Microbial Ecosystems from the Deepest Regions of the Terrestrial Deep Biosphere

NASA Astrophysics Data System (ADS)

Moser, D. P.

2011-12-01

Although recent discoveries from four continents support the existence of microbial ecosystems across vast regions of our planet's inner space, very little is known about the abundance, distribution, diversity, or ultimate depth limit of subsurface microbial life. These deep lithospheric inhabitants must contend with a variety of potential challenges including high temperature, pressure and salinity, extreme isolation, and low energy flux. Interestingly, although deep microbial ecosystems are assumed to be energy and nutrient limited, it is often difficult to identify any one limiting substrate and the energy for deep life is often present in relative abundance (e.g. as geologically-produced hydrogen or other reduced gases). Recently, the concept of radiation-supported deep microbial ecosystems has gained traction in the literature. In particular, one bacterium, a Firmicute denoted Candidatus Desulforudis audaxviator, has been shown to be prominent, and in cases dominate, in deep fracture fluids from across the Witwatersrand basin of South Africa, where it appears to persist by utilizing H2 and SO42- derived from radiochemical reactions in U-rich host rock. Until recently, these mines were thought to define the geographic limit of this genus and species; however, our recent North American detection of D. audaxviator in radioactive subsurface water resulting from underground nuclear tests both supports earlier assertions concerning the radiochemical lifestyle of D. audaxviator and greatly expands its range. Results such as these suggest that novel modes of life operating without inputs from the photosphere are possible, and thus may have implications for the likelihood of detecting life off the Earth (e.g. in the Martian subsurface). In addition to underground nuclear detonation cavities, this talk will consider insights gained from ongoing microbial ecology assessments from several to date unexplored deep ecosystems accessed via deep mines in the Black Hills (USA) and Canadian Shield (Canada) and exploratory boreholes in the Southern Great Basin (USA). The tantalizing possibility that several of these new potential habitats have exceeded some limit for life will be also be explored.

The Limits of Life in the Deep Subsurface - Implications for the Origin of Life

NASA Astrophysics Data System (ADS)

Baross, John

2013-06-01

There are very few environments on Earth where life is absent. Microbial life has proliferated into habitats that span nearly every imaginable physico-chemical variable. Only the availability of liquid water and temperature are known to prevent the growth of organisms. The other extreme physical and chemical variables, such as pH, pressure, high concentrations of solutes, damaging radiation, and toxic metals, are life-prohibiting factors for most organisms but not for all. The deep subsurface environments span all of the extreme conditions encountered by life including habitat conditions not yet explored, such as those that combine high temperature, high and low pH and extreme pressures. Some of the ``extremophile'' microorganisms inhabiting the deep subsurface environments have been shown to be among the most ``ancient'' of extant life. Their genomes and physiologies have led to a broader understanding of the geological settings of early life, the most ancient energy pathways, and the importance of water/rock interactions and tectonics in the origin and early evolution of life. The case can now be made that deep subsurface environments contributed to life's origin and provided the habitat(s) for the earliest microbial communities. However, there is much more to be done to further our understanding on the role of moderate to high pressures and temperatures on the chemical and biochemical ``steps'' leading to life, and on the evolution and physiology of both ancient and present-day subsurface microbial communities.

Comparative Study of Effects of CO 2 Concentration and pH on Microbial Communities from a Saline Aquifer, a Depleted Oil Reservoir, and a Freshwater Aquifer

DOE PAGES

Gulliver, Djuna M.; Lowry, Gregory V.; Gregory, Kelvin B.

2016-08-09

Injected CO 2 from geologic carbon storage is expected to impact the microbial communities of proposed storage sites, such as depleted oil reservoirs and deep saline aquifers, as well as overlying freshwater aquifers at risk of receiving leaking CO 2. Microbial community change in these subsurface sites may affect injectivity of CO 2, permanence of stored CO 2, and shallow subsurface water quality. The effect of CO 2 concentration on the microbial communities in fluid collected from a depleted oil reservoir and a freshwater aquifer was examined at subsurface pressures and temperatures. The community was exposed to 0%, 1%, 10%,more » and 100% pCO 2 for 56 days. Bacterial community structure was analyzed through 16S rRNA gene clone libraries, and total bacterial abundance was estimated through quantitative polymerase chain reaction. Changes in the microbial community observed in the depleted oil reservoir samples and freshwater samples were compared to previous results from CO 2-exposed deep saline aquifer fluids. Overall, results suggest that CO 2 exposure to microbial communities will result in pH-dependent population change, and the CO 2-selected microbial communities will vary among sites. In conclusion, this is the first study to compare the response of multiple subsurface microbial communities at conditions expected during geologic carbon storage, increasing the understanding of environmental drivers for microbial community changes in CO 2-exposed environments.« less

Comparative Study of Effects of CO 2 Concentration and pH on Microbial Communities from a Saline Aquifer, a Depleted Oil Reservoir, and a Freshwater Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulliver, Djuna M.; Lowry, Gregory V.; Gregory, Kelvin B.

Injected CO 2 from geologic carbon storage is expected to impact the microbial communities of proposed storage sites, such as depleted oil reservoirs and deep saline aquifers, as well as overlying freshwater aquifers at risk of receiving leaking CO 2. Microbial community change in these subsurface sites may affect injectivity of CO 2, permanence of stored CO 2, and shallow subsurface water quality. The effect of CO 2 concentration on the microbial communities in fluid collected from a depleted oil reservoir and a freshwater aquifer was examined at subsurface pressures and temperatures. The community was exposed to 0%, 1%, 10%,more » and 100% pCO 2 for 56 days. Bacterial community structure was analyzed through 16S rRNA gene clone libraries, and total bacterial abundance was estimated through quantitative polymerase chain reaction. Changes in the microbial community observed in the depleted oil reservoir samples and freshwater samples were compared to previous results from CO 2-exposed deep saline aquifer fluids. Overall, results suggest that CO 2 exposure to microbial communities will result in pH-dependent population change, and the CO 2-selected microbial communities will vary among sites. In conclusion, this is the first study to compare the response of multiple subsurface microbial communities at conditions expected during geologic carbon storage, increasing the understanding of environmental drivers for microbial community changes in CO 2-exposed environments.« less

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

PubMed Central

Graw, Michael F.; D'Angelo, Grace; Borchers, Matthew; Thurber, Andrew R.; Johnson, Joel E.; Zhang, Chuanlun; Liu, Haodong; Colwell, Frederick S.

2018-01-01

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics. PMID:29696012

Subsurface Environment Sampler for Improved In Situ Characterization of Subsurface Microbial Communities

NASA Astrophysics Data System (ADS)

Barnhart, E. P.; Ruppert, L. F.; Orem, W. H.; McIntosh, J. C.; Cunningham, A. B.; Fields, M. W.; Hiebert, R.; Hyatt, R.

2016-12-01

There is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by the extraction and transport of fossil fuels. This threat increases the need for improved groundwater monitoring and the ability to predict the extent to which microbial activity may remediate such contamination. The characterization of subsurface microbial communities could provide an ideal biomonitoring tool for the assessment of subsurface contamination due to prokaryotes environmental ubiquity, rapidity of response to environmental perturbation and the important role they play in hydrocarbon degradation and bioremediation. New DNA sequencing technologies provide the opportunity to cost-effectively identify the vast subsurface microbial ecosystem, but use of this new technology is restricted due to issues with sampling. Prior subsurface microbiology studies have relied on core samples that are expensive to obtain hard to collect aseptically and/or ground water samples that do not reflect in situ microbial densities or activities. The development of down-well incubation of sterile sediment with a Diffusive Microbial Sampler (DMS) has emerged as an alternative method to sample subsurface microbial communities that minimizes cost and contamination issues associated with traditional methods. We have designed a Subsurface Environment Sampler with a DMS module that could enable the anaerobic transport of the in situ microbial community from the field for laboratory bioremediation studies. This sampler could provide an inexpensive and standard method for subsurface microbial sampling which would make this tool useful for Federal, State, private and local agencies interested in monitoring contamination or the effectiveness of bioremediation activities in subsurface aquifers.

Impact disruption and recovery of the deep subsurface biosphere

USGS Publications Warehouse

Cockell, Charles S.; Voytek, Mary A.; Gronstal, Aaron L.; Finster, Kai; Kirshtein, Julie D.; Howard, Kieren; Reitner, Joachim; Gohn, Gregory S.; Sanford, Ward E.; Horton, J. Wright; Kallmeyer, Jens; Kelly, Laura; Powars, David S.

2012-01-01

Although a large fraction of the world's biomass resides in the subsurface, there has been no study of the effects of catastrophic disturbance on the deep biosphere and the rate of its subsequent recovery. We carried out an investigation of the microbiology of a 1.76 km drill core obtained from the ~35 million-year-old Chesapeake Bay impact structure, USA, with robust contamination control. Microbial enumerations displayed a logarithmic downward decline, but the different gradient, when compared to previously studied sites, and the scatter of the data are consistent with a microbiota influenced by the geological disturbances caused by the impact. Microbial abundance is low in buried crater-fill, ocean-resurge, and avalanche deposits despite the presence of redox couples for growth. Coupled with the low hydraulic conductivity, the data suggest the microbial community has not yet recovered from the impact ~35 million years ago. Microbial enumerations, molecular analysis of microbial enrichment cultures, and geochemical analysis showed recolonization of a deep region of impact-fractured rock that was heated to above the upper temperature limit for life at the time of impact. These results show how, by fracturing subsurface rocks, impacts can extend the depth of the biosphere. This phenomenon would have provided deep refugia for life on the more heavily bombarded early Earth, and it shows that the deeply fractured regions of impact craters are promising targets to study the past and present habitability of Mars.

Impact disruption and recovery of the deep subsurface biosphere.

PubMed

Cockell, Charles S; Voytek, Mary A; Gronstal, Aaron L; Finster, Kai; Kirshtein, Julie D; Howard, Kieren; Reitner, Joachim; Gohn, Gregory S; Sanford, Ward E; Horton, J Wright; Kallmeyer, Jens; Kelly, Laura; Powars, David S

2012-03-01

Although a large fraction of the world's biomass resides in the subsurface, there has been no study of the effects of catastrophic disturbance on the deep biosphere and the rate of its subsequent recovery. We carried out an investigation of the microbiology of a 1.76 km drill core obtained from the ∼35 million-year-old Chesapeake Bay impact structure, USA, with robust contamination control. Microbial enumerations displayed a logarithmic downward decline, but the different gradient, when compared to previously studied sites, and the scatter of the data are consistent with a microbiota influenced by the geological disturbances caused by the impact. Microbial abundance is low in buried crater-fill, ocean-resurge, and avalanche deposits despite the presence of redox couples for growth. Coupled with the low hydraulic conductivity, the data suggest the microbial community has not yet recovered from the impact ∼35 million years ago. Microbial enumerations, molecular analysis of microbial enrichment cultures, and geochemical analysis showed recolonization of a deep region of impact-fractured rock that was heated to above the upper temperature limit for life at the time of impact. These results show how, by fracturing subsurface rocks, impacts can extend the depth of the biosphere. This phenomenon would have provided deep refugia for life on the more heavily bombarded early Earth, and it shows that the deeply fractured regions of impact craters are promising targets to study the past and present habitability of Mars.

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA

PubMed Central

Osburn, Magdalena R.; LaRowe, Douglas E.; Momper, Lily M.; Amend, Jan P.

2014-01-01

The deep subsurface is an enormous repository of microbial life. However, the metabolic capabilities of these microorganisms and the degree to which they are dependent on surface processes are largely unknown. Due to the logistical difficulty of sampling and inherent heterogeneity, the microbial populations of the terrestrial subsurface are poorly characterized. In an effort to better understand the biogeochemistry of deep terrestrial habitats, we evaluate the energetic yield of chemolithotrophic metabolisms and microbial diversity in the Sanford Underground Research Facility (SURF) in the former Homestake Gold Mine, SD, USA. Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment. SURF provides access into an iron-rich Paleoproterozoic metasedimentary deposit that contains deeply circulating groundwater. Geochemical analyses of subsurface fluids reveal enormous geochemical diversity ranging widely in salinity, oxidation state (ORP 330 to −328 mV), and concentrations of redox sensitive species (e.g., Fe2+ from near 0 to 6.2 mg/L and Σ S2- from 7 to 2778μg/L). As a direct result of this compositional buffet, Gibbs energy calculations reveal an abundance of energy for microorganisms from the oxidation of sulfur, iron, nitrogen, methane, and manganese. Pyrotag DNA sequencing reveals diverse communities of chemolithoautotrophs, thermophiles, aerobic and anaerobic heterotrophs, and numerous uncultivated clades. Extrapolated across the mine footprint, these data suggest a complex spatial mosaic of subsurface primary productivity that is in good agreement with predicted energy yields. Notably, we report Gibbs energy normalized both per mole of reaction and per kg fluid (energy density) and find the later to be more consistent with observed physiologies and environmental conditions. Further application of this approach will significantly expand our understanding of the deep terrestrial biosphere. PMID:25429287

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE PAGES

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

2017-05-02

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Community dynamics of anaerobic bacteria in deep petroleum reservoirs

NASA Astrophysics Data System (ADS)

Hallmann, Christian; Schwark, Lorenz; Grice, Kliti

2008-09-01

The nature, activity and metabolism of microbes that inhabit the deep subsurface environment are a matter of ongoing debate. Primarily limited by temperature, little is known about secondary factors that restrict or enhance microbial activity or about the extent of a habitable environment deep below the surface. In particular, the degraders of chemically inert organic substrates remain elusive. Petroleum reservoirs can be regarded as natural bioreactors and are ideally suited for the study of microbial metabolism in the deep subsurface. Here we analyse series of oil samples that were biodegraded to different degrees. We find fatty acids after hydrolysis of purified crude oil fractions, indicating the presence of intact phospholipids and suggesting that indigenous bacteria inhabit petroleum reservoirs in sediment depths of up to 2,000m. A major change in bacterial community structure occurs after the removal of n-alkanes, indicating that more than one consortium is responsible for petroleum degradation. Our results suggest that further study of petroleum fluids will help understand bacterial metabolism and diversity in this habitat of the deep subsurface.

Genomic variation of subseafloor archaeal and bacterial populations from venting fluids at the Mid-Cayman Rise

NASA Astrophysics Data System (ADS)

Anderson, R. E.; Eren, A. M.; Stepanauskas, R.; Huber, J. A.; Reveillaud, J.

2015-12-01

Deep-sea hydrothermal vent systems serve as windows to a dynamic, gradient-dominated deep biosphere that is home to a wide diversity of archaea, bacteria, and viruses. Until recently the majority of these microbial lineages were uncultivated, resulting in a poor understanding of how the physical and geochemical context shapes microbial evolution in the deep subsurface. By comparing metagenomes, metatranscriptomes and single-cell genomes between geologically distinct vent fields, we can better understand the relationship between the environment and the evolution of subsurface microbial communities. An ideal setting in which to use this approach is the Mid-Cayman Rise, located on the world's deepest and slowest-spreading mid-ocean ridge, which hosts both the mafic-influenced Piccard and ultramafic-influenced Von Damm vent fields. Previous work has shown that Von Damm has higher taxonomic and metabolic diversity than Piccard, consistent with geochemical model expectations, and the fluids from all vents are enriched in hydrogen (Reveillaud et al., submitted). Mapping of both metagenomes and metatranscriptomes to a combined assembly showed very little overlap among the Von Damm samples, indicating substantial variability that is consistent with the diversity of potential metabolites in this ultramafic vent field. In contrast, the most consistently abundant and active lineage across the Piccard samples was Sulfurovum, a sulfur-oxidizing chemolithotroph that uses nitrate or oxygen as an electron acceptor. Moreover, analysis of point mutations within individual lineages suggested that Sulfurovumat Piccard is under strong selection, whereas microbial genomes at Von Damm were more variable. These results are consistent with the hypothesis that the subsurface environment at Piccard supports the emergence of a dominant lineage that is under strong selection pressure, whereas the more geochemically diverse microbial habitat at Von Damm creates a wider variety of stable ecological niches, facilitating higher diversity both within and between microbial lineages. By examining how the environment is imprinted into microbial genomes, we hope to gain insight into how subsurface microbial communities co-evolve with their environment in both the present and the deep past.

Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool

PubMed Central

Takai, Ken; Horikoshi, Koki

1999-01-01

Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible phylogenetic relationship among archaeal rRNA-encoded homing endonucleases. PMID:10584021

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust.

PubMed

Salas, Everett C; Bhartia, Rohit; Anderson, Louise; Hug, William F; Reid, Ray D; Iturrino, Gerardo; Edwards, Katrina J

2015-01-01

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 10(5) cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.

Deep and Ultra-deep Underground Observatory for In Situ Stress, Fluids, and Life

NASA Astrophysics Data System (ADS)

Boutt, D. F.; Wang, H.; Kieft, T. L.

2008-12-01

The question 'How deeply does life extend into the Earth?' forms a single, compelling vision for multidisciplinary science opportunities associated with physical and biological processes occurring naturally or in response to construction in the deep and ultra-deep subsurface environment of the Deep Underground Science and Engineering Laboratory (DUSEL) in the former Homestake mine. The scientific opportunity is to understand the interaction between the physical environment and microbial life, specifically, the coupling among (1) stress state and deformation; (2) flow and transport and origin of fluids; and (3) energy and nutrient sources for microbial life; and (4) microbial identity, diversity and activities. DUSEL-Homestake offers the environment in which these questions can be addressed unencumbered by competing human activities. Associated with the interaction among these variables are a number of questions that will be addressed at variety of depths and scales in the facility: What factors control the distribution of life as a function of depth and temperature? What patterns in microbial diversity, microbial activity and nutrients are found along this gradient? How do state variables (stress, strain, temperature, and pore pressure) and constitutive properties (permeability, porosity, modulus, etc.) vary with scale (space, depth, time) in a large 4D heterogeneous system: core - borehole - drift - whole mine - regional? How are fluid flow and stress coupled in a low-permeability, crystalline environment dominated by preferential flow paths? How does this interaction influence the distribution of fluids, solutes, gases, colloids, and biological resources (e.g. energy and nutritive substrates) in the deep continental subsurface? What is the interaction between geomechanics/geohydrology and microbiology (microbial abundance, diversity, distribution, and activities)? Can relationships elucidated within the mechanically and hydrologically altered subsurface habitat of the Homestake DUSEL be extrapolated to the pristine subsurface biosphere? In the absence of extensive intrusive investigations (drifts, mines, etc), can we characterize hydrogeologic and geomechanical processes in the subsurface? To what depth can we effectively characterize such processes, and what is the confidence in our interpretations? In addition to addressing these question in the 10-km3 of mine volume, the Homestake facility offers the deepest drilling platform in North America. The extant depth of 8000 feet can be doubled by drilling. An array of three or more 8,200 ft. boreholes, wire-line drilled from the 8,000 ft. level at Homestake will probe to at least 16,200 ft. below land surface, a depth at this location approaching the expected lower biosphere limit (e.g. the 120°C isotherm). Cores will be collected aseptically and then fracture patterns (e.g., orientation, aperture, etc.) will be determined and fracture fluids will be intensively sampled over time. Cores and fracture fluids will be analyzed for indigenous microbial communities, including their genetic elements, metabolic processes, and biosignatures.

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust

PubMed Central

Salas, Everett C.; Bhartia, Rohit; Anderson, Louise; Hug, William F.; Reid, Ray D.; Iturrino, Gerardo; Edwards, Katrina J.

2015-01-01

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 105 cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities. PMID:26617595

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.

PubMed

Ridley, Christina M; Voordouw, Gerrit

2018-06-01

Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

PubMed

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L; de Bruijn, Ino; Andersson, Anders F; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-10-14

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

PubMed Central

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; de Bruijn, Ino; Andersson, Anders F.; Leupin, Olivier X.; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present. PMID:27739431

Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs

PubMed Central

Liebensteiner, Martin G.; Tsesmetzis, Nicolas; Stams, Alfons J. M.; Lomans, Bartholomeus P.

2014-01-01

The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO2, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese-, and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (per)chlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (per)chlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (per)chlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (meta)genome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (per)chlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (per)chlorate for bioremediation, souring control, and microbial enhanced oil recovery are addressed. PMID:25225493

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt

PubMed Central

Jungbluth, Sean P; Bowers, Robert M; Lin, Huei-Ting; Cowen, James P; Rappé, Michael S

2016-01-01

Although little is known regarding microbial life within our planet's rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity. PMID:26872042

Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.

PubMed

Hubalek, Valerie; Wu, Xiaofen; Eiler, Alexander; Buck, Moritz; Heim, Christine; Dopson, Mark; Bertilsson, Stefan; Ionescu, Danny

2016-10-01

Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulliver, Djuna; Gregory, Kelvin B.; Lowry, Gregorgy V.

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 22 concentration and will create CO 2 concentration gradients that drivemore » changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2 exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2-altered microbial community may impact injectivity, permanence of stored CO 2, and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.« less

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulliver, Djuna M.; Gregory, Kelvin B.; Lowry, Gregory V.

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 2 concentration and will create CO 2 concentration gradients that drivemore » changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2-exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2-altered microbial community may impact injectivity, permanence of stored CO 2, and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.« less

Groundwater mixing at fracture intersections triggers massive iron-rich microbial mats

NASA Astrophysics Data System (ADS)

Bochet, O.; Le Borgne, T.; Bethencourt, L.; Aquilina, L.; Dufresne, A.; Pédrot, M.; Farasin, J.; Abbott, B. W.; Labasque, T.; Chatton, E.; Lavenant, N.; Petton, C.

2017-12-01

While most freshwater on Earth resides and flows in groundwater systems, these deep subsurface environments are often assumed to have little biogeochemical activity compared to surface environments. Here we report a massive microbial mat of iron-oxidizing bacteria, flourishing 60 meters below the surface, far below the mixing zone where most microbial activity is believed to occur. The abundance of microtubular structures in the mat hinted at the prevalence of of Leptothrix ochracea, but metagenomic analysis revealed a diverse consortium of iron-oxidizing bacteria dominated by unknown members of the Gallionellaceae family. This deep biogeochemical hot spot formed at the intersection of bedrock fractures, which maintain redox gradients by mixing water with different residence times and chemical compositions. Using measured fracture properties and hydrological conditions we developed a quantitative model to simulate the reactive zone where such deep hot spots could occur. While seasonal fluctuations are generally thought to decrease with depth, we found that meter-scale changes in water table level moved the depth of the reactive zone hundreds of meters because the microaerophilic threshold for ironoxidizers is highly sensitive to changes in mixing rates at fracture intersections. These results demonstrate that dynamic microbial communities can be sustained deep below the surface in bedrock fractures. Given the ubiquity of fractures at multiple scales in Earth's subsurface, such deep hot spots may strongly influence global biogeochemical cycles.

Gene expression in the deep biosphere.

PubMed

Orsi, William D; Edgcomb, Virginia P; Christman, Glenn D; Biddle, Jennifer F

2013-07-11

Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles, but deep biosphere activities are not well understood. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations and models of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

Nematoda from the terrestrial deep subsurface of South Africa.

PubMed

Borgonie, G; García-Moyano, A; Litthauer, D; Bert, W; Bester, A; van Heerden, E; Möller, C; Erasmus, M; Onstott, T C

2011-06-02

Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single-cell organisms, extending over three kilometres into the Earth's crust and comprising a significant fraction of the global biosphere. The constraints of temperature, energy, dioxygen and space seemed to preclude the possibility of more-complex, multicellular organisms from surviving at these depths. Here we report species of the phylum Nematoda that have been detected in or recovered from 0.9-3.6-kilometre-deep fracture water in the deep mines of South Africa but have not been detected in the mining water. These subsurface nematodes, including a new species, Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. Carbon-14 data indicate that the fracture water in which the nematodes reside is 3,000-12,000-year-old palaeometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits, and that they may control the microbial population density by grazing on fracture surface biofilm patches. Our results expand the known metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multicellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other planets in our Solar System.

Trends and future challenges in sampling the deep terrestrial biosphere.

PubMed

Wilkins, Michael J; Daly, Rebecca A; Mouser, Paula J; Trexler, Ryan; Sharma, Shihka; Cole, David R; Wrighton, Kelly C; Biddle, Jennifer F; Denis, Elizabeth H; Fredrickson, Jim K; Kieft, Thomas L; Onstott, Tullis C; Peterson, Lee; Pfiffner, Susan M; Phelps, Tommy J; Schrenk, Matthew O

2014-01-01

Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on "Trends and Future Challenges in Sampling The Deep Subsurface" was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation's Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.

Active subsurface cellular function in the Baltic Sea Basin, IODP Exp 347

NASA Astrophysics Data System (ADS)

Reese, B. K.; Zinke, L. A.; Bird, J. T.; Lloyd, K. G.; Marshall, I.; Amend, J.; Jørgensen, B. B.

2016-12-01

The Baltic Sea Basin is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of global temperature fluctuations over the course of several hundred thousand years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates (100-500 cm/1000 y) make this an ideal setting to understand the microbial structure of a deep biosphere community in a high-organic matter environment. The responses of deep sediment microbial communities to variations in conditions during and after deposition are poorly understood. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further define the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

Characterization of microbial communities in subsurface nuclear blast cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P; Czerwinski, Ken; Russell, Charles E

2010-07-13

This US Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P.; Bruckner, Jim; Fisher, Jen

2010-09-01

This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program’s Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere.

PubMed

Kimura, Hiroyuki; Ishibashi, Jun-Ichiro; Masuda, Harue; Kato, Kenji; Hanada, Satoshi

2007-04-01

International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117 degrees C) and surface seawater (29.9 degrees C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82 degrees C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84 degrees C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84 degrees C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers

PubMed Central

Kieft, Thomas L.; Kuloyo, Olukayode; Linage-Alvarez, Borja; van Heerden, Esta; Lindsay, Melody R.; Magnabosco, Cara; Wang, Wei; Wiggins, Jessica B.; Guo, Ling; Perlman, David H.; Kyin, Saw; Shwe, Henry H.; Harris, Rachel L.; Oh, Youmi; Yi, Min Joo; Purtschert, Roland; Slater, Greg F.; Ono, Shuhei; Wei, Siwen; Li, Long; Sherwood Lollar, Barbara; Onstott, Tullis C.

2016-01-01

Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2. Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH4 to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H2 oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface. PMID:27872277

Potential for Nitrogen Fixation and Nitrification in the Granite-Hosted Subsurface at Henderson Mine, CO

PubMed Central

Swanner, Elizabeth D.; Templeton, Alexis S.

2011-01-01

The existence of life in the deep terrestrial subsurface is established, yet few studies have investigated the origin of nitrogen that supports deep life. Previously, 16S rRNA gene surveys cataloged a diverse microbial community in subsurface fluids draining from boreholes 3000 feet deep at Henderson Mine, CO, USA (Sahl et al., 2008). The prior characterization of the fluid chemistry and microbial community forms the basis for the further investigation here of the source of NH4+. The reported fluid chemistry included N2, NH4+ (5–112 μM), NO2− (27–48 μM), and NO3− (17–72 μM). In this study, the correlation between low NH4+ concentrations in dominantly meteoric fluids and higher NH4+ in rock-reacted fluids is used to hypothesize that NH4+ is sourced from NH4+-bearing biotite. However, biotite samples from the host rocks and ore-body minerals were analyzed by Fourier transform infrared (FTIR) microscopy and none-contained NH4+. However, the nitrogenase-encoding gene nifH was successfully amplified from DNA of the fluid sample with high NH4+, suggesting that subsurface microbes have the capability to fix N2. If so, unregulated nitrogen fixation may account for the relatively high NH4+ concentrations in the fluids. Additionally, the amoA and nxrB genes for archaeal ammonium monooxygenase and nitrite oxidoreductase, respectively, were amplified from the high NH4+ fluid DNA, while bacterial amoA genes were not. Putative nitrifying organisms are closely related to ammonium-oxidizing Crenarchaeota and nitrite-oxidizing Nitrospira detected in other subsurface sites based upon 16S rRNA sequence analysis. Thermodynamic calculations underscore the importance of NH4+ as an energy source in a subsurface nitrification pathway. These results suggest that the subsurface microbial community at Henderson is adapted to the low nutrient and energy environment by their capability of fixing nitrogen, and that fixed nitrogen may support subsurface biomass via nitrification. PMID:22190904

Microbial Life of North Pacific Oceanic Crust

NASA Astrophysics Data System (ADS)

Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

2003-12-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep biosphere. Molecular microbial diversity is currently determined by cloning und comparative 16S rRNA gene analyses. The first results will also be presented. In summary, the low number of isolates, cultivated under aerobic conditions, is in good agreement with the common opinion that most of the bacteria within the deep biosphere are anaerobic. Thus, studies of microbial community structure in solid geological materials are feasible and constitute further evidence that continuing microbiological activity in the challenging exploration of the deep sub-seafloor biosphere environment is absolutely promising.

Deep aquifer prokaryotic community responses to CO2 geosequestration

NASA Astrophysics Data System (ADS)

Mu, A.; Moreau, J. W.

2015-12-01

Little is known about potential microbial responses to supercritical CO2 (scCO2) injection into deep subsurface aquifers, a currently experimental means for mitigating atmospheric CO2 pollution being trialed at several locations around the world. One such site is the Paaratte Formation of the Otway Basin (~1400 m below surface; 60°C; 2010 psi), Australia. Microbial responses to scCO2 are important to understand as species selection may result in changes to carbon and electron flow. A key aim is to determine if biofilm may form in aquifer pore spaces and reduce aquifer permeability and storage. This study aimed to determine in situ, using 16S rRNA gene, and functional metagenomic analyses, how the microbial community in the Otway Basin geosequestration site responded to experimental injection of 150 tons of scCO2. We demonstrate an in situ sampling approach for detecting deep subsurface microbial community changes associated with geosequestration. First-order level analyses revealed a distinct shift in microbial community structure following the scCO2 injection event, with proliferation of genera Comamonas and Sphingobium. Similarly, functional profiling of the formation revealed a marked increase in biofilm-associated genes (encoding for poly-β-1,6-N-acetyl-D-glucosamine). Global analysis of the functional gene profile highlights that scCO2 injection potentially degraded the metabolism of CH4 and lipids. A significant decline in carboxydotrophic gene abundance (cooS) and an anaerobic carboxydotroph OTU (Carboxydocella), was observed in post-injection samples. The potential impacts on the flow networks of carbon and electrons to heterotrophs are discussed. Our findings yield insights for other subsurface systems, such as hydrocarbon-rich reservoirs and high-CO2 natural analogue sites.

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

USGS Publications Warehouse

Sahl, J.W.; Schmidt, R.; Swanner, E.D.; Mandernack, K.W.; Templeton, A.S.; Kieft, Thomas L.; Smith, R.L.; Sanford, W.E.; Callaghan, R.L.; Mitton, J.B.; Spear, J.R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. Copyright ?? 2008, American Society for Microbiology. All Rights Reserved.

Subsurface Microbial Diversity in Deep-Granitic-Fracture Water in Colorado▿

PubMed Central

Sahl, Jason W.; Schmidt, Raleigh; Swanner, Elizabeth D.; Mandernack, Kevin W.; Templeton, Alexis S.; Kieft, Thomas L.; Smith, Richard L.; Sanford, William E.; Callaghan, Robert L.; Mitton, Jeffry B.; Spear, John R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This “Henderson candidate division” dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. PMID:17981950

Probing Metabolic Activity of Deep Subseafloor Life with NanoSIMS

NASA Astrophysics Data System (ADS)

Morono, Y.; Terada, T.; Itoh, M.; Inagaki, F.

2014-12-01

There are very few natural environments where life is absent in the Earth's surface biosphere. However, uninhabitable region is expected to be exist in the deep subsurface biosphere, of which extent and constraining factor(s) have still remained largly unknown. Scientific ocean drilling have revealed that microbial communities in sediments are generally phylogenetically distinct from known spieces isolated from the Earth's surface biosphere, and hence metabolic functions of the deep subseafloor life remain unknown. In addition, activity of subseafloor microbial cells are thought to be extraordinally slow, as indicated by limited supply of neutrient and energy substrates. To understand the limits of the Earth's subseafloor biosphere and metabolic functions of microbial populations, detection and quantification of the deeply buried microbial cells in geological habitats are fundamentary important. Using newly developed cell separation techniques as well as an discriminative cell detection system, the current quantification limit of sedimentary microbial cells approaches to 102 cells/cm3. These techniques allow not only to assess very small microbial population close to the subsurface biotic fringe, but also to separate and sort the target cells using flow cytometric cell sorter. Once the deep subseafloor microbial cells are detached from mineral grains and sorted, it opens new windows to subsequent molecular ecological and element/isotopic analyses. With a combined use of nano-scale secondary ion masspectrometry (NanoSIMS) and stable isotope-probing techniques, it is possible to detect and measure activity of substrate incorporation into biomass, even for extremely slow metabolic processes such as uncharacteriszed deep subseafloor life. For example, it was evidenced by NanoSIMS that at least over 80% of microbial cells at ~200 meters-deep, 460,000-year-old sedimentary habitat are indeed live, which substrate incooporation was found to be low (10-15 gC/cell/day) even under the lab incubation condition. Also microbial activity in ultraoligotrophic biosphere samples such as the South Pacific Gyre (i.e., IODP Expeditions 329) will be shown. Our results demonstrates metabolic potential of microbes that have been survived for geological timescale in extremely starved condition.

Actinobacterial diversity across a marine transgression in the deep subsurface off Shimokita Peninsula, Japan

NASA Astrophysics Data System (ADS)

Harrison, B. K.; Bailey, J. V.

2013-12-01

Sediment horizons represent a significant - but not permanent - barrier to microbial transport. Cells commonly attach to mineral surfaces in unconsolidated sediments. However, by taxis, growth, or passive migration under advecting fluids, some portion of the microbial community may transgress sedimentary boundaries. Few studies have attempted to constrain such transport of community signatures in the marine subsurface and its potential impact on biogeography. Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula recovered sediments over a greater than 1km interval representing a gradual decrease of terrestrial influence, from tidal to continental shelf depositional settings. This sequence represents a key opportunity to link subsurface microbial communities to lithological variability and investigate the permanence of community signatures characteristic of distinct depositional regimes. The phylogenetic connectivity between marine and terrestrially-influenced deposits may demonstrate to what degree sediments offer a substantial barrier to cell transport in the subsurface. Previous work has demonstrated that the Actinobacterial phylum is broadly distributed in marine sediments (Maldonado et al., 2005), present and active in the deep subsurface (Orsi et al., 2013), and that marine and terrestrial lineages may potentially be distinguished by 16S rRNA gene sequencing (e.g. Prieto-Davó et al., 2013). We report on Actinobacteria-specific 16S rRNA gene diversity recovered between 1370 and 2642 mbsf with high-throughput sequencing using the Illumina MiSeq platform, as well as selective assembly and analysis of environmental clone libraries.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

PubMed Central

Freedman, Adam J.E.; Tan, BoonFei

2017-01-01

Summary Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long‐term fate of sequestered scCO2, harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2‐water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling. PMID:28229521

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

DOE PAGES

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; ...

2016-10-14

A significant fraction (~ 20%) of microbial life is found in the terrestrial deep subsurface, yet the metabolic processes extant in those environments are poorly understood. Here we show that H 2, injected into the Opalinus Clay formation in a borehole located 300 meters below the surface, fuels a community of microorganisms with interconnected metabolisms. Metagenomic binning and metaproteomic analysis reveal a complete carbon cycle, driven by autotrophic hydrogen oxidizers. Dead biomass from these organisms is a substrate for a fermenting bacterium that produces acetate as a product. In turn, complete oxidizer heterotrophic sulfate- reducing bacteria utilize acetate and oxidizemore » it to CO 2, closing the cycle. This metabolic reconstruction sheds light onto a hydrogen-driven carbon cycle, and a sunlight-independent ecosystem in the deep subsurface.« less

Something new from something old? Fracking stimulated microbial processes

NASA Astrophysics Data System (ADS)

Wrighton, K. C.; Daly, R. A.; Hoyt, D.; Trexler, R.; McRae, J.; Wilkins, M.; Mouser, P. J.

2015-12-01

Hydraulic fracturing, colloquially known as "fracking", is employed for effective gas and oil recovery in deep shales. This process injects organisms and liquids from the surface into the deep subsurface (~2500 m), exposing microorganisms to high pressures, elevated temperatures, chemical additives, and brine-level salinities. Here we use assembly-based metagenomics to create a metabolic blueprint from an energy-producing Marcellus shale well over a 328-day period. Using this approach we ask the question: What abiotic and biotic factors drive microbial metabolism and thus biogeochemical cycling during natural gas extraction? We found that after 49 days, increased salinity in produced waters corresponded to a shift in the microbial community, with only organisms that encode salinity adaptations detected. We posit that organic compatible solutes, produced by organisms adapting to increased salinity, fuels a methylamine-driven ecosystem in fractured shale. This metabolic network ultimately results in biogenic methane production from members of Methanohalophilus and Methanolobus. Proton NMR validated these genomic hypotheses, with mono-methylamine being highest in the input material, but detected throughout the sampling. Beyond abiotic constraints, our genomic investigations revealed that viruses can be linked to key members of the microbial community, potentially releasing methylamine osmoprotectants and impacting bacterial strain variation. Collectively our results indicate that adaptation to high salinity, metabolism in the absence of oxidized electron acceptors, and viral predation are controlling factors mediating microbial community metabolism during hydraulic fracturing of the deep subsurface.

Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland

PubMed Central

Miettinen, Hanna; Kietäväinen, Riikka; Sohlberg, Elina; Numminen, Mikko; Ahonen, Lasse; Itävaara, Merja

2015-01-01

Pyhäsalmi mine in central Finland provides an excellent opportunity to study microbial and geochemical processes in a deep subsurface crystalline rock environment through near-vertical drill holes that reach to a depth of more than two kilometers below the surface. However, microbial sampling was challenging in this high-pressure environment. Nucleic acid yields obtained were extremely low when compared to the cell counts detected (1.4 × 104 cells mL−1) in water. The water for nucleic acid analysis went through high decompression (60–130 bar) during sampling, whereas water samples for detection of cell counts by microscopy could be collected with slow decompression. No clear cells could be identified in water that went through high decompression. The high-pressure decompression may have damaged part of the cells and the nucleic acids escaped through the filter. The microbial diversity was analyzed from two drill holes by pyrosequencing amplicons of the bacterial and archaeal 16S rRNA genes and from the fungal ITS regions from both DNA and RNA fractions. The identified prokaryotic diversity was low, dominated by Firmicute, Beta- and Gammaproteobacteria species that are common in deep subsurface environments. The archaeal diversity consisted mainly of Methanobacteriales. Ascomycota dominated the fungal diversity and fungi were discovered to be active and to produce ribosomes in the deep oligotrophic biosphere. The deep fluids from the Pyhäsalmi mine shared several features with other deep Precambrian continental subsurface environments including saline, Ca-dominated water and stable isotope compositions positioning left from the meteoric water line. The dissolved gas phase was dominated by nitrogen but the gas composition clearly differed from that of atmospheric air. Despite carbon-poor conditions indicated by the lack of carbon-rich fracture fillings and only minor amounts of dissolved carbon detected in formation waters, some methane was found in the drill holes. No dramatic differences in gas compositions were observed between different gas sampling methods tested. For simple characterization of gas composition the most convenient way to collect samples is from free flowing fluid. However, compared to a pressurized method a relative decrease in the least soluble gases may appear. PMID:26579109

Sulfur and iron cycling in deep-subsurface, coal bed-containing sediments off Shimokita (Japan)

NASA Astrophysics Data System (ADS)

Riedinger, N.; Smirnoff, M. N.; Gilhooly, W.; Phillips, S. C.; Lyons, T. W.; 337 Scientific Party, I.

2013-12-01

The main goal of IODP Expedition 337 was the identification and characterization of the deep coal bed biosphere and hydrocarbon system off the Shimokita Peninsula (Japan) in the northwestern Pacific using the D/V Chikyu. To accomplish this scientific objective, it was also necessary to investigate the inorganic biogeochemistry in order to identify possible electron acceptors and bio-essential nutrients. These biogeochemical parameters greatly influence both, the composition and abundance of microbial communities as well as the organic carbon cycle. In turn, the microbially mediated carbon cycle influences the diagenetic reactions in the subsurface, thus, altering geochemical and physical characteristics of the material. Here we present results from metal and sulfur geochemical analyses from the deep-subsurface sediments (about 1250 to 2466 mbsf) at Site C0020 off Shimokita. The measured concentrations of acid volatile sulfur (AVS) as well as chromium reducible sulfur (CRS) reflect the alteration of iron oxides to iron sulfides and indicate that the main sulfur-bearing phase in the investigated sediments is pyrite. Concentrations of intermediate sulfur species are minor and occur mainly in the coal-bearing interval. Our data show that the uppermost sediments contain higher amounts of pyrite (up to 1.2 wt.%) with an average of 0.5 wt.% compared to the deeper deposits (below about 1800 mbsf), which show an average of 0.16 wt.%. In contrast, iron oxide concentrations are highest in the deeper sediment sections (up to 0.4%), where pyrite concentrations are low. The alteration of iron oxides to sulfides in theses lower section was probably governed by the amount of available sulfide in the pore water. The occurrence of (bio-)reactive iron phases in these deeply buried sediments has implications for the deep biosphere as those minerals have the potential to serve as electron acceptors during burial, including reactions involving deep sourced electron donors, such as hydrogen and methane - related to the coal bed as the potential source. Thus, the deep subsurface coal beds off Shimokita provide an ideal environment to investigate microbial and metal interactions under extreme conditions.

Quantifying microbial activity in deep subsurface sediments using a tritium based hydrognease enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R.; Nickel, J.; Kallmeyer, J.

2012-12-01

Microbial life is widespread in Earth's subsurface and estimated to represent a significant fraction of Earth's total living biomass. However, very little is known about subsurface microbial activity and its fundamental role in biogeochemical cycles of carbon and other biologically important elements. Hydrogen is one of the most important elements in subsurface anaerobic microbial metabolism. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways. They either consume or produce protons for ATP synthesis. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy generating metabolic processes to electron acceptors such as CO2 or sulfate. H2ase enzyme targets a key metabolic compound in cellular metabolism therefore the assay can be used as a measure for total microbial activity without the need to identify any specific metabolic process. Using the highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey, in marine sediments of the Barents Sea and in deep subseafloor sediments from the Nankai Trough. H2ase activity could be quantified at all depths of all sites but the activity distribution varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3d-1 down to a depth of 1.60 m. At all sites the sulfate reduction rate profile followed the upper part of the H2ase activity profile until sulfate reduction reached the minimum detection limit (ca. 10 pmol cm-3d-1). H2ase activity could still be quantified after the decline of sulfate reduction, indicating that other microbial processes are becoming quantitatively more important. Similarly, H2ase activity could be quantified at greater depths (ca. 400 mbsf) in Nankai Trough sediments. Nankai Trough is one of the world's most geologically active accretionary wedges, where the Philippine Plate is subducting under the southwest of Japan. Due to the transient faulting, huge amounts of energy are liberated that enhance chemical transformations of organic and inorganic matter. An increase in H2ase activity could be observed at greater depth, which suggests that microbial activity is stimulated by the fault activity. Current techniques for the quantification of microbial activity in deep sediments have already reached their physical and technical limits and-in many cases- are still not sensitive enough to quantify extremely low rates of microbial activity. Additional to the quantification of specific processes, estimates of total microbial activity will provide valuable information on energy flux and microbial metabolism in the subsurface biosphere and other low-energy environments as well as help identifying hotspots of microbial activity. The tritium H2ase assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Molecular hydrogen: An abundant energy source for bacterial activity in nuclear waste repositories

NASA Astrophysics Data System (ADS)

Libert, M.; Bildstein, O.; Esnault, L.; Jullien, M.; Sellier, R.

A thorough understanding of the energy sources used by microbial systems in the deep terrestrial subsurface is essential since the extreme conditions for life in deep biospheres may serve as a model for possible life in a nuclear waste repository. In this respect, H 2 is known as one of the most energetic substrates for deep terrestrial subsurface environments. This hydrogen is produced from abiotic and biotic processes but its concentration in natural systems is usually maintained at very low levels due to hydrogen-consuming bacteria. A significant amount of H 2 gas will be produced within deep nuclear waste repositories, essentially from the corrosion of metallic components. This will consequently improve the conditions for microbial activity in this specific environment. This paper discusses different study cases with experimental results to illustrate the fact that microorganisms are able to use hydrogen for redox processes (reduction of O 2, NO3-, Fe III) in several waste disposal conditions. Consequences of microbial activity include: alteration of groundwater chemistry and shift in geochemical equilibria, gas production or consumption, biocorrosion, and potential modifications of confinement properties. In order to quantify the impact of hydrogen bacteria, the next step will be to determine the kinetic rate of the reactions in realistic conditions.

Some New Windows into Terrestrial Deep Subsurface Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Moser, D. P.

2011-12-01

Over the past several years, our group has surveyed the microbial ecology and biogeochemistry of a range of fracture rock subsurface ecosystems via deep mine boreholes in South Africa, the United States, and Canada; and boreholes from surface or deeply-sourced natural springs of the U.S. Great Basin. Collectively, these mostly unexplored habitats represent a wide range of geologic provinces, host rock types, aquatic chemistries, and the vast potential for biogeographic isolation. Thus, patterns of microbial diversity are of interest from the perspective of filling a fundamental knowledge gap; and while not necessarily expected, the detection of closely related microorganisms from geographically isolated settings would be noteworthy. Across these sample sets, microbial communities were invariably very low in biomass (e.g. 10e3 - 10e4 cells per mL) and dominated by deeply-branching bacterial lineages, particularly from the phyla Firmicutes and Nitrospira. In several cases, the Firmicutes have shown very close phylogenetic affiliations to lineages detected at divergent locations. For example, one abundant lineage from a new artesian well drilled into the Furnace Creek Fault of Death Valley, CA bears a very close phylogenetic relatedness to environmental DNA sequences (SSU rRNA gene) detected in one of the world's deepest mines (Tau Tona of South Africa) and what was North America's deepest gold mine (Homestake of South Dakota). Several radioactive wells from the Nevada National Security Site have produced rRNA gene sequences very close (e.g. greater than 99% identity) to that of Desulforudis audaxviator, a rarely detected microorganism thought to subsist as a single species ecosystem on the products of radiochemical reactions in deep crustal rocks from the South African Witwatersrand Basin. These sequences, along with more distantly related sequences from the marine subsurface (ridge flank basalt and mud volcanoes) and groundwater in Europe, hint at a role in certain hydrogen-rich subsurface settings for this group. Likewise, patterns of archaeal diversity across many of our Great Basin sites suggest shared deep lineages, particularly with the phylum, Thaumarchaeota. Here we will explore the possible significance of these patterns of diversity and discuss future research plans involving high throughput molecular techniques.

Cultivating the Deep Subsurface Microbiome

NASA Astrophysics Data System (ADS)

Casar, C. P.; Osburn, M. R.; Flynn, T. M.; Masterson, A.; Kruger, B.

2017-12-01

Subterranean ecosystems are poorly understood because many microbes detected in metagenomic surveys are only distantly related to characterized isolates. Cultivating microorganisms from the deep subsurface is challenging due to its inaccessibility and potential for contamination. The Deep Mine Microbial Observatory (DeMMO) in Lead, SD however, offers access to deep microbial life via pristine fracture fluids in bedrock to a depth of 1478 m. The metabolic landscape of DeMMO was previously characterized via thermodynamic modeling coupled with genomic data, illustrating the potential for microbial inhabitants of DeMMO to utilize mineral substrates as energy sources. Here, we employ field and lab based cultivation approaches with pure minerals to link phylogeny to metabolism at DeMMO. Fracture fluids were directed through reactors filled with Fe3O4, Fe2O3, FeS2, MnO2, and FeCO3 at two sites (610 m and 1478 m) for 2 months prior to harvesting for subsequent analyses. We examined mineralogical, geochemical, and microbiological composition of the reactors via DNA sequencing, microscopy, lipid biomarker characterization, and bulk C and N isotope ratios to determine the influence of mineralogy on biofilm community development. Pre-characterized mineral chips were imaged via SEM to assay microbial growth; preliminary results suggest MnO2, Fe3O4, and Fe2O3 were most conducive to colonization. Solid materials from reactors were used as inoculum for batch cultivation experiments. Media designed to mimic fracture fluid chemistry was supplemented with mineral substrates targeting metal reducers. DNA sequences and microscopy of iron oxide-rich biofilms and fracture fluids suggest iron oxidation is a major energy source at redox transition zones where anaerobic fluids meet more oxidizing conditions. We utilized these biofilms and fluids as inoculum in gradient cultivation experiments targeting microaerophilic iron oxidizers. Cultivation of microbes endemic to DeMMO, a system locally dominated by unclassified and candidate phyla, has the potential to yield novel subsurface organisms with unique physiologies. We intend to further utilize subsurface isolates to probe the effects of geochemical perturbations on biosignatures in future studies, thus broadening our understanding of subterranean ecosystems.

Subsurface metabolic potential on the Costa Rican Margin

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; Martino, A. J.; Bousses, K.; House, C. H.

2017-12-01

The distribution of archaea and bacteria and their associated metabolic abilities in the deep subseafloor are poorly understood. In order to explore this, we focused on samples from the Costa Rica margin IODP Expedition 334. The microbial community was analyzed via metagenomics in two different sites at multiple depths. At Site 1378, samples are from 2 meters below the sea floor (mbsf), 33 mbsf and 93 mbsf, and at Site 1379 from 22 mbsf to 45 mbsf. Whole community analysis of conserved gene markers in the metagenome show that the microbial community varies with depth, and drastically differs between the two geographically close sites. Thirty-two genomes were recovered from the metagenomic data with more than 30% completion. Archaea make 49% of all genomes recovered and over 90% of these recovered genomes belong to recently discovered and poorly characterized groups of Archaea. This study explored the relative dynamics of microbial communities in the deep biosphere and presents the metabolic potential of distinct subsurface biosphere archaeal groups.

Subsurface Biodegradation in a Fractured Basement Reservoir, Shropshire, UK

NASA Astrophysics Data System (ADS)

Parnell, John; Baba, Mas'ud; Bowden, Stephen; Muirhead, David

2017-04-01

Subsurface Biodegradation in a Fractured Basement Reservoir, Shropshire, UK. John Parnell, Mas'ud Baba, Stephen Bowden, David Muirhead Subsurface biodegradation in current oil reservoirs is well established, but there are few examples of fossil subsurface degradation. Biomarker compositions of viscous and solid oil residues ('bitumen') in fractured Precambrian and other basement rocks below the Carboniferous cover in Shropshire, UK, show that they are variably biodegraded. High levels of 25-norhopanes imply that degradation occurred in the subsurface. Lower levels of 25-norhopanes occur in active seepages. Liquid oil trapped in fluid inclusions in mineral veins in the fractured basement confirm that the oil was emplaced fresh before subsurface degradation. A Triassic age for the veins implies a 200 million year history of hydrocarbon migration in the basement rocks. The data record microbial colonization of a fractured basement reservoir, and add to evidence in modern basement aquifers for microbial activity in deep fracture systems. Buried basement highs may be especially favourable to colonization, through channelling fluid flow to shallow depths and relatively low temperatures

Stable, geochemically mediated biospheres in the Deep Mine Microbial Observatory, SD, USA

NASA Astrophysics Data System (ADS)

Osburn, M. R.; Casar, C. P.; Kruger, B.; Flynn, T. M.

2017-12-01

The terrestrial subsurface is a vast reservoir of life, hosting diverse microbial ecosystems with varying levels of connectivity to surface inputs. Understanding long term ecosystem dynamics within the subsurface biosphere is very challenging due to limitations in accessibility, sample availability, and slow microbial growth rates. The establishment of the Deep Mine Microbial Observatory (DeMMO) at the Sanford Underground Research Facility, SD, USA has allowed for bimonthly sampling for nearly two years at six sites spanning 250 to 1500 m below the surface. Here we present a time-resolved analysis of the geomicrobiology of the six DeMMO sites, which have been created from legacy mine boreholes modified to allow for controlled sampling. Our interdisciplinary approach includes analysis of passively draining fracture fluid for aqueous and gas geochemistry, DNA sequencing, microscopy, and isotopic measurements of organic and inorganic substrates. Fluid geochemistry varies significantly between sites, but is relatively stable over time for a given site, even through significant external perturbations such as drilling and installation of permanent sampling devices into the boreholes. The fluid-hosted microbial diversity follows these trends, with consistent populations present at each site through time, even through drilling events. For instance, the shallowest site (DeMMO 1) consistently hosts >30% uncharacterized phyla and >25% Omnitrophica whereas the deepest site (DeMMO 6) is dominated by Firmicutes and Bacterioidetes. Microbial diversity appears to respond to the availability of energy sources such as organic carbon, sulfate, sulfide, hydrogen, and iron. Carbon isotopic measurements reveal closed system behavior with significant recycling of organic carbon into the DIC pool. Together these observations suggest DeMMO hosts isolated subsurface microbial populations adapted to local geochemistry that are stable on yearlong timescales.

Looking For a Needle in the Haystack: Deciphering Indigenous 1.79 km Deep Subsurface Microbial Communities from Drilling Mud Contaminants Using 454 Pyrotag Sequencing

NASA Astrophysics Data System (ADS)

Dong, Y.; Cann, I.; Mackie, R.; Price, N.; Flynn, T. M.; Sanford, R.; Miller, P.; Chia, N.; Kumar, C. G.; Kim, P.; Sivaguru, M.; Fouke, B. W.

2010-12-01

Knowledge of the composition, structure and activity of microbial communities that live in deeply buried sedimentary rocks is fundamental to the future of subsurface biosphere stewardship as it relates to hydrocarbon exploration and extraction, carbon sequestration, gas storage and groundwater management. However, the study of indigenous subsurface microorganisms has been limited by the technical challenges of collecting deep formation water samples that have not been heavily contaminated by the mud used to drill the wells. To address this issue, a “clean-sampling method” deploying the newly developed Schlumberger Quicksilver MDT probe was used to collect a subsurface sample at a depth of 1.79 km (5872 ft) from an exploratory well within Cambrian-age sandstones in the Illinois Basin. This yielded a formation water sample that was determined to have less than 4% drilling mud contamination based on tracking changes in the aqueous geochemistry of the formation water during ~3 hours of pumping at depth prior to sample collection. A suite of microscopy and culture-independent molecular analyses were completed using the DNA extracted from microbial cells in the formation water, which included 454 amplicon pyrosequencing that targeted the V1-V3 hypervariable region of bacterial 16S rRNA gene sequences. Results demonstrated an extremely low diversity microbial community living in formation water at 1.79 km-depth. More than 95 % of the total V1-V3 pyrosequencing reads (n=11574) obtained from the formation water were affiliated with a halophilic γ-proteobacterium and most closely related to the genus Halomonas. In contrast, about 3 % of the V1-V3 sequences in the drilling mud library (n=13044) were classified as genus Halomonas but were distinctly different and distantly related to the formation water Halomonas detected at 1.79 km-depth. These results were consistent with those obtained using a suite of other molecular screens (e.g., Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and the initial full length 16S rRNA amplicon libraries) and bioinformatic analyses (e.g., 16S rRNA and Open Reading Frame (ORF) calls established from the 454 metagenomic community analyses). Functional pathway modeling is underway to evaluate the adaptation of this indigenous microbial community to the hydrologic and geologic history of the deep subsurface environment of the Illinois Basin.

A minimalistic microbial food web in an excavated deep subsurface clay rock.

PubMed

Bagnoud, Alexandre; de Bruijn, Ino; Andersson, Anders F; Diomidis, Nikitas; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

Clay rocks are being considered for radioactive waste disposal, but relatively little is known about the impact of microbes on the long-term safety of geological repositories. Thus, a more complete understanding of microbial community structure and function in these environments would provide further detail for the evaluation of the safety of geological disposal of radioactive waste in clay rocks. It would also provide a unique glimpse into a poorly studied deep subsurface microbial ecosystem. Previous studies concluded that microorganisms were present in pristine Opalinus Clay, but inactive. In this work, we describe the microbial community and assess the metabolic activities taking place within borehole water. Metagenomic sequencing and genome-binning of a porewater sample containing suspended clay particles revealed a remarkably simple heterotrophic microbial community, fueled by sedimentary organic carbon, mainly composed of two organisms: a Pseudomonas sp. fermenting bacterium growing on organic macromolecules and releasing organic acids and H2, and a sulfate-reducing Peptococcaceae able to oxidize organic molecules to CO(2). In Opalinus Clay, this microbial system likely thrives where pore space allows it. In a repository, this may occur where the clay rock has been locally damaged by excavation or in engineered backfills. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Rates of microbial metabolism in deep coastal plain aquifers

USGS Publications Warehouse

Chapelle, F.H.; Lovley, D.R.

1990-01-01

Rates of microbial metabolism in deep anaerobic aquifers of the Atlantic coastal plain of South Carolina were investigated by both microbiological and geochemical techniques. Rates of [2-14C]acetate and [U-14C]glucose oxidation as well as geochemical evidence indicated that metabolic rates were faster in the sandy sediments composing the aquifers than in the clayey sediments of the confining layers. In the sandy aquifer sediments, estimates of the rates of CO2 production (millimoles of CO2 per liter per year) based on the oxidation of [2-14C]acetate were 9.4 x 10-3 to 2.4 x 10-1 for the Black Creek aquifer, 1.1 x 10-2 for the Middendorf aquifer, and <7 x 10-5 for the Cape Fear aquifer. These estimates were at least 2 orders of magnitude lower than previously published estimates that were based on the accumulation of CO2 in laboratory incubations of similar deep subsurface sediments. In contrast, geochemical modeling of groundwater chemistry changes along aquifer flowpaths gave rate estimates that ranged from 10-4 to 10-6 mmol of CO2 per liter per year. The age of these sediments (ca. 80 million years) and their organic carbon content suggest that average rates of CO2 production could have been no more than 10-4 mmol per liter per year. Thus, laboratory incubations may greatly overestimate the in situ rates of microbial metabolism in deep subsurface environments. This has important implications for the use of laboratory incubations in attempts to estimate biorestoration capacities of deep aquifers. The rate estimates from geochemical modeling indicate that deep aquifers are among the most oligotrophic aquatic environments in which there is ongoing microbial metabolism.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

PubMed

Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

2017-06-01

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

PubMed Central

Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

2014-01-01

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

Linking Metabolism, Elemental Cycles, and Environmental Conditions in the Deep Biosphere: Growth of a Model Extremophile, Archaeoglobus fulgidus, Under High-Pressure Conditions

NASA Astrophysics Data System (ADS)

Oliver, G. C. M.; Cario, A.; Rogers, K. L.

2015-12-01

A majority of Earth's biosphere is hosted in subsurface environments where global-scale biogeochemical and energy cycles are driven by diverse microbial communities that operate on and are influenced by micro-scale environmental variables. While the subsurface hosts a variety of geochemical and geothermal conditions, elevated pressures are common to all subsurface ecosystems. Understanding how microbes adapt to and thrive in high-pressure environments is essential to linking microbial subsurface processes with global-scale cycles. Here we are using a model extremophile, Archaeoglobus fulgidus, to determine how elevated pressures affect the growth, metabolism, and physiology of subsurface microorganisms. A. fulgidus cycles carbon and sulfur via heterotrophic and autotrophic sulfate reduction in various high temperature and high-pressure niches including shallow marine vents, deep-sea hydrothermal vents, and deep oil reservoirs. Here we report the results of A. fulgidus growth experiments at optimum temperature, 83°C, and pressures up to 600 bars. Exponential growth was observed over the entire pressure range, though growth rates were diminished at 500 and 600 bars compared to ambient pressure experimental controls. At pressures up to 400 bars, cell density yields and growth rates were at least as high as ambient pressure controls. Elevated pressures and extended incubation times stimulated cell flocculation, a common stress response in this strain, and cellular morphology was affected at pressures exceeding 400 bars. These results suggest that A. fulgidus continues carbon, sulfur and energy cycling unaffected by elevated pressures up to 400 bars, representing a variety of subsurface environments. The ability of subsurface organisms to drive biogeochemical cycles at elevated pressures is a critical link between the surface and subsurface biospheres and understanding how species-scale processes operate under these conditions is a vital part of global-scale biogeochemical models.

Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes.

PubMed

Itävaara, M; Salavirta, H; Marjamaa, K; Ruskeeniemi, T

2016-01-01

Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities. Copyright © 2016 Elsevier Inc. All rights reserved.

Differential Bacterial Colonization of Volcanic Minerals in Deep Thermal Basalts

NASA Astrophysics Data System (ADS)

Smith, A. R.; Popa, R.; Fisk, M. R.; Nielsen, M.; Wheat, G.; Jannasch, H.; Fisher, A.; Sievert, S.

2010-04-01

There are reports of microbial weathering patterns in volcanic glass and minerals of both terrestrial and Martian origin. Volcanic minerals are colonized differentially in subsurface hydrothermal environments by a variety of physiological types.

Biofilm formation and potential for iron cycling in serpentinization-influenced groundwater of the Zambales and Coast Range ophiolites.

PubMed

Meyer-Dombard, D'Arcy R; Casar, Caitlin P; Simon, Alexander G; Cardace, Dawn; Schrenk, Matthew O; Arcilla, Carlo A

2018-05-01

Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems. Biofilms formed on rock cores from the Zambales ophiolite on surface and in-pit associations, confirming that organisms from serpentinizing systems can form biofilms in subsurface environments. Analysis by XPS and FTIR confirmed that enrichment culturing utilizing ferric iron growth substrates produced reduced, magnetic solids containing siderite, spinels, and FeO minerals. Microcosms and enrichment cultures supported organisms whose near relatives participate in iron redox transformations. Further, a potential 'principal' microbial community common to solid samples in serpentinizing systems was identified. These results indicate collectively that iron redox transformations should be more thoroughly and universally considered when assessing the function of terrestrial subsurface ecosystems driven by serpentinization.

Non-viable Microbial Community Structure and Geochemistry of Deep Subsurface Shales at Marcellus Shale Energy and Environment Laboratory

NASA Astrophysics Data System (ADS)

Akondi, R.; Trexler, R.; Sharma, S.; Mouser, P. J.; Pfiffner, S. M.

2016-12-01

The deep subsurface is known to harbor diverse communities of living microbes, and can therefore be expected to also harbor an equally diverse and likely different set of non-viable microbial populations. In this study, diglyceride fatty acids, (DGFA, biomarkers for non-viable microbes) as well as their compound specific isotopes (CSIA) were used to study the yield and variety of DGFAs in deep subsurface mid-Devonian sediments of different lithologies. Pristine sidewall cores were obtained from intervals in the Marcellus, Mahantango, and the Marcellus/Mahantango formation interface. The biomarkers were extracted and DGFAs were methylated to fatty acid methyl esters (FAMEs) and analyzed using GC-MS, while the CSIAs were performed using GC-irMS. Sediments were also analyzed for total organic carbon (TOC), stable carbon isotopic composition of organic carbon (δ13Corg), inorganic carbon (δ13Ccarb), and nitrogen (δ15Norg). TOC concentration was highest in the Marcellus and there was a general trend of increasing TOC from Mahantango to the Marcellus. The δ13Corg and δ13Ccarb increased and decreased respectively from Mahantango to the Marcellus while δ15Norg did not show any trend. The FAME profiles consisted of normal saturated, monounsaturated, polyunsaturated, branched, epoxy, terminally branched, hydroxyl, and dimethyl esters. The total biomass yield and variety of DGFA-FAME profiles were higher in the Mahantango compared to the samples from the Marcellus formation and Marcellus/Mahantango interface, suggesting the presence of more paleo-microbial activity in the less consolidated Mahantango formation. We attribute this to the smaller pore throat sizes within the Marcellus formation compared to the Mahantango formation. Since organic matter in the sediments is also one of the key sources of energy for microbial metabolism, bulk 13C and CSIA of the lipids will be used to understand the source(s) and pathways of the carbon cycling within the microbial communities.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea).

PubMed

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

PubMed Central

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin. PMID:26485717

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

PubMed

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-08-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H 2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H 2 , often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H 2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H 2 consumption and retardation of radionuclide migration.

Energy Requirements of Hydrogen-utilizing Microbes: A Boundary Condition for Subsurface Life

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christopher S.

2003-01-01

Microbial ecosystems based on the energy supplied by water-rock chemistry carry particular significance in the context of geo- and astrobiology. With no direct dependence on solar energy, lithotrophic microbes could conceivably penetrate a planetary crust to a depth limited only by temperature or pressure constraints (several kilometers or more). The deep lithospheric habitat is thereby potentially much greater in volume than its surface counterpart, and in addition offers a stable refuge against inhospitable surface conditions related to climatic or atmospheric evolution (e.g., Mars) or even high-energy impacts (e.g., early in Earth's history). The possibilities for a deep microbial biosphere are, however, greatly constrained by life s need to obtain energy at a certain minimum rate (the maintenance energy requirement) and of a certain minimum magnitude (the energy quantum requirement). The mere existence of these requirements implies that a significant fraction of the chemical free energy available in the subsurface environment cannot be exploited by life. Similar limits may also apply to the usefulness of light energy at very low intensities or long wavelengths. Quantification of these minimum energy requirements in terrestrial microbial ecosystems will help to establish a criterion of energetic habitability that can significantly constrain the prospects for life in Earth's subsurface, or on other bodies in the solar system. Our early work has focused on quantifying the biological energy quantum requirement for methanogenic archaea, as representatives of a plausible subsurface metabolism, in anoxic sediments (where energy availability is among the most limiting factors in microbial population growth). In both field and laboratory experiments utilizing these sediments, methanogens retain a remarkably consistent free energy intake, in the face of fluctuating environmental conditions that affect energy availability. The energy yields apparently required by methanogens in these sediment systems for sustained metabolism are about half that previously thought necessary. Lowered energy requirements would imply that a correspondingly greater proportion of the planetary subsurface could represent viable habitat for microorganisms.

Rates and extent of microbial debromination in the deep subseafloor biosphere

NASA Astrophysics Data System (ADS)

Berg, R. D.; Solomon, E. A.; Morris, R. M.

2013-12-01

Recent genomic and porewater geochemical data suggest that reductive dehalogenation of a wide range of halogenated organic compounds could represent an important energy source for deep subseafloor microbial communities. At continental slope sites worldwide, there is a remarkably linear relationship between porewater profiles of ammonium and bromide, indicating that the factors controlling the distribution and rates of dehalogenation have the potential to influence carbon and nitrogen cycling in the deep subsurface biosphere. Though this metabolic pathway could play an important role in the cycling of otherwise refractory pools of carbon and nitrogen in marine sediments and provide energy to microbial communities in the deep subsurface biosphere, the rates and extent of dehalogenation in marine sediments are poorly constrained. Here we report net reaction rate profiles of debromination activity in continental slope sediments, calculated from numerical modeling of porewater bromide profiles from several margins worldwide. The reaction rate profiles indicate three common zones of debromination activity in slope sediments: 1) low rates of debromination, and a potential bromine sink, in the upper sediment column correlating to the sulfate reduction zone, with net bromide removal rates from -3.6 x 10^-2 to -4.85 x 10^-1 μmol m^-2 yr^-1, 2) high rates of debromination from the sulfate-methane transition zone to ~40-100 mbsf, with net bromide release rates between 7.1 x 10^-2 to 3.9 x 10^-1 μmol m^-2 yr^-1, and 3) an inflection point at ~40-100 mbsf, below which net rates of debromination decrease by an order of magnitude and at several sites are indistinguishable from zero. These results indicate that dehalogenating activity is widely distributed in marine sediments, providing energy to fuel deep subseafloor microbial communities, with potentially important consequences for the global bromine and nitrogen cycles.

Microbial Community Shifts due to Hydrofracking: Observations from Field-Scale Observations and Laboratory-Scale Incubations

NASA Astrophysics Data System (ADS)

Mouser, P. J.; Ansari, M.; Hartsock, A.; Lui, S.; Lenhart, J.

2012-12-01

The use of fluids containing chemicals and variable water sources during the hydrofracking of unconventional shale is the source of considerable controversy due to perceived risks from altered subsurface biogeochemistry and the potential for contaminating potable water supplies. Rapid shifts in subsurface biogeochemistry are often driven by available macronutrients combined with the abundance and metabolic condition of the subsurface microbiota. While the depth that fracturing occurs in the Marcellus formation is reasonably deep to pose little risk to groundwater supplies, no published studies have systematically characterized the indigenous microbial population and how this community is altered through variable fluid management practices (e.g., chemical composition, source water makeup). In addition, limited information is available on how shallower microbial communities and geochemical conditions might be affected through the accidental release of these fluids to groundwater aquifers. Our measurements indicate field-applied and laboratory-generated fracking fluids contain levels of organic carbon greater than 300 mg/l and nitrogen concentrations greater than 80 mg/l that may differentially stimulate microbial growth in subsurface formations. In contrast to certain inorganic constituents (e.g., chloride) which increase in concentration through the flowback period; dissolved organic carbon levels decrease with time after the fracturing process through multiple attenuation processes (dilution, sorption, microbial utilization). Pyrosequencing data of the 16S rRNA gene indicate a shift from a more diverse source water microbial community to a less diverse community typical of a brine formation as time after fracturing increases. The introduction of varying percentages of a laboratory-generated fracking fluid to microcosm bottles containing groundwater and aquifer media stimulated biogeochemical changes similar to the introduction of landfill leachate, another wastewater containing elevated carbon, nitrogen, and complex organic constituents (e.g., decreased redox conditions, stepwise utilization of available terminal electron acceptors, enriched Fe(II) and sulfide concentrations). These research findings are important for understanding how fluids used during shale energy development may alter in situ microbial communities and provide insight into processes that attenuate the migration of these fluids in shallow aquifers and deep shale formations.

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. Amore » nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.« less

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

DOE PAGES

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.; ...

2018-01-29

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. Amore » nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.« less

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study

PubMed Central

Frank, Yulia A.; Kadnikov, Vitaly V.; Gavrilov, Sergey N.; Banks, David; Gerasimchuk, Anna L.; Podosokorskaya, Olga A.; Merkel, Alexander Y.; Chernyh, Nikolai A.; Mardanov, Andrey V.; Ravin, Nikolai V.; Karnachuk, Olga V.; Bonch-Osmolovskaya, Elizaveta A.

2016-01-01

The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles. PMID:28082967

Opportunities and challenges in studies of deep life (Invited)

NASA Astrophysics Data System (ADS)

Edwards, K. J.

2010-12-01

Over the past two decades, there has been an increasing awareness within the geological, microbiological, and oceanographic communities of the potentially vast microbial biosphere that is harbored beneath the surface of the Earth. With this awareness has come a mounting effort to study this potential biome - to better quantify biomass abundance, activity, and biogeochemical activity. In the Earth system, the largest deep subsurface biome is also the least accessible - the deep ocean subsurface biosphere. The oceanic deep biosphere also has greatest potential for influencing global scale biogeochemical processes -the carbon and energy cycles for example, and other elemental cycles. To address these topics and mount interdisciplinary efforts to study the deep subsurface marine biosphere, we have recently formed a center in support integrative, collaborative investigations. The national science foundation Center for Dark Biosphere Investigations (C-DEBI), has been initiated for the explicit purpose of resolving the extent, function, dynamics and implications of the subseafloor biosphere. This talk will discuss C-DEBI science, with focus on some of the opportunities and challenges in the study of deep life in the ocean, and the role that C-DEBI will play in meeting them

Trends and Future Challenges in Sampling the Deep Terrestrial Biosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, Michael J.; Daly, Rebecca; Mouser, Paula J.

2014-09-12

Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on “Trends and Future Challenges in Sampling The Deep Subsurface” was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty,more » and sponsored by The Ohio State University and the Sloan Foundation’s Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.« less

Exploring the Deep Biosphere in Ophiolite-hosted Systems: What Can Metabolic Processes in Surface Seeps Tell Us About Subsurface Ecosystems in Serpentinizing Fluids?

NASA Astrophysics Data System (ADS)

Meyer-Dombard, D. R.; Cardace, D.; Woycheese, K. M.; Vallalar, B.; Casar, C.; Simon, A.; Arcilla, C. A.

2016-12-01

Serpentinization in the subsurface produces highly reduced, high pH fluids that provide microbial habitats. It is assumed that these deep subsurface fluids contain copious H2 and CH4 gas, little/no inorganic carbon, and limited electron acceptors. As serpentinized fluids reach the oxygenated surface environment, microbial biomes shift and organisms capable of metabolizing O2 thrive (Woycheese et al., 2015). However, the relationship of microbial communities found in surface expressions of serpentinizing fluids to the subsurface biosphere is still a target of exploration. Our work in the Zambales ophiolite (Philippines) defines surface microbial habitats with geochemistry, targeted culturing efforts, and community analysis (Cardace et al., 2015; Woycheese et al., 2015). Springs range from pH 9-11.5, and contain 0.06-2 ppm DO, 0-3.7 ppm sulfide, 30-800 ppm silica. Gases include H2 and CH4 > 10uM, CO2 > 1 mM, and trace amounts of CO. These surface data allow prediction of the subsurface metabolic landscape. For example, Cardace et al., (2015) predicted that metabolism of iron is important in both biospheres. Growth media were designed to target iron reduction yielding heterotrophic and autotrophic iron reducers at high pH. Reduced iron minerals were produced in several cultures (Casar et al., sub.), and isolation efforts are underway. Shotgun metagenomic analysis shows the metabolic capacity for methanogenesis, suggesting microbial origins for some CH4 present. The enzymes methyl coenzyme M reductase, and formylmethanofuran dehydrogenase were detected, and relative abundance increased near the near-anoxic spring source. The metagenomes indicate carbon cycling at these sites is reliant on methanogenesis, acetogenesis, sulfate reduction, and H2 and CH4 oxidation. In this tropical climate, cellulose is also a likely carbon source; cellulose degrading isolates have been obtained. These results indicate a metabolically flexible community at the surface where serpentinizing fluids are expressed. The next step is to understand what these surface systems might tell us about the subsurface biosphere. References: Cardace et al., 2015 Frontiers in Extreme Microbiology 6: doi: 10.3389/fmicb.2015.00010 Woycheese et al., 2015 Frontiers in Extreme Microbiology 6: doi: 10.3389/fmicb.2015.00044

Feeding a subsurface biosphere: radiolysis and abiogenic energy sources

NASA Astrophysics Data System (ADS)

Onstott, T.

Noble gas analyses of ground water collected from the deep, fractured, basaltic andesite and quartzite Archean strata in South Africa suggest subsurface residence times ranging from tens to hundreds of millions of years. Hydraulically isolated compartments of highly saline water contain hundreds of μM concentrations of gas comprised primarily of C1-4 hydrocarbons, H2 and He, with minor Ar and N .2 Carbon and hydrogen isotopic analyses of the hydrocarbons suggest an abiogenic origin com atible with surface catalysed reductive assimilation (i.e. Fischer-Tropschp synthesis). H2 and He data suggest that the H2 is generated by subsurface radiolysis of water. One sample of a saline, isolated water/gas pocket agrees exactly with that predicted by radioactive decay of U, Th, K in the host rock and indicates a subsurface H2 production rate of 0.1 to 1 nM/yr. Other samples yielded less H2 than predicted and require a sink for this H2 . Possible sinks include microbial H2 oxidation and abiotic formation of hydrocarbons at rates slightly less than the H2 production rate. Highly diffusive H2 is essential for life in deep subsurface environments where only trace amounts of organic carbon exist. Lithoautotrophic microbes can acquire energy from the redox reactions involving H2 with other electron acceptors (Fe3 +, SO4 2 - or CO2 ), to synthesis organic carbon and can be fully independent of solar-driven photosynthesis. The microbial abundance in many of these ground water samples, however, is below our detection limit (<5000 cells/ml). This contrasts with shallow sedimentary aquifers where H2 levels of tens of nM are regulated by the coexistence of autotrophs/lithotrophs and heterotrophs for maximum efficiency of H2 utilization. The excessive H2 found in deep crustal environments implies that these microbial ecosystems are electron-acceptor and or substrate limited. The oxidants generated by water radiolysis interact with the reduced solid phases in the rock matrix, e.g. pyrite, producing potential electron acceptors, e.g. Fe3 +, that may be readily available for consumption by microbial communities than H . Nitrogen doesn't appear to be2 limited, because ammonia concentrations range upwards to tens of μM, but its origin remains a mystery. The unused H2 , CH4 and He continue to migrate upward to shallow aquifers. Microbial H2 oxidation may dominate over Fischer-Tropsch reactions in crustal environments where formation temperatures are <120o C; and vice versa for deeper crustal environments. This H2 cycle should be present on extraterrestrial bodies, producing potential chemical energy and crustal scale diffusive fluxes from the interaction subsurface ice/water and radiogenic decay.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

NASA Astrophysics Data System (ADS)

Jungbluth, Sean P.; Amend, Jan P.; Rappé, Michael S.

2017-03-01

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids.

PubMed

Jungbluth, Sean P; Amend, Jan P; Rappé, Michael S

2017-03-28

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

PubMed Central

Jungbluth, Sean P.; Amend, Jan P.; Rappé, Michael S.

2017-01-01

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation. PMID:28350381

Exploring Microbial Life in Oxic Sediments Underlying Oligotrophic Ocean Gyres

NASA Astrophysics Data System (ADS)

Ziebis, W.; Orcutt, B.; Wankel, S. D.; D'Hondt, S.; Szubin, R.; Kim, J. N.; Zengler, K.

2015-12-01

Oxygen, carbon and nutrient availability are defining parameters for microbial life. In contrast to organic-rich sediments of the continental margins, where high respiration rates lead to a depletion of O2 within a thin layer at the sediment surface, it was discovered that O2 penetrates several tens of meters into organic-poor sediments underlying oligotrophic ocean gyres. In addition, nitrate, another important oxidant, which usually disappears rapidly with depth in anoxic sediments, tends to accumulate above seawater concentrations in the oxic subsurface, reflecting the importance of nitrogen cycling processes, including both nitrification and denitrification. Two IODP drilling expeditions were vital for exploring the nature of the deep subsurface beneath oligotrophic ocean gyres, expedition 329 to the South Pacific Gyre (SPG) and expedition 336 to North Pond, located on the western flank of the Mid-Atlantic ridge beneath the North Atlantic Gyre. Within the ultra-oligotrophic SPG O2 penetrates the entire sediment column from the sediment-water interface to the underlying basement to depths of > 75 m. At North Pond, a topographic depression filled with sediment and surrounded by steep basaltic outcrops, O2 penetrates deeply into the sediment (~ 30 m) until it eventually becomes depleted. O2 also diffuses upward into the sediment from seawater circulating within the young crust underlying the sediment, resulting in a deep oxic layer several meters above the basalt. Despite low organic carbon contents microbial cells persist throughout the entire sediment column within the SPG (> 75 m) and at North Pond, albeit at low abundances. We explored the nature of the subsurface microbial communities by extracting intact cells from large volumes of sediment obtained from drill cores of the two expeditions. By using CARD-FiSH, amplicon (16s rRNA) and metagenome sequencing we shed light on the phylogenetic and functional diversity of the elusive communities residing in the deep oxic sediments of these two different areas. Given the global extent of this oxic subsurface studies of the diversity and metabolic potential of its biome, together with the analyses of porewater geochemical and isotopic composition, are beginning to reveal its role in global biogeochemical cycles.

Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex.

PubMed

Daae, F L; Økland, I; Dahle, H; Jørgensen, S L; Thorseth, I H; Pedersen, R B

2013-07-01

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions. © 2013 John Wiley & Sons Ltd.

Limitations of microbial hydrocarbon degradation at the Amon mud volcano (Nile deep-sea fan)

NASA Astrophysics Data System (ADS)

Felden, J.; Lichtschlag, A.; Wenzhöfer, F.; de Beer, D.; Feseker, T.; Pop Ristova, P.; de Lange, G.; Boetius, A.

2013-05-01

The Amon mud volcano (MV), located at 1250 m water depth on the Nile deep-sea fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulfate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition, and microbial activities over 3 yr, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulfide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. The low microbial activity in the hydrocarbon-vented areas of Amon MV is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer MV area is limited by hydrocarbon transport.

Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs.

PubMed

Brazelton, William J; Morrill, Penny L; Szponar, Natalie; Schrenk, Matthew O

2013-07-01

Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats.

Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs

PubMed Central

Morrill, Penny L.; Szponar, Natalie; Schrenk, Matthew O.

2013-01-01

Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats. PMID:23584766

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

PubMed Central

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-01-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration. PMID:28350393

Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface.

PubMed

Mouser, Paula J; Borton, Mikayla; Darrah, Thomas H; Hartsock, Angela; Wrighton, Kelly C

2016-11-01

Horizontal drilling and hydraulic fracturing are increasingly used for recovering energy resources in black shales across the globe. Although newly drilled wells are providing access to rocks and fluids from kilometer depths to study the deep biosphere, we have much to learn about microbial ecology of shales before and after 'fracking'. Recent studies provide a framework for considering how engineering activities alter this rock-hosted ecosystem. We first provide data on the geochemical environment and microbial habitability in pristine shales. Next, we summarize data showing the same pattern across fractured shales: diverse assemblages of microbes are introduced into the subsurface, eventually converging to a low diversity, halotolerant, bacterial and archaeal community. Data we synthesized show that the shale microbial community predictably shifts in response to temporal changes in geochemistry, favoring conservation of key microorganisms regardless of inputs, shale location or operators. We identified factors that constrain diversity in the shale and inhibit biodegradation at the surface, including salinity, biocides, substrates and redox. Continued research in this engineered ecosystem is required to assess additive biodegradability, quantify infrastructure biocorrosion, treat wastewaters that return to the surface and potentially enhance energy production through in situ methanogenesis. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Biogeography of serpentinite-hosted microbial ecosystems

NASA Astrophysics Data System (ADS)

Brazelton, W.; Cardace, D.; Fruh-Green, G.; Lang, S. Q.; Lilley, M. D.; Morrill, P. L.; Szponar, N.; Twing, K. I.; Schrenk, M. O.

2012-12-01

Ultramafic rocks in the Earth's mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H2). To date, however, the "serpentinite microbiome" is poorly constrained- almost nothing is known about the microbial diversity endemic to rocks actively undergoing serpentinization. Through the Census of Deep Life, we have obtained 16S rRNA gene pyrotag sequences from fluids and rocks from serpentinizing ophiolites in California, Canada, and Italy. The samples include high pH serpentinite springs, presumably representative of deeper environments within the ophiolite complex, wells which directly access subsurface aquifers, and rocks obtained from drill cores into serpentinites. These data represent a unique opportunity to examine biogeographic patterns among a restricted set of microbial taxa that are adapted to similar environmental conditions and are inhabiting sites with related geological histories. In general, our results point to potentially H2-utilizing Betaproteobacteria thriving in shallow, oxic-anoxic transition zones and anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These general taxonomic and biogeochemical trends were also observed in seafloor Lost City hydrothermal chimneys, indicating that we are beginning to identify a core serpentinite microbial community that spans marine and continental settings.

Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

PubMed

Anderson, Rika E; Sogin, Mitchell L; Baross, John A

2015-01-01

Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Exploring Genomic Diversity Using Metagenomics of Deep-Sea Subsurface Microbes from the Louisville Seamount and the South Pacific Gyre

NASA Astrophysics Data System (ADS)

Tully, B. J.; Sylvan, J. B.; Heidelberg, J. F.; Huber, J. A.

2014-12-01

There are many limitations involved with sampling microbial diversity from deep-sea subsurface environments, ranging from physical sample collection, low microbial biomass, culturing at in situ conditions, and inefficient nucleic acid extractions. As such, we are continually modifying our methods to obtain better results and expanding what we know about microbes in these environments. Here we present analysis of metagenomes sequences from samples collected from 120 m within the Louisville Seamount and from the top 5-10cm of the sediment in the center of the south Pacific gyre (SPG). Both systems are low biomass with ~102 and ~104 cells per cm3 for Louisville Seamount samples analyzed and the SPG sediment, respectively. The Louisville Seamount represents the first in situ subseafloor basalt and the SPG sediments represent the first in situ low biomass sediment microbial metagenomes. Both of these environments, subseafloor basalt and sediments underlying oligotrophic ocean gyres, represent large provinces of the seafloor environment that remain understudied. Despite the low biomass and DNA generated from these samples, we have generated 16 near complete genomes (5 from Louisville and 11 from the SPG) from the two metagenomic datasets. These genomes are estimated to be between 51-100% complete and span a range of phylogenetic groups, including the Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi, and unclassified bacterial groups. With these genomes, we have assessed potential functional capabilities of these organisms and performed a comparative analysis between the environmental genomes and previously sequenced relatives to determine possible adaptations that may elucidate survival mechanisms for these low energy environments. These methods illustrate a baseline analysis that can be applied to future metagenomic deep-sea subsurface datasets and will help to further our understanding of microbiology within these environments.

Microbes of deep marine sediments as viewed by metagenomics

NASA Astrophysics Data System (ADS)

Biddle, J.

2015-12-01

Ten years after the first deep marine sediment metagenome was produced, questions still exist about the nucleic acid sequences we have retrieved. Current data sets, including the Peru Margin, Costa Rica Margin and Iberian Margin show that consistently, data forms larger assemblies at depth due to the reduced complexity of the microbial community. But are these organisms active or preserved? At SMTZs, a change in the assembly statistics is noted, as well as an increase in cell counts, suggesting that cells are truly active. As depth increases, genome sizes are consistently large, suggesting that much like soil microbes, sedimentary microbes may maintain a larger reportorie of genomic potential. Functional changes are seen with depth, but at many sites are not correlated to specific geochemistries. Individual genomes show changes with depth, which raises interesting questions on how the subsurface is settled and maintained. The subsurface does have a distinct genomic signature, including unusual microbial groups, which we are now able to analyze for total genomic content.

Active fungi amidst a marine subsurface RNA paleome

NASA Astrophysics Data System (ADS)

Orsi, W.; Biddle, J.; Edgcomb, V.

2012-12-01

The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Since extracellular DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA signatures by amplicon pyrosequencing, metazoan, plant, and diatom rRNA signatures were recovered from marine sediments up to 2.7 million years old, suggesting that rRNA may be much more stable than previously considered in the marine subsurface. This finding confirms the concept of a paleome, extending it to include rRNA. Within the same dataset, unique profiles of fungi were found across a range of marine subsurface provinces exhibiting statistically significant correlations with total organic carbon (TOC), sulfide, and dissolved inorganic carbon (DIC). Sequences from metazoans, plants and diatoms showed different correlation patterns, consistent with a depth-controlled paleome. The fungal correlations with geochemistry allow the inference that some fungi are active and adapted for survival in the marine subsurface. A metatranscriptomic analysis of fungal derived mRNA confirms that fungi are metabolically active and utilize a range of organic and inorganic substrates in the marine subsurface.

Microbial diversity in Cenozoic sediments recovered from the Lomonosov Ridge in the Central Arctic basin.

PubMed

Forschner, Stephanie R; Sheffer, Roberta; Rowley, David C; Smith, David C

2009-03-01

The current understanding of microbes inhabiting deeply buried marine sediments is based largely on samples collected from continental shelves in tropical and temperate latitudes. The geographical range of marine subsurface coring was expanded during the Integrated Ocean Drilling Program Arctic Coring Expedition (IODP ACEX). This expedition to the ice-covered central Arctic Ocean successfully cored the entire 428 m sediment stack on the Lomonosov Ridge during August and September 2004. The recovered cores vary from siliciclastic sediment low in organic carbon (< 0.2%) to organic rich ( approximately 3%) black sediments that rapidly accumulated in the early middle Eocene. Three geochemical environments were characterized based on chemical analyses of porewater: an upper ammonium oxidation zone, a carbonate dissolution zone and a deep (> 200 m below sea floor) sulfate reduction zone. The diversity of microbes within each zone was assessed using 16S rRNA phylogenetic markers. Bacterial 16S rRNA genes were successfully amplified from each of the biogeochemical zones, while archaea was only amplified from the deep sulfate reduction zone. The microbial communities at each zone are phylogenetically different and are most closely related to those from other deep subsurface environments.

Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

PubMed Central

Holman, Hoi-Ying N.; DeSantis, Todd Z.; Wanner, Gerhard; Andersen, Gary L.; Perras, Alexandra K.; Meck, Sandra; Völkel, Jörg; Bechtel, Hans A.; Wirth, Reinhard; Moissl-Eichinger, Christine

2014-01-01

Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses. PMID:24971452

DUSEL and the future of deep terrestrial microbiology (Invited)

NASA Astrophysics Data System (ADS)

Onstott, T. C.; Peters, C. A.; Murdoch, L. C.; Elsworth, D.; Sonnenthal, E. L.; Kieft, T.; Boutt, D. F.; Germanovich, L.; Glaser, S. D.; Wang, H. F.; Roggenthen, B.; Lesko, K.; Cushman, P.; Stetler, L. D.; Bang, S.; Anderson, C.

2009-12-01

DUSEL will take advantage of the existing subsurface architecture of the deepest mine in the U.S. to provide a platform for launching new exploration into the deep terrestrial biosphere. Multi-year experiments are currently being designed to delineate the relationships between microbial diversity and activity and hydraulic connectivity, temperature, pressure, strain rate and multiphase fluids. Unlike the physics experiments, which will be located close to the center of the mine, most of these experiments will be located at the periphery in existing tunnels at 100 to 2400 m depth in order to access fluid fill fractures with boreholes. Hydrological models suggest that DUSEL could sample ~100 km3 volume for microbial biogeographic and transport studies. The high-capacity underground water filtration plant used to generate ultrapure water for neutrino detectors will readily supply water for microbiology coring projects reducing microbial contamination. This will be essential for the drilling platform located at 2400 m depth that will drill down to 7+ km and 120oC in search of the upper temperature limit for life. Another advantage of underground coring is that the drilling fluid pressure will be much less than that of the fracture water, which means that when the coring bit intersects a water-filled fracture, the fracture water will flow into the core barrel reducing the contamination of fracture surfaces in the cores. The ultra-low radiation background counting facility to be located at 1475 m depth will potentially enable 106 times improvement in the detection limit for subsurface microbial respiration rates using radioactive tracers. The Coupled Thermal-Hydrological-Mechanical-Chemical-Biological, block-heating experiment will examine how the microbial communities within fractures respond to the increased thermal and fluid flux. The Fracture Processes Facility is not only designed to determine what controls rock strength, but could also determine to what extent subsurface chemoautotrophic activity is regulated by tectonic episodicity. The DUSEL CO2 Facility will investigate how microbial activity is impacted by CO2 injection and whether microbial activity has a significant impact upon long-term sequestration of CO2. These three experiments represent a subset of the integrated suite of experiments planned for the first 5 years, but many more microbial experiments can be accommodated within DUSEL. With its unique experimental assets, km-scale spatial access and multi-decade observational lifetime, DUSEL will usher in the next generation of exploration into the deep terrestrial biosphere and not only reveal the answers to many of its well-hidden secrets, but perhaps to the origin of life itself.

Effects of remediation amendments on vadose zone microorganisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Hannah M.; Tilton, Fred A.

2012-08-10

Surfactant-based foam delivery technology has been studied to remediate Hanford 200 area deep vadose zone sediment. However, the surfactants and remediation amendments have an unknown effect on indigenous subsurface microorganisms. Microbial populations are important factors to consider in remediation efforts due to their potential to alter soil geochemistry. This project focuses on measuring microbial metabolic responses to remediation amendments in batch and column studies using Deep Vadose Zone Sediments. Initial studies of the microbes from Hanford 200 area deep vadose zone sediment showed surfactants sodium dodecyl sulfate (SDS) and cocamidopropyl betaine (CAPB) and remediation amendment calcium polysulfide (CPS) had nomore » affect on microbial growth using BiologTM Ecoplates. To move towards a more realistic field analog, soil columns were packed with Hanford 200 Area sediment. Once microbial growth in the column was verified by observing growth of the effluent solution on tryptic soy agar plates, remedial surfactants were injected into the columns, and the resulting metabolic diversity was measured. Results suggest surfactant sodium dodecyl sulfate (SDS) stimulates microbial growth. The soil columns were also visualized using X-ray microtomography to inspect soil packing and possibly probe for evidence of biofilms. Overall, BiologTM Ecoplates provide a rapid assay to predict effects of remediation amendments on Hanford 200 area deep vadose zone microorganisms.« less

Limitations of microbial hydrocarbon degradation at the Amon Mud Volcano (Nile Deep Sea Fan)

NASA Astrophysics Data System (ADS)

Felden, J.; Lichtschlag, A.; Wenzhöfer, F.; de Beer, D.; Feseker, T.; Pop Ristova, P.; de Lange, G.; Boetius, A.

2013-01-01

The Amon mud volcano (MV), located at 1250 m water depth on the Nile Deep Sea Fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulphate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition and microbial activities over three years, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulphide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. Furthermore, within three years, cell numbers and hydrocarbon degrading activity increased at the gas-seeping sites. The low microbial activity in the hydrocarbon-vented areas of Amon mud volcano is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer mud volcano area is limited by hydrocarbon transport.

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations

PubMed Central

Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

2016-01-01

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow ‘modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, ‘old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community. PMID:26484735

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

PubMed

Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

2016-05-01

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

Formation of recent Pb-Ag-Au mineralization by potential sub-surface microbial activity

NASA Astrophysics Data System (ADS)

Tornos, Fernando; Velasco, Francisco; Menor-Salván, César; Delgado, Antonio; Slack, John F.; Escobar, Juan Manuel

2014-08-01

Las Cruces is a base-metal deposit in the Iberian Pyrite Belt, one of the world’s best-known ore provinces. Here we report the occurrence of major Pb-Ag-Au mineralization resulting from recent sub-surface replacement of supergene oxyhydroxides by carbonate and sulphide minerals. This is probably the largest documented occurrence of recent microbial activity producing an ore assemblage previously unknown in supergene mineralizing environments. The presence of microbial features in the sulphides suggests that these may be the first-described natural bacteriomorphs of galena. The low δ13C values of the carbonate minerals indicate formation by deep anaerobic microbial processes. Sulphur isotope values of sulphides are interpreted here as reflecting microbial reduction in a system impoverished in sulphate. We suggest that biogenic activity has produced around 3.1 × 109 moles of reduced sulphur and 1010 moles of CO2, promoting the formation of ca. 1.19 Mt of carbonates, 114,000 t of galena, 638 t of silver sulphides and 6.5 t of gold.

Ocean Drilling Program Contributions to the Understanding of the Deep Subsurface Biosphere

NASA Astrophysics Data System (ADS)

Fisk, M. R.

2003-12-01

Tantalizing evidence for microbes in oceanic basalts has been reported for a few decades, but it was from rocks cored on Ocean Drilling Program (ODP) Leg 148 in 1993 that the first clear-cut evidence of microbial invasion of ocean basalts was obtained. (Work on ODP legs, starting with Leg 112 in 1986, had already revealed the presence of significant microbial biomass in sediments.) In 1997 ODP created the Deep Biosphere Program Planning Group to promote the investigation of the microbiology of the ocean crust. In 1999 ODP built a microbiology lab on the JOIDES Resolution, and used the lab that year (Legs 185 and 187) to test the amount of microbial contamination introduced into rocks during drilling and to establish cultures from cored basalts. These experiments have been repeated on several legs since then. The development of CORKs has permitted long-term sampling of subseafloor fluids, and microorganisms have been recovered from CORKed holes. Thus, ODP made it possible for the scientific community to address major questions about the biology of the igneous crust, such as, (1) What microbes are present? (2) How abundant are they? (3) How are they distributed? DNA from basalts and subseafloor fluids reveal what types of organisms are present. Cell abundance and biomass have been estimated based on cell counts and on organic content of basalts. Surveys of basalts in DSDP/ODP repositories indicate that microorganisms are ubiquitous in the igneous crust. Microorganisms are found in rocks that are close to 100° C. They are found as deep as 1500 m below the sea floor, and in rocks as young as a few years and as old as 170 million years. Because of the vast size of the habitat, microorganism, even if present in small numbers, could be a significant fraction of the Earth's biomass. In a short time ODP contributed to advances in our understanding of the oceanic subsurface biosphere. Answers to other significant questions such as: (1) How do the microorganisms live?, (2) What impact do subsurface microorganisms have on the surface biosphere? (3) And, what roles do the subsurface biosphere play in element cycling? will be answered by future drilling. The International Ocean Drilling Program (IODP) is in the enviable position of providing support to address these key questions about the Earth's subsurface biosphere.

Spatial Autocorrelation, Source Water and the Distribution of Total and Viable Microbial Abundances within a Crystalline Formation to a Depth of 800 m

PubMed Central

Beaton, E. D.; Stuart, Marilyne; Stroes-Gascoyne, Sim; King-Sharp, Karen J.; Gurban, Ioana; Festarini, Amy; Chen, Hui Q.

2017-01-01

Proposed radioactive waste repositories require long residence times within deep geological settings for which we have little knowledge of local or regional subsurface dynamics that could affect the transport of hazardous species over the period of radioactive decay. Given the role of microbial processes on element speciation and transport, knowledge and understanding of local microbial ecology within geological formations being considered as host formations can aid predictions for long term safety. In this relatively unexplored environment, sampling opportunities are few and opportunistic. We combined the data collected for geochemistry and microbial abundances from multiple sampling opportunities from within a proposed host formation and performed multivariate mixing and mass balance (M3) modeling, spatial analysis and generalized linear modeling to address whether recharge can explain how subsurface communities assemble within fracture water obtained from multiple saturated fractures accessed by boreholes drilled into the crystalline formation underlying the Chalk River Laboratories site (Deep River, ON, Canada). We found that three possible source waters, each of meteoric origin, explained 97% of the samples, these are: modern recharge, recharge from the period of the Laurentide ice sheet retreat (ca. ∼12000 years before present) and a putative saline source assigned as Champlain Sea (also ca. 12000 years before present). The distributed microbial abundances and geochemistry provide a conceptual model of two distinct regions within the subsurface associated with bicarbonate – used as a proxy for modern recharge – and manganese; these regions occur at depths relevant to a proposed repository within the formation. At the scale of sampling, the associated spatial autocorrelation means that abundances linked with geochemistry were not unambiguously discerned, although fine scale Moran’s eigenvector map (MEM) coefficients were correlated with the abundance data and suggest the action of localized processes possibly associated with the manganese and sulfate content of the fracture water. PMID:28974945

Fe-oxide grain coatings support bacterial Fe-reducing metabolisms in 1.7−2.0 km-deep subsurface quartz arenite sandstone reservoirs of the Illinois Basin (USA)

PubMed Central

Dong, Yiran; Sanford, Robert A.; Locke, Randall A.; Cann, Isaac K.; Mackie, Roderick I.; Fouke, Bruce W.

2014-01-01

The Cambrian-age Mt. Simon Sandstone, deeply buried within the Illinois Basin of the midcontinent of North America, contains quartz sand grains ubiquitously encrusted with iron-oxide cements and dissolved ferrous iron in pore-water. Although microbial iron reduction has previously been documented in the deep terrestrial subsurface, the potential for diagenetic mineral cementation to drive microbial activity has not been well studied. In this study, two subsurface formation water samples were collected at 1.72 and 2.02 km, respectively, from the Mt. Simon Sandstone in Decatur, Illinois. Low-diversity microbial communities were detected from both horizons and were dominated by Halanaerobiales of Phylum Firmicutes. Iron-reducing enrichment cultures fed with ferric citrate were successfully established using the formation water. Phylogenetic classification identified the enriched species to be related to Vulcanibacillus from the 1.72 km depth sample, while Orenia dominated the communities at 2.02 km of burial depth. Species-specific quantitative analyses of the enriched organisms in the microbial communities suggest that they are indigenous to the Mt. Simon Sandstone. Optimal iron reduction by the 1.72 km enrichment culture occurred at a temperature of 40°C (range 20–60°C) and a salinity of 25 parts per thousand (range 25–75 ppt). This culture also mediated fermentation and nitrate reduction. In contrast, the 2.02 km enrichment culture exclusively utilized hydrogen and pyruvate as the electron donors for iron reduction, tolerated a wider range of salinities (25–200 ppt), and exhibited only minimal nitrate- and sulfate-reduction. In addition, the 2.02 km depth community actively reduces the more crystalline ferric iron minerals goethite and hematite. The results suggest evolutionary adaptation of the autochthonous microbial communities to the Mt. Simon Sandstone and carries potentially important implications for future utilization of this reservoir for CO2 injection. PMID:25324834

Terrestrial Subsurface Ecosystem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, Michael J.; Fredrickson, Jim K.

2015-10-15

The Earth’s crust is a solid cool layer that overlays the mantle, with a varying thickness of between 30-50 km on continental plates, and 5-10 km on oceanic plates. Continental crust is composed of a variety of igneous, metamorphic, and sedimentary rocks that weather and re-form over geologic cycles lasting millions to billions of years. At the crust surface, these weathered minerals and organic material combine to produce a variety of soils types that provide suitable habitats and niches for abundant microbial diversity (see Chapter 4). Beneath this soil zone is the subsurface. Once thought to be relatively free ofmore » microorganisms, recent estimates have calculated that between 1016-1017 g C biomass (2-19% of Earth’s total biomass) may be present in this environment (Whitman et al., 1998;McMahon and Parnell, 2014). Microbial life in the subsurface exists across a wide range of habitats: in pores associated with relatively shallow unconsolidated aquifer sediments to fractures in bedrock formations that are more than a kilometer deep, where extreme lithostatic pressures and temperatures are encountered. While these different environments contain varying physical and chemical conditions, the absence of light is a constant. Despite this, diverse physiologies and metabolisms enable microorganisms to harness energy and carbon for growth in water-filled pore spaces and fractures. Carbon and other element cycles are driven by microbial activity, which has implications for both natural processes and human activities in the subsurface, e.g., bacteria play key roles in both hydrocarbon formation and degradation. Hydrocarbons are a major focus for human utilization of the subsurface, via oil and gas extraction and potential geologic CO2 sequestration. The subsurface is also utilized or being considered for sequestered storage of high-level radioactive waste from nuclear power generation and residual waste from past production of weapons grade nuclear materials. While our understanding of the subsurface is continually improving, it is clear that only a small fraction of microbial habitats have been sampled and studied. In this chapter, we will discuss these studies in the context of the distribution of microbial life in the subsurface, the stresses that microorganisms must overcome to survive in these environments, and the metabolic strategies that are employed to harness energy in a region of the planet far-removed from sunlight. Finally, we will consider both beneficial and deleterious effects of microbial activity in the subsurface on human activities in this environment.« less

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats.

PubMed

Dick, Gregory J; Anantharaman, Karthik; Baker, Brett J; Li, Meng; Reed, Daniel C; Sheik, Cody S

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales.

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats

PubMed Central

Dick, Gregory J.; Anantharaman, Karthik; Baker, Brett J.; Li, Meng; Reed, Daniel C.; Sheik, Cody S.

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales. PMID:23720658

Long-term fluid expulsion revealed by carbonate crusts and pockmarks connected to subsurface gas anomalies and palaeo-channels in the central North Sea

NASA Astrophysics Data System (ADS)

Chand, Shyam; Crémière, Antoine; Lepland, Aivo; Thorsnes, Terje; Brunstad, Harald; Stoddart, Daniel

2017-06-01

Gas seepage through the seafloor into the water column is inferred based on acoustic mapping, video observations and geochemical analyses at multiple locations in the Viking Graben and Utsira High areas of the central North Sea. Flares in the Viking Graben occur both inside and along the periphery of a submarine melt water channel where pockmarks (up to 500 m in diameter) and methane-derived carbonate crusts are found on the seafloor, indicating focussing of fluid flow in the vicinity of the channel. The flares can be related to gas accumulations close to the seafloor as well as in Quaternary and deeper strata, observed as high-amplitude reflections on seismic data. Many palaeo-channels, which act as accumulation zones, are observed in the subsurface of both the Viking Graben and Utsira High areas. The deeper origin of gas is partially supported by results of isotope analyses of headspace gas collected from sediment samples of the Viking Graben, which show a mixed microbial/thermogenic origin whereas isotope data on free seeping gas in the Viking Graben indicate a predominantly microbial origin. Based on these lines of evidence, a structure-controlled fluid flow model is proposed whereby hydrocarbons migrate in limited amount from deep thermogenic reservoirs along faults, and these deep fluids are strongly diluted by microbial methane. Moreover, the existence of subsurface pockmarks at several stratigraphic levels indicates long-term fluid flow, interpreted to be caused by gas hydrate destabilisation and stress-related high overpressures.

Genomic evidence for the Wood-Ljungdahl pathway for carbon fixation in warm basaltic ocean crust

NASA Astrophysics Data System (ADS)

Smith, A. R.; Fisk, M. R.; Mueller, R.; Colwell, F. S.; Mason, O. U.; Popa, R.

2016-12-01

Microbial life in the deep suboceanic aquifer can harness geochemical energy resulting from water-rock reactions and contribute to carbon cycling in the ocean via primary production, or chemosynthesis. Iron-bearing minerals such as olivine in oceanic crust can produce molecular hydrogen, small molecular weight hydrocarbons, and hydrogen sulfide as they react with seawater. Although this generally occurs in serpentinizing systems at very high temperatures deep in the subsurface, it has also been hypothesized to drive the subseafloor microbial ecosystems present in shallower basaltic aquifers. We present genome-based evidence for chemolithoautotrophic microbes present on the surface of olivine incubated in Juan de Fuca Ridge basaltic ocean crust for a 4-year period. These metagenome-derived genomes show dominant taxa capable of using both branches of the Wood-Ljungdahl pathway for carbon fixation and energy generation. This pathway uses molecular hydrogen potentially derived from the olivine surface as it reacts with seawater and CO2 which is inherent to seawater. These taxa were not reported from aquifer fluid samples, but have been found only in association with mineral surfaces in this study location. Most taxa in this simple community are distant relatives of cultured taxa; therefore this genome information is crucial to understanding how the subseafloor aquifer community is structured, how it obtains energy, how it cycles carbon, and gives us keys to help cultivate these organisms in the laboratory. Our findings also support the Subsurface Lithoautotrophic Microbial Ecosystem (SLiME) hypothesis and have implications for understanding life on early Earth and the potential for life in the Martian subsurface.

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-03-01

The Earth's Critical Zone (CZ) is the critical, outer shell of the Earth that provides an arena for the interplay of diverse physical, chemical, and biological processes that are fundamental for sustaining life. As microbes are the principle drivers of biogeochemical cycles, it is necessary to understand the biodiversity of the CZ unseen majority and their impact on life-sustaining processes. This review aims to summarize the factors controlling where microbes (prokaryotes and micro-eukaryotes) live within the CZ and what is known to date about their diversity and function. Microbes live in all regions of the CZ down to 5 km depth, but due to changing habitat complexity, e.g., variability in pore spaces, water, oxygen, and nutrients, their functional role changes with depth. The abundance of prokaryotes and micro-eukaryotes decreases from a maximum of 1010 or 107 cells g soil-1 up to eight orders of magnitude with depth. Symbiotic mycorrhizal fungi and free-living decomposers are best understood in soil habitats, where they are up to 103 cells g soil-1. However, little is known about their identity and impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that these organisms are either limited in space or nutrients or unable to cope with oxygen limitations. Since deep regions of the CZ are limited in the recent input of photosynthesis-derived carbon, microbes are dependent on deposited organic material or on chemolithoautotrophic metabolism that allows for the establishment of a complete food chain independent from the surface. However, the energy flux available might only allow cell growth over tens to thousands of years. The recent development of "omics" technologies has provided microbial ecologists with methods to link the composition and function of in situ microbial communities. We should expect new metabolic discoveries as we have a closer look utilizing a polyphasic approach into the microbial communities of the CZ. Thus, future work is still needed to link microbial biodiversity to the exact role of microbes in weathering and geochemical cycling in the CZ, especially in subsurface habitats.

Detection of microbes in the subsurface

NASA Technical Reports Server (NTRS)

White, David C.; Tunlid, Anders

1989-01-01

The search for evidence of microbial life in the deep subsurface of Earth has implications for the Mars Rover Sampling Return Missions program. If suitably protected environments can be found on Mars then the instrumentation to detect biomarkers could be used to examine the molecular details. Finding a lipid in Martian soil would represent possibly the simplest test for extant or extinct life. A device that could do a rapid extraction possibly using the supercritical fluid technology under development now with a detection of the carbon content would clearly indicate a sample to be returned.

Delving into the Deep Biosphere

NASA Astrophysics Data System (ADS)

Grim, S. L.; Sogin, M. L.; Boetius, A.; Briggs, B. R.; Brazelton, W. J.; D'Hondt, S. L.; Edwards, K. J.; Fisk, M. R.; Gaidos, E.; Gralnick, J.; Hinrichs, K.; Lazar, C.; Lavalleur, H.; Lever, M. A.; Marteinsson, V.; Moser, D. P.; Orcutt, B.; Pedersen, K.; Popa, R.; Ramette, A.; Schrenk, M. O.; Sylvan, J. B.; Smith, A. R.; Teske, A.; Walsh, E. A.; Colwell, F. S.

2013-12-01

The Census of Deep Life organized an international survey of microbial community diversity in terrestrial and marine deep subsurface environments. Habitats included subsurface continental fractured rock aquifers, volcanic and metamorphic subseafloor sedimentary units from the open ocean, subsurface oxic and anoxic sediments and underlying basaltic oceanic crust, and their overlying water columns. Our survey employed high-throughput pyrosequencing of the hypervariable V4-V6 16S rRNA gene of bacteria and archaea. We detected 1292 bacterial genera representing 40 phyla, and 99 archaeal genera from 30 phyla. Of these, a core group of thirteen bacterial genera occurred in every environment. A genus of the South African Goldmine Group (Euryarchaeota) was always present whenever archaea were detected. Members of the rare biosphere in one system often represented highly abundant taxa in other environments. Dispersal could account for this observation but mechanisms of transport remain elusive. Ralstonia (Betaproteobacteria) represented highly abundant taxa in marine communities and terrestrial rock, but generally low abundance organisms in groundwater. Some of these taxa could represent sample contamination, and their extensive distribution in several systems requires further assessment. An unknown Sphingobacteriales (Bacteroidetes) genus, Stenotrophomonas (Gammaproteobacteria), Acidovorax and Aquabacterium (both Betaproteobacteria), a Chlorobiales genus, and a TM7 genus were in the core group as well but more prevalent in terrestrial environments. Similarly, Bacillus (Firmicutes), a new cyanobacterial genus, Bradyrhizobium and Sphingomonas (both Alphaproteobacteria), a novel Acidobacteriaceae genus, and Variovorax (Betaproteobacteria) frequently occurred in marine systems but represented low abundance taxa in other environments. Communities tended to cluster by biome and material, and many genera were unique to systems. For example, certain Rhizobiales (Alphaproteobacteria) only occurred in groundwater, and select Firmicutes and actinobacterial taxa were specific to rock environments. We continue to investigate the ecological and physiological context of these organisms. By combining deep sequencing of microbial communities and geochemical and physical evaluations of their environments, we bring to light the diversity and scope of the deep biosphere and insight into the factors that determine the nature of these communities.

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy

PubMed Central

Pachiadaki, Maria G.; Rédou, Vanessa; Beaudoin, David J.; Burgaud, Gaëtan; Edgcomb, Virginia P.

2016-01-01

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere. PMID:27375571

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy.

PubMed

Pachiadaki, Maria G; Rédou, Vanessa; Beaudoin, David J; Burgaud, Gaëtan; Edgcomb, Virginia P

2016-01-01

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.

Microbial Community Responses to Organophosphate Substrate Additions in Contaminated Subsurface Sediments

PubMed Central

Martinez, Robert J.; Wu, Cindy H.; Beazley, Melanie J.; Andersen, Gary L.; Conrad, Mark E.; Hazen, Terry C.; Taillefert, Martial; Sobecky, Patricia A.

2014-01-01

Background Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. Methodology/Principal Findings Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO4 3−) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%–50% and 3%–17% of total detected Archaea and Bacteria, respectively. Conclusions/Significance This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration. PMID:24950228

Metagenomic Evidence for H2 Oxidation and H2 Production by Serpentinite-Hosted Subsurface Microbial Communities

PubMed Central

Brazelton, William J.; Nelson, Bridget; Schrenk, Matthew O.

2012-01-01

Ultramafic rocks in the Earth’s mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H2). In order to assess the potential for microbial H2 utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the Lost City hydrothermal field) and two continental serpentinite-hosted alkaline seeps (at the Tablelands Ophiolite, Newfoundland). Novel [NiFe]-hydrogenase sequences were identified at both the marine and continental sites, and in both cases, phylogenetic analyses indicated aerobic, potentially autotrophic Betaproteobacteria belonging to order Burkholderiales as the most likely H2-oxidizers. Both sites also yielded metagenomic evidence for microbial H2 production catalyzed by [FeFe]-hydrogenases in anaerobic Gram-positive bacteria belonging to order Clostridiales. In addition, we present metagenomic evidence at both sites for aerobic carbon monoxide utilization and anaerobic carbon fixation via the Wood–Ljungdahl pathway. In general, our results point to H2-oxidizing Betaproteobacteria thriving in shallow, oxic–anoxic transition zones and the anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These data demonstrate the feasibility of metagenomic investigations into novel subsurface habitats via surface-exposed seeps and indicate the potential for H2-powered primary production in serpentinite-hosted subsurface habitats. PMID:22232619

Metagenomic evidence for h(2) oxidation and h(2) production by serpentinite-hosted subsurface microbial communities.

PubMed

Brazelton, William J; Nelson, Bridget; Schrenk, Matthew O

2012-01-01

Ultramafic rocks in the Earth's mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H(2)). In order to assess the potential for microbial H(2) utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the Lost City hydrothermal field) and two continental serpentinite-hosted alkaline seeps (at the Tablelands Ophiolite, Newfoundland). Novel [NiFe]-hydrogenase sequences were identified at both the marine and continental sites, and in both cases, phylogenetic analyses indicated aerobic, potentially autotrophic Betaproteobacteria belonging to order Burkholderiales as the most likely H(2)-oxidizers. Both sites also yielded metagenomic evidence for microbial H(2) production catalyzed by [FeFe]-hydrogenases in anaerobic Gram-positive bacteria belonging to order Clostridiales. In addition, we present metagenomic evidence at both sites for aerobic carbon monoxide utilization and anaerobic carbon fixation via the Wood-Ljungdahl pathway. In general, our results point to H(2)-oxidizing Betaproteobacteria thriving in shallow, oxic-anoxic transition zones and the anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These data demonstrate the feasibility of metagenomic investigations into novel subsurface habitats via surface-exposed seeps and indicate the potential for H(2)-powered primary production in serpentinite-hosted subsurface habitats.

Characterizing Microbial Diversity and Function in Natural Subsurface CO2 Reservoir Systems for Applied Use in Geologic Carbon Sequestration Environments

NASA Astrophysics Data System (ADS)

Freedman, A.; Thompson, J. R.

2013-12-01

The injection of CO2 into geological formations at quantities necessary to significantly reduce CO2 emissions will represent an environmental perturbation on a continental scale. The extent to which biological processes may play a role in the fate and transport of CO2 injected into geological formations has remained an open question due to the fact that at temperatures and pressures associated with reservoirs targeted for sequestration CO2 exists as a supercritical fluid (scCO2), which has generally been regarded as a sterilizing agent. Natural subsurface accumulations of CO2 serve as an excellent analogue for studying the long-term effects, implications and benefits of CO2 capture and storage (CCS). While several geologic formations bearing significant volumes of nearly pure scCO2 phases have been identified in the western United States, no study has attempted to characterize the microbial community present in these systems. Because the CO2 in the region is thought to have first accumulated millions of years ago, it is reasonable to assume that native microbial populations have undergone extensive and unique physiological and behavioral adaptations to adjust to the exceedingly high scCO2 content. Our study focuses on the microbial communities associated with the dolomite limestone McElmo Dome scCO2 Field in the Colorado Plateau region, approximately 1,000 m below the surface. Fluid samples were collected from 10 wells at an industrial CO2 production facility outside Cortez, CO. Subsamples preserved on site in 3.7% formaldehyde were treated in the lab with Syto 9 green-fluorescent nucleic acid stain, revealing 3.2E6 to 1.4E8 microbial cells per liter of produced fluid and 8.0E9 cells per liter of local pond water used in well drilling fluids. Extracted DNAs from sterivex 0.22 um filters containing 20 L of sample biomass were used as templates for PCR targeting the 16S rRNA gene. 16S rRNA amplicons from these samples were cloned, sequenced and subjected to microbial community analysis to test the hypothesis that a low but non-zero diversity that includes taxa from other subsurface environments will be present, reflecting the extreme ecological selective pressures of scCO2. A wide range of phylogenies have been identified, including genera that fall within the Proteobacteria, Bacilli, and Clostridial classes. Several species identified by 16S BLAST best hits are also known to inhabit deep subsurface environments, preliminarily confirming that a non-zero diversity has been able to survive, and possibly thrive, in the extreme scCO2-exposed deep subsurface environment at McElmo Dome. It thus appears that at least a subsection of native subsurface community biota may withstand the severe stresses associated with the injection of scCO2 for long-term geologic carbon sequestration efforts.

Deep-Subterranean Microbial Habitats in the Hishikari Epithermal Gold Mine: Active Thermophilic Microbial Communities and Endolithic Ancient Microbial Relicts.

NASA Astrophysics Data System (ADS)

Hirayama, H.; Takai, K.; Inagaki, F.; Horikoshi, K.

2001-12-01

Deep subterranean microbial community structures in an epithermal gold-silver deposit, Hishikari gold mine, southern part of Kyusyu Japan, were evaluated through the combined use of enrichment culture methods and culture-independent molecular surveys. The geologic setting of the Hishikari deposit is composed of three lithologies; basement oceanic sediments of the Cretaceous Shimanto Supergroup, Quaternary andesites, and auriferous quartz vein. We studied the drilled core rock of these, and the geothermal hot waters from the basement aquifers collected by means of the dewatering system located at the deepest level in the mining sites. Culture-independent molecular phylogenetic analyses of PCR-amplified ribosomal DNA (rDNA) recovered from drilled cores suggested that the deep-sea oceanic microbial communities were present as ancient indigenous relicts confined in the Shimanto basement. On the other hand, genetic signals of active thermophilic microbial communities, mainly consisting of thermophilic hydrogen-oxidizer within Aquificales, thermophilic methanotroph within g-Proteobacteria and yet-uncultivated bacterium OPB37 within b-Proteobacteria, were detected with these of oceanic relicts from the subterranean geothermal hot aquifers (temp. 70-100ºC). Successful cultivation and FISH analyses strongly supported that these thermophilic lithotrophic microorganisms could be exactly active and they grew using geochemically produced hydrogen and methane gasses as nutrients. Based on these results, the deep-subsurface biosphere occurring in the Hishikari epithermal gold mine was delineated as endolithic ancient microbial relicts and modern habitats raising active lithotrophic thermophiles associated with the geological and geochemical features of the epithermal gold deposit.

Temperature and pressure adaptation of a sulfate reducer from the deep subsurface

PubMed Central

Fichtel, Katja; Logemann, Jörn; Fichtel, Jörg; Rullkötter, Jürgen; Cypionka, Heribert; Engelen, Bert

2015-01-01

Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment–basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure. PMID:26500624

Under the sea: microbial life in volcanic oceanic crust.

PubMed

Edwards, Katrina J; Wheat, C Geoffrey; Sylvan, Jason B

2011-09-06

Exploration of the microbiology in igneous, 'hard rock' oceanic crust represents a major scientific frontier. The igneous crust harbours the largest aquifer system on Earth, most of which is hydrologically active, resulting in a substantial exchange of fluids, chemicals and microorganisms between oceanic basins and crustal reservoirs. Study of the deep-subsurface biosphere in the igneous crust is technically challenging. However, technologies have improved over the past decade, providing exciting new opportunities for the study of deep-seated marine life, including in situ and cross-disciplinary experimentation in microbiology, geochemistry and hydrogeology. In this Progress article, we describe the recent advances, available technology and remaining challenges in the study of the marine intraterrestrial microbial life that is harboured in igneous oceanic crust.

A Microbial Oasis in the Hypersaline Atacama Subsurface Discovered by a Life Detector Chip: Implications for the Search for Life on Mars

PubMed Central

de Diego-Castilla, Graciela; Moreno-Paz, Mercedes; Blanco, Yolanda; Cruz-Gil, Patricia; Rodríguez-Manfredi, José A.; Fernández-Remolar, David; Gómez, Felipe; Gómez, Manuel J.; Rivas, Luis A.; Demergasso, Cecilia; Echeverría, Alex; Urtuvia, Viviana N.; Ruiz-Bermejo, Marta; García-Villadangos, Miriam; Postigo, Marina; Sánchez-Román, Mónica; Chong-Díaz, Guillermo; Gómez-Elvira, Javier

2011-01-01

Abstract The Atacama Desert has long been considered a good Mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. We performed a Mars analogue drilling campaign next to the Salar Grande (Atacama, Chile) in July 2009, and several cores and powder samples from up to 5 m deep were analyzed in situ with LDChip300 (a Life Detector Chip containing 300 antibodies). Here, we show the discovery of a hypersaline subsurface microbial habitat associated with halite-, nitrate-, and perchlorate-containing salts at 2 m deep. LDChip300 detected bacteria, archaea, and other biological material (DNA, exopolysaccharides, some peptides) from the analysis of less than 0.5 g of ground core sample. The results were supported by oligonucleotide microarray hybridization in the field and finally confirmed by molecular phylogenetic analysis and direct visualization of microbial cells bound to halite crystals in the laboratory. Geochemical analyses revealed a habitat with abundant hygroscopic salts like halite (up to 260 g kg−1) and perchlorate (41.13 μg g−1 maximum), which allow deliquescence events at low relative humidity. Thin liquid water films would permit microbes to proliferate by using detected organic acids like acetate (19.14 μg g−1) or formate (76.06 μg g−1) as electron donors, and sulfate (15875 μg g−1), nitrate (13490 μg g−1), or perchlorate as acceptors. Our results correlate with the discovery of similar hygroscopic salts and possible deliquescence processes on Mars, and open new search strategies for subsurface martian biota. The performance demonstrated by our LDChip300 validates this technology for planetary exploration, particularly for the search for life on Mars. Key Words: Atacama Desert—Life detection—Biosensor—Biopolymers—In situ measurement. Astrobiology 11, 969–996. PMID:22149750

A microbial oasis in the hypersaline Atacama subsurface discovered by a life detector chip: implications for the search for life on Mars.

PubMed

Parro, Victor; de Diego-Castilla, Graciela; Moreno-Paz, Mercedes; Blanco, Yolanda; Cruz-Gil, Patricia; Rodríguez-Manfredi, José A; Fernández-Remolar, David; Gómez, Felipe; Gómez, Manuel J; Rivas, Luis A; Demergasso, Cecilia; Echeverría, Alex; Urtuvia, Viviana N; Ruiz-Bermejo, Marta; García-Villadangos, Miriam; Postigo, Marina; Sánchez-Román, Mónica; Chong-Díaz, Guillermo; Gómez-Elvira, Javier

2011-12-01

The Atacama Desert has long been considered a good Mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. We performed a Mars analogue drilling campaign next to the Salar Grande (Atacama, Chile) in July 2009, and several cores and powder samples from up to 5 m deep were analyzed in situ with LDChip300 (a Life Detector Chip containing 300 antibodies). Here, we show the discovery of a hypersaline subsurface microbial habitat associated with halite-, nitrate-, and perchlorate-containing salts at 2 m deep. LDChip300 detected bacteria, archaea, and other biological material (DNA, exopolysaccharides, some peptides) from the analysis of less than 0.5 g of ground core sample. The results were supported by oligonucleotide microarray hybridization in the field and finally confirmed by molecular phylogenetic analysis and direct visualization of microbial cells bound to halite crystals in the laboratory. Geochemical analyses revealed a habitat with abundant hygroscopic salts like halite (up to 260 g kg(-1)) and perchlorate (41.13 μg g(-1) maximum), which allow deliquescence events at low relative humidity. Thin liquid water films would permit microbes to proliferate by using detected organic acids like acetate (19.14 μg g(-1)) or formate (76.06 μg g(-1)) as electron donors, and sulfate (15875 μg g(-1)), nitrate (13490 μg g(-1)), or perchlorate as acceptors. Our results correlate with the discovery of similar hygroscopic salts and possible deliquescence processes on Mars, and open new search strategies for subsurface martian biota. The performance demonstrated by our LDChip300 validates this technology for planetary exploration, particularly for the search for life on Mars.

Potential impact of Andrassy bentonite microbial diversity in the long-term performance of a deep nuclear waste repository

NASA Astrophysics Data System (ADS)

Tadza, M. Y. Mohd; Tadza, M. A. Mohd; Bag, R.; Harith, N. S. H.

2018-01-01

Copper and steel canning and bentonite buffer are normally forseen as the primary containment component of a deep nuclear waste repository. Distribution of microbes in subsurface environments have been found to be extensive and directly or indirectly may exert influence on waste canister corrosion and the mobility of radionuclides. The understanding of clays and microbial interaction with radionuclides will be useful in predicting the microbial impacts on the performance of the waste repositories. The present work characterizes the culture-dependent microbial diversity of Andrassy bentonite recovered from Tawau clay deposits. The evaluation of microbial populations shows the presence of a number of cultivable microbes (e.g. Staphylococcus, Micrococcus, Achromobacter, Bacillus, Paecilomyces, Trichoderma, and Fusarium). Additionally, a pigmented yeast strain Rhodotorula mucilaginosa was also recovered from the formation. Both Bacillus and Rhodotorula mucilaginosa have high tolerance towards U radiation and toxicity. The presence of Rhodotorula mucilaginosa in Andrassy bentonite might be able to change the speciation of radionuclides (e.g. uranium) in a future deep repository. However, concern over the presence of Fe (III) reduction microbes such as Bacillus also found in the formation could lead to corrosion of copper steel canister and affect the overall performance of the containment system.

Biogeochemical Cycle of Methanol in Anoxic Deep-Sea Sediments

PubMed Central

Yanagawa, Katsunori; Tani, Atsushi; Yamamoto, Naoya; Hachikubo, Akihiro; Kano, Akihiro; Matsumoto, Ryo; Suzuki, Yohey

2016-01-01

The biological flux and lifetime of methanol in anoxic marine sediments are largely unknown. We herein reported, for the first time, quantitative methanol removal rates in subsurface sediments. Anaerobic incubation experiments with radiotracers showed high rates of microbial methanol consumption. Notably, methanol oxidation to CO2 surpassed methanol assimilation and methanogenesis from CO2/H2 and methanol. Nevertheless, a significant decrease in methanol was not observed after the incubation, and this was attributed to the microbial production of methanol in parallel with its consumption. These results suggest that microbial reactions play an important role in the sources and sinks of methanol in subseafloor sediments. PMID:27301420

Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

NASA Astrophysics Data System (ADS)

Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

2011-12-01

The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum Proteobacteria) at 8%, and Formosa (phylum Bacteroidetes) at 7%. These lineages support a paradigm suggesting the importance of fermentation in the subsurface. However, this study extends the predicted range for fermentation below the shallow subsurface and into organic carbon limited marine sediments. Other previously characterized subsurface active populations from environments with higher organic carbon concentrations do not show similar levels of reduced diversity or predominance of fermentative populations. This study further emphasizes the spatial variability of microbial populations in the deep subsurface and highlights the need for continued exploration.

Organic and Inorganic Carbon in the Rio Tinto (Spain) Deep Subsurface System: a Possible Model for Subsurface Carbon and Lithoautotrophs on Mars.

NASA Astrophysics Data System (ADS)

Bonaccorsi, R.; Stoker, C. R.; MARTE Science Team

2007-12-01

The subsurface is the key environment for searching for life on planets lacking surface life. Subsurface ecosystems are of great relevance to astrobiology including the search for past/present life on Mars. Conditions on the Martian surface do not support biological activity but the subsurface might preserve organics and host subsurface life [1]. A key requirement for the analysis of subsurface samples on Mars is the ability to characterize organic vs. inorganic carbon pools. This information is needed to determine if the sample contains organic material of biological origin and/ or to establish if pools of inorganic carbon can support subsurface biospheres. The Mars Analog Rio Tinto Experiment (MARTE) performed deep drilling of cores i.e., down to 165-m depth, in a volcanically-hosted-massive-sulfide deposit at Rio Tinto, Spain, which is considered an important analog of the Sinus Meridiani site on Mars. Results from MARTE suggest the existence of a relatively complex subsurface life including aerobic and anaerobic chemoautotrophs, and strict anaerobic methanogens sustained by Fe and S minerals in anoxic conditions, which is an ideal model analog for a deep subsurface Martian environment. We report here on the distribution of organic (C-org: 0.01-0.3Wt% and inorganic carbon (IC = 0.01-7.0 Wt%) in a subsurface rock system including weathered/oxidized i.e., gossan, and unaltered pyrite stockwork. Cores were analyzed from 3 boreholes (BH-4, BH-7, and BH-8) that penetrated down to a depth of ~165 m into massive sulfide. Nearsurface phyllosilicate rich-pockets contain the highest amounts of organics (0.3Wt%) [2], while the deeper rocks contain the highest amount of carbonates. Assessing the amount of C pools available throughout the RT subsurface brings key insight on the type of trophic system sustaining its microbial ecosystem (i.e., heterotrophs vs. autotrophs) and the biogeochemical relationships that characterize a new type of subsurface biosphere at RT. This potentially novel biosphere on Earth could be used as a model to test for extant and extinct life on Mars. Furthermore, having found carbonates in an hyperacidic system (pH ~2.3) brings new insights on the possible occurrence of deep carbonates deposits under low-pH condition on Mars. [1] Boston, P.J., et al., 1992. Icarus 95,300-308; Bonaccorsi, Stoker and Sutter, 2007 Accepted with review in Astrobiology.

The nature and function of microbial enzymes in subsurface marine sediments

NASA Astrophysics Data System (ADS)

Steen, A. D.; Schmidt, J.

2016-02-01

Isotopic and genomic evidence indicates that marine sediments contain populations of active heterotrophic microorganisms which appear to metabolize old, detrital, apparently recalcitrant organic matter. In surface communities, heterotrophs use extracellular enzymes to access complex organic matter. In subsurface sediments, in which microbial doubling times can be on the order of hundreds or thousands of years, it is not clear whether extracellular enzymes could remain stable and active long enough to constitute a 'profitable' stragtegy for accessing complex organic carbon. Here we present evidence that a wide range of extracellular enzyme are active in subsurface sediments from two different environments: the White Oak River, NC, and deep (up to 80 m) sediments of the Baltic Sea Basin recovered from IODP Expedition 347. In the White Oak River, enzymes from deeper sediments appear to be better-adapted to highly-degraded organic matter than enzymes from surface sediments. In the Baltic Sea, preliminary data suggest that enzymes related to nitrogen acquisition are preferentially expressed. By characterizing the extracellular enzymes present in marine sediments, we hope to achieve a better understanding of the mechanisms that control sedimentary organic matter remineralization and preservation.

Technical Challenges of Drilling on Mars

NASA Technical Reports Server (NTRS)

Briggs, Geoffrey; Gross, Anthony; Condon, Estelle (Technical Monitor)

2002-01-01

In the last year, NASA's Mars science advisory committee (MEPAG: Mars Exploration Payload Advisory Group) has formally recommended that deep drilling be undertaken as a priority investigation to meet astrobiology and geology goals. This proposed new dimension in Mars exploration has come about for several reasons. Firstly, geophysical models of the martian subsurface environment indicate that we may well find liquid water (in the form of brines) under ground-ice at depths of several kilometers near the equator. On Earth we invariably find life forms associated with any environmental niche that supports liquid water. New data from the Mars Global Surveyor have shown that the most recent volcanism on Mars is very young so we cannot rule out contemporary volcanism -- in which case subsurface temperatures consistent with having water in its liquid phase may be found at relatively shallow depths. Secondly, in recent decades we have learned to our surprise that the Earth's subsurface (microbial) biosphere extends to depths of many kilometers and this discovery provides the basis for planning to explore the martian subsurface in search of ancient or even extant microbial life forms. We know (from Viking measurements) that all the biogenic elements (C, H, O, N, P, S) are available on Mars. What we therefore hope to learn is whether or not the evolution of life is inevitable given the necessary ingredients and, by implication, whether the Universe may be teeming with life. The feasibility of drilling deep into the surface of Mars has been the subject of increasing attention within NASA (and more recently among some of its international partners) for several years and this led to a broad-based feasibility study carried out by the Los Alamos National Laboratory and, subsequently, to the development of several hardware prototypes. This paper is intended to provide a general survey of that activity.

Significant contribution of Archaea to extant biomass in marine subsurface sediments.

PubMed

Lipp, Julius S; Morono, Yuki; Inagaki, Fumio; Hinrichs, Kai-Uwe

2008-08-21

Deep drilling into the marine sea floor has uncovered a vast sedimentary ecosystem of microbial cells. Extrapolation of direct counts of stained microbial cells to the total volume of habitable marine subsurface sediments suggests that between 56 Pg (ref. 1) and 303 Pg (ref. 3) of cellular carbon could be stored in this largely unexplored habitat. From recent studies using various culture-independent techniques, no clear picture has yet emerged as to whether Archaea or Bacteria are more abundant in this extensive ecosystem. Here we show that in subsurface sediments buried deeper than 1 m in a wide range of oceanographic settings at least 87% of intact polar membrane lipids, biomarkers for the presence of live cells, are attributable to archaeal membranes, suggesting that Archaea constitute a major fraction of the biomass. Results obtained from modified quantitative polymerase chain reaction and slot-blot hybridization protocols support the lipid-based evidence and indicate that these techniques have previously underestimated archaeal biomass. The lipid concentrations are proportional to those of total organic carbon. On the basis of this relationship, we derived an independent estimate of amounts of cellular carbon in the global marine subsurface biosphere. Our estimate of 90 Pg of cellular carbon is consistent, within an order of magnitude, with previous estimates, and underscores the importance of marine subsurface habitats for global biomass budgets.

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman.

PubMed

Rempfert, Kaitlin R; Miller, Hannah M; Bompard, Nicolas; Nothaft, Daniel; Matter, Juerg M; Kelemen, Peter; Fierer, Noah; Templeton, Alexis S

2017-01-01

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite ("gabbro," "alkaline peridotite," "hyperalkaline peridotite," and "gabbro/peridotite contact") that vary strongly in pH and the concentrations of H 2 , CH 4 , Ca 2+ , Mg 2+ , [Formula: see text], [Formula: see text], trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus , candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira , Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. These data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.

Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H 2, CH 4, Ca 2+, Mg 2+, NO 3 more » $-$, SO$$2-\\atop{4}$$, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. As a result, these data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.« less

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman

PubMed Central

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas; Nothaft, Daniel; Matter, Juerg M.; Kelemen, Peter; Fierer, Noah; Templeton, Alexis S.

2017-01-01

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H2, CH4, Ca2+, Mg2+, NO3-, SO42-, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. These data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites. PMID:28223966

Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman

DOE PAGES

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas; ...

2017-02-07

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H 2, CH 4, Ca 2+, Mg 2+, NO 3 more » $-$, SO$$2-\\atop{4}$$, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. As a result, these data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.« less

Viral Predation and Host Immunity Structure Microbial Communities in a Terrestrial Deep Subsurface, Hydraulically Fractured Shale System

NASA Astrophysics Data System (ADS)

Daly, R. A.; Mouser, P. J.; Trexler, R.; Wrighton, K. C.

2014-12-01

Despite a growing appreciation for the ecological role of viruses in marine and gut systems, little is known about their role in the terrestrial deep (> 2000 m) subsurface. We used assembly-based metagenomics to examine the viral component in fluids from hydraulically fractured Marcellus shale gas wells. Here we reconstructed microbial and viral genomes from samples collected 7, 82, and 328 days post fracturing. Viruses accounted for 4.14%, 0.92% and 0.59% of the sample reads that mapped to the assembly. We identified 6 complete, circularized viral genomes and an additional 92 viral contigs > 5 kb with a maximum contig size of 73.6 kb. A BLAST comparison to NCBI viral genomes revealed that 85% of viral contigs had significant hits to the viral order Caudovirales, with 43% of sequences belonging to the family Siphoviridae, 38% to Myoviridae, and 12% to Podoviridae. Enrichment of Caudovirales viruses was supported by a large number of predicted proteins characteristic of tailed viruses including terminases (TerL), tape measure, tail formation, and baseplate related proteins. The viral contigs included evidence of lytic and temperate lifestyles, with the 7 day sample having the greatest number of detected lytic viruses. Notably in this sample, the most abundant virus was lytic and its inferred host, a member of the Vibrionaceae, was not detected at later time points. Analyses of CRISPR sequences (a viral and foreign DNA immune system in bacteria and archaea), linked 18 viral contigs to hosts. CRISPR linkages increased through time and all bacterial and archaeal genomes recovered in the final time point had genes for CRISPR-mediated viral defense. The majority of CRISPR sequences linked phage genomes to several Halanaerobium strains, which are the dominant and persisting members of the community inferred to be responsible for carbon and sulfur cycling in these shales. Network analysis revealed that several viruses were present in the 82 and 328 day samples; this viral persistence is consistent with concomitant temporal stability in geochemistry and microbial community composition. Our findings suggest that after a disturbance (hydraulic fracturing) viral predation and host immunity is an important controller of microbial community structure, metabolism, and thus biogeochemical cycling in the deep subsurface.

Microbial Ecology of a Regional Flow System: Deep, Aerobic, Fractured Rock Aquifers of the US Basin and Range (Invited)

NASA Astrophysics Data System (ADS)

Moser, D. P.; Hamilton-Brehm, S.; Zhang, G.; Fisher, J.; Hughes, K.; Wheatley, A.; Thomas, J.; Zavarin, M.; Roberts, S. K.; Kryder, L.; McRae, R.; Howard, W.; Walker, J.; Federwisch, R.; King, M.; Friese, R.; Grim, S.; Amend, J.; Momper, L.; Sherwood Lollar, B.; Onstott, T. C.

2013-12-01

Recent decades have revealed anaerobic microbial ecosystems across a range of deep, continental settings; however, aerobic, regional aquifers represent a little-studied habitat for deep life. The US' Basin and Range Province is an extensional zone defined by deep, interconnected fracture systems that span multiple hydrologic basins and host regional aquifers. Here we describe a multi-basin microbiological assessment, applied to the Death Valley Regional Flow System (DVRFS). Our group has surveyed more than thirty deep boreholes (~ 1,000 m depth average) and deeply-sourced springs across a ~170 km inferred flow path from recharge areas in volcanic and carbonate rock highlands of the Nevada National Security Site (NNSS) and the Spring Mountains to discharge zones in Oasis, Amargosa, and Death Valleys. DVRFS waters were characterized by temperatures of 30 - 50 oC and the presence of dissolved O2 (4 - 8 mg/L in the recharge areas and ~0.2 - 2 mg/L in the discharge zones). Planktonic microbial populations, as tracked by molecular DNA approaches (e.g. 454 pyrotag), were of low abundance (e.g. ~ 10e3 ~10e6 per mL) and dominated by Proteobacteria and Nitrospirae. Archaea were also present and dominated by novel Thaumarchaeotes. Patterns of microbial diversity and the hypothesis that these patterns may have utility for recognition of hydrologic connectivity were assessed by statistical tools. At the species level, cosmopolitan, system-wide, and flow-path-specific groupings of both bacteria and archaea were detected. Even when in close proximity to aerobic springs and wells, sites sampling deep, hot, anaerobic groundwaters possessed completely distinct microbial populations (e.g. dominance by Firmicutes, ANME, and predicted methanogens). Among methodological refinements developed from this work, the repeated sampling of one deep borehole over a month-long pump test revealed that well-bore-associated contaminants required several days of pumping for complete removal and enabled the identification of the specific depth that produced most of the water. Our results reveal details of microbial community structure for a common, but little-studied microbial ecosystem and support the concept that regional flow systems possess distinct microbial populations, consistent with their geochemical and hydrologic characteristics. These results generally support the concept that microbial populations may have utility as amplifiable tracers for tracking the connectivity of fluids in the subsurface.

Deep Subsurface Microbial Communities Shaped by the Chicxulub Impactor

NASA Astrophysics Data System (ADS)

Cockell, C. S.; Coolen, M.; Schaefer, B.; Grice, K.; Gulick, S. P. S.; Morgan, J. V.; Kring, D. A.; Osinski, G.

2017-12-01

Fresh core material was obtained by drilling of the Chicxulub impact crater during IODP-ICDP Expedition 364 to assess the present-day biosphere in the crater structure. Cell enumerations through the core show that beneath the post-impact sedimentary rock there is a region of enhanced cell abundance that corresponds to the upper impact suevite layer (Units 1G/2A). We also observed a peak in cell numbers in samples at the bottom of suevite Unit 2C and between the suevitic and grainitoid interface (Unit 3/4). These patterns may reflect preferential movement of fluid and/or availability of nutrients and energy at interfaces. 16S rDNA analysis allows us to rule out contamination of the suevite material since no taxa associated with the drilling mud were observed. Two hundred and fifty microbial enrichments were established using diverse culture media for heterotrophs, autotrophs and chemolithotrophs at temperatures consistent with measured core temperatures. Six yielded growth in the breccia, lower breccia and upper granitoid layer and they affiliated with Acidiphilium, Thermoanaerobacteracea and Desulfohalbiaceae. The latter exhibited visible microbial sulfate-reduction. By contrast, the granitoid material exhibited low cell abundances, most samples were below direct cell detection. DNA extraction revealed pervasive low level contamination by drilling mud taxa, consistent with the highly fractured, high porosity of the impact-shocked granitoids. Few taxa can be attributed to an indigenous biota and no enrichments (at 60 and 70°C) yielded growth. These data show that even with a porosity approximately an order of magnitude greater than most unshocked granites, the uplifted granites have not experienced sufficient fluid flow to establish a significant deep biosphere. Paleosterilisation of the material during impact may have re-set colonisation and the material may have originally been below the depth at which temperatures exceeded the upper temperature limit for life. These data show that the deep biosphere can preserve the imprint of catastrophe long after these events. In this case, the distribution of deep subsurface microbial communities reflects the lithological sequence established during the substantial impact-induced geological rearrangements that occurred in the first hours of the Cenozoic.

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

Factors Effecting the Fate and Transport of CL-20 in the Vadose Zone and Groundwater: Final Report 2002 - 2004 SERDP Project CP-1255

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szecsody, James E.; Riley, Robert G.; Devary, Brooks J.

2005-06-01

This SERDP-funded project was initiated to investigate the fate of CL-20 in the subsurface environment, with a focus on identification and quantification of geochemical and microbial reactions of CL-20. CL-20 can be released to the surface and subsurface terrestrial environment by: a) manufacturing processes, b) munition storage, and c) use with low order detonation or unexploded ordnance. The risk of far-field subsurface migration was assessed through labora-tory experiments with a variety of sediments and subsurface materials to quantify processes that control CL-20 sorption-limited migration and degradation. Results of this study show that CL-20 will exhibit differing behavior in the subsurfacemore » terrestrial environment: 1. CL-20 on the sediment surface will photodegrade and interact with plants/animals (described in other SERDP projects CU 1254, 1256). CL-20 will exhibit greater sorption in humid sediments to organic matter. Transport will be solubility limited (i.e., low CL-20 aqueous solubility). 2. CL-20 infiltration into soils (<2 m) from spills will be subject to sorption to soil organic matter (if present), and low to high biodegradation rates (weeks to years) depending on the microbial population (greater in humid environment). 3. CL-20 in the vadose zone (>2 m) will be, in most cases, subject to low sorption and low degradation rates, so would persist in the subsurface environment and be at risk for deep migration. Low water content in arid regions will result in a decrease in both sorption and the degradation rate. Measured degradation rates in unsaturated sediments of years would result in significant subsurface migration distances. 4. CL-20 in groundwater will be subject to some sorption but likely very slow degradation rates. CL-20 sorption will be greater than RDX. Most CL-20 degradation will be abiotic (ferrous iron and other transition metals), because most deep subsurface systems have extremely low natural microbial populations. Degradation rates will range from weeks (iron reducing systems) to years. Although CL-20 will move rapidly through most sediments in the terrestrial environment, subsurface remediation can be utilized for cleanup. Transformation of CL-20 to intermediates can be rapidly accomplished under: a) reducing conditions (CL-20 4.1 min. half-life, RDX 18 min. half-life), b) alkaline (pH >10) conditions, and c) bioremediation with added nutrients. CL-20 degradation to intermediates may be insufficient to mitigate environmental impact, as the toxicity of many of these compounds is unknown. Biostimulation in oxic to reducing systems by carbon and nutrient addition can mineralize CL-20, with the most rapid rates occurring under reducing conditions.« less

Sorting Out the Ocean Crust Deep Biosphere with Single Cell Omics Approaches

NASA Astrophysics Data System (ADS)

Orcutt, B.; D'Angelo, T.; Goordial, J.; Jones, R. M.; Carr, S. A.

2017-12-01

Although oceanic crust comprises a large habitat for subsurface life, the structure, function, and dynamics of microbial communities living on rocks in the subsurface are poorly understood. Single cell level approaches can overcome limitations of low biomass in subsurface systems. Coupled with incubation experiments with amino acid orthologs, single cell level sorting can reveal high resolution information about identity, functional potential, and growth. Leveraging collaboration with the Single Cell Genomics Center and the Facility for Aquatic Cytometry at Bigelow Laboratory, we present recent results from single cell level sorting and -omics sequencing from several crustal environments, including the Atlantis Massif and the Juan de Fuca Ridge flank. We will also highlight new experiments conducted with samples recovered from the flank of the Mid-Atlantic Ridge.

Microbial DNA; a possible tracer of groundwater

NASA Astrophysics Data System (ADS)

Sugiyama, Ayumi; Segawa, Takuya; Furuta, Tsuyumi; Nagaosa, Kazuyo; Tsujimura, Maki; Kato, Kenji

2017-04-01

Though chemical analysis of groundwater shows an averaged value of chemistry of the examined water which was blended by various water with different sources and routes in subsurface environment, microbial DNA analysis may suggest the place where they originated, which may give information of the source and transport routes of the water examined. A huge amount of groundwater is stored in lava layer with maximum depth of 300m in Mt. Fuji (3,776m asl ), the largest volcanic mountain in Japan. Although the density of prokaryotes was low in the examined groundwater of Mt. Fuji, thermophilic prokaryotes as Thermoanaerobacterales, Gaiellales and Thermoplasmatales were significantly detected. They are optimally adapted to the temperature higher than 40oC. This finding suggests that at least some of the source of the examined groundwater was subsurface environment with 600m deep or greater, based on a temperature gradient of 4oC/100m and temperature of spring water ranges from 10 to 15oC in the foot of Mt. Fuji. This depth is far below the lava layer. Thus, the groundwater is not simply originated from the lava layer. In addition to those findings, we observed a very fast response of groundwater just a couple of weeks after the heavy rainfall exceeding 2 or 300 mm/event in Mt. Fuji. The fast response was suggested by a sharp increase in bacterial abundance in spring water located at 700m in height in the west foot of Mt. Fuji, where the average recharge elevation of groundwater was estimated to be 1,500m - 1,700m (Kato et. al. EGU 2016). This increase was mainly provided by soil bacteria as Burkholderiales, which might be detached from soil by strengthened subsurface flow caused by heavy rainfall. This suggests that heavy rainfall promotes shallow subsurface flow contributing to the discharge in addition to the groundwater in the deep aquifer. Microbial DNA, thus could give information about the route of the examined groundwater, which was never elucidated by analysis of chemical materials dissolved in groundwater. Though viral particle was employed as a tracer to chase the movement of groundwater, it doesn't tell the chemical and physical environmental condition where the particle was incorporated into groundwater. Thus, we propose microbial DNA as a new tracer to track the route of groundwater.

Isoprenoid quinones resolve the stratification of microbial redox processes in a biogeochemical continuum from the photic zone to deep anoxic sediments of the Black Sea.

PubMed

Becker, Kevin W; Elling, Felix J; Schröder, Jan M; Lipp, Julius S; Goldhammer, Tobias; Zabel, Matthias; Elvert, Marcus; Overmann, Jörg; Hinrichs, Kai-Uwe

2018-03-09

The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia-oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition. Importance Microorganisms play crucial roles in global biogeochemical cycles. Yet, we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy and anoxygenic photosynthesis in defined geochemical zones. Copyright © 2018 American Society for Microbiology.

Mineral Influence on Microbial Survival During Carbon Sequestration

NASA Astrophysics Data System (ADS)

Santillan, E. U.; Shanahan, T. M.; Wolfe, W. W.; Bennett, P.

2012-12-01

CO2 sequestered in a deep saline aquifer will perturb subsurface biogeochemistry by acidifying the groundwater and accelerating mineral diagenesis. Subsurface microbial communities heavily influence geochemistry through their metabolic processes, such as with dissimilatory iron reducing bacteria (DIRB). However, CO2 also acts as a sterilant and will perturb these communities. We investigated the role of mineralogy and its effect on the survival of microbes at high PCO2 conditions using the model DIRB Shewanella oneidensis MR-1. Batch cultures of Shewanella were grown to stationary phase and exposed to high PCO2 using modified Parr reactors. Cell viability was then determined by plating cultures after exposure. Results indicate that at low PCO2 (2 bar), growth and iron reduction are decreased and cell death occurs within 1 hour when exposed to CO2 pressures of 10 bar or greater. Further, fatty acid analysis indicates microbial lipid degradation with C18 fatty acids being the slowest lipids to degrade. When cultures were grown in the presence of rocks or minerals representative of the deep subsurface such as carbonates and silicates and exposed to 25 bar CO2, survival lasted beyond 2 hours. The most effective protecting substratum was quartz sandstone, with cultures surviving beyond 8 hours of CO2 exposure. Scanning electron microscope images reveal biofilm formation on the mineral surfaces with copious amounts of extracellular polymeric substances (EPS) present. EPS from these biofilms acts as a reactive barrier to the CO2, slowing the penetration of CO2 into cells and resulting in increased survival. When biofilm cultures were grown with Al and As to simulate the release of toxic metals from minerals such as feldspars and clays, survival time decreased, indicating mineralogy may also enhance microbial death. Biofilms were then grown on iron-coated quartz sand to determine conversely what influence biofilms may have on mineral dissolution during CO2 perturbation. Growth media was allowed to flow through a sand-packed column at a constant flow rate with pulses of liquid CO2 injected directly into the column. Preliminary data of dissolved iron measured from the effluent indicates that biofilm columns show a slight increase in dissolved iron concentrations before and after CO2 exposure in comparison to abiotic columns. These findings imply the important relationship between microbes and minerals during CO2 sequestration. The ability minerals have to contribute to the selection of microbes has important consequences to the survival of different microbial populations in the subsurface and the consequent biogeochemical changes that may happen.

Modified Lipid Extraction Methods for Deep Subsurface Shale

PubMed Central

Akondi, Rawlings N.; Trexler, Ryan V.; Pfiffner, Susan M.; Mouser, Paula J.; Sharma, Shikha

2017-01-01

Growing interest in the utilization of black shales for hydrocarbon development and environmental applications has spurred investigations of microbial functional diversity in the deep subsurface shale ecosystem. Lipid biomarker analyses including phospholipid fatty acids (PLFAs) and diglyceride fatty acids (DGFAs) represent sensitive tools for estimating biomass and characterizing the diversity of microbial communities. However, complex shale matrix properties create immense challenges for microbial lipid extraction procedures. Here, we test three different lipid extraction methods: modified Bligh and Dyer (mBD), Folch (FOL), and microwave assisted extraction (MAE), to examine their ability in the recovery and reproducibility of lipid biomarkers in deeply buried shales. The lipid biomarkers were analyzed as fatty acid methyl esters (FAMEs) with the GC-MS, and the average PL-FAME yield ranged from 67 to 400 pmol/g, while the average DG-FAME yield ranged from 600 to 3,000 pmol/g. The biomarker yields in the intact phospholipid Bligh and Dyer treatment (mBD + Phos + POPC), the Folch, the Bligh and Dyer citrate buffer (mBD-Cit), and the MAE treatments were all relatively higher and statistically similar compared to the other extraction treatments for both PLFAs and DGFAs. The biomarker yields were however highly variable within replicates for most extraction treatments, although the mBD + Phos + POPC treatment had relatively better reproducibility in the consistent fatty acid profiles. This variability across treatments which is associated with the highly complex nature of deeply buried shale matrix, further necessitates customized methodological developments for the improvement of lipid biomarker recovery. PMID:28790998

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

PubMed Central

Lau, Maggie C. Y.; Cameron, Connor; Magnabosco, Cara; Brown, C. Titus; Schilkey, Faye; Grim, Sharon; Hendrickson, Sarah; Pullin, Michael; Sherwood Lollar, Barbara; van Heerden, Esta; Kieft, Thomas L.; Onstott, Tullis C.

2014-01-01

Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes. PMID:25400621

Metabolic stratification driven by surface and subsurface interactions in a terrestrial mud volcano.

PubMed

Cheng, Ting-Wen; Chang, Yung-Hsin; Tang, Sen-Lin; Tseng, Ching-Hung; Chiang, Pei-Wen; Chang, Kai-Ti; Sun, Chih-Hsien; Chen, Yue-Gau; Kuo, Hung-Chi; Wang, Chun-Ho; Chu, Pao-Hsuan; Song, Sheng-Rong; Wang, Pei-Ling; Lin, Li-Hung

2012-12-01

Terrestrial mud volcanism represents the prominent surface geological feature, where fluids and hydrocarbons are discharged along deeply rooted structures in tectonically active regimes. Terrestrial mud volcanoes (MVs) directly emit the major gas phase, methane, into the atmosphere, making them important sources of greenhouse gases over geological time. Quantification of methane emission would require detailed insights into the capacity and efficiency of microbial metabolisms either consuming or producing methane in the subsurface, and establishment of the linkage between these methane-related metabolisms and other microbial or abiotic processes. Here we conducted geochemical, microbiological and genetic analyses of sediments, gases, and pore and surface fluids to characterize fluid processes, community assemblages, functions and activities in a methane-emitting MV of southwestern Taiwan. Multiple lines of evidence suggest that aerobic/anaerobic methane oxidation, sulfate reduction and methanogenesis are active and compartmentalized into discrete, stratified niches, resembling those in marine settings. Surface evaporation and oxidation of sulfide minerals are required to account for the enhanced levels of sulfate that fuels subsurface sulfate reduction and anaerobic methanotrophy. Methane flux generated by in situ methanogenesis appears to alter the isotopic compositions and abundances of thermogenic methane migrating from deep sources, and to exceed the capacity of microbial consumption. This metabolic stratification is sustained by chemical disequilibria induced by the mixing between upward, anoxic, methane-rich fluids and downward, oxic, sulfate-rich fluids.

Metabolic stratification driven by surface and subsurface interactions in a terrestrial mud volcano

PubMed Central

Cheng, Ting-Wen; Chang, Yung-Hsin; Tang, Sen-Lin; Tseng, Ching-Hung; Chiang, Pei-Wen; Chang, Kai-Ti; Sun, Chih-Hsien; Chen, Yue-Gau; Kuo, Hung-Chi; Wang, Chun-Ho; Chu, Pao-Hsuan; Song, Sheng-Rong; Wang, Pei-Ling; Lin, Li-Hung

2012-01-01

Terrestrial mud volcanism represents the prominent surface geological feature, where fluids and hydrocarbons are discharged along deeply rooted structures in tectonically active regimes. Terrestrial mud volcanoes (MVs) directly emit the major gas phase, methane, into the atmosphere, making them important sources of greenhouse gases over geological time. Quantification of methane emission would require detailed insights into the capacity and efficiency of microbial metabolisms either consuming or producing methane in the subsurface, and establishment of the linkage between these methane-related metabolisms and other microbial or abiotic processes. Here we conducted geochemical, microbiological and genetic analyses of sediments, gases, and pore and surface fluids to characterize fluid processes, community assemblages, functions and activities in a methane-emitting MV of southwestern Taiwan. Multiple lines of evidence suggest that aerobic/anaerobic methane oxidation, sulfate reduction and methanogenesis are active and compartmentalized into discrete, stratified niches, resembling those in marine settings. Surface evaporation and oxidation of sulfide minerals are required to account for the enhanced levels of sulfate that fuels subsurface sulfate reduction and anaerobic methanotrophy. Methane flux generated by in situ methanogenesis appears to alter the isotopic compositions and abundances of thermogenic methane migrating from deep sources, and to exceed the capacity of microbial consumption. This metabolic stratification is sustained by chemical disequilibria induced by the mixing between upward, anoxic, methane-rich fluids and downward, oxic, sulfate-rich fluids. PMID:22739492

Microbial Diversity Associated With Geochemical Changes in a Deep Subsurface Aquifer

NASA Astrophysics Data System (ADS)

Davidson, M. M.; Onstott, T. C.; Pratt, L. M.; Boice, E.; Southam, G.; Wanger, G.; Sherwood-Lollar, B.; Lippmann, J.; Seymoor, W.

2003-12-01

The microbial diversity of a 1.83km deep, thermophilic, fluid-filled subterranean fracture was monitored over a three and a half month period and correlated to observed changes in the geochemistry of the system. Three water samples were analyzed using 16S rDNA molecular techniques for microbial diversity, isotopic and geochemical composition. Gibbs' free energy of microbial redox reactions predicted that at in situ conditions sulfate reduction, methanogenesis and acetogenesis should be dominant metabolic pathways utilized by microbes, whereas Fe(III)-reduction should only have been favorable in the last sample. Noble gas isotopic data yielded a subsurface residence time of ˜10-100 Myr. and the non-meteoric δ D vs. δ 18O values were indicative of water-rock alteration at <100° C. δ 34S of sulfide and sulfate differed by 15‰ , consistent with fractionation by sulfate reducing bacteria. H2 concentrations declined with time, which in conjunction with the δ 34S data, suggested that hydrogenotrophic sulfate reducing bacteria dominate the community. This was compatible with 16S rDNA analysis, which yielded clones similar to Desulfotomaculum and Desulfofustis species appearing in the three 16S libraries. δ 13C and δ D values of CH4 and light hydrocarbons indicated methanogenic CH4 was mixing with abiogenically formed CH4. This is consistent with the presence of Archaeal 16S sequences similar to Methanosaeta and Methanosarcina species. The temporal increase in acetate concentration could be attributed to clone types similar to known acetogenic bacteria such as Moorella glycerini, which were present in the last sample. Clones similar to known Fe(III)-reducing bacteria such as Geovibrio species were observed in the first and last samples.

Viral activities and life cycles in deep subseafloor sediments.

PubMed

Engelhardt, Tim; Orsi, William D; Jørgensen, Bo Barker

2015-12-01

Viruses are highly abundant in marine subsurface sediments and can even exceed the number of prokaryotes. However, their activity and quantitative impact on microbial populations are still poorly understood. Here, we use gene expression data from published continental margin subseafloor metatranscriptomes to qualitatively assess viral diversity and activity in sediments up to 159 metres below seafloor (mbsf). Mining of the metatranscriptomic data revealed 4651 representative viral homologues (RVHs), representing 2.2% of all metatranscriptome sequence reads, which have close translated homology (average 77%, range 60-97% amino acid identity) to viral proteins. Archaea-infecting RVHs are exclusively detected in the upper 30 mbsf, whereas RVHs for filamentous inoviruses predominate in the deepest sediment layers. RVHs indicative of lysogenic phage-host interactions and lytic activity, notably cell lysis, are detected at all analysed depths and suggest a dynamic virus-host association in the marine deep biosphere studied here. Ongoing lytic viral activity is further indicated by the expression of clustered, regularly interspaced, short palindromic repeat-associated cascade genes involved in cellular defence against viral attacks. The data indicate the activity of viruses in subsurface sediment of the Peruvian margin and suggest that viruses indeed cause cell mortality and may play an important role in the turnover of subseafloor microbial biomass. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Intraterrestrial life in igneous ocean crust: advances, technologies, and the future (Invited)

NASA Astrophysics Data System (ADS)

Edwards, K. J.; Wheat, C. G.

2010-12-01

The “next frontier” of scientific investigation in the deep sub-seafloor microbial biosphere lies in a realm that has been a completely unexplored until just the past decade: the igneous oceanic crust. Problems that have hampered exploration of the “hard rock” marine deep biosphere have revolved around sample access (hard rock drilling is technologically complex), contamination (a major hurdle), momentum (why take on this challenge when the relatively “easier” marine muds also have been a frontier) and suspicion that microbes in more readily accessed using (simpler) non-drilling technologies - like vents - are truly are endemic of subsurface clades/activities. Since the late 1990’s, however, technologies and resultant studies on microbes in the igneous ocean crust deep biosphere have risen sharply, and offer a new and distinct view on this biome. Moreover, microbiologists are now taking leading roles in technological developments that are critically required to address this biosphere - interfacing and collaborating closely with engineers, genomic biologists, geologists, seismologists, and geochemists to accomplish logistically complex and long-term studies that bring observatory research to this deep realm. The future of this field for the least decade is rich - opportunities abound for microbiologists to play new roles in how we study microbiology in the deep subsurface in an oceanographic and Earth system science perspective.

Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems

PubMed Central

Pisapia, Céline; Gérard, Emmanuelle; Gérard, Martine; Lecourt, Léna; Lang, Susan Q.; Pelletier, Bernard; Payri, Claude E.; Monnin, Christophe; Guentas, Linda; Postec, Anne; Quéméneur, Marianne; Erauso, Gaël; Ménez, Bénédicte

2017-01-01

Despite their potential importance as analogs of primitive microbial metabolisms, the knowledge of the structure and functioning of the deep ecosystems associated with serpentinizing environments is hampered by the lack of accessibility to relevant systems. These hyperalkaline environments are depleted in dissolved inorganic carbon (DIC), making the carbon sources and assimilation pathways in the associated ecosystems highly enigmatic. The Prony Bay Hydrothermal Field (PHF) is an active serpentinization site where, similar to Lost City (Mid-Atlantic Ridge), high-pH fluids rich in H2 and CH4 are discharged from carbonate chimneys at the seafloor, but in a shallower lagoonal environment. This study aimed to characterize the subsurface microbial ecology of this environment by focusing on the earliest stages of chimney construction, dominated by the discharge of hydrothermal fluids of subseafloor origin. By jointly examining the mineralogy and the microbial diversity of the conduits of juvenile edifices at the micrometric scale, we find a central role of uncultivated bacteria belonging to the Firmicutes in the ecology of the PHF. These bacteria, along with members of the phyla Acetothermia and Omnitrophica, are identified as the first chimneys inhabitants before archaeal Methanosarcinales. They are involved in the construction and early consolidation of the carbonate structures via organomineralization processes. Their predominance in the most juvenile and nascent hydrothermal chimneys, and their affiliation with environmental subsurface microorganisms, indicate that they are likely discharged with hydrothermal fluids from the subseafloor. They may thus be representative of endolithic serpentinization-based ecosystems, in an environment where DIC is limited. In contrast, heterotrophic and fermentative microorganisms may consume organic compounds from the abiotic by-products of serpentinization processes and/or from life in the deeper subsurface. We thus propose that the Firmicutes identified at PHF may have a versatile metabolism with the capability to use diverse organic compounds from biological or abiotic origin. From that perspective, this study sheds new light on the structure of deep microbial communities living at the energetic edge in serpentinites and may provide an alternative model of the earliest metabolisms. PMID:28197130

Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems.

PubMed

Pisapia, Céline; Gérard, Emmanuelle; Gérard, Martine; Lecourt, Léna; Lang, Susan Q; Pelletier, Bernard; Payri, Claude E; Monnin, Christophe; Guentas, Linda; Postec, Anne; Quéméneur, Marianne; Erauso, Gaël; Ménez, Bénédicte

2017-01-01

Despite their potential importance as analogs of primitive microbial metabolisms, the knowledge of the structure and functioning of the deep ecosystems associated with serpentinizing environments is hampered by the lack of accessibility to relevant systems. These hyperalkaline environments are depleted in dissolved inorganic carbon (DIC), making the carbon sources and assimilation pathways in the associated ecosystems highly enigmatic. The Prony Bay Hydrothermal Field (PHF) is an active serpentinization site where, similar to Lost City (Mid-Atlantic Ridge), high-pH fluids rich in H 2 and CH 4 are discharged from carbonate chimneys at the seafloor, but in a shallower lagoonal environment. This study aimed to characterize the subsurface microbial ecology of this environment by focusing on the earliest stages of chimney construction, dominated by the discharge of hydrothermal fluids of subseafloor origin. By jointly examining the mineralogy and the microbial diversity of the conduits of juvenile edifices at the micrometric scale, we find a central role of uncultivated bacteria belonging to the Firmicutes in the ecology of the PHF. These bacteria, along with members of the phyla Acetothermia and Omnitrophica , are identified as the first chimneys inhabitants before archaeal Methanosarcinales . They are involved in the construction and early consolidation of the carbonate structures via organomineralization processes. Their predominance in the most juvenile and nascent hydrothermal chimneys, and their affiliation with environmental subsurface microorganisms, indicate that they are likely discharged with hydrothermal fluids from the subseafloor. They may thus be representative of endolithic serpentinization-based ecosystems, in an environment where DIC is limited. In contrast, heterotrophic and fermentative microorganisms may consume organic compounds from the abiotic by-products of serpentinization processes and/or from life in the deeper subsurface. We thus propose that the Firmicutes identified at PHF may have a versatile metabolism with the capability to use diverse organic compounds from biological or abiotic origin. From that perspective, this study sheds new light on the structure of deep microbial communities living at the energetic edge in serpentinites and may provide an alternative model of the earliest metabolisms.

Carbon mineralization in surface and subsurface soils in a subtropical mixed forest in central China

NASA Astrophysics Data System (ADS)

Liu, F.; Tian, Q.

2014-12-01

About a half of soil carbon is stored in subsurface soil horizons, their dynamics have the potential to significantly affect carbon balancing in terrestrial ecosystems. However, the main factors regulating subsurface soil carbon mineralization are poorly understood. As affected by mountain humid monsoon, the subtropical mountains in central China has an annual precipitation of about 2000 mm, which causes strong leaching of ions and nutrition. The objectives of this study were to monitor subsurface soil carbon mineralization and to determine if it is affected by nutrient limitation. We collected soil samples (up to 1 m deep) at three locations in a small watershed with three soil layers (0-10 cm, 10-30 cm, below 30 cm). For the three layers, soil organic carbon (SOC) ranged from 35.8 to 94.4 mg g-1, total nitrogen ranged from 3.51 to 8.03 mg g-1, microbial biomass carbon (MBC) ranged from 170.6 to 718.4 μg g-1 soil. We measured carbon mineralization with the addition of N (100 μg N/g soil), P (50 μg P/g soil), and liable carbon (glucose labeled by 5 atom% 13C, at five levels: control, 10% MBC, 50% MBC, 100% MBC, 200% MBC). The addition of N and P had negligible effects on CO2 production in surface soil layers; in the deepest soil layer, the addition of N and P decreased CO2 production from 4.32 to 3.20 μg C g-1 soil carbon h-1. Glucose addition stimulated both surface and subsurface microbial mineralization of SOC, causing priming effects. With the increase of glucose addition rate from 10% to 200% MBC, the primed mineralization rate increased from 0.19 to 3.20 μg C g-1 soil carbon h-1 (fifth day of glucose addition). The magnitude of priming effect increased from 28% to 120% as soil layers go deep compare to the basal CO2 production (fifth day of 200% MBC glucose addition, basal CO2 production rate for the surface and the deepest soil was 11.17 and 2.88 μg C g-1 soil carbon h-1). These results suggested that the mineralization of subsurface carbon is more sensitive to nutrient addition, and carbon mineralization in this layer is likely limited by carbon availability. Thus, any changes in environment conditions (global warming, nitrogen deposition, precipitation pattern change etc.) that affect the distribution of fresh carbon in soil profiles could then stimulate the release of deep soil carbon.

Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench.

PubMed

Tarn, Jonathan; Peoples, Logan M; Hardy, Kevin; Cameron, James; Bartlett, Douglas H

2016-01-01

Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1 m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in 34 bacterial and 4 archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats.

Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench

PubMed Central

Tarn, Jonathan; Peoples, Logan M.; Hardy, Kevin; Cameron, James; Bartlett, Douglas H.

2016-01-01

Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1 m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in 34 bacterial and 4 archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats. PMID:27242695

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust

PubMed Central

Robador, Alberto; Jungbluth, Sean P.; LaRowe, Douglas E.; Bowers, Robert M.; Rappé, Michael S.; Amend, Jan P.; Cowen, James P.

2015-01-01

The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with 35S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling. PMID:25642212

Deep subsurface life in Bengal Fan sediments (IODP Exp. 354)

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Heuer, V. B.; Elvert, M.; Kallmeyer, J.; Kitte, J. A.; Wörmer, L.; Hinrichs, K. U.

2017-12-01

We collected Bengal Fan sediment samples along a 8°N transect during International Ocean Discovery Program Expedition 354 (February - March 2015, Singapore - Colombo, Sri Lanka) to study subseafloor life in this, as yet unstudied, area. Among other biogeochemical parameters, we quantified microbial biomass by analyzing prokaryotic cells using epifluorescence microscopy after detaching cells from the sediment, and bacterial endospores by analyzing the diagnostic biomarker dipicolinic acid (DPA) by detection of fluorescence of the terbium-DPA complex. To gain understanding of total microbial activity, we quantified hydrogen utilization potential of hydrogenase enzymes, which are ubiquitous in subsurface microorganisms, by using a tritium assay. We measured highest cell concentrations of ca. 108 cells g-1 in shallow sediments close to the seafloor. These concentrations are one to two orders of magnitude lower than in most marine continental margin settings [1]. Similar to the global trend [1], cell concentrations decreased with depth according to a power-law function. Endospore concentrations scattered between ca. 105 and 107 cells g-1 sediment at all sites and depths. We could not observe a clear relationship of endospore concentration and sediment depth; instead, it appears to be linked to lithology and total organic carbon content. Bulk Hydrogenase enzyme activity ranged from nmolar to μmolar range of H2 g-1d-1. Similar to previous observations [2], per-cell hydrogen utilization depends on vertical biogeochemical zones, which could be due to the differences in hydrogen utilization requirements/efficiency of the respective metabolic processes such as sulfate reduction, methanogenesis, fermentation etc. Bengal fan is highly dynamic due to channel and levee systems and the sediments are dominated by turbidites, thick sand layers and hemipelagic deposits, which may control biogeochemical zonation. Based on our microbial biomass and activity data, we suggest that the nature, quality and origin of sedimentary material influence the deep subsurface life. [1] Kallmeyer et al., (2012) PNAS 109(40), 16213-16216 [2] Adhikari et al., (2016) Frontiers in Microbiology 7:8

Bacterial Growth, Necromass Turnover, And Endospore Abundance In The Deep Subseafloor Sediments Of The Greenland Shelf Using D:L Amino Acid Model.

NASA Astrophysics Data System (ADS)

Mhatre, S. S.; Braun, S.; Jaussi, M.; Røy, H.; Jørgensen, B. B.; Lomstein, B. A.

2015-12-01

The subsurface realm is colonized by a large number of microorganisms- about 3 × 1029. Microbial cells in these very stable and oligotrophic settings catabolize at a much slower rate than model organisms in nutrient rich cultures. The aim of this work was to use recently developed D:L-amino acid racemization model for studying the turnover times of microbial biomass and microbial necromass in a ~12,000 years old Greenland shelf marine sediment samples. Sediments were analyzed for total hydrolysable amino acids (THAA), the bacterial endospore marker dipicolinic acid (DPA), and amino acid enantiomers of aspartic acid. The percentage amino acid carbon content (%TAAC) and the percentage amino acid nitrogen content (%TAAN) were used for determining the degradation state of the organic matter. Endospores quantified using DPA quantification method were found to be as abundant as vegetative cells. The microbial necromass turnover times were thousand years, and biomass turnover times were in the range of tens to hundred years. Studies with deeper sediment cores will further improve our understanding of the energetic limits of life in the deep biosphere.

Microbial stowaways: Addressing oil spill impacts and the artificial reef effect on deep-sea microbiomes

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Salerno, J. L.; Blackwell, C. A.; Little, B.; McGown, C.; Fitzgerald, L. A.; Damour, M.

2016-02-01

Shipwrecks enhance macro-biological diversity in the deep ocean, but, to date, studies have not explored the reef effect on deep-sea microbiological diversity. This is an important concept to address in a restoration framework, as microbial biogeochemical function impacts recruitment and adhesion of higher trophic levels on artificial reefs. In addition, microbial biofilms influence the preservation of shipwrecks through biologically mediated corrosion. Oil and gas-related activities have potential to disrupt the base of the reef trophic web; therefore, bacterial diversity and gene function at six shipwrecks (3 steel-hulled; 3 wood-hulled) in the northern Gulf of Mexico was investigated as part of the GOM-SCHEMA (Shipwreck Corrosion, Hydrocarbon Exposure, Microbiology, and Archaeology) project. Sites were selected based on proximity to the Deepwater Horizon spill's subsurface plume, depth, hull type, and existing archaeological data. Classification of taxa in sediments adjacent to and at distance from wrecks, in water, and on experimental steel coupons was used to evaluate how the presence of shipwrecks and spill contaminants in the deep biosphere influenced diversity. At all sites, and in all sample types, Proteobacteria were most abundant. Biodiversity was highest in surface sediments and in coupon biofilms adjacent to two steel-hulled wrecks in the study (Halo and Anona) and decreased with sediment depth and distance from the wrecks. Sequences associated with the iron oxidizing Mariprofundus genus were elevated at steel-hulled sites, indicating wreck-specific environmental selection. Despite evidence of the reef effect on microbiomes, bacterial composition was structured primarily by proximity to the spill and secondarily by hull material at all sites. This study provides the first evidence of an artificial reef effect on deep-sea microbial communities and suggests that biodiversity and function of primary colonizers of shipwrecks may be impacted by the spill.

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes.

PubMed

Hoshino, Tatsuhiko; Toki, Tomohiro; Ijiri, Akira; Morono, Yuki; Machiyama, Hideaki; Ashi, Juichiro; Okamura, Kei; Inagaki, Fumio

2017-01-01

Submarine mud volcanoes (SMVs) are formed by muddy sediments and breccias extruded to the seafloor from a source in the deep subseafloor and are characterized by the discharge of methane and other hydrocarbon gasses and deep-sourced fluids into the overlying seawater. Although SMVs act as a natural pipeline connecting the Earth's surface and subsurface biospheres, the dispersal of deep-biosphere microorganisms and their ecological roles remain largely unknown. In this study, we investigated the microbial communities in sediment and overlying seawater at two SMVs located on the Ryukyu Trench off Tanegashima Island, southern Japan. The microbial communities in mud volcano sediments were generally distinct from those in the overlying seawaters and in the well-stratified Pacific margin sediments collected at the Peru Margin, the Juan de Fuca Ridge flank off Oregon, and offshore of Shimokita Peninsula, northeastern Japan. Nevertheless, in-depth analysis of different taxonomic groups at the sub-species level revealed that the taxon affiliated with Atribacteria , heterotrophic anaerobic bacteria that typically occur in organic-rich anoxic subseafloor sediments, were commonly found not only in SMV sediments but also in the overlying seawater. We designed a new oligonucleotide probe for detecting Atribacteria using the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). CARD-FISH, digital PCR and sequencing analysis of 16S rRNA genes consistently showed that Atribacteria are abundant in the methane plumes of the two SMVs (0.58 and 1.5 × 10 4 cells/mL, respectively) but not in surrounding waters, suggesting that microbial cells in subseafloor sediments are dispersed as "deep-biosphere seeds" into the ocean. These findings may have important implications for the microbial transmigration between the deep subseafloor biosphere and the hydrosphere.

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes

PubMed Central

Hoshino, Tatsuhiko; Toki, Tomohiro; Ijiri, Akira; Morono, Yuki; Machiyama, Hideaki; Ashi, Juichiro; Okamura, Kei; Inagaki, Fumio

2017-01-01

Submarine mud volcanoes (SMVs) are formed by muddy sediments and breccias extruded to the seafloor from a source in the deep subseafloor and are characterized by the discharge of methane and other hydrocarbon gasses and deep-sourced fluids into the overlying seawater. Although SMVs act as a natural pipeline connecting the Earth’s surface and subsurface biospheres, the dispersal of deep-biosphere microorganisms and their ecological roles remain largely unknown. In this study, we investigated the microbial communities in sediment and overlying seawater at two SMVs located on the Ryukyu Trench off Tanegashima Island, southern Japan. The microbial communities in mud volcano sediments were generally distinct from those in the overlying seawaters and in the well-stratified Pacific margin sediments collected at the Peru Margin, the Juan de Fuca Ridge flank off Oregon, and offshore of Shimokita Peninsula, northeastern Japan. Nevertheless, in-depth analysis of different taxonomic groups at the sub-species level revealed that the taxon affiliated with Atribacteria, heterotrophic anaerobic bacteria that typically occur in organic-rich anoxic subseafloor sediments, were commonly found not only in SMV sediments but also in the overlying seawater. We designed a new oligonucleotide probe for detecting Atribacteria using the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). CARD-FISH, digital PCR and sequencing analysis of 16S rRNA genes consistently showed that Atribacteria are abundant in the methane plumes of the two SMVs (0.58 and 1.5 × 104 cells/mL, respectively) but not in surrounding waters, suggesting that microbial cells in subseafloor sediments are dispersed as “deep-biosphere seeds” into the ocean. These findings may have important implications for the microbial transmigration between the deep subseafloor biosphere and the hydrosphere. PMID:28676800

Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula.

PubMed

Kobayashi, Tohru; Koide, Osamu; Mori, Kozue; Shimamura, Shigeru; Matsuura, Takae; Miura, Takeshi; Takaki, Yoshihiro; Morono, Yuki; Nunoura, Takuro; Imachi, Hiroyuki; Inagaki, Fumio; Takai, Ken; Horikoshi, Koki

2008-07-01

"A meta-enzyme approach" is proposed as an ecological enzymatic method to explore the potential functions of microbial communities in extreme environments such as the deep marine subsurface. We evaluated a variety of extra-cellular enzyme activities of sediment slurries and isolates from a deep subseafloor sediment core. Using the new deep-sea drilling vessel "Chikyu", we obtained 365 m of core sediments that contained approximately 2% organic matter and considerable amounts of methane from offshore the Shimokita Peninsula in Japan at a water depth of 1,180 m. In the extra-sediment fraction of the slurry samples, phosphatase, esterase, and catalase activities were detected consistently throughout the core sediments down to the deepest slurry sample from 342.5 m below seafloor (mbsf). Detectable enzyme activities predicted the existence of a sizable population of viable aerobic microorganisms even in deep subseafloor habitats. The subsequent quantitative cultivation using solid media represented remarkably high numbers of aerobic, heterotrophic microbial populations (e.g., maximally 4.4x10(7) cells cm(-3) at 342.5 mbsf). Analysis of 16S rRNA gene sequences revealed that the predominant cultivated microbial components were affiliated with the genera Bacillus, Shewanella, Pseudoalteromonas, Halomonas, Pseudomonas, Paracoccus, Rhodococcus, Microbacterium, and Flexibacteracea. Many of the predominant and scarce isolates produced a variety of extra-cellular enzymes such as proteases, amylases, lipases, chitinases, phosphatases, and deoxyribonucleases. Our results indicate that microbes in the deep subseafloor environment off Shimokita are metabolically active and that the cultivable populations may have a great potential in biotechnology.

Anaerobic decomposition of humic substances by Clostridium from the deep subsurface

PubMed Central

Ueno, Akio; Shimizu, Satoru; Tamamura, Shuji; Okuyama, Hidetoshi; Naganuma, Takeshi; Kaneko, Katsuhiko

2016-01-01

Decomposition of humic substances (HSs) is a slow and cryptic but non-negligible component of carbon cycling in sediments. Aerobic decomposition of HSs by microorganisms in the surface environment has been well documented; however, the mechanism of anaerobic microbial decomposition of HSs is not completely understood. Moreover, no microorganisms capable of anaerobic decomposition of HSs have been isolated. Here, we report the anaerobic decomposition of humic acids (HAs) by the anaerobic bacterium Clostridium sp. HSAI-1 isolated from the deep terrestrial subsurface. The use of 14C-labelled polycatechol as an HA analogue demonstrated that the bacterium decomposed this substance up to 7.4% over 14 days. The decomposition of commercial and natural HAs by the bacterium yielded lower molecular mass fractions, as determined using high-performance size-exclusion chromatography. Fourier transform infrared spectroscopy revealed the removal of carboxyl groups and polysaccharide-related substances, as well as the generation of aliphatic components, amide and aromatic groups. Therefore, our results suggest that Clostridium sp. HSAI-1 anaerobically decomposes and transforms HSs. This study improves our understanding of the anaerobic decomposition of HSs in the hidden carbon cycling in the Earth’s subsurface. PMID:26743007

Microbe-mediated transformations of marine dissolved organic matter during 2,100 years of natural incubation in the cold, oxic crust of the Mid-Atlantic Ridge.

NASA Astrophysics Data System (ADS)

Shah Walter, S. R.; Jaekel, U.; Huber, J. A.; Dittmar, T.; Girguis, P. R.

2015-12-01

On the western flank of the Mid-Atlantic Ridge, oxic seawater from the deep ocean is downwelled into the basaltic crust, supplying the crustal aquifer with an initial inoculum of organic matter and electron acceptors. Studies have shown that fluids circulating within the crust are minimally altered from original seawater, making this subsurface environment a unique natural experiment in which the fate of marine organic matter and the limitations of microbial adaptability in the context of reduced carbon supply can be examined. To make the subsurface crustal aquifer accessible, two CORK (Circulation Obviation Retrofit Kit) observatories have been installed at North Pond, a sediment-filled depression beneath the oligotrophic Sargasso Sea. Radiocarbon analysis of dissolved inorganic (DIC) and organic carbon (DOC) in samples recovered from these observatories show uncoupled aging between DOC and DIC with Δ14C values of DOC as low as -933‰ despite isolation from the open ocean for, at most, 2,100 years. This extreme value is part of a general trend of decreasing DOC δ13C and Δ14C values with increasing incubation time within the aquifer. Combined with reduced concentrations of DOC, our results argue for selective microbial oxidation of the youngest, most 13C-enriched components of downwelled DOC, possibly identifying these as characteristics of the more bioavailable fractions of deep-ocean dissolved organic matter. They also suggest that microbial oxidation during low-temperature hydrothermal circulation could be an important sink for aged marine dissolved organic matter.

Microbially-Enhanced Coal Bed Methane: Strategies for Increased Biogenic Production

NASA Astrophysics Data System (ADS)

Davis, K.; Barhart, E. P.; Schweitzer, H. D.; Cunningham, A. B.; Gerlach, R.; Hiebert, R.; Fields, M. W.

2014-12-01

Coal is the largest fossil fuel resource in the United States. Most of this coal is deep in the subsurface making it costly and potentially dangerous to extract. However, in many of these deep coal seams, methane, the main component of natural gas, has been discovered and successfully harvested. Coal bed methane (CBM) currently accounts for approximately 7.5% of the natural gas produced in the U.S. Combustion of natural gas produces substantially less CO2 and toxic emissions (e.g. heavy metals) than combustion of coal or oil thereby making it a cleaner energy source. In the large coal seams of the Powder River Basin (PRB) in southeast Montana and northeast Wyoming, CBM is produced almost entirely by biogenic processes. The in situ conversion of coal to CBM by the native microbial community is of particular interest for present and future natural gas sources as it provides the potential to harvest energy from coal seams with lesser environmental impacts than mining and burning coal. Research at Montana State University has shown the potential for enhancing the subsurface microbial processes that produce CBM. Long-term batch enrichments have investigated the methane enhancement potential of yeast extract as well as algal and cyanobacterial biomass additions with increased methane production observed with all three additions when compared to no addition. Future work includes quantification of CBM enhancement and normalization of additions. This presentation addresses the options thus far investigated for increasing CBM production and the next steps for developing the enhanced in situ conversion of coal to CBM.

Genetic legacy of the deep subsurface recorded in the outflow channel of a terrestrial serpentinizing seep (Luzon, the Philippines)

NASA Astrophysics Data System (ADS)

Woycheese, K. M.; Meyer-Dombard, D. R.; Cardace, D.; Arcilla, C. A.

2014-12-01

The deep subsurface microbial community represents the largest biome on Earth, yet accessing this deep biosphere is challenging. Fluids seep along fractures from aquifers that may support diverse microbial communities, living off hydrogen gas generated by radiolysis, serpentinization, or thermogenic reactions. A serpentinizing seep, emanating fluids as high as pH 11.27, was found to accrete meters-long carbonate terraces in the Zambales ophiolite range (Luzon, the Philippines). Samples were collected at several locations along the Poon Bato (PB) River, focusing primarily on the pools and terraces formed by carbonate rimstone (Figure 1). As serpentinizing fluids are exposed to the atmosphere, dynamic niches are established in surface sediments. We propose that the high pH, reducing, high Ca+2 fluid pool terraces reflect remnants of deep subsurface microbial communities, based on high-throughput 16S rRNA sequencing data. In total, eight samples were collected for environmental DNA analysis. Post-sequence analysis revealed a total of 927126 counts, with an average of 115890.75 counts per sample. Many taxa aligned with cultured representatives of serpentinizing seep-associated taxa, including Bacteroidetes, Clostrida, Chloroflexi, Methylococcales, and Xanthomonadales. Geochemical data indicates an average fluid temperature of 28.9°C, and pH that varies from 9.22-11.27. Total carbon wt.% of solids was highest in a shallow pool shaped by boulders, where calcite precipitation occurred over nearly every surface. Dissolved oxygen (DO%) was highest at PB1 main pool (60%), although a calcite skin had formed along the air-water interface. Dissolved inorganic carbon (DIC) at PB1 main pool was 1.3 ppm, while at PB2 main pool, the DIC was higher (6.0 ppm). The lack of calcite skin may allow more direct access to atmospheric carbon dioxide at PB2. The isotopic value of carbon-13 was depleted at PB1 relative to PB2 (δ13C VPDB -25.4 ‰ versus δ13C VPDB ‰ -17.5, respectively). The DOC concentration at PB1 main pool was 0.3 ppm and 1.15 ppm at PB2. Given the low DIC concentrations at PB1, it is suggested that heterotrophy may dominate over autotrophy in the system. This suggests that the highly reducing, high pH fluids emanating from fluid seeps at Poon Bato influence surface communities via inundation with serpentinizing fluid.

Microbes in deep marine sediments viewed through amplicon sequencing and metagenomics

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; Russell, J. A., III; Martino, A. J.

2016-12-01

Nearly twenty percent of microbial biomass on Earth can be found in the marine subsurface. The majority of this is concentrated on continental margins, which have been investigated by scientific drilling. On the Costa Rica Margin, Iberian Margin and Peru Margins, sediment samples have been investigated through DNA extraction followed by amplicon and metagenomic sequencing. Overall samples show a high degree of microbial diversity, including many lineages of newly defined groups. In this talk, metagenome assembled genomes of unusual lineages will be presented, including their relationships to shallower relatives. From Costa Rica, in particular, we have retrieved deep relatives of Lokiarchaeota and Thorarchaeota, as well as other deeply branching archaeal relatives. We discuss their genome similarities to both other archaea and eukaryotes. From the Iberian Margin, relatives of Atribacteria and Aerophobetes will be discussed. Finally, we will detail the knowledge lost or gained depending on whether samples are studied via amplicon sequencing or total metagenomics, as studies in other environments have shown that up to 15% of microbial diversity is ignored when samples are studied via amplicon sequencing alone.

Single cell genomic study of dehalogenating Chloroflexi from deep sea sediments of Peruvian Margin

NASA Astrophysics Data System (ADS)

Spormann, A.; Kaster, A.; Meyer-Blackwell, K.; Biddle, J.

2012-12-01

Dehalogenating Chloroflexi, such as Dehalococcoidites (Dhc), are members of the rare biosphere of deep sea sediments but were originally discovered as the key microbes mediating reductive dehalogenation of the prevalent groundwater contaminants tetrachloroethene and trichloroethene to ethene. Dhc are slow growing, highly niche adapted microbes that are specialized to organohalide respiration as the sole mode of energy conservation. These strictly anaerobic microbes depend on a supporting microbial community to mitigate electron donor and cofactor requirements among other factors. Molecular and genomic studies on the key enzymes for energy conservation, reductive dehalogenases, have provided evidence for rapid adaptive evolution in terrestrial environments. However, the metabolic life style of Dhc in the absence of anthropogenic contaminants, such as in pristine deep sea sediments, is still unknown. In order to provide fundamental insights into life style, genomic population structure and evolution of Dhc, we analyzed a non-contaminated deep sea sediment sample of the Peru Margin 1230 site collected 6 mbf by a metagenomic and single cell genomic. We present for the first time single cell genomic data on dehalogenating Chloroflexi, a significant microbial population in the poorly understood oligotrophic marine sub-surface environments.

Single cell genomic study of dehalogenating Chloroflexi in deep sea sediments of Peru Margin 1230

NASA Astrophysics Data System (ADS)

Kaster, A.; Meyer-Blackwell, K.; Biddle, J.; Spormann, A.

2012-12-01

Dehalogenating Chloroflexi, such as Dehalococcoidites (Dhc), are members of the rare biosphere of deep sea sediments but were originally discovered as the key microbes mediating reductive dehalogenation of the prevalent groundwater contaminants tetrachloroethene and trichloroethene to ethene. Dhc are slow growing, highly niche adapted microbes that are specialized to organohalide respiration as the sole mode of energy conservation. They are strictly anaerobic microbes that depend on a supporting microbial community for electron donor and cofactor requirements among other factors. Molecular and genomic studies on the key enzymes for energy conservation, reductive dehalogenases, have provided evidence for rapid adaptive evolution in terrestrial environments. However, the metabolic life style of Dhc in the absence of anthropogenic contaminants, such as in pristine deep sea sediments, is still unknown. In order to provide fundamental insights into life style, genomic population structure and evolution of Dhc, we analyzed a non-contaminated deep sea sediment sample of the Peru Margin 1230 site collected 6 mbsf by a metagenomic and single cell genomic approach. We present for the first time single cell genomic data on dehalogenating Chloroflexi, a significant microbial population in the poorly understood oligotrophic marine sub-surface environment.

Sulfur mass-independent fractionation in subsurface fracture waters indicates a long-standing sulfur cycle in Precambrian rocks.

PubMed

Li, L; Wing, B A; Bui, T H; McDermott, J M; Slater, G F; Wei, S; Lacrampe-Couloume, G; Lollar, B Sherwood

2016-10-27

The discovery of hydrogen-rich waters preserved below the Earth's surface in Precambrian rocks worldwide expands our understanding of the habitability of the terrestrial subsurface. Many deep microbial ecosystems in these waters survive by coupling hydrogen oxidation to sulfate reduction. Hydrogen originates from water-rock reactions including serpentinization and radiolytic decomposition of water induced by decay of radioactive elements in the host rocks. The origin of dissolved sulfate, however, remains unknown. Here we report, from anoxic saline fracture waters ∼2.4 km below surface in the Canadian Shield, a sulfur mass-independent fractionation signal in dissolved sulfate. We demonstrate that this sulfate most likely originates from oxidation of sulfide minerals in the Archaean host rocks through the action of dissolved oxidants (for example, HO · and H 2 O 2 ) themselves derived from radiolysis of water, thereby providing a coherent long-term mechanism capable of supplying both an essential electron donor (H 2 ) and a complementary acceptor (sulfate) for the deep biosphere.

Sulfur mass-independent fractionation in subsurface fracture waters indicates a long-standing sulfur cycle in Precambrian rocks

PubMed Central

Li, L.; Wing, B. A.; Bui, T. H.; McDermott, J. M.; Slater, G. F.; Wei, S.; Lacrampe-Couloume, G.; Lollar, B. Sherwood

2016-01-01

The discovery of hydrogen-rich waters preserved below the Earth's surface in Precambrian rocks worldwide expands our understanding of the habitability of the terrestrial subsurface. Many deep microbial ecosystems in these waters survive by coupling hydrogen oxidation to sulfate reduction. Hydrogen originates from water–rock reactions including serpentinization and radiolytic decomposition of water induced by decay of radioactive elements in the host rocks. The origin of dissolved sulfate, however, remains unknown. Here we report, from anoxic saline fracture waters ∼2.4 km below surface in the Canadian Shield, a sulfur mass-independent fractionation signal in dissolved sulfate. We demonstrate that this sulfate most likely originates from oxidation of sulfide minerals in the Archaean host rocks through the action of dissolved oxidants (for example, HO· and H2O2) themselves derived from radiolysis of water, thereby providing a coherent long-term mechanism capable of supplying both an essential electron donor (H2) and a complementary acceptor (sulfate) for the deep biosphere. PMID:27807346

The role microbial sulfate reduction in the direct mediation of sedimentary authigenic carbonate precipitation

NASA Astrophysics Data System (ADS)

Turchyn, A. V.; Walker, K.; Sun, X.

2016-12-01

The majority of modern deep marine sediments are bathed in water that is undersaturated with respect to calcium carbonate. However, within marine sediments changing chemical conditions, driven largely by the microbial oxidation of organic carbon in the absence of oxygen, lead to supersaturated conditions and drive calcium carbonate precipitation. This sedimentary calcium carbonate is often called `authigenic carbonate', and is found in the form of cements and disseminated crystals within the marine sedimentary pile. As this precipitation of this calcium carbonate is microbially mediated, identifying authigenic carbonate within the geological record and understanding what information its geochemical and/or isotopic signature may hold is key for understanding its importance and what information it may contain past life. However, the modern controls on authigenic carbonate precipitation remain enigmatic because the myriad of microbially mediated reactions occurring within sediments both directly and indirectly impact the proton balance. In this submission we present data from 25 ocean sediment cores spanning the globe where we explore the deviation from the stoichiometrically predicted relationships among alkalinity, calcium and sulfate concentrations. In theory for every mol of organic carbon reduced by sulfate, two mol of alkalinity is produced, and to precipitate subsurface calcium carbonate one mol of calcium is used to consume two mol of alkalinity. We use this data with a model to explore changes in carbonate saturation state with depth below the seafloor. Alkalinity changes in the subsurface are poorly correlated with changes in calcium concentrations, however calcium concentrations are directly and tightly coupled to changes in sulfate concentrations in all studied sites. This suggests a direct role for sulfate reducing bacteria in the precipitation of subsurface carbonate cements.

Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

PubMed Central

Lloyd, Karen G.; Albert, Daniel B.; Biddle, Jennifer F.; Chanton, Jeffrey P.; Pizarro, Oscar; Teske, Andreas

2010-01-01

Background Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. Methodology/Principal Findings We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat (∼400 cm and ∼10 cm from the mat's edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. Conclusions/Significance The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In contrast, 12–20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes. PMID:20090951

Variations in microbial carbon sources and cycling in the deep continental subsurface

NASA Astrophysics Data System (ADS)

Simkus, Danielle N.; Slater, Greg F.; Lollar, Barbara Sherwood; Wilkie, Kenna; Kieft, Thomas L.; Magnabosco, Cara; Lau, Maggie C. Y.; Pullin, Michael J.; Hendrickson, Sarah B.; Wommack, K. Eric; Sakowski, Eric G.; van Heerden, Esta; Kuloyo, Olukayode; Linage, Borja; Borgonie, Gaetan; Onstott, Tullis C.

2016-01-01

Deep continental subsurface fracture water systems, ranging from 1.1 to 3.3 km below land surface (kmbls), were investigated to characterize the indigenous microorganisms and elucidate microbial carbon sources and their cycling. Analysis of phospholipid fatty acid (PLFA) abundances and direct cell counts detected varying biomass that was not correlated with depth. Compound-specific carbon isotope analyses (δ13C and Δ14C) of the phospholipid fatty acids (PLFAs) and carbon substrates combined with genomic analyses did identify, however, distinct carbon sources and cycles between the two depth ranges studied. In the shallower boreholes at circa 1 kmbls, isotopic evidence indicated microbial incorporation of biogenic CH4 by the in situ microbial community. At the shallowest site, 1.05 kmbls in Driefontein mine, this process clearly dominated the isotopic signal. At slightly deeper depths, 1.34 kmbls in Beatrix mine, the isotopic data indicated the incorporation of both biogenic CH4 and dissolved inorganic carbon (DIC) derived from CH4 oxidation. In both of these cases, molecular genetic analysis indicated that methanogenic and methanotrophic organisms together comprised a small component (<5%) of the microbial community. Thus, it appears that a relatively minor component of the prokaryotic community is supporting a much larger overall bacterial community in these samples. In the samples collected from >3 kmbls in Tau Tona mine (TT107, TT109 Bh2), the CH4 had an isotopic signature suggesting a predominantly abiogenic origin with minor inputs from microbial methanogenesis. In these samples, the isotopic enrichments (δ13C and Δ14C) of the PLFAs relative to CH4 were consistent with little incorporation of CH4 into the biomass. The most 13C-enriched PLFAs were observed in TT107 where the dominant CO2-fixation pathway was the acetyl-CoA pathway by non-acetogenic bacteria. The differences in the δ13C of the PLFAs and the DIC and DOC for TT109 Bh2 were ∼-24‰ and 0‰, respectively. The dominant CO2-fixation pathways were 3-HP/4-HB cycle > acetyl-CoA pathway > reductive pentose phosphate cycle.

Continued evolution of Europa subsurface exploration technologies

NASA Technical Reports Server (NTRS)

Carsey, F. D.; Hecht, M. H.; Lane, A. L.; Mogensen, C.; Zimmerman, W.

2002-01-01

The Galileo results convincingly indicate that Europa has a deep salty ocean covered by a shell of water ice a few tens of kilometers thick; this physical description gives rise to a host of thoughtful speculation as to the nature of the ocean, its seafloor, and the likelihood of microbial life within it. We argue that this situation points to the high desirability of a series of in-situ missions to examine the ice and, ultimately, the ocean.

Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland.

PubMed

Sohlberg, Elina; Bomberg, Malin; Miettinen, Hanna; Nyyssönen, Mari; Salavirta, Heikki; Vikman, Minna; Itävaara, Merja

2015-01-01

The diversity and functional role of fungi, one of the ecologically most important groups of eukaryotic microorganisms, remains largely unknown in deep biosphere environments. In this study we investigated fungal communities in packer-isolated bedrock fractures in Olkiluoto, Finland at depths ranging from 296 to 798 m below surface level. DNA- and cDNA-based high-throughput amplicon sequencing analysis of the fungal internal transcribed spacer (ITS) gene markers was used to examine the total fungal diversity and to identify the active members in deep fracture zones at different depths. Results showed that fungi were present in fracture zones at all depths and fungal diversity was higher than expected. Most of the observed fungal sequences belonged to the phylum Ascomycota. Phyla Basidiomycota and Chytridiomycota were only represented as a minor part of the fungal community. Dominating fungal classes in the deep bedrock aquifers were Sordariomycetes, Eurotiomycetes, and Dothideomycetes from the Ascomycota phylum and classes Microbotryomycetes and Tremellomycetes from the Basidiomycota phylum, which are the most frequently detected fungal taxa reported also from deep sea environments. In addition some fungal sequences represented potentially novel fungal species. Active fungi were detected in most of the fracture zones, which proves that fungi are able to maintain cellular activity in these oligotrophic conditions. Possible roles of fungi and their origin in deep bedrock groundwater can only be speculated in the light of current knowledge but some species may be specifically adapted to deep subsurface environment and may play important roles in the utilization and recycling of nutrients and thus sustaining the deep subsurface microbial community.

A hydrogen-based subsurface microbial community dominated by methanogens

USGS Publications Warehouse

Chapelle, F.H.; O'Neil, Kyle; Bradley, P.M.; Methe, B.A.; Ciufo, S.A.; Knobel, L.L.; Lovley, D.R.

2002-01-01

The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem1-5. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16s ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

New Bio-Indicators for Long Term Natural Attenuation of Monoaromatic Compounds in Deep Terrestrial Aquifers.

PubMed

Aüllo, Thomas; Berlendis, Sabrina; Lascourrèges, Jean-François; Dessort, Daniel; Duclerc, Dominique; Saint-Laurent, Stéphanie; Schraauwers, Blandine; Mas, Johan; Patriarche, Delphine; Boesinger, Cécile; Magot, Michel; Ranchou-Peyruse, Anthony

2016-01-01

Deep subsurface aquifers despite difficult access, represent important water resources and, at the same time, are key locations for subsurface engineering activities for the oil and gas industries, geothermal energy, and CO2 or energy storage. Formation water originating from a 760 m-deep geological gas storage aquifer was sampled and microcosms were set up to test the biodegradation potential of BTEX by indigenous microorganisms. The microbial community diversity was studied using molecular approaches based on 16S rRNA genes. After a long incubation period, with several subcultures, a sulfate-reducing consortium composed of only two Desulfotomaculum populations was observed able to degrade benzene, toluene, and ethylbenzene, extending the number of hydrocarbonoclastic-related species among the Desulfotomaculum genus. Furthermore, we were able to couple specific carbon and hydrogen isotopic fractionation during benzene removal and the results obtained by dual compound specific isotope analysis (C = -2.4‰ ± 0.3‰; H = -57‰ ± 0.98‰; AKIEC: 1.0146 ± 0.0009, and AKIEH: 1.5184 ± 0.0283) were close to those obtained previously in sulfate-reducing conditions: this finding could confirm the existence of a common enzymatic reaction involving sulfate-reducers to activate benzene anaerobically. Although we cannot assign the role of each population of Desulfotomaculum in the mono-aromatic hydrocarbon degradation, this study suggests an important role of the genus Desulfotomaculum as potential biodegrader among indigenous populations in subsurface habitats. This community represents the simplest model of benzene-degrading anaerobes originating from the deepest subterranean settings ever described. As Desulfotomaculum species are often encountered in subsurface environments, this study provides some interesting results for assessing the natural response of these specific hydrologic systems in response to BTEX contamination during remediation projects.

Archaeal Viruses Contribute to the Novel Viral Assemblage Inhabiting Oceanic, Basalt-Hosted Deep Subsurface Crustal Fluids

NASA Astrophysics Data System (ADS)

Nigro, O. D.; Rappe, M. S.; Jungbluth, S.; Lin, H. T.; Steward, G.

2015-12-01

Fluids contained in the basalt-hosted deep subsurface of the world's oceans represent one of the most inaccessible and understudied biospheres on earth. Recent improvements in sampling infrastructure have allowed us to collect large volumes of crustal fluids (~104 L) from Circulation Obviation Retrofit Kits (CORKs) placed in boreholes located on the eastern flank of the Juan de Fuca Ridge (JdFR). We detected viruses within these fluids by TEM and epifluorescence microscopy in samples collected from 2010 to 2014. Viral abundance, determined by epifluorescence counts, indicated that concentrations of viruses in subsurface basement fluids (~105 ml-1) are lower than the overlying seawater, but are higher in abundance than microbial cells in the same samples. Analysis of TEM images revealed distinct viral morphologies (rod and spindle-shaped) that resemble the morphologies of viral families infecting archaea. There are very few, if any, direct observations of these viral morphologies in marine samples, although they have been observed in enrichment cultures and their signature genes detected in metagenomic studies from hydrothermal vents and marine sediments. Analysis of metagenomes from the JdFR crustal fluids revealed sequences with homology to archaeal viruses from the rudiviridae, bicaudaviridae and fuselloviridae. Prokaryotic communities in fluids percolating through the basaltic basement rock of the JdFR flank are distinct from those inhabiting the overlying sediments and seawater. Similarly, our data support the idea that the viral assemblage in these fluids is distinct from viral assemblages in other marine and terrestrial aquatic environments. Our data also suggest that viruses contribute to the mortality of deep subsurface prokaryotes through cell lysis, and viruses may alter the genetic potential of their hosts through the processes of lysogenic conversion and horizontal gene transfer.

Oil biodegradation. Water droplets in oil are microhabitats for microbial life.

PubMed

Meckenstock, Rainer U; von Netzer, Frederick; Stumpp, Christine; Lueders, Tillmann; Himmelberg, Anne M; Hertkorn, Norbert; Schmitt-Kopplin, Philipp; Harir, Mourad; Hosein, Riad; Haque, Shirin; Schulze-Makuch, Dirk

2014-08-08

Anaerobic microbial degradation of hydrocarbons, typically occurring at the oil-water transition zone, influences the quality of oil reservoirs. In Pitch Lake, Trinidad and Tobago--the world's largest asphalt lake--we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. Pyrotag sequencing of individual droplet microbiomes revealed complex methanogenic microbial communities actively degrading the oil into a diverse range of metabolites, as shown by nuclear magnetic resonance and Fourier transform ion cyclotron resonance mass spectrometry. High salinity and water-stable isotopes of the droplets indicate a deep subsurface origin. The 13.5% water content and the large surface area of the droplets represent an underestimated potential for biodegradation of oil away from the oil-water transition zone. Copyright © 2014, American Association for the Advancement of Science.

Deep subsurface microbiology of 64-71 million year old inactive seamounts along the Louisville Seamount Chain

NASA Astrophysics Data System (ADS)

Sylvan, J. B.; Morono, Y.; Grim, S.; Inagaki, F.; Edwards, K. J.

2013-12-01

One of the objectives of IODP Expedition 330, Louisville Seamount Trail, was to sample and learn about the subsurface biosphere in the Louisville Seamount Chain (LSC). Seamounts are volcanic constructs that are ubiquitous along the seafloor - models suggest there are >100,000 seamounts of >1 km in height globally (Wessel et al., 2010). Therefore, knowledge about microbiology in the LSC subsurface can broadly be interpreted as representative of much the seafloor. In addition, despite the fact that the vast majority of the sea floor is comprised of crust >10 Ma, the majority of work to date has focused on young sites with active hydrology. Our presentation summarizes work focusing on subsurface microbiology from two different LSC seamounts: holes U1374A (65-71 Ma) and U1376A (64 Ma). We here present data for microbial biomass in the LSC subsurface using a method we developed to quantify microbial biomass in subseafloor ocean crust. We also present results from pyrotag analysis of 15 samples from holes U1374A and holes U1376A, representing several different lithologies from 40-491 meters below seafloor (mbsf) in hole U1374A and from 29-174 mbsf in hole U1376A. Finally, we present preliminary analysis of metagenomic sequencing from three of the samples from Hole U1376A. Biomass was low in the subsurface of both seamounts, ranging from below detection to ~104 cells cm-3. Bacteria comprised >99% of the prokaryotic community in LSC subsurface samples, therefore, bacterial diversity was assessed through 454 pyrosequencing of the V4V6 region of the 16S rRNA gene. Rarefaction analysis indicates that bacterial communities from the LSC subsurface are low diversity, on the order of a few hundred operational taxonomic units per sample. The phyla Actinobacteria, Bacteroidetes, Firmicutes and the classes α-, β- and γ-Proteobacteria are most abundant in the LSC subsurface. Within these, the orders Actinomycetales, Sphingobacteriales, Bacillales and Burkholderiales are the most common. Samples from different lithologies in hole U1374A grouped together, indicating more similarity to each other than to samples from hole U1376A. However, samples from different lithologies in hole U1376A were not similar to other samples from the same site, indicating some differences in the microbial communities between the two seamounts. Preliminary analysis of the metagenomic data will provide further assessment of community structure and reveal likely metabolisms present in the LSC subsurface. Altogether, the biomass data, pyrotag analysis and metagenomic sequencing provide a well-balanced analysis of subsurface microbiology in an old oceanic crustal environment. Wessel, P., Sandwell, D. T. & Kim, S. S. (2010). The Global Seamount Census. Oceanography 23, 24-33.

Drilling effect on subsurface microbial community structure in groundwater from the -250 m gallery at the Horonobe Underground Research Laboratory, Japan

NASA Astrophysics Data System (ADS)

Ise, K.; Amano, Y.; Sasaki, Y.; Yoshikawa, H.

2014-12-01

The deep geological disposal system is regarded as the most secure and practical disposal method of high-level radioactive waste in the world. In this disposal system, preservation of reducing condition is one of the key requirements, because most of radionuclides have low solubilities in such condition. However, the host rocks near the shafts and galleries would be affected by oxidization during the construction and operation period of a repository (for about 50 years). Therefore, the recovery of reducing condition after closing the repository should be verified. During the recovery processes, it is considered that microbial activities play important roles, but the mechanisms are poorly understood. In this study, we monitored the changes in microbial communities by molecular method to evaluate microbial response toward the oxygen stress. The groundwater samples were collected from a borehole of 250 m depth at the Horonobe Underground Research Laboratory, for two years immediately after drilling of a borehole without any contamination as much as possible. Immediately after drilling of the borehole, the phylotype related to Arcobacter spp. was dominated about 65 % of the total clone library. Arcobacter spp. is known as sulfide oxidizer and which can growth chemoautotrophically. Half a year later, the phylotype related to Azoarcus spp. and Pseudomonas spp. known as nitrate reducing bacteria increased, instead of the phylotype related to Arcobacter spp. One year later, in addition to nitrate reducing bacteria, phylotype related to Dethiobacterspp. known as thiosulfate reducing bacteria was dominantly detected. Two years later, most of detected clones were related to uncultured species such as candidate division WS6 and JS1 which are detected frequently in deep-sea sediments. Our results indicate that these redox sequential reactions could contribute to the recovery and maintenance of reducing conditions and provide a conceptual model for evaluating the capacity to recover reducing conditions in subsurface environments after final geological disposal and the post-closure.

The deep, hot biosphere.

PubMed

Gold, T

1992-07-01

There are strong indications that microbial life is widespread at depth in the crust of the Earth, just as such life has been identified in numerous ocean vents. This life is not dependent on solar energy and photosynthesis for its primary energy supply, and it is essentially independent of the surface circumstances. Its energy supply comes from chemical sources, due to fluids that migrate upward from deeper levels in the Earth. In mass and volume it may be comparable with all surface life. Such microbial life may account for the presence of biological molecules in all carbonaceous materials in the outer crust, and the inference that these materials must have derived from biological deposits accumulated at the surface is therefore not necessarily valid. Subsurface life may be widespread among the planetary bodies of our solar system, since many of them have equally suitable conditions below, while having totally inhospitable surfaces. One may even speculate that such life may be widely disseminated in the universe, since planetary type bodies with similar subsurface conditions may be common as solitary objects in space, as well as in other solar-type systems.

Microbial habitability of Europa sustained by radioactive sources.

PubMed

Altair, Thiago; de Avellar, Marcio G B; Rodrigues, Fabio; Galante, Douglas

2018-01-10

There is an increasing interest in the icy moons of the Solar System due to their potential habitability and as targets for future exploratory missions, which include astrobiological goals. Several studies have reported new results describing the details of these moons' geological settings; however, there is still a lack of information regarding the deep subsurface environment of the moons. The purpose of this article is to evaluate the microbial habitability of Europa constrained by terrestrial analogue environments and sustained by radioactive energy provided by natural unstable isotopes. The geological scenarios are based on known deep environments on Earth, and the bacterial ecosystem is based on a sulfate-reducing bacterial ecosystem found 2.8 km below the surface in a basin in South Africa. The results show the possibility of maintaining the modeled ecosystem based on the proposed scenarios and provides directions for future models and exploration missions for a more complete evaluation of the habitability of Europa and of icy moons in general.

MICROBIAL ECOLOGY OF THE SUBSURFACE AT AN ABANDONED CREOSOTE WASTE SITE

EPA Science Inventory

The microbial ecology of pristine, slightly contaminated, and heavily contaminated subsurface materials, and four subsurface materials on the periphery of the plume at an abandoned creosote waste site was investigated. Except for the unsaturated zone of the heavily contaminated m...

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic.

PubMed

Krauze, Patryk; Kämpf, Horst; Horn, Fabian; Liu, Qi; Voropaev, Andrey; Wagner, Dirk; Alawi, Mashal

2017-01-01

The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO 2 at the surface that occurs in the form of CO 2 -rich mineral springs and wet and dry mofettes. So far, the influence of CO 2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO 2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas ) and iron (e.g., Gallionella, Sideroxydans ) cycling shaped the core community. Additionally, CO 2 -influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe 2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments.

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic

PubMed Central

Krauze, Patryk; Kämpf, Horst; Horn, Fabian; Liu, Qi; Voropaev, Andrey; Wagner, Dirk; Alawi, Mashal

2017-01-01

The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments. PMID:29321765

Diverse origins of Arctic and Subarctic methane point source emissions identified with multiply-substituted isotopologues

NASA Astrophysics Data System (ADS)

Douglas, P. M. J.; Stolper, D. A.; Smith, D. A.; Walter Anthony, K. M.; Paull, C. K.; Dallimore, S.; Wik, M.; Crill, P. M.; Winterdahl, M.; Eiler, J. M.; Sessions, A. L.

2016-09-01

Methane is a potent greenhouse gas, and there are concerns that its natural emissions from the Arctic could act as a substantial positive feedback to anthropogenic global warming. Determining the sources of methane emissions and the biogeochemical processes controlling them is important for understanding present and future Arctic contributions to atmospheric methane budgets. Here we apply measurements of multiply-substituted isotopologues, or clumped isotopes, of methane as a new tool to identify the origins of ebullitive fluxes in Alaska, Sweden and the Arctic Ocean. When methane forms in isotopic equilibrium, clumped isotope measurements indicate the formation temperature. In some microbial methane, however, non-equilibrium isotope effects, probably related to the kinetics of methanogenesis, lead to low clumped isotope values. We identify four categories of emissions in the studied samples: thermogenic methane, deep subsurface or marine microbial methane formed in isotopic equilibrium, freshwater microbial methane with non-equilibrium clumped isotope values, and mixtures of deep and shallow methane (i.e., combinations of the first three end members). Mixing between deep and shallow methane sources produces a non-linear variation in clumped isotope values with mixing proportion that provides new constraints for the formation environment of the mixing end-members. Analyses of microbial methane emitted from lakes, as well as a methanol-consuming methanogen pure culture, support the hypothesis that non-equilibrium clumped isotope values are controlled, in part, by kinetic isotope effects induced during enzymatic reactions involved in methanogenesis. Our results indicate that these kinetic isotope effects vary widely in microbial methane produced in Arctic lake sediments, with non-equilibrium Δ18 values spanning a range of more than 5‰.

Microbial monitoring during CO2 storage in deep subsurface saline aquifers in Ketzin, Germany

NASA Astrophysics Data System (ADS)

Wuerdemann, H.; Wandrey, M.; Fischer, S.; Zemke, K.; Let, D.; Zettlitzer, M.; Morozova, D.

2010-12-01

Investigations on subsurface saline aquifers have shown an active biosphere composed of diverse groups of microorganisms in the subsurface. Since microorganisms represent very effective geochemical catalysts, they may influence the process of CO2 storage significantly. In the frames of the EU Project CO2SINK a field laboratory to study CO2 storage into saline aquifer was operated. Our studies aim at monitoring of biological and biogeochemical processes and their impact on the technical effectiveness of CO2 storage technique. The interactions between microorganisms and the minerals of both the reservoir and the cap rock may cause changes to the structure and chemical composition of the rock formations, which may influence the reservoir permeability locally. In addition, precipitation and corrosion may be induced around the well affecting the casing and the casing cement. Therefore, analyses of the composition of microbial communities and its changes should contribute to an evaluation of the effectiveness and reliability of the long-term CO2 storage technique. In order to investigate processes in the deep biosphere caused by the injection of supercritical CO2, genetic fingerprinting (PCR SSCP Single-Strand-Conformation Polymorphism) and FISH (Fluorescence in situ Hybridisation) were used for identification and quantification of microorganisms. Although saline aquifers could be characterised as an extreme habitat for microorganisms due to reduced conditions, high pressure and salinity, a high number of diverse groups of microorganisms were detected with downhole sampling in the injection and observation wells at a depth of about 650m depth. Of great importance was the identification of the sulphate reducing bacteria, which are known to be involved in corrosion processes. Microbial monitoring during CO2 injection has shown that both quantity and diversity of microbial communities were strongly influenced by the CO2 injection. In addition, the indigenous microbial communities revealed a high adaptability to the changed environments after CO2 injection. In order to investigate processes in the rock substrate, long term CO2 exposure experiments on freshly drilled, pristine Ketzin reservoir core samples were accomplished for 24 months using sterile synthetic brine under in situ pressure and temperature conditions. The composition of the microbial community dominated by chemoorganotrophic bacteria and hydrogen oxidizing bacteria changed slightly under CO2 exposure. In addition, changes in porosities were observed with time. During the experiments porosity first increased due to mineral dissolution but then tend to decrease due to mineral precipitation. These mineralogical changes are consistent with changes in fluid composition during the course of the experiments that indicate notably increased K+, Ca2+, Mg2+, and SO4 2- concentrations. K+, Ca2+, Mg2+ concentrations exceeded the reservoir brine composition significantly and can be attributed to the CO2 exposure.

Microbial Stimulation and Succession following a Test Well Injection Simulating CO₂ Leakage into a Shallow Newark Basin Aquifer

PubMed Central

O’Mullan, Gregory; Dueker, M. Elias; Clauson, Kale; Yang, Qiang; Umemoto, Kelsey; Zakharova, Natalia; Matter, Juerg; Stute, Martin; Takahashi, Taro; Goldberg, David

2015-01-01

In addition to efforts aimed at reducing anthropogenic production of greenhouse gases, geological storage of CO2 is being explored as a strategy to reduce atmospheric greenhouse gas emission and mitigate climate change. Previous studies of the deep subsurface in North America have not fully considered the potential negative effects of CO2 leakage into shallow drinking water aquifers, especially from a microbiological perspective. A test well in the Newark Rift Basin was utilized in two field experiments to investigate patterns of microbial succession following injection of CO2-saturated water into an isolated aquifer interval, simulating a CO2 leakage scenario. A decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), and increased bacterial cell concentrations in the recovered water. 16S ribosomal RNA gene sequence libraries from samples collected before and after the test well injection were compared to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injections, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia and microbial taxa often noted to be associated with iron and sulfate reduction. The concurrence of increased microbial cell concentrations and rapid microbial community succession indicate significant changes in aquifer microbial communities immediately following the experimental CO2 leakage event. Samples collected one year post-injection were similar in cell number to the original background condition and community composition, although not identical, began to revert toward the pre-injection condition, indicating microbial resilience following a leakage disturbance. This study provides a first glimpse into the in situ successional response of microbial communities to CO2 leakage after subsurface injection in the Newark Basin and the potential microbiological impact of CO2 leakage on drinking water resources. PMID:25635675

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust

PubMed Central

Magnabosco, Cara; Ryan, Kathleen; Lau, Maggie C Y; Kuloyo, Olukayode; Sherwood Lollar, Barbara; Kieft, Thomas L; van Heerden, Esta; Onstott, Tullis C

2016-01-01

Subsurface microbial communities comprise a significant fraction of the global prokaryotic biomass; however, the carbon metabolisms that support the deep biosphere have been relatively unexplored. In order to determine the predominant carbon metabolisms within a 3-km deep fracture fluid system accessed via the Tau Tona gold mine (Witwatersrand Basin, South Africa), metagenomic and thermodynamic analyses were combined. Within our system of study, the energy-conserving reductive acetyl-CoA (Wood-Ljungdahl) pathway was found to be the most abundant carbon fixation pathway identified in the metagenome. Carbon monoxide dehydrogenase genes that have the potential to participate in (1) both autotrophic and heterotrophic metabolisms through the reversible oxidization of CO and subsequent transfer of electrons for sulfate reduction, (2) direct utilization of H2 and (3) methanogenesis were identified. The most abundant members of the metagenome belonged to Euryarchaeota (22%) and Firmicutes (57%)—by far, the highest relative abundance of Euryarchaeota yet reported from deep fracture fluids in South Africa and one of only five Firmicutes-dominated deep fracture fluids identified in the region. Importantly, by combining the metagenomics data and thermodynamic modeling of this study with previously published isotopic and community composition data from the South African subsurface, we are able to demonstrate that Firmicutes-dominated communities are associated with a particular hydrogeologic environment, specifically the older, more saline and more reducing waters. PMID:26325359

New Frontiers for Deep Fluids and Geobiology Research in the World's Oldest Rocks

NASA Astrophysics Data System (ADS)

Sherwood Lollar, B.; Li, L.; Wing, B. A.; Warr, O.; Sica, C. S.; Lollar, G. S.; Sutcliffe, N. C.; Telling, J.; Ballentine, C. J.; Giunta, T.; McDermott, J. M.

2016-12-01

Discovery of new environmental systems that facilitate investigation of biodiversity, microbial metabolism, life's adaptation to extreme conditions, and limits to life, have expanded our conception of Earth's habitability and informed search strategies for life elsewhere in the solar system. While chemolithotrophic microbial ecosystems in the marine biosphere have been investigated for decades, the geobiology of terrestrial systems is undergoing a recent expansion, in particular to include the > 70% of the continental lithosphere comprised of Precambrian rocks - the oldest rocks on Earth. Underground research laboratories and mines worldwide provide access to the deep subsurface in Precambrian settings, and targets for investigation of extant microbial ecosystems. Kidd Creek Mine located in Tmmins Ontario on the Canadian Shield is an iconic site. Investigation of fracture fluids here to 3 km revealed H2 production via radiolysis and serpentinization [1]; production of methane and higher hydrocarbons via abiotic organic synthesis [2]; and fracture fluids with mean residence times on the order of a billion years [3]. Recently, investigation of the sulfur cycle in these fluids has revealed a mass independent sulfur isotope signature in the dissolved sulfate, whereby oxidants from radiolysis oxidize Archean sulfide minerals, providing a mechanism to supply both electron donors (H2) and electron acceptors (sulfate) that could fuel a deep microbial biosphere [4]. Recent MPNs results demonstrate the presence of sulfate-reducing bacteria in these waters in the present day. Beginning in 2016 the deep levels at this site are providing access to international teams of researchers to collaborate with the University of Toronto in a multi-year program to characterize the deep CHONS cycles, as terrestrial geobiology continues to expand our understanding of the habitability of the Earth. [1] Sherwood Lollar et al. (2014) Nature 516,379-382. [2] Sherwood Lollar et al. (2002) Nature 416,522-524. [3] Holland et al. (2013) Nature 497,357-360. [4] Li et al. (2016) Nature Communications in press.

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

PubMed Central

Gründger, Friederike; Jiménez, Núria; Thielemann, Thomas; Straaten, Nontje; Lüders, Tillmann; Richnow, Hans-Hermann; Krüger, Martin

2015-01-01

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport. PMID:25852663

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

PubMed Central

Lesniewski, Ryan A; Jain, Sunit; Anantharaman, Karthik; Schloss, Patrick D; Dick, Gregory J

2012-01-01

Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3–4 times) and microbially mediated manganese oxidation rates (15–125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10–20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California. PMID:22695860

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs.

PubMed

Lesniewski, Ryan A; Jain, Sunit; Anantharaman, Karthik; Schloss, Patrick D; Dick, Gregory J

2012-12-01

Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3-4 times) and microbially mediated manganese oxidation rates (15-125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10-20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California.

Modeling Subsurface Behavior at the System Level: Considerations and a Path Forward

NASA Astrophysics Data System (ADS)

Geesey, G.

2005-12-01

The subsurface is an obscure but essential resource to life on Earth. It is an important region for carbon production and sequestration, a source and reservoir for energy, minerals and metals and potable water. There is a growing need to better understand subsurface possesses that control the exploitation and security of these resources. Our best models often fail to predict these processes at the field scale because of limited understanding of 1) the processes and the controlling parameters, 2) how processes are coupled at the field scale 3) geological heterogeneities that control hydrological, geochemical and microbiological processes at the field scale and 4) lack of data sets to calibrate and validate numerical models. There is a need for experimental data obtained at scales larger than those obtained at the laboratory bench that take into account the influence of hydrodynamics, geochemical reactions including complexation and chelation/adsorption/precipitation/ion exchange/oxidation-reduction/colloid formation and dissolution, and reactions of microbial origin. Furthermore, the coupling of each of these processes and reactions needs to be evaluated experimentally at a scale that produces data that can be used to calibrate numerical models so that they accurately describe field scale system behavior. Establishing the relevant experimental scale for collection of data from coupled processes remains a challenge and will likely be process-dependent and involve iterations of experimentation and data collection at different intermediate scales until the models calibrated with the appropriate date sets achieve an acceptable level of performance. Assuming that the geophysicists will soon develop technologies to define geological heterogeneities over a wide range of scales in the subsurface, geochemists need to continue to develop techniques to remotely measure abiotic reactions, while geomicrobiologists need to continue their development of complementary technologies to remotely measure microbial community parameters that define their key functions at a scale that accurately reflects their role in large scale subsurface system behavior. The practical questions that geomicrobiologist must answer in the short term are: 1) What is known about the activities of the dominant microbial populations or those of their closest relatives? 2) Which of these activities is likely to dominate under in situ conditions? In the process of answering these questions, researchers will obtain answers to questions of a more fundamental nature such as 1) How deep does "active" life extend below the surface of the seafloor and terrestrial subsurface? 2) How are electrons exchanged between microbial cells and solid phase minerals? 3) What is the metabolic state and mechanism of survival of "inactive" life forms in the subsurface? 4) What can genomes of life forms trapped in geological material tell us about evolution of life that current methods cannot? The subsurface environment represents a challenging environment to understand and model. As the need to understand subsurface processes increases and the technologies to characterize them become available, modeling subsurface behavior will approach the level of sophistication of models used today to predict behavior of other large scale systems such as the oceans.

Methanogenic degradation of petroleum hydrocarbons in subsurface environments remediation, heavy oil formation, and energy recovery.

PubMed

Gray, N D; Sherry, A; Hubert, C; Dolfing, J; Head, I M

2010-01-01

Hydrocarbons are common constituents of surface, shallow, and deep-subsurface environments. Under anaerobic conditions, hydrocarbons can be degraded to methane by methanogenic microbial consortia. This degradation process is widespread in the geosphere. In comparison with other anaerobic processes, methanogenic hydrocarbon degradation is more sustainable over geological time scales because replenishment of an exogenous electron acceptor is not required. As a consequence, this process has been responsible for the formation of the world's vast deposits of heavy oil, which far exceed conventional oil assets such as those found in the Middle East. Methanogenic degradation is also a potentially important component of attenuation in hydrocarbon contamination plumes. Studies of the organisms, syntrophic partnerships, mechanisms, and geochemical signatures associated with methanogenic hydrocarbon degradation have identified common themes and diagnostic markers for this process in the subsurface. These studies have also identified the potential to engineer methanogenic processes to enhance the recovery of energy assets as biogenic methane from residual oils stranded in petroleum systems. Copyright 2010 Elsevier Inc. All rights reserved.

Microbial colonisation in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

NASA Astrophysics Data System (ADS)

Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

2014-09-01

Colonisation of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focusing on settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associate vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soils types on the surface of the island. Total viable bacterial counts were performed with plate count at 22, 30 and 37 °C for all soils samples and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms aerobic and anaerobic bacteria. The deep subsurface biosphere was investigated by collecting liquid subsurface samples from a 182 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between N deficits and the number of microorganisms in surface soils samples. The lowest number of bacteria (1 × 104-1 × 105 g-1) was detected in almost pure pumice but the count was significant higher (1 × 106-1 × 109 g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 m and 172 m depth at 80 °C and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

Deep-Subsurface Marine Methane Hydrate Microbial Communities: Who's There and What Are They Doing?

NASA Astrophysics Data System (ADS)

Colwell, F.; Reed, D.; Fujita, Y.; Delwiche, M.; Blackwelder, D.; Uchida, T.; Fujii, T.; Lu, H.

2001-12-01

Natural gas hydrates are crystalline deposits of freshwater and primarily methane. They are estimated to represent a potentially vast reservoir of energy. Relatively little is known regarding microbial communities surrounding deep [>100 meters below sea floor (mbsf)] hydrate-bearing sediments. Deep sediment cores were collected in zones above, within, and below the hydrate bearing strata in an accretionary prism off the coast of Japan. Microorganisms were characterized using cultivation- and non-cultivation-based microbiological techniques to better understand the role that they play in the production and distribution of methane in gas hydrates. Direct counts show cell density at 105 cells/g throughout the hydrate strata. Lipid and 16S rDNA analyses indicate that diverse bacterial and archaeal microorganisms are represented throughout the strata. Acetate and hydrogen were utilized as an energy source for methane-producing microorganisms from each sediment depth. Although the methanogenic biomarker coenzyme M was not present above the detection limit in any of the samples, cloning and characterization of amplified 16S ribosomal RNA genes indicated the presence of methanogenic microorganisms related to the Methanobacteriales and Methanococcales. In addition, archaeal clones closely related to the hyperthermophilic Pyrodictiales were detected. Analysis of eubacterial clones indicated a more diverse eubacterial community compared to the archaea, including members from the groups of cyanobacteria, proteobacteria, gram positive bacteria, and flexibacter-cytophaga-bacteriodes. This study suggests that the diversity of microbial communities associated with the presence of methane in gas hydrate-rich deep marine sediments is greater than previously estimated.

Photosynthesis below the surface in a cryptic microbial mat

NASA Astrophysics Data System (ADS)

Rothschild, Lynn J.; Giver, Lorraine J.

2002-10-01

The discovery of subsurface communities has encouraged speculation that such communities might be present on planetary bodies exposed to harsh surface conditions, including the early Earth. While the astrobiology community has focused on the deep subsurface, near-subsurface environments are unique in that they provide some protection while allowing partial access to photosynthetically active radiation. Previously we identified near-surface microbial communities based on photosynthesis. Here we assess the productivity of such an ecosystem by measuring in situ carbon fixation rates in an intertidal marine beach through a diurnal cycle, and find them surprisingly productive. Gross fixation along a transect (99×1 m) perpendicular to the shore was highly variable and depended on factors such as moisture and mat type, with a mean of ~41 mg C fixed m[minus sign]2 day[minus sign]1. In contrast, an adjacent well-established cyanobacterial mat dominated by Lyngbya aestuarii was ~12 times as productive (~500 mg C fixed m[minus sign]2 day[minus sign]1). Measurements made of the Lyngbya mat at several times per year revealed a correlation between total hours of daylight and gross daily production. From these data, annual gross fixation was estimated for the Lyngbya mat and yielded a value of ~1.3×105 g m[minus sign]2 yr[minus sign]1. An analysis of pulse-chase data obtained in the study in conjunction with published literature on similar ecosystems suggests that subsurface interstitial mats may be an overlooked endogenous source of organic carbon, mostly in the form of excreted fixed carbon.

Homology between genes for aromatic hydrocarbon degradation in surface and deep-subsurface sphingomonas strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, E.; Aversano, P.J.; Zylstra, G.J.

The cloned genes for aromatic hydrocarbon degradation from Sphingomonas yanoikuyae B1 were utilized in Southern hybridization experiments with Sphingomonas strains from the surface and deep-subsurface environments. One hybridization pattern was obtained with BamHI-digested genomic DNAs for two surface strains, while a differing pattern was seen for five deep-subsurface strains. The cross-hybridizing genes were located in the chromosomes of the surface strains and on plasmids in the deep-subsurface strains. 31 refs., 3 figs., 1 tab.

Digging a Little Deeper: Microbial Communities, Molecular Composition and Soil Organic Matter Turnover along Tropical Forest Soil Depth Profiles

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; McFarlane, K. J.; Heckman, K. A.; Reed, S.; Green, E. A.; Nico, P. S.; Tfaily, M. M.; Wood, T. E.; Plante, A. F.

2016-12-01

Tropical forest soils store more carbon (C) than any other terrestrial ecosystem and exchange vast amounts of CO2, water, and energy with the atmosphere. Much of this C is leached and stored in deep soil layers where we know little about its fate or the microbial communities that drive deep soil biogeochemistry. Organic matter (OM) in tropical soils appears to be associated with mineral particles, suggesting deep soils may provide greater C stabilization. However, few studies have evaluated sub-surface soils in tropical ecosystems, including estimates of the turnover times of deep soil C, the sensitivity of this C to global environmental change, and the microorganisms involved. We quantified bulk C pools, microbial communities, molecular composition of soil organic matter, and soil radiocarbon turnover times from surface soils to 1.5m depths in multiple soil pits across the Luquillo Experimental Forest, Puerto Rico. Soil C, nitrogen, and root and microbial biomass all declined exponentially with depth; total C concentrations dropped from 5.5% at the surface to <0.5% at 140cm depth. High-throughput sequencing highlighted distinct microbial communities in surface soils (Acidobacteria and Proteobacteria) versus those below the active rooting zone (Verrucomicrobia and Thaumarchaea). High resolution mass spectrometry (FTICR-MS) analyses suggest a shift in the composition of OM with depth (especially in the water soluble fraction), an increase in oxidation, and decreasing H/C with depth (indicating higher aromaticity). Additionally, surface samples were rich in lignin-like compounds of plant origin that were absent with depth. Soil OM 14C and mean turnover times were variable across replicate horizons, ranging from 3-1500 years at the surface, to 5000-40,000 years at depth. In comparison to temperate deciduous forests, these 14C values reflect far older soil C. Particulate organic matter (free light fraction), with a relatively modern 14C was found in low but measureable concentration in even the deepest soil horizons. Our results indicate these tropical subsoils contain small but metabolically active microbial communities that are highly OM limited and may persist via degradation of recent inputs.

The Serpentinite Subsurface Microbiome

NASA Astrophysics Data System (ADS)

Schrenk, M. O.; Nelson, B. Y.; Brazelton, W. J.

2011-12-01

Microbial habitats hosted in ultramafic rocks constitute substantial, globally-distributed portions of the subsurface biosphere, occurring both on the continents and beneath the seafloor. The aqueous alteration of ultramafics, in a process known as serpentinization, creates energy rich, high pH conditions, with low concentrations of inorganic carbon which place fundamental constraints upon microbial metabolism and physiology. Despite their importance, very few studies have attempted to directly access and quantify microbial activities and distributions in the serpentinite subsurface microbiome. We have initiated microbiological studies of subsurface seeps and rocks at three separate continental sites of serpentinization in Newfoundland, Italy, and California and compared these results to previous analyses of the Lost City field, near the Mid-Atlantic Ridge. In all cases, microbial cell densities in seep fluids are extremely low, ranging from approximately 100,000 to less than 1,000 cells per milliliter. Culture-independent analyses of 16S rRNA genes revealed low-diversity microbial communities related to Gram-positive Firmicutes and hydrogen-oxidizing bacteria. Interestingly, unlike Lost City, there has been little evidence for significant archaeal populations in the continental subsurface to date. Culturing studies at the sites yielded numerous alkaliphilic isolates on nutrient-rich agar and putative iron-reducing bacteria in anaerobic incubations, many of which are related to known alkaliphilic and subsurface isolates. Finally, metagenomic data reinforce the culturing results, indicating the presence of genes associated with organotrophy, hydrogen oxidation, and iron reduction in seep fluid samples. Our data provide insight into the lifestyles of serpentinite subsurface microbial populations and targets for future quantitative exploration using both biochemical and geochemical approaches.

The subsurface record for the Anthropocene based on the global analysis of deep wells

NASA Astrophysics Data System (ADS)

Rose, K.

2016-12-01

While challenges persist in the characterization of Earth's subsurface, over two centuries of exploration resulting in more than six million deep wellbores, offer insights into these systems. Characteristics of the subsurface vary and can be analyzed on a variety of spatial scales using geospatial tools and methods. Characterization and prediction of subsurface properties, such as depth, thickness, porosity, permeability, pressure and temperature, are important for models and interpretations of the subsurface. Subsurface studies contribute to insights and understanding of natural system but also enable predictions and assessments of subsurface resources and support environmental and geohazard assessments. As the geo-data science landscape shifts, becoming more open, there are increasing opportunities to fill knowledge gaps, mine large, interrelated datasets, and develop innovative methods to improve our understanding of the subsurface and the impacts of its exploration. In this study, a global dataset of more than 6,000,000 deep subsurface wells has been assembled using ArcGIS and Access, which reflects to a first order, the cumulative representation of over two centuries of drilling. Wellbore data, in general represent the only portal for direct measurement and characterization of deep subsurface properties. As human engineering of the subsurface evolves from a focus on hydrocarbon resource development to include subsurface waste product disposal (e.g. CO2, industrial waste, etc) and production of other deep subsurface resources, such as heat and water resources, there is the increasing need to improve characterization techniques and understand local and global ramifications of anthropogenic interaction with the subsurface. Data and geospatial analyses are reviewed to constrain the extent to which human interactions, not just with Earth's surface systems, atmospheric and geologic, but subsurface systems will result in an enduring signature of human influences on the planet. Specifically, the extent and enduring signature of subsurface interactions with the planet, utilizing the four-dimensional, spatial and temporal, record for known deep wellbores is utilized.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites.

PubMed

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO 2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO 2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO 2 levels (sample groups I and II) and one control site with low CO 2 content (group III). Samples from sites with elevated CO 2 had pH ranging from 6.2 to 4.5 and samples from the low-CO 2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO 2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae , and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO 2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO 2 leakage from geologic storage sites.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites

PubMed Central

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F.; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites. PMID:29170659

Microbial Life Driving Low-Temperature Basalt Alteration in the Subsurface: Decoupling Abiotic Processes from Biologically-Mediated Rock Alteration

NASA Astrophysics Data System (ADS)

Moore, R.; Lecoeuvre, A.; Stephant, S.; Dupraz, S.; Ranchou-Peyruse, M.; Ranchou-Peyruse, A.; Gérard, E.; Ménez, B.

2017-12-01

Microorganisms are involved with specific rock alteration processes in the deep subsurface. It is a challenge to link any contribution microbial life may have on rock alteration with specific functions or phyla because many alteration features and secondary minerals produced by metabolic processes can also produce abiotically. Here, two flow-through experiments were designed to mimic the circulation of a CO2-rich fluid through crystalline basalt. In order to identify microbially-mediated alteration and be able to link it with specific metabolisms represented in the subsurface, a relatively fresh crystalline basalt substrate was subsampled, sterilized and used as the substrate for both experiments. In one experiment, the substrate was left sterile, and in the other it was inoculated with an enrichment culture derived from the same aquifer as the rock substrate. Initial results show that the inoculum contained Proteobacteria and Firmicutes, which have diverse metabolic potentials. Fluid and rock analyses before, during, and after the experiments show that mineralogy, fluid chemistry, and dissolution processes differ between the sterile and inoculated systems. In the inoculated experiment iron-rich orthopyroxenes were preferentially dissolved while in the sterile system clinopyroxenes and plagioclases both exhibited a higher degree of dissolution. Additionally, the patterns of CO2 consumption and production over the duration of both experiments is different. This suggest that in a low-temperature basalt system with microorganisms CO2 is either consumed to produce biomass, or that carbonates are produced and then subsequently preserved. This suite of results combined with molecular ecology analyses can be used to conclude that in low-temperature basalts microorganisms play an intrinsic role in rock alteration.

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-12-01

The Critical Zone (CZ) is the Earth's outer shell where all the fundamental physical, chemical, and biological processes critical for sustaining life occur and interact. As microbes in the CZ drive many of these biogeochemical cycles, understanding their impact on life-sustaining processes starts with an understanding of their biodiversity. In this review, we summarize the factors controlling where terrestrial CZ microbes (prokaryotes and micro-eukaryotes) live and what is known about their diversity and function. Microbes are found throughout the CZ, down to 5 km below the surface, but their functional roles change with depth due to habitat complexity, e.g. variability in pore spaces, water, oxygen, and nutrients. Abundances of prokaryotes and micro-eukaryotes decrease from 1010 or 107 cells g soil-1 or rock-1, or ml water-1 by up to eight orders of magnitude with depth. Although symbiotic mycorrhizal fungi and free-living decomposers have been studied extensively in soil habitats, where they occur up to 103 cells g soil-1, little is known regarding their identity or impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that they are limited in space, nutrients, are unable to cope with oxygen limitations, or some combination thereof. Since deep regions of the CZ have limited access to recent photosynthesis-derived carbon, microbes there depend on deposited organic material or a chemolithoautotrophic metabolism that allows for a complete food chain, independent from the surface, although limited energy flux means cell growth may take tens to thousands of years. Microbes are found in all regions of the CZ and can mediate important biogeochemical processes, but more work is needed to understand how microbial populations influence the links between different regions of the CZ and weathering processes. With the recent development of "omics" technologies, microbial ecologists have new methods that can be used to link the composition and function of in situ microbial communities. In particular, these methods can be used to search for new metabolic pathways that are relevant to biogeochemical nutrient cycling and determine how the activity of microorganisms can affect transport of carbon, particulates, and reactive gases between and within CZ regions.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

PubMed

Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

PubMed Central

Campbell, Barbara J.; Polson, Shawn W.; Zeigler Allen, Lisa; Williamson, Shannon J.; Lee, Charles K.; Wommack, K. Eric; Cary, S. Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments. PMID:23898323

Recalcitrant Carbonaceous Material: A Source of Electron Donors for Anaerobic Microbial Metabolisms in the Subsurface?

NASA Astrophysics Data System (ADS)

Nixon, S. L.; Montgomery, W.; Sephton, M. A.; Cockell, C. S.

2014-12-01

More than 90% of organic material on Earth resides in sedimentary rocks in the form of kerogens; fossilized organic matter formed through selective preservation of high molecular weight biopolymers under anoxic conditions. Despite its prevalence in the subsurface, the extent to which this material supports microbial metabolisms is unknown. Whilst aerobic microorganisms are known to derive energy from kerogens within shales, utilization in anaerobic microbial metabolisms that proliferate in the terrestrial subsurface, such as microbial iron reduction, has yet to be demonstrated. Data are presented from microbial growth experiments in which kerogens and shales were supplied as the sole electron donor source for microbial iron reduction by an enrichment culture. Four well-characterized kerogens samples (representative of Types I-IV, classified by starting material), and two shale samples, were assessed. Organic analysis was carried out to investigate major compound classes present in each starting material. Parallel experiments were conducted to test inhibition of microbial iron reduction in the presence of each material when the culture was supplied with a full redox couple. The results demonstrate that iron-reducing microorganisms in this culture were unable to use kerogens and shales as a source of electron donors for energy acquisition, despite the presence of compound classes known to support this metabolism. Furthermore, the presence of these materials was found to inhibit microbial iron reduction to varying degrees, with some samples leading to complete inhibition. These results suggest that recalcitrant carbonaceous material in the terrestrial subsurface is not available for microbial iron reduction and similar metabolisms, such as sulphate-reduction. Further research is needed to investigate the inhibition exerted by these materials, and to assess whether these findings apply to other microbial consortia. These results may have significant implications for the role of anaerobic microbial metabolisms in the subsurface terrestrial carbon cycle. Kerogens are chemically similar to organic material in carbonaceous chondrites. As such, further study may provide insight into the potential availability of organic compounds for microbial metabolisms operating in the subsurface of Mars.

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions

PubMed Central

Bukin, Sergei V.; Pavlova, Olga N.; Manakov, Andrei Y.; Kostyreva, Elena A.; Chernitsyna, Svetlana M.; Mamaeva, Elena V.; Pogodaeva, Tatyana V.; Zemskaya, Tamara I.

2016-01-01

The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids. PMID:27242716

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions.

PubMed

Bukin, Sergei V; Pavlova, Olga N; Manakov, Andrei Y; Kostyreva, Elena A; Chernitsyna, Svetlana M; Mamaeva, Elena V; Pogodaeva, Tatyana V; Zemskaya, Tamara I

2016-01-01

The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids.

Planetary science and exploration in the deep subsurface: results from the MINAR Program, Boulby Mine, UK

NASA Astrophysics Data System (ADS)

Payler, Samuel J.; Biddle, Jennifer F.; Coates, Andrew J.; Cousins, Claire R.; Cross, Rachel E.; Cullen, David C.; Downs, Michael T.; Direito, Susana O. L.; Edwards, Thomas; Gray, Amber L.; Genis, Jac; Gunn, Matthew; Hansford, Graeme M.; Harkness, Patrick; Holt, John; Josset, Jean-Luc; Li, Xuan; Lees, David S.; Lim, Darlene S. S.; McHugh, Melissa; McLuckie, David; Meehan, Emma; Paling, Sean M.; Souchon, Audrey; Yeoman, Louise; Cockell, Charles S.

2017-04-01

The subsurface exploration of other planetary bodies can be used to unravel their geological history and assess their habitability. On Mars in particular, present-day habitable conditions may be restricted to the subsurface. Using a deep subsurface mine, we carried out a program of extraterrestrial analog research - MINe Analog Research (MINAR). MINAR aims to carry out the scientific study of the deep subsurface and test instrumentation designed for planetary surface exploration by investigating deep subsurface geology, whilst establishing the potential this technology has to be transferred into the mining industry. An integrated multi-instrument suite was used to investigate samples of representative evaporite minerals from a subsurface Permian evaporite sequence, in particular to assess mineral and elemental variations which provide small-scale regions of enhanced habitability. The instruments used were the Panoramic Camera emulator, Close-Up Imager, Raman spectrometer, Small Planetary Linear Impulse Tool, Ultrasonic drill and handheld X-ray diffraction (XRD). We present science results from the analog research and show that these instruments can be used to investigate in situ the geological context and mineralogical variations of a deep subsurface environment, and thus habitability, from millimetre to metre scales. We also show that these instruments are complementary. For example, the identification of primary evaporite minerals such as NaCl and KCl, which are difficult to detect by portable Raman spectrometers, can be accomplished with XRD. By contrast, Raman is highly effective at locating and detecting mineral inclusions in primary evaporite minerals. MINAR demonstrates the effective use of a deep subsurface environment for planetary instrument development, understanding the habitability of extreme deep subsurface environments on Earth and other planetary bodies, and advancing the use of space technology in economic mining.

ANME-2D Archaea Catalyze Methane Oxidation in Deep Subsurface Sediments Independent of Nitrate Reduction

NASA Astrophysics Data System (ADS)

Hernsdorf, A. W.; Amano, Y.; Suzuki, Y.; Ise, K.; Thomas, B. C.; Banfield, J. F.

2015-12-01

Terrestrial sediments are an important global reservoir for methane. Microorganisms in the deep subsurface play a critical role in the methane cycle, yet much remains to be learned about their diversity and metabolisms. To provide more comprehensive insight into the microbiology of the methane cycle in the deep subsurface, we conducted a genome-resolved study of samples collected from the Horonobe Underground Research Laboratory (HURL), Japan. Groundwater samples were obtained from three boreholes from a depth range of between 140 m and 250 m in two consecutive years. Groundwater was filtered and metagenomic DNA extracted and sequenced, and the sequence data assembled. Based on the sequences of phylogenetically informative genes on the assembled fragments, we detected a high degree of overlap in community composition across a vertical transect within one borehole at the two sampling times. However, there was comparatively little similarity observed among communities across boreholes. Spatial and temporal abundance patterns were used in combination with tetranucleotide signatures of assembled genome fragments to bin the data and reconstruct over 200 unique draft genomes, of which 137 are considered to be of high quality (>90% complete). The deepest samples from one borehole were highly dominated by an archaeon identified as ANME-2D; this organism was also present at lower abundance in all other samples from that borehole. Also abundant in these microbial communities were novel members of the Gammaproteobacteria, Saccharibacteria (TM7) and Tenericute phyla. Notably, a ~2 Mbp draft genome for the ANME-2D archaeon was reconstructed. As expected, the genome encodes all of the genes predicted to be involved in the reverse methanogenesis pathway. In contrast with the previously reported ANME2-D genome, the HURL ANME-2D genome lacks the capacity to reduce nitrate. However, we identified many multiheme cytochromes with closest similarity to those of the known Fe-reducing/oxidizing archaeon Ferroglobus placidus. Thus, we suggest that ANME2-D may couple methane oxidation to reduction of ferric iron minerals in the sediment and may be generally important as a link between the iron and methane cycles in deep subsurface environments. Such information has important implications for modeling the global carbon cycle.

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor

PubMed Central

Fang, Jiasong; Kato, Chiaki; Runko, Gabriella M.; Nogi, Yuichi; Hori, Tomoyuki; Li, Jiangtao; Morono, Yuki; Inagaki, Fumio

2017-01-01

Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ. In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized. PMID:28220112

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor.

PubMed

Fang, Jiasong; Kato, Chiaki; Runko, Gabriella M; Nogi, Yuichi; Hori, Tomoyuki; Li, Jiangtao; Morono, Yuki; Inagaki, Fumio

2017-01-01

Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ . In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized.

Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters.

PubMed

Wu, Xiaofen; Pedersen, Karsten; Edlund, Johanna; Eriksson, Lena; Åström, Mats; Andersson, Anders F; Bertilsson, Stefan; Dopson, Mark

2017-03-23

Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide- and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria. Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.

New Bio-Indicators for Long Term Natural Attenuation of Monoaromatic Compounds in Deep Terrestrial Aquifers

PubMed Central

Aüllo, Thomas; Berlendis, Sabrina; Lascourrèges, Jean-François; Dessort, Daniel; Duclerc, Dominique; Saint-Laurent, Stéphanie; Schraauwers, Blandine; Mas, Johan; Patriarche, Delphine; Boesinger, Cécile; Magot, Michel; Ranchou-Peyruse, Anthony

2016-01-01

Deep subsurface aquifers despite difficult access, represent important water resources and, at the same time, are key locations for subsurface engineering activities for the oil and gas industries, geothermal energy, and CO2 or energy storage. Formation water originating from a 760 m-deep geological gas storage aquifer was sampled and microcosms were set up to test the biodegradation potential of BTEX by indigenous microorganisms. The microbial community diversity was studied using molecular approaches based on 16S rRNA genes. After a long incubation period, with several subcultures, a sulfate-reducing consortium composed of only two Desulfotomaculum populations was observed able to degrade benzene, toluene, and ethylbenzene, extending the number of hydrocarbonoclastic–related species among the Desulfotomaculum genus. Furthermore, we were able to couple specific carbon and hydrogen isotopic fractionation during benzene removal and the results obtained by dual compound specific isotope analysis (𝜀C = -2.4‰ ± 0.3‰; 𝜀H = -57‰ ± 0.98‰; AKIEC: 1.0146 ± 0.0009, and AKIEH: 1.5184 ± 0.0283) were close to those obtained previously in sulfate-reducing conditions: this finding could confirm the existence of a common enzymatic reaction involving sulfate-reducers to activate benzene anaerobically. Although we cannot assign the role of each population of Desulfotomaculum in the mono-aromatic hydrocarbon degradation, this study suggests an important role of the genus Desulfotomaculum as potential biodegrader among indigenous populations in subsurface habitats. This community represents the simplest model of benzene-degrading anaerobes originating from the deepest subterranean settings ever described. As Desulfotomaculum species are often encountered in subsurface environments, this study provides some interesting results for assessing the natural response of these specific hydrologic systems in response to BTEX contamination during remediation projects. PMID:26904000

Succession in the petroleum reservoir microbiome through an oil field production lifecycle.

PubMed

Vigneron, Adrien; Alsop, Eric B; Lomans, Bartholomeus P; Kyrpides, Nikos C; Head, Ian M; Tsesmetzis, Nicolas

2017-09-01

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H 2 S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.

Progression of methanogenic degradation of crude oil in the subsurface

USGS Publications Warehouse

Bekins, B.A.; Hostettler, F.D.; Herkelrath, W.N.; Delin, G.N.; Warren, E.; Essaid, H.I.

2005-01-01

Our results show that subsurface crude-oil degradation rates at a long-term research site were strongly influenced by small-scale variations in hydrologic conditions. The site is a shallow glacial outwash aquifer located near Bemidji in northern Minnesota that became contaminated when oil spilled from a broken pipeline in August 1979. In the study area, separate-phase oil forms a subsurface oil body extending from land surface to about 1 m (3.3 ft) below the 6-8-m (20-26 ft)-deep water table. Oil saturation in the sediments ranges from 10-20% in the vadose zone to 30-70% near the water table. At depths below 2 m (6.6 ft), degradation of the separate-phase crude oil occurs under methanogenic conditions. The sequence of methanogenic alkane degradation depletes the longer chain n-alkanes before the shorter chain n-alkanes, which is opposite to the better known aerobic sequence. The rates of degradation vary significantly with location in the subsurface. Oil-coated soils within 1.5 m (5 ft) of land surface have experienced little degradation where soil water saturation is less than 20%. Oil located 2-8 m (6.6-26 ft) below land surface in areas of higher recharge has been substantially degraded. The best explanation for the association between recharge and enhanced degradation seems to be increased downward transport of microbial growth nutrients to the oil body. This is supported by observations of greater microbial numbers at higher elevations in the oil body and significant decreases with depth in nutrient concentrations, especially phosphorus. Our results suggest that environmental effects may cause widely diverging degradation rates in the same spill, calling into question dating methods based on degradation state. Copyright ?? 2005. The American Association of Petroleum Geologists/Division of Environmental Geosciences. All rights reserved.

Sources of Hydrogen as Food for Deep Microbial Communities

NASA Technical Reports Server (NTRS)

Freund, Friedemann; Fonda, Mark (Technical Monitor)

1998-01-01

To survive in deep subsurface environments autolithotrophic microbial communities require a sustainable food supply. One possible source is H2 which forms when H2O reacts with ferrous iron at rock surfaces or mineral grain boundaries to produce H2 plus ferric iron. The amount of H2 that can be supplied in this way, however, is relatively small and may not last for more than a few hundred or thousand years. A much larger reservoir of H2 exists in the rocks, inside mineral grains, arising from an as yet little-known redox conversion that affects OH- in nominally anhydrous minerals. These OH- represent small amounts of "water" that become incorporated during crystallization in H2O-laden environments. A corollary of the H2 formation from OH- is the formation of peroxy, an oxidized form of oxygen. While the peroxy become part of the mineral structure, the H2 molecules are diffusively mobile and can escape from within the mineral grains, entering the intergranular space. Assuming cautiously realistic number densities of OH- undergoing the in situ redox conversion to H2 plus peroxy, a 10 km deep rock column is expected to contain enough H2 to allow for a constant degassing rate of 50-100 nmole H2 per day per sq cm over 30 million years.

Subsurface dolomite formation during post-depositional flow of sulphate-bearing fluids from underlying salt giants: Early Pliocene example at DSDP Leg 42A, Site 374, Ionian Abyssal Plain

NASA Astrophysics Data System (ADS)

McKenzie, Judith A.; Evans, Nick; Hodell, David; Aloisi, Giovanni; Vasconcelos, Crisogono

2017-04-01

Deciphering exact mechanisms for the formation of massive dolomite deposits has long been an enigma in sedimentary geology. The recognition that microbes can play a role in the dolomite precipitation process has added a new dimension to the study of the origin of dolomite formations in both shallow and deep-water environments. This scientific advance has evolved, particularly, through the investigation of dolomite-containing, organic-rich hemipelagic sediments cored on various continental margins during DSDP and ODP drilling campaigns, as well as intensive evaluations of modern hypersaline dolomite-precipitating environments with complementary culture experiments conducted in the laboratory. For example, the association of an active subsurface microbial community in contact with underlying brines of unknown origin leading to in situ dolomite precipitation has been observed in a Quaternary sequence of hemi-pelagic, organic carbon-rich sediments drilled on the Peru Margin, ODP Leg 201, Site 1229 (1). Specifically, it can be concluded that the long-term activity of subsurface microbes can be maintained by post-depositional flow of sulfate-bearing fluids from underlying large-scale evaporite deposits, or salt giants, promoting in situ dolomite precipitation. Another example of dolomite precipitation directly associated with the underlying Messinian salt giant was found at DSDP Leg 42A, Site 374 in the Ionian Abyssal Plain. Deep-sea drilling recovered a lowermost Pliocene sequence of diagenetically altered sediment (Unit II) separating the overlying Pliocene open-marine deposits (Unit I) and the underlying end Messinian dolomitic mudstone with gypsum layers (Unit III). The lower portion of this altered interval contained in Core 11, Section 2 (378.0 - 381.5 mbsf) comprises a dolomicrite with an unusual crystal morphology (2). The original interstitial water geochemical profiles indicate that a saline brine is diffusing upwards from below and into the dolomicrite sequence. There appears to be on-going bacterial sulfate reduction in this boundary zone between the evaporitic and normal pelagic sediments with a significant decrease in sulfate concentrations, whereas the chloride profile remains constant. It was concluded that the earliest Pliocene marine sediments of Unit II had been dolomitized after burial as a consequence of ionic migration across a steep Mg-concentration gradient (3). However, with the addition of a microbial factor into the study of the dolomite precipitation process, an alternate interpretation is possible. We propose that, at the location of DSDP Leg 42A, Site 374, modern subsurface dolomite precipitation is ongoing and the site is a "natural laboratory" in which to investigate the microbial phenomenon in the context of a giant evaporite deposit. This actualistic example may provide a new model for the origin of massive dolomite deposits associated with other salt giants in the rock record. (1) Meister, P., et al., 2007. Sedimentology, 54, 1007-1031. (2) Bernoulli, D. & Mélières, F., 1978. In: Hsü, K., Montadert, L. et al., 1978. Initial Reports of the Deep Sea Drilling Project, Volume 42, Part 1, 621-633. (3) McDuff, R.E., et al., 1978. In: Hsü, K., Montadert, L. et al., 1978. Initial Reports of the Deep Sea Drilling Project, Volume 42, Part 1, 561-568.

Does Aspartic Acid Racemization Constrain the Depth Limit of the Subsurface Biosphere?

NASA Technical Reports Server (NTRS)

Onstott, T C.; Magnabosco, C.; Aubrey, A. D.; Burton, A. S.; Dworkin, J. P.; Elsila, J. E.; Grunsfeld, S.; Cao, B. H.; Hein, J. E.; Glavin, D. P.;

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

PubMed

Onstott, T C; Magnabosco, C; Aubrey, A D; Burton, A S; Dworkin, J P; Elsila, J E; Grunsfeld, S; Cao, B H; Hein, J E; Glavin, D P; Kieft, T L; Silver, B J; Phelps, T J; van Heerden, E; Opperman, D J; Bada, J L

2014-01-01

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 °C and 1-2 years for 3 km depth and 54 °C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 °C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples. © 2013 John Wiley & Sons Ltd.

Ecohydrology of Deep Fractured Rocks at Homestake DUSEL

NASA Astrophysics Data System (ADS)

Kieft, T. L.; Boutt, D. F.; Murdoch, L. C.; Wang, H. F.

2009-12-01

The Deep Underground Science and Engineering Laboratory (DUSEL) at Homestake in SD will provide an unprecedented opportunity to study the terrestrial subsurface. Such a study could fundamentally change the way we view the origin and early evolution of life on Earth, the search for novel materials, and the generation of energy. Knowledge of subsurface life has come from only a few boreholes and deep mines. DUSEL will enable the first detailed study of a deep ecosystem in the context of the hydrology, geochemistry, and rock system state that sustain it. We are guided by the over-arching question: What controls the distribution and evolution of subsurface life? Our hypothesis is that these controls are dominated by processes related to geology, geochemistry, geomechanics, and hydrology. Themes of scaling and the development of facies, or zones of similar characteristics cut across all the processes. The ecohydrologic setting of DUSEL Homestake is characterized by a vast expanse of fractured metamorphic rock cut by 100s of km of tunnels and boreholes. Many km3 of the region have been highly affected by mining activities; adjacent regions are partially desaturated; and more distal regions are pristine and presumed to harbor indigenous microbial ecosystems. Simulations along with descriptions of the mine suggest division into zones, or ecohydrologic facies, where essential characteristics related to the requirements for life are expected to be similar. These ecohydrologic facies are a primary organizing principle for our investigation. The Deep EcoHydrology Experiment will consist of field studies supported by numerical simulations. The experimental activities include a particularly exciting opportunity to probe the lower limits of the biosphere using deep drilling technology deployed from the lowest reaches of the facility (2440 m below the surface). The use of the flooding/dewatering event as a tracer combined with hydrologic and mechanical stressors form a theme that cuts across many of the experimental activities. Five key experimental activities have been identified that will enable motivating hypotheses to be tested: 1) Initial Characterization, 2) Flow System, 3) Stress and Deformation, 4) Exploration, and 5) Cross-cutting activities. The International Continental Drilling Program has approved a preproposal for an ICDP ecohydrology project at DUSEL. The development of a long-term deep geosciences observatory at the Homestake DUSEL will revolutionize the field of deep sub-surface ecohydrology. The opportunities for young scientists and international participation in such a facility will be tremendous. Results from the work will have wide ranging implications as 20% of the current earth’s surface consists of a similar geologic setting. DUSEL will also facilitate experiential learning for K-12 through graduate school students working alongside world-class geoscientists.

Microbial communities in the deep subsurface

NASA Astrophysics Data System (ADS)

Krumholz, Lee R.

The diversity of microbial populations and microbial communities within the earth's subsurface is summarized in this review. Scientists are currently exploring the subsurface and addressing questions of microbial diversity, the interactions among microorganisms, and mechanisms for maintenance of subsurface microbial communities. Heterotrophic anaerobic microbial communities exist in relatively permeable sandstone or sandy sediments, located adjacent to organic-rich deposits. These microorganisms appear to be maintained by the consumption of organic compounds derived from adjacent deposits. Sources of organic material serving as electron donors include lignite-rich Eocene sediments beneath the Texas coastal plain, organic-rich Cretaceous shales from the southwestern US, as well as Cretaceous clays containing organic materials and fermentative bacteria from the Atlantic Coastal Plain. Additionally, highly diverse microbial communities occur in regions where a source of organic matter is not apparent but where igneous rock is present. Examples include the basalt-rich subsurface of the Columbia River valley and the granitic subsurface regions of Sweden and Canada. These subsurface microbial communities appear to be maintained by the action of lithotrophic bacteria growing on H2 that is chemically generated within the subsurface. Other deep-dwelling microbial communities exist within the deep sediments of oceans. These systems often rely on anaerobic metabolism and sulfate reduction. Microbial colonization extends to the depths below which high temperatures limit the ability of microbes to survive. Energy sources for the organisms living in the oceanic subsurface may originate as oceanic sedimentary deposits. In this review, each of these microbial communities is discussed in detail with specific reference to their energy sources, their observed growth patterns, and their diverse composition. This information is critical to develop further understanding of subsurface geochemical processes and to develop new approaches to subsurface remediation. Résumé La diversité des populations et des communautés microbiennes dans le sol et le sous-sol est présentée dans cet article. Les chercheurs s'interrogent fréquemment sur la diversité microbienne du sous-sol, sur les interactions entre organismes et sur les mécanismes qui permettent le maintien des communautés microbiennes souterraines. Il existe des communautés microbiennes anérobies hétérotrophes dans des grès ou dans des sédiments sableux relativement perméables, à proximité de dépôts riches en matières organiques. Ces micro-organismes semblent se maintenir grâce à la consommation de composés organiques provenant des dépôts organiques voisins. Les sources de matériel organique jouant le rôle de donneur d'électrons sont constituées par des sédiments éocènes riches en lignite situés sous la plaine littorale du Texas, les schistes riches en matières organiques du Crétacé du sud-ouest des États-Unis, ainsi que les argiles contenant des matériaux organiques et des bactéries de fermentation de la plaine littorale atlantique. En outre, il existe des communautés fortement diversifiées dans des régions où aucune source de matière organique n'existe, mais où sont présentes des roches ignées. Le sous-sol riche en basalte de la vallée de la Columbia au Canada et les régions granitiques de Suède en sont des exemples. Ces communautés microbiennes souterraines semblent se maintenir par l'action de bactéries lithotrophes se développant grâce à l'hydrogène qui est produit par réactions chimiques dans le sous-sol. Il existe d'autres communautés microbiennes de profondeur dans les sédiments profonds des océans. Ces systèmes sont souvent associés à un métabolisme anérobie et à une réduction des sulfates. La colonisation microbienne s'étend jusqu'à des profondeurs où les températures élevées limitent leur capacité de survie. Les sources d'énergie pour ces organismes vivant dans les fonds des océans peuvent être les dépôts sédimentaires océaniques. Dans cette revue, chacune des communautés microbiennes est discutée en détail en se référant spécifiquement à leurs sources d'énergie, au schéma observé de leur développement et à leur composition diversifiée. Cette information est donnée de façon critique dans le but d'améliorer la compréhension des processus géochimiques intervenant dans le sous-sol et de développer de nouvelles approches pour la dépollution souterraine. Resumen En este artículo se resume la diversidad de las poblaciones y comunidades microbianas en el subsuelo. A partir de exploraciones realizadas en el subsuelo, los científicos se están cuestionando en la actualidad aspectos relativos a la diversidad microbiana, las interacciones entre los distintos microorganismos y los mecanismos para el mantenimiento de las comunidades de microbios. Se ha comprobado la presencia de comunidades microbianas anaerobias y heterótrofas en areniscas relativamente permeables y en sedimentos arenosos ubicados cerca de depósitos ricos en materia orgánica, de la cual se alimentan. Algunas fuentes de material orgánico, que actúan como donantes de electrones, son: sedimentos del Eoceno ricos en lignito, bajo la planicie costera de Texas; pizarras del Cretácico ricas en materia orgánica, al sudoeste del país y arcillas cretácicas con materia orgánica y bacterias fermentativas, en la llanura Atlántica. También existen comunidades microbianas de gran diversidad en rocas ígneas, aunque la fuente de materia orgánica no es tan evidente. Algunos ejemplos son la subsuperficie del valle del Río Columbia, rico en basaltos, y las regiones graníticas de Suecia y Canadá. Estas comunidades microbianas subsuperficiales se mantienen por la acción de bacterias litotrópicas, que crecen en ambiente de H2, generado en la subsuperficie. También existen comunidades microbianas a gran profundidad, como por ejemplo en los sedimentos oceánicos. Estos sistemas subsisten con un metabolismo anaerobio en un ambiente sulfato-reductor. La colonización microbiana se extiende hasta profundidades tales que las altas temperaturas limitan su supervivencia. Las fuentes de energía para estos organismos pueden ser los depósitos sedimentarios oceánicos. En este artículo se discute cada una de estas comunidades en detalle, en particular sus fuentes de energía, su esquema de crecimiento y la diversidad de su composición. Esta información es de gran interés para permitir un mayor entendimiento de los procesos geoquímicos en profundidad y para desarrollar nuevos métodos de rehabilitación.

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.

PubMed

Li, Dong; Sharp, Jonathan O; Drewes, Jörg E

2016-01-01

To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.

Deep groundwater and potential subsurface habitats beneath an Antarctic dry valley

PubMed Central

Mikucki, J. A.; Auken, E.; Tulaczyk, S.; Virginia, R. A.; Schamper, C.; Sørensen, K. I.; Doran, P. T.; Dugan, H.; Foley, N.

2015-01-01

The occurrence of groundwater in Antarctica, particularly in the ice-free regions and along the coastal margins is poorly understood. Here we use an airborne transient electromagnetic (AEM) sensor to produce extensive imagery of resistivity beneath Taylor Valley. Regional-scale zones of low subsurface resistivity were detected that are inconsistent with the high resistivity of glacier ice or dry permafrost in this region. We interpret these results as an indication that liquid, with sufficiently high solute content, exists at temperatures well below freezing and considered within the range suitable for microbial life. These inferred brines are widespread within permafrost and extend below glaciers and lakes. One system emanates from below Taylor Glacier into Lake Bonney and a second system connects the ocean with the eastern 18 km of the valley. A connection between these two basins was not detected to the depth limitation of the AEM survey (∼350 m). PMID:25919365

Relevance of deep-subsurface microbiology for underground gas storage and geothermal energy production.

PubMed

Gniese, Claudia; Bombach, Petra; Rakoczy, Jana; Hoth, Nils; Schlömann, Michael; Richnow, Hans-Hermann; Krüger, Martin

2014-01-01

This chapter gives the reader an introduction into the microbiology of deep geological systems with a special focus on potential geobiotechnological applications and respective risk assessments. It has been known for decades that microbial activity is responsible for the degradation or conversion of hydrocarbons in oil, gas, and coal reservoirs. These processes occur in the absence of oxygen, a typical characteristic of such deep ecosystems. The understanding of the responsible microbial processes and their environmental regulation is not only of great scientific interest. It also has substantial economic and social relevance, inasmuch as these processes directly or indirectly affect the quantity and quality of the stored oil or gas. As outlined in the following chapter, in addition to the conventional hydrocarbons, new interest in such deep subsurface systems is rising for different technological developments. These are introduced together with related geomicrobiological topics. The capture and long-termed storage of large amounts of carbon dioxide, carbon capture and storage (CCS), for example, in depleted oil and gas reservoirs, is considered to be an important options to mitigate greenhouse gas emissions and global warming. On the other hand, the increasing contribution of energy from natural and renewable sources, such as wind, solar, geothermal energy, or biogas production leads to an increasing interest in underground storage of renewable energies. Energy carriers, that is, biogas, methane, or hydrogen, are often produced in a nonconstant manner and renewable energy may be produced at some distance from the place where it is needed. Therefore, storing the energy after its conversion to methane or hydrogen in porous reservoirs or salt caverns is extensively discussed. All these developments create new research fields and challenges for microbiologists and geobiotechnologists. As a basis for respective future work, we introduce the three major topics, that is, CCS, underground storage of gases from renewable energy production, and the production of geothermal energy, and summarize the current stat of knowledge about related geomicrobiological and geobiotechnological aspects in this chapter. Finally, recommendations are made for future research.

Tackling the Challenge of Deep Vadose Zone Remediation at the Hanford Site

NASA Astrophysics Data System (ADS)

Morse, J. G.; Wellman, D. M.; Gephart, R.

2010-12-01

The Central Plateau of the Hanford Site in Washington State contains some 800 waste disposal sites where 1.7 trillion liters of contaminated water was once discharged into the subsurface. Most of these sites received liquids from the chemical reprocessing of spent uranium fuel to recover plutonium. In addition, 67 single shell tanks have leaked or are suspected to have leaked 3.8 million liters of high alkali and aluminate rich cesium-contaminated liquids into the sediment. Today, this inventory of subsurface contamination contains an estimated 550,000 curies of radioactivity and 150 million kg (165,000 tons) of metals and hazardous chemicals. Radionuclides range from mobile 99Tc to more immobilized 137Cs, 241Am, uranium, and plutonium. A significant fraction of these contaminants likely remain within the deep vadose zone. Plumes of groundwater containing tritium, nitrate, 129I and other contaminants have migrated through the vadose zone and now extend outward from the Central Plateau to the Columbia River. During most of Hanford Site history, subsurface studies focused on groundwater monitoring and characterization to support waste management decisions. Deep vadose zone studies were not a priority because waste practices relied upon that zone to buffer contaminant releases into the underlying aquifer. Remediation of the deep vadose zone is now central to Hanford Site cleanup because these sediments can provide an ongoing source of contamination to the aquifer and therefore to the Columbia River. However, characterization and remediation of the deep vadose zone pose some unique challenges. These include sediment thickness; contaminant depth; coupled geohydrologic, geochemical, and microbial processes controlling contaminant spread; limited availability and effectiveness of traditional characterization tools and cleanup remedies; and predicting contaminant behavior and remediation performance over long time periods and across molecular to field scales. The U.S Department of Energy recognizes these challenges and is committed to a sustained, focused effort of continuing to apply existing technologies where feasible while investing and developing in new innovative, field-demonstrated capabilities supporting longer-term basic and applied research to establish the technical underpinning for solving intractable deep vadose zone problems and implementing final remedies. This approach will rely upon Multi-Project Teams focusing on coordinated projects across multiple DOE offices, programs, and site contractors plus the facilitation of basic and applied research investments through implementing a Deep Vadose Zone Applied Field Research Center and other scientific studies.

Seasonal dynamics in colored dissolved organic matter in the Mediterranean Sea: Patterns and drivers

NASA Astrophysics Data System (ADS)

Xing, Xiaogang; Claustre, Hervé; Wang, Haili; Poteau, Antoine; D`Ortenzio, Fabrizio

2014-01-01

Two autonomous profiling “Bio-Argo” floats were deployed in the northwestern and eastern sub-basins of the Mediterranean Sea in 2008. They recorded at high vertical (1 m) and temporal (5 day) resolution, the vertical distribution and seasonal variation of colored dissolved organic matter (CDOM), as well as of chlorophyll-a concentration and hydrological variables. The CDOM standing stock presented a clear seasonal dynamics with the progressive summer formation and winter destruction of subsurface CDOM maxima (YSM, for Yellow Substance Maximum). It was argued that subsurface CDOM is a by-product of phytoplankton, based on two main characteristics, (1) the YSM was located at the same depth than the deep chlorophyll maximum (DCM) and (2) the CDOM increased in summer parallels the decline in chlorophyll-a. These observations suggested an indirect but tight coupling between subsurface CDOM and phytoplankton via microbial activity or planktonic foodweb interactions. Moreover, the surface CDOM variations observed both by floats and MODIS displayed different seasonal dynamics from what recorded at subsurface one. This implies that CDOM standing stock can be hardly detected by satellite. It is worthnoting that surface CDOM was found to be more related to the sea surface temperature (SST) than chlorophyll-a concentration, suggesting its physical origin, in contrast to the biological origin of YSM and subsurface standing stocks.

Metabolic activity of subseafloor microbes in the South Pacific Gyre

NASA Astrophysics Data System (ADS)

Morono, Y.; Ito, M.; Terada, T.; Inagaki, F.

2013-12-01

The South Pacific Gyre (SPG) is characterized as the most oligotrophic open ocean environment. The sediment is rich in oxygen but poor in energy-sources such as reduced organic matter, and hence harbors very low numbers of microbial cells in relatively shallow subseafloor sediment (D'Hondt et al., 2009; Kallmeyer et al., 2012). In such an energy-limited sedimentary habitat, a small size of microbial community persists living functions with extraordinary low oxygen-consumption rate (Røy et al., 2012). During IODP Expedition 329, a series of sediment samples were successfully recovered from 7 drill sites (U1365-1371) from the seafloor to basement in the SPG, providing an unprecedented opportunity to study metabolic activity of the aerobic subseafloor microbial communities. We initiated incubation onboard by adding stable isotope-labeled substrates to the freshly collected sediment sample, such as 13C and/or 15N-labeled bicarbonate, glucose, amino acids, acetate, and ammonium under the (micro-) aerobic condition. One of the technological challenges in this study is to harvest microbial cells from very low-biomass sediment samples for the analysis using nano-scale secondary ion mass spectrometry (NanoSIMS). To address the technical issue, we improved existing cell separation technique for the SPG sediment samples with small inorganic zeolitic grains. By monitoring cell recovery rates through an image-based cell enumeration technique (Morono et al., 2009), we found that cell recovery rates in the SPG sediment samples are generally lower than those in other oceanographic settings (i.e., organic-rich ocean margin sediments). To gain higher cell recovery ratio, we applied multiple density gradient layers, resulting in the cell recovery ratio up to around 80-95% (Morono et al., in press). Then, using the newly developed cell separation technique, we successfully sorted enough number of microbial cells in small spots on the membrane (i.e., 103 to 105 cells per spot). NanoSIMS analysis showed incorporation of the supplemented stable isotope-labeled substrates after 1.5 year-incubation. The substrate incorporation rates of individual microbial cell ranged in average from 1/10 to 1/2 of those values previously observed in an organic-rich ocean margin sediment (Morono et al., 2011). References S. D'Hondt et al., Subseafloor sedimentary life in the South Pacific Gyre. Proc Natl Acad Sci USA 106, 11651 (2009) J. Kallmeyeret al., Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci USA 109, 16213 (2012) H. Røy et al., Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science 336, 922 (2012) Y. Morono et al. Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J 3, 503 (2009) Y. Morono et al., An Improved Cell Separation Technique for Marine Subsurface Sediments: Applications for High-throughput Analysis Using Flow Cytometry and Cell Sorting. Environ Microbiol, (2013) Y. Morono et al., Carbon and nitrogen assimilation in deep subseafloor microbial cells. Proc Natl Acad Sci USA 108, 18295 (2011)

The Deep Subsurface Biosphere in Igneous Ocean Crust: Frontier Habitats for Microbiological Exploration

PubMed Central

Edwards, Katrina J.; Fisher, Andrew T.; Wheat, C. Geoffrey

2011-01-01

We discuss ridge flank environments in the ocean crust as habitats for subseafloor microbial life. Oceanic ridge flanks, areas far from the magmatic and tectonic influence of seafloor spreading, comprise one of the largest and least explored microbial habitats on the planet. We describe the nature of selected ridge flank crustal environments, and present a framework for delineating a continuum of conditions and processes that are likely to be important for defining subseafloor microbial "provinces." The basis for this framework is three governing conditions that help to determine the nature of subseafloor biomes: crustal age, extent of fluid flow, and thermal state. We present a brief overview of subseafloor conditions, within the context of these three characteristics, for five field sites where microbial studies have been done, are underway, or have been proposed. Technical challenges remain and likely will limit progress in studies of microbial ridge flank ecosystems, which is why it is vital to select and design future studies so as to leverage as much general understanding as possible from work focused at a small number of sites. A characterization framework such that as presented in this paper, perhaps including alternative or additional physical or chemical characteristics, is essential for achieving the greatest benefit from multidisciplinary microbial investigations of oceanic ridge flanks. PMID:22347212

Microbial Fossils from Terrestrial Subsurface Hydrothermal Environments: Examples and Implications for Mars

NASA Technical Reports Server (NTRS)

Hofmann, Beda A.; Farmer, Jack; Chang, Sherwood (Technical Monitor)

1997-01-01

The recognition of biological signatures in ancient epithermal deposits has special relevance for studies of early blaspheme evolution and in exploring for past life on Mars. Recently, proposals for the existence of an extensive subsurface blaspheme on Earth, dominated by chemoautotrophic microbial life, has gained prominence. However, reports of fossilized microbial remains, or biosedimentary structures (e.g. stromatolites) from the deposits of ancient subsurface systems, are rare. Microbial preservation is favoured where high population densities co-exist with rapid mineral precipitation. Near-surface epithetical systems with strong gradients in temperature and redox are good candidates for the abundant growth and fossilization of microorganisms, and are also favorable environments for the precipitation of ore minerals. Therefore, we might expect microbial remain, to be particularly well preserved in various kinds of hydrothermal and diagenetic mineral precipitates that formed below the upper temperature limit for life (approx. 120 C).

The Potential for Low-Temperature Abiotic Hydrogen Generation and a Hydrogen-Driven Deep Biosphere

PubMed Central

Huang, Shanshan; Thorseth, Ingunn H.

2011-01-01

Abstract The release and oxidation of ferrous iron during aqueous alteration of the mineral olivine is known to reduce aqueous solutions to such extent that molecular hydrogen, H2, forms. H2 is an efficient energy carrier and is considered basal to the deep subsurface biosphere. Knowledge of the potential for H2 generation is therefore vital to understanding the deep biosphere on Earth and on extraterrestrial bodies. Here, we provide a review of factors that may reduce the potential for H2 generation with a focus on systems in the core temperature region for thermophilic to hyperthermophilic microbial life. We show that aqueous sulfate may inhibit the formation of H2, whereas redox-sensitive compounds of carbon and nitrogen are unlikely to have significant effect at low temperatures. In addition, we suggest that the rate of H2 generation is proportional to the dissolution rate of olivine and, hence, limited by factors such as reactive surface areas and the access of water to fresh surfaces. We furthermore suggest that the availability of water and pore/fracture space are the most important factors that limit the generation of H2. Our study implies that, because of large heat flows, abundant olivine-bearing rocks, large thermodynamic gradients, and reduced atmospheres, young Earth and Mars probably offered abundant systems where microbial life could possibly have emerged. Key Words: Serpentinization—Olivine—Hydrogen—Deep biosphere—Water—Mars. Astrobiology 11, 711–724. PMID:21923409

Biolog(TM) ID as compared to 16S ribosomal RNA ID for environmental isolates from the deep subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKinsey, P.C.

2000-05-05

The U.S. Dept of Energy (DOE) Subsurface Microbial Culture Collection (SMCC) contains nearly 10,000 strains of microorganisms isolated from terrestrial subsurface environments. Many of the aerobic, gram-negative, chemoheterotrophs isolated from the DOE Savannah River Site (SRS) have previously been identified by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. These SMCC isolates are currently being examined using Biolog GN Microplates and the Biolog Microstation System in order to gain knowledge of their metabolic capabilities and to compare Biolog IDs with 16S IDs. To accommodate the particular needs of these subsurface isolates, which are often incapable of growing undermore » high-nutrient conditions, Biolog's recommendations for inoculating isolates into Biolog GN Microplates have been altered. The isolates are grown on low nutrient media, sodium thioglycolate (3mM) is added to the culture media to inhibit capsule formation, and a low density of bacteria is inoculated into the microplate. Using these altered inoculation criteria, 60 percent of these SMCC isolates have a Biolog genus ID that matches the 16S rRNA ID. These results indicate that the Biolog System can be a good means of identifying unusual environmental isolates, even when recommended inoculation procedures are altered to accommodate particular isolate needs.« less

Fungal diversity from deep marine subsurface sediments (IODP 317, Canterbury Basin, New Zealand)

NASA Astrophysics Data System (ADS)

Redou, V.; Arzur, D.; Burgaud, G.; Barbier, G.

2012-12-01

Recent years have seen a growing interest regarding micro-eukaryotic communities in extreme environments as a third microbial domain after Bacteria and Archaea. However, knowledge is still scarce and the diversity of micro-eukaryotes in such environments remains hidden and their ecological role unknown. Our research program is based on the deep sedimentary layers of the Canterbury Basin in New Zealand (IODP 317) from the subsurface to the record depth of 1884 meters below seafloor. The objectives of our study are (i) to assess the genetic diversity of fungi in deep-sea sediments and (ii) identify the functional part in order to better understand the origin and the ecological role of fungal communities in this extreme ecosystem. Fingerprinting-based methods using capillary electrophoresis single-strand conformation polymorphism and denaturing high-performance liquid chromatography were used as a first step to raise our objectives. Molecular fungal diversity was assessed using amplification of ITS1 (Internal Transcribed Spacer 1) as a biomarker on 11 samples sediments from 3.76 to 1884 meters below seafloor. Fungal molecular signatures were detected throughout the sediment core. The phyla Ascomycota and Basidiomycota were revealed with DNA as well as cDNA. Most of the phylotypes are affiliated to environmental sequences and some to common fungal cultured species. The discovery of a present and metabolically active fungal component in this unique ecosystem allows some interesting first hypotheses that will be further combined to culture-based methods and deeper molecular methods (454 pyrosequencing) to highlight essential informations regarding physiology and ecological role of fungal communities in deep marine sediments.

Effects of subsurface aeration and trinexapac-ethyl application on soil microbial communities in a creeping bentgrass putting green

USGS Publications Warehouse

Feng, Y.; Stoeckel, D.M.; Van Santen, E.; Walker, R.H.

2002-01-01

The sensitivity of creeping bentgrass (Agrostis palustris Huds.) to the extreme heat found in the southeastern United States has led to the development of new greens-management methods. The purpose of this study was to examine the effects of subsurface aeration and growth regulator applications on soil microbial communities and mycorrhizal colonization rates in a creeping bentgrass putting green. Two cultivars (Crenshaw and Penncross), a growth regulator (trinexapacethyl), and subsurface aeration were evaluated in cool and warm seasons. Total bacterial counts were higher in whole (unsieved) soils than in sieved soils, indicating a richer rhizosphere soil environment. Mycorrhizal infection rates were higher in trinexapac-ethyl (TE) treated plants. High levels of hyphal colonization and relatively low arbuscule and vesicle occurrence were observed. Principal components analysis of whole-soil fatty acid methyl ester (FAME) profiles indicated that warm-season microbial populations in whole and sieved soils had similar constituents, but the populations differed in the cool season. FAME profiles did not indicate that subsurface aeration and TE application affected soil microbial community structure. This is the first reported study investigating the influences of subsurface aeration and TE application on soil microorganisms in a turfgrass putting green soil.

Microbial community assembly and evolution in subseafloor sediment.

PubMed

Starnawski, Piotr; Bataillon, Thomas; Ettema, Thijs J G; Jochum, Lara M; Schreiber, Lars; Chen, Xihan; Lever, Mark A; Polz, Martin F; Jørgensen, Bo B; Schramm, Andreas; Kjeldsen, Kasper U

2017-03-14

Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.

Trajectories of Microbial Community Function in Response to Accelerated Remediation of Subsurface Metal Contaminants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Firestone, Mary

Objectives of proposed research were to; Determine if the trajectories of microbial community composition and function following organic carbon amendment can be related to, and predicted by, key environmental determinants; Assess the relative importance of the characteristics of the indigenous microbial community, sediment, groundwater, and concentration of organic carbon amendment as the major determinants of microbial community functional response and bioremediation capacity; and Provide a fundamental understanding of the microbial community ecology underlying subsurface metal remediation requisite to successful application of accelerated remediation and long-term stewardship of DOE-IFC sites.

MODELING THREE-DIMENSIONAL SUBSURFACE FLOW, FATE AND TRANSPORT OF MICROBES AND CHEMICALS (3DFATMIC)

EPA Science Inventory

A three-dimensional model simulating the subsurface flow, microbial growth and degradation, microbial-chemical reaction, and transport of microbes and chemicals has been developed. he model is designed to solve the coupled flow and transport equations. asically, the saturated-uns...

An Evaluation of Subsurface Microbial Activity Conditional to Subsurface Temperature, Porosity, and Permeability at North American Carbon Sequestration Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, B.; Mordensky, S.; Verba, Circe

Several nations, including the United States, recognize global climate change as a force transforming the global ecosphere. Carbon dioxide (CO 2) is a greenhouse gas that contributes to the evolving climate. Reduction of atmospheric CO 2 levels is a goal for many nations and carbon sequestration which traps CO 2 in the Earth’s subsurface is one method to reduce atmospheric CO 2 levels. Among the variables that must be considered in developing this technology to a national scale is microbial activity. Microbial activity or biomass can change rock permeability, alter artificial seals around boreholes, and play a key role inmore » biogeochemistry and accordingly may determine how CO 2 is sequestered underground. Certain physical parameters of a reservoir found in literature (e.g., temperature, porosity, and permeability) may indicate whether a reservoir can host microbial communities. In order to estimate which subsurface formations may host microbes, this report examines the subsurface temperature, porosity, and permeability of underground rock formations that have high potential to be targeted for CO 2 sequestration. Of the 268 North American wellbore locations from the National Carbon Sequestration Database (NATCARB; National Energy and Technology Laboratory, 2015) and 35 sites from Nelson and Kibler (2003), 96 sequestration sites contain temperature data. Of these 96 sites, 36 sites have temperatures that would be favorable for microbial survival, 48 sites have mixed conditions for supporting microbial populations, and 11 sites would appear to be unfavorable to support microbial populations. Future studies of microbe viability would benefit from a larger database with more formation parameters (e.g. mineralogy, structure, and groundwater chemistry), which would help to increase understanding of where CO 2 sequestration could be most efficiently implemented.« less

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

PubMed Central

Booker, Anne E.; Borton, Mikayla A.; Daly, Rebecca A.; Welch, Susan A.; Nicora, Carrie D.; Hoyt, David W.; Wilson, Travis; Purvine, Samuel O.; Wolfe, Richard A.; Sharma, Shikha; Mouser, Paula J.; Cole, David R.; Lipton, Mary S.; Wrighton, Kelly C.

2017-01-01

ABSTRACT Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by a Halanaerobium strain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis of Halanaerobium isolate genomes and reconstructed genomes from metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using a Halanaerobium isolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentative Halanaerobium uses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCE Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as “souring”) is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary. PMID:28685163

Microbial Communities in Subpermafrost Saline Fracture Water at the Lupin Au Mine, Nunavut, Canada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Onstott, Tullis; McGown, Daniel; Bakermans, Corien

2009-01-01

We report the first investigation of a deep subpermafrost microbial ecosystem, a terrestrial analog for the Martian subsurface. Our multidisciplinary team analyzed fracture water collected at 890 and 1,130 m depths beneath a 540-m-thick permafrost layer at the Lupin Au mine (Nunavut, Canada). 14C, 3H, and noble gas isotope analyses suggest that the Na Ca Cl, suboxic, fracture water represents a mixture of geologically ancient brine, ~25-kyr-old, meteoric water and a minor modern talik-water component. Microbial planktonic concentrations were ~103 cells mL 1. Analysis of the 16S rRNA gene from extracted DNA and enrichment cultures revealed 42 unique operational taxonomicmore » units in 11 genera with Desulfosporosinus, Halothiobacillus, and Pseudomonas representing the most prominent phylotypes and failed to detect Archaea. The abundance of terminally branched and midchain-branched saturated fatty acids (5 to 15 mol%) was consistent with the abundance of Grampositive bacteria in the clone libraries. Geochemical data, the ubiquinone (UQ) abundance (3 to 11 mol%), and the presence of both aerobic and anaerobic bacteria indicated that the environment was suboxic, not anoxic. Stable sulfur isotope analyses of the fracture water detected the presence of microbial sulfate reduction, and analyses of the vein-filling pyrite indicated that it was in isotopic equilibrium with the dissolved sulfide. Free energy calculations revealed that sulfate reduction and sulfide oxidation via denitrification and not methanogenesis were the most thermodynamically viable consistent with the principal metabolisms inferred from the 16S rRNA community composition and with CH4 isotopic compositions. The sulfate-reducing bacteria most likely colonized the subsurface during the Pleistocene or earlier, whereas aerobic bacteria may have entered the fracture water networks either during deglaciation prior to permafrost formation 9,000 years ago or from the nearby talik through the hydrologic gradient created during mine dewatering. Although the absence of methanogens from this subsurface ecosystem is somewhat surprising, it may be attributable to an energy bottleneck that restricts their migration from surface permafrost deposits where they are frequently reported. These results have implications for the biological origin of CH4 on Mars.« less

Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4{degrees}C

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haldeman, D.L.; Amy, P.S.; White, D.C.

1994-08-01

The abundance of viable microorganisms recovered from deep subsurface volcanic rock samples increased after rock perturbation and storage for 1 week at 4{degrees}C, while the diversity and evenness of recoverable heterotrophic bacterial communities generally decreased. One sample of each morphologically distinct colony type, recovered both before and after storage of U12n rock samples, was purified and characterized by fatty acid methyl ester (MIDI) and API rapid NFT strips. As determined by MIDI cluster analysis, the composition of the recoverable microbial communities changed with storage of rock samples; some groups of organisms were recovered only before, only after, or at bothmore » sample times. In general, the isolates recovered only after storage of rock samples had a greater ability to utilize the carbohydrates included in API test strips and had faster generation times than isolates recovered only on initial plating. The nutritional versatility and faster growth rates of organisms recovered in higher proportions after sample storage provide evidence that some microbial community changes may be due to the proliferation of a few bacterial types. However, because some new genera are recovered only after storage, the possibility also exists that dormant bacterial types are resuscitated during sample perturbation and storage. 30 refs., 1 fig., 5 tabs.« less

Hydrogeologic controls on episodic H2 release from precambrian fractured rocks--energy for deep subsurface life on earth and mars.

PubMed

Sherwood Lollar, B; Voglesonger, K; Lin, L-H; Lacrampe-Couloume, G; Telling, J; Abrajano, T A; Onstott, T C; Pratt, L M

2007-12-01

Dissolved H(2) concentrations up to the mM range and H(2) levels up to 9-58% by volume in the free gas phase are reported for groundwaters at sites in the Precambrian shields of Canada and Finland. Along with previously reported dissolved H(2) concentrations up to 7.4 mM for groundwaters from the Witwatersrand Basin, South Africa, these findings indicate that deep Precambrian Shield fracture waters contain some of the highest levels of dissolved H(2) ever reported and represent a potentially important energy-rich environment for subsurface microbial life. The delta (2)H isotope signatures of H(2) gas from Canada, Finland, and South Africa are consistent with a range of H(2)-producing water-rock reactions, depending on the geologic setting, which include both serpentinization and radiolysis. In Canada and Finland, several of the sites are in Archean greenstone belts characterized by ultramafic rocks that have under-gone serpentinization and may be ancient analogues for serpentinite-hosted gases recently reported at the Lost City Hydrothermal Field and other hydrothermal seafloor deposits. The hydrogeologically isolated nature of these fracture-controlled groundwater systems provides a mechanism whereby the products of water-rock interaction accumulate over geologic timescales, which produces correlations between high H(2) levels, abiogenic hydrocarbon signatures, and the high salinities and highly altered delta (18)O and delta (2)H values of these groundwaters. A conceptual model is presented that demonstrates how periodic opening of fractures and resultant mixing control the distribution and supply of H(2) and support a microbial community of H(2)-utilizing sulfate reducers and methanogens.

CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough

PubMed Central

Wilkins, Michael J.; Hoyt, David W.; Marshall, Matthew J.; Alderson, Paul A.; Plymale, Andrew E.; Markillie, L. Meng; Tucker, Abby E.; Walter, Eric D.; Linggi, Bryan E.; Dohnalkova, Alice C.; Taylor, Ron C.

2014-01-01

Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using 13C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least 4 h, and at 80 bar CO2 for 2 h. The fraction of dead cells increased rapidly after 4 h at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process. PMID:25309528

CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, Michael J.; Hoyt, David W.; Marshall, Matthew J.

Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using 13C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurizedmore » batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least four hours, and at 80 bar CO2 for two hours. The fraction of dead cells increased rapidly after four hours at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process.« less

Evaluation of nutrient removal efficiency and microbial enzyme activity in a baffled subsurface-flow constructed wetland system

Treesearch

Lihua Cui; Ying Ouyang; Wenjie Gu; Weozhi Yang; Qiaoling Xu

2013-01-01

In this study, the enzyme activities and their relationships to domestic wastewater purification are investigated in four different types of subsurface-flow constructed wetlands (CWs), namely the traditional horizontal subsurface-flow, horizontal baffled subsurface-flow, vertical baffled subsurface-flow, and composite baffled subsurface-flow CWs. Results showed that...

Subseafloor Microbial Life in Venting Fluids from the Mid Cayman Rise Hydrothermal System

NASA Astrophysics Data System (ADS)

Huber, J. A.; Reveillaud, J.; Reddington, E.; McDermott, J. M.; Sylva, S. P.; Breier, J. A.; German, C. R.; Seewald, J.

2012-12-01

In hard rock seafloor environments, fluids emanating from hydrothermal vents are one of the best windows into the subseafloor and its resident microbial community. The functional consequences of an extensive population of microbes living in the subseafloor remains unknown, as does our understanding of how these organisms interact with one another and influence the biogeochemistry of the oceans. Here we report the abundance, activity, and diversity of microbes in venting fluids collected from two newly discovered deep-sea hydrothermal vents along the ultra-slow spreading Mid-Cayman Rise (MCR). Fluids for geochemical and microbial analysis were collected from the Von Damm and Piccard vent fields, which are located within 20 km of one another, yet have extremely different thermal, geological, and depth regimes. Geochemical data indicates that both fields are highly enriched in volatiles, in particular hydrogen and methane, important energy sources for and by-products of microbial metabolism. At both sites, total microbial cell counts in the fluids ranged in concentration from 5 x 10 4 to 3 x 10 5 cells ml-1 , with background seawater concentrations of 1-2 x 10 4 cells ml-1 . In addition, distinct cell morphologies and clusters of cells not visible in background seawater were seen, including large filaments and mineral particles colonized by microbial cells. These results indicate local enrichments of microbial communities in the venting fluids, distinct from background populations, and are consistent with previous enumerations of microbial cells in venting fluids. Stable isotope tracing experiments were used to detect utilization of acetate, formate, and dissolve inorganic carbon and generation of methane at 70 °C under anaerobic conditions. At Von Damm, a putatively ultra-mafic hosted site located at ~2200 m with a maximum temperature of 226 °C, stable isotope tracing experiments indicate methanogenesis is occurring in most fluid samples. No activity was detected in Piccard vent fluids, a basalt-hosted black smoker site located at ~4950 m with a maximum temperature of 403 °C. However, hyperthermophilic and thermophilic heterotrophs of the genus Thermococcus were isolated from Piccard vent fluids, but not Von Damm. These obligate anaerobes, growing optimally at 55-90 °C, are ubiquitous at hydrothermal systems and serve as a readily cultivable indicator organism of subseafloor populations. Finally, molecular analysis of vent fluids is on-going and will define the microbial population structure in this novel ecosystem and allow for direct comparisons with other deep-sea and subsurface habitats as part of our continuing efforts to explore the deep microbial biosphere on Earth.

viral abundance distribution in deep waters of the Northern of South China Sea

NASA Astrophysics Data System (ADS)

He, Lei; Yin, Kedong

2017-04-01

Little is known about the vertical distribution and interaction of viruses and bacteria in the deep ocean water column. The vertical distribution of viral-like particles and bacterial abundance was investigated in the deep water column in the South China Sea during September 2005 along with salinity, temperature and dissolved oxygen. There were double maxima in the ratio of viral to bacterial abundance (VBR) in the water column: the subsurface maximum located at 50-100 m near the pycnocline layer, and the deep maximum at 800-1000 m. At the subsurface maximum of VBR, both viral and bacterial abundance were maximal in the water column, and at the deep maximum of VBR, both viral and bacterial abundance were low, but bacterial abundance was relatively lower than viral abundance. The subsurface VBR maximum coincided with the subsurface chlorophyll maximum while the deep VBR maximum coincided with the minimum in dissolved oxygen (2.91mg L-1). Therefore, we hypothesize that the two maxima were formed by different mechanisms. The subsurface VBR maximum was formed due to an increase in bacterial abundance resulting from the stimulation of abundant organic supply at the subsurface chlorophyll maximum, whereas the deep VBR maximum was formed due to a decrease in bacterial abundance caused by more limitation of organic matter at the oxygen minimum. The evidence suggests that viruses play an important role in controlling bacterial abundance in the deep water column due to the limitation of organic matter supply. In turn, this slows down the formation of the oxygen minimum in which oxygen may be otherwise lower. The mechanism has a great implication that viruses could control bacterial decomposition of organic matter, oxygen consumption and nutrient remineralization in the deep oceans.

[Search for life in deep biospheres].

PubMed

Naganuma, Takeshi

2003-12-01

The life in deep biospheres bridges conventional biology and future exobiology. This review focuses the microbiological studies from the selected deep biospheres, i.e., deep-sea hydrothermal vents, sub-hydrothermal vents, terrestrial subsurface and a sub-glacier lake. The dark biospheres facilitate the emergence of organisms and communities dependent on chemolithoautotrophy, which are overwhelmed by photoautotrophy (photosynthesis) in the surface biospheres. The life at deep-sea hydrothermal vents owes much to chemolithoautotrophy based on the oxidation of sulfide emitted from the vents. It is likely that similarly active bodies such as the Jovian satellite Europa may have hydrothermal vents and associated biological communities. Anoxic or anaerobic condition is characteristic of deep subsurface biospheres. Subsurface microorganisms exploit available oxidants, or terminal electron acceptors (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, is about to be drill-penetrated for microbiological studies. These deep biosphere "platforms" provide new knowledge about the diversity and potential of the Earth's life. The expertise obtained from the deep biosphere expeditions will facilitate the capability of exobiologial exploration.

Microbial Metabolism in Serpentinite Fluids

NASA Astrophysics Data System (ADS)

Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

2013-12-01

Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid chemistry and microbial community composition. These experiments are expected to provide insight into the biogeochemical dynamics of the serpentinite subsurface at CROMO and represent a first step for developing metatranscriptomic and RNA-based Stable Isotope Probing (RNA-SIP) experiments to trace microbial activity at this site. [1] Brazelton et al. (2012) Frontiers in Microbiology 2:268

Contamination assessment in microbiological sampling of the Eyreville core, Chesapeake Bay impact structure

USGS Publications Warehouse

Gronstal, A.L.; Voytek, M.A.; Kirshtein, J.D.; Von der, Heyde; Lowit, M.D.; Cockell, C.S.

2009-01-01

Knowledge of the deep subsurface biosphere is limited due to difficulties in recovering materials. Deep drilling projects provide access to the subsurface; however, contamination introduced during drilling poses a major obstacle in obtaining clean samples. To monitor contamination during the 2005 International Continental Scientific Drilling Program (ICDP)-U.S. Geological Survey (USGS) deep drilling of the Chesapeake Bay impact structure, four methods were utilized. Fluorescent microspheres were used to mimic the ability of contaminant cells to enter samples through fractures in the core material during retrieval. Drilling mud was infused with a chemical tracer (Halon 1211) in order to monitor penetration of mud into cores. Pore water from samples was examined using excitation-emission matrix (EEM) fl uorescence spectroscopy to characterize dissolved organic carbon (DOC) present at various depths. DOC signatures at depth were compared to signatures from drilling mud in order to identify potential contamination. Finally, microbial contaminants present in drilling mud were identified through 16S ribosomal deoxyribonucleic acid (rDNA) clone libraries and compared to species cultured from core samples. Together, these methods allowed us to categorize the recovered core samples according to the likelihood of contamination. Twenty-two of the 47 subcores that were retrieved were free of contamination by all the methods used and were subsequently used for microbiological culture and culture-independent analysis. Our approach provides a comprehensive assessment of both particulate and dissolved contaminants that could be applied to any environment with low biomass. ?? 2009 The Geological Society of America.

Microbial control of the dark end of the biological pump

PubMed Central

2014-01-01

A fraction of the carbon captured by phytoplankton in the sunlit surface ocean sinks to depth as dead organic matter and faecal material. The microbial breakdown of this material in the subsurface ocean generates carbon dioxide. Collectively, this microbially mediated flux of carbon from the atmosphere to the ocean interior is termed the biological pump. In recent decades it has become clear that the composition of the phytoplankton community in the surface ocean largely determines the quantity and quality of organic matter that sinks to depth. This settling organic matter, however, is not sufficient to meet the energy demands of microbes in the dark ocean. Two additional sources of organic matter have been identified: non-sinking organic particles of debated origin that escape capture by sediment traps and exhibit stable concentrations throughout the dark ocean, and microbes that convert inorganic carbon into organic matter. Whether these two sources can together account for the significant mismatch between organic matter consumption and supply in the dark ocean remains to be seen. It is clear, however, that the microbial community of the deep ocean works in a fundamentally different way from surface water communities. PMID:24707320

Post-Viking microbiology: new approaches, new data, new insights

NASA Technical Reports Server (NTRS)

Nealson, K. H.

1999-01-01

In the 20 years since the Viking experiments, major advances have been made in the areas of microbial systematics, microbial metabolism, microbial survival capacity, and the definition of environments on earth, suggesting that life is more versatile and tenacious than was previously appreciated. Almost all niches on earth which have available energy, and which are compatible with the chemistry of carbon-carbon bonds, are known to be inhabited by bacteria. The oldest known bacteria on earth apparently evolved soon after the formation of the planet, and are heat loving, hydrogen and/or sulfur metabolizing forms. Among the two microbial domains (kingdoms) is a great deal of metabolic diversity, with members of these forms being able to grow on almost any known energy source, organic or inorganic, and to utilize an impressive array of electron acceptors for anaerobic respiration. Both hydrothermal environments and the deep subsurface environments have been shown to support large populations of bacteria, growing on energy supplied by geothermal energy, thus isolating these ecosystems from the rest of the global biogeochemical cycles. This knowledge, coupled with new insights into the history of the solar system, allow one to speculate on possible evolution and survival of life forms on Mars.

Post-Viking microbiology: new approaches, new data, new insights.

PubMed

Nealson, K H

1999-01-01

In the 20 years since the Viking experiments, major advances have been made in the areas of microbial systematics, microbial metabolism, microbial survival capacity, and the definition of environments on earth, suggesting that life is more versatile and tenacious than was previously appreciated. Almost all niches on earth which have available energy, and which are compatible with the chemistry of carbon-carbon bonds, are known to be inhabited by bacteria. The oldest known bacteria on earth apparently evolved soon after the formation of the planet, and are heat loving, hydrogen and/or sulfur metabolizing forms. Among the two microbial domains (kingdoms) is a great deal of metabolic diversity, with members of these forms being able to grow on almost any known energy source, organic or inorganic, and to utilize an impressive array of electron acceptors for anaerobic respiration. Both hydrothermal environments and the deep subsurface environments have been shown to support large populations of bacteria, growing on energy supplied by geothermal energy, thus isolating these ecosystems from the rest of the global biogeochemical cycles. This knowledge, coupled with new insights into the history of the solar system, allow one to speculate on possible evolution and survival of life forms on Mars.

Removal of microbial pathogens in a sandy gravel aquifer under forced-gradient subsurface flow conditions

NASA Astrophysics Data System (ADS)

Oudega, Thomas James; Derx, Julia; van Driezum, Inge; Cisneros, Anibal; Sommer, Regina; Kirschner, Alexander; Farnleitner, Andreas; Blaschke, Alfred Paul

2017-04-01

Subsurface media are being used around the world as a means to mitigate microbial contamination, but vary widely in their ability to remove pathogens. To help to provide accurate risk assessments of microbial contamination of groundwaters, and establish safe setback distances between receiving waters and disposal fields, this study aims to use aquifer tracer tests to evaluate the ability of subsurface media to attenuate these pathogens. The novelty of this work is the use of a variety of different tracer substances (e.g. phages, spores, microspheres, conservative tracers) together in field experiments. This will be done by means of injecting these substances under a forced gradient in a sandy gravel aquifer in Lobau, Austria. The extraction of the tracers will be monitored in a pumping well at a distrance of 50m downgradient. This will be able to provide us with insight to the characteristics of microbial transport and how the microorganisms react to the subsurface in the study site. Subsequent numerical modelling of the experiments can tell us more about quantification of subsurface processes such as attachment/detachment, inactivation and die-off of these substances. The first field experiment with conservative tracers (NaCl) has been carried out in December 2016, and subsequent tests are being planned for the next months.

Soil Physical Constraints on Intrinsic Biodegradation of Petroleum Vapors in a Layered Subsurface

PubMed Central

Kristensen, Andreas H.; Henriksen, Kaj; Mortensen, Lars; Scow, Kate M.; Moldrup, Per

2011-01-01

Naturally occurring biodegradation of petroleum hydrocarbons in the vadose zone depends on the physical soil environment influencing field-scale gas exchange and pore-scale microbial metabolism. In this study, we evaluated the effect of soil physical heterogeneity on biodegradation of petroleum vapors in a 16-m-deep, layered vadose zone. Soil slurry experiments (soil/water ratio 10:30 w/w, 25°C) on benzene biodegradation under aerobic and well-mixed conditions indicated that the biodegradation potential in different textured soil samples was related to soil type rather than depth, in the order: sandy loam > fine sand > limestone. Similarly, O2 consumption rates during in situ respiration tests performed at the site were higher in the sandy loam than in the fine sand, although the difference was less significant than in the slurries. Laboratory and field data generally agreed well and suggested a significant potential for aerobic biodegradation, even with nutrient-poor and deep subsurface conditions. In slurries of the sandy loam, the biodegradation potential declined with increasing in situ water saturation (i.e., decreasing air-filled porosity in the field). This showed a relation between antecedent undisturbed field conditions and the slurry biodegradation potential, and suggested airfilled porosity to be a key factor for the intrinsic biodegradation potential in the field. PMID:21617737

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

PubMed

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Some Ecological Mechanisms to Generate Habitability in Planetary Subsurface Areas by Chemolithotrophic Communities: The Ro Tinto Subsurface Ecosystem as a Model System

NASA Astrophysics Data System (ADS)

Fernández-Remolar, David C.; Gómez, Felipe; Prieto-Ballesteros, Olga; Schelble, Rachel T.; Rodríguez, Nuria; Amiols, Ricardo

2008-02-01

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Ro Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Ro Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.

Some ecological mechanisms to generate habitability in planetary subsurface areas by chemolithotrophic communities: the Río Tinto subsurface ecosystem as a model system.

PubMed

Fernández-Remolar, David C; Gómez, Felipe; Prieto-Ballesteros, Olga; Schelble, Rachel T; Rodríguez, Nuria; Amils, Ricardo

2008-02-01

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Río Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Río Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

DOE PAGES

Vigneron, Adrien; Alsop, Eric B.; Lomans, Bartholomeus P.; ...

2017-05-19

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of themore » entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H2S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.« less

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vigneron, Adrien; Alsop, Eric B.; Lomans, Bartholomeus P.

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of themore » entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H2S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.« less

An analysis of geothermal and carbonic springs in the western United States sustained by deep fluid inputs.

PubMed

Colman, D R; Garcia, J R; Crossey, L J; Karlstrom, K; Jackson-Weaver, O; Takacs-Vesbach, C

2014-01-01

Hydrothermal springs harbor unique microbial communities that have provided insight into the early evolution of life, expanded known microbial diversity, and documented a deep Earth biosphere. Mesothermal (cool but above ambient temperature) continental springs, however, have largely been ignored although they may also harbor unique populations of micro-organisms influenced by deep subsurface fluid mixing with near surface fluids. We investigated the microbial communities of 28 mesothermal springs in diverse geologic provinces of the western United States that demonstrate differential mixing of deeply and shallowly circulated water. Culture-independent analysis of the communities yielded 1966 bacterial and 283 archaeal 16S rRNA gene sequences. The springs harbored diverse taxa and shared few operational taxonomic units (OTUs) across sites. The Proteobacteria phylum accounted for most of the dataset (81.2% of all 16S rRNA genes), with 31 other phyla/candidate divisions comprising the remainder. A small percentage (~6%) of bacterial 16S rRNA genes could not be classified at the phylum level, but were mostly distributed in those springs with greatest inputs of deeply sourced fluids. Archaeal diversity was limited to only four springs and was primarily composed of well-characterized Thaumarchaeota. Geochemistry across the dataset was varied, but statistical analyses suggested that greater input of deeply sourced fluids was correlated with community structure. Those with lesser input contained genera typical of surficial waters, while some of the springs with greater input may contain putatively chemolithotrophic communities. The results reported here expand our understanding of microbial diversity of continental geothermal systems and suggest that these communities are influenced by the geochemical and hydrologic characteristics arising from deeply sourced (mantle-derived) fluid mixing. The springs and communities we report here provide evidence for opportunities to understand new dimensions of continental geobiological processes where warm, highly reduced fluids are mixing with more oxidized surficial waters. © 2013 John Wiley & Sons Ltd.

Saturated CO2 inhibits microbial processes in CO2-vented deep-sea sediments

NASA Astrophysics Data System (ADS)

de Beer, D.; Haeckel, M.; Neumann, J.; Wegener, G.; Inagaki, F.; Boetius, A.

2013-02-01

This study focused on biogeochemical processes and microbial activity in sediments of a natural deep-sea CO2 seepage area (Yonaguni Knoll IV hydrothermal system, Japan). The aim was to assess the influence of the geochemical conditions occurring in highly acidic and CO2 saturated sediments on sulphate reduction (SR) and anaerobic methane oxidation (AOM). Porewater chemistry was investigated from retrieved sediment cores and in situ by microsensor profiling. The sites sampled around a sediment-hosted hydrothermal CO2 vent were very heterogeneous in porewater chemistry, indicating a complex leakage pattern. Near the vents, droplets of liquid CO2 were observed to emanate from the sediments, and the pH reached approximately 4.5 in a sediment depth >6 cm, as determined in situ by microsensors. Methane and sulphate co-occurred in most sediment samples from the vicinity of the vents down to a depth of at least 3 m. However, SR and AOM were restricted to the upper 7-15 cm below seafloor, although neither temperature, low pH, nor the availability of methane and sulphate could be limiting microbial activity. We argue that the extremely high subsurface concentrations of dissolved CO2 (1000-1700 mM), through the ensuing high H2CO3 levels (approx. 1-2 mM) uncouples the proton-motive-force (PMF) and thus inhibits biological energy conservation by ATPase-driven phosphorylation. This limits life to the surface sediment horizons above the liquid CO2 phase, where less extreme conditions prevail. Our results may have to be taken into consideration in assessing the consequences of deep-sea CO2 sequestration on benthic element cycling and on the local ecosystem state.

Quantification of microbial activity in subsurface environments using a hydrogenase enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Nickel, J.; Kallmeyer, J.

2012-04-01

The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3 d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3 d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3 d-1 down to a depth of 1.60 m. At all sites the SRR profile followed the H2ase activity profile until SRR declined to values close to the minimum detection limit (~10 pmol cm-3 d-1). H2ase activity increased again after SRR declined, indicating that other microbial processes are becoming quantitatively more important. The H2ase and SRR data show that our assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Cultivation and diversity of fungi buried in the Baltic Sea sediments

NASA Astrophysics Data System (ADS)

Xiao, N.

2015-12-01

@font-face { "ＭＳ 明朝"; }@font-face { "Century"; }@font-face { "Century"; }@font-face { "@ＭＳ 明朝"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0mm 0mm 0.0001pt; text-align: justify; font-size: 12pt; ; }.MsoChpDefault { ; }div.WordSection1 { page: WordSection1; } Studies on molecular biological and cultivation have been done for the prokaryotic microbial community in the deep biosphere. Compare to the prokaryotic community, few attempts have been done for eukaryotic microbial community. Here we report the study on fungi buried in deep-subsurface sediments by approaches of both cultivation and molecular diversity survey. Cultivation targeting fungi has been done using a sequential sediment samples obtained from the Baltic Sea, Landsort Deep site during the IODP expedition 347. 6 culture media with different nutrition and salt concentration have been tried for the fungi cultivation. 50 isolates of fungi were obtained from the sediment samples. The surface sediments showed richness of fungi strains but not for the deep sediments. Internal Transcribed Spacer (ITS) regions of RNA genes were amplified and for the identification of the isolates. The isolates were classified to 11 different genera. Pseudeurotium bakeri was the dominant strain throughout the glacial and interglacial sediments. We also found different representative fungal strains from glacial and interglacial sediments, suggesting the cultivated strains are buried from different sources. The survey of fungal diversity was done by sequencing the 18S RNA genes in the total DNA extracted from selected sediment samples. Fungi community showed different cluster in the glacial and interglacial sediments.Our results revealed the presence and activity of fungi in the deep biosphere of the Baltic sea and provided evidence of fungal community response to the climate change.

Chase the direct impact of rainfall into groundwater in Mt. Fuji from multiple analyses including microbial DNA

NASA Astrophysics Data System (ADS)

Kato, Kenji; Sugiyama, Ayumi; Nagaosa, Kazuyo; Tsujimura, Maki

2016-04-01

A huge amount of groundwater is stored in subsurface environment of Mt. Fuji, the largest volcanic mountain in Japan. Based on the concept of piston flow transport of groundwater an apparent residence time was estimated to ca. 30 years by 36Cl/Cl ratio (Tosaki et al., 2011). However, this number represents an averaged value of the residence time of groundwater which had been mixed before it flushes out. We chased signatures of direct impact of rainfall into groundwater to elucidate the routes of groundwater, employing three different tracers; stable isotopic analysis (delta 18O), chemical analysis (concentration of silica) and microbial DNA analysis. Though chemical analysis of groundwater shows an averaged value of the examined water which was blended by various water with different sources and routes in subsurface environment, microbial DNA analysis may suggest the place where they originated, which may give information of the source and transport routes of the water examined. Throughout the in situ observation of four rainfall events showed that stable oxygen isotopic ratio of spring water and shallow groundwater obtained from 726m a.s.l. where the average recharge height of rainfall was between 1500 and 1800 m became higher than the values before a torrential rainfall, and the concentration of silica decreased after this event when rainfall exceeded 300 mm in precipitation of an event. In addition, the density of Prokaryotes in spring water apparently increased. Those changes did not appear when rainfall did not exceed 100 mm per event. Thus, findings shown above indicated a direct impact of rainfall into shallow groundwater, which appeared within a few weeks of torrential rainfall in the studied geological setting. In addition, increase in the density of Archaea observed at deep groundwater after the torrential rainfall suggested an enlargement of the strength of piston flow transport through the penetration of rainfall into deep groundwater. This finding was supported by difference in constituents of Archaea by predominance of Halobacteriales and Methanobacteriales, which were thought to be relatively tightly embedded in geological layer and were extracted from the environment to the examined groundwater. Microbial DNA thus could give information about the route of groundwater, which was never elucidated by analysis of chemical materials dissolved in groundwater.

Effects of Hydraulic Frac Fluids on Subsurface Microbial Communities in Gas Shales

NASA Astrophysics Data System (ADS)

Jiménez, Núria; Krüger, Martin

2014-05-01

Shale gas is being considered as a complementary energy resource to coal or other fossil fuels. The exploitation of unconventional gas reservoirs requires the use of advanced drilling techniques and hydraulic stimulation (fracking). During fracking operations, large amounts of fluids (fresh water, proppants and chemical additives) are injected at high pressures into the formations, to produce fractures and fissures, and thus to release gas from the source rock into the wellbore. The injected fluids partly remain in the formation, while about 20 to 40% of the originally injected fluid flows back to the surface, together with formation waters, sometimes containing dissolved hydrocarbons, high salt concentrations, etc. The overall production operation will likely affect and be affected by subsurface microbial communities associated to the shale formations. On the one hand microbial activity (like growth, biofilm formation) can cause unwanted processes like corrosion, clogging, etc. On the other hand, the introduction of frac fluids could either enhance microbial growth or cause toxicity to the shale-associated microbial communities. To investigate the potential impacts of changing environmental reservoir conditions, like temperature, salinity, oxgen content and pH, as well as the introduction of frac or geogenic chemicals on subsurface microbial communities, laboratory experiments under in situ conditions (i.e. high temperatures and pressures) are being conducted. Enrichment cultures with samples from several subsurface environments (e.g. shale and coal deposits, gas reservoirs, geothermal fluids) have been set up using a variety of carbon sources, including hydrocarbons and typical frac chemicals. Classical microbiological and molecular analysis are used to determine changes in the microbial abundance, community structure and function after the exposure to different single frac chemicals, "artificial" frac fluids or production waters. On the other hand, potential transformation reactions of frac or geogenic chemicals by subsurface microbiota and their lifetime are investigated. In our "fracking simulation" experiments, an increasing number of hydrocarbon-degrading or halophilic microorganisms is to be expected after exposure of subsurface communities to artificial production waters. Whereas the introduction of freshwater and of easily biodegradable substrates might favor the proliferation of fast-growing generalistic heterotrophs in shale-associated communities. Nevertheless toxicity of some of the frac components cannot be excluded.

Increased precipitation accelerates soil organic matter turnover associated with microbial community composition in topsoil of alpine grassland on the eastern Tibetan Plateau.

PubMed

Han, Conghai; Wang, Zongli; Si, Guicai; Lei, Tianzhu; Yuan, Yanli; Zhang, Gengxin

2017-10-01

Large quantities of carbon are stored in alpine grassland of the Tibetan Plateau, which is extremely sensitive to climate change. However, it remains unclear whether soil organic matter (SOM) in different layers responds to climate change analogously, and whether microbial communities play vital roles in SOM turnover of topsoil. In this study we measured and collected SOM turnover by the 14 C method in alpine grassland to test climatic effects on SOM turnover in soil profiles. Edaphic properties and microbial communities in the northwestern Qinghai Lake were investigated to explore microbial influence on SOM turnover. SOM turnover in surface soil (0-10 cm) was more sensitive to precipitation than that in subsurface layers (10-40 cm). Precipitation also imposed stronger effects on the composition of microbial communities in the surface layer than that in deeper soil. At the 5-10 cm depth, the SOM turnover rate was positively associated with the bacteria/fungi biomass ratio and the relative abundance of Acidobacteria, both of which are related to precipitation. Partial correlation analysis suggested that increased precipitation could accelerate the SOM turnover rate in topsoil by structuring soil microbial communities. Conversely, carbon stored in deep soil would be barely affected by climate change. Our results provide valuable insights into the dynamics and storage of SOM in alpine grasslands under future climate scenarios.

Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stegen, James C.; Konopka, Allan; McKinely, Jim

Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, diversity, and community composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial diversity—the number ofmore » microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.« less

Pathways for abiotic organic synthesis at submarine hydrothermal fields.

PubMed

McDermott, Jill M; Seewald, Jeffrey S; German, Christopher R; Sylva, Sean P

2015-06-23

Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H2-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH4 and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H2 generation during active serpentinization. Rather, our results indicate that CH4 found in vent fluids is formed in H2-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO2 reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond.

Pathways for abiotic organic synthesis at submarine hydrothermal fields

PubMed Central

McDermott, Jill M.; Seewald, Jeffrey S.; German, Christopher R.; Sylva, Sean P.

2015-01-01

Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H2-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH4 and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H2 generation during active serpentinization. Rather, our results indicate that CH4 found in vent fluids is formed in H2-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO2 reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond. PMID:26056279

Microbial Biogeography on the Legacies of Historical Events in the Arctic Subsurface Sediments

NASA Astrophysics Data System (ADS)

Han, Dukki; Nam, Seung-Il; Hur, Hor-Gil

2017-04-01

The Arctic marine environment consists of various microbial habitats. The niche preference of microbial assemblages in the Arctic Ocean has been surveyed with the modern environmental change by oceanographic traits such as sea-ice dynamics, current circulation, and sedimentation. The North Pacific inflow from the shallow and narrow Bering Strait is highly susceptible to sea-level fluctuations, and thus the water mass exchange mediated by the history of sea-ice between the North Pacific and the Chukchi Sea in the Arctic Ocean. Over geological timescale, the climate change may provide putative evidences for ecological niche for the Arctic microbial assemblages as well as geological records in response to the paleoclimate change. In the present study, the multidisciplinary approach, based on microbiology, geology, and geochemistry, was applied to survey the microbial assemblages in the Arctic subsurface sediments and help further integrate the microbial biogeography and biogeochemical patterns in the Arctic subsurface biosphere. Our results describe microbial assemblages with high-resolution paleoceanographic records in the Chukchi Sea sediment core (ARA02B/01A-GC; 5.4 mbsf) to show the processes that drive microbial biogeographic patterns in the Arctic subsurface sediments. We found microbial habitat preferences closely linked to Holocene paleoclimate records as well as geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. Especially, the vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota in the ARA02B/01A-GC consistent with the patterns of the known global SMTZs and Holocene sedimentary records, suggesting that in-depth microbiological profiles integrated with geological records may be indirectly useful for reconstructing Arctic paleoclimate changes. In the earliest phase of Mid Holocene in the ARA02B/01A-GC with concentrated crenarchaeol (a unique biomarker for Marine Group I Thaumarchaea), the most abundant archaeal population was Marine Group II Euryarchaeota rather than Marine Group I Thaumarchaea, suggesting that the interpretation of archaeal tetraether lipids in subsurface sediments needs careful consideration for paleoceanography. In conclusion, our findings have important implications for the availability of microbial biogeography in the sedimentary record. The present study offers a deeper understanding of the legacies of historical events during the Holocene and implies that the survey of microbial biogeography may be an appropriate tool to monitor potential effects from the climate change in the Arctic Ocean.

Changes in Root Decomposition Rates Across Soil Depths

NASA Astrophysics Data System (ADS)

Hicks Pries, C.; Porras, R. C.; Castanha, C.; Torn, M. S.

2016-12-01

Over half of global soil organic carbon (SOC) is stored in subsurface soils (>30 cm). Turnover times of soil organic carbon (SOC) increases with depth as evidenced by radiocarbon ages of 1,000 to more than 10,000 years in many deep soil horizons but the reasons for this increase are unclear. Many factors that potentially control SOC decomposition change with depth such as increased protection of SOC in aggregates or organo-mineral complexes and increased spatial heterogeneity of SOC "hotspots" like roots, which limit the accessibility of SOC to microbes. Lower concentrations of organic matter at depth may inhibit microbial activity due to energy limitation, and the microbial community itself changes with depth. To investigate how SOC decomposition differs with depth, we inserted a 13C-labeled fine root substrate into three depths (15, 50, and 90 cm) in a coniferous forest Alfisol and measured the root carbon remaining in particulate (>2 mm), bulk (< 2mm), free light, and mineral soil fractions over 2.5 years. We also characterized how the microbial community and SOC changed with depth. Initial rates of decomposition were unaffected by soil depth—50% of root carbon was lost from all depths within the first year. However, after 2.5 years, decomposition rates were affected by soil depth with only 15% of the root carbon remaining at 15 cm while 35% remained at 90 cm. Microbial communities, based on phospholipid fatty acid analysis, changed with depth—fungal biomarkers decreased whereas actinomycetes biomarkers increased. However, the preferences of different microbial groups for the 13C-labeled root carbon were consistent with depth. In contrast, the amount of mineral-associated SOC did not change with depth. Thus, decreased decomposition rates in this deep soil are not due to mineral associations limiting SOC availability, but may instead be due to changes in microbial communities, particularly in the microbes needed to carry out the later stages of root decomposition.

Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction

PubMed Central

Liang, Yuting; Van Nostrand, Joy D.; N′Guessan, Lucie A.; Peacock, Aaron D.; Deng, Ye; Long, Philip E.; Resch, C. Tom; Wu, Liyou; He, Zhili; Li, Guanghe; Hazen, Terry C.; Lovley, Derek R.

2012-01-01

To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation. PMID:22327592

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

PubMed Central

Oni, Oluwatobi E.; Schmidt, Frauke; Miyatake, Tetsuro; Kasten, Sabine; Witt, Matthias; Hinrichs, Kai-Uwe; Friedrich, Michael W.

2015-01-01

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30–530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments. PMID:26635758

Novel applications for biogeophysics: Prospects for detecting key subseafloor geomicrobiological processes or habitats

NASA Astrophysics Data System (ADS)

Colwell, F. S.; Ntarlagiannis, D.

2007-05-01

The new subdiscipline of biogeophysics has focused mostly on the geophysical signatures of microbial processes in contaminated subsurface environments usually undergoing remediation. However, the use of biogeophysics to examine the biogeochemistry of marine sediments has not yet been well-integrated into conceptual models that describe subseafloor processes. Current examples of geophysical measurements that have been used to detect geomicrobiological processes or infer their location in the seafloor include sound surveillance system (SOSUS)-derived data that detect seafloor eruptive events, deep and shallow cross-sectional seismic surveys that determine the presence of hydraulically conductive zones or gas-bearing sediments (e.g., bottom-simulating reflectors or bubble-rich strata), and thermal profiles. One possible area for innovative biogeophysical characterization of the seafloor involves determining the depth of the sulfate-methane interface (SMI) in locations where sulfate diffuses from the seawater and methane emanates from subsurface strata. The SMI demarcates a stratum where microbially-driven anaerobic methane oxidation (AMO) is dependent upon methane as an electron donor and sulfate as an electron acceptor. AMO is carried out by a recently defined, unique consortium of microbes that metabolically temper the flux of methane into the overlying seawater. The depth of the SMI is, respectively, shallow or deep according to whether a high or low rate of methane flux occurs from the deep sediments. Presently, the SMI can only be determined by direct measurements of methane and sulfate concentrations in the interstitial waters or by molecular biological techniques that target the microbes responsible for creating the SMI. Both methods require collection and considerable analysis of sediment samples. Therefore, detection of the SMI by non-destructive methods would be advantageous. As a key biogeochemical threshold in marine sediments, the depth of the SMI defines methane charge in marine sediments, whether it is from dissolved methane or from methane hydrates. As such, a biogeophysical strategy for determining SMI depth would represent an important contribution to assessing methane charge with respect to climate change, sediment stability, or potential energy resources.

Bacteriophage lytic to Desulfovibrio aespoeensis isolated from deep groundwater.

PubMed

Eydal, Hallgerd S C; Jägevall, Sara; Hermansson, Malte; Pedersen, Karsten

2009-10-01

Viruses were earlier found to be 10-fold more abundant than prokaryotes in deep granitic groundwater at the Aspö Hard Rock Laboratory (HRL). Using a most probable number (MPN) method, 8-30 000 cells of sulphate-reducing bacteria per ml were found in groundwater from seven boreholes at the Aspö HRL. The content of lytic phages infecting the indigenous bacterium Desulfovibrio aespoeensis in Aspö groundwater was analysed using the MPN technique for phages. In four of 10 boreholes, 0.2-80 phages per ml were found at depths of 342-450 m. Isolates of lytic phages were made from five cultures. Using transmission electron microscopy, these were characterized and found to be in the Podoviridae morphology group. The isolated phages were further analysed regarding host range and were found not to infect five other species of Desulfovibrio or 10 Desulfovibrio isolates with up to 99.9% 16S rRNA gene sequence identity to D. aespoeensis. To further analyse phage-host interactions, using a direct count method, growth of the phages and their host was followed in batch cultures, and the viral burst size was calculated to be approximately 170 phages per lytic event, after a latent period of approximately 70 h. When surviving cells from infected D. aespoeensis batch cultures were inoculated into new cultures and reinfected, immunity to the phages was found. The parasite-prey system found implies that viruses are important for microbial ecosystem diversity and activity, and for microbial numbers in deep subsurface groundwater.

Uranium Biomineralization By Natural Microbial Phosphatase Activities in the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taillefert, Martial

This project investigated the geochemical and microbial processes associated with the biomineralization of radionuclides in subsurface soils. During this study, it was determined that microbial communities from the Oak Ridge Field Research subsurface are able to express phosphatase activities that hydrolyze exogenous organophosphate compounds and result in the non-reductive bioimmobilization of U(VI) phosphate minerals in both aerobic and anaerobic conditions. The changes of the microbial community structure associated with the biomineralization of U(VI) was determined to identify the main organisms involved in the biomineralization process, and the complete genome of two isolates was sequenced. In addition, it was determined thatmore » both phytate, the main source of natural organophosphate compounds in natural environments, and polyphosphate accumulated in cells could also be hydrolyzed by native microbial population to liberate enough orthophosphate and precipitate uranium phosphate minerals. Finally, the minerals produced during this process are stable in low pH conditions or environments where the production of dissolved inorganic carbon is moderate. These findings suggest that the biomineralization of U(VI) phosphate minerals is an attractive bioremediation strategy to uranium bioreduction in low pH uranium-contaminated environments. These efforts support the goals of the SBR long-term performance measure by providing key information on "biological processes influencing the form and mobility of DOE contaminants in the subsurface".« less

Characterisation of microbial biocoenosis in vertical subsurface flow constructed wetlands.

PubMed

Tietz, Alexandra; Kirschner, Alexander; Langergraber, Günter; Sleytr, Kirsten; Haberl, Raimund

2007-07-15

In this study a quantitative description of the microbial biocoenosis in subsurface vertical flow constructed wetlands fed with municipal wastewater was carried out. Three different methods (substrate induced respiration, ATP measurement and fumigation-extraction) were applied to measure the microbial biomass at different depths of planted and unplanted systems. Additionally, bacterial biomass was determined by epifluorescence microscopy and productivity was measured via (14)C leucine incorporation into bacterial biomass. All methods showed that >50% of microbial biomass and bacterial activity could be found in the first cm and about 95% in the first 10 cm of the filter layer. Bacterial biomass in the first 10 cm of the filter body accounted only for 16-19% of the total microbial biomass. Whether fungi or methodical uncertainties are mainly responsible for the difference between microbial and bacterial biomass remains to be examined. A comparison between the purification performance of planted and unplanted pilot-scale subsurface vertical flow constructed wetlands (PSCWs) showed no significant difference with the exception of the reduction of enterococci. The microbial biomass in all depths of the filter body was also not different in planted and unplanted systems. Compared with data from soils the microbial biomass in the PSCWs was high, although the specific surface area of the used sandy filter material available for biofilm growth was lower, especially in the beginning of the set-up of the PSCWs, due to missing clay and silt fraction.

Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobecky, Patricia A; Taillefert, Martial

This final technical report describes results and findings from a research project to examine the role of microbial phosphohydrolase enzymes in naturally occurring subsurface microorganisms for the purpose of promoting the immobilization of the radionuclide uranium through the production of insoluble uranium phosphate minerals. The research project investigated the microbial mechanisms and the physical and chemical processes promoting uranium biomineralization and sequestration in oxygenated subsurface soils. Uranium biomineralization under aerobic conditions can provide a secondary biobarrier strategy to immobilize radionuclides should the metal precipitates formed by microbial dissimilatory mechanisms remobilize due to a change in redox state.

Biofilm-induced calcium carbonate precipitation: application in the subsurface

NASA Astrophysics Data System (ADS)

Phillips, A. J.; Eldring, J.; Lauchnor, E.; Hiebert, R.; Gerlach, R.; Mitchell, A. C.; Esposito, R.; Cunningham, A. B.; Spangler, L.

2012-12-01

We have investigated mitigation strategies for sealing high permeability regions, like fractures, in the subsurface. This technology has the potential to, for example, improve the long-term security of geologically-stored carbon dioxide (CO2) by sealing fractures in cap rocks or to mitigate leakage pathways to prevent contamination of overlying aquifers from hydraulic fracturing fluids. Sealing technologies using low-viscosity fluids are advantageous since they potentially reduce the necessary injection pressures and increase the radius of influence around injection wells. In this technology, aqueous solutions and suspensions are used to promote microbially-induced mineral precipitation which can be applied in subsurface environments. To this end, a strategy was developed to twice seal a hydraulically fractured, 74 cm (2.4') diameter Boyles Sandstone core, collected in North-Central Alabama, with biofilm-induced calcium carbonate (CaCO3) precipitates under ambient pressures. Sporosarcina pasteurii biofilms were established and calcium and urea containing reagents were injected to promote saturation conditions favorable for CaCO3 precipitation followed by growth reagents to resuscitate the biofilm's ureolytic activity. Then, in order to evaluate this process at relevant deep subsurface pressures, a novel high pressure test vessel was developed to house the 74 cm diameter core under pressures as high as 96 bar (1,400 psi). After determining that no impact to the fracture permeability occurred due to increasing overburden pressure, the fractured core was sealed under subsurface relevant pressures relating to 457 meters (1,500 feet) below ground surface (44 bar (650 psi) overburden pressure). After fracture sealing under both ambient and subsurface relevant pressure conditions, the sandstone core withstood three times higher well bore pressure than during the initial fracturing event, which occurred prior to biofilm-induced CaCO3 mineralization. These studies suggest biofilm-induced CaCO3 precipitation technologies may potentially seal and strengthen high permeability regions or fractures (either natural or induced) in the subsurface. Novel high pressure test vessel to investigate biogeochemical processes under relevant subsurface scales and pressures.

Ecogenomic characterization of a marine microorganism belonging to a Firmicutes lineage that is widespread in both terrestrial and oceanic subsurface environments

NASA Astrophysics Data System (ADS)

Jungbluth, S.; Glavina del Rio, T.; Tringe, S. G.; Stepanauskas, R.; Rappe, M. S.

2015-12-01

Large-volumes of basalt-hosted fluids from the sediment-covered subseafloor were collected in July 2011 from a horizon extending 29-117 meters below the sediment-rock interface at borehole 1362B, as well as from a deep horizon extending 193-292 meters below the sediment-rock interface at borehole 1362A, which are two of the latest generation of borehole observatories on the Juan de Fuca Ridge flank in the Northeast Pacific Ocean. Environmental DNA was sequenced from one fluid sample collected from each borehole, and a genomic bin related to the terrestrial Candidatus Desulforudis audaxviator lineage within the Firmicutes phylum of bacteria was identified. The near-complete bacterial genome, herein named Candidatus Desulfopertinax inferamarinus, is composed of six scaffolds totaling 1.78 Mbp in length. Despite vast differences in geography and environment of origin, phylogenomic analysis indicate that D. inferamarinus and D. audaxviator form a monophyletic clade to the exclusion of all other sequenced genomes. Similar to its terrestrial relative, the draft genome of the marine D. inferamarinus revealed a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that is capable of synthesizing all amino acids and fixing inorganic carbon via the Wood-Ljungdahl pathway. Unlike the terrestrial clade, relatively few integrases and transposases were identified. The marine genome described here provides evidence that a life-style adapted to the isolated deep subsurface environment is a general feature of the broader, globally-distributed Desulforudis/Desulfopertinax lineage and provides insight into the adaptations required for microbial life in the marine versus terrestrial deep biospheres.

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological measurements

NASA Astrophysics Data System (ADS)

Bochet, O.; Dufresne, A.; Pédrot, M.; Chatton, E.; Labasque, T.; Ben Maamar, S.; Burté, L.; de la Bernardie, J.; Guihéneuf, N.; Lavenant, N.; Petton, C.; Bour, O.; Aquilina, L.; Le Borgne, T.

2015-12-01

Biofilms play a major role in controlling the fluxes and reactivity of chemical species transported in hydro-logical systems. Micro-organisms require both electron donors and electron acceptors for cellular growth, proliferation and maintenance of their metabolic functions. The mechanisms controlling these reactions derive from the interactions occurring at the micro-scale that depend on mineral compositions, the biota of subsurface environment, but also fluid mixing, which determines the local concentrations of nutriments, electron donors and electron acceptors. Hence, mixing zones between oxygen and nutriment rich shallow groundwater and mineralized deep groundwater are often considered as potential hotspots of microbial activity, although relatively few field data document flow distributions, transport properties, chemical gradients and micro-organisms distributions across these mixing interfaces. Here we investigate the origin of a localized biofilm development observed in the fractured granite aquifer at the Ploemeur observatory (H+ network hplus.ore.fr).This biofilm composed of ferro-oxidizing bacteria is observed in an 130m deep artesian well. Borehole video logs show an important colonization of the well by the biofilm in the shallower part (0 to 60m), while it is inexistent in the deeper part (60 to 130m). As flow is localized in a few deep and shallow fractures, we presume that the spatial distribution of biofilm is controlled by mixing between shallow and deep groundwater. To verify this hypothesis we conducted a field campaign with joint characterization of the flow and chemical composition of water flowing from the different fractures, as well as the microbiological composition of the biofilm at different depth, using pyrosequencing techniques. We will discuss in this presentation the results of this interdisciplinary dataset and their implications for the occurrence of hotspots of microbiological activity in the subsurface.

Crude oil treatment leads to shift of bacterial communities in soils from the deep active layer and upper permafrost along the China-Russia Crude Oil Pipeline route.

PubMed

Yang, Sizhong; Wen, Xi; Zhao, Liang; Shi, Yulan; Jin, Huijun

2014-01-01

The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils.

Crude Oil Treatment Leads to Shift of Bacterial Communities in Soils from the Deep Active Layer and Upper Permafrost along the China-Russia Crude Oil Pipeline Route

PubMed Central

Yang, Sizhong; Wen, Xi; Zhao, Liang; Shi, Yulan; Jin, Huijun

2014-01-01

The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils. PMID:24794099

Cave speleothems as repositories of microbial biosignatures

NASA Astrophysics Data System (ADS)

Miller, Ana Z.; Jurado, Valme; Pereira, Manuel F. C.; Fernández, Octavio; Calaforra, José M.; Dionísio, Amélia; Saiz-Jimenez, Cesareo

2015-04-01

The need to better understand the biodiversity, origins of life on Earth and on other planets, and the wide applications of the microbe-mineral interactions have led to a rapid expansion of interest in subsurface environments. Recently reported results indicated signs of an early wet Mars and rather recent volcanic activity which suggest that Mars's subsurface can house organic molecules or traces of microbial life, making the search for microbial life on Earth's subsurface even more compelling. Caves on Earth are windows into the subsurface that harbor a wide variety of mineral-utilizing microorganisms, which may contribute to the formation of biominerals and unusual microstructures recognized as biosignatures. These environments contain a wide variety of redox interfaces and stable physicochemical conditions, which enhance secondary mineral precipitation and microbial growth under limited organic nutrient inputs. Enigmatic microorganisms and unusual mineral features have been found associated with secondary mineral deposits or speleothems in limestone caves and lava tubes. In this study, Field Emission Scanning Electron Microscopy (FESEM) and Energy Dispersive X-ray spectroscopy (EDS) analyses were conducted on cave speleothem samples to assess microbe-mineral interactions, evaluate biogenicity, as well as to describe unusual mineral formations and microbial features. Microbial mats, extracellular polymeric substances, tubular empty sheaths, mineralized cells, filamentous fabrics, as well as "cell-sized" etch pits or microborings produced by bacterial cells were observed on minerals. These features evidence microbe-mineral interactions and may represent mineralogical signatures of life. We can thus consider that caves on Earth are plausible repositories of terrestrial biosignatures where we can look for microbial signatures. Acknowledgments: AZM acknowledges the support from the Marie Curie Intra-European Fellowship within the 7th European Community Framework Programme (PIEF-GA-2012-328689- DECAVE). The authors acknowledge the Spanish Ministry of Economy and Competitiveness (project CGL2013-41674-P) for financial support.

In-Well Sediment Incubators to Evaluate Microbial Community Stability and Dynamics following Bioimmobilization of Uranium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldwin, Brett R.; Peacock, Aaron D.; Gan, M.

2009-09-23

An in-situ incubation device (ISI) was developed in order to investigate the stability and dynamics of sediment associated microbial communities to prevailing subsurface oxidizing or reducing conditions. Here we describe the use of these devices at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site. During the 7 month deployment oxidized Rifle aquifer background sediments (RABS) were deployed in previously biostimulated wells under iron reducing conditions, cell densities of known iron reducing bacteria including Geobacteraceae increased significantly showing the microbial community response to local subsurface conditions. PLFA profiles of RABS following in situ deployment were strikingly similar to thosemore » of adjacent sediment cores suggesting ISI results could be extrapolated to the native material of the test plots. Results for ISI deployed reduced sediments showed only slight changes in community composition and pointed toward the ability of the ISIs to monitor microbial community stability and response to subsurface conditions.« less

Monitoring microbial growth and activity using spectral induced polarization and low-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Zhang, Chi; Keating, Kristina; Revil, Andre

2015-04-01

Microbes and microbial activities in the Earth's subsurface play a significant role in shaping subsurface environments and are involved in environmental applications such as remediation of contaminants in groundwater and oil fields biodegradation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface. It is critical to monitor and determine the fate and transportation of microorganisms in the subsurface during such applications. Recent geophysical studies demonstrate the potential of two innovative techniques, spectral induced polarization (SIP) and low-field nuclear magnetic resonance (NMR), for monitoring microbial growth and activities in porous media. The SIP measures complex dielectric properties of porous media at low frequencies of exciting electric field, and NMR studies the porous structure of geologic media and characterizes fluids subsurface. In this laboratory study, we examined both SIP and NMR responses from bacterial growth suspension as well as suspension mixed with silica sands. We focus on the direct contribution of microbes to the SIP and NMR signals in the absence of biofilm formation or biomineralization. We used Zymomonas mobilis and Shewanella oneidensis (MR-1) for SIP and NMR measurements, respectively. The SIP measurements were collected over the frequency range of 0.1 - 1 kHz on Z. mobilis growth suspension and suspension saturated sands at different cell densities. SIP data show two distinct peaks in imaginary conductivity spectra, and both imaginary and real conductivities increased as microbial density increased. NMR data were collected using both CPMG pulse sequence and D-T2 mapping to determine the T2-distribution and diffusion properties on S. oneidensis suspension, pellets (live and dead), and suspension mixed with silica sands. NMR data show a decrease in the T2-distribution in S. oneidensis suspension saturated sands as microbial density increase. A clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets was also observed. These results will provide a basis for understanding the effect of microbes within geologic media on SIP and low-field NMR measurements. This research suggests that both SIP and NMR have the potential to monitor microbial growth and activities in the subsurface and could provide spatiotemporal variations in bacterial abundance in porous media.

Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate.

PubMed

Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge M; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2016-01-01

CO2 sequestration in deep-subsurface formations including oil reservoirs is a potential measure to reduce the CO2 concentration in the atmosphere. However, the fate of the CO2 and the ecological influences in carbon dioxide capture and storage (CDCS) facilities is not understood clearly. In the current study, the fate of CO2 (in bicarbonate form; 0∼90 mM) with 10 mM of formate as electron donor and carbon source was investigated with high-temperature production water from oilfield in China. The isotope data showed that bicarbonate could be reduced to methane by methanogens and major pathway of methanogenesis could be syntrophic formate oxidation coupled with CO2 reduction and formate methanogenesis under the anaerobic conditions. The bicarbonate addition induced the shift of microbial community. Addition of bicarbonate and formate was associated with a decrease of Methanosarcinales, but promotion of Methanobacteriales in all treatments. Thermodesulfovibrio was the major group in all the samples and Thermacetogenium dominated in the high bicarbonate treatments. The results indicated that CO2 from CDCS could be transformed to methane and the possibility of microbial CO2 conversion for enhanced microbial energy recovery in oil reservoirs.

Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate

PubMed Central

Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge M.; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2016-01-01

CO2 sequestration in deep-subsurface formations including oil reservoirs is a potential measure to reduce the CO2 concentration in the atmosphere. However, the fate of the CO2 and the ecological influences in carbon dioxide capture and storage (CDCS) facilities is not understood clearly. In the current study, the fate of CO2 (in bicarbonate form; 0∼90 mM) with 10 mM of formate as electron donor and carbon source was investigated with high-temperature production water from oilfield in China. The isotope data showed that bicarbonate could be reduced to methane by methanogens and major pathway of methanogenesis could be syntrophic formate oxidation coupled with CO2 reduction and formate methanogenesis under the anaerobic conditions. The bicarbonate addition induced the shift of microbial community. Addition of bicarbonate and formate was associated with a decrease of Methanosarcinales, but promotion of Methanobacteriales in all treatments. Thermodesulfovibrio was the major group in all the samples and Thermacetogenium dominated in the high bicarbonate treatments. The results indicated that CO2 from CDCS could be transformed to methane and the possibility of microbial CO2 conversion for enhanced microbial energy recovery in oil reservoirs. PMID:27047478

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales.

PubMed

Sierra-Garcia, Isabel Natalia; Dellagnezze, Bruna M; Santos, Viviane P; Chaves B, Michel R; Capilla, Ramsés; Santos Neto, Eugenio V; Gray, Neil; Oliveira, Valeria M

2017-01-01

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

Heterotrophic potential of Atribacteria from deep marine Antarctic sediment

NASA Astrophysics Data System (ADS)

Carr, S. A.; Orcutt, B.; Mandernack, K. W.; Spear, J. R.

2015-12-01

Bacteria belonging to the newly classified candidate phylum "Atribacteria" (formerly referred to as "OP9" and "JS1") are common in anoxic methane-rich sediments. However, the metabolic functions and biogeochemical role of these microorganisms in the subsurface remains unrealized due to the lack of pure culture representatives. This study observed a steady increase of Atribacteria-related sequences with increasing sediment depth throughout the methane-rich zone of the Adélie Basin, Antarctica (according to a 16S rRNA gene survey). To explore the functional potential of Atribacteria in this basin, samples from various depths (14, 25 and 97 meters below seafloor), were subjected to metagenomic sequencing. Additionally, individual cells were separated from frozen, unpreserved sediment for whole genome amplification. The successful isolation and sequencing of a single-amplified Atribacteria genome from these unpreserved sediments demonstrates a future use of single cell techniques with previously collected and frozen sediments. Our resulting single-cell amplified genome, combined with metagenomic interpretations, provides our first insights to the functional potential of Atribacteria in deep subsurface settings. As observed for non-marine Atribacteria, genomic analyses suggest a heterotrophic metabolism, with Atribacteria potentially producing fermentation products such as acetate, ethanol and CO2. These products may in turn support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacteria in anoxic methane-rich sediments.

Distribution of microbial biomass and potential for anaerobic respiration in Hanford Site 300 Area subsurface sediment.

PubMed

Lin, Xueju; Kennedy, David; Peacock, Aaron; McKinley, James; Resch, Charles T; Fredrickson, James; Konopka, Allan

2012-02-01

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The nosZ gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most nosZ sequences were affiliated with Ochrobactrum anthropi (97 sequence similarity) or had a nearest neighbor of Achromobacter xylosoxidans (90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the dsrA gene and Geobacteraceae had the highest relative abundance. The majority of dsrA genes detected near the interface were related to Desulfotomaculum spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling.

Distribution of Microbial Biomass and Potential for Anaerobic Respiration in Hanford Site 300 Area Subsurface Sediment

PubMed Central

Lin, Xueju; Kennedy, David; Peacock, Aaron; McKinley, James; Resch, Charles T.; Fredrickson, James

2012-01-01

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The nosZ gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most nosZ sequences were affiliated with Ochrobactrum anthropi (97 sequence similarity) or had a nearest neighbor of Achromobacter xylosoxidans (90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the dsrA gene and Geobacteraceae had the highest relative abundance. The majority of dsrA genes detected near the interface were related to Desulfotomaculum spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling. PMID:22138990

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life

PubMed Central

Sheik, Cody S.; Reese, Brandi Kiel; Twing, Katrina I.; Sylvan, Jason B.; Grim, Sharon L.; Schrenk, Matthew O.; Sogin, Mitchell L.; Colwell, Frederick S.

2018-01-01

Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset. PMID:29780369

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

PubMed

Sheik, Cody S; Reese, Brandi Kiel; Twing, Katrina I; Sylvan, Jason B; Grim, Sharon L; Schrenk, Matthew O; Sogin, Mitchell L; Colwell, Frederick S

2018-01-01

Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium , Aquabacterium , Ralstonia , and Acinetobacter . While the top five most frequently observed genera were Pseudomonas , Propionibacterium , Acinetobacter , Ralstonia , and Sphingomonas . The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth's deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.

Effects of Jet Fuel Spills on the Microbial Community of Soil †

PubMed Central

Song, Hong-Gyu; Bartha, Richard

1990-01-01

Hydrocarbon residues, microbial numbers, and microbial activity were measured and correlated in loam soil contaminated by jet fuel spills resulting in 50 and 135 mg of hydrocarbon g of soil−1. Contaminated soil was incubated at 27°C either as well-aerated surface soil or as poorly aerated subsurface soil. In the former case, the effects of bioremediation treatment on residues, microbial numbers, and microbial activity were also assessed. Hydrocarbon residues were measured by quantitative gas chromatography. Enumerations included direct counts of metabolically active bacteria, measurement of mycelial length, plate counts of aerobic heterotrophs, and most probable numbers of hydrocarbon degraders. Activity was assessed by fluorescein diacetate (FDA) hydrolysis. Jet fuel disappeared much more rapidly from surface soil than it did from subsurface soil. In surface soil, microbial numbers and mycelial length were increased by 2 to 2.5 orders of magnitude as a result of jet fuel contamination alone and by 3 to 4 orders of magnitude as a result of the combination of jet fuel contamination and bioremediation. FDA hydrolysis was stimulated by jet fuel and bioremediation, but was inhibited by jet fuel alone. The latter was traced to an inhibition of the FDA assay by jet fuel biodegradation products. In subsurface soil, oxygen limitation strongly attenuated microbial responses to jet fuel. An increase in the most probable numbers of hydrocarbon degraders was accompanied by a decline in other aerobic heterotrophs, so that total plate counts changed little. The correlations between hydrocarbon residues, microbial numbers, and microbial activity help in elucidating microbial contributions to jet fuel elimination from soil. PMID:16348138

Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments

PubMed Central

2016-01-01

Sediments within the Okinawa back-arc basin overlay a subsurface hydrothermal network, creating intense temperature gradients with sediment depth and potential limits for microbial diversity. We investigated taxonomic changes across 45 m of recovered core with a temperature gradient of 3°C/m from the dynamic Iheya North Hydrothermal System. The interval transitions sharply from low-temperature marine mud to hydrothermally altered clay at 10 meters below seafloor (mbsf). Here, we present taxonomic results from an analysis of the 16S rRNA gene that support a conceptual model in which common marine subsurface taxa persist into the subsurface, while high temperature adapted archaeal taxa show localized peaks in abundances in the hydrothermal clay horizons. Specifically, the bacterial phylum Chloroflexi accounts for a major proportion of the total microbial community within the upper 10 mbsf, whereas high temperature archaea (Terrestrial Hot Spring Crenarchaeotic Group and methanotrophic archaea) appear in varying local abundances in deeper, hydrothermal clay horizons with higher in situ temperatures (up to 55°C, 15 mbsf). In addition, geochemical evidence suggests that methanotrophy may be occurring in various horizons. There is also relict DNA (i.e., DNA preserved after cell death) that persists in horizons where the conditions suitable for microbial communities have ceased. PMID:28096736

The deep, hot biosphere: Twenty-five years of retrospection.

PubMed

Colman, Daniel R; Poudel, Saroj; Stamps, Blake W; Boyd, Eric S; Spear, John R

2017-07-03

Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a "deep, hot biosphere" in the Earth's crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings. Furthermore, it has become apparent that much of this life is dependent on lithogenically sourced high-energy compounds to sustain productivity. A vast diversity of uncultivated microorganisms has been detected in subsurface environments, and we show that H 2 , CH 4 , and CO feature prominently in many of their predicted metabolisms. Despite 25 years of intense study, key questions remain on life in the deep subsurface, including whether it is endemic and the extent of its involvement in the anaerobic formation and degradation of hydrocarbons. Emergent data from cultivation and next-generation sequencing approaches continue to provide promising new hints to answer these questions. As Gold suggested, and as has become increasingly evident, to better understand the subsurface is critical to further understanding the Earth, life, the evolution of life, and the potential for life elsewhere. To this end, we suggest the need to develop a robust network of interdisciplinary scientists and accessible field sites for long-term monitoring of the Earth's subsurface in the form of a deep subsurface microbiome initiative.

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Booker, Anne E.; Borton, Mikayla A.; Daly, Rebecca A.

ABSTRACT Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance ofHalanaerobiumstrains within thein situmicrobial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by aHalanaerobiumstrain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis ofHalanaerobiumisolate genomes and reconstructed genomes frommore » metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using aHalanaerobiumisolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentativeHalanaerobiumuses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCEAlthough thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as “souring”) is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary.« less

Modern water/rock reactions in Oman hyperalkaline peridotite aquifers and implications for microbial habitability

NASA Astrophysics Data System (ADS)

Miller, Hannah M.; Matter, Jürg M.; Kelemen, Peter; Ellison, Eric T.; Conrad, Mark E.; Fierer, Noah; Ruchala, Tyler; Tominaga, Masako; Templeton, Alexis S.

2016-04-01

The Samail ophiolite in Oman is undergoing modern hydration and carbonation of peridotite and may host a deep subsurface biosphere. Previous investigations of hyperalkaline fluids in Oman have focused on fluids released at surface seeps, which quickly lose their reducing character and precipitate carbonates upon contact with the O2/CO2-rich atmosphere. In this work, geochemical analysis of rocks and fluids from the subsurface provides new insights into the operative reactions in serpentinizing aquifers. Serpentinite rock and hyperalkaline fluids (pH > 10), which exhibit millimolar concentrations of Ca2+, H2 and CH4, as well as variable sulfate and nitrate, were accessed from wells situated in mantle peridotite near Ibra and studied to investigate their aqueous geochemistry, gas concentrations, isotopic signatures, mineralogy, Fe speciation and microbial community composition. The bulk mineralogy of drill cuttings is dominated by olivine, pyroxene, brucite, serpentine and magnetite. At depth, Fe-bearing brucite is commonly intermixed with serpentine, whereas near the surface, olivine and brucite are lost and increased magnetite and serpentine is detected. Micro-Raman spectroscopy reveals at least two distinct generations of serpentine present in drill cuttings recovered from several depths from two wells. Fe K-edge X-ray absorption near-edge spectroscopy (XANES) analysis of the lizardite shows a strong tetrahedral Fe coordination, suggesting a mixture of both Fe(II) and Fe(III) in the serpentine. Magnetite veins are also closely associated with this second generation serpentine, and 2-10 μm magnetite grains overprint all minerals in the drill cuttings. Thus we propose that the dissolved H2 that accumulates in the subsurface hyperalkaline fluids was evolved through low temperature oxidation and hydration of relict olivine, as well as destabilization of pre-existing brucite present in the partially serpentinized dunites and harzburgites. In particular, we hypothesize that Fe-bearing brucite is currently reacting with dissolved silica in the aquifer fluids to generate late-stage magnetite, additional serpentine and dissolved H2. Dissolved CH4 in the fluids exhibits the most isotopically heavy carbon in CH4 reported in the literature thus far. The CH4 may have formed through abiotic reduction of dissolved CO2 or through biogenic pathways under extreme carbon limitation. The methane isotopic composition may have also been modified by significant methane oxidation. 16S rRNA sequencing of DNA recovered from filtered hyperalkaline well fluids reveals an abundance of Meiothermus, Thermodesulfovibrionaceae (sulfate-reducers) and Clostridia (fermenters). The fluids also contain candidate phyla OP1 and OD1, as well as Methanobacterium (methanogen) and Methylococcus sp. (methanotroph). The composition of these microbial communities suggests that low-temperature hydrogen and methane generation, coupled with the presence of electron acceptors such as nitrate and sulfate, sustains subsurface microbial life within the Oman ophiolite.

The Search for Sustainable Subsurface Habitats on Mars, and the Sampling of Impact Ejecta

NASA Astrophysics Data System (ADS)

Ivarsson, Magnus; Lindgren, Paula

2010-07-01

On Earth, the deep subsurface biosphere of both the oceanic and the continental crust is well known for surviving harsh conditions and environments characterized by high temperatures, high pressures, extreme pHs, and the absence of sunlight. The microorganisms of the terrestrial deep biosphere have an excellent capacity for adapting to changing geochemistry, as the alteration of the crust proceeds and the conditions of their habitats slowly change. Despite an almost complete isolation from surface conditions and the surface biosphere, the deep biosphere of the crustal rocks has endured over geologic time. This indicates that the deep biosphere is a self-sufficient system, independent of the global events that occur at the surface, such as impacts, glaciations, sea level fluctuations, and climate changes. With our sustainable terrestrial subsurface biosphere in mind, the subsurface on Mars has often been suggested as the most plausible place to search for fossil Martian life, or even present Martian life. Since the Martian surface is more or less sterile, subsurface settings are the only place on Mars where life could have been sustained over geologic time. To detect a deep biosphere in the Martian basement, drilling is a requirement. However, near future Mars sample return missions are limited by the mission's payload, which excludes heavy drilling equipment and restrict the missions to only dig the topmost meter of the Martian soil. Therefore, the sampling and analysis of Martian impact ejecta has been suggested as a way of accessing the deeper Martian subsurface without using heavy drilling equipment. Impact cratering is a natural geological process capable of excavating and exposing large amounts of rock material from great depths up to the surface. Several studies of terrestrial impact deposits show the preservation of pre-impact biosignatures, such as fossilized organisms and chemical biological markers. Therefore, if the Martian subsurface contains a record of life, it is reasonable to assume that biosignatures derived from the Martian subsurface could also be preserved in the Martian impact ejecta.

Discriminative detection and enumeration of microbial life in marine subsurface sediments.

PubMed

Morono, Yuki; Terada, Takeshi; Masui, Noriaki; Inagaki, Fumio

2009-05-01

Detection and enumeration of microbial life in natural environments provide fundamental information about the extent of the biosphere on Earth. However, it has long been difficult to evaluate the abundance of microbial cells in sedimentary habitats because non-specific binding of fluorescent dye and/or auto-fluorescence from sediment particles strongly hampers the recognition of cell-derived signals. Here, we show a highly efficient and discriminative detection and enumeration technique for microbial cells in sediments using hydrofluoric acid (HF) treatment and automated fluorescent image analysis. Washing of sediment slurries with HF significantly reduced non-biological fluorescent signals such as amorphous silica and enhanced the efficiency of cell detachment from the particles. We found that cell-derived SYBR Green I signals can be distinguished from non-biological backgrounds by dividing green fluorescence (band-pass filter: 528/38 nm (center-wavelength/bandwidth)) by red (617/73 nm) per image. A newly developed automated microscope system could take a wide range of high-resolution image in a short time, and subsequently enumerate the accurate number of cell-derived signals by the calculation of green to red fluorescence signals per image. Using our technique, we evaluated the microbial population in deep marine sediments offshore Peru and Japan down to 365 m below the seafloor, which provided objective digital images as evidence for the quantification of the prevailing microbial life. Our method is hence useful to explore the extent of sub-seafloor life in the future scientific drilling, and moreover widely applicable in the study of microbial ecology.

Radiochemically-supported microbial communities. A potential mechanism for biocolloid production of importance to actinide transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P.; Hamilton-Brehm, Scott D.; Fisher, Jenny C.

The work described here revealed the presence of diverse microbial communities located across 19 subsurface sites at the NNSS/NTTR and nearby locations. Overall, the diversity of microorganisms was high for subsurface habitats and variable between sites. As of this writing, preparations are being made to combine the Illumina sequences and 16S rRNA clone libraries with other non-NNSS/NTTR well sites of Southern Nevada Regional Flow System for a publication manuscript describing our very broad landscape scale survey of subsurface microbial diversity. Isolates DRI-13 and DRI-14 remain to be fully characterized and named in accordance with the conventions established by Bergey's Manualmore » of Systematic Bacteriology. In preparation to be published, these microorganisms will be submitted to the American Type Culture Collection (ATCC) and the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ).It is anticipated that the data resulting from this study in combination with other data sets that will allow us to produce a number of publications that will be impactful to the subsurface microbiology community.« less

In-Situ Contained And Of Volatile Soil Contaminants

DOEpatents

Varvel, Mark Darrell

2005-12-27

The invention relates to a novel approach to containing and removing toxic waste from a subsurface environment. More specifically the present invention relates to a system for containing and removing volatile toxic chemicals from a subsurface environment using differences in surface and subsurface pressures. The present embodiment generally comprises a deep well, a horizontal tube, at least one injection well, at least one extraction well and a means for containing the waste within the waste zone (in-situ barrier). During operation the deep well air at the bottom of well (which is at a high pressure relative to the land surface as well as relative to the air in the contaminated soil) flows upward through the deep well (or deep well tube). This stream of deep well air is directed into the horizontal tube, down through the injection tube(s) (injection well(s)) and into the contaminate plume where it enhances volatization and/or removal of the contaminants.

In-Situ Containment and Extraction of Volatile Soil Contaminants

DOEpatents

Varvel, Mark Darrell

2005-12-27

The invention relates to a novel approach to containing and removing toxic waste from a subsurface environment. More specifically the present invention relates to a system for containing and removing volatile toxic chemicals from a subsurface environment using differences in surface and subsurface pressures. The present embodiment generally comprises a deep well, a horizontal tube, at least one injection well, at least one extraction well and a means for containing the waste within the waste zone (in-situ barrier). During operation the deep well air at the bottom of well (which is at a high pressure relative to the land surface as well as relative to the air in the contaminated soil) flows upward through the deep well (or deep well tube). This stream of deep well air is directed into the horizontal tube, down through the injection tube(s) (injection well(s)) and into the contaminate plume where it enhances volatization and/or removal of the contaminants.

Functional Microbial Diversity Explains Groundwater Chemistry in a Pristine Aquifer

EPA Science Inventory

Microbial communities inhabiting anoxic aquifers catalyze critical biogeochemical reactions in the subsurface, yet little is known about how their community structure correlates with groundwater chemistry. In this study, we described the composition of microbial communities in th...

Finding the best windows: An apparent environmental threshold determines which diffuse flows are dominated by subsurface microbes

NASA Astrophysics Data System (ADS)

Olins, H. C.; Rogers, D.; Scholin, C. A.; Preston, C. J.; Vidoudez, C.; Ussler, W.; Pargett, D.; Jensen, S.; Roman, B.; Birch, J. M.; Girguis, P. R.

2014-12-01

Hydrothermal vents are hotspots of microbial primary productivity often described as "windows into the subsurface biosphere." High temperature vents have received the majority of research attention, but cooler diffuse flows are as, if not more, important a source of heat and chemicals to the overlying ocean. We studied patterns of in situ gene expression and co-registered geochemistry in order to 1) describe the diversity and physiological poise of active microbial communities that span thermal and geochemical gradients from active diffuse flow to background vent field seawater, and 2) determine to what extent seawater or subsurface microbes were active throughout this environment. Analyses of multiple metatranscriptomes from 5 geochemically distinct sites (some from samples preserved in situ) show that proximate diffuse flows showed strikingly different transcription profiles. Specifically, caldera background and some diffuse flows were similar, both dominated by seawater-derived Gammaproteobacteria despite having distinct geochemistries. Intra-field community shows evidence of increased primary productivity throughout the entire vent field and not just at individual diffuse flows. In contrast, a more spatially limited, Epsilonproteobacteria-dominated transcription profile from the most hydrothermally-influenced diffuse flow appeared to be driven by the activity of vent-endemic microbes, likely reflecting subsurface microbial activity. We suggest that the microbial activity within many diffuse flow vents is primarily attributable to seawater derived Gammaproteobacterial sulfur oxidizers, while in certain other flows vent-endemic Epsilonproteobactiera are most active. These data reveal a diversity in microbial activity at diffuse flows that has not previously been recognized, and reshapes our thinking about the relative influence that different microbial communities may have on local processes (such as primary production) and potentially global biogeochemical cycles.

Investigation of North Pond crustal fluids by poised potential methods

NASA Astrophysics Data System (ADS)

Jones, R. M.; Orcutt, B.

2017-12-01

Microbes are present in the deep subsurface but their rates of activity, potential metabolisms and roles in the environment are still largely unknown. The marine deep crustal subsurface accounts for approximately 2.3x1018 m2 of the earth's volume, making this environment potentially significant to earth processes despite low productivity inherent in resource limited conditions. This has implications for geochemical cycling and exploring limits of life, linking to the `follow the energy' approach for defining habitability on earth and further afield. Most resources for life in the marine deep crust originate from rock. One subset of lithotrophic interactions involves direct transfer between electron acceptors and donors embedded in minerals and microbes. In this investigation, poised potential methods such as chronoamperometry were used to investigate mineral-microbe electron transfer interactions in the context of North Pond, a Mid-Atlantic ridge site representative of cool, sediment-covered basalts that make up the majority of the deep marine subsurface. Electrodes were poised at potentials corresponding approximately to particular lithotrophic oxidation reactions to enrich for sub-sections of North Pond deep subsurface fluid communities that were associated with direct electron transfer at these potentials.

The deep, hot biosphere: Twenty-five years of retrospection

PubMed Central

Colman, Daniel R.; Poudel, Saroj; Stamps, Blake W.; Boyd, Eric S.; Spear, John R.

2017-01-01

Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a “deep, hot biosphere” in the Earth’s crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings. Furthermore, it has become apparent that much of this life is dependent on lithogenically sourced high-energy compounds to sustain productivity. A vast diversity of uncultivated microorganisms has been detected in subsurface environments, and we show that H2, CH4, and CO feature prominently in many of their predicted metabolisms. Despite 25 years of intense study, key questions remain on life in the deep subsurface, including whether it is endemic and the extent of its involvement in the anaerobic formation and degradation of hydrocarbons. Emergent data from cultivation and next-generation sequencing approaches continue to provide promising new hints to answer these questions. As Gold suggested, and as has become increasingly evident, to better understand the subsurface is critical to further understanding the Earth, life, the evolution of life, and the potential for life elsewhere. To this end, we suggest the need to develop a robust network of interdisciplinary scientists and accessible field sites for long-term monitoring of the Earth’s subsurface in the form of a deep subsurface microbiome initiative. PMID:28674200

Optical fiber-mediated photosynthesis for enhanced subsurface oxygen delivery.

PubMed

Lanzarini-Lopes, Mariana; Delgado, Anca G; Guo, Yuanming; Dahlen, Paul; Westerhoff, Paul

2018-03-01

Remediation of polluted groundwater often requires oxygen delivery into subsurface to sustain aerobic bacteria. Air sparging or injection of oxygen containing solutions (e.g., hydrogen peroxide) into the subsurface are common. In this study visible light was delivered into the subsurface using radially emitting optical fibers. Phototrophic organisms grew near the optical fiber in a saturated sand column. When applying light in on-off cycles, dissolved oxygen (DO) varied from super saturation levels of >15 mg DO/L in presence of light to under-saturation (<5 mg DO/L) in absence of light. Non-photosynthetic bacteria dominated at longer radial distances from the fiber, presumably supported by soluble microbial products produced by the photosynthetic microorganisms. The dissolved oxygen variations alter redox condition changes in response to light demonstrate the potential to biologically deliver oxygen into the subsurface and support a diverse microbial community. The ability to deliver oxygen and modulate redox conditions on diurnal cycles using solar light may provide a sustainable, long term strategy for increasing dissolved oxygen levels in subsurface environments and maintaining diverse biological communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isolation and Metabolic Characteristics of Previously Uncultured Members of the Order Aquificales in a Subsurface Gold Mine

PubMed Central

Takai, Ken; Hirayama, Hisako; Sakihama, Yuri; Inagaki, Fumio; Yamato, Yu; Horikoshi, Koki

2002-01-01

Culture-dependent and -independent techniques were combined to characterize the physiological properties and the ecological impacts of culture-resistant phylotypes of thermophiles within the order Aquificales from a subsurface hot aquifer of a Japanese gold mine. Thermophilic bacteria phylogenetically associated with previously uncultured phylotypes of Aquificales were successfully isolated. 16S ribosomal DNA clone analysis of the entire microbial DNA assemblage and fluorescence in situ whole-cell hybridization analysis indicated that the isolates dominated the microbial population in the subsurface aquifer. The isolates were facultatively anaerobic, hydrogen- or sulfur/thiosulfate-oxidizing, thermophilic chemolithoautotrophs utilizing molecular oxygen, nitrate, ferric iron, arsenate, selenate, and selenite as electron acceptors. Their versatile energy-generating systems may reflect the geochemical conditions of their habitat in the geothermally active subsurface gold mine. PMID:12039766

High CO2 subsurface environment enriches for novel microbial lineages capable of autotrophic carbon fixation

NASA Astrophysics Data System (ADS)

Probst, A. J.; Jerett, J.; Castelle, C. J.; Thomas, B. C.; Sharon, I.; Brown, C. T.; Anantharaman, K.; Emerson, J. B.; Hernsdorf, A. W.; Amano, Y.; Suzuki, Y.; Tringe, S. G.; Woyke, T.; Banfield, J. F.

2015-12-01

Subsurface environments span the planet but remain little understood from the perspective of the capacity of the resident organisms to fix CO2. Here we investigated the autotrophic capacity of microbial communities in range of a high-CO2 subsurface environments via analysis of 250 near-complete microbial genomes (151 of them from distinct species) that represent the most abundant organisms over a subsurface depth transect. More than one third of the genomes belonged to the so-called candidate phyla radiation (CPR), which have limited metabolic capabilities. Approximately 30% of the community members are autotrophs that comprise 70% of the microbiome with metabolism likely supported by sulfur and nitrogen respiration. Of the carbon fixation pathways, the Calvin Benson Basham Cycle was most common, but the Wood-Ljungdhal pathway was present in the greatest phylogenetic diversity of organisms. Unexpectedly, one organism from a novel phylum sibling to the CPR is predicted to fix carbon by the reverse TCA cycle. The genome of the most abundant organism, an archaeon designated "Candidatus Altiarchaeum hamiconexum", was also found in subsurface samples from other continents including Europe and Asia. The archaeon was proven to be a carbon fixer using a novel reductive acetyl-CoA pathway. These results provide evidence that carbon dioxide is the major carbon source in these environments and suggest that autotrophy in the subsurface represents a substantial carbon dioxide sink affecting the global carbon cycle.

High-pressure hydrogen respiration in hydrothermal vent samples from the deep biosphere

NASA Astrophysics Data System (ADS)

Morgan-Smith, D.; Schrenk, M. O.

2013-12-01

Cultivation of organisms from the deep biosphere has met with many challenges, chief among them the ability to replicate this extreme environment in a laboratory setting. The maintenance of in situ pressure levels, carbon sources, and gas concentrations are important, intertwined factors which may all affect the growth of subsurface microorganisms. Hydrogen in particular is of great importance in hydrothermal systems, but in situ hydrogen concentrations are largely disregarded in attempts to culture from these sites. Using modified Hungate-type culture tubes (Bowles et al. 2011) within pressure-retaining vessels, which allow for the dissolution of higher concentrations of gas than is possible with other culturing methods, we have incubated hydrothermal chimney and hydrothermally-altered rock samples from the Lost City and Mid-Cayman Rise hydrothermal vent fields. Hydrogen concentrations up to 15 mmol/kg have been reported from Lost City (Kelley et al. 2005), but data are not yet available from the recently-discovered Mid-Cayman site, and the elevated concentration of 30 mmol/kg is being used in all incubations. We are using a variety of media types to enrich for various metabolic pathways including iron and sulfur reduction under anoxic or microaerophilic conditions. Incubations are being carried out at atmospheric (0.1 MPa), in situ (9, 23, or 50 MPa, depending on site), and elevated (50 MPa) pressure levels. Microbial cell concentrations, taxonomic diversity, and metabolic activities are being monitored during the course of these experiments. These experiments will provide insight into the relationships between microbial activities, pressure, and gas concentrations typical of deep biosphere environments. Results will inform further culturing studies from both fresh and archived samples. References cited: Bowles, M.W., Samarkin, V.A., Joye, S.B. 2011. Improved measurement of microbial activity in deep-sea sediments at in situ pressure and methane concentration. Limnology and Oceanography Methods 9:499-506 Kelley, D.S., Karson, J.A., Früh-Green, G.L., Yoerger, D.R., Shank, T.M., et al. 2005. A Serpentinite-Hosted Ecosystem: The Lost City Hydrothermal Field. Science 307:1428-1434

The giant cold-water coral mound as a nested microbial/metazoan system: physical, chemical, biological and geological picture (ESF EuroDiversity MiCROSYSTEMS)

NASA Astrophysics Data System (ADS)

Henriet, J. P.; Microsystems Team

2009-04-01

The MiCROSYSTEMS project under the ESF EUROCORES EuroDiversity scheme is a holistic and multi-scale approach in studying microbial diversity and functionality in a nested microbial/metazoan system, which thrives in deep waters: the giant cold-water coral mound. Studies on prolific cold-water coral sites have been carried out from the canyons of the Bay of Biscay to the fjords of the Norwegian margin, while the Pen Duick carbonate mound province off Morocco developed into a joint natural lab for studying in particular the impact of biogeochemical and microbial processes on modern sedimentary diagenesis within the reef sediments, in complement to the studies on I0DP Exp. 307 cores (Challenger Mound, off Ireland). Major outcomes of this research can be summarized as follows. • IODP Exp. 307 on Challenger Mound had revealed a significant prokaryotic community both within and beneath the carbonate mound. MiCROSYSTEMS unveils a remarkable degree of compartmentalization in such community from the seawater, the coral skeleton surface and mucus to the reef sediments. The occurrence of such multiple and distinct microbial compartments associated with cold-water coral ecosystems promotes opportunities for microbial diversity in the deep ocean. • New cases of co-habitation of cold-water corals and giant deep-water oysters were discovered in the Bay of Biscay, which add a new facet of macrofaunal diversity to cold-water coral reef systems. • The discovery of giant, ancient coral graveyards on the Moroccan mounds not only fuels the debate about natural versus anthropogenic mass extinction, but these open frameworks simultaneously invite for the study of bio-erosion and early diagenesis, in particular organo-mineralization, and of the possible role and significance of these thick, solid rubble patches in 3D mound-building and consolidation. • The assessment of the carbonate budget of a modern cold-water coral mound (Challenger Mound) reveals that only 33 to 40 wt % of carbonate is derived from corals and suggests a selective enrichment of the hemipelagic carbonate fraction, compared to adjacent sediment drift deposits. • The detection of allochthonous fluids, in particular brines, in the pore space of the surficial mound sediments on the Pen Duick Escarpment hints towards the presence of salt deposits deep underneath, and simultaneously provides the first direct evidence of advective fluid transfer from the deep, throughout the mound substrate and the full mound height. Potential stratigraphic pathways leading from the deeper basinal realms directly to the mound setting have been imaged in a spectacular way through high-resolution pseudo-3D seismic imaging. Geophysical signatures of free gas accumulations have been detected a few hundreds of meters below the mound base, but low concentrations of methane and the absence of lipid biomarkers from methane-dependent prokaryotes suggest low fluxes of methane-derived carbon and thus very small rates of anaerobic oxidation of methane (AOM) in the immediate mound subsurface. Local changes in the sediment biogeochemistry are most likely dictated by slow diffusive fluid transfer, operating in a heterogeneous way in the subsurface. • Cultivation experiments with sediments from microbially active mound zones have allowed to study microbially induced carbonate precipitation and provide a tool for the interpretation of carbonate mineralogy. The development and operation of a continuous high-pressure bioreactor (100 bars) allows to simulate in an ex situ mode the impact of environmental parameter changes onto the functioning of relevant microbial communities. • The detected influx of sulfate in mound sediments implies that bacterial sulfate reduction can be the dominant anaerobic carbon mineralization process. Groundwater flow modeling suggests that currents impinging on the escarpment and the flanks of an exposed mound can account for a significant influx and transport of sulfate through convective fluid transfer within the mound sediments. Oceanic currents consequently provide not only a major control on the external flux of nutrients to the mound-building communities, but they also potentially drive internal flow in the mound. The extant hydrodynamic climate of the mound setting is documented through long-term lander deployments and CTD stations: the current records reveal a significant tidal and seasonal variability. The past environmental record over the last 400 ka is documented in a most comprehensive sedimentary archive, sampled with long cores at the foot of the Pen Duick Escarpment during the MD169 ‘MiCROSYSTEMS' cruise in July 2008. • MiCROSYSTEMS has significantly contributed to the successful submission of IODP proposal 673-Full, which should (i) document the whole-mound architecture and the mound setting on Pen Duick Escarpment as well as a most comprehensive stratigraphic record on a reference site at the foot of the escarpment, (ii) reveal the full spatial pattern in microbial diversity, activity and functionality throughout the mound and underneath, and (iii) unravel the plumbing system of a mound and the dynamic interaction between advective, convective and diffusive transfers of organic and inorganic compounds, which impact on biogeochemical equilibria, microbial activity and early diagenetic processes.

Marine Subsurface Microbial Communities Across a Hydrothermal Gradient in Okinawa Trough Sediments

NASA Astrophysics Data System (ADS)

Brandt, L. D.; Hser Wah Saw, J.; Ettema, T.; House, C. H.

2015-12-01

IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 meters below sea floor (mbsf). Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 mbsf. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data shows a shift over 15 mbsf from a heterogeneous community of cosmopolitan marine subsurface taxa toward an archaeal-dominated community in the deepest horizons of the predicted biosphere. Notably, the phylum Chloroflexi represents a substantial taxon through most horizons, where it appears to be replaced below 10 mbsf by punctuations of thermophilic and methanotrophic Archaea and Miscellaneous Crenarchaeotic Group abundances. DNA from the aforementioned transition horizons was further analyzed using metagenomic sequencing. Preliminary taxonomic analysis of the metagenomic data agrees well with amplicon data in capturing the shift in relative abundance of Archaea increasing with depth. Additionally, reverse gyrase, a gene found exclusively in hyperthermophilic microorganisms, was recovered only in the metagenome of the deepest horizon. A BLAST search of this protein sequence against the GenBank non-redudnant protein database produced top hits with reverse gyrase from Thermococcus and Pyrococcus, which are known thermophiles. Up until now, thermophiles and hyperthermophiles have been studied in cultured hydrothermal vent fluid samples, or have been identified from 16S rRNA taxonomic analyses. These recovered genes provide direct evidence for a pervasive subsurface hyperthermophilic biosphere in off-axis hydrothermal sediments.

Growth Inhibition and Stimulation of Shewanella oneidensis MR-1 by Surfactants and Calcium Polysulfide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bailey, Kathryn L.; Tilton, Fred A.; Jansik, Danielle P.

2012-06-14

Foam delivery technology (FDT) uses surfactant based foam to immobilize subsurface contaminants in situ. Where traditional approaches are impractical, FDT has the potential to overcome many of the technical challenges facing the remediation of contaminated deep vadose zone environments. However, little is known about the effects these reactive chemicals may have on microorganisms inhabiting the contaminated subsurface. In addition, there are currently no standard assays to assess microbial responses to subsurface remedial treatments while these agents are under development. The objective of this study was to develop a rapid laboratory assay to assess the potential growth inhibition and/or stimulation ofmore » microorganisms following exposure to candidate FDT components. Calcium polysulfide (CPS) and several surfactants (i.e. sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB) and NINOL40-CO) have diverse chemistries and are candidate components of FDT. Shewanella oneidensis MR-1 cultures were exposed to a range of concentrations of these chemicals to determine the minimum bactericidal concentration (MBC) and the growth and viability potential of these components. Concentrations of SDS higher than 700 {micro}M were toxic to S. oneidensis MR-1 growth over the course of four days of exposure. The relative acute toxicity order for these compounds was SDS>>CPS>>NINOL40-CO>SLES-CAPB. Dose dependent growth decreases (20 to 100 mM) were observed in the CAPB and SLES treated cultures and both CPS and NINOL 40-CO were toxic at all concentrations tested (1.45 to 7.25 mM CPS). Both SLES (20 to 100 mM) and SDS at lower concentrations (20 to 500 {micro}M) were stimulatory to S. oneidensis MR-1 indicating a capacity to be used as a carbon source. These studies also identified potentially key component characteristics, such as precipitate formation and oxygen availability, which may prove valuable in assessing the response of subsurface microorganisms. This benchtop system provides a capability to assess adverse microbial-remediation responses and contributes to the development of in situ remedial chemistries before they are deployed in the field.« less

Growth inhibition and stimulation of Shewanella oneidensis MR-1 by surfactants and calcium polysulfide.

PubMed

Bailey, Kathryn L; Tilton, Fred; Jansik, Danielle P; Ergas, Sarina J; Marshall, Matthew J; Miracle, Ann L; Wellman, Dawn M

2012-06-01

Foam delivery technology (FDT) uses surfactant based foam to immobilize subsurface contaminants in situ. Where traditional approaches are impractical, FDT has the potential to overcome many of the technical challenges facing the remediation of contaminated deep vadose zone environments. However, little is known about the effects these reactive chemicals may have on microorganisms inhabiting the contaminated subsurface. In addition, there are currently no standard assays to assess microbial responses to subsurface remedial treatments while these agents are under development. The objective of this study was to develop a rapid laboratory assay to assess the potential growth inhibition and/or stimulation of microorganisms following exposure to candidate FDT components. Calcium polysulfide (CPS) and several surfactants (i.e. sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB) and NINOL40-CO) have diverse chemistries and are candidate components of FDT. Shewanella oneidensis MR-1 cultures were exposed to a range of concentrations of these chemicals to determine the minimum bactericidal concentration (MBC) and the growth and viability potential of these components. Concentrations of SDS higher than 700 μM were toxic to S. oneidensis MR-1 growth over the course of four days of exposure. The relative acute toxicity order for these compounds was SDS > CPS > NINOL 40-CO>SLES≥CAPB. Dose dependent growth decreases (20-100mM) were observed in the CAPB and SLES treated cultures and both CPS and NINOL 40-CO were toxic at all concentrations tested (1.45-7.25 mM CPS). Both SLES (20-100mM) and SDS at lower concentrations (20-500 μM) were stimulatory to S. oneidensis MR-1 indicating a capacity to be used as a carbon source. These studies also identified potentially key component characteristics, such as precipitate formation and oxygen availability, which may prove valuable in assessing the response of subsurface microorganisms. This benchtop system provides a capability to assess adverse microbial-remediation responses and contributes to the development of in situ remedial chemistries before they are deployed in the field. Copyright © 2012 Elsevier Inc. All rights reserved.

Preliminary biological sampling of GT3 and BT1 cores and the microbial community dynamics of existing subsurface wells

NASA Astrophysics Data System (ADS)

Kraus, E. A.; Stamps, B. W.; Rempfert, K. R.; Ellison, E. T.; Nothaft, D. B.; Boyd, E. S.; Templeton, A. S.; Spear, J. R.

2017-12-01

Subsurface microbial life is poorly understood but potentially very important to the search for life on other planets as well as increasing our understanding of Earth's geobiological processes. Fluids and rocks of actively serpentinizing subsurface environments are a recent target of biological study due to their apparent ubiquity across the solar system. Areas of serpentinization can contain high concentrations of molecular hydrogen, H2, that can serve as the dominant fuel source for subsurface microbiota. Working with the Oman Drilling Project, DNA and RNA were extracted from fluids of seven alkaline wells and two rock cores from drill sites GT3 and BT1 within the Samail ophiolite. DNA and cDNA (produced via reverse transcription from the recovered RNA) were sequenced using universal primers to identify microbial life across all three domains. Alkaline subsurface fluids support a microbial community that changes with pH and host-rock type. In peridotite with pH values of >11, wells NSHQ 14 and WAB 71 have high relative abundances of Meiothermus, Methanobacterium, the family Nitrospiraceae, and multiple types of the class Dehalococcoidia. While also hosted in peridotite but at pH 8.5, wells WAB 104 and 105 have a distinct, more diverse microbial community. This increased variance in community make-up is seen in wells that sit near/at the contact of gabbro and peridotite formations as well. Core results indicate both sampled rock types host a very low biomass environment subject to multiple sources of contamination during the drilling process. Suggestions for contaminant reduction, such as having core handlers wear nitrile gloves and flame-sterilizing the outer surfaces of core rounds for biological sampling, would have minimal impact to overall ODP coreflow and maximize the ability to better understand in situ microbiota in this low-biomass serpentinizing subsurface environment. While DNA extraction was successful with gram amounts of crushed rock, much can be done to improve yields and reduce contamination sources for Phase II drilling.

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

PubMed Central

Twing, Katrina I.; Brazelton, William J.; Kubo, Michael D. Y.; Hyer, Alex J.; Cardace, Dawn; Hoehler, Tori M.; McCollom, Tom M.; Schrenk, Matthew O.

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments. PMID:28298908

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

PubMed

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

[Microbes on the edge of global biosphere].

PubMed

Naganuma, T

2000-12-01

The search for life on the edge of global biosphere is a frontier to bridge conventional bio/ecology and exo/astrobiology. This communication reviews the foci of microbiological studies on the inhabitants of the selected "edges", i.e., deep-sea, deep subsurface and Antarctic habitats. The deep-sea is characterized as the no-light (non-photosynthetic) habitat, and the primary production is mostly due to the chemosynthetic autotrophy at the hydrothermal vents and methane-rich seeps. Formation of the chemosynthesis-dependent animal communities in the deep leads to the idea that such communities may be found in "ocean" of the Jovian satellite, Europa. The oxygen minimal layer (OML) in mid-water provides another field of deep-sea research. Modern OML is a relatively thin layer, found between the water depth of 200 and 1000 m, but was much thicker during the periods of oceanic anoxia events (OAEs) in the past. The history of oceanic biosphere is regarded as the cycle of OAE and non-OAE periods, and the remnants of the past OAEs may be seen in the modem OML. Anoxic (no-O2) condition is also characteristic of deep subsurface biosphere. Microorganisms in deep subsurface biosphere exploit every available oxidant, or terminal electron acceptor (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Subsurface of hydrothermal vents, or sub-vent biosphere, may house brine (high salt) habitats and halophilic microorganisms. Some sub-vent halophiles were phylogenetically closely similar to the ones found in the Antarctic habitats which are extremely dry by the liophilizing climate. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, has been a target of "life in extreme environments" and is about to be drill-penetrated for microbiological studies. These 'microbiological platforms' will provide new knowledge about the diversity and potential of the Earth's life and facilitate the capability of astrobiologial exploration.

Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge

PubMed Central

Zhang, Xinxu; Fang, Jing; Bach, Wolfgang; Edwards, Katrina J.; Orcutt, Beth N.; Wang, Fengping

2016-01-01

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement. PMID:27199959

2500 high-quality genomes reveal that the biogeochemical cycles of C, N, S and H are cross-linked by metabolic handoffs in the terrestrial subsurface

NASA Astrophysics Data System (ADS)

Anantharaman, K.; Brown, C. T.; Hug, L. A.; Sharon, I.; Castelle, C. J.; Shelton, A.; Bonet, B.; Probst, A. J.; Thomas, B. C.; Singh, A.; Wilkins, M.; Williams, K. H.; Tringe, S. G.; Beller, H. R.; Brodie, E.; Hubbard, S. S.; Banfield, J. F.

2015-12-01

Microorganisms drive the transformations of carbon compounds in the terrestrial subsurface, a key reservoir of carbon on earth, and impact other linked biogeochemical cycles. Our current knowledge of the microbial ecology in this environment is primarily based on 16S rRNA gene sequences that paint a biased picture of microbial community composition and provide no reliable information on microbial metabolism. Consequently, little is known about the identity and metabolic roles of the uncultivated microbial majority in the subsurface. In turn, this lack of understanding of the microbial processes that impact the turnover of carbon in the subsurface has restricted the scope and ability of biogeochemical models to capture key aspects of the carbon cycle. In this study, we used a culture-independent, genome-resolved metagenomic approach to decipher the metabolic capabilities of microorganisms in an aquifer adjacent to the Colorado River, near Rifle, CO, USA. We sequenced groundwater and sediment samples collected across fifteen different geochemical regimes. Sequence assembly, binning and manual curation resulted in the recovery of 2,542 high-quality genomes, 27 of which are complete. These genomes represent 1,300 non-redundant organisms comprising both abundant and rare community members. Phylogenetic analyses involving ribosomal proteins and 16S rRNA genes revealed the presence of up to 34 new phyla that were hitherto unknown. Less than 11% of all genomes belonged to the 4 most commonly represented phyla that constitute 93% of all currently available genomes. Genome-specific analyses of metabolic potential revealed the co-occurrence of important functional traits such as carbon fixation, nitrogen fixation and use of electron donors and electron acceptors. Finally, we predict that multiple organisms are often required to complete redox pathways through a complex network of metabolic handoffs that extensively cross-link subsurface biogeochemical cycles.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

DOE PAGES

Jungbluth, Sean P.; Glavina del Rio, Tijana; Tringe, Susannah G.; ...

2017-04-06

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “more » Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “ Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Finally, our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.« less

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jungbluth, Sean P.; Glavina del Rio, Tijana; Tringe, Susannah G.

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “more » Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “ Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Finally, our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.« less

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

PubMed Central

Glavina del Rio, Tijana; Tringe, Susannah G.; Stepanauskas, Ramunas

2017-01-01

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments. PMID:28396823

Microbial Growth under Supercritical CO2

PubMed Central

Peet, Kyle C.; Freedman, Adam J. E.; Hernandez, Hector H.; Britto, Vanya; Boreham, Chris; Ajo-Franklin, Jonathan B.

2015-01-01

Growth of microorganisms in environments containing CO2 above its critical point is unexpected due to a combination of deleterious effects, including cytoplasmic acidification and membrane destabilization. Thus, supercritical CO2 (scCO2) is generally regarded as a sterilizing agent. We report isolation of bacteria from three sites targeted for geologic carbon dioxide sequestration (GCS) that are capable of growth in pressurized bioreactors containing scCO2. Analysis of 16S rRNA genes from scCO2 enrichment cultures revealed microbial assemblages of varied complexity, including representatives of the genus Bacillus. Propagation of enrichment cultures under scCO2 headspace led to isolation of six strains corresponding to Bacillus cereus, Bacillus subterraneus, Bacillus amyloliquefaciens, Bacillus safensis, and Bacillus megaterium. Isolates are spore-forming, facultative anaerobes and capable of germination and growth under an scCO2 headspace. In addition to these isolates, several Bacillus type strains grew under scCO2, suggesting that this may be a shared feature of spore-forming Bacillus spp. Our results provide direct evidence of microbial activity at the interface between scCO2 and an aqueous phase. Since microbial activity can influence the key mechanisms for permanent storage of sequestered CO2 (i.e., structural, residual, solubility, and mineral trapping), our work suggests that during GCS microorganisms may grow and catalyze biological reactions that influence the fate and transport of CO2 in the deep subsurface. PMID:25681188

Calculating in situ degradation rates of hydrocarbon compounds in deep waters of the Gulf of Mexico.

PubMed

Thessen, Anne E; North, Elizabeth W

2017-09-15

Biodegradation is an important process for hydrocarbon weathering that influences its fate and transport, yet little is known about in situ biodegradation rates of specific hydrocarbon compounds in the deep ocean. Using data collected in the Gulf of Mexico below 700m during and after the Deepwater Horizon oil spill, we calculated first-order degradation rate constants for 49 hydrocarbons and inferred degradation rate constants for an additional 5 data-deficient hydrocarbons. Resulting calculated (not inferred) half-lives of the hydrocarbons ranged from 0.4 to 36.5days. The fastest degrading hydrocarbons were toluene (k=-1.716), methylcyclohexane (k=-1.538), benzene (k=-1.333), and C1-naphthalene (k=-1.305). The slowest degrading hydrocarbons were the large straight-chain alkanes, C-26 through C-33 (k=-0.0494 through k=-0.007). Ratios of C-18 to phytane supported the hypothesis that the primary means of degradation in the subsurface was microbial biodegradation. These degradation rate constants can be used to improve models describing the fate and transport of hydrocarbons in the event of an accidental deep ocean oil spill. Copyright © 2017 Elsevier Ltd. All rights reserved.

Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobecky, Patricia A.

2015-04-06

In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Areamore » 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.« less

Evidence for Seismogenic Hydrogen Gas, a Potential Microbial Energy Source on Earth and Mars.

PubMed

McMahon, Sean; Parnell, John; Blamey, Nigel J F

2016-09-01

The oxidation of molecular hydrogen (H2) is thought to be a major source of metabolic energy for life in the deep subsurface on Earth, and it could likewise support any extant biosphere on Mars, where stable habitable environments are probably limited to the subsurface. Faulting and fracturing may stimulate the supply of H2 from several sources. We report the H2 content of fluids present in terrestrial rocks formed by brittle fracturing on fault planes (pseudotachylites and cataclasites), along with protolith control samples. The fluids are dominated by water and include H2 at abundances sufficient to support hydrogenotrophic microorganisms, with strong H2 enrichments in the pseudotachylites compared to the controls. Weaker and less consistent H2 enrichments are observed in the cataclasites, which represent less intense seismic friction than the pseudotachylites. The enrichments agree quantitatively with previous experimental measurements of frictionally driven H2 formation during rock fracturing. We find that conservative estimates of current martian global seismicity predict episodic H2 generation by Marsquakes in quantities useful to hydrogenotrophs over a range of scales and recurrence times. On both Earth and Mars, secondary release of H2 may also accompany the breakdown of ancient fault rocks, which are particularly abundant in the pervasively fractured martian crust. This study strengthens the case for the astrobiological investigation of ancient martian fracture systems. Deep biosphere-Faults-Fault rocks-Seismic activity-Hydrogen-Mars. Astrobiology 16, 690-702.

Putting the Deep Biosphere on the Map for Oceanography Courses: Gas Hydrates As a Case Study for the Deep Biosphere

NASA Astrophysics Data System (ADS)

Sikorski, J. J.; Briggs, B. R.

2014-12-01

The ocean is essential for life on our planet. It covers 71% of the Earth's surface, is the source of the water we drink, the air we breathe, and the food we eat. Yet, the exponential growth in human population is putting the ocean and thus life on our planet at risk. However, based on student evaluations from our introductory oceanography course it is clear that our students have deficiencies in ocean literacy that impact their ability to recognize that the ocean and humans are inextricably connected. Furthermore, life present in deep subsurface marine environments is also interconnected to the study of the ocean, yet the deep biosphere is not typically covered in undergraduate oceanography courses. In an effort to improve student ocean literacy we developed an instructional module on the deep biosphere focused on gas hydrate deposits. Specifically, our module utilizes Google Earth and cutting edge research about microbial life in the ocean to support three inquiry-based activities that each explore different facets of gas hydrates (i.e. environmental controls, biologic controls, and societal implications). The relevant nature of the proposed module also makes it possible for instructors of introductory geology courses to modify module components to discuss related topics, such as climate, energy, and geologic hazards. This work, which will be available online as a free download, is a solid contribution toward increasing the available teaching resources focused on the deep biosphere for geoscience educators.

Exploration of a Subsurface Biosphere in a Volcanic Massive Sulfide: Results of the Mars Analog Rio Tinto Drilling Experiment

NASA Astrophysics Data System (ADS)

Stoker, C. R.; Stevens, T.; Amils, R.; Fernandez, D.

2005-12-01

Biological systems on Earth require three key ingredients-- liquid water, an energy source, and a carbon source, that are found in very few extraterrestrial environments. Previous examples of independent subsurface ecosystems have been found only in basalt aquifers. Such lithotrophic microbial ecosystems (LME) have been proposed as models for steps in the early evolution of Earth's biosphere and for potential biospheres on other planets where the surface is uninhabitable, such as Mars and Europa.. The Mars Analog Rio Tinto Experiment (MARTE) has searched in a volcanic massive sulfide deposit in Rio Tinto Spain for a subsurface biosphere capable of living without sunlight or oxygen and found a subsurface ecosystem driven by the weathering of the massive sulfide deposit (VMS) in which the rock matrix provides sufficient resources to support microbial metabolism, including the vigorous production of H2 by water-rock interactions. Microbial production of methane and sulfate occurred in the sulfide orebody and microbial production of methane and hydrogen sulfide continued in an anoxic plume downgradient from the sulfide ore. Organic carbon concentrations in the parent rock were too low to support microbes. The Rio Tinto system thus represents a new type of subsurface ecosystem with strong relevance for exobiological studies. Commercial drilling was used to reach the aquifer system at 100 m depth and conventional laboratory techniques were used to identify and characterize the biosphere. Then, the life search strategy that led to successful identification of this biosphere was applied to the development of a robotic drilling, core handling, inspection, subsampling, and life detection system built on a prototype planetary lander that was deployed in Rio Tinto Spain in September 2005 to test the capability of a robotic drilling system to search for subsurface life. A remote science team directed the simulation and analyzed the data from the MARTE robotic drill. The results of this experiment have important implications for the strategy for searching for life on Mars.

Microbial community stratification controlled by the subseafloor fluid flow and geothermal gradient at the Iheya North hydrothermal field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331).

PubMed

Yanagawa, Katsunori; Breuker, Anja; Schippers, Axel; Nishizawa, Manabu; Ijiri, Akira; Hirai, Miho; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2014-10-01

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the Chloroflexi and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I Thaumarchaeota dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Microbial Community Stratification Controlled by the Subseafloor Fluid Flow and Geothermal Gradient at the Iheya North Hydrothermal Field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331)

PubMed Central

Breuker, Anja; Schippers, Axel; Nishizawa, Manabu; Ijiri, Akira; Hirai, Miho; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2014-01-01

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the Chloroflexi and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I Thaumarchaeota dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments. PMID:25063666

An investigation of the sensitivity of low-field nuclear magnetic resonance to microbial growth and activity

NASA Astrophysics Data System (ADS)

Zhang, C.; Keating, K.

2014-12-01

Microbes and microbial processes play a significant role in shaping subsurface environments and are involved in applications ranging from microbially enhanced oil recovery to soil and groundwater contaminant remediation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface; however, due to the complexity of subsurface systems,it is difficult to monitor the growth of microbes and microbial activity in porous media. The focus of this research is to determine if low-field nuclear magnetic resonance (NMR), a method used in well logging to characterize fluids in hydrocarbon reservoirs or water in aquifers, can be used to directly detect the presence and the growth of microbes in geologic media. In this laboratory study, low-field NMR (2 MHz) relaxation measurements were collected on microbial suspensions with measured densities (i.e. biomasses), microbial pellets (live and dead), and inoculated silica. We focus on the direct contribution of microbes to the NMR signals in the absence of biomineralization. Shewanella oneidensis (MR-1), a facultative metal reducer known to play an important role in subsurface environments, were used as a model organism and were inoculated under aerobic condition. Data were collected using a CPMG pulse sequence, which was to determine the T2-distribution, and using a gradient spin-echo (PGSE) plus CPMG pulse sequence, which was used to encode diffusion properties and determine the effective diffusion-spin-spin relaxation correlation (D-T2) plot. Our data show no obvious change in the T2-distribution as S. oneidensis density varied in suspension, but show a clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets. A decrease in the T2-distribution is observed in the inoculated sand column. These results will provide a basis for understanding the effect of microbes within geologic media on low-field NMR measurements. This research is necessary to determine if NMR measurements can ultimately to be used to monitor microbial growth and activity in oil reservoirs or contaminated aquifers.

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological characterization

NASA Astrophysics Data System (ADS)

Bochet, Olivier; Le Borgne, Tanguy; Pédrot, Mathieu; Labasque, Thierry; Lavenant, Nicolas; Petton, Christophe; Dufresne, Alexis; Ben Maamar, Sarah; Chatton, Eliot; De la Bernardie, Jérôme; Aquilina, Luc

2015-04-01

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological characterization Olivier Bochet1, Tanguy Le Borgne1, Mathieu Pédrot1, Thierry Labasque1, Nicolas Lavenant1, Christophe Petton1, Alexis Dufresne2,Sarah Ben Maamar1-2, Eliot Chatton1, Jérôme de la Bernardie1, Luc Aquilina1 1: Géosciences Rennes, CNRS UMR 6118, Université de Rennes 1, Campus de Beaulieu bât 14B, Rennes, France 2: Ecobio, CNRS UMR 6553, Université de Rennes 1, Campus de Beaulieu, bât 14, Rennes, France Biofilms play a major role in controlling the fluxes and reactivity of chemical species transported in hydrological systems. Their development can have either positive impacts on groundwater quality (e.g. attenuation of contaminants under natural or stimulated conditions), or possible negative effects on subsurface operations (e.g. bio-clogging of geothermal dipoles or artificial recharge systems). Micro-organisms require both electron donors and electron acceptors for cellular growth, proliferation and maintenance of their metabolic functions. The mechanisms controlling these reactions derive from the interactions occurring at the micro-scale that depend on mineral compositions, the biota of subsurface environment, but also fluid mixing, which determines the local concentrations of nutriments, electron donors and electron acceptors. Hence, mixing zones between oxygen and nutriment rich shallow groundwater and mineralized deep groundwater are often considered as potential hotspots of microbial activity, although relatively few field data document flow distributions, transport properties, chemical gradients and micro-organisms distributions across these mixing interfaces. Here we investigate the origin of a localized biofilm development observed in the fractured granite aquifer at the Ploemeur observatory (H+ network hplus.ore.fr).This biofilm composed of ferro-oxidizing bacteria is observed in an 130m deep artesian well. Borehole video logs show an important colonization of the well by the biofilm in the shallower part (0 to 60m), while it is inexistent in the deeper part (60 to 130m). As flow is localized in a few deep and shallow fractures, we presume that the spatial distribution of biofilm is controlled by mixing between shallow and deep groundwater. To verify this hypothesis we conducted a field campaign with joint characterization of the flow and chemical composition of water flowing from the different fractures, as well as the microbiological composition of the biofilm at different depth, using pyrosequencing techniques. We will discuss in this presentation the results of this interdisciplinary dataset and their implications for the occurrence of hotspots of microbiological activity in the subsurface.

Using Nitrogen Limiting Growth Conditions to Remove Atrazine from Groundwater: Laboratory Studies

USDA-ARS?s Scientific Manuscript database

In the past microbial redox reactions have been the driving mechanism behind in situ bioremediations that use a carbon substrate. This is because subsurface microbial activity is generally restricted by electron (e-) donor availability and microbial activity, growth and respiration, can be stimulat...

Distinguishing Indigenous from Contaminating Microorganisms in Rock Samples from a Deep Au Mine in South Africa

NASA Technical Reports Server (NTRS)

Onstott, T. C.; Moser, D. P.; Fredrickson, J. K.; Pfiffner, S. M.; Phelps, T. J.; White, D. C.; Peacock, A.; Balkwill, D.; Hoover, R. B.; Krumholz, L.;

Relative contributions of microbial and infrastructure heat at a crude oil-contaminated site

NASA Astrophysics Data System (ADS)

Warren, Ean; Bekins, Barbara A.

2018-04-01

Biodegradation of contaminants can increase the temperature in the subsurface due to heat generated from exothermic reactions, making temperature observations a potentially low-cost approach for determining microbial activity. For this technique to gain more widespread acceptance, it is necessary to better understand all the factors affecting the measured temperatures. Biodegradation has been occurring at a crude oil-contaminated site near Bemidji, Minnesota for 39 years, creating a quasi-steady-state plume of contaminants and degradation products. A model of subsurface heat generation and transport helps elucidate the contribution of microbial and infrastructure heating to observed temperature increases at this site. We created a steady-state, two-dimensional, heat transport model using previous-published parameter values for physical, chemical and biodegradation properties. Simulated temperature distributions closely match the observed average annual temperatures measured in the contaminated area at the site within less than 0.2 °C in the unsaturated zone and 0.4 °C in the saturated zone. The model results confirm that the observed subsurface heat from microbial activity is due primarily to methane oxidation in the unsaturated zone resulting in a 3.6 °C increase in average annual temperature. Another important source of subsurface heat is from the active, crude-oil pipelines crossing the site. The pipelines impact temperatures for a distance of 200 m and contribute half the heat. Model results show that not accounting for the heat from the pipelines leads to overestimating the degradation rates by a factor of 1.7, demonstrating the importance of identifying and quantifying all heat sources. The model results also highlighted a zone where previously unknown microbial activity is occurring at the site.

Relative contributions of microbial and infrastructure heat at a crude oil-contaminated site.

PubMed

Warren, Ean; Bekins, Barbara A

2018-04-01

Biodegradation of contaminants can increase the temperature in the subsurface due to heat generated from exothermic reactions, making temperature observations a potentially low-cost approach for determining microbial activity. For this technique to gain more widespread acceptance, it is necessary to better understand all the factors affecting the measured temperatures. Biodegradation has been occurring at a crude oil-contaminated site near Bemidji, Minnesota for 39 years, creating a quasi-steady-state plume of contaminants and degradation products. A model of subsurface heat generation and transport helps elucidate the contribution of microbial and infrastructure heating to observed temperature increases at this site. We created a steady-state, two-dimensional, heat transport model using previous-published parameter values for physical, chemical and biodegradation properties. Simulated temperature distributions closely match the observed average annual temperatures measured in the contaminated area at the site within less than 0.2 °C in the unsaturated zone and 0.4 °C in the saturated zone. The model results confirm that the observed subsurface heat from microbial activity is due primarily to methane oxidation in the unsaturated zone resulting in a 3.6 °C increase in average annual temperature. Another important source of subsurface heat is from the active, crude-oil pipelines crossing the site. The pipelines impact temperatures for a distance of 200 m and contribute half the heat. Model results show that not accounting for the heat from the pipelines leads to overestimating the degradation rates by a factor of 1.7, demonstrating the importance of identifying and quantifying all heat sources. The model results also highlighted a zone where previously unknown microbial activity is occurring at the site. Published by Elsevier B.V.

Subsurface high resolution definition of subsurface heterogeneity for understanding the biodynamics of natural field systems: Advancing the ability for scaling to field conditions. 1998 annual progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Majer, E.L.; Brockman, F.J.

1998-06-01

'This research is an integrated physical (geophysical and hydrologic) and microbial study using innovative geophysical imaging and microbial characterization methods to identify key scales of physical heterogeneities that affect the biodynamics of natural subsurface environments. Data from controlled laboratory and in-situ experiments at the INEEL Test Area North (TAN) site are being used to determine the dominant physical characteristics (lithologic, structural, and hydrologic) that can be imaged in-situ and correlated with microbial properties. The overall goal of this research is to contribute to the understanding of the interrelationships between transport properties and spatially varying physical, chemical, and microbiological heterogeneity. Themore » outcome will be an improved understanding of the relationship between physical and microbial heterogeneity, thus facilitating the design of bioremediation strategies in similar environments. This report summarizes work as of May 1998, the second year of the project. This work is an extension of basic research on natural heterogeneity first initiated within the DOE/OHER Subsurface Science Program (SSP) and is intended to be one of the building blocks of an integrated and collaborative approach with an INEEL/PNNL effort aimed at understanding the effect of physical heterogeneity on transport properties and biodynamics in natural systems. The work is closely integrated with other EMSP projects at INEEL (Rick Colwell et al.) and PNNL (Fred Brockman and Jim Fredrickson).'« less

Microbial community response to the CO2 injection and storage in the saline aquifer, Ketzin, Germany

NASA Astrophysics Data System (ADS)

Morozova, Daria; Zettlitzer, Michael; Vieth, Andrea; Würdemann, Hilke

2010-05-01

The concept of CO2 capture and storage in the deep underground is currently receiving great attention as a consequence of the effects of global warming due to the accumulation of carbon dioxide gas in the atmosphere. The EU funded CO2SINK project is aimed as a pilot storage of CO2 in a saline aquifer located near Ketzin, Germany. One of the main aims of the project is to develop efficient monitoring procedures for assessing the processes that are triggered in the reservoir by CO2 injection. This study reveals analyses of the composition and activity of the microbial community of a saline CO2 storage aquifer and its response to CO2 injection. The availability of CO2 has an influence on the metabolism of both heterotrophic microorganisms, which are involved in carbon cycle, and lithoautotrophic microorganisms, which are able to use CO2 as the sole carbon source and electron acceptor. Injection of CO2 in the supercritical state (temperature above 31.1 °C, pressure above 72.9 atm) may induce metabolic shifts in the microbial communities. Furthermore, bacterial population and activity can be strongly influenced by changes in pH value, pressure, temperature, salinity and other abiotic factors, which will be all influenced by CO2 injection into the deep subsurface. Analyses of the composition of microbial communities and its changes should contribute to an evaluation of the effectiveness and reliability of the long-term CO2 storage technique. The interactions between microorganisms and the minerals of both the reservoir and the cap rock may cause major changes to the structure and chemical composition of the rock formations, which would influence the permeability within the reservoir. In addition, precipitation and corrosion may occur around the well affecting the casing and the casing cement. By using Fluorescence in situ Hybridisation (FISH) and molecular fingerprinting such as Polymerase-Chain-Reaction Single-Strand-Conformation Polymorphism (PCR-SSCP) and Denaturing Gradient Gel Electrophoresis (PCR-DGGE), we have shown that the microbial community was strongly influenced by CO2 injection. Before CO2 arrival, up to 6x106 cells ml-1 were detected by DAPI-staining at a depth of 647 m below the surface. The microbial community was dominated by the domain Bacteria, with Proteobacteria and Firmicutes as the most abundant phyla. Representatives of the sulphate-reducing bacteria, extremophilic and fermenting bacteria were identified. After CO2 injection, our study revealed temporal outcompetition of sulphate-reducing bacteria by methanogenic archaea. In addition, an enhanced activity of the microbial population after five months CO2 storage indicated that the bacterial community was able to adapt to the extreme conditions of the deep biosphere and to the extreme changes of these conditions. In order to draw broader conclusions about the microbial community in the deep biosphere, more intensive sampling and methodologies are necessary. The limiting factors such as high expenses of the downhole sampling and time-consuming analyses should be taken into consideration. This study can thus provide only an early insight into the community structure and its changes due to the CO2 injection. Further studies on the activity, quantity and physiology of these microbial communities using molecular cloning and real-time PCR are in progress.

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredrickson, Jim K.; Balkwill, David L.; Romine, Margaret F.

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteriamore » cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.« less

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

PubMed

Fredrickson, J K; Balkwill, D L; Romine, M F; Shi, T

1999-10-01

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteria cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.

Linking microbial assemblages to paleoenvironmental conditions from the Holocene and Last Glacial Maximum times in Laguna Potrok Aike sediments, Argentina

NASA Astrophysics Data System (ADS)

Vuillemin, Aurele; Ariztegui, Daniel; Leavitt, Peter R.; Bunting, Lynda

2014-05-01

Laguna Potrok Aike is a closed basin located in the southern hemisphere's mid-latitudes (52°S) where paleoenvironmental conditions were recorded as temporal sedimentary sequences resulting from variations in the regional hydrological regime and geology of the catchment. The interpretation of the limnogeological multiproxy record developed during the ICDP-PASADO project allowed the identification of contrasting time windows associated with the fluctuations of Southern Westerly Winds. In the framework of this project, a 100-m-long core was also dedicated to a detailed geomicrobiological study which aimed at a thorough investigation of the lacustrine subsurface biosphere. Indeed, aquatic sediments do not only record past climatic conditions, but also provide a wide range of ecological niches for microbes. In this context, the influence of environmental features upon microbial development and survival remained still unexplored for the deep lacustrine realm. Therefore, we investigated living microbes throughout the sedimentary sequence using in situ ATP assays and DAPI cell count. These results, compiled with pore water analysis, SEM microscopy of authigenic concretions and methane and fatty acid biogeochemistry, provided evidence for a sustained microbial activity in deep sediments and pinpointed the substantial role of microbial processes in modifying initial organic and mineral fractions. Finally, because the genetic material associated with microorganisms can be preserved in sediments over millennia, we extracted environmental DNA from Laguna Potrok Aike sediments and established 16S rRNA bacterial and archaeal clone libraries to better define the use of DNA-based techniques in reconstructing past environments. We focused on two sedimentary horizons both displaying in situ microbial activity, respectively corresponding to the Holocene and Last Glacial Maximum periods. Sequences recovered from the productive Holocene record revealed a microbial community adapted to subsaline conditions producing methane with a high potential of organic matter degradation. In contrast, sediments rich in volcanic detritus from the Last Glacial Maximum showed a substantial presence of lithotrophic microorganisms and sulphate-reducing bacteria mediating authigenic minerals. Together, these features suggested that microbial communities developed in response to climatic control of lake and catchment productivity at the time of sediment deposition. Prevailing climatic conditions exerted a hierarchical control on the microbial composition of lake sediments by regulating the influx of organic and inorganic material to the lake basin, which in turn determined water column chemistry, production and sedimentation of particulate material, resulting in the different niches sheltering these microbial assemblages. Moreover, it demonstrated that environmental DNA can constitute sedimentary archives of phylogenetic diversity and diagenetic processes over tens of millennia.

Ridge-flank crustal microbiology investigated with long-term borehole observatories

NASA Astrophysics Data System (ADS)

Orcutt, B. N.; Bach, W.; Becker, K.; Edwards, K. J.; Fisher, A. T.; Haddad, A.; Hulme, S.; Teske, A.; Toner, B.; Wheat, C. G.

2011-12-01

The ridge flank environment represents an important habitat for microbial life on Earth, considering its size and chemical disequilibria between circulating fluids and rocks. However, the potential for this habitat to harbor life, and the characteristics that such life might have, are poorly known at present. Furthermore, the interactions of microbial communities across deep sediment-basement interfaces are not well-characterized. Subseafloor borehole observatories provide a novel platform for sampling and monitoring the microbiology of the crustal ridge flank environment. We present current results from a series of subsurface microbial colonization experiments using borehole observatories on the eastern flank of the Juan de Fuca Ridge, as well as analysis of samples collected on a transect away from a seawater-recharging seamount on this ridge flank. These results are compared to the microbiology of observatories installed in the Costa Rica Rift flank with similar fluid composition and temperatures (i.e. anoxic and warm). We will also discuss on-going experiments on the western-flank of the Mid-Atlantic Ridge, where formation fluids in basement are oxic and cool. Results from these experiments represent some of the extremes in crustal fluid conditions, paving the way for additional studies that are needed to address the importance of this biome as a carbon reservoir and a mechanism for crustal alteration.

Structure and function of subsurface microbial communities affecting radionuclide transport and bioimmobilization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostka, Joel E.; Prakash, Om; Green, Stefan J.

2012-05-01

Our objectives were to: 1) isolate and characterize novel anaerobic prokaryotes from subsurface environments exposed to high levels of mixed contaminants (U(VI), nitrate, sulfate), 2) elucidate the diversity and distribution of metabolically active metal- and nitrate-reducing prokaryotes in subsurface sediments, and 3) determine the biotic and abiotic mechanisms linking electron transport processes (nitrate, Fe(III), and sulfate reduction) to radionuclide reduction and immobilization. Mechanisms of electron transport and U(VI) transformation were examined under near in situ conditions in sediment microcosms and in field investigations. Field sampling was conducted at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee. Themore » ORFRC subsurface is exposed to mixed contamination predominated by uranium and nitrate. In short, we effectively addressed all 3 stated objectives of the project. In particular, we isolated and characterized a large number of novel anaerobes with a high bioremediation potential that can be used as model organisms, and we are now able to quantify the function of subsurface sedimentary microbial communities in situ using state-of-the-art gene expression methods (molecular proxies).« less

Biological formation of ethane and propane in the deep marine subsurface.

PubMed

Hinrichs, Kai-Uwe; Hayes, John M; Bach, Wolfgang; Spivack, Arthur J; Hmelo, Laura R; Holm, Nils G; Johnson, Carl G; Sylva, Sean P

2006-10-03

Concentrations and isotopic compositions of ethane and propane in cold, deeply buried sediments from the southeastern Pacific are best explained by microbial production of these gases in situ. Reduction of acetate to ethane provides one feasible mechanism. Propane is enriched in (13)C relative to ethane. The amount is consistent with derivation of the third C from inorganic carbon dissolved in sedimentary pore waters. At typical sedimentary conditions, the reactions yield free energy sufficient for growth. Relationships with competing processes are governed mainly by the abundance of H(2). Production of C(2) and C(3) hydrocarbons in this way provides a sink for acetate and hydrogen but upsets the general belief that hydrocarbons larger than methane derive only from thermal degradation of fossil organic material.

Biological formation of ethane and propane in the deep marine subsurface

PubMed Central

Hinrichs, Kai-Uwe; Hayes, John M.; Bach, Wolfgang; Spivack, Arthur J.; Hmelo, Laura R.; Holm, Nils G.; Johnson, Carl G.; Sylva, Sean P.

2006-01-01

Concentrations and isotopic compositions of ethane and propane in cold, deeply buried sediments from the southeastern Pacific are best explained by microbial production of these gases in situ. Reduction of acetate to ethane provides one feasible mechanism. Propane is enriched in 13C relative to ethane. The amount is consistent with derivation of the third C from inorganic carbon dissolved in sedimentary pore waters. At typical sedimentary conditions, the reactions yield free energy sufficient for growth. Relationships with competing processes are governed mainly by the abundance of H2. Production of C2 and C3 hydrocarbons in this way provides a sink for acetate and hydrogen but upsets the general belief that hydrocarbons larger than methane derive only from thermal degradation of fossil organic material. PMID:16990430

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

PubMed Central

Kawai, Mikihiko; Futagami, Taiki; Toyoda, Atsushi; Takaki, Yoshihiro; Nishi, Shinro; Hori, Sayaka; Arai, Wataru; Tsubouchi, Taishi; Morono, Yuki; Uchiyama, Ikuo; Ito, Takehiko; Fujiyama, Asao; Inagaki, Fumio; Takami, Hideto

2014-01-01

Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere. PMID:24624126

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes.

PubMed

Kawai, Mikihiko; Futagami, Taiki; Toyoda, Atsushi; Takaki, Yoshihiro; Nishi, Shinro; Hori, Sayaka; Arai, Wataru; Tsubouchi, Taishi; Morono, Yuki; Uchiyama, Ikuo; Ito, Takehiko; Fujiyama, Asao; Inagaki, Fumio; Takami, Hideto

2014-01-01

Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.

Recovery Act: Understanding the Impact of CO 2 Injection on the Subsurface Microbial Community in an Illinois Basin CCS Reservoir: Integrated Student Training in Geoscience and Geomicrobiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fouke, Bruce

An integrated research and teaching program was developed to provide cross--disciplinary training opportunities in the emerging field of carbon capture and storage (CCS) for geobiology students attending the University of Illinois Urbana-­Champaign (UIUC). Students from across the UIUC campus participated, including those from the departments of Geology, Microbiology, Biochemistry, Civil and Environmental Engineering, Animal Sciences and the Institute for Genomic Biology. The project took advantage of the unique opportunity provided by the drilling and sampling of the large-­scale Phase III CCS demonstration Illinois Basin - Decatur Project (IBDP) in the central Illinois Basin at nearby Decatur, Illinois. The IBPD ismore » under the direction of the Illinois State Geological Survey (ISGS, located on the UIUC campus) and the Midwest Geological Sequestration Consortium (MGSC). The research component of this project focused on the subsurface sampling and identification of microbes inhabiting the subsurface Cambrian-­age Mt. Simon Sandstone. In addition to formation water collected from the injection and monitoring wells, sidewall rock cores were collected and analyzed to characterize the cements and diagenetic features of the host Mt. Simon Sandstone. This established a dynamic geobiological framework, as well as a comparative baseline, for future studies of how CO 2 injection might affect the deep microbial biosphere at other CCS sites. Three manuscripts have been prepared as a result of these activities, which are now being finalized for submission to top-­tier international peer-­reviewed research journals. The training component of this project was structured to ensure that a broad group of UIUC students, faculty and staff gained insight into CCS issues. An essential part of this training was that the UIUC faculty mentored and involved undergraduate and graduate students, as well as postdocs and research scientists, at all stages of the project in order to develop CCS-­focused classroom and field courses, as well as seminars. This program provided an excellent opportunity for participants to develop the background necessary to establish longer-­term research in CCS-­related geology and microbial ecology. Further, the program provided an ongoing dynamic platform to foster long-term collaboration with the regional ISGS and MGSC sequestration partnership, while offering hands-­on, applied learning experiences.« less

Metabolic potential of a Novel Gram-Negative, Spore-forming, and Putatively Sulfate-Reducing Bacterium in the Continental Subsurface

NASA Astrophysics Data System (ADS)

Lau, C. Y. M.; Becraft, E. D.; Cason, E. D.; Borgonie, G.; Kieft, T. L.; Li, L.; van Heerden, E.; Jarett, J.; Woyke, T.; Stepanauskas, R.; Onstott, T. C.

2017-12-01

Anaerobic sulfate reduction is among the most thermodynamically favorable biochemical reactions in the deep subsurface environments. Phylogenetically and functionally diverse sulfate-reducing bacteria (SRB) within Deltaproteobacteria and Firmicutes have been reported. However, only few of them have been isolated in pure cultures for detailed physiological characterization. Previous studies showed that fracture fluid samples from the 1 km-deep borehole DR5IPC (Driefontein gold mine, South Africa) harbored novel SRB, as indicated by the low percentages (84% and 90%) of identity of the 16S ribosomal RNA clone sequences to known SRB. To overcome the challenge of low cultivability, we employed next-generation sequencing to unveil the metabolic potential of these novel SRB. Metagenomic assembly and binning yielded seven >50% complete genomes including a methylotrophic SRB belonging to Deltaproteobacteria (DR5_3) and two draft genomes representing an uncultivated phylum, tentatively "Driefonteinae" (DR5_4 and DR5_5). They accounted for 3%, 2% and 18% of all metagenomic reads. Three single-cell assembled genomes (SAGs) sharing 99% of average nucleotide identity (ANI) with DR5_5 were obtained. Analysis of the protein-coding genes in DR5_5 and related SAGs indicated that "Driefonteinae" possesses dissimilatory sulfite reductase genes (dsrAB), suggesting that sulfate would be the terminal electron acceptor. Whereas it may use diverse electron acceptors such as carbon monoxide, acetate, lactate and formate. A near-complete collection of genes for Wood-Ljungdahl pathway and genes for partial pentose phosphate pathway, glycolysis and tricarboxylic acid cycle further showed that "Driefonteinae" may live a mixotrophic life style. It is evident that archaeal genes related to methanogens were acquired through horizontal gene transfer. Phenotypically, "Driefonteinae" has a Gram-negative cell wall and flagella. The ability of forming spores would enable this microorganism to endure adverse conditions. Genomic analysis has provided an invaluable avenue to reveal novel microbial players in the subsurface sulfur cycle.

Natural dissolved organic matter dynamics in karstic aquifer: O'Leno Sink-Rise system, Florida, USA

NASA Astrophysics Data System (ADS)

Jin, J.; Zimmerman, A. R.

2010-12-01

Natural dissolved organic matter (NDOM) dynamics in karstic aquifer remain poorly understood due to the inaccessibility and heterogeneity of the subsurface. Because the Santa Fe River sinks into the Floridan Aquifer and emerges 6 km down gradient, the O'Leno Sink-Rise system in Northern Florida provides an ideal setting to study NDOM transformation in groundwater. Water samples were collected at both high and low temporal resolutions over 3 years from the River Sink, Rise, and a series of shallow and deep wells. Analyses of dissolved organic and inorganic carbon, stable isotopic, and spectrophotometry (excitation-emission matrix or EEM) show that reversals of hydrologic head gradient in the conduit and matrix are closely related to the delivery of NDOM to the aquifer. In addition, the relative influence of biotic and abiotic processes varies along spatiotemporal gradients; regions of the aquifer with greatest connectivity to surface water (new NDOM and terminal electron acceptor supply) see the most microbial transformation of NDOM, while those with least connectivity see relatively greater abiotic transformation of NDOM. A source water mixing model was established for the Sink-Rise system using Mg2+ and SO42- concentrations from three end-members identified as allogenic recharge, upwelling deep water, and shallow groundwater of the Upper Floridan Aquifer. Biogeochemical processes were quantified after accounting for changes that occurred due to source water mixing, according to the model. In addition to NDOM remineralization by subsurface microbes which occurred mostly during wet periods, adsorption of NDOM onto aquifer materials as well as release of NDOM from aquifer materials was also observed. During wet periods when DOC-rich conduit water entered the matrix, progressive NDOM remineralization was found along the preferential flow paths from the conduits into the matrices. Both biotic and abiotic NDOM transformation processes were found to control channel dissolution and thus the subsurface geomorphology, all of which are linked to hydrology and climate patterns.

Depositionally controlled recycling of iron and sulfur in marine sediments and its isotopic consequences

NASA Astrophysics Data System (ADS)

Riedinger, N.; Formolo, M.; Arnold, G. L.; Vossmeyer, A.; Henkel, S.; Sawicka, J.; Kasten, S.; Lyons, T. W.

2011-12-01

The continental margin off Uruguay and Argentina is characterized by highly dynamic depositional conditions. This variable depositional regime significantly impacts the biogeochemical cycles of iron and sulfur. Mass deposit related redeposition of reduced minerals can lead to the reoxidation of these phases and thus to an overprint of their geochemical primary signatures. Due to rapid burial these oxidized phases are still present in deeper subsurface sediments. To study the effects of sediment relocation on the sulfur and iron inventory we collected shallow and deep subsurface sediment samples via multicorer and gravity cores, respectively, in the western Argentine Basin during the RV Meteor Expedition M78/3 in May-July 2009. The samples were retrieved from shelf, slope and deep basin sites. The concentration and sulfur isotope composition of acid volatile sulfur (AVS), chromium reducible sulfur (CRS), elemental sulfur and total organic sulfur were determined. Furthermore, sequential iron extraction techniques were applied assess the distribution of iron oxide phases within the sediment. The investigated sediments are dominated by terrigenous inputs, with high amounts of reactive ferric iron minerals and only low concentrations of calcium carbonate. Total organic carbon concentrations show strong variation in the shallow subsurface sediments ranging between approximately 0.7 and 6.4 wt% for different sites. These concentrations do not correlate with water depths. Pore water accumulations of hydrogen sulfide are restricted to an interval at the sulfate-methane transition (SMT) zone a few meters below the sediment surface. In these deeper subsurface sediments pyrite is precipitated in this zone of hydrogen sulfide excess, whereas the accumulation of authigenic AVS and elemental sulfur (up to 2000 ppm) occurs at the upper and lower boundary of the sulfidic zone due the reaction of iron oxides with limited amounts of sulfide. Furthermore, our preliminary results indicate that there is a link between modern deposition in the shallow subsurface sediments and the long-term signals being buried and preserved in the deep subsurface layers. The data show that the burial of elemental sulfur into deep subsurface sediments can fuel the deep biosphere and has consequences for isotopic overprints tied, for example, to oxidation and disproportionation processes in the deeper sediments.

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay

PubMed Central

Jochum, Lara M.; Chen, Xihan; Lever, Mark A.; Loy, Alexander; Jørgensen, Bo Barker; Schramm, Andreas

2017-01-01

ABSTRACT Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community. PMID:28939599

Investigating the hydrological origins of Blood Falls - geomicrobiological insights into a briny subglacial Antarctic aquifer

NASA Astrophysics Data System (ADS)

Mikucki, J.; Tulaczyk, S. M.; Purcell, A. M.; Dachwald, B.; Lyons, W. B.; Welch, K. A.; Auken, E.; Dugan, H. A.; Walter, J. I.; Pettit, E. C.; Doran, P. T.; Virginia, R. A.; Schamper, C.; Foley, N.; Feldmann, M.; Espe, C.; Ghosh, D.; Francke, G.

2015-12-01

Subglacial waters tend to accumulate solutes from extensive rock-water interactions, which, when released to the surface, can provide nutrients to surface ecosystems providing a 'hot spot' for microbial communities. Blood Falls, an iron-rich, saline feature at the terminus of Taylor Glacier in the McMurdo Dry Valleys, Antarctica is a well-studied subglacial discharge. Here we present an overview of geophysical surveys, thermomechanical drilling exploration and geomicrobiological analyses of the Blood Falls system. A helicopter-borne transient electromagnetic system (SkyTEM) flown over the Taylor Glacier revealed a surprisingly extensive subglacial aquifer and indicates that Blood Falls may be the only surface manifestation of this extensive briny groundwater. Ground-based temperature sensing and GPR data combined with the helicopter-borne TEM data enabled targeted drilling into the englacial conduit that delivers brine to the surface. During the 2014-15 austral summer field season, we used a novel ice-melting drill (the IceMole) to collect englacial brine for geomicrobiological analyses. Results from previously collected outflow and more recent samples indicate that the brine harbors a metabolically active microbial community that persists, despite cold, dark isolation. Isotope geochemistry and molecular analysis of functional genes from BF suggested that a catalytic or 'cryptic' sulfur cycle was linked to iron reduction. Recent metagenomic analysis confirms the presence of numerous genes involved in oxidative and reductive sulfur transformations. Metagenomic and metabolic activity data also indicate that subglacial dark CO2 fixation occurs via various pathways. Genes encoding key steps in CO2 fixation pathways including the Calvin Benson Basham and Wood Ljungdahl pathway were present and brine samples showed measureable uptake of 14C-labeled bicarbonate. These results support the notion that, like the deep subsurface, subglacial environments are chemosynthetic, deriving energy in part by cycling iron and sulfur compounds. Collectively our interdisciplinary dataset indicates that subsurface brines are widespread in the Taylor Valley polar desert and this previously unknown groundwater network likely supports unique microbial life.

Investigating the potential for subsurface primary production fueled by serpentinization

NASA Astrophysics Data System (ADS)

Brazelton, W. J.; Nelson, B. Y.; Schrenk, M. O.

2011-12-01

Ultramafic rocks in the Earth's mantle represent a tremendous reservoir of carbon and reducing power. Tectonic uplift of these materials into the crust can result in serpentinization, a highly exothermic geochemical reaction that releases hydrogen gas (H2) and promotes the abiogenic synthesis of organic molecules. The extent and activity of microbial communities in serpentinite-hosted subsurface habitats is almost entirely unknown, but they clearly have great potential to host extensive sunlight-independent primary production fueled by H2 and abiotic carbon compounds. We have been testing this hypothesis at several sites of serpentinization around the globe utilizing a suite of techniques including metagenomics, 16S rRNA pyrotag sequencing, and stable isotope tracing experiments. All four of our study sites, which include deep-sea hydrothermal vents, terrestrial alkaline springs, and continental drill holes, are characteristically low in archaeal and bacterial genetic diversity. In carbonate chimneys of the Lost City hydrothermal field (Mid-Atlantic Ridge), for example, a single archaeal phylotype dominates the biofilm community. Stable isotope tracing experiments indicated that these archaeal biofilms are capable of both production and anaerobic oxidation of methane at 80C and pH 10. Both production and oxidation were stimulated by H2, suggesting a possible syntrophic relationship among cells within the biofilm. Preliminary results from similar stable isotope tracing experiments at terrestrial alkaline seeps at the Tablelands Ophiolite (Newfoundland), Ligurian springs (Italy), and McLaughlin Reserve (California) have indicated the potential for microbial activity fueled by H2 and acetate. Furthermore, recent metagenomic sequencing of fluids from the Tablelands and Ligurian springs have revealed genomic potential for chemolithotrophy powered by iron reduction with H2. In summary, these data support the potential for extensive microbial activity fueled by serpentinization, and further characterization of the endemic organisms (now underway) is likely to reveal novel physiological adaptations to the unusual conditions of serpentinite-hosted habitats.

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

PubMed Central

Jungbluth, Sean P; Grote, Jana; Lin, Huei-Ting; Cowen, James P; Rappé, Michael S

2013-01-01

Despite its immense size, logistical and methodological constraints have largely limited microbiological investigations of the subseafloor basement biosphere. In this study, a unique sampling system was used to collect fluids from the subseafloor basaltic crust via a Circulation Obviation Retrofit Kit (CORK) observatory at Integrated Ocean Drilling Program borehole 1301A, located at a depth of 2667 m in the Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Here, a fluid delivery line directly accesses a 3.5 million years old basalt-hosted basement aquifer, overlaid by 262 m of sediment, which serves as a barrier to direct exchange with bottom seawater. At an average of 1.2 × 104 cells ml−1, microorganisms in borehole fluids were nearly an order of magnitude less abundant than in surrounding bottom seawater. Ribosomal RNA genes were characterized from basement fluids, providing the first snapshots of microbial community structure using a high-integrity fluid delivery line. Interestingly, microbial communities retrieved from different CORKs (1026B and 1301A) nearly a decade apart shared major community members, consistent with hydrogeological connectivity. However, over three sampling years, the dominant gene clone lineage changed from relatives of Candidatus Desulforudis audaxviator within the bacterial phylum Firmicutes in 2008 to the Miscellaneous Crenarchaeotic Group in 2009 and a lineage within the JTB35 group of Gammaproteobacteria in 2010, and statistically significant variation in microbial community structure was observed. The enumeration of different phylogenetic groups of cells within borehole 1301A fluids supported our observation that the deep subsurface microbial community was temporally dynamic. PMID:22791235

Impact on the deep biosphere of CO2 geological sequestration in (ultra)mafic rocks and retroactive consequences on its fate

NASA Astrophysics Data System (ADS)

Ménez, Bénédicte; Gérard, Emmanuelle; Rommevaux-Jestin, Céline; Dupraz, Sébastien; Guyot, François; Arnar Alfreősson, Helgi; Reynir Gíslason, Sigurőur; Sigurőardóttir, Hólmfríiur

2010-05-01

Due to their reactivity and high potential of carbonation, mafic and ultramafic rocks constitute targets of great interest to safely and permanently sequestrate anthropogenic CO2 and thus, limit the potential major environmental consequences of its increasing atmospheric level. In addition, subsurface (ultra)mafic environments are recognized to harbor diverse and active microbial populations that may be stimulated or decimated following CO2 injection (± impurities) and subsequent acidification. However, the nature and amplitude of the involved biogeochemical pathways are still unknown. To avoid unforeseen consequences at all time scales (e.g. reservoir souring and clogging, bioproduction of H2S and CH4), the impact of CO2 injection on deep biota with unknown ecology, and their retroactive effects on the capacity and long-term stability of CO2 storage sites, have to be determined. We present here combined field and experimental investigations focused on the Icelandic pilot site, implemented in the Hengill area (SW Iceland) at the Hellisheidi geothermal power plant (thanks to the CarbFix program, a consortium between the University of Iceland, Reykjavik Energy, the French CNRS of Toulouse and Columbia University in N.Y., U.S.A. and to the companion French ANR-CO2FIX project). This field scale injection of CO2 charged water is here designed to study the feasibility of storing permanently CO2 in basaltic rocks and to optimize industrial methods. Prior to the injection, the microbiological initial state was characterized through regular sampling at various seasons (i.e., October '08, July '09, February '10). DNA was extracted and amplified from the deep and shallow observatory wells, after filtration of 20 to 30 liters of groundwater collected in the depth interval 400-980 m using a specifically developed sampling protocol aiming at reducing contamination risks. An inventory of living indigenous bacteria and archaea was then done using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). The stratigraphic levels targeted to store the injected CO2 as aqueous phase harbor numerous new species close to cultivable species belonging to the genus Thermus or Proteobacteria species known to be linked in particular with the hydrogen and iron cycles. After injection, the evolution of these microbial communities will be monitored using the Denaturing Gradient Gel Electrophoresis technique. Beyond the ecological impact of storing high levels of CO2 in deep environments, particularly important is the ability of intraterrestrial microbes to potentially interact with the injected fluids. For example, carbonation has been shown to be strongly influenced by microbiological activities that can locally modify pH and induce nucleation of solid carbonates. To improve the understanding of these processes and to better constrain the influence of deep biota on the evolving chemical and petrophysical properties of the reservoir, an experimental and numerical modeling is carried out in parallel, using model strains representative of the subsurface (including acetogens, sulphate and iron reducing bacteria), as single-species or consortia. A set of batch experiments in presence of crushed olivine or basalts was especially designed to evaluate how microbial activity could overcome the slow kinetics of mineral-fluid reactions and reduce the energy needed to hasten the carbonation process.

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA

PubMed Central

Read, Kaitlyn J. H.; Hughes, Evan M.; Spilde, Michael N.

2017-01-01

Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. Actinobacteria dominated in all cave samples, with 39% from caves and 21% from surface soils. Proteobacteria made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were Nitrospirae (7%) followed by minor phyla (7%), compared to surface soils with Bacteroidetes (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community. PMID:28199330

Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

NASA Astrophysics Data System (ADS)

Hunter, K. S.; Van Cappellen, P.

2000-01-01

Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

Plasmid incidence in bacteria from deep subsurface sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredrickson, J.K.; Hicks, R.J.; Li, S.W.

Bacteria were isolated from deep terrestrial subsurface sediments underlying the coastal plain of South Carolina. A total of 163 isolates from deep sediments, surface soil, and return drill muds were examined for plasmid DNA content and resistance to the antibiotics penicillin, ampicillin, carbenicillin, streptomycin, kanamycin, and tetracycline. MICs of Cu{sup 2+}, Cr{sup 3+}, and Hg{sup 2+} for each isolate were also determined. The overall frequency of plasmid occurrence in the subsurface bacteria was 33%. Resistance was most frequent to penicillin (70% of all isolates), ampicillin (49%), and carbenicillin (32%) and was concluded to be related to the concentrations of themore » individual antibiotics in the disks used for assaying resistance and to the production of low levels of {beta}-lactamase. The frequencies of resistance to penicillin and ampicillin were significantly greater for isolates bearing plasmids than for plasmidless isolates; however, resistance was not transferable to penicillin-sensitive Escherichia coli. Hybridization of subsurface bacterial plasmids and chromosomal DNA with a whole-TOL-plasmid (pWWO) probe revealed some homology of subsurface bacterial plasmid and chromosomal DNAs, indicating a potential for those bacterial to harbor catabolic genes on plasmids or chromosomes. The incidences of antibiotic resistance and MICs of metals for subsurface bacteria were significantly different from those drill mud bacteria, ruling out the possibility that bacteria from sediments were derived from drill muds.« less

Subsurface conditions in hydrothermal vents inferred from diffuse flow composition, and models of reaction and transport

NASA Astrophysics Data System (ADS)

Larson, B. I.; Houghton, J. L.; Lowell, R. P.; Farough, A.; Meile, C. D.

2015-08-01

Chemical gradients in the subsurface of mid-ocean ridge hydrothermal systems create an environment where minerals precipitate and dissolve and where chemosynthetic organisms thrive. However, owing to the lack of easy access to the subsurface, robust knowledge of the nature and extent of chemical transformations remains elusive. Here, we combine measurements of vent fluid chemistry with geochemical and transport modeling to give new insights into the under-sampled subsurface. Temperature-composition relationships from a geochemical mixing model are superimposed on the subsurface temperature distribution determined using a heat flow model to estimate the spatial distribution of fluid composition. We then estimate the distribution of Gibb's free energies of reaction beneath mid oceanic ridges and by combining flow simulations with speciation calculations estimate anhydrite deposition rates. Applied to vent endmembers observed at the fast spreading ridge at the East Pacific Rise, our results suggest that sealing times due to anhydrite formation are longer than the typical time between tectonic and magmatic events. The chemical composition of the neighboring low temperature flow indicates relatively uniform energetically favorable conditions for commonly inferred microbial processes such as methanogenesis, sulfate reduction and numerous oxidation reactions, suggesting that factors other than energy availability may control subsurface microbial biomass distribution. Thus, these model simulations complement fluid-sample datasets from surface venting and help infer the chemical distribution and transformations in subsurface flow.

Evolution of Hydrocarbon-Degrading Microbial Communities in the Aftermath of the Deepwater Horizon Oil Well Blowout in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Andersen, G.; Dubinsky, E. A.; Chakraborty, R.; Hollibaugh, J. T.; Hazen, T. C.

2012-12-01

The Deepwater Horizon oil spill created large plumes of dispersed oil and gas that remained deep in the water column and stimulated growth of several deep-sea bacteria that can degrade hydrocarbons at cold temperatures. We tracked microbial community composition before, during and after the 83-day spill to determine relationships between microbial dynamics, and hydrocarbon and dissolved-oxygen concentrations. Dominant bacteria in plumes shifted drastically over time and were dependent on the concentration of hydrocarbons, and the relative quantities of insoluble and soluble oil fractions. Unmitigated flow from the wellhead early in the spill resulted in the highest concentrations of oil and relatively more n-alkanes suspended in the plume as small oil droplets. These conditions resulted in near complete dominance by alkane-degrading Oceanospirillales, Pseudomonas and Shewanella. Six-weeks into the spill overall hydrocarbon concentrations in the plume decreased and were almost entirely composed of BTEX after management actions reduced emissions into the water column. These conditions corresponded with the emergence of Colwellia, Pseudoalteromonas, Cycloclasticus and Halomonas that are capable of degrading aromatic compounds. After the well was contained dominant plume bacteria disappeared within two weeks after the spill and transitioned to an entirely different set of bacteria dominated by Flavobacteria, Methylophaga, Alteromonas and Rhodobacteraceae that were found in anomalous oxygen depressions throughout August and are prominent degraders of both high molecular weight organic matter as well as hydrocarbons. Bio-Sep beads amended with volatile hydrocarbons from MC-252 oil were used from August through September to create hydrocarbon-amended traps for attracting oil-degrading microbes in situ. Traps were placed at multiple depths on a drilling rig about 600-m from the original MC-252 oil spill site. Microbes were isolated on media using MC-252 oil as the sole carbon source and characterized. Pure cultures were obtained from bacteria similar to those found to dominate hydrocarbon plumes and anomalous oxygen depressions by molecular community analysis. Respirometry studies confirmed that the isolates were able to metabolize the MC-252 oil. Our results from both molecular and culture analysis indicate that indigenous psychrophilic consortia of microorganisms thriving at 5°C from the oil-plume depth water were able to rapidly respond to dispersed oil at depth. The microbial community was highly dynamic and structured by changes in hydrocarbon composition over time. The spill caused sustained alterations in subsurface microbial communities and impacted the deep ocean for at least months after well containment.

Evidence for Methyl-Compound-Activated Life in Coal Bed System 2 km Below Sea Floor

NASA Astrophysics Data System (ADS)

Trembath-reichert, E.; Morono, Y.; Dawson, K.; Wanger, G.; Bowles, M.; Heuer, V.; Hinrichs, K. U.; Inagaki, F.; Orphan, V. J.

2014-12-01

IODP Expedition 337 set the record for deepest marine scientific drilling down to 2.4 kmbsf. This cruise also had the unique opportunity to retrieve deep cores from the Shimokita coal bed system in Japan with the aseptic and anaerobic conditions necessary to look for deep life. Onboard scientists prepared nearly 1,700 microbiology samples shared among five different countries to study life in the deep biosphere. Samples spanned over 1 km in sampling depths and include representatives of shale, sandstone, and coal lithologies. Findings from previous IODP and deep mine expeditions suggest the genetic potential for methylotrophy in the deep subsurface, but it has yet to be observed in incubations. A subset of Expedition 337 anoxic incubations were prepared with a range of 13C-methyl substrates (methane, methylamine, and methanol) and maintained near in situ temperatures. To observe 13C methyl compound metabolism over time, we monitored the δ13C of the dissolved inorganic carbon (by-product of methyl compound metabolism) over a period of 1.5 years. Elemental analysis (EA), ion chromatograph (IC), 13C volatile fatty acid (VFA), and mineral-associated microscopy data were also collected to constrain initial and endpoint conditions in these incubations. Our geochemical evidence suggests that the coal horizon incubated with 13C-methane showed the highest activity of all methyl incubations. This provides the first known observation of methane-activated metabolism in the deep biosphere, and suggests there are not only active cells in the deeply buried terrigenous coal bed at Shimokita, but the presence of a microbial community activated by methylotrophic compounds.

A System for Incubations at High Gas Partial Pressure

PubMed Central

Sauer, Patrick; Glombitza, Clemens; Kallmeyer, Jens

2012-01-01

High-pressure is a key feature of deep subsurface environments. High partial pressure of dissolved gasses plays an important role in microbial metabolism, because thermodynamic feasibility of many reactions depends on the concentration of reactants. For gases, this is controlled by their partial pressure, which can exceed 1 MPa at in situ conditions. Therefore, high hydrostatic pressure alone is not sufficient to recreate true deep subsurface in situ conditions, but the partial pressure of dissolved gasses has to be controlled as well. We developed an incubation system that allows for incubations at hydrostatic pressure up to 60 MPa, temperatures up to 120°C, and at high gas partial pressure. The composition and partial pressure of gasses can be manipulated during the experiment. To keep costs low, the system is mainly made from off-the-shelf components with only very few custom-made parts. A flexible and inert PVDF (polyvinylidene fluoride) incubator sleeve, which is almost impermeable for gases, holds the sample and separates it from the pressure fluid. The flexibility of the incubator sleeve allows for sub-sampling of the medium without loss of pressure. Experiments can be run in both static and flow-through mode. The incubation system described here is usable for versatile purposes, not only the incubation of microorganisms and determination of growth rates, but also for chemical degradation or extraction experiments under high gas saturation, e.g., fluid–gas–rock-interactions in relation to carbon dioxide sequestration. As an application of the system we extracted organic compounds from sub-bituminous coal using H2O as well as a H2O–CO2 mixture at elevated temperature (90°C) and pressure (5 MPa). Subsamples were taken at different time points during the incubation and analyzed by ion chromatography. Furthermore we demonstrated the applicability of the system for studies of microbial activity, using samples from the Isis mud volcano. We could detect an increase in sulfate reduction rate upon the addition of methane to the sample. PMID:22347218

Subsurface Nitrogen-Cycling Microbial Communities at Uranium Contaminated Sites in the Colorado River Basin

NASA Astrophysics Data System (ADS)

Cardarelli, E.; Bargar, J.; Williams, K. H.; Dam, W. L.; Francis, C.

2015-12-01

Throughout the Colorado River Basin (CRB), uranium (U) persists as a relic contaminant of former ore processing activities. Elevated solid-phase U levels exist in fine-grained, naturally-reduced zone (NRZ) sediments intermittently found within the subsurface floodplain alluvium of the following Department of Energy-Legacy Management sites: Rifle, CO; Naturita, CO; and Grand Junction, CO. Coupled with groundwater fluctuations that alter the subsurface redox conditions, previous evidence from Rifle, CO suggests this resupply of U may be controlled by microbially-produced nitrite and nitrate. Nitrification, the two-step process of archaeal and bacterial ammonia-oxidation followed by bacterial nitrite oxidation, generates nitrate under oxic conditions. Our hypothesis is that when elevated groundwater levels recede and the subsurface system becomes anoxic, the nitrate diffuses into the reduced interiors of the NRZ and stimulates denitrification, the stepwise anaerobic reduction of nitrate/nitrite to dinitrogen gas. Denitrification may then be coupled to the oxidation of sediment-bound U(IV) forming mobile U(VI), allowing it to resupply U into local groundwater supplies. A key step in substantiating this hypothesis is to demonstrate the presence of nitrogen-cycling organisms in U-contaminated, NRZ sediments from the upper CRB. Here we investigate how the diversity and abundances of nitrifying and denitrifying microbial populations change throughout the NRZs of the subsurface by using functional gene markers for ammonia-oxidation (amoA, encoding the α-subunit of ammonia monooxygenase) and denitrification (nirK, nirS, encoding nitrite reductase). Microbial diversity has been assessed via clone libraries, while abundances have been determined through quantitative polymerase chain reaction (qPCR), elucidating how relative numbers of nitrifiers (amoA) and denitrifiers (nirK, nirS) vary with depth, vary with location, and relate to uranium release within NRZs in sediment cores spanning the upper CRB. Early findings from Rifle, CO indicate elevated abundances of ammonia-oxidizers seem to correlate with elevated uranium concentrations emphasizing the critical need to understand how nitrogen-cycling organisms influence subsurface U redox chemistry and mobility.

US Air Force 1989 Research Initiation Program . Volume 1.

DTIC Science & Technology

1992-06-25

microbial ecology of contaminated soils. 27-5 Thomas and coworkers (1989) studied microbial activity at a creosote waste site and demonstrated that...provide information essential for an understanding of the microbial ecology of contaminated soils, they do not address the microbiology of...substrates. Appl. Environ. Microbiol. 49:711-713. Thomas, J. M., M. D. Lee, M. J. Scott and C. H. Ward. 1989. Microbial ecology of the subsurface Lt an

Temperature change affected groundwater quality in a confined marine aquifer during long-term heating and cooling.

PubMed

Saito, Takeshi; Hamamoto, Shoichiro; Ueki, Takashi; Ohkubo, Satoshi; Moldrup, Per; Kawamoto, Ken; Komatsu, Toshiko

2016-05-01

Global warming and urbanization together with development of subsurface infrastructures (e.g. subways, shopping complexes, sewage systems, and Ground Source Heat Pump (GSHP) systems) will likely cause a rapid increase in the temperature of relatively shallow groundwater reservoirs (subsurface thermal pollution). However, potential effects of a subsurface temperature change on groundwater quality due to changed physical, chemical, and microbial processes have received little attention. We therefore investigated changes in 34 groundwater quality parameters during a 13-month enhanced-heating period, followed by 14 months of natural or enhanced cooling in a confined marine aquifer at around 17 m depth on the Saitama University campus, Japan. A full-scale GSHP test facility consisting of a 50 m deep U-tube for circulating the heat-carrying fluid and four monitoring wells at 1, 2, 5, and 10 m from the U-tube were installed, and groundwater quality was monitored every 1-2 weeks. Rapid changes in the groundwater level in the area, especially during the summer, prevented accurate analyses of temperature effects using a single-well time series. Instead, Dual-Well Analysis (DWA) was applied, comparing variations in subsurface temperature and groundwater chemical concentrations between the thermally-disturbed well and a non-affected reference well. Using the 1 m distant well (temperature increase up to 7 °C) and the 10 m distant well (non-temperature-affected), the DWA showed an approximately linear relationships for eight components (B, Si, Li, dissolved organic carbon (DOC), Mg(2+), NH4(+), Na(+), and K(+)) during the combined 27 months of heating and cooling, suggesting changes in concentration between 4% and 31% for a temperature change of 7 °C. Copyright © 2016 Elsevier Ltd. All rights reserved.

Final Technical Report: Viral Infection of Subsurface Microorganisms and Metal/Radionuclide Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Karrie A.; Bender, Kelly S.; Li, Yusong

Microbially mediated metabolisms have been identified as a significant factor either directly or indirectly impacting the fate and transport of heavy metal/radionuclide contaminants. To date microorganisms have been isolated from contaminated environments. Examination of annotated finished genome sequences of many of these subsurface isolates from DOE sites, revealed evidence of prior viral infection. To date the role that viruses play influencing microbial mortality and the resulting community structure which directly influences biogeochemical cycling in soils and sedimentary environments remains poorly understood. The objective of this exploratory study was to investigate the role of viral infection of subsurface bacteria and themore » formation of contaminant-bearing viral particles. This objective was approached by examining the following working hypotheses: (i) subsurface microorganisms are susceptible to viral infections by the indigenous subsurface viral community, and (ii) viral surfaces will adsorb heavy metals and radionuclides. Our results have addressed basic research needed to accomplish the BER Long Term Measure to provide sufficient scientific understanding such that DOE sites would be able to incorporate coupled physical, chemical and biological processes into decision making for environmental remediation or natural attenuation and long-term stewardship by establishing viral-microbial relationships on the subsequent fate and transport of heavy metals and radionuclides. Here we demonstrated that viruses play a significant role in microbial mortality and community structure in terrestrial subsurface sedimentary systems. The production of viral-like particles within subsurface sediments in response to biostimulation with dissolved organic carbon and a terminal electron acceptor resulted in the production of viral-like particles. Organic carbon alone did not result in significant viral production and required the addition of a terminal electron acceptor (nitrate), indicating that nutrients are not limiting viral production, but rather substrates that can be converted into energy for host metabolism. Our results also revealed that cell abundance was not correlated to the mineralization of organic carbon, but rather viruses were positively correlated with carbon mineralization. This is a result of viral-mediated cell lysis and demonstrates that viruses are sensitive indicators of microbial activity. Viruses as an indicator of microbial activity was not unique to batch culture studies as results obtained from an in situ field experiment conducted at the DOE Old Rifle Field site. This study revealed that viral abundance increased in response to the injection of oxygenated groundwater and influx of dissolved organic carbon whereas cell abundance changes were minimal. However, the extent to which viral-mediated cell lysis alters organic matter pools subsequently influencing microbial community structure and biogeochemical function remains a critical question in subsurface biogeochemical cycling. The production of significant numbers of viruses in groundwater has implications for nanoparticulate metal as well as carbon transport in groundwater. We have demonstrated that the virus surface is reactive and will adsorb heavy metals. Thus viruses can promote colloidal contaminant mobility. Interestingly, the presence of heavy metals has a positive effect on infectivity of the phage, increasing phage infection which could lead to further production of viruses. Together, the results indicate that the sorption of metals to the surface of viruses could not only contribute to nanoparticulate metal as well as carbon transport but could also enhance infectivity further contributing to cell lysis which could subsequently influence biogeochemical cycling. As more viruses infect host microbial populations the high concentration of metals would enhance infection, resulting in cell lysis, and decreasing the metabolically active host population while yielding greater numbers of viruses capable of transporting contaminats. Additional studies will be necessary to further establish the potential relationship(s) between viruses, cells, carbon, and metals/radionuclides to provide sufficient scientific understanding to incorporate coupled physical, chemical, and biological processes into agent based and reactive transport models.« less

Clays and Carbonates in a Groundwater-Fed 3.8 Ga Martian Lake: Insights to Subsurface Habitability on Mars

NASA Technical Reports Server (NTRS)

Michalski, Joseph; Niles, Paul

2015-01-01

On Earth, the deep biosphere remains a largely unexplored, but clearly important carbon reservoir. Results from some uplifted central peaks in craters on Mars indicate that substantial carbon was also present at depth and might have helped sustain a deep biosphere. In fact, many factors relevant to deep biosphere habitability are more favorable on Mars than on Earth (e.g. porosity of the crust, geothermal gradient). Future exploration of Mars should include landing sites where materials have been exhumed from depth by meteor impact or basins where subsurface fluids have emerged, carrying clues to subsurface habitability. One of the most astrobiologically interesting sites on Mars McLaughlin Crater, a 93 km-diameter impact crater that formed approximately 4 b.y. ago. On the floor of the crater is a stratigraphic section of subhorizontal, layered sedimentary rocks with strong spectroscopic evidence for Fe-rich clay minerals and Mg-rich carbonates, which we interpret as ancient lacustrine deposits. The fluids that formed these materials likely originated in the subsurface, based on the paucity of channels leading into the crater basin and the fact that this is one of the deepest basins on Mars - a good candidate to have experienced upwelling of subsurface fluids. Therefore, the deposits within McLaughlin crater provide insight into subsurface processes on Mars. In this presentation, we will discuss the habitability of the martian subsurface as well as the geology of McLaughlin Crater and the possibility to detect biomarkers at that site with a future landed mission.

Close association of active nitrifiers with Beggiatoa mats covering deep-sea hydrothermal sediments.

PubMed

Winkel, Matthias; de Beer, Dirk; Lavik, Gaute; Peplies, Jörg; Mußmann, Marc

2014-06-01

Hydrothermal sediments in the Guaymas Basin are covered by microbial mats that are dominated by nitrate-respiring and sulphide-oxidizing Beggiatoa. The presence of these mats strongly correlates with sulphide- and ammonium-rich fluids venting from the subsurface. Because ammonium and oxygen form opposed gradients at the sediment surface, we hypothesized that nitrification is an active process in these Beggiatoa mats. Using biogeochemical and molecular methods, we measured nitrification and determined the diversity and abundance of nitrifiers. Nitrification rates ranged from 74 to 605 μmol N l(-1)  mat day(-1), which exceeded those previously measured in hydrothermal plumes and other deep-sea habitats. Diversity and abundance analyses of archaeal and bacterial ammonia monooxygenase subunit A genes, archaeal 16S ribosomal RNA pyrotags and fluorescence in situ hybridization confirmed that ammonia- and nitrite-oxidizing microorganisms were associated with Beggiatoa mats. Intriguingly, we observed cells of bacterial and potential thaumarchaeotal ammonia oxidizers attached to narrow, Beggiatoa-like filaments. Such a close spatial coupling of nitrification and nitrate respiration in mats of large sulphur bacteria is novel and may facilitate mat-internal cycling of nitrogen, thereby reducing loss of bioavailable nitrogen in deep-sea sediments. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Evaluation of positron emission tomography as a method to visualize subsurface microbial processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kinsella K.; Schlyer D.; Kinsella, K.

2012-01-18

Positron emission tomography (PET) provides spatiotemporal monitoring in a nondestructive manner and has higher sensitivity and resolution relative to other tomographic methods. Therefore, this technology was evaluated for its application to monitor in situ subsurface bacterial activity. To date, however, it has not been used to monitor or image soil microbial processes. In this study, PET imaging was applied as a 'proof-of-principle' method to assess the feasibility of visualizing a radiotracer labeled subsurface bacterial strain (Rahnella sp. Y9602), previously isolated from uranium contaminated soils and shown to promote uranium phosphate precipitation. Soil columns packed with acid-purified simulated mineral soils weremore » seeded with 2-deoxy-2-[{sup 18}F]fluoro-d-glucose ({sup 18}FDG) labeled Rahnella sp. Y9602. The applicability of [{sup 18}F]fluoride ion as a tracer for measuring hydraulic conductivity and {sup 18}FDG as a tracer to identify subsurface metabolically active bacteria was successful in our soil column studies. Our findings indicate that positron-emitting isotopes can be utilized for studies aimed at elucidating subsurface microbiology and geochemical processes important in contaminant remediation.« less

The Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation

PubMed Central

Teske, Andreas; de Beer, Dirk; McKay, Luke J.; Tivey, Margaret K.; Biddle, Jennifer F.; Hoer, Daniel; Lloyd, Karen G.; Lever, Mark A.; Røy, Hans; Albert, Daniel B.; Mendlovitz, Howard P.; MacGregor, Barbara J.

2016-01-01

The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region. PMID:26925032

Immunological techniques as tools to characterize the subsurface microbial community at a trichloroethylene contaminated site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fliermans, C.B.; Dougherty, J.M.; Franck, M.M.

Effective in situ bioremediation strategies require an understanding of the effects pollutants and remediation techniques have on subsurface microbial communities. Therefore, detailed characterization of a site`s microbial communities is important. Subsurface sediment borings and water samples were collected from a trichloroethylene (TCE) contaminated site, before and after horizontal well in situ air stripping and bioventing, as well as during methane injection for stimulation of methane-utilizing microorganisms. Subsamples were processed for heterotrophic plate counts, acridine orange direct counts (AODC), community diversity, direct fluorescent antibodies (DFA) enumeration for several nitrogen-transforming bacteria, and Biolog {reg_sign} evaluation of enzyme activity in collected water samples.more » Plate counts were higher in near-surface depths than in the vadose zone sediment samples. During the in situ air stripping and bioventing, counts increased at or near the saturated zone, remained elevated throughout the aquifer, but did not change significantly after the air stripping. Sporadic increases in plate counts at different depths as well as increased diversity appeared to be linked to differing lithologies. AODCs were orders of magnitude higher than plate counts and remained relatively constant with depth except for slight increases near the surface depths and the capillary fringe. Nitrogen-transforming bacteria, as measured by serospecific DFA, were greatly affected both by the in situ air stripping and the methane injection. Biolog{reg_sign} activity appeared to increase with subsurface stimulation both by air and methane. The complexity of subsurface systems makes the use of selective monitoring tools imperative.« less

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

PubMed Central

Quaiser, Achim; Zivanovic, Yvan; Moreira, David; López-García, Purificación

2011-01-01

To extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the Sea of Marmara, the gateway between the Eastern Mediterranean and the Black Seas. Data from small subunit ribosomal RNA (SSU rRNA) gene libraries and direct pyrosequencing of the same samples indicated that Gamma- and Alpha-proteobacteria, followed by Bacteroidetes, dominated the bacterial fraction in Marmara deep-sea plankton, whereas Planctomycetes, Delta- and Gamma-proteobacteria were the most abundant groups in high bacterial-diversity sediment. Group I Crenarchaeota/Thaumarchaeota dominated the archaeal plankton fraction, although group II and III Euryarchaeota were also present. Eukaryotes were highly diverse in SSU rRNA gene libraries, with group I (Duboscquellida) and II (Syndiniales) alveolates and Radiozoa dominating plankton, and Opisthokonta and Alveolates, sediment. However, eukaryotic sequences were scarce in pyrosequence data. Archaeal amo genes were abundant in plankton, suggesting that Marmara planktonic Thaumarchaeota are ammonia oxidizers. Genes involved in sulfate reduction, carbon monoxide oxidation, anammox and sulfatases were over-represented in sediment. Genome recruitment analyses showed that Alteromonas macleodii ‘surface ecotype', Pelagibacter ubique and Nitrosopumilus maritimus were highly represented in 1000 m-deep plankton. A comparative analysis of Marmara metagenomes with ALOHA deep-sea and surface plankton, whale carcasses, Peru subsurface sediment and soil metagenomes clustered deep-sea Marmara plankton with deep-ALOHA plankton and whale carcasses, likely because of the suboxic conditions in the deep Marmara water column. The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles. PMID:20668488

Microbial transport and fate in the subsurface: An introduction to the special collection

USDA-ARS?s Scientific Manuscript database

Microorganisms constitute the almost exclusive form of life in the earth’s subsurface (not including caves), particularly at depths exceeding the soil horizon. While of broad interest to ecology and geology, scientific interest in the fate and transport of microorganisms, particularly those introduc...

ADAPTATION OF SUBSURFACE MICROBIAL BIOFILM COMMUNITIES IN RESPONSE TO CHEMICAL STRESSORS

EPA Science Inventory

The impact of this work will help improve our understanding of how subsurface biofilm communities respond to chemical stressors that are likely to be present at hazardous waste sites. Ultimately, these results can be used to determine more effective ways to insure proper envir...

Subsurface geomicrobiology of the Iberian Pyritic Belt, a terrestrial analogue of Mars

NASA Astrophysics Data System (ADS)

Amils, Ricardo

Terrestrial subsurface geomicrobiology is a matter of growing interest on many levels. From a fundamental point of view, it seeks to determine whether life can be sustained in the absence of radiation. From an astrobiological point of view, it is an interesting model for early life on Earth, as well as a representation of life as it could occur in other planetary bodies, e.g., Mars. Ŕ Tinto is an unusual extreme acidic environment due to its size, constant acidic pH, high ıo concentration of heavy metals and high level of microbial diversity. Ŕ Tinto rises in the core of ıo the Iberian Pyritic Belt (IPB), one of the biggest sulfidic ore deposits in the world. Today it is clear that the extreme characteristics of Ŕ Tinto are not due to acid mine drainage resulting ıo from mining activity. To explore the hypothesis that a continuous underground reactor of chemolithotrophic microorganisms thriving in the rich sulfidic minerals of the IPB is responsible for the extreme conditions found in the river, a drilling project has been developed to detect evidence of subsurface microbial activity and potential resources to support these microbial communities in situ from retrieved cores (MARTE project). Preliminary results clearly show that there is an active subsurface geomicrobiology in the Iberian Pyritic Belt associated to places were ground waters intersects the sulfidic ore body.

Utilization of subsurface microbial electrochemical systems to elucidate the mechanisms of competition between methanogenesis and microbial iron(III)/humic acid reduction in Arctic peat soils

NASA Astrophysics Data System (ADS)

Friedman, E. S.; Miller, K.; Lipson, D.; Angenent, L. T.

2012-12-01

High-latitude peat soils are a major carbon reservoir, and there is growing concern that previously dormant carbon from this reservoir could be released to the atmosphere as a result of continued climate change. Microbial processes, such as methanogenesis and carbon dioxide production via iron(III) or humic acid reduction, are at the heart of the carbon cycle in Arctic peat soils [1]. A deeper understanding of the factors governing microbial dominance in these soils is crucial for predicting the effects of continued climate change. In previous years, we have demonstrated the viability of a potentiostatically-controlled subsurface microbial electrochemical system-based biosensor that measures microbial respiration via exocellular electron transfer [2]. This system utilizes a graphite working electrode poised at 0.1 V NHE to mimic ferric iron and humic acid compounds. Microbes that would normally utilize these compounds as electron acceptors donate electrons to the electrode instead. The resulting current is a measure of microbial respiration with the electrode and is recorded with respect to time. Here, we examine the mechanistic relationship between methanogenesis and iron(III)- or humic acid-reduction by using these same microbial-three electrode systems to provide an inexhaustible source of alternate electron acceptor to microbes in these soils. Chamber-based carbon dioxide and methane fluxes were measured from soil collars with and without microbial three-electrode systems over a period of four weeks. In addition, in some collars we simulated increased fermentation by applying acetate treatments to understand possible effects of continued climate change on microbial processes in these carbon-rich soils. The results from this work aim to increase our fundamental understanding of competition between electron acceptors, and will provide valuable data for climate modeling scenarios. 1. Lipson, D.A., et al., Reduction of iron (III) and humic substances plays a major role in anaerobic respiration in an Arctic peat soil. Journal of Geophysical Research-Biogeosciences, 2010. 115. 2. Friedman, E.S., et al., A cost-effective and field-ready potentiostat that poises subsurface electrodes to monitor bacterial respiration. Biosensors and Bioelectronics, 2012. 32(1): p. 309-313.

Biogeochemistry of microbial coal-bed methane

USGS Publications Warehouse

Strc, D.; Mastalerz, Maria; Dawson, K.; MacAlady, J.; Callaghan, A.V.; Wawrik, B.; Turich, C.; Ashby, M.

2011-01-01

Microbial methane accumulations have been discovered in multiple coal-bearing basins over the past two decades. Such discoveries were originally based on unique biogenic signatures in the stable isotopic composition of methane and carbon dioxide. Basins with microbial methane contain either low-maturity coals with predominantly microbial methane gas or uplifted coals containing older, thermogenic gas mixed with more recently produced microbial methane. Recent advances in genomics have allowed further evaluation of the source of microbial methane, through the use of high-throughput phylogenetic sequencing and fluorescent in situ hybridization, to describe the diversity and abundance of bacteria and methanogenic archaea in these subsurface formations. However, the anaerobic metabolism of the bacteria breaking coal down to methanogenic substrates, the likely rate-limiting step in biogenic gas production, is not fully understood. Coal molecules are more recalcitrant to biodegradation with increasing thermal maturity, and progress has been made in identifying some of the enzymes involved in the anaerobic degradation of these recalcitrant organic molecules using metagenomic studies and culture enrichments. In recent years, researchers have attempted lab and subsurface stimulation of the naturally slow process of methanogenic degradation of coal. Copyright ?? 2011 by Annual Reviews. All rights reserved.

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems.

PubMed

Babatunde, A O; Miranda-CasoLuengo, Raul; Imtiaz, Mehreen; Zhao, Y Q; Meijer, Wim G

2016-08-01

This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems (CWs). Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100gBOD5/(m(2)·day), similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus (P), the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10gP/(m(2)·day) based on the performance results obtained within the first 16months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance. Copyright © 2016. Published by Elsevier B.V.

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

PubMed

Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

2015-10-01

Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

Orenia metallireducens sp. nov. strain Z6, a Novel Metal-reducing [member of the Phylum] Firmicute from the Deep Subsurface

DOE PAGES

Dong, Yiran; Sanford, Robert A.; Boyanov, Maxim I.; ...

2016-08-26

A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H 2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C).more » At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe 2O 3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe 3(PO 4) 2] and siderite (FeCO 3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. In conclusion, these distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov.« less

Lessons from Suiyo Seamount studies, for understanding extreme (ancient?) microbial ecosystems in the deep-sea hydrothermal fields

NASA Astrophysics Data System (ADS)

Maruyama, A.; Higashi, Y.; Sunamura, M.; Urabe, T.

2004-12-01

Deep-sea hydrothermal ecosystems are driven with various geo-thermally modified, mainly reduced, compounds delivered from extremely hot subsurface environments. To date, several unique microbes including thermophilic archaeons have been isolated from/around vent chimneys. However, there is little information about microbes in over-vent and sub-vent fields. Here, we report several new findings on microbial diversity and ecology of the Suiyo Seamount that locates on the Izu-Bonin Arc in the northwest Pacific Ocean, as a result of the Japanese Archaean Park project, with special concern to the sub-vent biosphere. At first, we succeeded to reveal a very unique microbial ecosystem in hydrothermal plume reserved within the outer rim of the seamount crater, that is, it consisted of almost all metabolically active microbes belonged to only two Bacteria phylotypes, probably of sulfur oxidizers. In the center of the caldera seafloor (ca. 1,388-m deep) consisted mainly of whitish sands and pumices, we found many small chimneys (ca. 5-10 cm) and bivalve colonies distributed looking like gray to black patches. These geo/ecological features of the seafloor were supposed to be from a complex mixing of hydrothermal venting and strong water current near the seafloor. Through quantitative FISH analysis for various environmental samples, one of the two representative groups in the plume was assessed to be from some of the bivalve colonies. Using the Benthic Multi-coring System (BMS), total 10 points were drilled and 6 boreholes were maintained with stainless or titanium casing pipes. In the following submersible surveys, newly developed catheter- and column-type in situ growth chambers were deployed in and on the boreholes, respectively, for collecting indigenous sub-vent microbes. Finally, we succeeded to detect several new phylotypes of microbes in these chamber samples, e.g., within epsilon-Proteobacteria, a photosynthetic group of alpha-Proteobacteria, and hyperthermophile-related Euryarchaea. By the FISH analysis, however, some specific members of Bacteria that differed from those in the chamber samples were occasionally abundant in hot vent fluids. In clone library analysis of column-type chamber samples, we also found very unique vertical profiles in the community of Archaea, i.e., rich in uncultivable Marine Group I & II members in the upper and middle columns situated at a warm vent site, while heterotrophic thermophiles in the middle and bottom. In a bottom column sample from a hot vent site, hyperthermophilic anaerobes were detected. From these results, we will propose a vertical profile model for the sub-vent Archaea community. From geophysical, geochemical and geological surveys, this sub-vent ecosystem is supposed to be restricted in a shallow subsurface region. Whether these unique ecosystems are general in hydrothermal fields over the sea or specific only to this submarine volcano will be discussed.

Issues in subsurface exploration of ice sheets

NASA Technical Reports Server (NTRS)

French, L.; Carsey, F.; Zimmerman, W.

2000-01-01

Exploration of the deep subsurface ice sheets of Earth, Mars, Europa, and Titan has become a major consideration in addressing scientific objectives in climate change, extremophile biology, exobiology,chemical weathering, planetary evolution and ice dynamics.

LIPID ANALYSIS TO DETERMINE THE EFFECT OF A SOURCE REMEDIAL TECHNOLOGY IN MICROBIAL ECOLOGY

EPA Science Inventory

Microbial community structures and related changes in the subsurface environment were investigated following in situ chemical oxidation (ISCO) treatment at Launch Complex 34, Cape Canaveral Air Station, Florida. The site has dense non-aqueous phase (DNAPL) concentrations of TCE ...

Using N-Limiting Growth Conditions to Remove Atrazine from Groundwater: Laboratory Studies.

USDA-ARS?s Scientific Manuscript database

Typically, respiratory redox reactions are the driving mechanism behind in situ bioremediations that use a carbon substrate. This is because electron (e-) donor availability generally restricts subsurface microbial activity. Thus, microbial growth and respiration can be greatly stimulated by the a...

Microbial structures in an Alpine Thermal Spring - Microscopic techniques for the examination of Biofilms in a Subsurface Environment

NASA Astrophysics Data System (ADS)

Dornmayr-Pfaffenhuemer, Marion; Pierson, Elisabeth; Janssen, Geert-Jan; Stan-Lotter, Helga

2010-05-01

The research into extreme environments hast important implications for biology and other sciences. Many of the organisms found there provide insights into the history of Earth. Life exists in all niches where water is present in liquid form. Isolated environments such as caves and other subsurface locations are of interest for geomicrobiological studies. And because of their "extra-terrestrial" conditions such as darkness and mostly extreme physicochemical state they are also of astrobiological interest. The slightly radioactive thermal spring at Bad Gastein (Austria) was therefore examined for the occurrence of subsurface microbial communities. The surfaces of the submerged rocks in this warm spring were overgrown by microbial mats. Scanning electron microscopy (SEM) performed by the late Dr. Wolfgang Heinen revealed an interesting morphological diversity in biofilms found in this environment (1, 2). Molecular analysis of the community structure of the radioactive subsurface thermal spring was performed by Weidler et al. (3). The growth of these mats was simulated using sterile glass slides which were exposed to the water stream of the spring. Those mats were analysed microscopically. Staining, using fluorescent dyes such as 4',6-Diamidino-2-phenylindol (DAPI), gave an overview of the microbial diversity of these biofilms. Additional SEM samples were prepared using different fixation protocols. Scanning confocal laser microscopy (SCLM) allowed a three dimensional view of the analysed biofilms. This work presents some electron micrographs of Dr. Heinen and additionally new microscopic studies of the biofilms formed on the glass slides. The appearances of the new SEM micrographs were compared to those of Dr. Heinen that were done several years ago. The morphology and small-scale distribution in the microbial mat was analyzed by fluorescence microscopy. The examination of natural biomats and biofilms grown on glass slides using several microscopical techniques suggest that the thermal springs in the Central Alps near Bad Gastein represent a novel and unique habitat for microbial life. Results obtained during these studies revealed reproducibility of Dr. Heinen's micrographs. Hollow reticulated filaments and flat ribbons with parallel hexagonal chambers (web-structures) were found repeatedly. Given the chance that subsurface environments represent a potent opportunity to detect life on planetary bodies it is of big interest to search for representative biosignatures found on earth today. References: 1. Lauwers A. M. & Heinen W. (1985) Mikroskopie (Wien) 42, 94-101. 2. Heinen W. & Lauwers A. M. (1985) Mikroskopie (Wien) 42, 124-134. 3. Weidler G. W., Dornmayr-Pfaffenhuemer M., Gerbl F. W., Heinen W., Stan-Lotter H. (2007) AEM 73, 259-270.

Drilling Automation Demonstrations in Subsurface Exploration for Astrobiology

NASA Technical Reports Server (NTRS)

Glass, Brian; Cannon, H.; Lee, P.; Hanagud, S.; Davis, K.

2006-01-01

This project proposes to study subsurface permafrost microbial habitats at a relevant Arctic Mars-analog site (Haughton Crater, Devon Island, Canada) while developing and maturing the subsurface drilling and drilling automation technologies that will be required by post-2010 missions. It builds on earlier drilling technology projects to add permafrost and ice-drilling capabilities to 5m with a lightweight drill that will be automatically monitored and controlled in-situ. Frozen cores obtained with this drill under sterilized protocols will be used in testing three hypotheses pertaining to near-surface physical geology and ground H2O ice distribution, viewed as a habitat for microbial life in subsurface ice and ice-consolidated sediments. Automation technologies employed will demonstrate hands-off diagnostics and drill control, using novel vibrational dynamical analysis methods and model-based reasoning to monitor and identify drilling fault states before and during faults. Three field deployments, to a Mars-analog site with frozen impact crater fallback breccia, will support science goals, provide a rigorous test of drilling automation and lightweight permafrost drilling, and leverage past experience with the field site s particular logistics.

Performance Indicators for Uranium Bioremediation in the Subsurface: Basis and Assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, Philip E.; Yabusaki, Steven B.

2006-12-29

The purpose of this letter report is to identify performance indicators for in situ engineered bioremediation of subsurface uranium (U) contamination. This report focuses on in situ treatment of groundwater by biostimulation of extant in situ microbial populations (see http://128.3.7.51/NABIR/generalinfo/primers_guides/03_NABIR_primer.pdf for background information on bioremediation of metals and radionuclides). The treatment process involves amendment of the subsurface with an electron donor such as acetate, lactate, ethanol or other organic compound such that in situ microorganisms mediate the reduction of U(VI) to U(IV). U(VI) precipitates as uraninite or other insoluble U phase. Uranium is thus immobilized in place by such processesmore » and is subject to reoxidation that may remobilize the reduced uranium. Related processes include augmenting the extant subsurface microbial populations, addition of electron acceptors, and introduction of chemically reducing materials such as zero-valent Fe. While metrics for such processes may be similar to those for in situ biostimulation, these related processes are not directly in the scope of this letter report.« less

Insight from Genomics on Biogeochemical Cycles in a Shallow-Sea Hydrothermal System

NASA Astrophysics Data System (ADS)

Lu, G. S.; Amend, J.

2015-12-01

Shallow-sea hydrothermal ecosystems are dynamic, high-energy systems influenced by sunlight and geothermal activity. They provide accessible opportunities for investigating thermophilic microbial biogeochemical cycles. In this study, we report biogeochemical data from a shallow-sea hydrothermal system offshore Paleochori Bay, Milos, Greece, which is characterized by a central vent covered by white microbial mats with hydrothermally influenced sediments extending into nearby sea grass area. Geochemical analysis and deep sequencing provide high-resolution information on the geochemical patterns, microbial diversity and metabolic potential in a two-meter transect. The venting fluid is elevated in temperature (~70oC), low in pH (~4), and enriched in reduced species. The geochemical pattern shows that the profile is affected by not only seawater dilution but also microbial regulation. The microbial community in the deepest section of vent core (10-12 cm) is largely dominated by thermophilic archaea, including a methanogen and a recently described Crenarcheon. Mid-core (6-8 cm), the microbial community in the venting area switches to the hydrogen utilizer Aquificae. Near the sediment-water interface, anaerobic Firmicutes and Actinobacteria dominate, both of which are commonly associated with subsurface and hydrothermal sites. All other samples are dominated by diverse Proteobacteria. The sulfate profile is strongly correlated with the population size of delta- and episilon-proteobactia. The dramatic decrease in concentrations of As and Mn in pore fluids as a function of distance from the vent suggests that in addition to seawater dilution, microorganisms are likely transforming these and other ions through a combination of detoxification and catabolism. In addition, high concentrations of dissolved Fe are only measurable in the shallow sea grass area, suggesting that iron-transforming microorganisms are controlling Fe mobility, and promoting biomineralization. Taken together, these samples represent the effects of submarine venting on sediment microbial communities both vertically and horizontally in the predicted fluid flow path, and will provide a detailed investigation of genetic potential for biogeochemical cycling at Paleochori Bay.

Bioremediation of uranium-contaminated groundwater: a systems approach to subsurface biogeochemistry.

PubMed

Williams, Kenneth H; Bargar, John R; Lloyd, Jonathan R; Lovley, Derek R

2013-06-01

Adding organic electron donors to stimulate microbial reduction of highly soluble U(VI) to less soluble U(IV) is a promising strategy for immobilizing uranium in contaminated subsurface environments. Studies suggest that diagnosing the in situ physiological status of the subsurface community during uranium bioremediation with environmental transcriptomic and proteomic techniques can identify factors potentially limiting U(VI) reduction activity. Models which couple genome-scale in silico representations of the metabolism of key microbial populations with geochemical and hydrological models may be able to predict the outcome of bioremediation strategies and aid in the development of new approaches. Concerns remain about the long-term stability of sequestered U(IV) minerals and the release of co-contaminants associated with Fe(III) oxides, which might be overcome through targeted delivery of electrons to select microorganisms using in situ electrodes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Seasonal change in precipitation, snowpack, snowmelt, soil water and streamwater chemistry, northern Michigan

USGS Publications Warehouse

Stottlemyer, R.; Toczydlowski, D.

1999-01-01

We have studied weekly precipitation, snowpack, snowmelt, soil water and streamwater chemistry throughout winter for over a decade in a small (176 ha) northern Michigan watershed with high snowfall and vegetated by 60 to 80 year-old northern hardwoods. In this paper, we examine physical, chemical, and biological processes responsible for observed seasonal change in streamwater chemistry based upon intensive study during winter 1996-1997. The objective was to define the contributions made to winter and spring streamwater chemical concentration and flux by processes as snowmelt, over-winter forest floor and surface soil mineralization, immobilization, and exchange, and subsurface flowpath. The forest floor and soil were unfrozen beneath the snowpack which permitted most snowmelt to enter. Over-winter soil mineralization and other biological processes maintain shallow subsurface ion and dissolved organic carbon (DOC) reservoirs. Small, but steady, snowmelt throughout winter removed readily mobilized soil NO3- which resulted in high over-winter streamwater concentrations but little flux. Winter soil water levels and flowpaths were generally deep which increased soil water and streamwater base cation (C(B)), HCO3-, and Si concentrations. Spring snowmelt increased soil water levels and removal of ions and DOC from the biologically active forest floor and shallow soils. The snowpack solute content was a minor component in determining streamwater ion concentration or flux during and following peak snowmelt. Exchangeable ions, weakly adsorbed anions, and DOC in the forest floor and surface soils dominated the chemical concentration and flux in soil water and streamwater. Following peak snowmelt, soil microbial immobilization and rapidly increased plant uptake of limiting nutrients removed nearly all available nitrogen from soil water and streamwater. During the growing season high evapotranspiration increased subsurface flowpath depth which in turn removed weathering products, especially C(B), HCO3-, and Si, from deeper soils. Soil water was a major component in the hydrologic and chemical budgets.We have studied weekly precipitation, snowpack, snowmelt, soil water and streamwater chemistry throughout winter for over a decade in a small (176 ha) northern Michigan watershed with high snowfall and vegetated by 60 to 80 year-old northern hardwoods. In this paper, we examine physical, chemical, and biological processes responsible for observed seasonal change in streamwater chemistry based upon intensive study during winter 1996-1997. The objective was to define the contributions made to winter and spring streamwater chemical concentration and flux by processes as snowmelt, over-winter forest floor and surface soil mineralization, immobilization, and exchange, and subsurface flowpath. The forest floor and soils were unfrozen beneath the snowpack which permitted most snowmelt to enter. Over-winter soil mineralization and other biological processes maintain shallow subsurface ion and dissolved organic carbon (DOC) reservoirs. Small, but steady, snowmelt throughout winter removed readily mobilized soil NO3- which resulted in high over-winter streamwater concentrations but little flux. Winter soil water levels and flowpaths were generally deep which increased soil water and streamwater base cation (CB), HCO3-, and Si concentrations. Spring snowmelt increased soil water levels and removal of ions and DOC from the biologically active forest floor and shallow soils. The snowpack solute content was a minor component in determining streamwater ion concentration or flux during and following peak snowmelt. Exchangeable ions, weakly adsorbed anions, and DOC in the forest floor and surface soils dominated the chemical concentration and flux in soil water and streamwater. Following peak snowmelt, soil microbial immobilization and rapidly increased plant uptake of limiting nutrients removed nearly all available nitrogen from soil water and streamwater. D

Microbial degradation of crude oil and some model hydrocarbons

USGS Publications Warehouse

Chang, Fu-Hsian; Noben, N.N.; Brand, Danny; Hult, Marc F.

1988-01-01

Research on microbial degradation of crude oil in the shallow subsurface at a spill site near Bemidji, Minn. (fig. C-l), began in 1983 (Hull, 1984; Chang and Ehrlich, 1984). The rate and extent of crude oil and model hydrocarbon biodegradation by the indigenous microbial community was measured in the laboratory at several concentrations of inorganic nutrients, conditions of oxygen availability, incubation temperatures, and incubation time.

The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Methe, Barbara; Lipton, Mary; Mahadevan, Krishna

Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives ofmore » this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling development. The model as created is capable of predicting the response of the community structure in changing environments such as anoxic/oxic conditions or limitations by carbon or nutrients. The ability to more accurately model these responses is critical to understanding carbon and energy flows in an ecosystem is critical towards improving our ability to make predictions that can be used to design more efficient remediation and management strategies, and better understand the implications of environmental perturbations on these ecosystems.« less

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Donald; Nolan, Jason; Williams, Kenneth H.

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.« less

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

DOE PAGES

Pan, Donald; Nolan, Jason; Williams, Kenneth H.; ...

2017-07-11

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.« less

Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Kenneth H.; Kemna, Andreas; Wilkins, Michael J.

2009-08-05

Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1more » Hz) andwasdependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous phase response were enriched in Fe(II), dissolved sulfide, and cell-associated FeS nanoparticles. The accumulation of mineral precipitates and electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the anomalous IP response and revealing the usefulness of multifrequency IP measurements for monitoring mineralogical and geochemical changes accompanying stimulated subsurface bioremediation.« less

[Effects of intensive management on soil C and N pools and soil enzyme activities in Moso bamboo plantations.

PubMed

Yang, Meng; Li, Yong Fu; Li, Yong Chun; Xiao, Yong Heng; Yue, Tian; Jiang, Pei Kun; Zhou, Guo Mo; Liu, Juan

2016-11-18

In order to elucidate the effects of intensive management on soil carbon pool, nitrogen pool, enzyme activities in Moso bamboo (Phyllostachys pubescens) plantations, we collected soil samples from the soil surface (0-20 cm) and subsurface (20-40 cm) layers in the adjacent Moso bamboo plantations with extensive and intensive managements in Sankou Township, Lin'an City, Zhejiang Province. We determined different forms of C, N and soil invertase, urease, catalase and acid phosphatase activities. The results showed that long-term intensive management of Moso bamboo plantations significantly decreased the content and storage of soil organic carbon (SOC), with the SOC storage in the soil surface and subsurface layers decreased by 13.2% and 18.0%, respectively. After 15 years' intensive management of Masoo bamboo plantations, the contents of soil water soluble carbon (WSOC), hot water soluble carbon (HWSOC), microbial carbon (MBC) and readily oxidizable carbon (ROC) were significantly decreased in the soil surface and subsurface layers. The soil N storage in the soil surface and subsurface layers in intensively managed Moso bamboo plantations increased by 50.8% and 36.6%, respectively. Intensive management significantly increased the contents of nitrate-N (NO 3 - -N) and ammonium-N (NH 4 + -N), but decreased the contents of water-soluble nitrogen (WSON) and microbial biomass nitrogen (MBN). After 15 years' intensive management of Masoo bamboo plantations, the soil invertase, urease, catalase and acid phosphatase activities in the soil surface layer were significantly decreased, the soil acid phosphatase activity in the soil subsurface layer were significantly decreased, and other enzyme activities in the soil subsurface layer did not change. In conclusion, long-term intensive management led to a significant decline of soil organic carbon storage, soil labile carbon and microbial activity in Moso bamboo plantations. Therefore, we should consider the use of organic fertilizer in the intensive mana-gement process for the sustainable management of Moso bamboo plantations in the future.

First Microbial Community Assessment of Borehole Fluids from the Deep Underground Science and Engineering Laboratory (DUSEL)

NASA Astrophysics Data System (ADS)

Moser, D. P.; Anderson, C.; Bang, S.; Jones, T. L.; Boutt, D.; Kieft, T.; Sherwood Lollar, B.; Murdoch, L. C.; Pfiffner, S. M.; Bruckner, J.; Fisher, J. C.; Newburn, J.; Wheatley, A.; Onstott, T. C.

2010-12-01

Fluid and gas samples were collected from two flowing boreholes at the 4100 (1,250 m) and 4850 ft (1478 m) levels of the former Homestake Gold Mine in Lead, South Dakota. Service- and flood water samples were also collected as comparative benchmarks. With a maximum depth of 8,000 ft, (2,438 m), this mine currently hosts the Sanford Laboratory and is the proposed location for the US Deep Underground Science and Engineering Laboratory (DUSEL). The uncased 4100L hole is a legacy of mining; whereas, the cased 4850 hole was drilled in 2009 in support of large cavity construction. Both were packered or valved to exclude mine air and sampled anaerobically using aseptic technique. Physical measurements, aquatic and dissolved gas chemistry, cell counts, and microbial community assessments (SSU rRNA libraries) were performed on all samples. This study represents the first at Sanford Lab/DUSEL specifically focused on the deep biosphere rather than mine microbiology. Fluids from the two holes differed markedly, with that from 4100L being characterized by NaHCO3 and 4850 by Na2SO4. pH values of 8.2 vs. 7.5, conductivities (μS) of 1790 vs. 7667 and alkalinities (mg/L) of 767 vs. 187 were obtained from 4100L and 4850, respectively. As expected, the deeper 4850L hole had the higher temperature (38 vs. 30 oC). Neither had measureable nitrate, but both had similar dissolved organic C (DOC) concentrations (0.8 vs. 0.9 mg/L). Sulfate was present at 337 vs. 4,470 mg/L in 4100L and 4850L. Major dissolved gases were N2 (91 and 81 vol%), O2 (12 and 16 vol%) and CH4 (0.07 and 3.35 vol%) in 4100L and 4850L. The δ13C of CH4 was -51 and -56.7 permil in 4100L and 4850, respectively. The uncorrected 14C age of DIC was calculated at 25,310 (+/- 220) and 47,700 (+/-3,100) years for the two fluids. Cell counts were 5.9e3 and 2.01e5 in 4100L and 4850. Microbial community structure was diverse in both holes and distinct from that of service water. A large proportion of rRNA library clones were Proteobacteria and closely related to known or expected aerobes including: Thiobacillus, Siderooxidans, Leptothrix, Hydrogenophaga, Pseaudomonas, Methylomonas and Thiothrix, consistent with possible mine water or air contamination. Conversely, Deltaproteobacteria and Firmicute clones, often very closely related to others detected from deep mine or sediment habitats, suggests a deep subsurface component as well. Archaeal clones from 4100L were dominated by a deeply-branching clade with no cultivated representatives; whereas, those from 4850 were mostly related to known methanogens (e.g. Methanolobus). Collectively, this dataset suggests mixed end-member or deeply-sourced water partially overprinted by mine-related artifacts. However, until more is known concerning the deep hydrogeology of this system, it will be difficult to ascertain indigenous from impacted microbial communities in DUSEL.

Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere.

PubMed

Fullerton, Heather; Moyer, Craig L

2016-05-15

Chloroflexi small-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylum Chloroflexi is represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurface Chloroflexi Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurface Chloroflexi single amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nine Chloroflexi SAGs (seven of which are from the order Anaerolineales) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of the Chloroflexi SAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the seven Anaerolineales SAGs contains a distinct reductive dehalogenase homologous (rdhA) gene. Through the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, the Chloroflexi These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examined Chloroflexi SAGs, our genomes (several are from the order Anaerolineales) were recovered from a hydrothermally driven system and therefore provide a unique window into the metabolic potential of this type of habitat. In addition, a reductive dehalogenase gene (rdhA) has been directly linked to marine subsurface Chloroflexi, suggesting that reductive dehalogenation is not limited to the class Dehalococcoidia This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group. Copyright © 2016 Fullerton and Moyer.

Microbial reduction of structural Fe3+ in nontronite by a thermophilic bacterium and its role in promoting the smectite to illite reaction

USGS Publications Warehouse

Zhang, G.; Dong, H.; Kim, J.; Eberl, D.D.

2007-01-01

The illitization process of Fe-rich smectite (nontronite NAu-2) promoted by microbial reduction of structural Fe3+ was investigated by using a thermophilic metal-reducing bacterium, Thermoanaerobacter ethanolicus, isolated from the deep subsurface. T. ethanolicus was incubated with lactate as the sole electron donor and structural Fe3+ in nontronite as the sole electron acceptor, and anthraquinone-2, 6-disulfonate (AQDS) as an electron shuttle in a growth medium (pH 6.2 and 9.2, 65 ??C) with or without an external supply of Al and K sources. With an external supply of Al and K, the extent of reduction of Fe3+ in NAu-2 was 43.7 and 40.4% at pH 6.2 and 9.2, respectively. X-ray diffraction and scanning and transmission electron microscopy revealed formation of discrete illite at pH 9.2 with external Al and K sources, while mixed layers of illite/smectite or highly charged smectite were detected under other conditions. The morphology of biogenic illite evolved from lath and flake to pseudo-hexagonal shape. An external supply of Al and K under alkaline conditions enhances the smectite-illite reaction during microbial Fe3+ reduction of smectite. Biogenic SiO2 was observed as a result of bioreduction under all conditions. The microbially promoted smectite-illite reaction proceeds via dissolution of smectite and precipitation of illite. Thermophilic iron reducing bacteria have a significant role in promoting the smectite to illite reaction under conditions common in sedimentary basins.

Seasonal switchgrass ecotype contributions to soil organic carbon, deep soil microbial community composition and rhizodeposit uptake during an extreme drought

USDA-ARS?s Scientific Manuscript database

The importance of rhizodeposit C and associated microbial communities in deep soil C stabilization is relatively unknown. Phenotypic variability in plant root biomass could impact C cycling through belowground plant allocation, rooting architecture, and microbial community abundance and composition...

Characterisation of DOC and its relation to the deep terrestrial biosphere

NASA Astrophysics Data System (ADS)

Vieth, Andrea; Vetter, Alexandra; Sachse, Anke; Horsfield, Brian

2010-05-01

The deep subsurface is populated by a large number of microorganisms playing a pivotal role in the carbon cycling. The question arises as to the origin of the potential carbon sources that support deep microbial communities and their possible interactions within the deep subsurface. As the carbon sources need to be dissolved in formation fluids to become available to microorganisms, the dissolved organic carbon (DOC) needs further characterisation as regards concentration, structural as well as molecular composition and origin. The Malm carbonates in the Molasse basin of southern Germany are of large economic potential as they are targets for both hydrocarbon and geothermal exploration (ANDREWS et al., 1987). Five locations that differ in their depth of the Malm aquifer between 220 m and 3445 m below surface have been selected for fluid sampling. The concentration and the isotopic composition of the DOC have been determined. To get a better insight into the structural composition of the DOC, we also applied size exclusion chromatography and quantified the amount of low molecular weight organic acids (LMWOA) by ion chromatography. With increasing depth of the aquifer the formation fluids show increasing salinity as chloride concentrations increase from 2 to 300 mg/l and also the composition of the DOC changes. Water samples from greater depth (>3000 m) showed that the DOC mainly consists of LMWOA (max. 83 %) and low percentages of neutral compounds (alcohols, aldehyde, ketones, amino acids) as well as "building blocks". Building blocks have been described to be the oxidation intermediates from humic substances to LMWOA. With decreasing depth of the aquifer, the DOC of the fluid becomes increasingly dominated by neutral compounds and the percentage of building blocks increases to around 27%. The fluid sample from 220 m depth still contains a small amount of humic substances. The DOC of formation fluids in some terrestrial sediments may originate from organic-rich layers like coals and source rocks which may provide carbon sources for the deep biosphere by leaching water soluble organic compounds. We investigated the potential of a series of Eocene-Pleistocene coals, mudstones and sandstones from New Zealand with different maturities (Ro between 0.29 and 0.39) and total organic carbon content (TOC) regarding their potential to release such compounds. The water extraction of these New Zealand coals using Soxhlet apparatus resulted in yields of LMWOA that may feed the local deep terrestrial biosphere over geological periods of time (VIETH et al., 2008). However, the DOC of the water extracts mainly consisted of humic substances. To investigate the effect of thermal maturity of the organic matter as well as the effect of the organic matter type on the extraction yields, we examined additional coal samples (Ro between 0.29 and 0.80) and source rock samples from low to medium maturity (Ro between 0.3 to 1.1). Within our presentation we would like to show the compositional diversity and variability of dissolved organic compounds in natural formation fluids as well as in water extracts from a series of very different lithologies and discuss their effects on the carbon cycling in the deep terrestrial subsurface. References: Andrews, J. N., Youngman, M. J., Goldbrunner, J. E., and Darling, W. G., 1987. The geochemistry of formation waters in the Molasse Basin of Upper Austria. Environmental Geology 10, 43-57. Vieth, A., Mangelsdorf, K., Sykes, R., and Horsfield, B., 2008. Water extraction of coals - potential to estimate low molecular weight organic acids as carbon feedstock for the deep terrestrial biosphere? Organic Geochemistry 39, 985-991.

EVALUATION OF COMMERCIAL, MICROBIAL-BASED PRODUCTS TO TREAT PARAFFIN DEPOSITION IN TANK BOTTOMS AND OIL PRODUCTION EQUIPMENT

EPA Science Inventory

Introduction:

Paraffins are naturally-occurring components of crude oils, but often form solids within oil reservoirs and on oil production equipment when oil is harvested from hot subsurface temperatures to the cooler surface environments. Microbial t...

Pilot-scale vadose zone microbial biobarriers removed nitrate leaching from a cattle corral

USDA-ARS?s Scientific Manuscript database

activities that involve animal wastes can result in the contamination of subsurface soils by nitrates. In saturated or nearly saturated soils microbial biobarriers are a common method used to remove contaminants from water. This field study was conducted beneath a cattle pen in northeast Colorado a...

Genetic analysis of stress responses in soil bacteria for enhanced bioremediation of mixed contaminants. 1997 annual progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, K.K.

'To provide increased knowledge of stress responses of indigenous microbes at contaminated sites as well as using microbes as molecular probes for monitoring the performance and effectiveness of bioremediation, the authors propose to identify the stress-inducible genes and promoters from two soil bacteria, Deinococcus radiodurans and Sphingomonas F199. These organisms represent two phylogenetically distinct groups of soil bacteria, each of which has specific features of interest for bioremediation. D. radiodurans exhibits high resistance to external stress; F199 is a deep subsurface (Savannah River Site) organism with unique degradative capabilities. Research Statement To realize the full potential of bioremediation, an understandingmore » of microbial community and individual bacterial responses to the stresses encountered at contaminated sites is needed. Knowledge about genetic responses of soil and subsurface bacteria to environmental stresses, which include low nutrients, low oxygen, and mixed pollutants, will allow extrapolation of basic principles to field applications either using indigenous bacteria or genetically engineered microorganisms. Defining bacterial responses to those stresses presents an opportunity for improving bioremediation strategies, and should contribute to environmental management and restoration actions that would reduce the cost and time required to achieve DOE''s cleanup goals.'« less

The contribution of the Precambrian continental lithosphere to global H2 production.

PubMed

Lollar, Barbara Sherwood; Onstott, T C; Lacrampe-Couloume, G; Ballentine, C J

2014-12-18

Microbial ecosystems can be sustained by hydrogen gas (H2)-producing water-rock interactions in the Earth's subsurface and at deep ocean vents. Current estimates of global H2 production from the marine lithosphere by water-rock reactions (hydration) are in the range of 10(11) moles per year. Recent explorations of saline fracture waters in the Precambrian continental subsurface have identified environments as rich in H2 as hydrothermal vents and seafloor-spreading centres and have suggested a link between dissolved H2 and the radiolytic dissociation of water. However, extrapolation of a regional H2 flux based on the deep gold mines of the Witwatersrand basin in South Africa yields a contribution of the Precambrian lithosphere to global H2 production that was thought to be negligible (0.009 × 10(11) moles per year). Here we present a global compilation of published and new H2 concentration data obtained from Precambrian rocks and find that the H2 production potential of the Precambrian continental lithosphere has been underestimated. We suggest that this can be explained by a lack of consideration of additional H2-producing reactions, such as serpentinization, and the absence of appropriate scaling of H2 measurements from these environments to account for the fact that Precambrian crust represents over 70 per cent of global continental crust surface area. If H2 production via both radiolysis and hydration reactions is taken into account, our estimate of H2 production rates from the Precambrian continental lithosphere of 0.36-2.27 × 10(11) moles per year is comparable to estimates from marine systems.

Methods for microbial filtration of fluids

DOEpatents

Carman, Margaret L.; Jackson, Kenneth J.; Knapp, Richard B.; Knezovich, John P.; Shah, Nilesh N.; Taylor, Robert T.

1996-01-01

Novel methods for purifying contaminated subsurface groundwater are disclosed. The method is involves contacting the contaminated subsurface groundwater with methanotrophic or heterotrophic microorganisms which produce contaminant-degrading enzymes. The microorganisms are derived from surface cultures and are injected into the ground so as to act as a biofilter. The contaminants which may be treated include organic or metallic materials and radionuclides.

Microbial Diversity of Groundwater from Deep Subsurface Environment

NASA Astrophysics Data System (ADS)

Lin, L.; Onstott, T. C.; Hall, J.

2002-12-01

The subsurface environment harbors one of the most abundant reservoirs of biomass on Earth. The distribution of microbial ecosystems and the diversity of microbial metabolisms there remained poorly understood due to lack of detailed sampling over three-dimensional space with extremely heterogeneous characteristics. South African Au mines, however, provide the best access in the world to various types of groundwater and rocks at depths up to 4 km below surface. In this study, we present our recent analyses of microbial community structure of groundwater (with residence time of several million years) collected from depths between 850 to 1500 mbsl of Beatrix Au mine, South Africa. Five groundwater samples were collected anaerobically from freshly drilling boreholes with flow rates of 1 to 38 L/min. Cells were concentrated through filtration and total DNA were extracted from filters and PCR-amplified with primers targeting 16S rDNA gene. The amplicons were cloned and digested with restriction enzymes to identify the unique clone type. Sequences were obtained through direct sequencing of representative clones and compared with the closest matching sequences deposited in the gene bank for the construction of phylogenetic tree. The archaeal signatures were only found in one sample and close to the lineage of methanosarcina. The most predominant ribotype was similar to the environmental clone found in the same mine under the species level while the rest of ribotypes were either close to those capable of methanogenesis from long-chain alkanes or found in rice field or were distant from other environmental clones reported in previous study (Takai et al., 2001). The bacterial community exhibited a wide range of diversity among samples. Most samples were dominated by sequences close to alpha proteobacteria with various proportions of beta, gamma proteobacteria and environmental clones. A significant proportion of sequences close to thermophilic delta proteobacteria and clostridia were observed from one of the deepest samples. Since the in-situ water or rock temperature at sampling location is below the temperature range for thermophilic bacteria, this might indicate that the microorganisms once colonizing in the deeper and hotter portion of crust were transported upward with hydrothermal fluid and preserved in the sealed water pocket for a time scale of millions of years.

Heat Stress Dictates Microbial Lipid Composition along a Thermal Gradient in Marine Sediments

PubMed Central

Sollich, Miriam; Yoshinaga, Marcos Y.; Häusler, Stefan; Price, Roy E.; Hinrichs, Kai-Uwe; Bühring, Solveig I.

2017-01-01

Temperature exerts a first-order control on microbial populations, which constantly adjust the fluidity and permeability of their cell membrane lipids to minimize loss of energy by ion diffusion across the membrane. Analytical advances in liquid chromatography coupled to mass spectrometry have allowed the detection of a stunning diversity of bacterial and archaeal lipids in extreme environments such as hot springs, hydrothermal vents and deep subsurface marine sediments. Here, we investigated a thermal gradient from 18 to 101°C across a marine sediment field and tested the hypothesis that cell membrane lipids provide a major biochemical basis for the bioenergetics of archaea and bacteria under heat stress. This paper features a detailed lipidomics approach with the focus on membrane lipid structure-function. Membrane lipids analyzed here include polar lipids of bacteria and polar and core lipids of archaea. Reflecting the low permeability of their ether-linked isoprenoids, we found that archaeal polar lipids generally dominate over bacterial lipids in deep layers of the sediments influenced by hydrothermal fluids. A close examination of archaeal and bacterial lipids revealed a membrane quandary: not only low permeability, but also increased fluidity of membranes are required as a unified property of microbial membranes for energy conservation under heat stress. For instance, bacterial fatty acids were composed of longer chain lengths in concert with higher degree of unsaturation while archaea modified their tetraethers by incorporation of additional methyl groups at elevated sediment temperatures. It is possible that these configurations toward a more fluidized membrane at elevated temperatures are counterbalanced by the high abundance of archaeal glycolipids and bacterial sphingolipids, which could reduce membrane permeability through strong intermolecular hydrogen bonding. Our results provide a new angle for interpreting membrane lipid structure-function enabling archaea and bacteria to survive and grow in hydrothermal systems. PMID:28878741

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2.

PubMed

Jin, Qusheng; Kirk, Matthew F

2016-01-01

Geological carbon sequestration captures CO 2 from industrial sources and stores the CO 2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO 2 concentration. This study uses biogeochemical modeling to explore the influence of CO 2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO 2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO 2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO 2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO 2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses.

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2

PubMed Central

Jin, Qusheng; Kirk, Matthew F.

2016-01-01

Geological carbon sequestration captures CO2 from industrial sources and stores the CO2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO2 concentration. This study uses biogeochemical modeling to explore the influence of CO2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses. PMID:27909425

Search for life on Mars.

PubMed

Brack, A; Clancy, P; Fitton, B; Hoffmann, B; Horneck, G; Kurat, G; Maxwell, J; Ori, G; Pillinger, C; Raulin, F; Thomas, N; Westall, F

1998-06-01

A multi-user integrated suite of instruments designed to optimize the search for evidence of life on Mars is described. The package includes: -Surface inspection and surface environment analysis to identify the potential Mars landing sites, to inspect the surface geology and mineralogy, to search for visible surficial microbial macrofossils, to study the surface radiation budget and surface oxidation processes, to search for niches for extant life. -Subsurface sample acquisition by core drilling -Analysis of surface and subsurface minerals and organics to characterize the surface mineralogy, to analyse the surface and subsurface oxidants, to analyse the mineralogy of subsurface aliquots, to analyse the organics present in the subsurface aliquots (elemental and molecular composition, isotopes, chirality). -Macroscopic and microscopic inspection of subsurface aliquots to search for life's indicators (paleontological, biological, mineralogical) and to characterize the mineralogy of the subsurface aliquots. The study is led by ESA Manned Spaceflight and Microgravity Directorate.

Novel determination of radon-222 velocity in deep subsurface rocks and the feasibility to using radon as an earthquake precursor

NASA Astrophysics Data System (ADS)

Zafrir, Hovav; Ben Horin, Yochai; Malik, Uri; Chemo, Chaim; Zalevsky, Zeev

2016-09-01

A novel technique utilizing simultaneous radon monitoring by gamma and alpha detectors to differentiate between the radon climatic driving forces and others has been improved and used for deep subsurface investigation. Detailed long-term monitoring served as a proxy for studying radon movement within the shallow and deep subsurface, as well as for analyzing the effect of various parameters of the radon transport pattern. The main achievements of the investigation are (a) determination, for the first time, of the radon movement velocity within rock layers at depths of several tens of meters, namely, 25 m/h on average; (b) distinguishing between the diurnal periodical effect of the ambient temperature and the semidiurnal effect of the ambient pressure on the radon temporal spectrum; and (c) identification of a radon random preseismic anomaly preceding the Nuweiba, M 5.5 earthquake of 27 June 2015 that occurred within Dead Sea Fault Zone.

Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

NASA Astrophysics Data System (ADS)

Masum, Shakil A.; Thomas, Hywel R.

2018-06-01

To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment.

PubMed

Lomstein, Bente Aa; Langerhuus, Alice T; D'Hondt, Steven; Jørgensen, Bo B; Spivack, Arthur J

2012-03-18

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach--the D:L-amino-acid model--to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.

An in vivo Investigation into Temperature-Controlled Stratification of Sub-Seafloor Populations

NASA Astrophysics Data System (ADS)

McClelland, H. L. O.; Morono, Y.; Fike, D. A.; Bradley, A. S.

2017-12-01

The deep subsurface is characterized by a paucity of carbon substrates and biologically exploitable chemical potential energy. These metabolic challenges can be exacerbated by high temperatures, due to increased costs of cellular maintenance. Though sparse, microbial life persists in such environments, however, the degree to which temperature gradients result in the stratification extremophilic sub-seafloor populations is poorly understood. During Expedition 370, we established a matrix of incubation experiments with sediment samples taken from 8 depths corresponding to in situ temperatures of approximately 37, 50, 60, 70, 80, 90, 100 and 110°C, which were incubated in oxygen-free, acetate- and sulfate- supplemented, artificial seawater at temperatures of 37, 50, 60, 70 and 80°C. Substrates include large isotopic labels. Following separation from the sediment, cells were analyzed using SIMS, allowing estimates of biomass synthesis rates. We are interested in discussing potential future experiments and collaborations using this resource.

Laboratory controls of precursor and temperature on the kinetics and isotopic fractionations of microbial methane for deep subsurface environments

NASA Astrophysics Data System (ADS)

Ling, Y.; Lin, L.; Wang, P.; Sun, C.

2009-12-01

In subsurface environments, the mineralization of organic carbon involves complex interactions among geological and microbial processes. As the most reduced form and the shortest hydrocarbon chain, methane, is the final product of both microbial degradation and thermal-cracking of organic matter, it serves as the connection of carbon cycles between different reservoirs. Of various mechanisms for methane formation, microbial methane constitutes 85% of the total methane inventory investigated by far. However, the mechanisms and resultant carbon isotope fingerprints of methanogenesis in environments still remained largely unknown. The types of precursors and temperature might be the most critical factors governing methanogenesis. Lots of studies have been investigating the mechanisms responsible for methanogenesis by pure cultures, but it still remains obscure with regard to which precursors are predominantly utilized by methanogens in natural settings. The effect of temperature is especially prominent for anoxic sediments within which the temperature increases with depth in accordance with the local geotherm. Commonly observed temperatures for methanogenesis span from ambient temperature to 90OC, a temperature range for most diagenetic reactions. In order to address how different precursors would be activated for microbially catalytic methane formation upon different temperatures, we incubated the sediments collected from Kuan-Tzu-Ling hot spring at temperatures up to 90OC. Five precursors including acetate, formate, methanol, methylamine, and hydrogen were added with the inocula to stimulate methanogenesis and inhibit fermentation, and were monitored together with methane production through time. Results of this experiments indicated that methanogenesis was positive at temperatures from room temperature to 80OC and precursors investigated despite substantial variations in the maximum rates and yields. In the experiment supplied with hydrogen and formate, methanogenic rates were rapid at all temperatures. Maximum methane production rates occurred at 40~50OC for incubations with methanol, 40~60OC for incubation with acetate, and 50OC for those with methylamine. The patterns of carbon isotopic compositions on methane were either consistent with the prediction of the Rayleigh fractionation in a closed system, trending toward more depleted through time or invariant through time, suggesting variable physiological responses and microbial assemblages to precursor additions. The obtained ɛ values were 0~-12‰ for incubations with acetate, -16~-45‰ for incubations with hydrogen, -50~-80‰ for incubations with methanol, and -87~-115‰ for incubations with methylamine. Acetoclastic methanogenesis appears to fractionate carbon isotopes at the smallest magnitude. This when combined with the results from positive controls and the field observation suggests that acetoclastic methanogenesis produced methane with isotopic signatures comparable with those with thermogenic in origin and contributed significantly to the total methane inventory in the Kuan-Tzu-Ling hotspring area.

Ultramafics-Hydrothermalism-Hydrogenesis-HyperSLiME (UltraH3) Linkage is a key for Occurrence of Last Universal Common Ancestral (LUCA) Community: Where is it, Lost City or Kairei (Rainbow)?

NASA Astrophysics Data System (ADS)

Takai, K.; Inagaki, F.; Nakamura, K.; Suzuki, K.; Kumagai, H.

2005-12-01

Deep-sea hydrothermal system has been recognized one of the most plausible places for origin of life in this planet. This hypothesis has been supported by evidences from multidisciplinary scientific fields. In geology, it has been demonstrated that the potentially most ancient microbial fossils are retrieved from the paleoenvironment, that might be related with deep-sea hydrothermal systems in the Archean. Chemical reactions suggesting prebiotic chemical evolution (synthesis of amino acids, nucleic acids and hydrocarbon, and polymerization of these molecules) are observed under the simulated physical and chemical conditions of the deep-sea hydrothermal vents in the laboratory. In addition, phylogenetic analyses of all the lives in this planet have clearly revealed that hyperthermophiles inhabiting deep-sea hydrothermal systems represent the deepest lineage of the life. Supposed that the Archean deep-sea hydrothermal system hosted the origin of life, what was the first life? We are pursuing the energy metabolism of our last universal common ancestor (LUCA) and the environmental settings hosting the LUCA. It is definitely expected that the genesis of LUCA occurred at high temperatures of locally organics-rich microenvironment around deep-sea hydrothermal field and the first energy metabolism depended on fermentation of simple amino acids, organic acids and sugars. However, these organics were immediately consumed by the hyperthermophilic LUCA activity. Inheritance of the LUCA needed to evolve the energy and carbon acquisitions to more stable and efficient mode. Chemolithoautotrophy might be the best because a plenty of reductive gas components were always provided by the hydrothermal activity. Hyperthermophilic chemolithoautotrophs could serve as the primary producers and could foster the heterotrophic fellows. This was the genesis of the last universal common ancestral (LUCA) community of life. We hypothesize that the LUCA community was metabolically approximated to hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) currently discovered beneath the Central Indian Ridge hydrothermal field. The environmental settings for the occurrence of HyperSLiME are now being characterized and an important linkage among the occurrence of HyperSLiME, extraordinary amount of hydrogen in the hydrothermal fluids and ultramfics-hosted hydrothermal systems is proposed. This ultramafics-hydrothermalism-hydrogen-HyperSLiME (UltraH3) linkage is very likely a key for the genesis of the LUCA community. We would like to discuss the possible UltraH3 linkage in the Archean earth. In addition, we would like to discuss which of modern deep-sea hydrothermal systems is the most plausible proxy for the Archean LUCA habitats.

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE PAGES

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.; ...

2016-01-22

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

PubMed

Kwon, Man Jae; O'Loughlin, Edward J; Boyanov, Maxim I; Brulc, Jennifer M; Johnston, Eric R; Kemner, Kenneth M; Antonopoulos, Dionysios A

2016-01-01

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.

Community Characterization of Microbial Populations Found at a Cold Water Sulfidic Spring in the Canadian High Arctic

NASA Astrophysics Data System (ADS)

Trivedi, C.; Lau, G. E.; Templeton, A. S.; Grasby, S. E.; Spear, J. R.

2015-12-01

The unique environment on Europa makes it an ideal target for astrobiological investigation. One such earth-based analogue to aid in this investigation is the sulfur-dominated glacial spring system found at Borup Fiord Pass (BFP), Ellesmere Island, Nunavut, Canada. In this system, subsurface microbial sulfate reduction produces hydrogen sulfide, which is transported through the glacier along spring channels [1]. As the surface oxidation of H2S occurs, resultant deposition of elemental sulfur (S0) and other minerals becomes visible (attached image). The energy released from these reactions can support potential microbial metabolisms and may be a valuable representation of microbial processes occurring on Europa. The resulting sulfur minerals provide sensitive records of dynamic atmospheric, geological, hydrological, chemical, and biological processes on planetary surfaces. Moreover, we expect that the S0-rich deposits of this glacial spring system will serve as a mineralogical record for biological activity and will provide a valuable tool for recognizing potential sulfur-based life on Europa. During a recent collaborative expedition (2014) to BFP, samples were taken from the toe of the glacier in an area called the 'Blister Crust' (attached image). At this location, glacial channels reach the surface, representing an active interface between subsurface and surface processes. Initial geochemical characterization at the site revealed high amounts of aqueous sulfide (1.8 mM) and hydrogen (29 nM), which likely serve as the electron donation potential in the system. Furthermore, preliminary 16S rRNA gene sequencing has shown a high abundance of the genus Sulfurimonas, which is a known sulfur metabolizer. Our research seeks to further characterize microbial communities found at this interface in order to elucidate information regarding in situ sulfur cycling and the potential to tie this into subsurface/surface processes on Europa. Continued work will provide guidance into potential astrobiological targets on the surface of Europa, predominantly in regions where subsurface fluids interact with surface icings. References: [1] Grasby S. E. et al. (2003) Astrobiology, 3(3), 583-596.

Microbial life in cold, hydrologically active oceanic crustal fluids

NASA Astrophysics Data System (ADS)

Meyer, J. L.; Jaekel, U.; Girguis, P. R.; Glazer, B. T.; Huber, J. A.

2012-12-01

It is estimated that at least half of Earth's microbial biomass is found in the deep subsurface, yet very little is known about the diversity and functional roles of these microbial communities due to the limited accessibility of subseafloor samples. Ocean crustal fluids, which may have a profound impact on global nutrient cycles given the large volumes of water moving through the crustal aquifer, are particularly difficult to sample. Access to uncontaminated ocean crustal fluids is possible with CORK (Circulation Obviation Retrofit Kit) observatories, installed through the Integrated Ocean Drilling Program (IODP). Here we present the first microbiological characterization of the formation fluids from cold, oxygenated igneous crust at North Pond on the western flank of the Mid Atlantic Ridge. Fluids were collected from two CORKs installed at IODP boreholes 1382A and 1383C and include fluids from three different depth horizons within oceanic crust. Collection of borehole fluids was monitored in situ using an oxygen optode and solid-state voltammetric electrodes. In addition, discrete samples were analyzed on deck using a comparable lab-based system as well as a membrane-inlet mass spectrometer to quantify all dissolved volatiles up to 200 daltons. The instruments were operated in parallel and both in situ and shipboard geochemical measurements point to a highly oxidized fluid, revealing an apparent slight depletion of oxygen in subsurface fluids (~215μM) relative to bottom seawater (~245μM). We were unable to detect reduced hydrocarbons, e.g. methane. Cell counts indicated the presence of roughly 2 x 10^4 cells per ml in all fluid samples, and DNA was extracted and amplified for the identification of both bacterial and archaeal community members. The utilization of ammonia, nitrate, dissolved inorganic carbon, and acetate was measured using stable isotopes, and oxygen consumption was monitored to provide an estimate of the rate of respiration per cell per day. These results provide the first dataset describing the diversity of microbes present in cold, oxygenated ocean crustal fluids and the biogeochemical processes they mediate in the subseafloor.

Dissolved Organic Carbon Cycling and Transformation Dynamics in A Northern Forested Peatland

NASA Astrophysics Data System (ADS)

Tfaily, M. M.; Lin, X.; Chanton, P. R.; Steinweg, J.; Esson, K.; Kostka, J. E.; Cooper, W. T.; Schadt, C. W.; Hanson, P. J.; Chanton, J.

2013-12-01

Peatlands sequester one-third of all soil carbon and currently act as major sinks of atmospheric carbon dioxide. The ability to predict or simulate the fate of stored carbon in response to climatic disruption remains hampered by our limited understanding of the controls of carbon turnover and the composition and functioning of peatland microbial communities. A combination of advanced analytical chemistry and microbiology approaches revealed that organic matter reactivity and microbial community dynamics were closely coupled in an extensive field dataset compiled at the S1 bog site established for the SPRUCE program, Marcell Experimental Forest (MEF). The molecular composition and decomposition pathways of dissolved organic carbon (DOC) were contrasted using parallel factor (PARAFAC)-modeled excitation emission fluorescence spectroscopy (EEMS) and FT-ICR MS. The specific UV absorbance (SUVA) at 254 nm was calculated as an indicator of aromaticity. Fluorescence intensity ratios (BIX and FI) were used to infer the relative contributions from solid phase decomposition and microbial production. Distributions of bulk DOC, its stable (δ13C) and radioactive (Δ14C) isotopic composition were also utilized to infer information on its dynamics and transformation processes. Strong vertical stratification was observed in organic matter composition, the distribution of mineralization products (CO2, CH4), respiration rates, and decomposition pathways, whereas smaller variations were observed between sites. A decline in the aromaticity of pore water DOC was accompanied by an increase in microbially-produced DOC. Solid phase peat, on the other hand, became more humified and highly aromatic with depth. These observations were consistent with radiocarbon data that showed that the radiocarbon signatures of microbial respiration products in peat porewaters more closely resemble those of DOC rather than solid peat, indicating that carbon from recent photosynthesis is fueling the majority of the decomposition, even in the subsurface. Stable isotope geochemistry paralleled with vertical changes in methanogen community composition to reveal a mid-depth maximum in acetoclastic methanogenesis, while hydrogenotrophic methanogenesis appears to dominate deeper peat layers. Archaea increased in relative abundance with depth, comprising up to 60 % of the microbial community in the deep peat below 75 cm depth. The Crenarchaeota, Archaea that are not known to produce methane, are suggested to play a critical role in the carbon cycle of deeper peat layers. This is corroborated by evidence from a C isotope mass balance, which indicates that processes other than methanogenesis (fermentation, anaerobic respiration) predominate in the deep peat leading to dominance of CO2 production at depth.

Microbial ecology of deep-water mid-Atlantic canyons

USGS Publications Warehouse

Kellogg, Christina A.

2011-01-01

The research described in this fact sheet will be conducted from 2012 to 2014 as part of the U.S. Geological Survey's DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) Program. This integrated, multidisciplinary effort will be investigating a variety of topics related to unique and fragile deep-sea ecosystems from the microscopic level to the ecosystem level. One goal is to improve understanding, at the microbiological scale, of the benthic communities (including corals) that reside in and around mid-Atlantic canyon habitats and their associated environments. Specific objectives include identifying and characterizing the microbial associates of deep-sea corals, characterizing the microbial biofilms on hard substrates to better determine their role in engineering the ecosystem, and adding a microbial dimension to benthic community structure and function assessments by characterizing micro-eukaryotes, bacteria, and archaea in deep-sea sediments.

Microbial survival in deep space environment.

NASA Technical Reports Server (NTRS)

Silverman, G. J.

1971-01-01

Review of the knowledge available on the extent to which microorganisms (mainly microbial spores, vegetative cells, and fungi) are capable of surviving the environment of deep space, based on recent simulation experiments of deep space. A description of the experimental procedures used is followed by a discussion of deep space ecology, the behavior of microorganisms in ultrahigh vacuum, and factors influencing microbial survival. It is concluded that, so far, simulation experiments have proved far less lethal to microorganisms than to other forms of life. There are, however, wide gaps in the knowledge available, and no accurate predictions can as yet be made on the degree of lethality that might be incurred by a microbial population on a given mission. Therefore, sterilization of spacecraft surfaces is deemed necessary if induced panspermia (i.e., interplanetary life propagation) is to be avoided.

Methods for microbial filtration of fluids

DOEpatents

Carman, M.L.; Jackson, K.J.; Knapp, R.B.; Knezovich, J.P.; Shah, N.N.; Taylor, R.T.

1996-01-30

Novel methods for purifying contaminated subsurface groundwater are disclosed. The method is involves contacting the contaminated subsurface groundwater with methanotrophic or heterotrophic microorganisms which produce contaminant-degrading enzymes. The microorganisms are derived from surface cultures and are injected into the ground so as to act as a biofilter. The contaminants which may be treated include organic or metallic materials and radionuclides. 8 figs.

Subsurface Microbes Expanding the Tree of Life

ScienceCinema

Banfield, Jillian

2018-02-14

Jillian Banfield, Ph.D., UC Berkeley Professor and Berkeley Lab Earth Sciences Division staff scientist and long-time user of the DOE Joint Genome Institute’s resources shares her perspective on how the DOE JGI helps advance her research addressing knowledge gaps related to the roles of subsurface microbial communities in biogeochemical cycling. The video was filmed near the town of Rifle, Colorado at the primary field site for Phase I of the Subsurface Systems Scientific Focus Area 2.0 sponsored by the DOE Office of Biological and Environmental Research.

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

PubMed

Long, Philip E; Williams, Kenneth H; Hubbard, Susan S; Banfield, Jillian F

2016-08-01

Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis.

PubMed

Wu, Jieying; Gao, Weimin; Zhang, Weiwen; Meldrum, Deirdre R

2011-01-01

Limitation in sample quality and quantity is one of the big obstacles for applying metatranscriptomic technologies to explore gene expression and functionality of microbial communities in natural environments. In this study, several amplification methods were evaluated for whole-transcriptome amplification of deep-sea microbial samples, which are of low cell density and high impurity. The best amplification method was identified and incorporated into a complete protocol to isolate and amplify deep-sea microbial samples. In the protocol, total RNA was first isolated by a modified method combining Trizol (Invitrogen, CA) and RNeasy (QIAGEN, CA) method, amplified with a WT-Ovation™ Pico RNA Amplification System (NuGEN, CA), and then converted to double-strand DNA from single-strand cDNA with a WT-Ovation™ Exon Module (NuGEN, CA). The products from the whole-transcriptome amplification of deep-sea microbial samples were assessed first through random clone library sequencing. The BLAST search results showed that marine-based sequences are dominant in the libraries, consistent with the ecological source of the samples. The products were then used for next-generation Roche GS FLX Titanium sequencing to obtain metatranscriptome data. Preliminary analysis of the metatranscriptomic data showed good sequencing quality. Although the protocol was designed and demonstrated to be effective for deep-sea microbial samples, it should be applicable to similar samples from other extreme environments in exploring community structure and functionality of microbial communities. Copyright © 2010 Elsevier B.V. All rights reserved.

Simulating pathways of subsurface oil in the Faroe-Shetland Channel using an ocean general circulation model.

PubMed

Main, C E; Yool, A; Holliday, N P; Popova, E E; Jones, D O B; Ruhl, H A

2017-01-15

Little is known about the fate of subsurface hydrocarbon plumes from deep-sea oil well blowouts and their effects on processes and communities. As deepwater drilling expands in the Faroe-Shetland Channel (FSC), oil well blowouts are a possibility, and the unusual ocean circulation of this region presents challenges to understanding possible subsurface oil pathways in the event of a spill. Here, an ocean general circulation model was used with a particle tracking algorithm to assess temporal variability of the oil-plume distribution from a deep-sea oil well blowout in the FSC. The drift of particles was first tracked for one year following release. Then, ambient model temperatures were used to simulate temperature-mediated biodegradation, truncating the trajectories of particles accordingly. Release depth of the modeled subsurface plumes affected both their direction of transport and distance travelled from their release location, and there was considerable interannual variability in transport. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Surface assessment of CaF2 deep-ultraviolet and vacuum-ultraviolet optical components by the quasi-Brewster angle technique.

PubMed

Wang, Jue; Maier, Robert L

2006-08-01

The requirements for optical components have drastically increased for the deep-ultraviolet and vacuum-ultraviolet spectral regions. Low optical loss, high laser damage threshold, and long lifetime fluoride optics are required for microlithographic applications. A nondestructive quasi-Brewster angle technique (qBAT) has been developed for evaluating the quality of optical surfaces including both top surface and subsurface information. By using effective medium approximation, the negative quasi-Brewster angle shift at wavelengths longer than 200 nm has been used to model the distribution of subsurface damage, whereas the positive quasi-Brewster angle shift for wavelengths shorter than 200 nm has been explained by subsurface contamination. The top surface roughness depicted by the qBAT is consistent with atomic force microscopy measurements. The depth and the microporous structure of the subsurface damage measured by the qBAT has been confirmed by magnetorheological finishing. The technique has been extended to evaluate both polished and antireflection-coated CaF(2) components.

Rapid Response of Eastern Mediterranean Deep Sea Microbial Communities to Oil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Jiang; Techtmann, Stephen M.; Woo, Hannah L.

Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage. 16S rRNA amplicon sequencing was combined with GeoChip metagenomic analysis to monitor themore » microbial community changes to the crude oil and dispersant in on-ship microcosms set up immediately after water collection. After 3 days of incubation at 14 °C, the microbial communities from two different water depths: 824 m and 1210 m became dominated by well-known oil degrading bacteria. The archaeal population and the overall microbial community diversity drastically decreased. Similarly, GeoChip metagenomic analysis revealed a tremendous enrichment of genes related to oil biodegradation, which was consistent with the results from the DWH oil spill. These results highlight a rapid microbial adaption to oil contamination in the deep E. Med., and indicate strong oil biodegradation potentia« less

Data on subsurface storage of liquid waste near Pensacola, Florida, 1963-1980

USGS Publications Warehouse

Hull, R.W.; Martin, J.B.

1982-01-01

Since 1963, when industrial waste was first injected into the subsurface in northwest Florida, considerable data have been collected relating to the geochemistry of subsurface waste storage. This report presents hydrogeologic data on two subsurface waste storage. This report presents hydrogeologic data on two subsurface storage systems near Pensacola, Fla., which inject liquid industrial waste through deep wells into a saline aquifer. Injection sites are described giving a history of well construction, injection, and testing; geologic data from cores and grab samples; hydrographs of injection rates, volume, pressure, and water levels; and chemical and physical data from water-quality samples collected from injection and monitor wells. (USGS)

Deep-Sea Microbes: Linking Biogeochemical Rates to -Omics Approaches

NASA Astrophysics Data System (ADS)

Herndl, G. J.; Sintes, E.; Bayer, B.; Bergauer, K.; Amano, C.; Hansman, R.; Garcia, J.; Reinthaler, T.

2016-02-01

Over the past decade substantial progress has been made in determining deep ocean microbial activity and resolving some of the enigmas in understanding the deep ocean carbon flux. Also, metagenomics approaches have shed light onto the dark ocean's microbes but linking -omics approaches to biogeochemical rate measurements are generally rare in microbial oceanography and even more so for the deep ocean. In this presentation, we will show by combining metagenomics, -proteomics and biogeochemical rate measurements on the bulk and single-cell level that deep-sea microbes exhibit characteristics of generalists with a large genome repertoire, versatile in utilizing substrate as revealed by metaproteomics. This is in striking contrast with the apparently rather uniform dissolved organic matter pool in the deep ocean. Combining the different -omics approaches with metabolic rate measurements, we will highlight some major inconsistencies and enigmas in our understanding of the carbon cycling and microbial food web structure in the dark ocean.

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume.

PubMed

Dick, Gregory J; Tebo, Bradley M

2010-05-01

Hydrothermal plumes are hot spots of microbial biogeochemistry in the deep ocean, yet little is known about the diversity or ecology of microorganisms inhabiting plumes. Recent biogeochemical evidence shows that Mn(II) oxidation in the Guaymas Basin (GB) hydrothermal plume is microbially mediated and suggests that the plume microbial community is distinct from deep-sea communities. Here we use a molecular approach to compare microbial diversity in the GB plume and in background deep seawater communities, and cultivation to identify Mn(II)-oxidizing bacteria from plumes and sediments. Despite dramatic differences in Mn(II) oxidation rates between plumes and background seawater, microbial diversity and membership were remarkably similar. All bacterial clone libraries were dominated by Gammaproteobacteria and archaeal clone libraries were dominated by Crenarchaeota. Two lineages, both phylogenetically related to methanotrophs and/or methylotrophs, were consistently over-represented in the plume. Eight Mn(II)-oxidizing bacteria were isolated, but none of these or previously identified Mn(II) oxidizers were abundant in clone libraries. Taken together with Mn(II) oxidation rates measured in laboratory cultures and in the field, these results suggest that Mn(II) oxidation in the GB hydrothermal plume is mediated by genome-level dynamics (gene content and/or expression) of microorganisms that are indigenous and abundant in the deep sea but have yet to be unidentified as Mn(II) oxidizers.

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Z.; Deng, Y.; Nostrand, J.D. Van

2011-06-15

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in U.S. history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared to outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep-sea. Various other microbial functional genes relevant to carbon, nitrogen, phosphorus, sulfurmore » and iron cycling, metal resistance, and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could play a significant role in biodegradation of oil spills in deep-sea environments.« less

SUBSURFACE PROPERTY RIGHTS: IMPLICATIONS FOR GEOLOGIC CO2 STORAGE

EPA Science Inventory

The paper discusses subsurface property rights as they apply to geologic sequestration (GS) of carbon dioxide (CO2). GS projects inject captured CO2 into deep (greater than ~1 km) geologic formations for the explicit purpose of avoiding atmospheric emission of CO2. Because of the...

SUBSURFACE PROPERTY RIGHTS: IMPLICATIONS FOR GEOLOGIC CO2 SEQUESTRATION

EPA Science Inventory

The chapter discusses subsurface property rights as they apply to geologic sequestration (GS) of carbon dioxide (CO2). GS projects inject captured CO2 into deep (greater than ~1 km) geologic formations for the explicit purpose of avoiding atmospheric emission of CO2. Because of t...

Deep sea microbial fuel cell output as a proxy for microbial activity

NASA Astrophysics Data System (ADS)

Richter, K.; George, R.; Hardy, K. R.

2016-02-01

Abstract: Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The current is chiefly limited by the rate of microbial metabolism at the anode and serves as a proxy for microbial activity. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions and studies of important environmental parameters that affect fuel cell performance. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>4000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. We are pursuing a field efforts to deploy a microbial fuel cell in progressively deeper water, record in situ power and temperature over several weeks, and retrieve the fuel cell along with sediment samples for analysis. We are also pursuing a laboratory effort to build a matching microbial fuel cell in a pressure vessel capable of matching the pressure and temperature of deep water, and stocking the pressure vessel with deep water sediment in order to take measurements analogous to those in the field. We also hope to determine whether bacteria growing on the anode are different from bacteria growing in the bulk sediment via DNA analysis. The current progress and results from this work at SPAWAR will be presented.

Isolation and Characterization of Electrochemically Active Subsurface Delftia and Azonexus Species

PubMed Central

Jangir, Yamini; French, Sarah; Momper, Lily M.; Moser, Duane P.; Amend, Jan P.; El-Naggar, Mohamed Y.

2016-01-01

Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Extracellular electron transfer (EET) is a metabolic strategy that microorganisms can deploy to meet the challenges of interacting with redox-active surfaces. Though mechanistically characterized in a few metal-reducing bacteria, the role, extent, and diversity of EET in subsurface ecosystems remains unclear. Since this process can be mimicked on electrode surfaces, it opens the door to electrochemical techniques to enrich for and quantify the activities of environmental microorganisms in situ. Here, we report the electrochemical enrichment of microorganisms from a deep fractured-rock aquifer in Death Valley, CA, USA. In experiments performed in mesocosms containing a synthetic medium based on aquifer chemistry, four working electrodes (WEs) were poised at different redox potentials (272, 373, 472, 572 mV vs. SHE) to serve as electron acceptors, resulting in anodic currents coupled to the oxidation of acetate during enrichment. The anodes were dominated by Betaproteobacteria from the families Comamonadaceae and Rhodocyclaceae. A representative of each dominant family was subsequently isolated from electrode-associated biomass. The EET abilities of the isolated Delftia strain (designated WE1-13) and Azonexus strain (designated WE2-4) were confirmed in electrochemical reactors using WEs poised at 522 mV vs. SHE. The rise in anodic current upon inoculation was correlated with a modest increase in total protein content. Both genera have been previously observed in mixed communities of microbial fuel cell enrichments, but this is the first direct measurement of their electrochemical activity. While alternate metabolisms (e.g., nitrate reduction) by these organisms were previously known, our observations suggest that additional ‘hidden’ interactions with external electron acceptors are also possible. Electrochemical approaches are well positioned to dissect such extracellular interactions that may be prevalent in the subsurface. PMID:27242768

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

PubMed Central

Heidelberg, John F.

2016-01-01

ABSTRACT The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. IMPORTANCE This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. PMID:27208118

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments.

PubMed

Tully, Benjamin J; Heidelberg, John F

2016-07-15

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. Copyright © 2016 Tully and Heidelberg.

Deep-sea piezosphere and piezophiles: geomicrobiology and biogeochemistry.

PubMed

Fang, Jiasong; Zhang, Li; Bazylinski, Dennis A

2010-09-01

The deep-sea piezosphere accounts for approximately 75% of the total ocean volume and hosts active and diverse biological communities. Evidence obtained thus far suggests that the microbial biomass present in the piezosphere is significant. Continued international interest in exploring the deep ocean provides impetus to increase our understanding of the deep-sea piezosphere and of the influence of piezophilic microbial communities on the global ocean environment and on biogeochemical cycling occurring in the deep sea. Here, we review the diversity, metabolic characteristics, geomicrobiology and biogeochemistry of the deep-sea piezophiles. Copyright 2010 Elsevier Ltd. All rights reserved.

Results from Field Testing the RIMFAX GPR on Svalbard.

NASA Astrophysics Data System (ADS)

Hamran, S. E.; Amundsen, H. E. F.; Berger, T.; Carter, L. M.; Dypvik, H.; Ghent, R. R.; Kohler, J.; Mellon, M. T.; Nunes, D. C.; Paige, D. A.; Plettemeier, D.; Russell, P.

2017-12-01

The Radar Imager for Mars' Subsurface Experiment - RIMFAX is a Ground Penetrating Radar being developed for NASÁs MARS 2020 rover mission. The principal goals of the RIMFAX investigation are to image subsurface structures, provide context for sample sites, derive information regarding subsurface composition, and search for ice or brines. In meeting these goals, RIMFAX will provide a view of the stratigraphic section and a window into the geological and environmental history of Mars. To verify the design an Engineering Model (EM) of the radar was tested in the field in the spring 2017. Different sounding modes on the EM were tested in different types of subsurface geology on Svalbard. Deep soundings were performed on polythermal glaciers down to a couple of hundred meters. Shallow soundings were used to map a ground water table in the firn area of a glacier. A combination of deep and shallow soundings was used to image buried ice under a sedimentary layer of a couple of meters. Subsurface sedimentary layers were imaged down to more than 20 meters in sand stone permafrost. This presentation will give an overview of the RIMFAX investigation, describe the development of the radar system, and show results from field tests of the radar.

Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site

PubMed Central

Green, Stefan J.; Prakash, Om; Jasrotia, Puja; Overholt, Will A.; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M.; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

2012-01-01

The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment. PMID:22179233

Investigating the Differences in the Total and Active Microbial Community of Mid-Atlantic Ridge Sediments

NASA Astrophysics Data System (ADS)

Sobol, M. S.; Zinke, L. A.; Orcutt, B.; Mills, H. J.; Edwards, K. J.; Girguis, P. R.; Reese, B. K.

2016-02-01

Microbes in the marine deep subsurface are key mediators of many geochemical cycles. It is important to understand how microbial communities and the diversity of those communities impacts geochemical cycling. Sediment cores were collected from IODP (Integrated Ocean Drilling Program) Expedition 336 to the western flank of the mid-Atlantic ridge also referred to as North Pond. The dissolved oxygen concentration decreased with depth for 60-70 mbsf, followed by a sharp increase in oxygen until it terminated at the basement. The 16S rRNA genes (DNA) and transcripts (RNA) were extracted simultaneously using a method designed by Reese et al. (2013) to differentiate between the total and active microbial community structures, respectively, as well as correlate the putative metabolism with the geochemistry. We observed many differences between the active and total communities. Sequences most closely related to Cyanobacteria were found to dominate the total community at both sites, but were found in small numbers in the active community. The most abundant phyla in the active community were Alphaproteobacteria, which suggests that they may have high activity even though the abundance was not as great in the total community. This suggests that, even in small numbers, bacteria are capable of contributing greatly to their environment. Principal Component Analysis (PCA) and Singular Value Decomposition (SVD) showed that iron-reducing bacteria in the active (RNA) community correlated strongly with solid phase iron oxides. SVD also showed that the putative nitrate reducers in the active community were found in greater abundance where porewater NO3- and NO2- total concentrations were elevated. Overall, the active (RNA) community correlated significantly with the geochemistry whereas the total (DNA) community did not. Therefore, RNA analysis yields a more accurate representation of how microbial communities impact geochemical cycling.

Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells.

PubMed

Cluff, Maryam A; Hartsock, Angela; MacRae, Jean D; Carter, Kimberly; Mouser, Paula J

2014-06-03

Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process.

Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lovley, Derek R.

2012-11-28

The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities inmore » a diversity of soils and sediments.« less

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

PubMed

Klier, Christine

2012-03-06

The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

The biogeochemical fate of nickel during microbial ISA degradation; implications for nuclear waste disposal.

PubMed

Kuippers, Gina; Boothman, Christopher; Bagshaw, Heath; Ward, Michael; Beard, Rebecca; Bryan, Nicholas; Lloyd, Jonathan R

2018-06-08

Intermediate level radioactive waste (ILW) generally contains a heterogeneous range of organic and inorganic materials, of which some are encapsulated in cement. Of particular concern are cellulosic waste items, which will chemically degrade under the conditions predicted during waste disposal, forming significant quantities of isosaccharinic acid (ISA), a strongly chelating ligand. ISA therefore has the potential to increase the mobility of a wide range of radionuclides via complex formation, including Ni-63 and Ni-59. Although ISA is known to be metabolized by anaerobic microorganisms, the biodegradation of metal-ISA complexes remains unexplored. This study investigates the fate of a Ni-ISA complex in Fe(III)-reducing enrichment cultures at neutral pH, representative of a microbial community in the subsurface. After initial sorption of Ni onto Fe(III)oxyhydroxides, microbial ISA biodegradation resulted in >90% removal of the remaining Ni from solution when present at 0.1 mM, whereas higher concentrations of Ni proved toxic. The microbial consortium associated with ISA degradation was dominated by close relatives to Clostridia and Geobacter species. Nickel was preferentially immobilized with trace amounts of biogenic amorphous iron sulfides. This study highlights the potential for microbial activity to help remove chelating agents and radionuclides from the groundwater in the subsurface geosphere surrounding a geodisposal facility.

Comparison of Bacterial Diversity in Azorean and Hawai’ian Lava Cave Microbial Mats

PubMed Central

MARSHALL HATHAWAY, JENNIFER J.; GARCIA, MATTHEW G.; BALASCH, MONICA MOYA; SPILDE, MICHAEL N.; STONE, FRED D.; DAPKEVICIUS, MARIA DE LURDES N. E.; AMORIM, ISABEL R.; GABRIEL, ROSALINA; BORGES, PAULO A. V.; NORTHUP, DIANA E.

2015-01-01

Worldwide, lava caves host colorful microbial mats. However, little is known about the diversity of these microorganisms, or what role they may play in the subsurface ecosystem. White and yellow microbial mats were collected from four lava caves each on the Azorean island of Terceira and the Big Island of Hawai’i, to compare the bacterial diversity found in lava caves from two widely separated archipelagos in two different oceans at different latitudes. Scanning electron microscopy of mat samples showed striking similarities between Terceira and Hawai’ian microbial morphologies. 16S rRNA gene clone libraries were constructed to determine the diversity within these lava caves. Fifteen bacterial phyla were found across the samples, with more Actinobacteria clones in Hawai’ian communities and greater numbers of Acidobacteria clones in Terceira communities. Bacterial diversity in the subsurface was correlated with a set of factors. Geographical location was the major contributor to differences in community composition (at the OTU level), together with differences in the amounts of organic carbon, nitrogen and copper available in the lava rock that forms the cave. These results reveal, for the first time, the similarity among the extensive bacterial diversity found in lava caves in two geographically separate locations and contribute to the current debate on the nature of microbial biogeography. PMID:26924866

Biogeographic congruency among bacterial communities from terrestrial sulfidic springs

PubMed Central

Headd, Brendan; Engel, Annette S.

2014-01-01

Terrestrial sulfidic springs support diverse microbial communities by serving as stable conduits for geochemically diverse and nutrient-rich subsurface waters. Microorganisms that colonize terrestrial springs likely originate from groundwater, but may also be sourced from the surface. As such, the biogeographic distribution of microbial communities inhabiting sulfidic springs should be controlled by a combination of spring geochemistry and surface and subsurface transport mechanisms, and not necessarily geographic proximity to other springs. We examined the bacterial diversity of seven springs to test the hypothesis that occurrence of taxonomically similar microbes, important to the sulfur cycle, at each spring is controlled by geochemistry. Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. Among the putative sulfide-oxidizing groups (Epsilonproteobacteria and Gammaproteobacteria), up to 83% of the sequences from geochemically similar springs clustered together. Abundant populations of Hydrogenimonas-like or Sulfurovum-like spp. (Epsilonproteobacteria) occurred with abundant Thiothrix and Thiofaba spp. (Gammaproteobacteria), but Arcobacter-like and Sulfurimonas spp. (Epsilonproteobacteria) occurred with less abundant gammaproteobacterial populations. These distribution patterns confirmed that geochemistry rather than biogeography regulates bacterial dominance at each spring. Potential biogeographic controls were related to paleogeologic sedimentation patterns that could control long-term microbial transport mechanisms that link surface and subsurface environments. Knowing the composition of a core sulfidic spring microbial community could provide a way to monitor diversity changes if a system is threatened by anthropogenic processes or climate change. PMID:25250021

Microbial community assembly patterns under incipient conditions in a basaltic soil system

NASA Astrophysics Data System (ADS)

Sengupta, A.; Stegen, J.; Alves Meira Neto, A.; Wang, Y.; Chorover, J.; Troch, P. A. A.; Maier, R. M.

2017-12-01

In sub-surface environments, the biotic components are critically linked to the abiotic processes. However, there is limited understanding of community establishment, functional associations, and community assembly processes of such microbes in sub-surface environments. This study presents the first analysis of microbial signatures in an incipient terrestrial basalt soil system conducted under controlled conditions. A sub-meter scale sampling of a soil mesocosm revealed the contrasting distribution patterns of simple soil parameters such as bulk density and electrical conductivity. Phylogenetic analysis of 16S rRNA gene indicated the presence of a total 40 bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and highest abundance of Proteobacteria throughout the system. Community diversity patterns were inferred to be dependent on depth profile and average water content in the system. Predicted functional gene analysis suggested mixotrophy lifestyles with both autotrophic and heterotrophic metabolisms, likelihood of a unique salt tolerant methanogenic pathway with links to novel Euryarchea, signatures of an incomplete nitrogen cycle, and predicted enzymes of extracellular iron (II) to iron (III) conversion followed by intracellular uptake, transport and regulation. Null modeling revealed microbial community assembly was predominantly governed by variable selection, but the influence of the variable selection did not show systematic spatial structure. The presence of significant heterogeneity in predicted functions and ecologically deterministic shifts in community composition in a homogeneous incipient basalt highlights the complexity exhibited by microorganisms even in the simplest of environmental systems. This presents an opportunity to further develop our understanding of how microbial communities establish, evolve, impact, and respond in sub-surface environments.

Drip irrigation research update at NPRL

USDA-ARS?s Scientific Manuscript database

Drip irrigation research has been conducted since 1998 at NPRL. Systems include deep subsurface drip irrigation (SSDI), surface drip irrigation (SDI), and shallow subsurface drip irrigation (S3DI). Results have shown that SDI and S3DI are more economical to install than SSDI. SDI systems have more r...

SUBSURFACE PROPERTY RIGHTS: IMPLICATIONS FOR GEOLOGIC CO2 SEQUESTRATION (PRESENTATION)

EPA Science Inventory

The paper discusses subsurface property rights as they apply to geologic sequestration (GS) of carbon dioxide (CO2). GS projects inject captured CO2 into deep (greater than ~1 km) geologic formations for the explicit purpose of avoiding atmospheric emission of CO2. Because of the...

Long-Duration Orbit Exposure Experiment with Sub-Surface Microorganism from a Mars Terrestrial Analog

NASA Astrophysics Data System (ADS)

Davila, A. F.; Lim, D.; Fairen, A. G.; Uceda, E. R.; Zavaleta, J.; McKay, C.

2007-07-01

Orbit Exposure Experiments (OEE) allow us to test the possibility of life transfer between planets and moons. Deep sub-surface microorganisms may be the best candidates to survive long-term exposure to space conditions. A long duration OEE is proposed to test our hypothesis.

Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

PubMed Central

Sanford, Robert A.; Boyanov, Maxim I.; Kemner, Kenneth M.; O'Loughlin, Edward J.; Chang, Yun-juan; Locke, Randall A.; Weber, Joseph R.; Egan, Sheila M.; Mackie, Roderick I.; Cann, Isaac; Fouke, Bruce W.

2016-01-01

ABSTRACT A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov. IMPORTANCE A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack of c-type cytochromes typically affiliated with iron reduction in Geobacter and Shewanella species, and (iii) being the only member of the Halanaerobiales capable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes. PMID:27565620

Hydrogen in rocks: an energy source for deep microbial communities

NASA Technical Reports Server (NTRS)

Freund, Friedemann; Dickinson, J. Thomas; Cash, Michele

2002-01-01

To survive in deep subsurface environments, lithotrophic microbial communities require a sustainable energy source such as hydrogen. Though H2 can be produced when water reacts with fresh mineral surfaces and oxidizes ferrous iron, this reaction is unreliable since it depends upon the exposure of fresh rock surfaces via the episodic opening of cracks and fissures. A more reliable and potentially more voluminous H2 source exists in nominally anhydrous minerals of igneous and metamorphic rocks. Our experimental results indicate that H2 molecules can be derived from small amounts of H2O dissolved in minerals in the form of hydroxyl, OH- or O3Si-OH, whenever such minerals crystallized in an H2O-laden environment. Two types of experiments were conducted. Single crystal fracture experiments indicated that hydroxyl pairs undergo an in situ redox conversion to H2 molecules plus peroxy links, O3Si/OO\\SiO3. While the peroxy links become part of the mineral structure, the H2 molecules diffused out of the freshly fractured mineral surfaces. If such a mechanism occurred in natural settings, the entire rock column would become a volume source of H2. Crushing experiments to facilitate the outdiffusion of H2 were conducted with common crustal igneous rocks such as granite, andesite, and labradorite. At least 70 nmol of H2/g diffused out of coarsely crushed andesite, equivalent at standard pressure and temperature to 5,000 cm3 of H2/m3 of rock. In the water-saturated, biologically relevant upper portion of the rock column, the diffusion of H2 out of the minerals will be buffered by H2 saturation of the intergranular water film.

Regional Mapping and Resource Assessment of Shallow Gas Hydrates of Japan Sea - METI Launched 3 Years Project in 2013.

NASA Astrophysics Data System (ADS)

Matsumoto, R.

2014-12-01

Agency of Natural Resources and Energy of METI launched a 3 years shallow gas hydrate exploration project in 2013 to make a precise resource assessment of shallow gas hydrates in the eastern margin of Japan Sea and around Hokkaido. Shallow gas hydrates of Japan Sea occur in fine-grained muddy sediments of shallow subsurface of mounds and gas chimneys in the form of massive nodular to platy accumulation. Gas hydrate bearing mounds are often associated with active methane seeps, bacterial mats and carbonate concretions and pavements. Gases of gas hydrates are derived either from deep thermogenic, shallow microbial or from the mixed gases, contrasting with totally microbial deep-seated stratigraphically controlled hydrates. Shallow gas hydrates in Japan Sea have not been considered as energy resource due to its limited distribution in narrow Joetsu basin. However recently academic research surveys have demonstrated regional distribution of gas chimney and hydrate mound in a number of sedimentary basins along the eastern margin of Japan Sea. Regional mapping of gas chimney and hydrate mound by means of MBES and SBP surveys have confirmed that more than 200 gas chimneys exist in 100 km x 100 km area. ROV dives have identified dense accumulation of hydrates on the wall of half collapsed hydrate mound down to 30 mbsf. Sequential LWD and shallow coring campaign in the Summer of 2014, R/V Hakurei, which is equipped with Fugro Seacore R140 drilling rig, drilled through hydrate mounds and gas chimneys down to the BGHS (base of gas hydrate stability) level and successfully recovered massive gas hydrates bearing sediments from several horizons.

A passive low frequency instrument for radio wave sounding the subsurface oceans of the Jovian icy moons: An instrument concept

NASA Astrophysics Data System (ADS)

Hartogh, P.; Ilyushin, Ya. A.

2016-10-01

Exploration of subsurface oceans on Jovian icy moons is a key issue of the icy moons' geology. Electromagnetic wave propagation is the only way to probe their icy mantles from the orbit. In the present paper, a principal concept of a passive interferometric instrument for deep sounding of the icy moons' crust is proposed. Its working principle is measuring and correlating Jupiter's radio wave emissions with reflections from the deep sub-surface of the icy moons. A number of the functional aspects of the proposed experiment are studied, in particular, impact of the wave scattering on the surface terrain on the instrument performance and digital sampling of the noisy signal. Results of the test of the laboratory prototype of the instrument are also presented in the paper.

Remote Sensing of Subsurface Microbial Transformations

NASA Astrophysics Data System (ADS)

Williams, K. H.; Ntarlagiannis, D.; Slater, L.; Long, P.; Dohnalkova, A.; Hubbard, S. S.; Banfield, J. F.

2004-12-01

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to detect microbial dynamics in real time with high spatial resolution. Here we have used non-invasive geophysical methods to monitor biomineralization and related processes during biostimulation at both laboratory and field scales. Alterations in saturated sediment characteristics resulting from microbe-mediated transformations were concomitant with changes in complex resistivity, spontaneous potential, and acoustic wave signatures. Variability in complex resistivity and acoustic wave amplitudes appears tied to the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. In contrast, time-varying spontaneous potentials appear primarily sensitive to the electrochemical gradients resulting from metabolic pathways, such as iron- and sulfate-reduction. Furthermore, they enable us to track mobile fronts of active respiration that arise due to microbial chemotaxis. In this way, geophysical data may be used to image the distribution of mineral precipitates, biomass, and biogeochemical fronts evolving over time and suggest the ability to remotely monitor contaminated aquifers undergoing bioremediation.

Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids

NASA Astrophysics Data System (ADS)

Purkamo, Lotta; Bomberg, Malin; Kietäväinen, Riikka; Salavirta, Heikki; Nyyssönen, Mari; Nuppunen-Puputti, Maija; Ahonen, Lasse; Kukkonen, Ilmo; Itävaara, Merja

2016-05-01

The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible "keystone" genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.

Influence of microorganisms on the oxidation state distribution of multivalent actinides under anoxic conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reed, Donald Timothy; Borkowski, Marian; Lucchini, Jean - Francois

2010-12-10

The fate and potential mobility of multivalent actinides in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium, uranium and neptunium are the near-surface multivalent contaminants of concern and are also key contaminants for the deep geologic disposal of nuclear waste. Their mobility is highly dependent on their redox distribution at their contamination source as well as along their potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity.more » Under anoxic conditions, indirect and direct bioreduction mechanisms exist that promote the prevalence of lower-valent species for multivalent actinides. Oxidation-state-specific biosorption is also an important consideration for long-term migration and can influence oxidation state distribution. Results of ongoing studies to explore and establish the oxidation-state specific interactions of soil bacteria (metal reducers and sulfate reducers) as well as halo-tolerant bacteria and Archaea for uranium, neptunium and plutonium will be presented. Enzymatic reduction is a key process in the bioreduction of plutonium and uranium, but co-enzymatic processes predominate in neptunium systems. Strong sorptive interactions can occur for most actinide oxidation states but are likely a factor in the stabilization of lower-valent species when more than one oxidation state can persist under anaerobic microbiologically-active conditions. These results for microbiologically active systems are interpreted in the context of their overall importance in defining the potential migration of multivalent actinides in the subsurface.« less

Evidence for Seismogenic Hydrogen Gas, a Potential Microbial Energy Source on Earth and Mars

NASA Astrophysics Data System (ADS)

McMahon, Sean; Parnell, John; Blamey, Nigel J. F.

2016-09-01

The oxidation of molecular hydrogen (H2) is thought to be a major source of metabolic energy for life in the deep subsurface on Earth, and it could likewise support any extant biosphere on Mars, where stable habitable environments are probably limited to the subsurface. Faulting and fracturing may stimulate the supply of H2 from several sources. We report the H2 content of fluids present in terrestrial rocks formed by brittle fracturing on fault planes (pseudotachylites and cataclasites), along with protolith control samples. The fluids are dominated by water and include H2 at abundances sufficient to support hydrogenotrophic microorganisms, with strong H2 enrichments in the pseudotachylites compared to the controls. Weaker and less consistent H2 enrichments are observed in the cataclasites, which represent less intense seismic friction than the pseudotachylites. The enrichments agree quantitatively with previous experimental measurements of frictionally driven H2 formation during rock fracturing. We find that conservative estimates of current martian global seismicity predict episodic H2 generation by Marsquakes in quantities useful to hydrogenotrophs over a range of scales and recurrence times. On both Earth and Mars, secondary release of H2 may also accompany the breakdown of ancient fault rocks, which are particularly abundant in the pervasively fractured martian crust. This study strengthens the case for the astrobiological investigation of ancient martian fracture systems.

Mineralization of Bacteria in Terrestrial Basaltic Rocks: Comparison With Possible Biogenic Features in Martian Meteorite Allan Hills 84001

NASA Technical Reports Server (NTRS)

Thomas-Keprta, K. L.; McKay, D. S.; Wentworth, S. J.; Stevens, T. O.; Taunton, A. E.; Allen, C. C.; Gibson, E. K., Jr.; Romanek, C. S.

1998-01-01

The identification of biogenic features altered by diagenesis or mineralization is important in determining whether specific features in terrestrial rocks and in meteorites may have a biogenic origin. Unfortunately, few studies have addressed the formation of biogenic features in igneous rocks, which may be important to these phenomena, including the controversy over possible biogenic features in basaltic martian meteorite ALH84001. To explore the presence of biogenic features in igneous rocks, we examined microcosms growing in basaltic small-scale experimental growth chambers or microcosms. Microbial communities were harvested from aquifers of the Columbia River Basalt (CRB) group and grown in a microcosm containing unweathered basalt chips and groundwater (technique described in. These microcosms simulated natural growth conditions in the deep subsurface of the CRB, which should be a good terrestrial analog for any putative martian subsurface ecosystem that may have once included ALH84001. Here we present new size measurements and photomicrographs comparing the putative martian fossils to biogenic material in the CRB microcosms. The range of size and shapes of the biogenic features on the CRB microcosm chips overlaps with and is similar to those on ALH84001 chips. Although this present work does not provide evidence for the biogenicity of ALH84001 features, we believe that, based on criteria of size, shape, and general morphology, a biogenic interpretation for the ALH84001 features remains plausible.

Microbial physiology-based model of ethanol metabolism in subsurface sediments

NASA Astrophysics Data System (ADS)

Jin, Qusheng; Roden, Eric E.

2011-07-01

A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

Microbial Methanogenesis In Laboratory Incubations Of Coal: Implications For A Sustainable Energy Resource In Subsurface Coalbeds

NASA Astrophysics Data System (ADS)

Harris, S. H.; Barker, C. E.; Smith, R. L.

2005-12-01

Methane desorbed from subsurface coalseams contributes about 8% of the total natural gas produced in the US. This value is expected to increase over the next several years as a growing proportion of energy demands are supplied from unconventional reservoirs. Isotopic analyses of gas samples from several geographically separate coalbeds indicates a substantial proportion of the sorbed methane is biogenic in origin. Furthermore, previous studies have shown the ability of microbial consortia to degrade coal in aerobic laboratory incubations. These findings suggests the stimulation of microbial methane production in subsurface coals may provide a sustainable source of domestic energy. To address this prospect, we assessed the ability of indigenous microbial populations to produce methane in coal maintained under anaerobic conditions in the laboratory and investigated factors that influenced the rate and extent of the process. Several freshly collected coals of different rank were examined for their ability to support methanogenesis in mineral medium alone or amended with different nutrients such as hydrogen (4 kPa), formate (20 mM), or acetate (25mM). Microbial methane production was distinguished from abiotic desorption by subtracting methane generated in replicate incubations that contained bromoethanesulfonic acid (5 mM), an inhibitor of methanogenesis. The extent and rate of methane production varied among the different coals. A relatively shallow (400 m), immature coal exhibited a rate of 700 nmole CH4*day-1*g coal-1, a value comparable to previous observations of contaminated sediments. Methane production was negligible in a deeper, relatively mature (650 m) coal obtained from the same borehole although the same material exhibited a rate of about 80 nmole CH4*day-1*g coal-1 after a formate amendment. In contrast, hydrogen proved to be ineffective as a methanogenic substrate, although this electron donor was rapidly consumed in coal incubations. A filter-sterilized warm water extract of spent coal renewed methanogenesis in incubations no longer generating methane, suggesting the cessation of methane production was not due to moribund cells or the accumulation of an inhibitory compound, but rather the lack of suitable electron donor. Viable methanogenic consortia were present in most of the coal samples examined in this study and their activity could be enhanced by electron donor amendment, which presumably supports microbial growth. Furthermore, the observation of rapid hydrogen consumption uncoupled from methanogenesis suggests competition exists for this compound. The success of efforts to stimulate methanogenesis in subsurface coalbeds will likely be influenced by the nature of the electron donor.

Analysis of Low-Biomass Microbial Communities in the Deep Biosphere.

PubMed

Morono, Y; Inagaki, F

2016-01-01

Over the past few decades, the subseafloor biosphere has been explored by scientific ocean drilling to depths of about 2.5km below the seafloor. Although organic-rich anaerobic sedimentary habitats in the ocean margins harbor large numbers of microbial cells, microbial populations in ultraoligotrophic aerobic sedimentary habitats in the open ocean gyres are several orders of magnitude less abundant. Despite advances in cultivation-independent molecular ecological techniques, exploring the low-biomass environment remains technologically challenging, especially in the deep subseafloor biosphere. Reviewing the historical background of deep-biosphere analytical methods, the importance of obtaining clean samples and tracing contamination, as well as methods for detecting microbial life, technological aspects of molecular microbiology, and detecting subseafloor metabolic activity will be discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Martian CH(4): sources, flux, and detection.

PubMed

Onstott, T C; McGown, D; Kessler, J; Lollar, B Sherwood; Lehmann, K K; Clifford, S M

2006-04-01

Recent observations have detected trace amounts of CH(4) heterogeneously distributed in the martian atmosphere, which indicated a subsurface CH(4) flux of ~2 x 10(5) to 2 x 10(9) cm(2) s(1). Four different origins for this CH(4) were considered: (1) volcanogenic; (2) sublimation of hydrate- rich ice; (3) diffusive transport through hydrate-saturated cryosphere; and (4) microbial CH(4) generation above the cryosphere. A diffusive flux model of the martian crust for He, H(2), and CH(4) was developed based upon measurements of deep fracture water samples from South Africa. This model distinguishes between abiogenic and microbial CH(4) sources based upon their isotopic composition, and couples microbial CH(4) production to H(2) generation by H(2)O radiolysis. For a He flux of approximately 10(5) cm(2) s(1) this model yields an abiogenic CH(4) flux and a microbial CH(4) flux of approximately 10(6) and approximately 10(9) cm(2) s(1), respectively. This flux will only reach the martian surface if CH(4) hydrate is saturated in the cryosphere; otherwise it will be captured within the cryosphere. The sublimation of a hydrate-rich cryosphere could generate the observed CH(4) flux, whereas microbial CH(4) production in a hypersaline environment above the hydrate stability zone only seems capable of supplying approximately 10(5) cm(2) s(1) of CH(4). The model predicts that He/H(2)/CH(4)/C(2)H(6) abundances and the C and H isotopic values of CH(4) and the C isotopic composition of C(2)H(6) could reveal the different sources. Cavity ring-down spectrometers represent the instrument type that would be most capable of performing the C and H measurements of CH(4) on near future rover missions and pinpointing the cause and source of the CH(4) emissions.

Research Performed at NETL on the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

Deep below our feet, lies the unique and complex world of the subsurface. A world that is improving the lives of Americans and brimming with the potential to generate even greater benefits through NETL research. NETL research supports industry by improving resource extraction while also helping to make carbon storage safe and more effective.

Autonomous, Retrievable, Deep Sea Microbial Fuel Cell

NASA Astrophysics Data System (ADS)

Richter, K.

2014-12-01

Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The open circuit voltage is approximately 0.8 v. The voltage between electrodes is operationally kept at 0.4 v with a potentiastat. The current is chiefly limited by the rate of microbial metabolism at the anode. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>1000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. One question we are asking is whether MFC power output from deep water sediments repressurized and chilled in the laboratory comparable to those measured in situ. If yes, mapping the power potential of deep sea sediments may be made much easier, requiring sediment grabs and lab tests rather than deployment and retrieval of fuel cells. Another question we are asking is whether in situ temperature and total organic carbon in the deep sea sediment can predict MFC power. If yes, then we can make use of the large collection of publicly available, deep sea oceanographic measurements to make these predictions, foregoing expensive work at sea. These regressions will be compared to those derived from shallow water measurements.

Dynamic Autoinoculation and the Microbial Ecology of a deep Water Hydrocarbon Irruption

DTIC Science & Technology

2012-12-11

gas hydrate) likely altered plume com- position near the source, leavrngintruswrscknimatedbythemost soluble compounds, such as gases (2-4, 9, 10, 12...well. These results may reconcile disparate observations of the physical dynamics and microbial community structure of the deep plume . Model...feeds bacterial metabolism and cellular growth. We focused entirely on the deep plume horizon spanning 1,000-1,300 m water depth, applying