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

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water

PubMed Central

Frank, Alexander H.; Garcia, Juan A. L.; Herndl, Gerhard J.

2016-01-01

Summary To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep‐water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses. PMID:26914787

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points

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

Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.

2015-03-01

We explored the impact of the starting community composition and structure on ecosystem response to perturbations using organic carbon amendment experiments. Subsurface sediment was partitioned into flow-through columns, and the microbial communities were initially stimulated in situ by addition of acetate as a carbon and electron donor source. This drove community richness and evenness down, and pushed the system into a new biogeochemical state characterized by iron reduction. Reconstructed near-full-length 16S rRNA gene sequence analysis indicated a concomitant enrichment of Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After 10 to 12 days, acetate was exchange for lactate in a subset of columns.more » Following the clear onset of sulfate reduction (35 days after acetate-amendment), acetate was substituted for lactate in additional columns. Acetatestimulated communities differed markedly during each biogeochemical regime and at each lactate-switch. Regardless, however, of when communities were switched to lactate, they followed comparable trajectories with respect to composition and structure, with convergence evident one week after each switch, and marked after one month of lactate amendment. During sulfate reduction all treatments were enriched in Firmicutes and a number of species likely involved in sulfate reduction (notably Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum). Lactate treatments were distinguished by substantially lower relative abundances of Desulfotomaculum and Bacteroidetes, and enrichments of Psychrosinus and Clostridiales species. Results imply that the structure of the starting community was not significant in controlling organism selection in community succession.« less

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China

PubMed Central

Wu, Yucheng; Tan, Liangcheng; Liu, Wuxing; Wang, Baozhan; Wang, Jianjun; Cai, Yanjun; Lin, Xiangui

2015-01-01

Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments. PMID:25870592

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China.

PubMed

Wu, Yucheng; Tan, Liangcheng; Liu, Wuxing; Wang, Baozhan; Wang, Jianjun; Cai, Yanjun; Lin, Xiangui

2015-01-01

Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments.

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.

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water.

PubMed

Frank, Alexander H; Garcia, Juan A L; Herndl, Gerhard J; Reinthaler, Thomas

2016-06-01

To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep-water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach

PubMed Central

Crespo-Medina, Melitza; Twing, Katrina I.; Kubo, Michael D. Y.; Hoehler, Tori M.; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O.

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems. PMID:25452748

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach.

PubMed

Crespo-Medina, Melitza; Twing, Katrina I; Kubo, Michael D Y; Hoehler, Tori M; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite-hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

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

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.

The importance of subsurface geology for water source and vegetation communities in Cherokee Marsh, Wisconsin

USGS Publications Warehouse

Kurtz, A.M.; Bahr, J.M.; Carpenter, Q.J.; Hunt, R.J.

2007-01-01

Restoration of disturbed wetland systems is an important component of wetland mitigation, yet uncertainty remains about how hydrologic processes affect biologic processes and wetlands patterns. To design more effective restoration strategies and re-establish native plant communities in disturbed wetlands, it is imperative to understand undisturbed systems. A site within Cherokee Marsh located in Madison, Wisconsin, USA, contains a relatively undisturbed area of wetland consisting of plant communities common within the prairie landscape including a fen, sedge meadow, and shallow marsh. These distinct communities are found within an area of minimal topographic relief, yet transitions from one community to the next occur over short distances. This study sought to characterize the geologic, hydrologic, and chemical gradients associated with these shifts in vegetation to gain insight into the factors controlling the spatial differences in dominant plant species, which could be critical for restoration success. Vegetation analyses revealed a transition of dominant sedge species, which appeared to correspond to changes in hydrology from a ground-water dominated to a surface-water dominated system (as determined by water isotopes). Along the same vegetation transect, subsurface coring results show a heterogeneous composition of peat and till with lateral and vertical variations in stratigraphy, which relates to variability in ground-water discharge as evidenced by hydroperiods and stable isotope composition. Applications of this type of approach throughout the glaciated terrains of the midwestern and northeastern United States and Canada can improve future wetland restoration and management. ?? 2007, The Society of Wetland Scientists.

Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences.

PubMed

Zhang, Xiaoying; Hu, Bill X; Ren, Hejun; Zhang, Jin

2018-08-15

The gradient distribution of microbial communities has been detected in profiles along many natural environments. In a mangrove seedlings inhabited mudflat, the microbes drive a variety of biogeochemical processes and are associated with a dramatically changed environment across the tidal zones of mudflat. A better understanding of microbial composition, diversity and associated functional profiles in relation to physicochemical influences could provide more insights into the ecological functions of microbes in a coastal mangrove ecosystem. In this study, the variation of microbial community along successive tidal flats inhabited by mangrove seedlings were characterized based on the 16S rDNA gene sequences, and then the factors that shape the bacterial and archaeal communities were determined. Results showed that the tidal cycles strongly influence the distribution of bacterial and archaeal communities. Dissimilarity and gradient distribution of microbial communities were found among high tidal flat, mid-low tidal flat and seawater. Discrepancies were also as well observed from the surface to subsurface layers specifically in the high tidal flat. For example, Alphaproteobacteria displayed an increasing trend from low tidal to high tidal flat and vice versa for Deltaproteobacteria; Cyanobacteria and Thaumarchaeota were more dominant in the surface layer than the subsurface. In addition, by classifying the microorganisms into metabolic functional groups, we were able to identify the biogeochemical pathway that was dominant in each zone. The (oxygenic) photoautotrophy and nitrate reduction were enhanced in the mangrove inhabited mid tidal flat. It revealed the ability of xenobiotic metabolism microbes to degrade, transform, or accumulate environmental hydrocarbon pollutants in seawater, increasing sulfur-related respiration from high tidal to low tidal flat. An opposite distribution was found for major nitrogen cycling processes. The shift of both composition and function of microbial communities were significantly related to light, oxygen availability and total dissolved nitrogen instead of sediment types or salinity. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

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

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

Regional-scale drivers of marine nematode distribution in Southern Ocean continental shelf sediments

NASA Astrophysics Data System (ADS)

Hauquier, Freija; Verleyen, Elie; Tytgat, Bjorn; Vanreusel, Ann

2018-07-01

Many marine meiofauna taxa seem to possess cosmopolitan species distributions, despite their endobenthic lifestyle and restricted long-distance dispersal capacities. In light of this paradox we used a metacommunity framework to study spatial turnover in free-living nematode distribution and assess the importance of local environmental conditions in explaining differences between communities in surface and subsurface sediments of the Southern Ocean continental shelf. We analysed nematode community structure in two sediment layers (0-3 cm and 3-5 cm) of locations maximum 2400 km apart. We first focused on a subset of locations to evaluate whether the genus level is sufficiently taxonomically fine-grained to study large-scale patterns in nematode community structure. We subsequently used redundancy and variation partitioning analyses to quantify the unique and combined effects of local environmental conditions and spatial descriptors on genus-level community composition. Macroecological patterns in community structure were highly congruent at the genus and species level. Nematode community composition was highly divergent between both depth strata, likely as a result of local abiotic conditions. Variation in community structure between the different regions largely stemmed from turnover (i.e. genus/species replacement) rather than nestedness (i.e. genus/species loss). The level of turnover among communities increased with geographic distance and was more pronounced in subsurface layers compared to surface sediments. Variation partitioning analysis revealed that both environmental and spatial predictors significantly explained variation in community structure. Moreover, the shared fraction of both sets of variables was high, which suggested a substantial amount of spatially structured environmental variation. Additionally, the effect of space independent of environment was much higher than the effect of environment independent of space, which shows the importance of including spatial descriptors in meiofauna and nematode community ecology. Large-scale assessment of free-living nematode diversity and abundance in the Southern Ocean shelf zone revealed strong horizontal and vertical spatial structuring in response to local environmental conditions, in combination with (most likely) dispersal limitation.

Diverse archaeal community of a bat guano pile in Domica Cave (Slovak Karst, Slovakia).

PubMed

Chronáková, A; Horák, A; Elhottová, D; Kristůfek, V

2009-09-01

The molecular diversity of Archaea in a bat guano pile in Cave Domica (Slovakia), temperate cave ecosystem with significant bat colony (about 1600 individuals), was examined. The guano pile was created mainly by an activity of the Mediterranean horseshoe bat (Rhinolophus euryale) and provides a source of organic carbon and other nutrients in the oligotrophic subsurface ecosystem. The upper and the basal parts of guano surface were sampled where the latter one had higher pH and higher admixture of limestone bedrock and increased colonization of invertebrates. The relative proportion of Archaea determined using CARD-FISH in both parts was 3.5-3.9 % (the basal and upper part, respectively). The archaeal community was dominated by non-thermophilic Crenarchaeota (99 % of clones). Phylogenetic analysis of 115 16S rDNA sequences revealed the presence of Crenarchaeota previously isolated from temperate surface soils (group 1.1b, 62 clones), deep subsurface acid waters (group 1.1a, 52 clones) and Euryarchaeota (1 clone). Four of the analyzed sequences were found to have little similarity to those in public databases. The composition of both archaeal communities differed, with respect to higher diversity of Archaea in the upper part of the bat guano pile. High diversity archaeal population is present in the bat guano deposit and consists of both soil- and subsurface-born Crenarchaeota.

Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru

PubMed Central

Biddle, Jennifer F.; Lipp, Julius S.; Lever, Mark A.; Lloyd, Karen G.; Sørensen, Ketil B.; Anderson, Rika; Fredricks, Helen F.; Elvert, Marcus; Kelly, Timothy J.; Schrag, Daniel P.; Sogin, Mitchell L.; Brenchley, Jean E.; Teske, Andreas; House, Christopher H.; Hinrichs, Kai-Uwe

2006-01-01

Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane–carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100–2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea. PMID:16505362

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.

The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents.

PubMed

Sercu, Bram; Jones, Antony D G; Wu, Cindy H; Escobar, Mauricio H; Serlin, Carol L; Knapp, Timothy A; Andersen, Gary L; Holden, Patricia A

2013-01-01

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.

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.

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.

A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿†

PubMed Central

Gihring, Thomas M.; Zhang, Gengxin; Brandt, Craig C.; Brooks, Scott C.; Campbell, James H.; Carroll, Susan; Criddle, Craig S.; Green, Stefan J.; Jardine, Phil; Kostka, Joel E.; Lowe, Kenneth; Mehlhorn, Tonia L.; Overholt, Will; Watson, David B.; Yang, Zamin; Wu, Wei-Min; Schadt, Christopher W.

2011-01-01

Subsurface amendments of slow-release substrates (e.g., emulsified vegetable oil [EVO]) are thought to be a pragmatic alternative to using short-lived, labile substrates for sustained uranium bioimmobilization within contaminated groundwater systems. Spatial and temporal dynamics of subsurface microbial communities during EVO amendment are unknown and likely differ significantly from those of populations stimulated by soluble substrates, such as ethanol and acetate. In this study, a one-time EVO injection resulted in decreased groundwater U concentrations that remained below initial levels for approximately 4 months. Pyrosequencing and quantitative PCR of 16S rRNA from monitoring well samples revealed a rapid decline in groundwater bacterial community richness and diversity after EVO injection, concurrent with increased 16S rRNA copy levels, indicating the selection of a narrow group of taxa rather than a broad community stimulation. Members of the Firmicutes family Veillonellaceae dominated after injection and most likely catalyzed the initial oil decomposition. Sulfate-reducing bacteria from the genus Desulforegula, known for long-chain fatty acid oxidation to acetate, also dominated after EVO amendment. Acetate and H2 production during EVO degradation appeared to stimulate NO3−, Fe(III), U(VI), and SO42− reduction by members of the Comamonadaceae, Geobacteriaceae, and Desulfobacterales. Methanogenic archaea flourished late to comprise over 25% of the total microbial community. Bacterial diversity rebounded after 9 months, although community compositions remained distinct from the preamendment conditions. These results demonstrated that a one-time EVO amendment served as an effective electron donor source for in situ U(VI) bioreduction and that subsurface EVO degradation and metal reduction were likely mediated by successive identifiable guilds of organisms. PMID:21764967

A limited microbial consortium is responsible for extended bioreduction of uranium in a contaminated aquifer.

PubMed

Gihring, Thomas M; Zhang, Gengxin; Brandt, Craig C; Brooks, Scott C; Campbell, James H; Carroll, Susan; Criddle, Craig S; Green, Stefan J; Jardine, Phil; Kostka, Joel E; Lowe, Kenneth; Mehlhorn, Tonia L; Overholt, Will; Watson, David B; Yang, Zamin; Wu, Wei-Min; Schadt, Christopher W

2011-09-01

Subsurface amendments of slow-release substrates (e.g., emulsified vegetable oil [EVO]) are thought to be a pragmatic alternative to using short-lived, labile substrates for sustained uranium bioimmobilization within contaminated groundwater systems. Spatial and temporal dynamics of subsurface microbial communities during EVO amendment are unknown and likely differ significantly from those of populations stimulated by soluble substrates, such as ethanol and acetate. In this study, a one-time EVO injection resulted in decreased groundwater U concentrations that remained below initial levels for approximately 4 months. Pyrosequencing and quantitative PCR of 16S rRNA from monitoring well samples revealed a rapid decline in groundwater bacterial community richness and diversity after EVO injection, concurrent with increased 16S rRNA copy levels, indicating the selection of a narrow group of taxa rather than a broad community stimulation. Members of the Firmicutes family Veillonellaceae dominated after injection and most likely catalyzed the initial oil decomposition. Sulfate-reducing bacteria from the genus Desulforegula, known for long-chain fatty acid oxidation to acetate, also dominated after EVO amendment. Acetate and H(2) production during EVO degradation appeared to stimulate NO(3)(-), Fe(III), U(VI), and SO(4)(2-) reduction by members of the Comamonadaceae, Geobacteriaceae, and Desulfobacterales. Methanogenic archaea flourished late to comprise over 25% of the total microbial community. Bacterial diversity rebounded after 9 months, although community compositions remained distinct from the preamendment conditions. These results demonstrated that a one-time EVO amendment served as an effective electron donor source for in situ U(VI) bioreduction and that subsurface EVO degradation and metal reduction were likely mediated by successive identifiable guilds of organisms.

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

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.

Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer.

PubMed

Bagwell, Christopher E; Liu, Xuaduan; Wu, Liyou; Zhou, Jizhong

2006-03-01

The impact of legacy nuclear waste on the compositional diversity and distribution of sulfate-reducing bacteria in a heavily contaminated subsurface aquifer was examined. dsrAB clone libraries were constructed and restriction fragment length polymorphism (RFLP) analysis used to evaluate genetic variation between sampling wells. Principal component analysis identified nickel, nitrate, technetium, and organic carbon as the primary variables contributing to well-to-well geochemical variability, although comparative sequence analysis showed the sulfate-reducing bacteria community structure to be consistent throughout contaminated and uncontaminated regions of the aquifer. Only 3% of recovered dsrAB gene sequences showed apparent membership to the Deltaproteobacteria. The remainder of recovered sequences may represent novel, deep-branching lineages that, to our knowledge, do not presently contain any cultivated members; although corresponding phylotypes have recently been reported from several different marine ecosystems. These findings imply resiliency and adaptability of sulfate-reducing bacteria to extremes in environmental conditions, although the possibility for horizontal transfer of dsrAB is also discussed.

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.

The bacterial community composition of the surface microlayer in a high mountain lake.

PubMed

Hörtnagl, Paul; Pérez, Maria Teresa; Zeder, Michael; Sommaruga, Ruben

2010-09-01

The existence of bacterioneuston in aquatic ecosystems is well established, but little is known about its composition and dynamics, particularly in lakes. The bacterioneuston underlies extreme conditions at the air-water boundary, which may influence its dynamics in a different way compared with the bacterioplankton. In this study, we assessed quantitative changes in major bacterial groups of the surface microlayer (SML) (upper 900 microm) and the underlying water (ULW) (0.2-0.5 m depth) of an alpine lake during two consecutive ice-free seasons. Analysis of the bacterial community composition was done using catalyzed reporter deposition FISH with oligonucleotide probes. In addition, several physicochemical parameters were measured to characterize these two water layers. Dissolved organic carbon was consistently enriched in the SML and the dissolved organic matter pool presented clear signals of photodegradation and photobleaching. The water temperature was generally colder in the SML than in the subsurface. The bacterial community of the SML and the ULW was dominated by Betaproteobacteria and Actinobacteria. The bacterial community composition was associated with different combinations of physicochemical factors in these two layers, but temporal changes showed similar trends in both layers over the two seasons. Our results identify the SML of alpine lakes as a microhabitat where specific bacterial members such as of Betaproteobacteria seem to be efficient colonizers.

Copepod communities from surface and ground waters in the everglades, south Florida

USGS Publications Warehouse

Bruno, M.C.; Cunningham, K.J.; Perry, S.A.

2003-01-01

We studied species composition and individual abundance of copepods in the surficial aquifer northeast of Everglades National Park. We identified the spatial distribution of subsurface habitats by assessing the depth of the high porosity layers in the limestone along a canal system, and we used copepods to assess the exchange between surface water and ground water along canal banks, at levels in the wells where high porosity connections to the canals exist. Surface- and ground-water taxa were defined, and species composition was related to areal position, sampling depth, and time. Subsurface copepod communities were dominated by surface copepods that disperse into the aquifer following the groundwater seepage along canal L-31N. The similarities in species composition between wells along canal reaches, suggest that copepods mainly enter ground water horizontally along canals via active and passive dispersal. Thus, the copepod populations indicate continuous connections between surface- and ground waters. The most abundant species were Orthocyclops modestus, Arctodiaptomus floridanus, Mesocyclops edax, and Thermocyclops parvus, all known in literature from surface habitats; however, these species have been collected in ground water in ENP. Only two stygophiles were collected: Diacylcops nearcticus and Diacyclops crassicaudis brachycercus. Restoration of the Everglades ecosystem requires a mosaic of data to reveal a complete picture of this complex system. The use of copepods as indicators of seepage could be a tool in helping to assess the direction and the duration of surface and ground water exchange.

Compositions produced using an in situ heat treatment process

DOEpatents

Roes, Augustinus Wilhelmus Maria; Nair, Vijay; Munsterman, Erwin Hunh; Van Bergen, Petrus Franciscus; Van Den Berg, Franciscus Gondulfus Antonius

2013-05-28

Methods for treating a subsurface formation and compositions produced therefrom are described herein. At least one method for producing hydrocarbons from a subsurface formation includes providing heat to the subsurface formation using an in situ heat treatment process. One or more formation particles may be formed during heating of the subsurface formation. Fluid that includes hydrocarbons and the formation particles may be produced from the subsurface formation. The formation particles in the produced fluid may include cenospheres and have an average particle size of at least 0.5 micrometers.

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog

PubMed Central

Sapers, Haley M.; Ronholm, Jennifer; Raymond-Bouchard, Isabelle; Comrey, Raven; Osinski, Gordon R.; Whyte, Lyle G.

2017-01-01

While many habitable niches on Earth are characterized by permanently cold conditions, little is known about the spatial structure of seasonal communities and the importance of substrate-cell associations in terrestrial cyroenvironments. Here we use the 16S rRNA gene as a marker for genetic diversity to compare two visually distinct but spatially integrated surface microbial mats on Axel Heiberg Island, Canadian high arctic, proximal to a perennial saline spring. This is the first study to describe the bacterial diversity in microbial mats on Axel Heiberg Island. The hypersaline springs on Axel Heiberg represent a unique analog to putative subsurface aquifers on Mars. The Martian subsurface represents the longest-lived potentially habitable environment on Mars and a better understanding of the microbial communities on Earth that thrive in analog conditions will help direct future life detection missions. The microbial mats sampled on Axel Heiberg are only visible during the summer months in seasonal flood plains formed by melt water and run-off from the proximal spring. Targeted-amplicon sequencing revealed that not only does the bacterial composition of the two mat communities differ substantially from the sediment community of the proximal cold spring, but that the mat communities are distinct from any other microbial community in proximity to the Arctic springs studied to date. All samples are dominated by Gammaproteobacteria: Thiotichales is dominant within the spring samples while Alteromonadales comprises a significant component of the mat communities. The two mat samples differ in their Thiotichales:Alteromonadales ratio and contribution of Bacteroidetes to overall diversity. The red mats have a greater proportion of Alteromonadales and Bacteroidetes reads. The distinct bacterial composition of the mat bacterial communities suggests that the spring communities are not sourced from the surface, and that seasonal melt events create ephemerally habitable niches with distinct microbial communities in the Canadian high arctic. The finding that these surficial complex microbial communities exist in close proximity to perennial springs demonstrates the existence of a transiently habitable niche in an important Mars analog site. PMID:29312221

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog.

PubMed

Sapers, Haley M; Ronholm, Jennifer; Raymond-Bouchard, Isabelle; Comrey, Raven; Osinski, Gordon R; Whyte, Lyle G

2017-01-01

While many habitable niches on Earth are characterized by permanently cold conditions, little is known about the spatial structure of seasonal communities and the importance of substrate-cell associations in terrestrial cyroenvironments. Here we use the 16S rRNA gene as a marker for genetic diversity to compare two visually distinct but spatially integrated surface microbial mats on Axel Heiberg Island, Canadian high arctic, proximal to a perennial saline spring. This is the first study to describe the bacterial diversity in microbial mats on Axel Heiberg Island. The hypersaline springs on Axel Heiberg represent a unique analog to putative subsurface aquifers on Mars. The Martian subsurface represents the longest-lived potentially habitable environment on Mars and a better understanding of the microbial communities on Earth that thrive in analog conditions will help direct future life detection missions. The microbial mats sampled on Axel Heiberg are only visible during the summer months in seasonal flood plains formed by melt water and run-off from the proximal spring. Targeted-amplicon sequencing revealed that not only does the bacterial composition of the two mat communities differ substantially from the sediment community of the proximal cold spring, but that the mat communities are distinct from any other microbial community in proximity to the Arctic springs studied to date. All samples are dominated by Gammaproteobacteria: Thiotichales is dominant within the spring samples while Alteromonadales comprises a significant component of the mat communities. The two mat samples differ in their Thiotichales:Alteromonadales ratio and contribution of Bacteroidetes to overall diversity. The red mats have a greater proportion of Alteromonadales and Bacteroidetes reads. The distinct bacterial composition of the mat bacterial communities suggests that the spring communities are not sourced from the surface, and that seasonal melt events create ephemerally habitable niches with distinct microbial communities in the Canadian high arctic. The finding that these surficial complex microbial communities exist in close proximity to perennial springs demonstrates the existence of a transiently habitable niche in an important Mars analog site.

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.

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...

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.

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.

Uranium reduction and microbial community development in response to stimulation with different electron donors.

PubMed

Barlett, Melissa; Moon, Hee Sun; Peacock, Aaron A; Hedrick, David B; Williams, Kenneth H; Long, Philip E; Lovley, Derek; Jaffe, Peter R

2012-07-01

Stimulating microbial reduction of soluble U(VI) to less soluble U(IV) shows promise as an in situ bioremediation strategy for uranium contaminated groundwater, but the optimal electron donors for promoting this process have yet to be identified. The purpose of this study was to better understand how the addition of various electron donors to uranium-contaminated subsurface sediments affected U(VI) reduction and the composition of the microbial community. The simple electron donors, acetate or lactate, or the more complex donors, hydrogen-release compound (HRC) or vegetable oil, were added to the sediments incubated in flow-through columns. The composition of the microbial communities was evaluated with quantitative PCR probing specific 16S rRNA genes and functional genes, phospholipid fatty acid analysis, and clone libraries. All the electron donors promoted U(VI) removal, even though the composition of the microbial communities was different with each donor. In general, the overall biomass, rather than the specific bacterial species, was the factor most related to U(VI) removal. Vegetable oil and HRC were more effective in stimulating U(VI) removal than acetate. These results suggest that the addition of more complex organic electron donors could be an excellent option for in situ bioremediation of uranium-contaminated groundwater.

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.

Investigations of subsurface flow constructed wetlands and associated geomaterial resources in the Akumal and Reforma regions, Quintana Roo, Mexico

NASA Astrophysics Data System (ADS)

Krekeler, Mark P. S.; Probst, Pete; Samsonov, Misha; Tselepis, Cynthia M.; Bates, William; Kearns, Lance E.; Maynard, J. Barry

2007-12-01

Subsurface flow constructed wetlands in the village of Akumal, Quintana Roo, Mexico were surveyed to determine the general status of the wetland systems and provide baseline information for long term monitoring and further study. Twenty subsurface flow wetlands were surveyed and common problems observed in the systems were overloading, poor plant cover, odor, and no secondary containment. Bulk mineral composition of aggregate from two subsurface flow constructed wetlands was determined to consist solely of calcite using bulk powder X-ray diffraction. Some soil structure is developed in the aggregate and aggregate levels in wetlands drop at an estimated rate between 3 and 10 cm/year for overloaded wetlands owing to dissolution. Mineral composition from fresh aggregate samples commonly is a mixture of calcite and aragonite. Trace amounts of Pb, Zn, Co, and Cr were observed in fresh aggregate. Coefficients of permeability ( k) varied from 0.006 to 0.027 cm/s with an average values being 0.016 cm/s. Grain size analysis of fresh aggregate samples indicates there are unimodal and multimodal size distributions in the samples with modes in the coarse and fine sand being common. Investigations of other geologic media from the Reforma region indicate that a dolomite with minor amounts of Fe-oxide and palygorskite is abundant and may be a better aggregate source that the current materials used. A Ca-montmorillonite bed was identified in the Reforma region as well and this unit is suitable to serve as a clay liner to prevent leaks for new and existing wetland systems. These newly discovered geologic resources should aid in the improvement of subsurface flow constructed wetlands in the region. Although problems do exist in these wetlands with respect to design, these systems represent a successful implementation of constructed wetlands at a community level in developing regions.

Subsurface In Situ Elemental Composition Measurements with PING

NASA Technical Reports Server (NTRS)

Parsons, Ann; McClanahan, Timothy; Bodnarik, Julia; Evans, Larry; Nowicki, Suzanne; Schweitzer, Jeffrey; Starr, Richard

2013-01-01

This paper describes the Probing In situ with Neutron and Gamma rays (PING) instrument, that can measure the subsurface elemental composition in situ for any rocky body in the solar system without the need for digging into the surface. PING consists of a Pulsed Neutron Generator (PNG), a gamma ray spectrometer and neutron detectors. Subsurface elements are stimulated by high-energy neutrons to emit gamma rays at characteristic energies. This paper will show how the detection of these gamma rays results in a measurement of elemental composition. Examples of the basalt to granite ratios for aluminum and silicon abundance are provided.

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.

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

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

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

Complete Subsurface Elemental Composition Measurements With PING

NASA Technical Reports Server (NTRS)

Parsons, A. M.

2012-01-01

The Probing In situ with Neutrons and Gamma rays (PING) instrument will measure the complete bulk elemental composition of the subsurface of Mars as well as any other solid planetary body. PING can thus be a highly effective tool for both detailed local geochemistry science investigations and precision measurements of Mars subsurface reSOurces in preparation for future human exploration. As such, PING is thus fully capable of meeting a majority of both ncar and far term elements in Challenge #1 presented for this conference. Measuring the ncar subsurface composition of Mars will enable many of the MEPAG science goals and will be key to filling an important Strategic Knowledge Gap with regard to In situ Resources Utilization (ISRU) needs for human exploration. [1, 2] PING will thus fill an important niche in the Mars Exploration Program.

Isolated ecosystems on supercooled scree slopes in subalpine environments - interaction between permafrost, soil and vegetation

NASA Astrophysics Data System (ADS)

Schwindt, Daniel; Kozák, Johanna-Luise; Kohlpaintner, Michael

2017-04-01

In the central European Alps, permafrost can be expected in altitudes above 2300 m a.s.l., where mean annual air temperatures are below -1°C. However, attributed to the thermally induced "chimney effect", isolated permafrost lenses can be found in scree slopes far below the timberline where mean annual air temperature is positive. Usually the supercooled subsurface appears as lenses at the foot of talus slopes, covered by a thick layer of organic material and a unique vegetation composition most obviously characterized by dwarf grown trees ("Hexenwäldli") and azonal plant species. The fact that mean annual air temperature is positive and therefore can be excluded as a driving factor makes these sites unique for studying interdependencies between a supercooled subsurface, plant adaptation and vegetation sociology as well as the soil development. Three study sites in the Swiss Alps, differing in altitude and substrate (granite, dolomite, limestone) were investigated. Studies covered the permafrost-affected central parts of the slope as well as the surrounding areas. For characterizing distribution and temporal variability of ground ice geophysical methods were applied (electrical resistivity- and seismic refraction tomography). Temperature data loggers were used for monitoring the thermal regime (air-, surface- and soil temperatures). Chemical parameters (pH, C/N ratio) and nutrient contents (N, P, Ca, Mg, Mn, K) were analyzed in different depth levels. Plant communities were analyzed with the Braun-Blanquet method. To characterize physiognomic adaptation of trees, transects have been determined parallel to slope, measuring tree height, diameter and age. Results show a strong spatial correlation between frozen ground, formation of a thick organic layer (Tangelhumus), azonal plant species distribution and pronounced dwarfing of trees. Surrounding areas with unfrozen subsurface show an - for the particular altitude - expected species and soil composition and normal forest growth. Ellenberg pointer values in central parts of the study sites showed a strong plant adaption to cold temperatures. However, plant sociological analysis did not indicate one clear azonal community, but two different permafrost-plant-communities, one adapted to acidic and the other to calcareous substrates. Dwarf grown trees (e.g. spruce, 63cm high, 122 years old) could be found in permafrost-affected areas of all study sites, while the same species developed normally in the surroundings. Main factor for the physiognomic adaptation seems to be the low temperature in the rooting zone and the correlated shorter vegetation period, as air temperatures and nutrient supplies between the permafrost affected area and its surroundings are comparable. Pronounced interdependencies between frozen ground distribution, vegetation cover and soil development could be verified for all sites. The supercooled subsurface causes reduced decomposition of organic material as well as dwarfing of trees. In return, Tangelhumus and dwarfed trees positively affect supercooling. Dry organic material thermally insulates the subsurface during summer and prevents/delays thawing, while the high thermal conductivity of the moist or frozen Tangelhumus enhances heat flow and supercooling in winter. In addition, dwarfed trees prevent the formation of a consistent insulating snow cover optimizing thermal fluxes between atmosphere and subsurface.

Temperature and Redox Effect on Mineral Colonization in Juan de Fuca Ridge Flank Subsurface Crustal Fluids

PubMed Central

Baquiran, Jean-Paul M.; Ramírez, Gustavo A.; Haddad, Amanda G.; Toner, Brandy M.; Hulme, Samuel; Wheat, Charles G.; Edwards, Katrina J.; Orcutt, Beth N.

2016-01-01

To examine microbe-mineral interactions in subsurface oceanic crust, we evaluated microbial colonization on crustal minerals that were incubated in borehole fluids for 1 year at the seafloor wellhead of a crustal borehole observatory (IODP Hole U1301A, Juan de Fuca Ridge flank) as compared to an experiment that was not exposed to subsurface crustal fluids (at nearby IODP Hole U1301B). In comparison to previous studies at these same sites, this approach allowed assessment of the effects of temperature, fluid chemistry, and/or mineralogy on colonization patterns of different mineral substrates, and an opportunity to verify the approach of deploying colonization experiments at an observatory wellhead at the seafloor instead of within the borehole. The Hole U1301B deployment did not have biofilm growth, based on microscopy and DNA extraction, thereby confirming the integrity of the colonization design against bottom seawater intrusion. In contrast, the Hole U1301A deployment supported biofilms dominated by Epsilonproteobacteria (43.5% of 370 16S rRNA gene clone sequences) and Gammaproteobacteria (29.3%). Sequence analysis revealed overlap in microbial communities between different minerals incubated at the Hole U1301A wellhead, indicating that mineralogy did not separate biofilm structure within the 1-year colonization experiment. Differences in the Hole U1301A wellhead biofilm community composition relative to previous studies from within the borehole using similar mineral substrates suggest that temperature and the diffusion of dissolved oxygen through plastic components influenced the mineral colonization experiments positioned at the wellhead. This highlights the capacity of low abundance crustal fluid taxa to rapidly establish communities on diverse mineral substrates under changing environmental conditions such as from temperature and oxygen. PMID:27064928

Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization

DOE PAGES

Oates, Lawrence G.; Duncan, David S.; Sanford, Gregg R.; ...

2016-10-03

The choice of crops and their management can strongly influence soil microbial communities and their processes. Here, we used lipid biomarker profiling to characterize how soil microbial composition of five potential bioenergy cropping systems diverged from a common baseline five years after they were established. The cropping systems we studied included an annual system (continuous no-till corn) and four perennial crops (switchgrass, miscanthus, hybrid poplar, and restored prairie). Partial- and no-stover removal were compared for the corn system, while N-additions were compared to unfertilized plots for the perennial cropping systems. Arbuscular mycorrhizal fungi (AMF) and Gram-negative biomass was higher inmore » unfertilized perennial grass systems, especially in switchgrass and prairie. Gram-positive bacterial biomass decreased in all systems relative to baseline values in surface soils (0–10 cm), but not subsurface soils (10–25 cm). Overall microbial composition was similar between the two soil depths. Our findings demonstrate the capacity of unfertilized perennial cropping systems to recreate microbial composition found in undisturbed soil environments and indicate how strongly agroecosystem management decisions such as N addition and plant community composition can influence soil microbial assemblages.« less

Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization

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

Oates, Lawrence G.; Duncan, David S.; Sanford, Gregg R.

The choice of crops and their management can strongly influence soil microbial communities and their processes. Here, we used lipid biomarker profiling to characterize how soil microbial composition of five potential bioenergy cropping systems diverged from a common baseline five years after they were established. The cropping systems we studied included an annual system (continuous no-till corn) and four perennial crops (switchgrass, miscanthus, hybrid poplar, and restored prairie). Partial- and no-stover removal were compared for the corn system, while N-additions were compared to unfertilized plots for the perennial cropping systems. Arbuscular mycorrhizal fungi (AMF) and Gram-negative biomass was higher inmore » unfertilized perennial grass systems, especially in switchgrass and prairie. Gram-positive bacterial biomass decreased in all systems relative to baseline values in surface soils (0–10 cm), but not subsurface soils (10–25 cm). Overall microbial composition was similar between the two soil depths. Our findings demonstrate the capacity of unfertilized perennial cropping systems to recreate microbial composition found in undisturbed soil environments and indicate how strongly agroecosystem management decisions such as N addition and plant community composition can influence soil microbial assemblages.« less

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

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.

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

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

The influence of subsurface porosity and bedrock composition on ecosystem productivity and drought resilience in the Sierra Nevada Batholith, California

NASA Astrophysics Data System (ADS)

Riebe, C. S.; Callahan, R. P.; Goulden, M.; Pasquet, S.; Flinchum, B. A.; Taylor, N. J.; Holbrook, W. S.

2017-12-01

The availability of water and nutrients in soil and weathered rock influences the distribution of Earth's terrestrial life and regulates ecosystem vulnerability to land use and climate change. We explored these relationships by combining geochemical and geophysical measurements at three mid-elevation sites in the Sierra Nevada, California. Forest cover correlates strongly with bedrock composition across the sites, implying strong lithologic control on the ecosystem. We evaluated two hypotheses about bedrock-ecosystem connections: 1) that bedrock composition influences vegetation by moderating plant-essential nutrient supply; and 2) that bedrock composition influences the degree of subsurface weathering, which influences vegetation by controlling subsurface water-storage capacity. To quantify subsurface water-holding capacity, we used seismic refraction surveys to infer gradients in P and S-wave velocity structure, which reveal variations in porosity when coupled together in a Hertz-Mindlin rock-physics model. We combined the geophysical data on porosity with bedrock bulk geochemistry measured in previous work to evaluate the influence of water-holding capacity and nutrient supply on ecosystem productivity, which we quantified using remote sensing. Our results show that more than 80% of the variance in ecosystem productivity can be explained by differences in bedrock phosphorus concentration and subsurface porosity, with phosphorus content being the dominant explanatory variable. This suggests that bedrock composition exerts a strong bottom-up control on ecosystem productivity through its influence on nutrient supply and weathering susceptibility, which in turn influences porosity. We show that vegetation vulnerability to drought stress and mortality can be explained in part by variations in subsurface water-holding capacity and rock-derived nutrient supply.

Microbial population and functional dynamics associated with surface potential and carbon metabolism

PubMed Central

Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Phan, Tony; Wanger, Greg; Nealson, Kenneth H; Sekiguchi, Yuji; Gorby, Yuri A; Bretschger, Orianna

2014-01-01

Microbial extracellular electron transfer (EET) to solid surfaces is an important reaction for metal reduction occurring in various anoxic environments. However, it is challenging to accurately characterize EET-active microbial communities and each member's contribution to EET reactions because of changes in composition and concentrations of electron donors and solid-phase acceptors. Here, we used bioelectrochemical systems to systematically evaluate the synergistic effects of carbon source and surface redox potential on EET-active microbial community development, metabolic networks and overall electron transfer rates. The results indicate that faster biocatalytic rates were observed under electropositive electrode surface potential conditions, and under fatty acid-fed conditions. Temporal 16S rRNA-based microbial community analyses showed that Geobacter phylotypes were highly diverse and apparently dependent on surface potentials. The well-known electrogenic microbes affiliated with the Geobacter metallireducens clade were associated with lower surface potentials and less current generation, whereas Geobacter subsurface clades 1 and 2 were associated with higher surface potentials and greater current generation. An association was also observed between specific fermentative phylotypes and Geobacter phylotypes at specific surface potentials. When sugars were present, Tolumonas and Aeromonas phylotypes were preferentially associated with lower surface potentials, whereas Lactococcus phylotypes were found to be closely associated with Geobacter subsurface clades 1 and 2 phylotypes under higher surface potential conditions. Collectively, these results suggest that surface potentials provide a strong selective pressure, at the species and strain level, for both solid surface respirators and fermentative microbes throughout the EET-active community development. PMID:24351938

New Insights on Subsurface Imaging of Carbon Nanotubes in Polymer Composites via Scanning Electron Microscopy

NASA Technical Reports Server (NTRS)

Zhao, Minhua; Ming, Bin; Kim, Jae-Woo; Gibbons, Luke J.; Gu, Xiaohong; Nguyen, Tinh; Park, Cheol; Lillehei, Peter T.; Villarrubia, J. S.; Vladar, Andras E.;

Contents and composition of organic matter in subsurface soils affected by land use and soil mineralogy

NASA Astrophysics Data System (ADS)

Ellerbrock, Ruth H.; Kaiser, Michael

2010-05-01

Land use and mineralogy affect the ability of surface as well as subsurface soils to sequester organic carbon and their contribution to mitigate the greenhouse effect. This study aimed to investigate the long-term impact of land use (i.e., arable and forest) and soil mineralogy on contents and composition of soil organic matter (SOM) from subsurface soils. Seven soils different in mineralogy (Albic and Haplic Luvisol, Colluvic and Haplic Regosol, Haplic and Vertic Cambisol, Haplic Stagnosol) were selected within Germany. Soil samples were taken from forest and adjacent arable sites. First, particulate and water soluble organic matter were separated from the subsurface soil samples. From the remaining solid residues the OM(PY) fractions were separated, analyzed for its OC content (OCPY) and characterized by FTIR spectroscopy. For the arable subsurface soils multiple regression analyses indicate significant positive relationships between the soil organic carbon contents and the contents of i) exchangeable Ca and oxalate soluble Fe, and Alox contents. Further for the neutral arable subsurface soils the contents OCPY weighted by its C=O contents were found to be related to the contents of Ca indicating interactions between OM(PY) and Ca cations. For the forest subsurface soils (pH <5) the OCPY contents were positively related with the contents of Na-pyrophosphate soluble Fe and Al. For the acidic forest subsurface soils such findings indicate interactions between OM(PY) and Fe3+ and Al3+ cations. The effects of land use and soil mineralogy on contents and composition of SOM and OM(PY) will be discussed.

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...

Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

PubMed Central

Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

2012-01-01

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments.

PubMed

Laverock, Bonnie; Smith, Cindy J; Tait, Karen; Osborn, A Mark; Widdicombe, Steve; Gilbert, Jack A

2010-12-01

Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction fragment length polymorphism analysis was used to investigate variation in the structure of bacterial communities in sediment bioturbated by the burrowing shrimp Upogebia deltaura or Callianassa subterranea. Analyses of 229 sediment samples revealed significant differences between bacterial communities inhabiting shrimp burrows and those inhabiting ambient surface and subsurface sediments. Bacterial communities in burrows from both shrimp species were more similar to those in surface-ambient than subsurface-ambient sediment (R=0.258, P<0.001). The presence of shrimp was also associated with changes in bacterial community structure in surrounding surface sediment, when compared with sediments uninhabited by shrimp. Bacterial community structure varied with burrow depth, and also between individual burrows, suggesting that the shrimp's burrow construction, irrigation and maintenance behaviour affect the distribution of bacteria within shrimp burrows. Subsequent sequence analysis of bacterial 16S rRNA genes from surface sediments revealed differences in the relative abundance of bacterial taxa between shrimp-inhabited and uninhabited sediments; shrimp-inhabited sediment contained a higher proportion of proteobacterial sequences, including in particular a twofold increase in Gammaproteobacteria. Chao1 and ACE diversity estimates showed that taxon richness within surface bacterial communities in shrimp-inhabited sediment was at least threefold higher than that in uninhabited sediment. This study shows that bioturbation can result in significant structural and compositional changes in sediment bacterial communities, increasing bacterial diversity in surface sediments and resulting in distinct bacterial communities even at depth within the burrow. In an area of high macrofaunal abundance, this could lead to alterations in the microbial transformations of important nutrients at the sediment-water interface.

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.

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

Bacterial Communities in the Groundwater of Xikuangshan Antimony Mine, China

NASA Astrophysics Data System (ADS)

Wu, M.; Wang, H.; Wang, N.; Wang, M.

2017-12-01

Xikuangshan (XKS) is the biggest antimony (Sb) mine around the word, which causes serious environmental contamination due to the mining actives. To fully understand the bacterial compositions in the groundwater around the mining area in XKS and their correlation with environmental factors, groundwater samples were collected and subject to 16S rDNA high throughput sequencing. Results indicated that Proteobacteria (especially Gamma-Proteobacteria) dominated bacterial communities in high-Sb groundwater samples, whereas Bacteroidetes predominated in low-Sb groundwater. Furthermore, antimony concentration was found to be the most significant factor shaping bacterial communities (P=0.002) with an explanation of 9.16% of the variation. Other factors such as pH, contents of Mg, Ca and orthophosphate were also observed to significantly correlate with bacterial communities. This was the first report to show the important impact of Sb concentration on bacterial community structure in the groundwater in the mining area. Our results will enhance the understanding of subsurface biogeochemical processes mediated by microbes.

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

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.

Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest.

PubMed

Du, Can; Geng, Zengchao; Wang, Qiang; Zhang, Tongtong; He, Wenxiang; Hou, Lin; Wang, Yueling

2017-09-01

Microbial communities in subsurface soil are specialized for their environment, which is distinct from that of the surface communities. However, little is known about the microbial communities (bacteria and fungi) that exist in the deeper soil horizons. Vertical changes in microbial alpha-diversity (Chao1 and Shannon indices) and community composition were investigated at four soil depths (0-10, 10-20, 20-40, and 40-60 cm) in a natural secondary forest of Betula albosinensis by high-throughput sequencing of the 16S and internal transcribed spacer rDNA regions. The numbers of operational taxonomic units (OTUs), and the Chao1 and Shannon indices decreased in the deeper soil layers. Each soil layer contained both mutual and specific OTUs. In the 40-60 cm soil layer, 175 and 235 specific bacterial and fungal OTUs were identified, respectively. Acidobacteria was the most dominant bacterial group in all four soil layers, but reached its maximum at 40-60 cm (62.88%). In particular, the 40-60 cm soil layer typically showed the highest abundance of the fungal genus Inocybe (47.46%). The Chao1 and Shannon indices were significantly correlated with the soil organic carbon content. Redundancy analysis indicated that the bacterial communities were closely correlated with soil organic carbon content (P = 0.001). Collectively, these results indicate that soil nutrients alter the microbial diversity and relative abundance and affect the microbial composition.

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

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.

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.

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.

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability.

PubMed

Brannen-Donnelly, Kathleen; Engel, Annette S

2015-01-01

Unchanging physicochemical conditions and nutrient sources over long periods of time in cave and karst subsurface habitats, particularly aquifers, can support stable ecosystems, termed autochthonous microbial endokarst communities (AMEC). AMEC existence is unknown for other karst settings, such as epigenic cave streams. Conceptually, AMEC should not form in streams due to faster turnover rates and seasonal disturbances that have the capacity to transport large quantities of water and sediment and to change allochthonous nutrient and organic matter sources. Our goal was to investigate whether AMEC could form and persist in hydrologically active, epigenic cave streams. We analyzed bacterial diversity from cave water, sediments, and artificial substrates (Bio-Traps®) placed in the cave at upstream and downstream locations. Distinct communities existed for the water, sediments, and Bio-Trap® samplers. Throughout the study period, a subset of community members persisted in the water, regardless of hydrological disturbances. Stable habitat conditions based on flow regimes resulted in more than one contemporaneous, stable community throughout the epigenic cave stream. However, evidence for AMEC was insufficient for the cave water or sediments. Community succession, specifically as predictable exogenous heterotrophic microbial community succession, was evident from decreases in community richness from the Bio-Traps®, a peak in Bio-Trap® community biomass, and from changes in the composition of Bio-Trap® communities. The planktonic community was compositionally similar to Bio-Trap® initial colonizers, but the downstream Bio-Trap® community became more similar to the sediment community at the same location. These results can help in understanding the diversity of planktonic and attached microbial communities from karst, as well as microbial community dynamics, stability, and succession during disturbance or contamination responses over time.

[Characterizing composition and transformation of dissolved organic matter in subsurface wastewater infiltration system].

PubMed

Wang, Li-Jun; Liu, Yu-Zhong; Zhang, Lie-Yu; Xi, Bei-Dou; Xia, Xun-Feng; Liu, Ya-Ru

2013-08-01

In the present study, the soil column with radius of 30 cm and height of 200 cm was used to simulate a subsurface wastewater infiltration system. Under the hydraulic loading of 4 cm x d(-1), composition and transformation of dissolved organic matter (DOM) from different depths were analyzed in a subsurface wastewater infiltration system for treatment of septic tank effluent using three-dimensional excitation emission matrix fluorescence spectroscopy (3D-EEM) with regional integration analysis (FRI). The results indicate that: (1) from different depth, the composition of DOM was also different; influent with the depth of 0.5 m was mainly composed of protein-like substances, and that at other depths was mainly composed of humic- and fulvic-like substances. (2) DOM stability gradually increased and part of the nonbiodegradable organic matter can be removed during organic pollutants degradation process. (3) Not only the organic pollutants concentration was reduced effectively, but also the stability of the DOM improved in subsurface wastewater infiltration system.

Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions.

PubMed

Serkebaeva, Yulia M; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

2013-01-01

Northern peatlands play a key role in the global carbon and water budget, but the bacterial diversity in these ecosystems remains poorly described. Here, we compared the bacterial community composition in the surface (0-5 cm depth) and subsurface (45-50 cm) peat layers of an acidic (pH 4.0) Sphagnum-dominated wetland, using pyrosequencing of 16S rRNA genes. The denoised sequences (37,229 reads, average length ∼430 bp) were affiliated with 27 bacterial phyla and corresponded to 1,269 operational taxonomic units (OTUs) determined at 97% sequence identity. Abundant OTUs were affiliated with the Acidobacteria (35.5±2.4% and 39.2±1.2% of all classified sequences in surface and subsurface peat, respectively), Alphaproteobacteria (15.9±1.7% and 25.8±1.4%), Actinobacteria (9.5±2.0% and 10.7±0.5%), Verrucomicrobia (8.5±1.4% and 0.6±0.2%), Planctomycetes (5.8±0.4% and 9.7±0.6%), Deltaproteobacteria (7.1±0.4% and 4.4%±0.3%), and Gammaproteobacteria (6.6±0.4% and 2.1±0.1%). The taxonomic patterns of the abundant OTUs were uniform across all the subsamples taken from each peat layer. In contrast, the taxonomic patterns of rare OTUs were different from those of the abundant OTUs and varied greatly among subsamples, in both surface and subsurface peat. In addition to the bacterial taxa listed above, rare OTUs represented the following groups: Armatimonadetes, Bacteroidetes, Chlamydia, Chloroflexi, Cyanobacteria, Elusimicrobia, Fibrobacteres, Firmicutes, Gemmatimonadetes, Spirochaetes, AD3, WS1, WS4, WS5, WYO, OD1, OP3, BRC1, TM6, TM7, WPS-2, and FCPU426. OTU richness was notably higher in the surface layer (882 OTUs) than in the anoxic subsurface peat (483 OTUs), with only 96 OTUs common to both data sets. Most members of poorly studied phyla, such as the Acidobacteria, Verrucomicrobia, Planctomycetes and the candidate division TM6, showed a clear preference for growth in either oxic or anoxic conditions. Apparently, the bacterial communities in surface and subsurface layers of northern peatlands are highly diverse and taxonomically distinct, reflecting the different abiotic conditions in microhabitats within the peat profile.

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.

Observation to Theory in Deep Subsurface Microbiology Research: Can We Piece It Together?

NASA Astrophysics Data System (ADS)

Colwell, F. S.; Thurber, A. R.

2016-12-01

Three decades of observations of microbes in deep environments have led to startling discoveries of life in the subsurface. Now, a few theoretical frameworks exist that help to define Stygian life. Temperature, redox gradients, productivity (e.g., in the overlying ocean), and microbial power requirements are thought to determine the distribution of microbes in the subsurface. Still, we struggle to comprehend the spatial and temporal spectra of Earth processes that define how deep microbe communities survive. Stommel diagrams, originally used to guide oceanographic sampling, may be useful in depicting the subsurface where microbial communities are impacted by co-occurring spatial and temporal phenomena that range across exponential scales. Spatially, the geological settings that influence the activity and distribution of microbes range from individual molecules or minerals all the way up to the planetary-scale where geological formations, occupying up to 105 km3, dictate the bio- and functional geography of microbial communities. Temporally, life in the subsurface may respond in time units familiar to humans (e.g., seconds to days) or to events that unfold over hundred millennial time periods. While surface community dynamics are underpinned by solar and lunar cycles, these cycles only fractionally dictate survival underground where phenomena like tectonic activity, isostatic rebound, and radioactive decay are plausible drivers of microbial life. Geological or planetary processes that occur on thousand or million year cycles could be uniquely important to microbial viability in the subsurface. Such an approach aims at a holistic comprehension of the interaction of Earth system dynamics with microbial ecology.

Taxonomic and functional patterns of macrobenthic communities on a high-Arctic shelf: A case study from the Laptev Sea

NASA Astrophysics Data System (ADS)

Kokarev, V. N.; Vedenin, A. A.; Basin, A. B.; Azovsky, A. I.

2017-11-01

The studies of functional structure of high-Arctic Ecosystems are scarce. We used data on benthic macrofauna from 500-km latitudinal transect in the eastern Laptev Sea, from the Lena delta to the continental shelf break, to describe spatial patterns in species composition, taxonomic and functional structure in relation to environmental factors. Both taxonomy-based approach and Biological Trait analysis yielded similar results and showed general depth-related gradient in benthic diversity and composition. This congruence between taxonomical and functional dimensions of community organization suggests that the same environmental factors (primarily riverine input and regime of sedimentation) have similar effect on both community structure and functioning. BTA also revealed a distinct functional structure of stations situated at the Eastern Lena valley, with dominance of motile, burrowing sub-surface deposit-feeders and absence of sedentary tube-dwelling forms. The overall spatial distribution of benthic assemblages corresponds well to that described there in preceding decades, evidencing the long-term stability of bottom ecosystem. Strong linear relationship between species and traits diversity, however, indicates low functional redundancy, which potentially makes the ecosystem susceptible to a species loss or structural shifts.

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.

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.

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.

Effects of 6 months of aging in water on hardness and surface roughness of two microhybrid dental composites.

PubMed

de Moraes, Rafael Ratto; Marimon, José Laurindo Machado; Schneider, Luis Felipe; Sinhoreti, Mário Alexandre Coelho; Correr-Sobrinho, Lourenço; Bueno, Márcia

2008-06-01

This study assessed the effect of 6 months of aging in water on surface roughness and surface/subsurface hardness of two microhybrid resin composites. Filtek Z250 and Charisma were tested. Cylindrical specimens were obtained and stored in distilled water for 24 hours or 6 months, at 37 degrees C. For Knoop hardness evaluation, the specimens were transversely wet-flattened, and indentations were made on surface and subsurface layers. Data were submitted to three-way ANOVA and Tukey's test (alpha < or = 0.05). Surface roughness baseline measurements were made at 24 hours and repeated after 6 months of storage. Data were submitted to repeated measures ANOVA and Tukey's test (alpha < or = 0.05). Surface hardness (KHN, kg/mm(2)) means (+/- standard deviation) ranged from 55 +/- 1 to 49 +/- 4 for Z250 and from 50 +/- 2 to 41 +/- 3 for Charisma, at 24 hours and 6 months, respectively. Subsurface means ranged from 58 +/- 2 to 61 +/- 3 for Z250 and from 50 +/- 1 to 54 +/- 2 for Charisma, at 24 hours and 6 months. For both composites, the aged specimens presented significantly softer surfaces (p < 0.01). For the subsurface hardness, alteration after storage was detected only for Charisma, which presented a significant rise in hardness (p < 0.01). Z250 presented significantly harder surface and subsurface layers in comparison with Charisma. Surface roughness (Ra, mum) means ranged from 0.07 +/- 0.00 to 0.07 +/- 0.01 for Z250 and from 0.06 +/- 0.01 to 0.07 +/- 0.01 for Charisma, at 24 hours and 6 months, respectively. For both composites, no significant roughness alteration was detected during the study (p= 0.386). The 6-month period of storage in water presented a significant softening effect on the surfaces of the composites, although no significant deleterious alteration was detected for the subsurface hardness. In addition, the storage period had no significant effect on the surface roughness of the materials.

A New Approach to Predict Microbial Community Assembly and Function Using a Stochastic, Genome-Enabled Modeling Framework

NASA Astrophysics Data System (ADS)

King, E.; Brodie, E.; Anantharaman, K.; Karaoz, U.; Bouskill, N.; Banfield, J. F.; Steefel, C. I.; Molins, S.

2016-12-01

Characterizing and predicting the microbial and chemical compositions of subsurface aquatic systems necessitates an understanding of the metabolism and physiology of organisms that are often uncultured or studied under conditions not relevant for one's environment of interest. Cultivation-independent approaches are therefore important and have greatly enhanced our ability to characterize functional microbial diversity. The capability to reconstruct genomes representing thousands of populations from microbial communities using metagenomic techniques provides a foundation for development of predictive models for community structure and function. Here, we discuss a genome-informed stochastic trait-based model incorporated into a reactive transport framework to represent the activities of coupled guilds of hypothetical microorganisms. Metabolic pathways for each microbe within a functional guild are parameterized from metagenomic data with a unique combination of traits governing organism fitness under dynamic environmental conditions. We simulate the thermodynamics of coupled electron donor and acceptor reactions to predict the energy available for cellular maintenance, respiration, biomass development, and enzyme production. While `omics analyses can now characterize the metabolic potential of microbial communities, it is functionally redundant as well as computationally prohibitive to explicitly include the thousands of recovered organisms into biogeochemical models. However, one can derive potential metabolic pathways from genomes along with trait-linkages to build probability distributions of traits. These distributions are used to assemble groups of microbes that couple one or more of these pathways. From the initial ensemble of microbes, only a subset will persist based on the interaction of their physiological and metabolic traits with environmental conditions, competing organisms, etc. Here, we analyze the predicted niches of these hypothetical microbes and assess the ability of a stochastically assembled community of organisms to predict subsurface biogeochemical dynamics.

Compositions produced using an in situ heat treatment process

DOEpatents

Roes, Augustinus Wilhelmus Maria [Houston, TX; Nair, Vijay [Katy, TX; Munsterman, Erwin Henh [Amsterdam, NL; Van Bergen, Petrus Franciscus [Amsterdam, NL; Van Den Berg, Franciscus Gondulfus Antonius

2009-10-20

Systems, methods, and heaters for treating a subsurface formation are described herein. At least one method for producing hydrocarbons from a subsurface formation includes providing heat to the subsurface formation using an in situ heat treatment process. One or more formation particles may be formed during heating of the subsurface formation. Fluid that includes hydrocarbons and the formation particles may be produced from the subsurface formation. The formation particles in the produced fluid may include cenospheres and have an average particle size of at least 0.5 micrometers.

Estimating and mapping ecological processes influencing microbial community assembly

PubMed Central

Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

2015-01-01

Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth. PMID:25983725

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

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

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

Hamada, Yuki; Gilbert, Jack A.; Larsen, Peter E.

2014-04-01

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and belowground ecosystems. However, the integration of biophysical and soil remote sensing withmore » geospatial information about the e nvironment holds great promise for mapping SMC biogeography. Additional research needs invol ve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.« less

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

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

Hamada, Yuki; Gilbert, Jack A.; Larsen, Peter E.

2014-04-01

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and below-ground ecosystems. However, the integration of biophysical and soil remote sensing withmore » geospatial information about the environment holds great promise for mapping SMC biogeography. Additional research needs involve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.« less

Radioactive waste management complex low-level waste radiological composite analysis

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

McCarthy, J.M.; Becker, B.H.; Magnuson, S.O.

1998-05-01

The composite analysis estimates the projected cumulative impacts to future members of the public from the disposal of low-level radioactive waste (LLW) at the Idaho National Engineering and Environmental Laboratory (INEEL) Radioactive Waste Management Complex (RWMC) and all other sources of radioactive contamination at the INEEL that could interact with the LLW disposal facility to affect the radiological dose. Based upon the composite analysis evaluation, waste buried in the Subsurface Disposal Area (SDA) at the RWMC is the only source at the INEEL that will significantly interact with the LLW facility. The source term used in the composite analysis consistsmore » of all historical SDA subsurface disposals of radionuclides as well as the authorized LLW subsurface disposal inventory and projected LLW subsurface disposal inventory. Exposure scenarios evaluated in the composite analysis include all the all-pathways and groundwater protection scenarios. The projected dose of 58 mrem/yr exceeds the composite analysis guidance dose constraint of 30 mrem/yr; therefore, an options analysis was conducted to determine the feasibility of reducing the projected annual dose. Three options for creating such a reduction were considered: (1) lowering infiltration of precipitation through the waste by providing a better cover, (2) maintaining control over the RWMC and portions of the INEEL indefinitely, and (3) extending the period of institutional control beyond the 100 years assumed in the composite analysis. Of the three options investigated, maintaining control over the RWMC and a small part of the present INEEL appears to be feasible and cost effective.« less

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

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.

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

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.

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

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

PubMed Central

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

2017-01-01

Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5′-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs. PMID:28638372

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

Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.

Across a set of ecological communities connected to each other through organismal dispersal (a ‘meta-community’), turnover in composition is governed by (ecological) Drift, Selection, and Dispersal Limitation. Quantitative estimates of these processes remain elusive, but would represent a common currency needed to unify community ecology. Using a novel analytical framework we quantitatively estimate the relative influences of Drift, Selection, and Dispersal Limitation on subsurface, sediment-associated microbial meta-communities. The communities we study are distributed across two geologic formations encompassing ~12,500m3 of uranium-contaminated sediments within the Hanford Site in eastern Washington State. We find that Drift consistently governs ~25% of spatial turnovermore » in community composition; Selection dominates (governing ~60% of turnover) across spatially-structured habitats associated with fine-grained, low permeability sediments; and Dispersal Limitation is most influential (governing ~40% of turnover) across spatially-unstructured habitats associated with coarse-grained, highly-permeable sediments. Quantitative influences of Selection and Dispersal Limitation may therefore be predictable from knowledge of environmental structure. To develop a system-level conceptual model we extend our analytical framework to compare process estimates across formations, characterize measured and unmeasured environmental variables that impose Selection, and identify abiotic features that limit dispersal. Insights gained here suggest that community ecology can benefit from a shift in perspective; the quantitative approach developed here goes beyond the ‘niche vs. neutral’ dichotomy by moving towards a style of natural history in which estimates of Selection, Dispersal Limitation and Drift can be described, mapped and compared across ecological systems.« less

Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site.

PubMed

Lin, Xueju; Kennedy, David; Fredrickson, Jim; Bjornstad, Bruce; Konopka, Allan

2012-02-01

Microbial diversity in subsurface sediments at the Hanford Site 300 Area near Richland, Washington state (USA) was investigated by analysing 21 samples recovered from depths of 9-52 m. Approximately 8000 near full-length 16S rRNA gene sequences were analysed across geological strata that include a natural redox transition zone. These strata included the oxic coarse-grained Hanford formation, fine-grained oxic and anoxic Ringold Formation sediments, and the weathered basalt group. We detected 1233 and 120 unique bacterial and archaeal OTUs (operational taxonomic units at the 97% identity level) respectively. Microbial community structure and richness varied substantially across the different geological strata. Bacterial OTU richness (Chao1 estimator) was highest (> 700) in the upper Hanford formation, and declined to about 120 at the bottom of the Hanford formation. Just above the Ringold oxic-anoxic interface, richness was about 325 and declined to less than 50 in the deeper reduced zones. The deeper Ringold strata were characterized by a preponderance (c. 90%) of Proteobacteria. The bacterial community in the oxic sediments contained not only members of nine well-recognized phyla but also an unusually high proportion of three candidate divisions (GAL15, NC10 and SPAM). Additionally, 13 novel phylogenetic orders were identified within the Deltaproteobacteria, a clade rich in microbes that carry out redox transformations of metals that are important contaminants on the Hanford Site. © 2011 Society for Applied Microbiology and Blackwell Publishing 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.

2013-01-01

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.

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.

The influence of Critical Zone structure on runoff paths, seasonal water storage, and ecosystem composition

NASA Astrophysics Data System (ADS)

Hahm, W. J.; Dietrich, W. E.; Rempe, D.; Dralle, D.; Dawson, T. E.; Lovill, S.; Bryk, A.

2017-12-01

Understanding how subsurface water storage mediates water availability to ecosystems is crucial for elucidating linkages between water, energy, and carbon cycles from local to global scales. Earth's Critical Zone (the CZ, which extends from the top of the vegetation canopy downward to fresh bedrock) includes fractured and weathered rock layers that store and release water, thereby contributing to ecosystem water supplies, and yet are not typically represented in land-atmosphere models. To investigate CZ structural controls on water storage dynamics, we intensively studied field sites in a Mediterranean climate where winter rains arrive months before peak solar energy availability, resulting in strong summertime ecosystem reliance on stored subsurface water. Intra-hillslope and catchment-wide observations of CZ water storage capacity across a lithologic boundary in the Franciscan Formation of the Northern California Coast Ranges reveal large differences in the thickness of the CZ and water storage capacity that result in a stark contrast in plant community composition and stream behavior. Where the CZ is thick, rock moisture storage supports forest transpiration and slow groundwater release sustains baseflow and salmon populations. Where the CZ is thin, limited water storage is used by an oak savanna ecosystem, and streams run dry in summer due to negligible hillslope drainage. At both sites, wet season precipitation replenishes the dynamic storage deficit generated during the summer dry season, with excess winter rains exiting the watersheds via storm runoff as perched groundwater fracture flow at the thick-CZ site and saturation overland flow at the thin-CZ site. Annual replenishment of subsurface water storage even in severe drought years may lead to ecosystem resilience to climatic perturbations: during the 2011-2015 drought there was not widespread forest die-off in the study area.

Estimating and mapping ecological processes influencing microbial community assembly

DOE PAGES

Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; ...

2015-05-01

Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recentlymore » developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.« less

Characterizing near-surface elemental layering on Mars using gamma-ray spectroscopy: A proof-of-principle experiment

NASA Astrophysics Data System (ADS)

Peplowski, Patrick N.; Wilson, Jack T.; Beck, Andrew W.; Burks, Morgan; Goldsten, John O.; Lawrence, David J.

2018-01-01

Gamma-ray spectroscopy investigations characterize the chemical composition of planetary surfaces by measuring element-characteristic gamma rays with energies of ∼100 keV to ∼9 MeV. Over this energy range, the mean free path of a gamma ray varies from about 1 to 25 cm, therefore gamma-ray measurements sample subsurface composition. Many elements emit gamma rays at multiple, often widely spaced energies, so gamma-ray measurements can in principle also be used to identify depth-dependent variations in subsurface composition. We report results from laboratory measurements and radiation transport modeling designed to demonstrate this capability. The laboratory measurements verified the presence of depth-dependent gamma-ray signatures, and were then used to benchmark radiation transport simulations that were used to model realistic Mars-like scenarios. The models indicate that compositionally distinct subsurface deposits, buried to depths of ∼80 cm (125 g/cm2), can be identified using gamma-ray measurements. Going beyond identification to characterization (burial depth, relative composition of the layers) of the deposits requires knowledge of the vertical and horizontal variability in the water content of the near-surface surface materials, the local Galactic Cosmic Ray environment (magnitude and energy distribution), the depth-dependent neutron flux, gamma-ray production cross sections, and knowledge of the composition and column density of the atmosphere. The results of our experiments and models provided a basis for examining the utility of using orbiter- and lander-based gamma-ray measurements to identify subsurface deposits on Mars.

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

Studying Phobos subsurface structure elementary composition by neutron and gamma-rays spectrometers "NS HEND" from "Phobos-Grunt" mission.

NASA Astrophysics Data System (ADS)

Kozyrev, S. Alexander; Litvak, Maxim; Malakhov, Alexey; Mokrousov, Maxim; Mitrofanov, Igor; Sanin, Anton; Schulz, Rita; Shvetsov, Valery; Rogozhin, Alexander; Timoshenko, Genagy; Tretyakov, Vladislav; Vostrukhin, Andrey

The Neutron Spectrometer HEND (NS HEND) has been proposed for studying elemental com-position of Phobos (the Mars's moon) regolith by "Phobos-Grunt" mission. NS HEND have been selected by the Federal Space Agency of Russia for the Lander of the "Phobos-Grunt" mission scheduled for launch in 2011. The shallow subsurface of Phobos might be studied by observations of induced nuclear gamma-ray lines and neutron emission. Secondary gamma-rays and neutrons are produced by energetic Galactic Cosmic Rays within 1-2 meter layer of subsur-face. The knowledge of the spectral density of neutrons in addition to measurements of nuclear gamma lines allows to deconvolve concentrations of soil-constituting elements. That is why nuclear instruments include both the segment for detection of gamma ray lines and segment of neutron spectrometer for the measurement of the neutron leakage spectra. Moreover, mea-surements of neutrons at 2.2 MeV line will also allow to study the content of hydrogen within subsurface layer about 1 meter deep. This instrument, will be able to provide observational data for composition of Phobos regolith and content of natural radioactive elements K, U and Th, and also for content of hydrogen or water ice in the Phobos subsurface. At present, the flight units of NS HEND instrument is manufactured, tested and current go through physical calibration.

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.

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

The Microbial Contribution to Shale Gas: How Much Have They Done, and How Fast Can They Do It?

NASA Astrophysics Data System (ADS)

Martini, A. M.

2014-12-01

Over the past few decades, the importance of microbial contributions to our natural gas supply has been widely recognized, even leading to efforts to enhance the rate of methanogenesis in reservoirs whether the substrate is oil, coal or the organic matter in shale. The identification of biogenic gas was first established with gas compositional and isotopic data. More recently, molecular genomic data has been applied, giving us a glimpse into bacterial and archaeal communities in the subsurface, both in reservoirs where the microbial community was expected by the geochemical signature, but also in flowback waters from formations where there was no indication of anything other than thermogenic gas. With these microbes, it is not so much a question of "build it and they will come", but more that the community lies in wait for conditions to improve and allow them to flourish. Conditions for microbial methanogenesis are well constrained: temperatures up to ~80oC, low sulfate concentration, and chloride concentrations under 2M. However, these are rather expansive boundaries and within each range there lies constant turnover in population density as well specific microbial abundances. In addition, the rates at which these microbes are able convert complex organic matter into methane depend upon environmental conditions. Confounding our evaluation of these subsurface communities is the effect that production incurs. Over the past two decades, wells under production in the Antrim Shale have exhibited changes in the geochemistry of formation fluids, most notably a drop in dissolved inorganic carbon of ~10mM. Gas chemistry has also shifted, with increasing concentrations of carbon dioxide that have also become more enriched in 13C, while the co-produced methane has become more depleted in 13C over the 20 years that these few wells have been monitored. Perhaps not unsurprisingly, the microbial community has also shifted with the water's chemical evolution. Most intriguing is the correlation of the deuterium in the water to the methane, where CO2-reduction seems to remain the dominant methanogenic pathway and the gas composition is responding to changes in the water source. This may signify a relatively high proportion of recently produced methane in the system.

Can Surface Seeps Elucidate Carbon Cycling in Terrestrial Subsurface Ecosystems in Ophiolite-hosted Serpentinizing Fluids?

NASA Astrophysics Data System (ADS)

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

2017-12-01

Serpentinization in ophiolite-hosted regimes produces highly reduced, high pH fluids that are often characterized as having copious H2 and CH4 gas, little/no inorganic carbon, and limited electron acceptors. Subsurface microbial biomes shift as deeply-sourced fluids reach the oxygenated surface environment, where organisms capable of metabolizing O2 thrive (Woycheese et al., 2015). The relationship, connection, and communication between surface expressions (such as fluid seeps) and the subsurface biosphere is still largely unexplored. Our work in the Zambales and Palawan ophiolites (Philippines) defines surface habitats with geochemistry, targeted culturing efforts, and community analysis (Cardace et al., 2015; Woycheese et al., 2015). Fluids in the spring sources are largely `typical' and fall in the pH range of 9-11.5 with measurable gas escaping from the subsurface (H2 and CH4 > 10uM, CO2 > 1 mM; Cardace et al., 2015). Outflow channels extend from the source pools. These surface data encourage prediction of the subsurface metabolic landscape. To understand how carbon cycling in the subsurface and surface environments might be related, we focus on community analysis, culturing, and the geochemical context of the ecosystem. Shotgun metagenomic analyses indicate carbon cycling is reliant on methanogenesis, acetogenesis, sulfate reduction, and H2 and CH4 oxidation. Methyl coenzyme M reductase, and formylmethanofuran dehydrogenase were detected, and relative abundance increased near the near-anoxic spring source. In this tropical climate, cellulose is also a likely carbon source, possibly even in the subsurface. Enrichment cultures [pH 8-12] and strains [pH 8-10] from Zambales springs show degradation of cellulose and production of cellulase. DIC, DOC, and 13C of solid substrates show mixed autotrophic/heterotrophic activity. Results indicate a metabolically flexible surface community, and suggest details about carbon cycling in the subsurface.

Scaling isotopic emissions and microbes across a permafrost thaw landscape

NASA Astrophysics Data System (ADS)

Varner, R. K.; Palace, M. W.; Saleska, S. R.; Bolduc, B.; Braswell, B. H., Jr.; Crill, P. M.; Chanton, J.; DelGreco, J.; Deng, J.; Frolking, S. E.; Herrick, C.; Hines, M. E.; Li, C.; McArthur, K. J.; McCalley, C. K.; Persson, A.; Roulet, N. T.; Torbick, N.; Tyson, G. W.; Rich, V. I.

2017-12-01

High latitude peatlands are a significant source of atmospheric methane. This source is spatially and temporally heterogeneous, resulting in a wide range of emission estimates for the atmospheric budget. Increasing atmospheric temperatures are causing degradation of underlying permafrost, creating changes in surface soil moisture, the surface and sub-surface hydrological patterns, vegetation and microbial communities, but the consequences to rates and magnitudes of methane production and emissions are poorly accounted for in global budgets. We combined field observations, multi-source remote sensing data and biogeochemical modeling to predict methane dynamics, including the fraction derived from hydrogenotrophic versus acetoclastic microbial methanogenesis across Stordalen mire, a heterogeneous discontinuous permafrost wetland located in northernmost Sweden. Using the field measurement validated Wetland-DNDC biogeochemical model, we estimated mire-wide CH4 and del13CH4 production and emissions for 2014 with input from field and unmanned aerial system (UAS) image derived vegetation maps, local climatology and water table from insitu and remotely sensed data. Model simulated methanogenic pathways correlate with sequence-based observations of methanogen community composition in samples collected from across the permafrost thaw landscape. This approach enables us to link below ground microbial community composition with emissions and indicates a potential for scaling across broad areas of the Arctic region.

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

Cultivation Of Deep Subsurface Microbial Communities

NASA Astrophysics Data System (ADS)

Obrzut, Natalia; Casar, Caitlin; Osburn, Magdalena R.

2018-01-01

The potential habitability of surface environments on other planets in our solar system is limited by exposure to extreme radiation and desiccation. In contrast, subsurface environments may offer protection from these stressors and are potential reservoirs for liquid water and energy that support microbial life (Michalski et al., 2013) and are thus of interest to the astrobiology community. The samples used in this project were extracted from the Deep Mine Microbial Observatory (DeMMO) in the former Homestake Mine at depths of 800 to 2000 feet underground (Osburn et al., 2014). Phylogenetic data from these sites indicates the lack of cultured representatives within the community. We used geochemical data to guide media design to cultivate and isolate organisms from the DeMMO communities. Media used for cultivation varied from heterotrophic with oxygen, nitrate or sulfate to autotrophic media with ammonia or ferrous iron. Environmental fluid was used as inoculum in batch cultivation and strains were isolated via serial transfers or dilution to extinction. These methods resulted in isolating aerobic heterotrophs, nitrate reducers, sulfate reducers, ammonia oxidizers, and ferric iron reducers. DNA sequencing of these strains is underway to confirm which species they belong to. This project is part of the NASA Astrobiology Institute Life Underground initiative to detect and characterize subsurface microbial life; by characterizing the intraterrestrials, the life living deep within Earth’s crust, we aim to understand the controls on how and where life survives in subsurface settings. Cultivation of terrestrial deep subsurface microbes will provide insight into the survival mechanisms of intraterrestrials guiding the search for these life forms on other planets.

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

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.

A Geostatistical Toolset for Reconstructing Louisiana's Coastal Stratigraphy using Subsurface Boring and Cone Penetrometer Test Data

NASA Astrophysics Data System (ADS)

Li, A.; Tsai, F. T. C.; Jafari, N.; Chen, Q. J.; Bentley, S. J.

2017-12-01

A vast area of river deltaic wetlands stretches across southern Louisiana coast. The wetlands are suffering from a high rate of land loss, which increasingly threats coastal community and energy infrastructure. A regional stratigraphic framework of the delta plain is now imperative to answer scientific questions (such as how the delta plain grows and decays?) and to provide information to coastal protection and restoration projects (such as marsh creation and construction of levees and floodwalls). Through years, subsurface investigations in Louisiana have been conducted by state and federal agencies (Louisiana Department of Natural Resources, United States Geological Survey, United States Army Corps of Engineers, etc.), research institutes (Louisiana Geological Survey, LSU Coastal Studies Institute, etc.), engineering firms, and oil-gas companies. This has resulted in the availability of various types of data, including geological, geotechnical, and geophysical data. However, it is challenging to integrate different types of data and construct three-dimensional stratigraphy models in regional scale. In this study, a set of geostatistical methods were used to tackle this problem. An ordinary kriging method was used to regionalize continuous data, such as grain size, water content, liquid limit, plasticity index, and cone penetrometer tests (CPTs). Indicator kriging and multiple indicator kriging methods were used to regionalize categorized data, such as soil classification. A compositional kriging method was used to regionalize compositional data, such as soil composition (fractions of sand, silt and clay). Stratigraphy models were constructed for three cases in the coastal zone: (1) Inner Harbor Navigation Canal (IHNC) area: soil classification and soil behavior type (SBT) stratigraphies were constructed using ordinary kriging; (2) Middle Barataria Bay area: a soil classification stratigraphy was constructed using multiple indicator kriging; (3) Lower Barataria Bay and Lower Breton Sound areas: a soil texture stratigraphy was constructed using soil compositional data and compositional kriging. Cross sections were extracted from the three-dimensional stratigraphy models to reveal spatial distributions of different stratigraphic features.

Modeling of Composite Scenes Using Wires, Plates and Dielectric Parallelized (WIPL-DP)

DTIC Science & Technology

2006-06-01

formation and solves the data communications problem. The ability to perform subsurface imaging to depths of 200’ have already been demonstrated by...perform subsurface imaging to depths of 200’ have already been demonstrated by Brown in [3] and presented in Figure 3 above. Furthermore, reference [3...transmitter platform for use in image formation and solves the data communications problem. The ability to perform subsurface imaging to depths of 200

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.

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

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 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

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.

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient.

PubMed

Eldridge, David J; Delgado-Baquerizo, Manuel; Woodhouse, Jason N; Neilan, Brett A

2016-11-01

The effects of mammalian ecosystem engineers on soil microbial communities and ecosystem functions in terrestrial ecosystems are poorly known. Disturbance from livestock has been widely reported to reduce soil function, but disturbance by animals that forage in the soil may partially offset these negative effects of livestock, directly and/or indirectly by shifting the composition and diversity of soil microbial communities. Understanding the role of disturbance from livestock and ecosystem engineers in driving soil microbes and functions is essential for formulating sustainable ecosystem management and conservation policies. We compared soil bacterial community composition and enzyme concentrations within four microsites: foraging pits of two vertebrates, the indigenous short-beaked echidna (Tachyglossus aculeatus) and the exotic European rabbit (Oryctolagus cuniculus), and surface and subsurface soils along a gradient in grazing-induced disturbance in an arid woodland. Microbial community composition varied little across the disturbance gradient, but there were substantial differences among the four microsites. Echidna pits supported a lower relative abundance of Acidobacteria and Cyanobacteria, but a higher relative abundance of Proteobacteria than rabbit pits and surface microsites. Moreover, these microsite differences varied with disturbance. Rabbit pits had a similar profile to the subsoil or the surface soils under moderate and high, but not low disturbance. Overall, echidna foraging pits had the greatest positive effect on function, assessed as mean enzyme concentrations, but rabbits had the least. The positive effects of echidna foraging on function were indirectly driven via microbial community composition. In particular, increasing activity was positively associated with increasing relative abundance of Proteobacteria, but decreasing Acidobacteria. Our study suggests that soil disturbance by animals may offset, to some degree, the oft-reported negative effects of grazing-induced disturbance on soil function. Further, our results suggest that most of this effect will be derived from echidnas, with little positive effects due to rabbits. Activities that enhance the habitat for echidnas or reduce rabbit populations are likely to have a positive effect on soil function in these systems. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation

PubMed Central

Beaton, E. D.; Stevenson, Bradley S.; King-Sharp, Karen J.; Stamps, Blake W.; Nunn, Heather S.; Stuart, Marilyne

2016-01-01

Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth’s biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the differential historical events that have influenced the current bacterial composition. Categorizing the study site into smaller regions of interest of more closely spaced fractures, or of potentially hydraulically connected fractures, might improve the resolution of an analysis to reveal environmental influences that have shaped these bacterial communities. PMID:27999569

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation.

PubMed

Beaton, E D; Stevenson, Bradley S; King-Sharp, Karen J; Stamps, Blake W; Nunn, Heather S; Stuart, Marilyne

2016-01-01

Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth's biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the differential historical events that have influenced the current bacterial composition. Categorizing the study site into smaller regions of interest of more closely spaced fractures, or of potentially hydraulically connected fractures, might improve the resolution of an analysis to reveal environmental influences that have shaped these bacterial 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

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.

A Subsurface Soil Composition and Physical Properties Experiment to Address Mars Regolith Stratigraphy

NASA Technical Reports Server (NTRS)

Richter, L.; Sims, M.; Economou, T.; Stoker, C.; Wright, I.; Tokano, T.

2004-01-01

Previous in-situ measurements of soil-like materials on the surface of Mars, in particular during the on-going Mars Exploration Rover missions, have shown complex relationships between composition, exposure to the surface environment, texture, and local rocks. In particular, a diversity in both compositional and physical properties could be established that is interpreted to be diagnostic of the complex geologic history of the martian surface layer. Physical and chemical properties vary laterally and vertically, providing insight into the composition of rocks from which soils derive, and environmental conditions that led to soil formation. They are central to understanding whether habitable environments existed on Mars in the distant past. An instrument the Mole for Soil Compositional Studies and Sampling (MOCSS) - is proposed to allow repeated access to subsurface regolith on Mars to depths of up to 1.5 meters for in-situ measurements of elemental composition and of physical and thermophysical properties, as well as for subsurface sample acquisition. MOCSS is based on the compact PLUTO (PLanetary Underground TOol) Mole system developed for the Beagle 2 lander and incorporates a small X-ray fluorescence spectrometer within the Mole which is a new development. Overall MOCSS mass is approximately 1.4 kilograms. Taken together, the MOCSS science data support to decipher the geologic history at the landing site as compositional and textural stratigraphy if they exist - can be detected at a number of places if the MOCSS were accommodated on a rover such as MSL. Based on uncovered stratigraphy, the regional sequence of depositional and erosional styles can be constrained which has an impact on understanding the ancient history of the Martian near-surface layer, considering estimates of Mars soil production rates of 0.5... 1.0 meters per billion years on the one hand and Mole subsurface access capability of approximately 1.5 meters. An overview of the MOCSS, XRS instrument accomodation and the impact that these instruments have on Mars science is discussed.

A Miniaturized Spectrometer for Optimized Selection of Subsurface Samples for Future MSR Missions

NASA Astrophysics Data System (ADS)

De Sanctis, M. C.; Altieri, F.; De Angelis, S.; Ferrari, M.; Frigeri, A.; Biondi, D.; Novi, S.; Antonacci, F.; Gabrieli, R.; Paolinetti, R.; Villa, F.; Ammannito, A.; Mugnuolo, R.; Pirrotta, S.

2018-04-01

We present the concept of a miniaturized spectrometer based on the ExoMars2020/Ma_MISS experiment. Coupled with a drill tool, it will allow an assessment of subsurface composition and optimize the selection of martian samples with a high astrobiological potential.

Stability of surface and subsurface hydrogen on and in Au/Ni near-surface alloys

DOE PAGES

Celik, Fuat E.; Mavrikakis, Manos

2015-01-12

Periodic, self-consistent DFT-GGA (PW91) calculations were used to study the interaction of hydrogen atoms with the (111) surfaces of substitutional near-surface alloys (NSAs) of Au and Ni with different surface layer compositions and different arrangements of Au atoms in the surface layer. The effect of hydrogen adsorption on the surface and in the first and second subsurface layers of the NSAs was studied. Increasing the Au content in the surface layer weakens hydrogen binding on the surface, but strengthens subsurface binding, suggesting that the distribution of surface and subsurface hydrogen will be different than that on pure Ni(111). While themore » metal composition of the surface layer has an effect on the binding energy of hydrogen on NSA surfaces, the local composition of the binding site has a stronger effect. For example, fcc hollow sites consisting of three Ni atoms bind H nearly as strongly as on Ni(111), and fcc sites consisting of three Au atoms bind H nearly as weakly as on Au(111). Sites with one or two Au atoms show intermediate binding energies. The preference of hydrogen for three-fold Ni hollow sites alters the relative stabilities of different surface metal atom arrangements, and may provide a driving force for adsorbate-induced surface rearrangement.« less

Stability of Surface and Subsurface Hydrogen on and in Au/Ni Near-Surface Alloys

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

Celik, Fuat E.; Mavrikakis, Manos

2015-10-01

Periodic, self-consistent DFT-GGA (PW91) calculations were used to study the interaction of hydrogen atoms with the (111) surfaces of substitutional near-surface alloys (NSAs) of Au and Ni with different surface layer compositions and different arrangements of Au atoms in the surface layer. The effect of hydrogen adsorption on the surface and in the first and second subsurface layers of the NSAs was studied. Increasing the Au content in the surface layer weakens hydrogen binding on the surface, but strengthens subsurface binding, suggesting that the distribution of surface and subsurface hydrogen will be different than that on pure Ni(111). While themore » metal composition of the surface layer has an effect on the binding energy of hydrogen on NSA surfaces, the local composition of the binding site has a stronger effect. For example, fcc hollow sites consisting of three Ni atoms bind H nearly as strongly as on Ni(111), and fcc sites consisting of three Au atoms bind H nearly as weakly as on Au(111). Sites with one or two Au atoms show intermediate binding energies. The preference of hydrogen for three-fold Ni hollow sites alters the relative stabilities of different surface metal atom arrangements, and may provide a driving force for adsorbate-induced surface rearrangement.« less

Stability of surface and subsurface hydrogen on and in Au/Ni near-surface alloys

NASA Astrophysics Data System (ADS)

Celik, Fuat E.; Mavrikakis, Manos

2015-10-01

Periodic, self-consistent DFT-GGA (PW91) calculations were used to study the interaction of hydrogen atoms with the (111) surfaces of substitutional near-surface alloys (NSAs) of Au and Ni with different surface layer compositions and different arrangements of Au atoms in the surface layer. The effect of hydrogen adsorption on the surface and in the first and second subsurface layers of the NSAs was studied. Increasing the Au content in the surface layer weakens hydrogen binding on the surface, but strengthens subsurface binding, suggesting that the distribution of surface and subsurface hydrogen will be different than that on pure Ni(111). While the metal composition of the surface layer has an effect on the binding energy of hydrogen on NSA surfaces, the local composition of the binding site has a stronger effect. For example, fcc hollow sites consisting of three Ni atoms bind H nearly as strongly as on Ni(111), and fcc sites consisting of three Au atoms bind H nearly as weakly as on Au(111). Sites with one or two Au atoms show intermediate binding energies. The preference of hydrogen for three-fold Ni hollow sites alters the relative stabilities of different surface metal atom arrangements, and may provide a driving force for adsorbate-induced surface rearrangement.

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.

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

Effect of biostimulants on 2,4,6-trinitrotoluene (TNT) degradation and bacterial community composition in contaminated aquifer sediment enrichments.

PubMed

Fahrenfeld, Nicole; Zoeckler, Jeffrey; Widdowson, Mark A; Pruden, Amy

2013-04-01

2,4,6-Trinitrotoluene (TNT) is a toxic and persistent explosive compound occurring as a contaminant at numerous sites worldwide. Knowledge of the microbial dynamics driving TNT biodegradation is limited, particularly in native aquifer sediments where it poses a threat to water resources. The purpose of this study was to quantify the effect of organic amendments on anaerobic TNT biodegradation rate and pathway in an enrichment culture obtained from historically contaminated aquifer sediment and to compare the bacterial community dynamics. TNT readily biodegraded in all microcosms, with the highest biodegradation rate obtained under the lactate amended condition followed by ethanol amended and naturally occurring organic matter (extracted from site sediment) amended conditions. Although a reductive pathway of TNT degradation was observed across all conditions, denaturing gradient gel electrophoresis (DGGE) analysis revealed distinct bacterial community compositions. In all microcosms, Gram-negative γ- or β-Proteobacteria and Gram-positive Negativicutes or Clostridia were observed. A Pseudomonas sp. in particular was observed to be stimulated under all conditions. According to non-metric multidimensional scaling analysis of DGGE profiles, the microcosm communities were most similar to heavily TNT-contaminated field site sediment, relative to moderately and uncontaminated sediments, suggesting that TNT contamination itself is a major driver of microbial community structure. Overall these results provide a new line of evidence of the key bacteria driving TNT degradation in aquifer sediments and their dynamics in response to organic carbon amendment, supporting this approach as a promising technology for stimulating in situ TNT bioremediation in the subsurface.

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater.

PubMed

Holmes, Dawn E; Giloteaux, Ludovic; Williams, Kenneth H; Wrighton, Kelly C; Wilkins, Michael J; Thompson, Courtney A; Roper, Thomas J; Long, Philip E; Lovley, Derek R

2013-07-01

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

PubMed Central

Holmes, Dawn E; Giloteaux, Ludovic; Williams, Kenneth H; Wrighton, Kelly C; Wilkins, Michael J; Thompson, Courtney A; Roper, Thomas J; Long, Philip E; Lovley, Derek R

2013-01-01

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey–predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies. PMID:23446832

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

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

Holmes, Dawn; Giloteaux, L.; Williams, Kenneth H.

2013-07-28

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well-recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, acetate amendments initially promoted the growth of metal-reducing Geobacter species followed by the growthmore » of sulfate-reducers, as previously observed. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater prior to the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the amoeboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity, and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.« less

Fiber Optic Thermal Health Monitoring of Composites

NASA Technical Reports Server (NTRS)

Wu, Meng-Chou; Winfree, William P.; Moore, Jason P.

2010-01-01

A recently developed technique is presented for thermographic detection of flaws in composite materials by performing temperature measurements with fiber optic Bragg gratings. Individual optical fibers with multiple Bragg gratings employed as surface temperature sensors were bonded to the surfaces of composites with subsurface defects. The investigated structures included a 10-ply composite specimen with subsurface delaminations of various sizes and depths. Both during and following the application of a thermal heat flux to the surface, the individual Bragg grating sensors measured the temporal and spatial temperature variations. The data obtained from grating sensors were analyzed with thermal modeling techniques of conventional thermography to reveal particular characteristics of the interested areas. Results were compared with the calculations using numerical simulation techniques. Methods and limitations for performing in-situ structural health monitoring are discussed.

Fiber Optic Thermographic Detection of Flaws in Composites

NASA Technical Reports Server (NTRS)

Wu, Meng-Chou; Winfree, William P.

2009-01-01

Optical fibers with multiple Bragg gratings bonded to surfaces of structures were used for thermographic detection of subsurface defects in structures. The investigated structures included a 10-ply composite specimen with subsurface delaminations of various sizes and depths. Both during and following the application of a thermal heat flux to the surface, the individual Bragg grating sensors measured the temporal and spatial temperature variations. The obtained data were analyzed with thermal modeling to reveal particular characteristics of the interested areas. These results were found to be consistent with the simulation results.

Geochemical and physical drivers of microbial community structure in hot spring ecosystems

NASA Astrophysics Data System (ADS)

Havig, J. R.; Hamilton, T. L.; Boyd, E. S.; Meyer-Dombard, D. R.; Shock, E.

2012-12-01

Microbial communities in natural systems are typically characterized using samples collected from a single time point, thereby neglecting the temporal dynamics that characterize natural systems. The composition of these communities obtained from single point samples is then related to the geochemistry and physical parameters of the environment. Since most microbial life is adapted to a relatively narrow ecological niche (multiplicity of physical and chemical parameters that characterize a local habitat), these assessments provide only modest insight into the controls on community composition. Temporal variation in temperature or geochemical composition would be expected to add another dimension to the complexity of niche space available to support microbial diversity, with systems that experience greater variation supporting a greater biodiversity until a point where the variability is too extreme. . Hot springs often exhibit significant temporal variation, both in physical as well as chemical characteristics. This is a result of subsurface processes including boiling, phase separation, and differential mixing of liquid and vapor phase constituents. These characteristics of geothermal systems, which vary significantly over short periods of time, provide ideal natural laboratories for investigating how i) the extent of microbial community biodiversity and ii) the composition of those communities are shaped by temporal fluctuations in geochemistry. Geochemical and molecular samples were collected from 17 temporally variable hot springs across Yellowstone National Park, Wyoming. Temperature measurements using data-logging thermocouples, allowing accurate determination of temperature maximums, minimums, and ranges for each collection site, were collected in parallel, along with multiple geochemical characterizations as conditions varied. There were significant variations in temperature maxima (54.5 to 90.5°C), minima (12.5 to 82.5°C), and range (3.5 to 77.5°C) for the hot spring environments that spanned ranges of pH values (2.2 to 9.0) and geochemical compositions. We characterized the abundance, composition, and phylogenetic diversity of bacterial and archaeal 16S rRNA gene assemblages in sediment/biofilm samples collected from each site. 16S data can be used as proxy for metabolic dissimilarity. We predict that temporally fluctuating environments should provide additional complexity to the system (additional niche space) capable of supporting additional taxa, which should lead to greater 16S rRNA gene diversity. However, systems with too much variability should collapse the diversity. Thus, one would expect an optimal system for variability, with respect to 16S phylogenetic diversity. Community ecology tools were then applied to model the relative influence of physical and chemical characteristics (including temperature dynamics) on the local biodiversity. The results reveal unique insight into the role of temporal environmental variation in the development of biodiverse communities and provide a platform for predicting the response of an ecosystem to temperature perturbation.

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

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

A large column analog experiment of stable isotope variations during reactive transport: II. Carbon mass balance, microbial community structure and predation

NASA Astrophysics Data System (ADS)

Druhan, Jennifer L.; Bill, Markus; Lim, HsiaoChien; Wu, Cindy; Conrad, Mark E.; Williams, Kenneth H.; DePaolo, Donald J.; Brodie, Eoin L.

2014-01-01

Here we report a combined analysis of carbon mass balance based on isotopic labeling and microbiological characterization during organic carbon stimulated bioreduction of a subsurface sediment in a large laboratory column experimental system. This combination of approaches allows quantification of both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Carbon isotope mass balance facilitated by the use of 13C-labeled acetate as the electron donor showed evidence for a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data clearly demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples collected weekly over the duration of the 43-day amendment at <20 cm intervals along the flow path were analyzed for microbial composition by pyrosequencing of ribosomal RNA genes. The microbial community composition was transient, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identified in the partitioning of carbon isotopes. This study demonstrates evidence for predator-prey relationships that impact subsurface microbial community dynamics and provides a novel indication of the impact of this relationship on the flux of carbon through a system via the microbial biomass pool. Overall, our approach provides high temporal and spatial sampling resolution at field relevant flow rates, while minimizing effects of mixing and transverse dispersion. The result is a quantitative carbon budget accounting for a diversity of processes that should be considered for inclusion in reactive transport models that aim to predict carbon turnover, nutrient flux, and redox reactions in natural and stimulated subsurface systems. the mobilization of previously stabilized, sediment-bound carbon; a carbon mass balance for a through-flowing sediment column over the course of a 43-day amendment using 13C-labeled acetate; a phylogenetic microbial community structure at <20 cm sampling resolution with distance away from the organic carbon source weekly over the 43-day amendment; protozoan grazing on the active Geobacteraceae population and the rapid turnover of microbial biomass carbon as a secondary cycling pathway. Such a high resolution, combined analysis of microbial populations and the associated carbon mass balance in a through-flowing system at field relevant flow rates provides novel, quantitative insights into the interface between biogeochemical cycling and bulk carbon fluxes in the near-surface environment.

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria

PubMed Central

Bienhold, Christina; Zinger, Lucie; Boetius, Antje; Ramette, Alban

2016-01-01

The deep ocean floor covers more than 60% of the Earth’s surface, and hosts diverse bacterial communities with important functions in carbon and nutrient cycles. The identification of key bacterial members remains a challenge and their patterns of distribution in seafloor sediment yet remain poorly described. Previous studies were either regionally restricted or included few deep-sea sediments, and did not specifically test biogeographic patterns across the vast oligotrophic bathyal and abyssal seafloor. Here we define the composition of this deep seafloor microbiome by describing those bacterial operational taxonomic units (OTU) that are specifically associated with deep-sea surface sediments at water depths ranging from 1000–5300 m. We show that the microbiome of the surface seafloor is distinct from the subsurface seafloor. The cosmopolitan bacterial OTU were affiliated with the clades JTB255 (class Gammaproteobacteria, order Xanthomonadales) and OM1 (Actinobacteria, order Acidimicrobiales), comprising 21% and 7% of their respective clades, and about 1% of all sequences in the study. Overall, few sequence-abundant bacterial types were globally dispersed and displayed positive range-abundance relationships. Most bacterial populations were rare and exhibited a high degree of endemism, explaining the substantial differences in community composition observed over large spatial scales. Despite the relative physicochemical uniformity of deep-sea sediments, we identified indicators of productivity regimes, especially sediment organic matter content, as factors significantly associated with changes in bacterial community structure across the globe. PMID:26814838

A reference data set of hillslope rainfall-runoff response, Panola Mountain Research Watershed, United States

USGS Publications Warehouse

Tromp-van, Meerveld; James, A.L.; McDonnell, Jeffery J.; Peters, N.E.

2008-01-01

Although many hillslope hydrologic investigations have been conducted in different climate, topographic, and geologic settings, subsurface stormflow remains a poorly characterized runoff process. Few, if any, of the existing data sets from these hillslope investigations are available for use by the scientific community for model development and validation or conceptualization of subsurface stormflow. We present a high-resolution spatial and temporal rainfall-runoff data set generated from the Panola Mountain Research Watershed trenched experimental hillslope. The data set includes surface and subsurface (bedrock surface) topographic information and time series of lateral subsurface flow at the trench, rainfall, and subsurface moisture content (distributed soil moisture content and groundwater levels) from January to June 2002. Copyright 2008 by the American Geophysical Union.

Microbes, Minerals and Electrodes at the Sanford Underground Research Facility (SURF): Electrochemistry 4100 ft below the surface.

NASA Astrophysics Data System (ADS)

Rowe, A. R.; Abuyen, K.; Casar, C. P.; Osburn, M. R.; Kruger, B.; El-Naggar, M.; Amend, J.

2017-12-01

Little is known about the importance of mineral oxidation processes in subsurface environments. This stems, in part from our limited insight into the biochemistry of many of these metabolisms, especially where redox interactions with solid surfaces is concerned. To this aim, we have been developing electrochemical cultivation techniques, to target enrichment and isolation of microbes capable of oxidative extracellular electron transfer (oxEET)—transfer of electrons from the exterior of the cell to the interior. Our previous worked focused on marine sediments; using an electrode poised at a given redox potential to isolate mineral-oxidizing microbes. Electrode oxidizing microbes isolated from these enrichments belong to the genera Thioclava, Marinobacter, Halomonas, Idiomarina, Thalassospira, and Pseudamonas; organisms commonly detected in marine and deep sea sediments but not generally associated with mineral, sulfur and/or iron oxidation. At the Sanford Underground Research Facility (SURF) in Leed, South Dakota, we have been utilizing similar electrocultivation techniques to understand: 1) the potential for mineral oxidation by subsurface microbes, 2) their selective colonization on mineral vs. electrode surfaces, as well as 3) the community composition of microbes capable of these metabolic interactions. An electrochemical and mineral enrichment scheme was designed and installed into a sulfidic groundwater flow, located at the 4100 ft level of the former gold mine. The communities enriched on electrodes (graphite and indium tin oxide coated glass) and minerals (sulfur, pyrite, and schists from the location) were compared to the long-term ground water microbial community observed. Ultimately, these observations will help inform the potential activity of a lithotrophic microbes in situ and will in turn guide our culturing efforts.

Electrically Conducting, Ca-Rich Brines, Rather Than Water, Expected in the Martian Subsurface

NASA Technical Reports Server (NTRS)

Burt, D. M.; Knauth, L. P.

2003-01-01

If Mars ever possessed a salty liquid hydrosphere, which later partly evaporated and froze down, then any aqueous fluids left near the surface could have evolved to become dense eutectic brines. Eutectic brines, by definition, are the last to freeze and the first to melt. If CaC12-rich, such brines can remain liquid until temperatures below 220 K, close to the average surface temperature of Mars. In the Martian subsurface, in intimate contact with the Ca-rich basaltic regolith, NaC1-rich early brines should have reacted to become Ca-rich. Fractional crystallization (freezing) and partial melting would also drive brines toward CaC12-rich compositions. In other words, eutectic brine compositions could be present in the shallow subsurface of Mars, for the same reasons that eutectic magma compositions are common on Earth. Don Juan Pond, Antarctica, a CaC12-rich eutectic brine, provides a possible terrestrial analog, particularly because it is fed from a basaltic aquifer. Owing to their relative density and fluid nature, brines in the Martian regolith should eventually become sandwiched between ice above and salts beneath. A thawing brine sandwich provides one explanation (among many) for the young gullies recently attributed to seepage of liquid water on Mars. Whether or not brine seepage explains the gullies phenomenon, dense, CaC12-rich brines are to be expected in the deep subsurface of Mars, although they might be somewhat diluted (temperatures permitting) and of variable salt composition. In any case, they should be good conductors of electricity.

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.

Unique microbial community in drilling fluids from Chinese continental scientific drilling

USGS Publications Warehouse

Zhang, Gengxin; Dong, Hailiang; Jiang, Hongchen; Xu, Zhiqin; Eberl, Dennis D.

2006-01-01

Circulating drilling fluid is often regarded as a contamination source in investigations of subsurface microbiology. However, it also provides an opportunity to sample geological fluids at depth and to study contained microbial communities. During our study of deep subsurface microbiology of the Chinese Continental Scientific Deep drilling project, we collected 6 drilling fluid samples from a borehole from 2290 to 3350 m below the land surface. Microbial communities in these samples were characterized with cultivation-dependent and -independent techniques. Characterization of 16S rRNA genes indicated that the bacterial clone sequences related to Firmicutes became progressively dominant with increasing depth. Most sequences were related to anaerobic, thermophilic, halophilic or alkaliphilic bacteria. These habitats were consistent with the measured geochemical characteristics of the drilling fluids that have incorporated geological fluids and partly reflected the in-situ conditions. Several clone types were closely related to Thermoanaerobacter ethanolicus, Caldicellulosiruptor lactoaceticus, and Anaerobranca gottschalkii, an anaerobic metal-reducer, an extreme thermophile, and an anaerobic chemoorganotroph, respectively, with an optimal growth temperature of 50–68°C. Seven anaerobic, thermophilic Fe(III)-reducing bacterial isolates were obtained and they were capable of reducing iron oxide and clay minerals to produce siderite, vivianite, and illite. The archaeal diversity was low. Most archaeal sequences were not related to any known cultivated species, but rather to environmental clone sequences recovered from subsurface environments. We infer that the detected microbes were derived from geological fluids at depth and their growth habitats reflected the deep subsurface conditions. These findings have important implications for microbial survival and their ecological functions in the deep subsurface.

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

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.

GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer

USGS Publications Warehouse

Lu, Zhenmei; He, Zhili; Parisi, Victoria A.; Kang, Sanghoon; Deng, Ye; Van Nostrand, Joy D.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Suflita, Joseph M.; Zhou, Jizhong

2012-01-01

The functional gene diversity and structure of microbial communities in a shallow landfill leachate-contaminated aquifer were assessed using a comprehensive functional gene array (GeoChip 3.0). Water samples were obtained from eight wells at the same aquifer depth immediately below a municipal landfill or along the predominant downgradient groundwater flowpath. Functional gene richness and diversity immediately below the landfill and the closest well were considerably lower than those in downgradient wells. Mantel tests and canonical correspondence analysis (CCA) suggested that various geochemical parameters had a significant impact on the subsurface microbial community structure. That is, leachate from the unlined landfill impacted the diversity, composition, structure, and functional potential of groundwater microbial communities as a function of groundwater pH, and concentrations of sulfate, ammonia, and dissolved organic carbon (DOC). Historical geochemical records indicate that all sampled wells chronically received leachate, and the increase in microbial diversity as a function of distance from the landfill is consistent with mitigation of the impact of leachate on the groundwater system by natural attenuation mechanisms.

Subsurface damage detection in non-ferrous systems using 3D synchronous magnetic inspection

NASA Astrophysics Data System (ADS)

Gray, David; Berry, David

2018-04-01

Prime Photonics is developing a non-destructive inspection (NDI) technology, 3-D synchronous magnetic imaging system (3-D SMIS), that uses synchronous detection of magnetic signatures resulting from ultrasonic excitation to measure both surface and subsurface flaws in conductive structures. 3-D SMIS is showing promise in a wide range of NDI/NDE uses including characterizing surface-breaking cracks in ferrous and non-ferrous materials, locating and characterizing subsurface cracks within nonferrous conductive materials (Ti 6-4 and carbon fiber composites), and characterization of subsurface residual stresses. The technology offers a non-contact, high resolution inspection technique that does not require austere environments, and can accommodate non-planar specimen geometries.

Application of the Quadrupole Method for Simulation of Passive Thermography

NASA Technical Reports Server (NTRS)

Winfree, William P.; Zalameda, Joseph N.; Gregory, Elizabeth D.

2017-01-01

Passive thermography has been shown to be an effective method for in-situ and real time nondestructive evaluation (NDE) to measure damage growth in a composite structure during cyclic loading. The heat generation by subsurface flaw results in a measurable thermal profile at the surface. This paper models the heat generation as a planar subsurface source and calculates the resultant temperature profile at the surface using a three dimensional quadrupole. The results of the model are compared to finite element simulations of the same planar sources and experimental data acquired during cyclic loading of composite specimens.

Antibiotic resistance and community analysis of surface and subsurface drainage waters in the South Fork Iowa River watershed

USDA-ARS?s Scientific Manuscript database

The Midwest is a center for swine production leading to application of swine manure onto lands that have artificial subsurface drainage. Previous reports have indicated elevated levels of antibiotic resistance genes (ARGs) in surface water and groundwater around confined animal feeding operations w...

Antibiotic resistance and community analysis of surface and subsurface drainage waters in the South Fork Iowa River watershed

USDA-ARS?s Scientific Manuscript database

The Midwest is a center for swine production leading to application of swine manure onto lands that have artificial subsurface drainage. Previous reports have indicated elevated levels of antibiotic resistance genes (ARGs) in surface water and groundwater around confined animal feeding operations wh...

Evidence of a dynamic microbial community structure and predation through combined microbiological and stable isotope characterization

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Bill, M.; Lim, H. C.; Wu, C.; Conrad, M. E.; Williams, K. H.; DePaolo, D. J.; Brodie, E.

2014-12-01

The speciation, reactivity and mobility of carbon in the near surface environment is intimately linked to the prevalence, diversity and dynamics of native microbial populations. We utilize this relationship by introducing 13C-labeled acetate to sediments recovered from a shallow aquifer system to track both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Results demonstrate a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples analyzed weekly for microbial composition by pyrosequencing of ribosomal RNA genes showed a transient microbial community structure, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identifiable in the partitioning of carbon isotopes. The impact of predator-prey relationships on subsurface microbial community dynamics and therefore the flux of carbon through a system via the microbial biomass pool suggests a diversity of processes that should be considered for inclusion in reactive transport models that aim to predict carbon turnover, nutrient flux, and redox reactions in natural and stimulated subsurface systems.

Microbial communities at the borehole observatory on the Costa Rica Rift flank (Ocean Drilling Program Hole 896A).

PubMed

Nigro, Lisa M; Harris, Kate; Orcutt, Beth N; Hyde, Andrew; Clayton-Luce, Samuel; Becker, Keir; Teske, Andreas

2012-01-01

The microbiology of subsurface, hydrothermally influenced basaltic crust flanking mid-ocean ridges has remained understudied, due to the difficulty in accessing the subsurface environment. The instrumented boreholes resulting from scientific ocean drilling offer access to samples of the formation fluids circulating through oceanic crust. We analyzed the phylogenetic diversity of bacterial communities of fluid and microbial mat samples collected in situ from the observatory at Ocean Drilling Program Hole 896A, drilled into ~6.5 million-year-old basaltic crust on the flank of the Costa Rica Rift in the equatorial Pacific Ocean. Bacterial 16S rRNA gene sequences recovered from borehole fluid and from a microbial mat coating the outer surface of the fluid port revealed both unique and shared phylotypes. The dominant bacterial clones from both samples were related to the autotrophic, sulfur-oxidizing genus Thiomicrospira. Both samples yielded diverse gamma- and alphaproteobacterial phylotypes, as well as members of the Bacteroidetes, Planctomycetes, and Verrucomicrobia. Analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL and cbbM) from the sampling port mat and from the borehole fluid demonstrated autotrophic carbon assimilation potential for in situ microbial communities; most cbbL genes were related to those of the sulfur-oxidizing genera Thioalkalivibrio and Thiomicrospira, and cbbM genes were affiliated with uncultured phylotypes from hydrothermal vent plumes and marine sediments. Several 16S rRNA gene phylotypes from the 896A observatory grouped with phylotypes recovered from seawater-exposed basalts and sulfide deposits at inactive hydrothermal vents, but there is little overlap with hydrothermally influenced basaltic boreholes 1026B and U1301A on the Juan de Fuca Ridge flank, suggesting that site-specific characteristics of Hole 896A (i.e., seawater mixing into borehole fluids) affect the microbial community composition.

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

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.

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.

Changes in deep-sea carbonate-hosted microbial communities associated with high and low methane flux

NASA Astrophysics Data System (ADS)

Case, D. H.; Steele, J. A.; Chadwick, G.; Mendoza, G. F.; Levin, L. A.; Orphan, V. J.

2012-12-01

Methane seeps on continental shelves are rich in authigenic carbonates built of methane-derived carbon. These authigenic carbonates are home to micro- and macroscopic communities whose compositions are thus far poorly constrained but are known to broadly depend on local methane flux. The formation of authigenic carbonates is itself a result of microbial metabolic activity, as associations of anaerobic methane oxidizing archaea (ANME) and sulfate reducing bacteria (SRB) in the sediment subsurface increase both dissolved inorganic carbon (DIC) and alkalinity in pore waters. This 1:1 increase in DIC and alkalinity promotes the precipitation of authigenic carbonates. In this study, we performed in situ manipulations to test the response of micro- and macrofaunal communities to a change in methane flux. Methane-derived authigenic carbonates from two locations at Hydrate Ridge, OR, USA (depth range 595-604 mbsl), were transplanted from "active" cold seep sites (high methane flux) to "inactive" background sites (low methane flux), and vise versa, for one year. Community diversity surveys using T-RFLP and 16S rRNA clone libraries revealed how both bacterial and archaeal assemblages respond to this change in local environment, specifically demonstrating reproducible shifts in different ANME groups (ANME-1 vs. ANME-2). Animal assemblage composition also shifted during transplantation; gastropod representation increased (relative to control rocks) when substrates were moved from inactive to active sites and polychaete, crustacean and echinoderm representation increased when substrates were moved from active to inactive sites. Combined with organic and inorganic carbon δ13C measurements and mineralogy, this unique in situ experiment demonstrates that authigenic carbonates are viable habitats, hosting microbial and macrofaunal communities capable of responding to changes in external environment over relatively short time periods.

Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline▿†

PubMed Central

Park, Hyung Soo; Chatterjee, Indranil; Dong, Xiaoli; Wang, Sheng-Hung; Sensen, Christoph W.; Caffrey, Sean M.; Jack, Thomas R.; Boivin, Joe; Voordouw, Gerrit

2011-01-01

Pipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) of Pseudomonas not found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereas Deltaproteobacteria of the genera Desulfomicrobium and Desulfocapsa were not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) of Methanobacteriaceae archaea but increased fractions of sulfate-reducing Desulfomicrobium (18% and 48%) and of bisulfite-disproportionating Desulfocapsa (35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters. PMID:21856836

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.

Flooding forested groundwater recharge areas modifies microbial communities from top soil to groundwater table.

PubMed

Schütz, Kirsten; Nagel, Peter; Vetter, Walter; Kandeler, Ellen; Ruess, Liliane

2009-01-01

Subsurface microorganisms are crucial for contaminant degradation and maintenance of groundwater quality. This study investigates the microbial biomass and community composition [by phospholipid fatty acids (PLFAs)], as well as physical and chemical soil characteristics at woodland flooding sites of an artificial groundwater recharge system used for drinking water production. Vertical soil profiles to c. 4 m at two watered and one nonwatered site were analyzed. The microbial biomass was equal in watered and nonwatered sites, and considerable fractions (25-42%) were located in 40-340 cm depth. The microbial community structure differed significantly between watered and nonwatered sites, predominantly below 100 cm depth. Proportions of the bacterial PLFAs 16:1omega5, 16:1omega7, cy17:0 and 18:1omega9t, and the long-chained PLFAs 22:1omega9 and 24:1omega9 were more prominent at the watered sites, whereas branched, saturated PLFAs (iso/anteiso) dominated at the nonwatered site. PLFA community indices indicated stress response (trans/cis ratio), higher nutrient availability (unsaturation index) and changes in membrane fluidity (iso/anteiso ratio) due to flooding. In conclusion, water recharge processes led to nutrient input and altered environmental conditions, which resulted in a highly active and adapted microbial community residing in the vadose zone that effectively degraded organic compounds.

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

USGS Publications Warehouse

Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

2007-01-01

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Zones of life in the subsurface of hydrothermal vents: A synthesis

NASA Astrophysics Data System (ADS)

Larson, B. I.; Houghton, J.; Meile, C. D.

2011-12-01

Subsurface microbial communities in Mid-ocean Ridge (MOR) hydrothermal systems host a wide array of unique metabolic strategies, but the spatial distribution of biogeochemical transformations is poorly constrained. Here we present an approach that reexamines chemical measurements from diffuse fluids with models of convective transport to delineate likely reaction zones. Chemical data have been compiled from bare basalt surfaces at a wide array of mid-ocean ridge systems, including 9°N, East Pacific Rise, Axial Seamount, Juan de Fuca, and Lucky Strike, Mid-Atlantic Ridge. Co-sampled end-member fluid from Ty (EPR) was used to constrain reaction path models that define diffuse fluid compositions as a function of temperature. The degree of mixing between hot vent fluid (350 deg. C) and seawater (2 deg. C) governs fluid temperature, Fe-oxide mineral precipitation is suppressed, and aqueous redox reactions are prevented from equilibrating, consistent with sluggish kinetics. Quartz and pyrite are predicted to precipitate, consistent with field observations. Most reported samples of diffuse fluids from EPR and Axial Seamount fall along the same predicted mixing line only when pyrite precipitation is suppressed, but Lucky Strike fluids do not follow the same trend. The predicted fluid composition as a function of temperature is then used to calculate the free energy available to autotrophic microorganisms for a variety of catabolic strategies in the subsurface. Finally, the relationships between temperature and free energy is combined with modeled temperature fields (Lowell et al., 2007 Geochem. Geophys., Geosys.) over a 500 m x 500 m region extending downward from the seafloor and outward from the high temperature focused hydrothermal flow to define areas that are energetically most favorable for a given metabolic process as well as below the upper temperature limit for life (~120 deg. C). In this way, we can expand the relevance of geochemical model predictions of bioenergetics by predicting functionally-defined 'Zones of Life' and placing them spatially within the boundary of the 120 deg. C isotherm, estimating the extent of subsurface biosphere beneath mid-ocean ridge hydrothermal systems. Preliminary results indicate that methanogenesis yields the most energy per kg of vent fluid, consistent with the elevated CH4(aq) seen at all three sites, but may be constrained by temperatures too hot for microbial life while available energy from the oxidation of Fe(II) peaks near regions of the crust that are more hospitable.

Trace Element and Cu Isotopic Tracers of Subsurface Flow and Transport in Wastewater Irrigated Soils

NASA Astrophysics Data System (ADS)

Carte, J.; Fantle, M. S.

2017-12-01

An understanding of subsurface flow paths is critical for quantifying the fate of contaminants in wastewater irrigation systems. This study investigates the subsurface flow of wastewater by quantifying the distribution of trace contaminants in wastewater irrigated soils. Soil samples were collected from the upper 1m of two wetlands at Penn State University's wastewater irrigation site, at which all effluent from the University's wastewater treatment plant has been sprayed since 1983. Major and trace element and Cu isotopic composition were determined for these samples, in addition to wastewater effluent and bedrock samples. The upper 20 cm of each wetland shows an enrichment of Bi, Cd, Cr, Cu, Mo, Ni, Pb, and Zn concentrations relative to deep (>1m) soils at the site by a factor of 1.7-3.5. Each wetland also has a subsurface clay rich horizon with Bi, Cu, Li, Ni, Pb, and Zn concentrations enriched by a factor of 1.4 to 5 relative to deep soils. These subsurface horizons directly underlie intervals that could facilitate preferential effluent flow: a gravel layer in one wetland, and a silty loam with visible mottling, an indication of dynamic water saturation, in the other. Trace metal concentrations in other horizons from both wetlands fall in the range of the deep soils. Significant variability in Cu isotopic composition is present in soils from both wetlands, with δ65Cu values ranging from 0.74‰ to 5.09‰. Soil δ65Cu correlates well with Cu concentrations, with lighter δ65Cu associated with higher concentrations. The Cu isotopic composition of the zones of metal enrichment are comparable to the ostensible average wastewater effluent δ65Cu value (0.61‰), while other horizons have considerably heavier δ65Cu values. We hypothesize that wastewater is the source of the metal enrichments, as each of the enriched elements are present as contaminants in wastewater, and the enrichments are located in clay-rich horizons conducive to trace metal immobilization due to adsorption. This hypothesis will be further tested by modeling with the reactive transport code CrunchTope. This study provides evidence that trace element and isotopic composition of soils can be useful tracers of subsurface hydrologic pathways and elemental fate and transport.

The metal oxide fraction of pelagic sediment in the equatorial North Pacific Ocean: A source of metals in ferromanganese nodules

USGS Publications Warehouse

Piper, D.Z.

1988-01-01

Pelagic sediment recovered at DOMES Site A in the equatorial North Pacific (151??W, 9?? 15???N) consists of a surface homogeneous layer, approximately 10 cm thick, overlying a strongly mottled layer that is lighter in color. The radiolarian composition of both units is Quaternary. In areas where this sediment was only a few centimeters thick, the underlying sediment was early Tertiary. Clay mineralogy and major oxide composition of the two Quaternary sediments are uniform. Their similarity to continental shale suggests that the sediment has a terrigenous source. Clay mineralogy and major oxide composition of the Tertiary sediment also are uniform, although they differ markedly from the Quarternary sediment. In contrast to the major oxides, concentrations of Mn, Co, Cu, and Ni soluble in hydroxylamine hydrochlorideacetic acid are strongly different in the surface and subsurface Quaternary sediment. Mn and Ni exhibit pronounced depletions in the subsurface sediment, Ni slightly more than Mn. Cu is also depleted in the subsurface sediment, but less than Mn. It is also depleted in the subsurface Tertiary sediment, whereas the Mn concentration remains high. Concentration of Co relative to Mn increases into the subsurface Quaternary sediment to a constant Co:Mn ratio of 3 ?? 10-2. The trivalent REE (the REE exclusive of Ce) and Fe exhibit little down-core variation. Distribution of elements in these sediments is closely related to their concentration in associated surface ferromanganese nodules. The nodules are of two distinct types: those from the area where the Quaternary sediment is relatively thick have ??-MnO2 as the dominant manganese mineral. The ratios of Ni:Mn, Cu:Mn, and Fe:Mn in these nodules approximate the corresponding ratios of the soluble fraction of surface sediment. Todorokite is the dominant mineral of nodules recovered from areas where the Quaternary sediment is thin. Relatively high Cu/Mn, Ni/Mn, and low Fe/Mn ratios of these nodules mirror differences between the soluble fraction of surface and subsurface Quaternary sediment. These compositional trends of sediment and nodules at DOMES Site A reflect a diagenetic origin for the todorokite nodules and a predominantly hydrogenous origin for the ??-MnO2 nodules. ?? 1988.

Debates - Stochastic subsurface hydrology from theory to practice: Introduction

NASA Astrophysics Data System (ADS)

Rajaram, Harihar

2016-12-01

This paper introduces the papers in the "Debates - Stochastic Subsurface Hydrology from Theory to Practice" series. Beginning in the 1970s, the field of stochastic subsurface hydrology has been an active field of research, with over 3500 journal publications, of which over 850 have appeared in Water Resources Research. We are fortunate to have insightful contributions from four groups of distinguished authors who discuss the reasons why the advanced research framework established in stochastic subsurface hydrology has not impacted the practice of groundwater flow and transport modeling and design significantly. There is reasonable consensus that a community effort aimed at developing "toolboxes" for applications of stochastic methods will make them more accessible and encourage practical applications.

Fourier transform infrared spectral detection of life in polar subsurface environments and its application to Mars exploration.

PubMed

Preston, Louisa J; Johnson, Diane; Cockell, Charles S; Grady, Monica M

2015-09-01

Cryptoendolithic lichen communities of the Dry Valleys, Antarctica, survive in an extremely inhospitable environment, finding refuge in microscopic niches where conditions suitable for life exist. Such "within-rock" communities may have evolved on Mars when conditions for life on the surface deteriorated to such an extent that they could no longer survive. Fourier transform infrared spectroscopy of unprepared whole-rock Antarctic Beacon sandstones was used to vertically profile molecular vibrations of fatty acids, proteins, and carboxylic acids created by endolithic communities. Spectral biosignatures were found localized to lichen-rich areas and were absent in crustal regions and the bulk rock substrate. These cryptoendolithic profiles will aid similar spectroscopic investigations of organic biosignatures during future Martian subsurface studies and will help in the identification of similar communities in other localities across the Earth.

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

Introduction of a Ground Penetrating Radar System for Subsurface Investigation in Balik Pulau, Penang Island

NASA Astrophysics Data System (ADS)

Teoh, YJ; Bruka, MA; Idris, NM; Ismail, NA; Muztaza, NM

2018-04-01

Ground penetrating radar (GPR) are non-invasive geophysical techniques that enhance studies of the shallow subsurface. The purposes of this work are to study the subsurface composition of Balik Pulau area in Penang Island and to identify shallow subsurface geology features. Data acquisition for GPR is by using 250 MHz antenna to cover 200m survey line at Jalan Tun Sardon, Balik Pulau. GPR survey was divided into ten sections at 20 m each. Results from GPR shows that there is low EM reflection along the first 40 m of the survey line. Intense EM reflections were recorded along the distance 40 m to 100 m. Less noticeable radar reflections recorded along 100 m to 200 m distance of the survey line. As a conclusion, clear signal of radar wave reflection indicates dry region of the subsurface. Meanwhile, low signal of radar wave reflection indicates highly weathered granitic soil or clay of the subsurface.

Long term drainage alters plant biodiversity and soil C- and N-storage

NASA Astrophysics Data System (ADS)

Wolf, K.; Bol, R.; Dungait, J. A. J.; Dixon, L.; Dhanoa, D.; Beaumont, D.; Wiesenberg, G. L. B.

2012-04-01

Moisture and slope position can have a strong influence on soil properties and plant communities. In a long term permanent grassland experiment, sub-surface drainage was introduced in 1982 on some plots of Rowden Moor at North Wyke (SW UK). The soil is a Stagnic vertic Cambisol with a dense clay layer at shallow depth. After drainage the plant community had shifted from a Lolium perenne dominated grassland with patches of Juncus sp. towards a typical grassland plant community dominated by Lolium perenne and Trifolium sp. In addition, soil carbon and nitrogen concentrations significantly decreased. This is related to a smaller contribution of plant-derived organic matter to soil due to the change in plant community structure, and the enhanced mineralization of soil organic matter (SOM) under lower soil moisture. However, for C:N ratios neither plants nor soil did reveal any drainage related change arguing for an identical degradability of plant and soil organic matter. Furthermore the δ13C values tend to get more negative in soil, which could be related to the changing plant community. For δ15N no changes were observed, which was surprising as increase δ15N values were expected due to the increase in legumes on the drained plot. Changes in the chemical composition of SOM were also examined using compositional changes of soil n-alkanes. A shift in the alkane abundance occurs from the upper part of the slope (dominated by n-C31), to the bottom parts (n-C29 enriched). The carbon preference index and average chain length of alkanes correlated between undrained and drained plots and decreased down slope. Similarly, several alkane ratios like n-C27/n-C31 declined, due to the enhanced mineralization. Hence, the molecular pattern changed on the one hand due to changing contribution of plant derived organic matter and on the other hand because of changing preservation of organic matter in soil. The study showed that drainage has a long term effect on the plant community leading to depletion in C- and N-contents and a change in the chemical composition of SOM.

In-situ Subsurface Soil Analyzer

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

Ulmer, Chris

The Department of Energy’s (DOE’s) Terrestrial Ecosystem Science (TES) program is seeking improved sensor systems for monitoring hydro-biogeochemical processes in complex subsurface environments. The TES program is specifically interested in acquiring chemical and structural information regarding the type and nature of the hydration and redox states of subsurface chemical species. The technology should be able to perform on-site and real-time measurements to provide information not available using current sample acquisition and preservation processes. To address the needs of the DOE and the terrestrial science community, Physical Optics Corporation (POC) worked on the development of a new In-Situ Subsurface Soil Analyzermore » (ISSA) based on magnetic resonance technologies. Benchtop testing was performed to assess the feasibility of continuous wave electron pair resonance (CW-EPR) detection of chemical species in subsurface soil systems.« less

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.

Distribution of phytobenthos in the Yakima River basin, Washington, in relation to geology, land use, and other environmental factors

USGS Publications Warehouse

Leland, Harry V.

1995-01-01

Benthic-algal distributions in the Yakima River, Washington, basin were, examined in relation to geology, land use, water chemistry, and stream habitat using indicator-species classification (TWINSPAN) and canonical correspondence analysis (CCA). Algal assemblages identified byTWINSPAN were each associated with a narrow range of water-quality conditions. In the Cascade geologic province, where timber harvest and grazing are the dominant land uses, differences in community structure (CCA site scores) and concentrations of major ions (Ca and Mg) and nutrients (solute P, SiO2 and inorganic N) varied with dominant rock type of the basin. In agricultural areas of the Columbia Plateau province, differences in phytobenthos structure were based primarily on the degree of enrichment of dissolved solids, inorganic N, and solute P from irrigation-return flows and subsurface drainage. Habitat characteristics strongly correlated with community structure included reach altitude, turbidity, substratum embeddedness (Columbia Plateau), large woody-debris density (Cascade Range), and composition and density of the riparian vegetation. Algal biomass (AFDM) correlated with composition and density of the riparian vegetation but not with measured chemical-constituent concentrations. Nitrogen limitation in streams of the Cascade Range favored nitrogen-fixing blue-green algae and diatoms with endosymbiotic blue-greens, whereas nitrogen heterotrophs were abundant in agricultural areas of the Columbia Plateau.

Distribution of phytobenthos in the Yakima River basin, Washington, in relation to geology, land use and other environmental factors

USGS Publications Warehouse

Leland, Harry V.

1995-01-01

Benthic-algal distributions in the Yakima River, Washington, basin were, examined in relation to geology, land use, water chemistry, and stream habitat using indicator-species classification (TWINSPAN) and canonical correspondence analysis (CCA). Algal assemblages identified byTWINSPAN were each associated with a narrow range of water-quality conditions. In the Cascade geologic province, where timber harvest and grazing are the dominant land uses, differences in community structure (CCA site scores) and concentrations of major ions (Ca and Mg) and nutrients (solute P, SiO2 and inorganic N) varied with dominant rock type of the basin. In agricultural areas of the Columbia Plateau province, differences in phytobenthos structure were based primarily on the degree of enrichment of dissolved solids, inorganic N, and solute P from irrigation-return flows and subsurface drainage. Habitat characteristics strongly correlated with community structure included reach altitude, turbidity, substratum embeddedness (Columbia Plateau), large woody-debris density (Cascade Range), and composition and density of the riparian vegetation. Algal biomass (AFDM) correlated with composition and density of the riparian vegetation but not with measured chemical-constituent concentrations. Nitrogen limitation in streams of the Cascade Range favored nitrogen-fixing blue-green algae and diatoms with endosymbiotic blue-greens, whereas nitrogen heterotrophs were abundant in agricultural areas of the Columbia Plateau.

Searching for an Acidic Aquifer in the Rio Tinto Basin: First Geobiology Results of MARTE Project

NASA Technical Reports Server (NTRS)

Fernandez-Remolar, D. C.; Prieto-Ballesteros, O.; Stoker, C.

2004-01-01

Among the conceivable modern habitats to be explored for searching life on Mars are those potentially developed underground. Subsurface habitats are currently environments that, under certain physicochemical circumstances, have high thermal and hydrochemical stability [1, 2]. In planets like Mars lacking an atmospheric shield, such systems are obviously protected against radiation, which strongly alters the structure of biological macromolecules. Low porosity but fractured aquifers currently emplaced inside ancient volcano/sedimentary and hydrothermal systems act as excellent habitats [3] due to its thermal and geochemical properties. In these aquifers the temperature is controlled by a thermal balance between conduction and advection processes, which are driven by the rock composition, geological structure, water turnover of aquifers and heat generation from geothermal processes or chemical reactions [4]. Moreover, microbial communities based on chemolithotrophy can obtain energy by the oxidation of metallic ores that are currently associated to these environments. Such a community core may sustain a trophic web composed of non-autotrophic forms like heterotrophic bacteria, fungi and protozoa.

Effects of coal mining, forestry, and road construction on southern Appalachian stream invertebrates and habitats.

PubMed

Gangloff, Michael M; Perkins, Michael; Blum, Peter W; Walker, Craig

2015-03-01

Coal has been extracted via surface and sub-surface mining for decades throughout the Appalachian Mountains. New interest in ridge-top mining has raised concerns about possible waterway impacts. We examined effects of forestry, mining, and road construction-based disturbance on physico-chemistry and macroinvertebrate communities in east-central Tennessee headwater streams. Although 11 of 30 sites failed Tennessee's biocriteria scoring system, invertebrate richness was moderately high and we did not find significant differences in any water chemistry or habitat parameters between sites with passing and failing scores. However, conductivity and dissolved solid concentrations appeared elevated in the majority of study streams. Principal components (PCs) analysis indicated that six PCs accounted for ~77 % of among-site habitat variability. One PC associated with dissolved oxygen and specific conductance explained the second highest proportion of among-site variability after catchment area. Specific conductance was not correlated with catchment area but was strongly correlated with mining activity. Composition and success of multivariate models using habitat PCs to predict macroinvertebrate metrics was highly variable. PC scores associated with water chemistry and substrate composition were most frequently included in significant models. These results suggest that impacts of historical and current coal mining remain a source of water quality and macroinvertebrate community impairment in this region, but effects are subtle. Our results suggest that surface mining may have chronic and system-wide effects on habitat conditions and invertebrate communities in Cumberland Plateau streams.

Asset management to support urban land and subsurface management.

PubMed

Maring, Linda; Blauw, Maaike

2018-02-15

Pressure on urban areas increases by demographic and climate change. To enable healthy, adaptive and liveable urban areas different strategies are needed. One of the strategies is to make better use of subsurface space and its functions. Asset management of the Subsurface (AMS) contributes to this. Asset management provides transparency of trade-offs between performance, cost and risks throughout the entire lifecycle of these assets. AMS is based on traditional asset management methods, but it does not only take man-made assets in the subsurface into account. AMS also considers the natural functions that the subsurface, including groundwater, has to offer (ecosystem services). A Dutch community of practice consisting of national and municipal authorities, a consultancy-engineering and a research institute are developing AMS in practice in order to 1) enhance the urban underground space planning (using its benefits, avoiding problems) and 2) use, manage and maintain the (urban) subsurface and its functions. The method is currently still under development. Copyright © 2017 Elsevier B.V. All rights reserved.

A composite numerical model for assessing subsurface transport of oily wastes and chemical constituents

NASA Astrophysics Data System (ADS)

Panday, S.; Wu, Y. S.; Huyakorn, P. S.; Wade, S. C.; Saleem, Z. A.

1997-02-01

Subsurface fate and transport models are utilized to predict concentrations of chemicals leaching from wastes into downgradient receptor wells. The contaminant concentrations in groundwater provide a measure of the risk to human health and the environment. The level of potential risk is currently used by the U.S. Environmental Protection Agency to determine whether management of the wastes should conform to hazardous waste management standards. It is important that the transport and fate of contaminants is simulated realistically. Most models in common use are inappropriate for simulating the migration of wastes containing significant fractions of nonaqueous-phase liquids (NAPLs). The migration of NAPL and its dissolved constituents may not be reliably predicted using conventional aqueous-phase transport simulations. To overcome this deficiency, an efficient and robust regulatory assessment model incorporating multiphase flow and transport in the unsaturated and saturated zones of the subsurface environment has been developed. The proposed composite model takes into account all of the major transport processes including infiltration and ambient flow of NAPL, entrapment of residual NAPL, adsorption, volatilization, degradation, dissolution of chemical constituents, and transport by advection and hydrodynamic dispersion. Conceptually, the subsurface is treated as a composite unsaturated zone-saturated zone system. The composite simulator consists of three major interconnected computational modules representing the following components of the migration pathway: (1) vertical multiphase flow and transport in the unsaturated zone; (2) areal movement of the free-product lens in the saturated zone with vertical equilibrium; and (3) three-dimensional aqueous-phase transport of dissolved chemicals in ambient groundwater. Such a composite model configuration promotes computational efficiency and robustness (desirable for regulatory assessment applications). Two examples are presented to demonstrate the model verification and a site application. Simulation results obtained using the composite modeling approach are compared with a rigorous numerical solution and field observations of crude oil saturations and plume concentrations of total dissolved organic carbon at a spill site in Minnesota, U.S.A. These comparisons demonstrate the ability of the present model to provide realistic depiction of field-scale situations.

Subsurface microbial habitats on Mars

NASA Technical Reports Server (NTRS)

Boston, P. J.; Mckay, C. P.

1991-01-01

We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.

[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.

Monitoring and Quantifying Subsurface Ice and Water Content in Permafrost Regions Based on Geophysical Data Sets

NASA Astrophysics Data System (ADS)

Hauck, C.; Bach, M.; Hilbich, C.

2007-12-01

Based on recent observational evidence of climate change in permafrost regions, it is now recognised that a detailed knowledge of the material composition of the subsurface in permafrost regions is required for modelling of the future evolution of the ground thermal regime and an assessment of the hazard potential due to degrading permafrost. However, due to the remote location of permafrost areas and the corresponding difficulties in obtaining high-quality data sets of the subsurface, knowledge about the material composition in permafrost areas is scarce. In frozen ground subsurface material may consist of four different phases: rock/soil matrix, unfrozen pore water, ice and air-filled pore space. Applications of geophysical techniques for determining the subsurface composition are comparatively cheap and logistically feasible alternatives to the single point information from boreholes. Due to the complexity of the subsurface a combination of complementary geophysical methods (e.g. electrical resistivity tomography (ERT) and refraction seismic tomography) is often favoured to avoid ambiguities in the interpretation of the results. The indirect nature of geophysical soundings requires a relation between the measured variable (electrical resistivity, seismic velocity) and the rock-, water-, ice- and air content. In this contribution we will present a model which determines the volumetric fractions of these four phases from tomographic electrical and seismic data sets. The so-called 4-phase model is based on two well-known geophysical mixing rules using observed resistivity and velocity data as input data on a 2-dimensional grid. Material properties such as resistivity and P- wave velocity of the host rock material and the pore water have to be known beforehand. The remaining free model parameters can be determined by a Monte-Carlo approach, the results of which are used additionally as indicator for the reliability of the model results. First results confirm the good model performance for various field cases in permafrost research. Especially the 2- dimensional monitoring and detection of ground ice and air cavities in the blocky surface layer was substantially improved. Validation of the model results was obtained using borehole and energy balance data from different permafrost sites.

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.

Method and apparatus for subsurface exploration

NASA Technical Reports Server (NTRS)

Wilcox, Brian (Inventor)

2002-01-01

A subsurface explorer (SSX) for exploring beneath the terrestrial surface of planetary bodies such as the Earth, Mars, or comets. This exploration activity utilizes appropriate sensors and instrument to evaluate the composition, structure, mineralogy and possibly biology of the subsurface medium, as well as perhaps the ability to return samples of that medium back to the surface. The vehicle comprises an elongated skin or body having a front end and a rear end, with a nose piece at the front end for imparting force to composition material of the planetary body. Force is provided by a hammer mechanism to the back side of a nose piece from within the body of the vehicle. In the preferred embodiment, a motor spins an intermediate shaft having two non-uniform threads along with a hammer which engages these threads with two conical rollers. A brake assembly halts the rotation of the intermediate shaft, causing the conical roller to spin down the non-uniform thread to rapidly and efficiently convert the rotational kinetic energy of the hammer into translational energy.

Hillslope characterization: Identifying key controls on local-scale plant communities' distribution using remote sensing and subsurface data fusion.

NASA Astrophysics Data System (ADS)

Falco, N.; Wainwright, H. M.; Dafflon, B.; Leger, E.; Peterson, J.; Steltzer, H.; Wilmer, C.; Williams, K. H.; Hubbard, S. S.

2017-12-01

Mountainous watershed systems are characterized by extreme heterogeneity in hydrological and pedological properties that influence biotic activities, plant communities and their dynamics. To gain predictive understanding of how ecosystem and watershed system evolve under climate change, it is critical to capture such heterogeneity and to quantify the effect of key environmental variables such as topography, and soil properties. In this study, we exploit advanced geophysical and remote sensing techniques - coupled with machine learning - to better characterize and quantify the interactions between plant communities' distribution and subsurface properties. First, we have developed a remote sensing data fusion framework based on the random forest (RF) classification algorithm to estimate the spatial distribution of plant communities. The framework allows the integration of both plant spectral and structural information, which are derived from multispectral satellite images and airborne LiDAR data. We then use the RF method to evaluate the estimated plant community map, exploiting the subsurface properties (such as bedrock depth, soil moisture and other properties) and geomorphological parameters (such as slope, curvature) as predictors. Datasets include high-resolution geophysical data (electrical resistivity tomography) and LiDAR digital elevation maps. We demonstrate our approach on a mountain hillslope and meadow within the East River watershed in Colorado, which is considered to be a representative headwater catchment in the Upper Colorado Basin. The obtained results show the existence of co-evolution between above and below-ground processes; in particular, dominant shrub communities in wet and flat areas. We show that successful integration of remote sensing data with geophysical measurements allows identifying and quantifying the key environmental controls on plant communities' distribution, and provides insights into their potential changes in the future climate conditions.

Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota

PubMed Central

Waddell, Evan J.; Elliott, Terran J.; Sani, Rajesh K.; Vahrenkamp, Jefferey M.; Roggenthen, William M.; Anderson, Cynthia M.; Bang, Sookie S.

2013-01-01

Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil–like sample. Geochemical analyses indicated that both samples were high in sulfur, rich in nitrogen and salt, but with significantly different metal concentrations. Microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (OTUs) belonging to the archaeal phylum Thaumarchaeota typically identified from marine environments, and one OTU to a potentially novel phylum that falls sister to Thaumarchaeota. To our knowledge this is only the second report of Thaumarchaeota in a terrestrial environment. The majority of the clones from Archaea sequence libraries fell into two closely related OTUs and grouped most closely to an ammonia–oxidizing, carbon–fixing and halophilic thaumarchaeote genus, Nitrosopumilus. The two samples showed neither Euryarchaeota nor Crenarchaeota members that were often identified from other subsurface terrestrial ecosystems. Bacteria OTUs containing the highest percentage of sequences were related to sulfur-oxidizing bacteria of the orders Chromatiales and Thiotrichales. Community members of Bacteria from individual Homestake ecosystems were heterogeneous and distinctive to each community with unique phylotypes identified within each sample. PMID:20662386

Oceanographic structure drives the assembly processes of microbial eukaryotic communities.

PubMed

Monier, Adam; Comte, Jérôme; Babin, Marcel; Forest, Alexandre; Matsuoka, Atsushi; Lovejoy, Connie

2015-03-17

Arctic Ocean microbial eukaryote phytoplankton form subsurface chlorophyll maximum (SCM), where much of the annual summer production occurs. This SCM is particularly persistent in the Western Arctic Ocean, which is strongly salinity stratified. The recent loss of multiyear sea ice and increased particulate-rich river discharge in the Arctic Ocean results in a greater volume of fresher water that may displace nutrient-rich saltier waters to deeper depths and decrease light penetration in areas affected by river discharge. Here, we surveyed microbial eukaryotic assemblages in the surface waters, and within and below the SCM. In most samples, we detected the pronounced SCM that usually occurs at the interface of the upper mixed layer and Pacific Summer Water (PSW). Poorly developed SCM was seen under two conditions, one above PSW and associated with a downwelling eddy, and the second in a region influenced by the Mackenzie River plume. Four phylogenetically distinct communities were identified: surface, pronounced SCM, weak SCM and a deeper community just below the SCM. Distance-decay relationships and phylogenetic structure suggested distinct ecological processes operating within these communities. In the pronounced SCM, picophytoplanktons were prevalent and community assembly was attributed to water mass history. In contrast, environmental filtering impacted the composition of the weak SCM communities, where heterotrophic Picozoa were more numerous. These results imply that displacement of Pacific waters to greater depth and increased terrigenous input may act as a control on SCM development and result in lower net summer primary production with a more heterotroph dominated eukaryotic microbial community.

Microbial Diversity in a Permanently Cold and Alkaline Environment in Greenland

PubMed Central

Glaring, Mikkel A.; Vester, Jan K.; Lylloff, Jeanette E.; Abu Al-Soud, Waleed; Sørensen, Søren J.; Stougaard, Peter

2015-01-01

The submarine ikaite columns located in the Ikka Fjord in Southern Greenland represent a unique, permanently cold (less than 6°C) and alkaline (above pH 10) environment and are home to a microbial community adapted to these extreme conditions. The bacterial and archaeal community inhabiting the ikaite columns and surrounding fjord was characterised by high-throughput pyrosequencing of 16S rRNA genes. Analysis of the ikaite community structure revealed the presence of a diverse bacterial community, both in the column interior and at the surface, and very few archaea. A clear difference in overall taxonomic composition was observed between column interior and surface. Whereas the surface, and in particular newly formed ikaite material, was primarily dominated by Cyanobacteria and phototrophic Proteobacteria, the column interior was dominated by Proteobacteria and putative anaerobic representatives of the Firmicutes and Bacteroidetes. The results suggest a stratification of the ikaite columns similar to that of classical soda lakes, with a light-exposed surface inhabited by primary producers and an anoxic subsurface. This was further supported by identification of major taxonomic groups with close relatives in soda lake environments, including members of the genera Rhodobaca, Dethiobacter, Thioalkalivibrio and Tindallia, as well as very abundant groups related to uncharacterised environmental sequences originally isolated from Mono Lake in California. PMID:25915866

Microbial diversity in a permanently cold and alkaline environment in Greenland.

PubMed

Glaring, Mikkel A; Vester, Jan K; Lylloff, Jeanette E; Al-Soud, Waleed Abu; Sørensen, Søren J; Stougaard, Peter

2015-01-01

The submarine ikaite columns located in the Ikka Fjord in Southern Greenland represent a unique, permanently cold (less than 6°C) and alkaline (above pH 10) environment and are home to a microbial community adapted to these extreme conditions. The bacterial and archaeal community inhabiting the ikaite columns and surrounding fjord was characterised by high-throughput pyrosequencing of 16S rRNA genes. Analysis of the ikaite community structure revealed the presence of a diverse bacterial community, both in the column interior and at the surface, and very few archaea. A clear difference in overall taxonomic composition was observed between column interior and surface. Whereas the surface, and in particular newly formed ikaite material, was primarily dominated by Cyanobacteria and phototrophic Proteobacteria, the column interior was dominated by Proteobacteria and putative anaerobic representatives of the Firmicutes and Bacteroidetes. The results suggest a stratification of the ikaite columns similar to that of classical soda lakes, with a light-exposed surface inhabited by primary producers and an anoxic subsurface. This was further supported by identification of major taxonomic groups with close relatives in soda lake environments, including members of the genera Rhodobaca, Dethiobacter, Thioalkalivibrio and Tindallia, as well as very abundant groups related to uncharacterised environmental sequences originally isolated from Mono Lake in California.

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

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period.

PubMed

Postec, Anne; Quéméneur, Marianne; Bes, Méline; Mei, Nan; Benaïssa, Fatma; Payri, Claude; Pelletier, Bernard; Monnin, Christophe; Guentas-Dombrowsky, Linda; Ollivier, Bernard; Gérard, Emmanuelle; Pisapia, Céline; Gérard, Martine; Ménez, Bénédicte; Erauso, Gaël

2015-01-01

Active carbonate chimneys from the shallow marine serpentinizing Prony Hydrothermal Field were sampled 3 times over a 6 years period at site ST09. Archaeal and bacterial communities composition was investigated using PCR-based methods (clone libraries, Denaturating Gel Gradient Electrophoresis, quantitative PCR) targeting 16S rRNA genes, methyl coenzyme M reductase A and dissimilatory sulfite reductase subunit B genes. Methanosarcinales (Euryarchaeota) and Thaumarchaea were the main archaeal members. The Methanosarcinales, also observed by epifluorescent microscopy and FISH, consisted of two phylotypes that were previously solely detected in two other serpentinitzing ecosystems (The Cedars and Lost City Hydrothermal Field). Surprisingly, members of the hyperthermophilic order Thermococcales were also found which may indicate the presence of a hot subsurface biosphere. The bacterial community mainly consisted of Firmicutes, Chloroflexi, Alpha-, Gamma-, Beta-, and Delta-proteobacteria and of the candidate division NPL-UPA2. Members of these taxa were consistently found each year and may therefore represent a stable core of the indigenous bacterial community of the PHF chimneys. Firmicutes isolates representing new bacterial taxa were obtained by cultivation under anaerobic conditions. Our study revealed diverse microbial communities in PHF ST09 related to methane and sulfur compounds that share common populations with other terrestrial or submarine serpentinizing ecosystems.

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

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.

Untangling the biological contributions to soil stability in semiarid shrublands

USGS Publications Warehouse

Chaudhary, V. Bala; Bowker, Matthew A.; O'Dell, Thomas E.; Grace, James B.; Redman, Andrea E.; Rillig, Matthias C.; Johnson, Nancy C.

2009-01-01

Communities of plants, biological soil crusts (BSCs), and arbuscular mycorrhizal (AM) fungi are known to influence soil stability individually, but their relative contributions, interactions, and combined effects are not well understood, particularly in arid and semiarid ecosystems. In a landscape-scale field study we quantified plant, BSC, and AM fungal communities at 216 locations along a gradient of soil stability levels in southern Utah, USA. We used multivariate modeling to examine the relative influences of plants, BSCs, and AM fungi on surface and subsurface stability in a semiarid shrubland landscape. Models were found to be congruent with the data and explained 35% of the variation in surface stability and 54% of the variation in subsurface stability. The results support several tentative conclusions. While BSCs, plants, and AM fungi all contribute to surface stability, only plants and AM fungi contribute to subsurface stability. In both surface and subsurface models, the strongest contributions to soil stability are made by biological components of the system. Biological soil crust cover was found to have the strongest direct effect on surface soil stability (0.60; controlling for other factors). Surprisingly, AM fungi appeared to influence surface soil stability (0.37), even though they are not generally considered to exist in the top few millimeters of the soil. In the subsurface model, plant cover appeared to have the strongest direct influence on soil stability (0.42); in both models, results indicate that plant cover influences soil stability both directly (controlling for other factors) and indirectly through influences on other organisms. Soil organic matter was not found to have a direct contribution to surface or subsurface stability in this system. The relative influence of AM fungi on soil stability in these semiarid shrublands was similar to that reported for a mesic tallgrass prairie. Estimates of effects that BSCs, plants, and AM fungi have on soil stability in these models are used to suggest the relative amounts of resources that erosion control practitioners should devote to promoting these communities. This study highlights the need for system approaches in combating erosion, soil degradation, and arid-land desertification.

Dual-Use Applications of Infrared Sensitive Materials

DTIC Science & Technology

1993-06-01

only limit to MCT-based detectors’ market potential is in price. Specialty systems for subsurface imaging (such as buried storage tanks, toxic wastes...and assessment of automotive paint damaged by rust or stone impacts. Since automotive paint is a multi-layered coating, it lends itself to subsurface ... imaging , as well as aerospace aluminum and epoxy composites. Another family of non-destructive evaluation techniques which could use infrared detectors

Implications of Polishing Techniques in Quantitative X-Ray Microanalysis

PubMed Central

Rémond, Guy; Nockolds, Clive; Phillips, Matthew; Roques-Carmes, Claude

2002-01-01

Specimen preparation using abrasives results in surface and subsurface mechanical (stresses, strains), geometrical (roughness), chemical (contaminants, reaction products) and physical modifications (structure, texture, lattice defects). The mechanisms involved in polishing with abrasives are presented to illustrate the effects of surface topography, surface and subsurface composition and induced lattice defects on the accuracy of quantitative x-ray microanalysis of mineral materials with the electron probe microanalyzer (EPMA). PMID:27446758

Microbial production and oxidation of methane in deep subsurface

NASA Astrophysics Data System (ADS)

Kotelnikova, Svetlana

2002-10-01

The goal of this review is to summarize present studies on microbial production and oxidation of methane in the deep subterranean environments. Methane is a long-living gas causing the "greenhouse" effect in the planet's atmosphere. Earlier, the deep "organic carbon poor" subsurface was not considered as a source of "biogenic" methane. Evidence of active methanogenesis and presence of viable methanogens including autotrophic organisms were obtained for some subsurface environments including water-flooded oil-fields, deep sandy aquifers, deep sea hydrothermal vents, the deep sediments and granitic groundwater at depths of 10 to 2000 m below sea level. As a rule, the deep subterranean microbial populations dwell at more or less oligotrophic conditions. Molecular hydrogen has been found in a variety of subsurface environments, where its concentrations were significantly higher than in the tested surface aquatic environments. Chemolithoautotrophic microorganisms from deep aquifers that could grow on hydrogen and carbon dioxide can act as primary producers of organic carbon, initiating heterotrophic food chains in the deep subterranean environments independent of photosynthesis. "Biogenic" methane has been found all over the world. On the basis of documented occurrences, gases in reservoirs and older sediments are similar and have the isotopic character of methane derived from CO 2 reduction. Groundwater representing the methanogenic end member are characterized by a relative depletion of dissolved organic carbon (DOC) in combination with an enrichment in 13C in inorganic carbon, which is consistent with the preferential reduction of 12CO 2 by autotrophic methanogens or acetogens. The isotopic composition of methane formed via CO 2 reduction is controlled by the δ13C of the original CO 2 substrate. Literature data shows that CH 4 as heavy as -40‰ or -50‰ can be produced by the microbial reduction of isotopically heavy CO 2. Produced methane may be oxidized microbially to carbon dioxide. Microbial methane oxidation is a biogeochemical process that limits the release of methane, a greenhouse gas from anaerobic environments. Anaerobic methane oxidation plays an important role in marine sediments. Similar processes may take place in deep subsurface and thus fuel the deep microbial community. Organisms or consortia responsible for anaerobic methane oxidation have not yet been cultured, although diverse aerobic methanotrophs have been isolated from a variety of underground niches. The presence of aerobic methanotrophs in the anoxic subsurface remains to be explained. The presence of methane in the deep subsurface have been shown all over the world. The flux of gases between the deep subsurface and the atmosphere is driven by the concentration gradient from depth to the atmosphere. However, methane is consumed by methanotrophs on the way of its evolution in oxidized environments and is transformed to organic form, available for further microbial processing. When the impact of subsurface environments to global warming is estimated, it is necessary to take into account the activity of methane-producing Archaea and methane-oxidizing biofilters in groundwater. Microbial production and oxidation of methane is involved in the carbon cycle in the deep subsurface environments.

Sources of fatty acids in Lake Michigan surface microlayers and subsurface waters

NASA Astrophysics Data System (ADS)

Meyers, Philip A.; Owen, Robert M.

1980-11-01

Fatty acid and organic carbon contents have been measured in the particulate and dissolved phases of surface microlayer and subsurface water samples collected from Lake Michigan. Concentrations are highest close to fluvial sources and lowest in offshore areas, yet surface/subsurface fractionation is lowest near river mouths and highest in open lake locations. These gradients plus accompanying fatty acid compositional changes indicate that river-borne organic materials are important constituents of coastal Lake Michigan microlayers and that sinking and turbulent resuspension of particulates affect surface film characteristics. Lake neuston and plankton contribute organic components which partially replace potamic materials removed by sinking.

Subsurface earthworm casts can be important soil microsites specifically influencing the growth of grassland plants.

PubMed

Zaller, Johann G; Wechselberger, Katharina F; Gorfer, Markus; Hann, Patrick; Frank, Thomas; Wanek, Wolfgang; Drapela, Thomas

Earthworms (Annelida: Oligochaeta) deposit several tons per hectare of casts enriched in nutrients and/or arbuscular mycorrhizal fungi (AMF) and create a spatial and temporal soil heterogeneity that can play a role in structuring plant communities. However, while we begin to understand the role of surface casts, it is still unclear to what extent plants utilize subsurface casts. We conducted a greenhouse experiment using large mesocosms (volume 45 l) to test whether (1) soil microsites consisting of earthworm casts with or without AMF (four Glomus taxa) affect the biomass production of 11 grassland plant species comprising the three functional groups grasses, forbs, and legumes, (2) different ecological groups of earthworms (soil dwellers- Aporrectodea caliginosa vs. vertical burrowers- Lumbricus terrestris ) alter potential influences of soil microsites (i.e., four earthworms × two subsurface microsites × two AMF treatments). Soil microsites were artificially inserted in a 25-cm depth, and afterwards, plant species were sown in a regular pattern; the experiment ran for 6 months. Our results show that minute amounts of subsurface casts (0.89 g kg -1 soil) decreased the shoot and root production of forbs and legumes, but not that of grasses. The presence of earthworms reduced root biomass of grasses only. Our data also suggest that subsurface casts provide microsites from which root AMF colonization can start. Ecological groups of earthworms did not differ in their effects on plant production or AMF distribution. Taken together, these findings suggest that subsurface earthworm casts might play a role in structuring plant communities by specifically affecting the growth of certain functional groups of plants.

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.

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.

Natural and microcosm phytoneuston communities of Sequim Bay, Washington

NASA Astrophysics Data System (ADS)

Hardy, John T.; Valett, Melee

1981-01-01

The sea surface microlayer (upper 56 μm) of Sequim Bay, Washington was sampled using a glass plate collector. At the same stations, water was collected from 10 cm deep through a glass tube. The surface microlayer algal community differed significantly in several respects from the subsurface community. The mean ratio of microlayer phytoneuston to subsurface phytoplankton density (M/S ratio) was 7·8±10·9, and at one station with a visible slick reached 32·0. The rank order of individual species abundances differed significantly between the phytoneuston and phytoplankton. Outdoor tanks with a slow flow-through of seawater produced dense microlayer communities. Within 7 days, the tanks had an M/S ratio of 500. In terms of species rank order, the tank neuston are similar to field neuston, but differ significantly from tank plankton communities. Tank and field plankton communities are not significantly different either in total abundance or species rank order. These results indicate that natural phytoneuston communities can be duplicated with only minor species differences in the laboratory and used for controlled studies of the fate of pollutants passing into or through the air-sea interface.

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

Beneath the surface: Characteristics of oceanic ecosystems under weak mixing conditions A theoretical investigation

NASA Astrophysics Data System (ADS)

Beckmann, Aike; Hense, Inga

2007-12-01

This study considers an important biome in aquatic environments, the subsurface ecosystem that evolves under low mixing conditions, from a theoretical point of view. Employing a conceptual model that involves phytoplankton, a limiting nutrient and sinking detritus, we use a set of key characteristics (thickness, depth, biomass amplitude/productivity) to qualitatively and quantitatively describe subsurface biomass maximum layers (SBMLs) of phytoplankton. These SBMLs are defined by the existence of two community compensation depths in the water column, which confine the layer of net community production; their depth coincides with the upper nutricline. Analysing the results of a large ensemble of simulations with a one-dimensional numerical model, we explore the parameter dependencies to obtain fundamental steady-state relationships that connect primary production, mortality and grazing, remineralization, vertical diffusion and detrital sinking. As a main result, we find that we can distinguish between factors that determine the vertically integrated primary production and others that affect only depth and shape (thickness and biomass amplitude) of this subsurface production layer. A simple relationship is derived analytically, which can be used to estimate the steady-state primary productivity in the subsurface oligotrophic ocean. The fundamental nature of the results provides further insight into the dynamics of these “hidden” ecosystems and their role in marine nutrient cycling.

A multi-omics and imaging approach to understand soil organic matter composition and its interaction with microbes.

NASA Astrophysics Data System (ADS)

Tfaily, M. M.; Walker, L. R.; Kyle, J. E.; Chu, R. K.; Dohnalkova, A.; Tolic, N.; Orton, D.; Robinson, E. R.; Paša-Tolić, L.; Hess, N. J.

2015-12-01

The focus on soil C dynamics is currently relevant as researchers and policymakers strive to understand the feedbacks between ecosystem stress and climate change. Successful development of molecular profiles that link soil microbiology with soil carbon (C) dynamics to ascertain soil vulnerability and resilience to climate change would have great impact on assessments of soil ecosystems in response to climate change. Additionally, a better understanding of the soil C dynamics would improve climate modeling, and fate and transport of carbon across terrestrial, subsurface and atmospheric interfaces. Unravelling the wide range of possible interactions between and within the microbial communities, with minerals and organic compounds in the terrestrial ecosystem requires a multimodal, molecular approach. Here we report on the use of a combination of several molecular 'omics' approaches: metabolomics, metallomics, lipidomics, and proteomics coupled with a suite of high resolution imaging, and X-ray diffraction crystallographic techniques, as a novel methodology to understand SOM composition, and its interaction with microbial communities in different ecosystems, including C associated with mineral surfaces. The findings of these studies provide insights into the SOM persistence and microbial stabilization of carbon in ecosystems and reveal the powerful coupling of a multi-scale of techniques. Examples of this approach will be presented from field studies of simulated climate change, and laboratory column-grown Pinus resinosa mesocosms.

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.

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

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

Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

USGS Publications Warehouse

Holmes, Dawn E.; O'Neil, Regina A.; Vrionis, Helen A.; N'Guessan, Lucie A.; Ortiz-Bernad, Irene; Larrahondo, Maria J.; Adams, Lorrie A.; Ward, Joy A.; Nicoll , Julie S.; Nevin, Kelly P.; Chavan, Milind A.; Johnson, Jessica P.; Long, Philip E.; Lovely, Derek R.

2007-01-01

There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.

Composition and structure of the shallow subsurface of Ceres revealed by crater morphology

NASA Astrophysics Data System (ADS)

Bland, Michael T.; Raymond, Carol A.; Schenk, Paul M.; Fu, Roger R.; Kneissl, Thomas; Pasckert, Jan Hendrik; Hiesinger, Harry; Preusker, Frank; Park, Ryan S.; Marchi, Simone; King, Scott D.; Castillo-Rogez, Julie C.; Russell, Christopher T.

2016-07-01

Before NASA’s Dawn mission, the dwarf planet Ceres was widely believed to contain a substantial ice-rich layer below its rocky surface. The existence of such a layer has significant implications for Ceres’s formation, evolution, and astrobiological potential. Ceres is warmer than icy worlds in the outer Solar System and, if its shallow subsurface is ice-rich, large impact craters are expected to be erased by viscous flow on short geologic timescales. Here we use digital terrain models derived from Dawn Framing Camera images to show that most of Ceres’s largest craters are several kilometres deep, and are therefore inconsistent with the existence of an ice-rich subsurface. We further show from numerical simulations that the absence of viscous relaxation over billion-year timescales implies a subsurface viscosity that is at least one thousand times greater than that of pure water ice. We conclude that Ceres’s shallow subsurface is no more than 30% to 40% ice by volume, with a mixture of rock, salts and/or clathrates accounting for the other 60% to 70%. However, several anomalously shallow craters are consistent with limited viscous relaxation and may indicate spatial variations in subsurface ice content.

Composition and structure of the shallow subsurface of Ceres revealed by crater morphology

USGS Publications Warehouse

Bland, Michael T.; Carol A. Raymond,; Schenk, Paul M.; Roger R. Fu,; Thomas Kneisl,; Hendrick Pasckert, Jan; Hiesinger, Harald; Frank Preusker,; Ryan S. Park,; Simone Marchi,; Scott King,; Castillo-Rogez, Julie C.; Christopher T. Russell,

2016-01-01

Before NASA’s Dawn mission, the dwarf planet Ceres was widely believed to contain a substantial ice-rich layer below its rocky surface. The existence of such a layer has significant implications for Ceres’s formation, evolution, and astrobiological potential. Ceres is warmer than icy worlds in the outer Solar System and, if its shallow subsurface is ice-rich, large impact craters are expected to be erased by viscous flow on short geologic timescales. Here we use digital terrain models derived from Dawn Framing Camera images to show that most of Ceres’s largest craters are several kilometres deep, and are therefore inconsistent with the existence of an ice-rich subsurface. We further show from numerical simulations that the absence of viscous relaxation over billion-year timescales implies a subsurface viscosity that is at least one thousand times greater than that of pure water ice. We conclude that Ceres’s shallow subsurface is no more than 30% to 40% ice by volume, with a mixture of rock, salts and/or clathrates accounting for the other 60% to 70%. However, several anomalously shallow craters are consistent with limited viscous relaxation and may indicate spatial variations in subsurface ice content.

Photosynthetic oxygen production in a warmer ocean: the Sargasso Sea as a case study.

PubMed

Richardson, Katherine; Bendtsen, Jørgen

2017-09-13

Photosynthetic O 2 production can be an important source of oxygen in sub-surface ocean waters especially in permanently stratified oligotrophic regions of the ocean where O 2 produced in deep chlorophyll maxima (DCM) is not likely to be outgassed. Today, permanently stratified regions extend across approximately 40% of the global ocean and their extent is expected to increase in a warmer ocean. Thus, predicting future ocean oxygen conditions requires a better understanding of the potential response of photosynthetic oxygen production to a warmer ocean. Based on our own and published observations of water column processes in oligotrophic regions, we develop a one-dimensional water column model describing photosynthetic oxygen production in the Sargasso Sea to quantify the importance of photosynthesis for the downward flux of O 2 and examine how it may be influenced in a warmer ocean. Photosynthesis is driven in the model by vertical mixing of nutrients (including eddy-induced mixing) and diazotrophy and is found to substantially increase the downward O 2 flux relative to physical-chemical processes alone. Warming (2°C) surface waters does not significantly change oxygen production at the DCM. Nor does a 15% increase in re-mineralization rate (assuming Q 10  = 2; 2°C warming) have significant effect on net sub-surface oxygen accumulation. However, changes in the relative production of particulate (POM) and dissolved organic material (DOM) generate relatively large changes in net sub-surface oxygen production. As POM/DOM production is a function of plankton community composition, this implies plankton biodiversity and food web structure may be important factors influencing O 2 production in a warmer ocean.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'. © 2017 The Author(s).

Photosynthetic oxygen production in a warmer ocean: the Sargasso Sea as a case study

NASA Astrophysics Data System (ADS)

Richardson, Katherine; Bendtsen, Jørgen

2017-08-01

Photosynthetic O2 production can be an important source of oxygen in sub-surface ocean waters especially in permanently stratified oligotrophic regions of the ocean where O2 produced in deep chlorophyll maxima (DCM) is not likely to be outgassed. Today, permanently stratified regions extend across approximately 40% of the global ocean and their extent is expected to increase in a warmer ocean. Thus, predicting future ocean oxygen conditions requires a better understanding of the potential response of photosynthetic oxygen production to a warmer ocean. Based on our own and published observations of water column processes in oligotrophic regions, we develop a one-dimensional water column model describing photosynthetic oxygen production in the Sargasso Sea to quantify the importance of photosynthesis for the downward flux of O2 and examine how it may be influenced in a warmer ocean. Photosynthesis is driven in the model by vertical mixing of nutrients (including eddy-induced mixing) and diazotrophy and is found to substantially increase the downward O2 flux relative to physical-chemical processes alone. Warming (2°C) surface waters does not significantly change oxygen production at the DCM. Nor does a 15% increase in re-mineralization rate (assuming Q10 = 2; 2°C warming) have significant effect on net sub-surface oxygen accumulation. However, changes in the relative production of particulate (POM) and dissolved organic material (DOM) generate relatively large changes in net sub-surface oxygen production. As POM/DOM production is a function of plankton community composition, this implies plankton biodiversity and food web structure may be important factors influencing O2 production in a warmer ocean. This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.

Biodiversity of polycyclic aromatic hydrocarbon-degrading bacteria from deep sea sediments of the Middle Atlantic Ridge.

PubMed

Cui, Zhisong; Lai, Qiliang; Dong, Chunming; Shao, Zongze

2008-08-01

The bacteria involved in the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in deep sea subsurface environments are largely unknown. In order to reveal their biodiversity, sediments from 2.2 m under the bottom surface at a water depth of 3542 m were sampled on the Middle Atlantic Ridge with a gravity column sampler. The sediments were promptly enriched with either crude oil or a mixture of PAHs (naphthalene, phenanthrene and pyrene) as the sole carbon source, and further enriched with the PAH mixture mentioned above in the lab. The resulting consortia were named C2CO and C2PPN respectively. Their bacterial composition was analysed with plate cultivation, PCR-DGGE and 16S rDNA library analysis. On plates, isolates belonging to Pseudoalteromonas, Halomonas, Marinobacter, Thalassospira and Tistrella dominated the culturable populations. With PCR-DGGE, five major bands closely related to Cycloclasticus, Alteromonas, Thalassospira, Alcanivorax and Rhodospirillaceae were detected in consortium C2CO, while only one major band of Cycloclasticus was detected in consortium C2PPN. In addition, the dynamics of community structure in response to aromatic substrate alterations were examined. As a result, three ribotypes of Cycloclasticus were detected by 16S rDNA library analysis, one which played a key role in phenanthrene degradation; two Alteromonas bacteria dominated the naphthalene reselected consortium. Although bacteria of the two genera grew as the main members of the communities, none of them were isolated, probably owing to their poor cultivability. These results confirm that bacteria of Cycloclasticus are important obligate PAH degraders in marine environments, and coexist with other degrading bacteria that inhabit the deep subsurface sediment of the Atlantic. This supports the view that PAH accumulation and bioattenuation occur in remote areas consistently and continuously.

Biodiversity of polycyclic aromatic hydrocarbon-degrading bacteria from deep sea sediments of the Middle Atlantic Ridge

PubMed Central

Cui, Zhisong; Lai, Qiliang; Dong, Chunming; Shao, Zongze

2008-01-01

The bacteria involved in the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in deep sea subsurface environments are largely unknown. In order to reveal their biodiversity, sediments from 2.2 m under the bottom surface at a water depth of 3542 m were sampled on the Middle Atlantic Ridge with a gravity column sampler. The sediments were promptly enriched with either crude oil or a mixture of PAHs (naphthalene, phenanthrene and pyrene) as the sole carbon source, and further enriched with the PAH mixture mentioned above in the lab. The resulting consortia were named C2CO and C2PPN respectively. Their bacterial composition was analysed with plate cultivation, PCR-DGGE and 16S rDNA library analysis. On plates, isolates belonging to Pseudoalteromonas, Halomonas, Marinobacter, Thalassospira and Tistrella dominated the culturable populations. With PCR-DGGE, five major bands closely related to Cycloclasticus, Alteromonas, Thalassospira, Alcanivorax and Rhodospirillaceae were detected in consortium C2CO, while only one major band of Cycloclasticus was detected in consortium C2PPN. In addition, the dynamics of community structure in response to aromatic substrate alterations were examined. As a result, three ribotypes of Cycloclasticus were detected by 16S rDNA library analysis, one which played a key role in phenanthrene degradation; two Alteromonas bacteria dominated the naphthalene reselected consortium. Although bacteria of the two genera grew as the main members of the communities, none of them were isolated, probably owing to their poor cultivability. These results confirm that bacteria of Cycloclasticus are important obligate PAH degraders in marine environments, and coexist with other degrading bacteria that inhabit the deep subsurface sediment of the Atlantic. This supports the view that PAH accumulation and bioattenuation occur in remote areas consistently and continuously. PMID:18445026

Trace Elements Affect Methanogenic Activity and Diversity in Enrichments from Subsurface Coal Bed Produced Water

PubMed Central

Ünal, Burcu; Perry, Verlin Ryan; Sheth, Mili; Gomez-Alvarez, Vicente; Chin, Kuk-Jeong; Nüsslein, Klaus

2012-01-01

Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R2 = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community. PMID:22590465

Quantification of Microbial Communities in Subsurface Marine Sediments of the Black Sea and off Namibia.

PubMed

Schippers, Axel; Kock, Dagmar; Höft, Carmen; Köweker, Gerrit; Siegert, Michael

2012-01-01

Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 m below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises Meteor 72-5 and 76-1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, catalyzed reporter deposition - fluorescence in situ hybridization (CARD-FISH) and quantitative real-time PCR (Q-PCR). Total cell counts decreased with depths from 10(9) to 10(10) cells/mL at the sediment surface to 10(7)-10(9) cells/mL below one meter depth. Based on CARD-FISH and Q-PCR analyses overall similar proportions of Bacteria and Archaea were found. The down-core distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes (16S and 18S rRNA) as well as functional genes involved in different biogeochemical processes was quantified using Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 as well as the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were highly abundant. Less abundant but detectable in most of the samples were Eukarya as well as the metal and sulfate-reducing Geobacteraceae (only in the Benguela upwelling influenced sediments). The functional genes cbbL, encoding for the large subunit of RuBisCO, the genes dsrA and aprA, indicative of sulfate-reducers as well as the mcrA gene of methanogens were detected in the Benguela upwelling and Black Sea sediments. Overall, the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

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.

Diversity of Microbial Communities in Production and Injection Waters of Algerian Oilfields Revealed by 16S rRNA Gene Amplicon 454 Pyrosequencing

PubMed Central

Lenchi, Nesrine; İnceoğlu, Özgül; Kebbouche-Gana, Salima; Gana, Mohamed Lamine; Llirós, Marc; Servais, Pierre; García-Armisen, Tamara

2013-01-01

The microorganisms inhabiting many petroleum reservoirs are multi-extremophiles capable of surviving in environments with high temperature, pressure and salinity. Their activity influences oil quality and they are an important reservoir of enzymes of industrial interest. To study these microbial assemblages and to assess any modifications that may be caused by industrial practices, the bacterial and archaeal communities in waters from four Algerian oilfields were described and compared. Three different types of samples were analyzed: production waters from flooded wells, production waters from non-flooded wells and injection waters used for flooding (water-bearing formations). Microbial communities of production and injection waters appeared to be significantly different. From a quantitative point of view, injection waters harbored roughly ten times more microbial cells than production waters. Bacteria dominated in injection waters, while Archaea dominated in production waters. Statistical analysis based on the relative abundance and bacterial community composition (BCC) revealed significant differences between production and injection waters at both OTUs0.03 and phylum level. However, no significant difference was found between production waters from flooded and non-flooded wells, suggesting that most of the microorganisms introduced by the injection waters were unable to survive in the production waters. Furthermore, a Venn diagram generated to compare the BCC of production and injection waters of one flooded well revealed only 4% of shared bacterial OTUs. Phylogenetic analysis of bacterial sequences indicated that Alpha-, Beta- and Gammaproteobacteria were the main classes in most of the water samples. Archaeal sequences were only obtained from production wells and each well had a unique archaeal community composition, mainly belonging to Methanobacteria, Methanomicrobia, Thermoprotei and Halobacteria classes. Many of the bacterial genera retrieved had already been reported as degraders of complex organic molecules and pollutants. Nevertheless, a large number of unclassified bacterial and archaeal sequences were found in the analyzed samples, indicating that subsurface waters in oilfields could harbor new and still-non-described microbial species. PMID:23805243

Diversity and Function of Methanotrophic Bacteria in Caves

NASA Astrophysics Data System (ADS)

Webster, K.; Schimmelmann, A.; Lennon, J. T.

2016-12-01

Despite representing the second largest sink for the atmospheric greenhouse gas methane (CH4), the methanotrophic organisms responsible for atmospheric CH4 consumption have eluded cultivation. High-throughput studies of methanotrophic communities present an opportunity to learn novel details about the organisms responsible, yet such studies have rarely been conducted. Recent observations of subatmospheric CH4 concentrations in cave-air have led to the hypothesis that methanotrophs are active over large spatial scales in the subsurface. Karst terrains cover between 10 - 20 % of the terrestrial surface area and offer abundant cave-related methanotrophic habitat due to the exchange of air with the atmosphere. We collected 42 cave soil samples from 20 caves to test the hypothesis that subterranean methanotrophy removes CH4 from cave-air. Methanotrophs were found in 90 % of samples, notably in locations with subatmospheric CH4­ concentrations. Methylocystaceae were present in caves and accounted for 92 % of the methanotrophic community on average (median), however almost all of the observations were of unidentified Methylocystaceae. Abundances of uncultured and unidentified members of the Methylococcales were correlated with cave-air CH4 concentrations suggesting that some Methylococcales may contribute to atmospheric CH4 oxidation. Individual caves had a strong influence on the observed methanotrophic community composition accounting for 77 % of the variance in the assemblage. Nevertheless, cave-air CH4 concentrations were predictive of the methanotrophic community composition accounting for 5 % of the variation. Our findings also are suggestive of CH4-fueled microbial food webs. For example, abundances of known methylotrophic organisms were correlated with cave-air CH4 concentrations. This may suggest that some methylotrophs contribute to atmospheric CH4 oxidation or that molecules produced in the CH4 oxidation pathway, like methanol, are leaked from methanotrophic cells allowing for the growth of methylotrophs. Our results suggest that uncultivated and unidentified methanotrophs are responsible for subatmospheric CH4 concentrations in caves and have secondary influences on the cave-microbial community structure.

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.

Influence of dissimilatory metal reduction on fate of organic and metal contaminants in the subsurface

USGS Publications Warehouse

Lovely, Derek R.; Anderson, Robert T.

2000-01-01

Geobacter become dominant members of the microbial community when Fe(III)-reducing conditions develop as the result of organic contamination, or when Fe(III) reduction is artificially stimulated. These results suggest that further understanding of the ecophysiology of Geobacter species would aid in better prediction of the natural attenuation of organic contaminants under anaerobic conditions and in the design of strategies for the bioremediation of subsurface metal contamination.

A constant flux of diverse thermophilic bacteria into the cold Arctic seabed.

PubMed

Hubert, Casey; Loy, Alexander; Nickel, Maren; Arnosti, Carol; Baranyi, Christian; Brüchert, Volker; Ferdelman, Timothy; Finster, Kai; Christensen, Flemming Mønsted; Rosa de Rezende, Júlia; Vandieken, Verona; Jørgensen, Bo Barker

2009-09-18

Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 10(8) spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis, fermentation, and sulfate reduction upon induction at 50 degrees C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may broadly influence microbial community composition in the marine environment.

Oceanographic structure drives the assembly processes of microbial eukaryotic communities

PubMed Central

Monier, Adam; Comte, Jérôme; Babin, Marcel; Forest, Alexandre; Matsuoka, Atsushi; Lovejoy, Connie

2015-01-01

Arctic Ocean microbial eukaryote phytoplankton form subsurface chlorophyll maximum (SCM), where much of the annual summer production occurs. This SCM is particularly persistent in the Western Arctic Ocean, which is strongly salinity stratified. The recent loss of multiyear sea ice and increased particulate-rich river discharge in the Arctic Ocean results in a greater volume of fresher water that may displace nutrient-rich saltier waters to deeper depths and decrease light penetration in areas affected by river discharge. Here, we surveyed microbial eukaryotic assemblages in the surface waters, and within and below the SCM. In most samples, we detected the pronounced SCM that usually occurs at the interface of the upper mixed layer and Pacific Summer Water (PSW). Poorly developed SCM was seen under two conditions, one above PSW and associated with a downwelling eddy, and the second in a region influenced by the Mackenzie River plume. Four phylogenetically distinct communities were identified: surface, pronounced SCM, weak SCM and a deeper community just below the SCM. Distance–decay relationships and phylogenetic structure suggested distinct ecological processes operating within these communities. In the pronounced SCM, picophytoplanktons were prevalent and community assembly was attributed to water mass history. In contrast, environmental filtering impacted the composition of the weak SCM communities, where heterotrophic Picozoa were more numerous. These results imply that displacement of Pacific waters to greater depth and increased terrigenous input may act as a control on SCM development and result in lower net summer primary production with a more heterotroph dominated eukaryotic microbial community. PMID:25325383

Glass fiber addition strengthens low-density ablative compositions

NASA Technical Reports Server (NTRS)

Chandler, H. H.

1974-01-01

Approximately 15% of E-glass fibers was added to compositions under test and greatly improved char stability. Use of these fibers also reduced thermal strains which, in turn, minimized char shrinkage and associated cracks, subsurface voids, and disbonds. Increased strength allows honeycomb core reinforcement to be replaced by equivalent amount of glass fibers.

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.

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.

Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquifer

NASA Astrophysics Data System (ADS)

Danczak, Robert; Yabusaki, Steven; Williams, Kenneth; Fang, Yilin; Hobson, Chad; Wilkins, Michael

2016-05-01

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a six-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species in reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period

PubMed Central

Postec, Anne; Quéméneur, Marianne; Bes, Méline; Mei, Nan; Benaïssa, Fatma; Payri, Claude; Pelletier, Bernard; Monnin, Christophe; Guentas-Dombrowsky, Linda; Ollivier, Bernard; Gérard, Emmanuelle; Pisapia, Céline; Gérard, Martine; Ménez, Bénédicte; Erauso, Gaël

2015-01-01

Active carbonate chimneys from the shallow marine serpentinizing Prony Hydrothermal Field were sampled 3 times over a 6 years period at site ST09. Archaeal and bacterial communities composition was investigated using PCR-based methods (clone libraries, Denaturating Gel Gradient Electrophoresis, quantitative PCR) targeting 16S rRNA genes, methyl coenzyme M reductase A and dissimilatory sulfite reductase subunit B genes. Methanosarcinales (Euryarchaeota) and Thaumarchaea were the main archaeal members. The Methanosarcinales, also observed by epifluorescent microscopy and FISH, consisted of two phylotypes that were previously solely detected in two other serpentinitzing ecosystems (The Cedars and Lost City Hydrothermal Field). Surprisingly, members of the hyperthermophilic order Thermococcales were also found which may indicate the presence of a hot subsurface biosphere. The bacterial community mainly consisted of Firmicutes, Chloroflexi, Alpha-, Gamma-, Beta-, and Delta-proteobacteria and of the candidate division NPL-UPA2. Members of these taxa were consistently found each year and may therefore represent a stable core of the indigenous bacterial community of the PHF chimneys. Firmicutes isolates representing new bacterial taxa were obtained by cultivation under anaerobic conditions. Our study revealed diverse microbial communities in PHF ST09 related to methane and sulfur compounds that share common populations with other terrestrial or submarine serpentinizing ecosystems. PMID:26379636

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points: Microbial community succession and disturbance

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

Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.

2014-04-18

Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacteriummore » and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.« 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

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.

Modular evaluation method for subsurface activities (MEMSA). A novel approach for integrating social acceptance in a permit decision-making process for subsurface activities

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

Os, Herman W.A. van, E-mail: h.w.a.van.os@rug.nl; Herber, Rien, E-mail: rien.herber@rug.nl; Scholtens, Bert, E-mail: l.j.r.scholtens@rug.nl

We investigate how the decision support system ‘Modular Evaluation Method Subsurface Activities’ (MEMSA) can help facilitate an informed decision-making process for permit applications of subsurface activities. To this end, we analyze the extent the MEMSA approach allows for a dialogue between stakeholders in a transparent manner. We use the exploration permit for the underground gas storage facility at the Pieterburen salt dome (Netherlands) as a case study. The results suggest that the MEMSA approach is flexible enough to adjust to changing conditions. Furthermore, MEMSA provides a novel way for identifying structural problems and possible solutions in permit decision-making processes formore » subsurface activities, on the basis of the sensitivity analysis of intermediate rankings. We suggest that the planned size of an activity should already be specified in the exploration phase, because this would allow for a more efficient use of the subsurface as a whole. We conclude that the host community should be involved to a greater extent and in an early phase of the permit decision-making process, for example, already during the initial analysis of the project area of a subsurface activity. We suggest that strategic national policy goals are to be re-evaluated on a regular basis, in the form of a strategic vision for the subsurface, to account for timing discrepancies between the realization of activities and policy deadlines, because this discrepancy can have a large impact on the necessity and therefore acceptance of a subsurface activity.« less

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

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

Exploring the links between groundwater quality and bacterial communities near oil and gas extraction activities.

PubMed

Santos, Inês C; Martin, Misty S; Reyes, Michelle L; Carlton, Doug D; Stigler-Granados, Paula; Valerio, Melissa A; Whitworth, Kristina W; Hildenbrand, Zacariah L; Schug, Kevin A

2018-03-15

Bacterial communities in groundwater are very important as they maintain a balanced biogeochemical environment. When subjected to stressful environments, for example, due to anthropogenic contamination, bacterial communities and their dynamics change. Studying the responses of the groundwater microbiome in the face of environmental changes can add to our growing knowledge of microbial ecology, which can be utilized for the development of novel bioremediation strategies. High-throughput and simpler techniques that allow the real-time study of different microbiomes and their dynamics are necessary, especially when examining larger data sets. Matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) is a workhorse for the high-throughput identification of bacteria. In this work, groundwater samples were collected from a rural area in southern Texas, where agricultural activities and unconventional oil and gas development are the most prevalent anthropogenic activities. Bacterial communities were assessed using MALDI-TOF MS, with bacterial diversity and abundance being analyzed with the contexts of numerous organic and inorganic groundwater constituents. Mainly denitrifying and heterotrophic bacteria from the Phylum Proteobacteria were isolated. These microorganisms are able to either transform nitrate into gaseous forms of nitrogen or degrade organic compounds such as hydrocarbons. Overall, the bacterial communities varied significantly with respect to the compositional differences that were observed from the collected groundwater samples. Collectively, these data provide a baseline measurement of bacterial diversity in groundwater located near anthropogenic surface and subsurface activities. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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.

Spreadsheet log analysis in subsurface geology

USGS Publications Warehouse

Doveton, J.H.

2000-01-01

Most of the direct knowledge of the geology of the subsurface is gained from the examination of core and drill-cuttings recovered from boreholes drilled by the petroleum and water industries. Wireline logs run in these same boreholes generally have been restricted to tasks of lithostratigraphic correlation and thee location of hydrocarbon pay zones. However, the range of petrophysical measurements has expanded markedly in recent years, so that log traces now can be transformed to estimates of rock composition. Increasingly, logs are available in a digital format that can be read easily by a desktop computer and processed by simple spreadsheet software methods. Taken together, these developments offer accessible tools for new insights into subsurface geology that complement the traditional, but limited, sources of core and cutting observations.

Bromus tectorum invasion alters nitrogen dynamics in an undisturbed arid grassland ecosystem

USGS Publications Warehouse

Sperry, L.J.; Belnap, J.; Evans, R.D.

2006-01-01

The nonnative annual grass Bromus tectorum has successfully replaced native vegetation in many arid and semiarid ecosystems. Initial introductions accompanied grazing and agriculture, making it difficult to separate the effects of invasion from physical disturbance. This study examined N dynamics in two recently invaded, undisturbed vegetation associations (C3 and C4). The response of these communities was compared to an invaded/disturbed grassland. The invaded/disturbed communities had higher surface NH4+ input in spring, whereas there were no differences for surface input of NO3-. Soil inorganic N was dominated by NH4+, but invaded sites had greater subsurface soil NO3-. Invaded sites had greater total soil N at the surface four years post-invasion in undisturbed communities, but total N was lower in the invaded/disturbed communities. Soil ??15N increased with depth in the noninvaded and recently invaded communities, whereas the invaded/disturbed communities exhibited the opposite pattern. Enriched foliar ??15N values suggest that Bromus assimilated subsurface NO3-, whereas the native grasses were restricted to surface N. A Rayleigh distillation model accurately described decomposition patterns in the noninvaded communities where soil N loss is accompanied by increasing soil ??15N; however, the invaded/disturbed communities exhibited the opposite pattern, suggesting redistribution of N within the soil profile. This study suggests that invasion has altered the mechanisms driving nitrogen dynamics. Bromus litter decomposition and soil NO3- concentrations were greater in the invaded communities during periods of ample precipitation, and NO3- leached from the surface litter, where it was assimilated by Bromus. The primary source of N input in these communities is a biological soil crust that is removed with disturbance, and the lack of N input by the biological soil crust did not balance N loss, resulting in reduced total N in the invaded/disturbed communities. Bromus produced a positive feedback loop by leaching NO3- from decomposing Bromus litter to subsurface soil layers, accessing that deep-soil N pool with deep roots and returning that N to the surface as biomass and subsequent litter. Lack of new inputs combined with continued loss will result in lower total soil N, evidenced by the lower total soil N in the invaded/disturbed communities. ?? 2006 by the Ecological Society of America.

Optical method and apparatus for detection of surface and near-subsurface defects in dense ceramics

DOEpatents

Ellingson, William A.; Brada, Mark P.

1995-01-01

A laser is used in a non-destructive manner to detect surface and near-subsurface defects in dense ceramics and particularly in ceramic bodies with complex shapes such as ceramic bearings, turbine blades, races, and the like. The laser's wavelength is selected based upon the composition of the ceramic sample and the laser can be directed on the sample while the sample is static or in dynamic rotate or translate motion. Light is scattered off surface and subsurface defects using a preselected polarization. The change in polarization angle is used to select the depth and characteristics of surface/subsurface defects. The scattered light is detected by an optical train consisting of a charge coupled device (CCD), or vidicon, television camera which, in turn, is coupled to a video monitor and a computer for digitizing the image. An analyzing polarizer in the optical train allows scattered light at a given polarization angle to be observed for enhancing sensitivity to either surface or near-subsurface defects. Application of digital image processing allows subtraction of digitized images in near real-time providing enhanced sensitivity to subsurface defects. Storing known "feature masks" of identified defects in the computer and comparing the detected scatter pattern (Fourier images) with the stored feature masks allows for automatic classification of detected defects.

Ma_MISS on ExoMars: Mineralogical Characterization of the Martian Subsurface

NASA Astrophysics Data System (ADS)

De Sanctis, Maria Cristina; Altieri, Francesca; Ammannito, Eleonora; Biondi, David; De Angelis, Simone; Meini, Marco; Mondello, Giuseppe; Novi, Samuele; Paolinetti, Riccardo; Soldani, Massimo; Mugnuolo, Raffaele; Pirrotta, Simone; Vago, Jorge L.; Ma_MISS Team

2017-07-01

The Ma_MISS (Mars Multispectral Imager for Subsurface Studies) experiment is the visible and near infrared (VNIR) miniaturized spectrometer hosted by the drill system of the ExoMars 2020 rover. Ma_MISS will perform IR spectral reflectance investigations in the 0.4-2.2 μm range to characterize the mineralogy of excavated borehole walls at different depths (between 0 and 2 m). The spectral sampling is about 20 nm, whereas the spatial resolution over the target is 120 μm. Making use of the drill's movement, the instrument slit can scan a ring and build up hyperspectral images of a borehole. The main goal of the Ma_MISS instrument is to study the martian subsurface environment. Access to the martian subsurface is crucial to our ability to constrain the nature, timing, and duration of alteration and sedimentation processes on Mars, as well as habitability conditions. Subsurface deposits likely host and preserve H2O ice and hydrated materials that will contribute to our understanding of the H2O geochemical environment (both in the liquid and in the solid state) at the ExoMars 2020 landing site. The Ma_MISS spectral range and sampling capabilities have been carefully selected to allow the study of minerals and ices in situ before the collection of samples. Ma_MISS will be implemented to accomplish the following scientific objectives: (1) determine the composition of subsurface materials, (2) map the distribution of subsurface H2O and volatiles, (3) characterize important optical and physical properties of materials (e.g., grain size), and (4) produce a stratigraphic column that will inform with regard to subsurface geological processes. The Ma_MISS findings will help to refine essential criteria that will aid in our selection of the most interesting subsurface formations from which to collect samples.

Geophysical imaging of watershed subsurface patterns and prediction of soil texture and water holding capacity

USDA-ARS?s Scientific Manuscript database

The extent to which soil resource availability, nutrients or moisture, contro1 the structure, function and diversity of plant communities has aroused considerableinterest in the past decade, and remains topical in light of global change. Numerous plant communities are controlled either by water or s...

Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars.

PubMed

Mickol, Rebecca L; Laird, Sarah K; Kral, Timothy A

2018-04-23

Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My) freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable micro-environments within the martian subsurface. On Earth, microbial communities are often active at sub-freezing temperatures within permafrost, especially within the active layer, which experiences large ranges in temperature. With warming global temperatures, the effect of thawing permafrost communities on the release of greenhouse gases such as carbon dioxide and methane becomes increasingly important. Studies examining the community structure and activity of microbial permafrost communities on Earth can also be related to martian permafrost environments, should life have developed on the planet. Here, two non-psychrophilic methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii , were tested for their ability to survive long-term (~4 year) exposure to freeze/thaw cycles varying in both temperature and duration, with implications both for climate change on Earth and possible life on Mars.

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.

Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition

PubMed Central

Toth, Courtney R. A.; Gieg, Lisa M.

2018-01-01

Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32) or heavy crude oil (°API = 16). Over the course of 17 months, we conducted routine analytical (GC, GC-MS) and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing) surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella), along with syntrophic bacteria (Syntrophus), methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”). Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems. PMID:29354103

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.

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.

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.

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

The Cartridge Theory: a description of the functioning of horizontal subsurface flow constructed wetlands for wastewater treatment, based on modelling results.

PubMed

Samsó, Roger; García, Joan

2014-03-01

Despite the fact that horizontal subsurface flow constructed wetlands have been in operation for several decades now, there is still no clear understanding of some of their most basic internal functioning patterns. To fill this knowledge gap, on this paper we present what we call "The Cartridge Theory". This theory was derived from simulation results obtained with the BIO_PORE model and explains the functioning of urban wastewater treatment wetlands based on the interaction between bacterial communities and the accumulated solids leading to clogging. In this paper we start by discussing some changes applied to the biokinetic model implemented in BIO_PORE (CWM1) so that the growth of bacterial communities is consistent with a well-known population dynamics models. This discussion, combined with simulation results for a pilot wetland system, led to the introduction of "The Cartridge Theory", which states that the granular media of horizontal subsurface flow wetlands can be assimilated to a generic cartridge which is progressively consumed (clogged) with inert solids from inlet to outlet. Simulations also revealed that bacterial communities are poorly distributed within the system and that their location is not static but changes over time, moving towards the outlet as a consequence of the progressive clogging of the granular media. According to these findings, the life-span of constructed wetlands corresponds to the time when bacterial communities are pushed as much towards the outlet that their biomass is not anymore sufficient to remove the desirable proportion of the influent pollutants. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Habitat Inspection Scanner, Bio-Structure Scanner, and In Situ Sub-Surface Composition Sensor

NASA Technical Reports Server (NTRS)

VanSteenberg, Michael

2004-01-01

The extension of dielectric and inductive spectroscopy into in situ observations represents a significant exploration-enabling tool. This technology can be widely applied from microscopic to macroscopic. Dielectrometry and inductometry can measure sub-surface composition and its distribution. The primary environment that we cannot easily explored is the sub-surface of solid bodies. Weather as part of our equipment that we bring with us, or the locations we are exploring. These fundamental questions lie at the core of the exploration Initiative. To answer them we must use a whole host of complimentary tools including those that allow us to practically examine the sub-surface environment. A nondestructive approach offers significant advantages for both the initial identification of likely samples but also the monitoring of ecosystems and crew health. These include materials characterization, nondestructive inspection, and process quality control, damage monitoring, and hidden object detection and identification. The identification of natural resources such as water on the Moon or Mars is of great importance to the utilization of local resource in the support of human exploration crews. On the macroscopic scale, the understanding of what resources are available and how they are distributed is of primary importance to their productive utilization. Even if initial explorations do not require the use of local resources to succeed, eventual settlement and commercial development will. The routine examination of the structural integrity (micro cracks, leaks) of hi.inafi habitats in harsh envkmments ww!d also be enabled.

Working Smarter Not Harder - Developing a Virtual Subsurface Data Framework for U.S. Energy R&D

NASA Astrophysics Data System (ADS)

Rose, K.; Baker, D.; Bauer, J.; Dehlin, M.; Jones, T. J.; Rowan, C.

2017-12-01

The data revolution has resulted in a proliferation of resources that span beyond commercial and social networking domains. Research, scientific, and engineering data resources, including subsurface characterization, modeling, and analytical datasets, are increasingly available through online portals, warehouses, and systems. Data for subsurface systems is still challenging to access, discontinuous, and varies in resolution. However, with the proliferation of online data there are significant opportunities to advance access and knowledge of subsurface systems. The Energy Data eXchange (EDX) is an online platform designed to address research data needs by improving access to energy R&D products through advanced search capabilities. In addition, EDX hosts private, virtualized computational workspaces in support of multi-organizational R&D. These collaborative workspaces allow teams to share working data resources and connect to a growing number of analytical tools to support research efforts. One recent application, a team digital data notebook tool, called DataBook, was introduced within EDX workspaces to allow teams to capture contextual and structured data resources. Starting with DOE's subsurface R&D community, the EDX team has been developing DataBook to support scientists and engineers working on subsurface energy research, allowing them to contribute and curate both structured and unstructured data and knowledge about subsurface systems. These resources span petrophysical, geologic, engineering, geophysical, interpretations, models, and analyses associated with carbon storage, water, oil, gas, geothermal, induced seismicity and other subsurface systems to support the development of a virtual subsurface data framework. The integration of EDX and DataBook allows for these systems to leverage each other's best features, such as the ability to interact with other systems (Earthcube, OpenEI.net, NGDS, etc.) and leverage custom machine learning algorithms and capabilities to enhance user experience, make access and connection to relevant subsurface data resources more efficient for research teams to use, analyze and draw insights. Ultimately, the public and private resources in EDX seek to make subsurface energy research more efficient, reduce redundancy, and drive innovation.

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.

Using electrokinetic phenomena and electrical resistance tomography to characterize the movement of subsurface fluids

DOEpatents

Ramirez, Abelardo L.; Cooper, John F.; Daily, William D.

1996-01-01

This invention relates generally to the remote detections of subsurface liquid contaminants using in combination a geophysical technique known as ERT and an EKS. Electrokinetic transport is used to enhance the ability of electrical resistance tomography (ERT) to detect position and movement of subsurface contaminant liquids, particles or ions. ERT images alone are difficult to interpret because of natural inhomogeneities in soil composition and electrical properties. By subtracting two or more ERT images obtained before and after field induced movement, a high contrast image of a plume of distinct electrokinetic properties can be seen. The invention is applicable to important subsurface characterization problems including, as examples, (1) detection of liquid-saturated plumes of contaminants such as those associated with leaks from underground storage tanks containing hazardous concentrated electrolytes, (2) detection and characterization of soils contaminated with organic pollutants such as droplets of gasoline; and (3) monitoring the progress of electrokinetic containment or clean up of underground contamination.

Using electrokinetic phenomena and electrical resistance tomography to characterize the movement of subsurface fluids

DOEpatents

Ramirez, A.L.; Cooper, J.F.; Daily, W.D.

1996-02-27

This invention relates generally to the remote detections of subsurface liquid contaminants using in combination a geophysical technique known as ERT and an EKS. Electrokinetic transport is used to enhance the ability of electrical resistance tomography (ERT) to detect position and movement of subsurface contaminant liquids, particles or ions. ERT images alone are difficult to interpret because of natural inhomogeneities in soil composition and electrical properties. By subtracting two or more ERT images obtained before and after field induced movement, a high contrast image of a plume of distinct electrokinetic properties can be seen. The invention is applicable to important subsurface characterization problems including, as examples, (1) detection of liquid-saturated plumes of contaminants such as those associated with leaks from underground storage tanks containing hazardous concentrated electrolytes, (2) detection and characterization of soils contaminated with organic pollutants such as droplets of gasoline; and (3) monitoring the progress of electrokinetic containment or clean up of underground contamination. 1 fig.

Lead isotopes and trace metals in dust at Yucca Mountain

USGS Publications Warehouse

Kwak, Loretta; Neymark, Leonid A.; Peterman, Zell E.

2008-01-01

Lead (Pb)-isotope compositions and trace-metal concentrations were determined for samples of dust collected from underground and surface locations at and near the proposed radioactive waste repository at Yucca Mountain, Nevada. Rare earth element concentrations in the dust samples from the underground tunnels are similar to those in wholerock samples of the repository host rocks (Miocene Tiva Canyon Tuff and Topopah Spring Tuff), supporting interpretation that the subsurface dust is mainly composed of rock comminuted during tunnel construction. Other trace metals (arsenic, cadmium, cobalt, chromium, copper, manganese, nickel, lead, antimony, thallium, and zinc) are variably enriched in the subsurface dust samples relative to the average concentrations in the host rocks. Average concentrations of arsenic and lead in dust samples, high concentrations of which can cause corrosion of waste canisters, have enrichment factors from 1.2 to 1.6 and are insignificant relative to the range of concentrations for these metals observed in the host rock samples. Most dust samples from surface sites also are enriched in many of these trace metals relative to average repository host rocks. At least some of these enrichments may be artifacts of sampling. Plotted on a 208Pb/206Pb-207Pb/206Pb graph, Pb-isotope compositions of dust samples from underground sites form a mixing line extending from host-rock Pb-isotope compositions towards compositions of many of the dust samples from surface sites; however, combined Pb concentration and isotope data indicate the presence of a Pbenriched component in the subsurface dust that is not derived from host rock or surface dust and may derive from anthropogenic materials introduced into the underground environment.

Coupled Spatiotemporal Dynamics of Microbial Community Ecology, Biogeochemistry, and Hydrologic Mixing

NASA Astrophysics Data System (ADS)

Stegen, J.; Johnson, T. C.; Fredrickson, J.; Wilkins, M.; Konopka, A.; Nelson, W.; Arntzen, E.; Chrisler, W.; Chu, R. K.; Fansler, S.; Kennedy, D.; Resch, T.; Tfaily, M. M.

2015-12-01

The hyporheic zone (HZ) is a critical ecosystem component that links terrestrial, surface water, and groundwater ecosystems. A dominant feature of the HZ is groundwater-surface water mixing and the input of terrestrially—as well as aquatically—derived organic carbon. In many systems the HZ has a relatively small spatial extent, but in larger riverine systems groundwater-surface water mixing can occur 100s of meters beyond the surface water shoreline; we consider these more distal locations to be within the 'subsurface interaction zone' (SIZ) as they are beyond the traditional HZ. Microbial communities in the HZ and SIZ drive biogeochemical processes in these system components, yet relatively little is known about the ecological processes that drive HZ and SIZ microbial communities. Here, we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected through space (400m spatial extent) and time (7 month temporal extent) within the Hanford Site 300 Area. These data streams were integrated to evaluate how the influence of groundwater-surface water mixing on microbial communities changes when moving from the HZ to the broader SIZ. Our results indicate that groundwater-surface water mixing (i) consistently stimulated heterotrophic respiration, but only above a threshold of surface water intrusion, (ii) did not stimulate denitrification, (iii) caused deterministic shifts in HZ microbial communities due to changes in organic carbon composition, and (iv) did not cause shifts in SIZ microbial communities. These results suggest that microbial communities and the biogeochemical processes they drive are impacted by groundwater-surface water mixing primarily in the HZ and to a lesser extent in the SIZ.

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

DOE PAGES

Castelle, Cindy J.; Hug, Laura A.; Wrighton, Kelly C.; ...

2013-08-27

Microorganisms in the subsurface represent a substantial but poorly understood component of the Earth’s biosphere. Subsurface environments are complex and difficult to characterize; thus, their microbiota have remained as a ‘dark matter’ of the carbon and other biogeochemical cycles. Here we deeply sequence two sediment-hosted microbial communities from an aquifer adjacent to the Colorado River, CO, USA. No single organism represents more than ~1% of either community. Remarkably, many bacteria and archaea in these communities are novel at the phylum level or belong to phyla lacking a sequenced representative. The dominant organism in deeper sediment, RBG-1, is a member ofmore » a new phylum. On the basis of its reconstructed complete genome, RBG-1 is metabolically versatile. Its wide respiration-based repertoire may enable it to respond to the fluctuating redox environment close to the water table. We document extraordinary microbial novelty and the importance of previously unknown lineages in sediment biogeochemical transformations.« less

MSL DAN Science Investigation: Physical Simulation of DAN

NASA Technical Reports Server (NTRS)

Jun, Insoo

2012-01-01

The main objective of the proposed investigation is to study the characteristics (i.e., hydrogen content, soil composition, layer-structure, etc.) of sub-surface and the surface radiation (neutron in particular) environment.

Nonlinearities in the Evolutional Distinctions Between El Niño and La Niña Types

NASA Astrophysics Data System (ADS)

Ashok, K.; Shamal, M.; Sahai, A. K.; Swapna, P.

2017-12-01

Using the HadISST, SODA reanalysis, and various other observed and reanalyzed data sets for the period 1950-2010, we explore nonlinearities in the subsurface evolutional distinctions between El Niño types and La Niña types from a few seasons before the onset. Cluster analysis carried out over both summer and winter suggests that while the warm-phased events of both types are distinguishable, several cold phased events are clustered together. Further, we apply a joint Self-Organizing Map (SOM) analysis using the monthly sea surface temperature anomaly (SSTA) and thermocline-depth anomalies in tropical Pacific (TP). Results reveal that the evolutionary paths of El Niño Modoki (EM) and El Niño (EL) are, broadly, different. Subsurface temperature composites of EL and EM show different onset characteristics. During an EL, warm anomaly in the west spreads eastward along the thermocline and reaches the surface in the east in March-May of year(0). During an EM, warm anomaly already exists in the central tropical Pacific and then reaches the surface in the east in September-November of year(0). Composited SSTAs during La Niña (LN) and La Niña Modoki (LM) are distinguishable only at 80% confidence level, but the composited subsurface temperature anomalies show differences in the location of the coldest anomaly as well as evolution at 90% confidence level. Thus, the El Niño flavor distinction is potentially predictable at longer leads.

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.

Remineralization of demineralized enamel via calcium phosphate nanocomposite.

PubMed

Weir, M D; Chow, L C; Xu, H H K

2012-10-01

Secondary caries remains the main problem limiting the longevity of composite restorations. The objective of this study was to investigate the remineralization of demineralized human enamel in vitro via a nanocomposite containing nanoparticles of amorphous calcium phosphate (NACP). NACP were synthesized by a spray-drying technique and incorporated into a dental resin. First, caries-like subsurface enamel lesions were created via an acidic solution. Then, NACP nanocomposite or a commercial fluoride-releasing control composite was placed on the demineralized enamel, along with control enamel without a composite. These specimens were then treated with a cyclic demineralization/remineralization regimen for 30 days. Quantitative microradiography showed typical enamel subsurface demineralization before cyclic demineralization/remineralization treatment, and significant remineralization in enamel under the NACP nanocomposite after the demineralization/remineralization treatment. The NACP nanocomposite had the highest enamel remineralization (mean ± SD; n = 6) of 21.8 ± 3.7%, significantly higher than the 5.7 ± 6.9% for fluoride-releasing composite (p < 0.05). The enamel group without composite had further demineralization of -26.1 ± 16.2%. In conclusion, a novel NACP nanocomposite was effective in remineralizing enamel lesions in vitro. Its enamel remineralization was 4-fold that of a fluoride-releasing composite control. Combined with the good mechanical and acid-neutralization properties reported earlier, the new NACP nanocomposite is promising for remineralization of demineralized tooth structures.

Remineralization of Demineralized Enamel via Calcium Phosphate Nanocomposite

PubMed Central

Weir, M.D.; Chow, L.C.; Xu, H.H.K.

2012-01-01

Secondary caries remains the main problem limiting the longevity of composite restorations. The objective of this study was to investigate the remineralization of demineralized human enamel in vitro via a nanocomposite containing nanoparticles of amorphous calcium phosphate (NACP). NACP were synthesized by a spray-drying technique and incorporated into a dental resin. First, caries-like subsurface enamel lesions were created via an acidic solution. Then, NACP nanocomposite or a commercial fluoride-releasing control composite was placed on the demineralized enamel, along with control enamel without a composite. These specimens were then treated with a cyclic demineralization/remineralization regimen for 30 days. Quantitative microradiography showed typical enamel subsurface demineralization before cyclic demineralization/remineralization treatment, and significant remineralization in enamel under the NACP nanocomposite after the demineralization/remineralization treatment. The NACP nanocomposite had the highest enamel remineralization (mean ± SD; n = 6) of 21.8 ± 3.7%, significantly higher than the 5.7 ± 6.9% for fluoride-releasing composite (p < 0.05). The enamel group without composite had further demineralization of −26.1 ± 16.2%. In conclusion, a novel NACP nanocomposite was effective in remineralizing enamel lesions in vitro. Its enamel remineralization was 4-fold that of a fluoride-releasing composite control. Combined with the good mechanical and acid-neutralization properties reported earlier, the new NACP nanocomposite is promising for remineralization of demineralized tooth structures. PMID:22933607

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

PubMed

Kinsman-Costello, L E; Sheik, C S; Sheldon, N D; Allen Burton, G; Costello, D M; Marcus, D; Uyl, P A Den; Dick, G J

2017-03-01

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH communities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling. © 2016 John Wiley & Sons Ltd.

The impact of catchment source group classification on the accuracy of sediment fingerprinting outputs.

PubMed

Pulley, Simon; Foster, Ian; Collins, Adrian L

2017-06-01

The objective classification of sediment source groups is at present an under-investigated aspect of source tracing studies, which has the potential to statistically improve discrimination between sediment sources and reduce uncertainty. This paper investigates this potential using three different source group classification schemes. The first classification scheme was simple surface and subsurface groupings (Scheme 1). The tracer signatures were then used in a two-step cluster analysis to identify the sediment source groupings naturally defined by the tracer signatures (Scheme 2). The cluster source groups were then modified by splitting each one into a surface and subsurface component to suit catchment management goals (Scheme 3). The schemes were tested using artificial mixtures of sediment source samples. Controlled corruptions were made to some of the mixtures to mimic the potential causes of tracer non-conservatism present when using tracers in natural fluvial environments. It was determined how accurately the known proportions of sediment sources in the mixtures were identified after unmixing modelling using the three classification schemes. The cluster analysis derived source groups (2) significantly increased tracer variability ratios (inter-/intra-source group variability) (up to 2122%, median 194%) compared to the surface and subsurface groupings (1). As a result, the composition of the artificial mixtures was identified an average of 9.8% more accurately on the 0-100% contribution scale. It was found that the cluster groups could be reclassified into a surface and subsurface component (3) with no significant increase in composite uncertainty (a 0.1% increase over Scheme 2). The far smaller effects of simulated tracer non-conservatism for the cluster analysis based schemes (2 and 3) was primarily attributed to the increased inter-group variability producing a far larger sediment source signal that the non-conservatism noise (1). Modified cluster analysis based classification methods have the potential to reduce composite uncertainty significantly in future source tracing studies. Copyright © 2016 Elsevier Ltd. 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.

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation.

PubMed

Li, Bing; Wu, Wei-Min; Watson, David B; Cardenas, Erick; Chao, Yuanqing; Phillips, D H; Mehlhorn, Tonia; Lowe, Kenneth; Kelly, Shelly D; Li, Pengsong; Tao, Huchun; Tiedje, James M; Criddle, Craig S; Zhang, Tong

2018-05-01

A site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilized in situ through intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A paired t test indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion. Castellaniella had the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing genera Geothrix , Desulfovibrio , Ferribacterium , and Geobacter decreased significantly, whereas the denitrifying Acidovorax abundance increased significantly after groundwater invasion. Additionally, seven genera, i.e., Castellaniella , Ignavibacterium , Simplicispira , Rhizomicrobium , Acidobacteria Gp1, Acidobacteria Gp14, and Acidobacteria Gp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions. IMPORTANCE High-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites. Copyright © 2018 American Society for Microbiology.

Optical method and apparatus for detection of surface and near-subsurface defects in dense ceramics

DOEpatents

Ellingson, W.A.; Brada, M.P.

1995-06-20

A laser is used in a non-destructive manner to detect surface and near-subsurface defects in dense ceramics and particularly in ceramic bodies with complex shapes such as ceramic bearings, turbine blades, races, and the like. The laser`s wavelength is selected based upon the composition of the ceramic sample and the laser can be directed on the sample while the sample is static or in dynamic rotate or translate motion. Light is scattered off surface and subsurface defects using a preselected polarization. The change in polarization angle is used to select the depth and characteristics of surface/subsurface defects. The scattered light is detected by an optical train consisting of a charge coupled device (CCD), or vidicon, television camera which, in turn, is coupled to a video monitor and a computer for digitizing the image. An analyzing polarizer in the optical train allows scattered light at a given polarization angle to be observed for enhancing sensitivity to either surface or near-subsurface defects. Application of digital image processing allows subtraction of digitized images in near real-time providing enhanced sensitivity to subsurface defects. Storing known ``feature masks`` of identified defects in the computer and comparing the detected scatter pattern (Fourier images) with the stored feature masks allows for automatic classification of detected defects. 29 figs.

Investigation of lunar maria structure from cross-analysis of GRAIL gravity and Kaguya radar data

NASA Astrophysics Data System (ADS)

Zuber, M. T.; Ermakov, A.; Smith, D. E.; Mastroguiseppe, M.; Raguso, M.

2016-12-01

The Lunar Radar Sounder (LRS) on JAXA's Kaguya spacecraft investigated the subsurface structure of the Moon to a depth of a few km. GRAIL gravity models are potentially sensitive to subsurface structure at such depths. GRAIL gravity and LRS radar data are complementary since both are sensitive to density/compositional heterogeneities. Cross-correlation of GRAIL and LRS data has the potential to produce new constraints on the structure and evolution of the lunar maria. Originally, subsurface reflections within the lunar maria were detected with Lunar Sounder Experiment aboard Apollo 17. Subsurface layering was attributed to multiple episodes of volcanism. Later, Kaguya's LRS produced similar measurements but with global-scale coverage. Laboratory measurements show that density variations among mare basalts can be up to 200 kg m-3 or 7%. The LRS measurements have detected subsurface reflection in the upper 1 km of the crust. Combining these two estimates and using the Bouguer slab approximation, we estimate that anomalies of order 1-10 mGal are expected due to potentially varying density of surface and/or subsurface horizons. This accuracy is achievable with the latest GRAIL gravity models. The LRS surface backscattering power is indicative of surface and near sub-surface dielectric properties, which are sensitive to target density and roughness. We investigate the northwestern part of the Procellarum basin because it is the region with the strongest signal-to-noise ratios in gravity models within maria. To examine shallow subsurface structure, we map the surface received power by tracking the first return of radar echoes and compare it with gravity gradients, which are particularly sensitive to small-scale structures.

Radar Imaging of Europa's Subsurface Properties and Processes: The View from Earth

NASA Astrophysics Data System (ADS)

Blankenship, D. D.; Moore, W. B.; Young, D. A.; Peters, M. E.

2007-12-01

A primary objective of future Europa studies will be to characterize the distribution of shallow subsurface water as well as to identify any ice-ocean interface. Another objective will be to understand the formation of surface and subsurface features associated with interchange processes between any ocean and the surface. Achieving these objectives will require either direct or inferred knowledge of the position of any ice/water interfaces as well as any brine or layer pockets. We will review the hypothesized processes that control the thermal, compositional and structural (TCS) properties, and therefore the dielectric character, of the subsurface of Europa's icy shell. Our approach will be to extract the TCS properties for various subsurface processes thought to control the formation of major surface (e.g., ridges/bands, lenticulae, chaos, cratering...) and subsurface (e.g., rigid shell eutectics, diapirs, accretionary lenses ...) features on Europa. We will then assess the spectrum of analog processes and TCS properties represented by Earth's cryosphere including both Arctic and Antarctic ice sheets, ice shelves and valley glaciers. There are few complete analogs over the full TCS space but, because of the wide range of ice thickness, impurities and strain rates for Earth's cryosphere, there are many more analogs than many Earth and planetary researchers might imagine for significant portions of this space (e.g., bottom crevasses, marine ice shelf/subglacial lake accretion, surging polythermal glaciers...).Our ultimate objective is to use these Earth analog studies to define the radar imaging approach for Europa's subsurface that will be most useful for supporting/refuting the hypotheses for the formation of major surface/subsurface features as well as for "pure" exploration of Europa's icy shell and its interface with the underlying ocean.

Exobiological Exploration of Europa (E3) Europa Lander

NASA Technical Reports Server (NTRS)

Stillwagen, F. H.; Manvi, Ramachandra; Seywald, Hans; Park, Sang-Young; Kolacinski, Rick

2002-01-01

The search for life outside Earth's protected atmosphere is a compelling testament to the quest by mankind to determine if "we" are alone in the universe. The phenomenal success of the NASA Galileo spacecraft has indicated that the moons of Jupiter, and most notably Europa, may indeed contain subsurface liquid under an icy surface. This speculation of a salty liquid subsurface fuels expert opinions that biological products may exist. The Revolutionary Aerospace Systems Concepts (RASC) effort at Langley Research Center, initiated by NASA Headquarters, pushes NASA and the Aerospace/Science community to target advanced evolutionary technology usage to provide a Europa Lander concept targeted for completion within the next 50 years. The study effort indicates the use of certain advanced technologies to achieve a subsurface penetrator and liquid explorer in the approximately 2040 timeframe.

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.

Pyrosequencing reveals benthic bacteria changes responsing to heavy deposition of Microcystis scum in lab — searching bacteria for bloom control

NASA Astrophysics Data System (ADS)

Tang, Yali; Cheng, Dongmei; Guan, Baohua; Zhang, Xiufeng; Liu, Zhengwen; Liu, Zejun

2017-05-01

Bacteria capable of degrading cyanobacteria Microcystis are crucial for determining the ecological consequences of Microcystis blooms in freshwater lakes. Scum derived from Microcystis blooms tends to accumulate in bays of large lakes and then sink to the sediments where it is finally consumed by benthic bacteria. Understanding the response of benthic bacterial communities to massive Microcystis deposition events may help identify the bacteria best suited to Microcystis hydrolyzation and even bloom control. For that purpose, an experimental system was set up in which intact sediment cores were incubated in the laboratory with normal and heavy deposits of Microcystis detritus. Pyrosequencing was performed in order to describe a phylogenetic inventory of bacterial communities in samples taken at 0-1, 1-2 and 2-3 cm depths in incubated sediments and in original untreated sediment. A hierarchical cluster tree was constructed expose differences between sediments. Similarity percentage calculations were also performed to identify the bacterial species contributing to variation. The results of this study suggest that: (1) deposition of Microcystis scums exerts a strong effect on the bacterial community composition in the surface (0-1 cm) and sub-surface (1-2 cm) sediment layers; (2) bacterial community responses to Microcystis detritus deposition vary across vertical gradients. A list of bacteria with potential roles in Microcystis degradation was compiled. These findings may inform the development of future measures for Microcystis bloom control in lakes.

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

DOE PAGES

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.; ...

2016-05-11

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a 6-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Thus, reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.« less

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

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

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a 6-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Thus, reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.« less

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.

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.

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

DOE PAGES

Hug, Laura A.; Thomas, Brian C.; Sharon, Itai; ...

2015-07-22

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re-construct high-quality draft genomes from complex samples. Here, we applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla withmore » no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin Benson Bassham, Wood Ljungdahl or 3-hydroxyproprionate/4-hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium-oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. Finally, this organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange of geochemical resources.« less

A New Method and Mass-Spectrometric Instrument for Extraterrestrial Microbial Life Detection Using the Elemental Composition Analyses of Martian Regolith and Permafrost/Ice

NASA Astrophysics Data System (ADS)

Managadze, G. G.; Safronova, A. A.; Luchnikov, K. A.; Vorobyova, E. A.; Duxbury, N. S.; Wurz, P.; Managadze, N. G.; Chumikov, A. E.; Khamizov, R. Kh.

2017-05-01

We propose a new technique for the detection of microorganisms by elemental composition analyses of a sample extracted from regolith, permafrost, and ice of extraterrestrial bodies. We also describe the design of the ABIMAS instrument, which consists of the onboard time-of-flight laser mass-reflectron (TOF LMR) and the sample preparation unit (SPU) for biomass extraction. This instrument was initially approved to fly on board the ExoMars 2020 lander mission. The instrument can be used to analyze the elemental composition of possible extraterrestrial microbial communities and compare it to that of terrestrial microorganisms. We have conducted numerous laboratory studies to confirm the possibility of biomass identification via the following biomarkers: P/S and Ca/K ratios, and C and N abundances. We underline that only the combination of these factors will allow one to discriminate microbial samples from geological ones. Our technique has been tested experimentally in numerous laboratory trials on cultures of microorganisms and polar permafrost samples as terrestrial analogues for martian polar soils. We discuss various methods of extracting microorganisms and sample preparation. The developed technique can be used to search for and identify microorganisms in different martian samples and in the subsurface of other planets, satellites, comets, and asteroids—in particular, Europa, Ganymede, and Enceladus.

Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia

PubMed Central

Gérard, Emmanuelle; Moreira, David; Philippot, Pascal; Van Kranendonk, Martin J.; López-García, Purificación

2009-01-01

Background Several abiotic processes leading to the formation of life-like signatures or later contamination with actual biogenic traces can blur the interpretation of the earliest fossil record. In recent years, a large body of evidence showing the occurrence of diverse and active microbial communities in the terrestrial subsurface has accumulated. Considering the time elapsed since Archaean sedimentation, the contribution of subsurface microbial communities postdating the rock formation to the fossil biomarker pool and other biogenic remains in Archaean rocks may be far from negligible. Methodology/Principal Findings In order to evaluate the degree of potential contamination of Archean rocks by modern microorganisms, we looked for the presence of living indigenous bacteria in fresh diamond drillcores through 2,724 Myr-old stromatolites (Tumbiana Formation, Fortescue Group, Western Australia) using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). We analyzed drillcore samples from 4.3 m and 66.2 m depth, showing signs of meteoritic alteration, and also from deeper “fresh” samples showing no apparent evidence for late stage alteration (68 m, 78.8 m, and 99.3 m). We also analyzed control samples from drilling and sawing fluids and a series of laboratory controls to establish a list of potential contaminants introduced during sample manipulation and PCR experiments. We identified in this way the presence of indigenous bacteria belonging to Firmicutes, Actinobacteria, and Alpha-, Beta-, and Gammaproteobacteria in aseptically-sawed inner parts of drillcores down to at least 78.8 m depth. Conclusions/Significance The presence of modern bacterial communities in subsurface fossil stromatolite layers opens the possibility that a continuous microbial colonization had existed in the past and contributed to the accumulation of biogenic traces over geological timescales. This finding casts shadow on bulk analyses of early life remains and makes claims for morphological, chemical, isotopic, and biomarker traces syngenetic with the rock unreliable in the absence of detailed contextual analyses at microscale. PMID:19396360

Single step transformation of sulphur to Li2S2/Li2S in Li-S batteries

PubMed Central

Helen, M.; Reddy, M. Anji; Diemant, Thomas; Golla-Schindler, Ute; Behm, R. Jürgen; Kaiser, Ute; Fichtner, Maximilian

2015-01-01

Lithium-sulphur batteries have generated tremendous research interest due to their high theoretical energy density and potential cost-effectiveness. The commercial realization of Li-S batteries is still hampered by reduced cycle life associated with the formation of electrolyte soluble higher-order polysulphide (Li2Sx, x = 4–8) intermediates, leading to capacity fading, self-discharge, and a multistep voltage profile. Herein, we have realized a practical approach towards a direct transformation of sulphur to Li2S2/Li2S in lithium-sulphur batteries by alteration of the reaction pathway. A coconut shell derived ultramicroporous carbon-sulphur composite cathode has been used as reaction directing template for the sulphur. The lithiation/delithiation and capacity fading mechanism of microporous carbon confined sulphur composite was revealed by analyzing the subsurface using X-ray photoelectron spectroscopy. No higher-order polysulphides were detected in the electrolyte, on the surface, and in the subsurface of the cathode composite. The altered reaction pathway is reflected by a single-step profile in the discharge/charge of a lithium-sulphur cell. PMID:26173723

Is the genetic landscape of the deep subsurface biosphere affected by viruses?

PubMed

Anderson, Rika E; Brazelton, William J; Baross, John A

2011-01-01

Viruses are powerful manipulators of microbial diversity, biogeochemistry, and evolution in the marine environment. Viruses can directly influence the genetic capabilities and the fitness of their hosts through the use of fitness factors and through horizontal gene transfer. However, the impact of viruses on microbial ecology and evolution is often overlooked in studies of the deep subsurface biosphere. Subsurface habitats connected to hydrothermal vent systems are characterized by constant fluid flux, dynamic environmental variability, and high microbial diversity. In such conditions, high adaptability would be an evolutionary asset, and the potential for frequent host-virus interactions would be high, increasing the likelihood that cellular hosts could acquire novel functions. Here, we review evidence supporting this hypothesis, including data indicating that microbial communities in subsurface hydrothermal fluids are exposed to a high rate of viral infection, as well as viral metagenomic data suggesting that the vent viral assemblage is particularly enriched in genes that facilitate horizontal gene transfer and host adaptability. Therefore, viruses are likely to play a crucial role in facilitating adaptability to the extreme conditions of these regions of the deep subsurface biosphere. We also discuss how these results might apply to other regions of the deep subsurface, where the nature of virus-host interactions would be altered, but possibly no less important, compared to more energetic hydrothermal systems.

Is the Genetic Landscape of the Deep Subsurface Biosphere Affected by Viruses?

PubMed Central

Anderson, Rika E.; Brazelton, William J.; Baross, John A.

2011-01-01

Viruses are powerful manipulators of microbial diversity, biogeochemistry, and evolution in the marine environment. Viruses can directly influence the genetic capabilities and the fitness of their hosts through the use of fitness factors and through horizontal gene transfer. However, the impact of viruses on microbial ecology and evolution is often overlooked in studies of the deep subsurface biosphere. Subsurface habitats connected to hydrothermal vent systems are characterized by constant fluid flux, dynamic environmental variability, and high microbial diversity. In such conditions, high adaptability would be an evolutionary asset, and the potential for frequent host–virus interactions would be high, increasing the likelihood that cellular hosts could acquire novel functions. Here, we review evidence supporting this hypothesis, including data indicating that microbial communities in subsurface hydrothermal fluids are exposed to a high rate of viral infection, as well as viral metagenomic data suggesting that the vent viral assemblage is particularly enriched in genes that facilitate horizontal gene transfer and host adaptability. Therefore, viruses are likely to play a crucial role in facilitating adaptability to the extreme conditions of these regions of the deep subsurface biosphere. We also discuss how these results might apply to other regions of the deep subsurface, where the nature of virus–host interactions would be altered, but possibly no less important, compared to more energetic hydrothermal systems. PMID:22084639

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.

Marine biogeochemistry: Methylmercury manufacture

NASA Astrophysics Data System (ADS)

Cossa, Daniel

2013-10-01

The neurotoxin methylmercury can accumulate in marine food webs, contaminating seafood. An analysis of the isotopic composition of fish in the North Pacific suggests that much of the mercury that enters the marine food web originates from low-oxygen subsurface waters.

Sources of dissolved salts in the central Murray Basin, Australia

USGS Publications Warehouse

Jones, B.F.; Hanor, J.S.; Evans, W.R.

1994-01-01

Large areas of the Australian continent contain scattered saline lakes underlain by shallow saline groundwaters of regional extent and debated origin. The normative salt composition of subsurface pore fluids extracted by squeezing cores collected during deep drilling at Piangil West 2 in the central Murray Basin in southeastern Australia, and of surface and shallow subsurface brines produced by subaerial evaporation in the nearby Lake Tyrrell systems, helps constrain interpretation of the origin of dissolved solutes in the groundwaters of this part of the continent. Although regional sedimentation in the Murray Basin has been dominantly continental except for a marine transgression in Oligocene-Pliocene time, most of the solutes in saline surface and subsurface waters in the central Murray Basin have a distinctly marine character. Some of the Tyrrell waters, to the southwest of Piangil West 2, show the increase in NaCl and decrease in sulfate salts expected with evaporative concentration and gypsum precipitation in an ephemeral saline lake or playa environment. The salt norms for most of the subsurface saline waters at Piangil West 2 are compatible with the dilution of variably fractionated marine bitterns slightly depleted in sodium salts, similar to the more evolved brines at Lake Tyrrell, which have recharged downward after evaporation at the surface and then dissolved a variable amount of gypsum at depth. Apparently over the last 0.5 Ma significant quantities of marine salt have been blown into the Murray Basin as aerosols which have subsequently been leached into shallow regional groundwater systems basin-wide, and have been transported laterally into areas of large evaporative loss in the central part of the basin. This origin for the solutes helps explain why the isotopic compositions of most of the subsurface saline waters at Piangil West 2 have a strong meteoric signature, whereas the dissolved salts in these waters appear similar to a marine assemblage. ?? 1994.

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.

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

Oxidative particle mixtures for groundwater treatment

DOEpatents

Siegrist, Robert L.; Murdoch, Lawrence C.

2000-01-01

The invention is a method and a composition of a mixture for degradation and immobilization of contaminants in soil and groundwater. The oxidative particle mixture and method includes providing a material having a minimal volume of free water, mixing at least one inorganic oxidative chemical in a granular form with a carrier fluid containing a fine grained inorganic hydrophilic compound and injecting the resulting mixture into the subsurface. The granular form of the inorganic oxidative chemical dissolves within the areas of injection, and the oxidative ions move by diffusion and/or advection, therefore extending the treatment zone over a wider area than the injection area. The organic contaminants in the soil and groundwater are degraded by the oxidative ions, which form solid byproducts that can sorb significant amounts of inorganic contaminants, metals, and radionuclides for in situ treatment and immobilization of contaminants. The method and composition of the oxidative particle mixture for long-term treatment and immobilization of contaminants in soil and groundwater provides for a reduction in toxicity of contaminants in a subsurface area of contamination without the need for continued injection of treatment material, or for movement of the contaminants, or without the need for continuous pumping of groundwater through the treatment zone, or removal of groundwater from the subsurface area of contamination.

Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

NASA Astrophysics Data System (ADS)

Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun-ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken

2013-07-01

We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations) was nearly constant (250 μM) throughout the stream. Based on the level of detectable dissolved molecular oxygen (O2) of the stream water (⩾38 μM) along with metabolic measurements, it was predicted that nitrification by thermophilic AOA and NOB components in the microbial mats that were exposed to the stream water would constrain the concentrations and isotopic ratios of ΣNH3, NO2- and NO3- of the stream water. The δ15N value of ΣNH3 increased from 0‰ to 7‰ with decreasing concentration, which was consistent with the previously reported isotopic fractionation for microbial ΣNH3 oxidation. In contrast, the δ15N value of NO2- was 22‰ lighter than that of NO3- in the steam water at the same site, indicating an inverse isotopic fractionation for microbial NO2- oxidation. The variation in concentrations and δ15N values of ΣNH3, NO2- and NO3- was largely explained using a two-step nitrification model, and the apparent nitrogen isotopic fractionations of ΣNH3 oxidation and NO2- oxidation were estimated to be 0.986 and 1.020, respectively. In the interstitial water within the microbial mats, the compositional and isotopic properties of TIN at the downstream site indicated potential denitrification by the anaerobic microbial components. The geochemically deduced transition of microbial nitrogen metabolism was substantiated through cultivation-independent microbiological analyses.

Imaging in vivo secondary caries and ex vivo dental biofilms using cross-polarization optical coherence tomography

PubMed Central

Lenton, Pat; Rudney, Joel; Chen, Ruoqiong; Fok, Alex; Aparicio, Conrado; Jones, Robert S.

2012-01-01

Objectives Conventional diagnostic methods frequently detect only late stage enamel demineralization under composite resin restorations. The objective of this study is to examine the subsurface tooth-composite interface and to assess for the presence of secondary caries in pediatric patients using a novel Optical Coherence Tomography System with an intraoral probe. Methods A newly designed intraoral cross polarization swept source optical coherence tomography (CP-OCT) imaging system was used to examine the integrity of the enamel-composite interfaces in vivo. Twenty two pediatric subjects were recruited with either recently placed or long standing composite restorations in their primary teeth. To better understand how bacterial biofilms cause demineralization at the interface, we also used the intraoral CP-OCT system to assess ex vivo bacterial biofilm growth on dental composites. Results As a positive control, cavitated secondary carious interfaces showed a 18.2 dB increase (p<0.001), or over 1-2 orders of magnitude higher, scattering than interfaces associated with recently placed composite restorations. Several long standing composite restorations, which appeared clinically sound, had a marked increase in scattering than recently placed restorations. This suggests the ability of CP-OCT to assess interfacial degradation such as early secondary caries prior to cavitation. CP-OCT was also able to image ex vivo biofilms on dental composites and assess their thickness. Significance This paper shows that CP-OCT imaging using a beam splitter based design can examine the subsurface interface of dental composites in human subjects. Furthermore, the probe dimensions and acquisition speed of the CP-OCT system allowed for analysis of caries development in children. PMID:22578989

Application of an in-situ soil sampler for assessing subsurface biogeochemical dynamics in a diesel-contaminated coastal site during soil flushing operations.

PubMed

Kwon, Man Jae; O'Loughlin, Edward J; Ham, Baknoon; Hwang, Yunho; Shim, Moojoon; Lee, Soonjae

2018-01-15

Subsurface biogeochemistry and contaminant dynamics during the remediation of diesel-contamination by in-situ soil flushing were investigated at a site located in a coastal region. An in-situ sampler containing diesel-contaminated soils separated into two size fractions (<0.063- and <2-mm) was utilized in two monitoring wells: DH1 (located close to the injection and extraction wells for in-situ soil flushing) and DH2 (located beyond sheet piles placed to block the transport of leaked diesel). Total petroleum hydrocarbon (TPH) concentrations and biogeochemical properties were monitored both in soil and groundwater for six months. A shift occurred in the groundwater type from Ca-HCO 3 to Na-Cl due to seawater intrusion during intense pumping, while the concentrations of Ni, Cu, Co, V, Cr, and Se increased substantially following surfactant (TWEEN 80) injection. The in-situ sampler with fine particles was more sensitive to variations in conditions during the remedial soil flushing process. In both wells, soil TPH concentrations in the <0.063-mm fraction were much higher than those in the <2-mm fraction. Increases in soil TPH in DH1 were consistent with the expected outcomes following well pumping and surfactant injection used to enhance TPH extraction. However, the number of diesel-degrading microorganisms decreased after surfactant injection. 16S-rRNA gene-based analysis also showed that the community composition and diversity depended on both particle size and diesel contamination. The multidisciplinary approach to the contaminated site assessments showed that soil flushing with surfactant enhanced diesel extraction, but negatively impacted in-situ diesel biodegradation as well as groundwater quality. The results also suggest that the in-situ sampler can be an effective monitoring tool for subsurface biogeochemistry as well as contaminant dynamics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evidence of remediation-induced alteration of subsurface poly- and perfluoroalkyl substance distribution at a former firefighter training area.

PubMed

McGuire, Meghan E; Schaefer, Charles; Richards, Trenton; Backe, Will J; Field, Jennifer A; Houtz, Erika; Sedlak, David L; Guelfo, Jennifer L; Wunsch, Assaf; Higgins, Christopher P

2014-06-17

Poly- and perfluoroalkyl substances (PFASs) are a class of fluorinated chemicals that are utilized in firefighting and have been reported in groundwater and soil at several firefighter training areas. In this study, soil and groundwater samples were collected from across a former firefighter training area to examine the extent to which remedial activities have altered the composition and spatial distribution of PFASs in the subsurface. Log Koc values for perfluoroalkyl acids (PFAAs), estimated from analysis of paired samples of groundwater and aquifer solids, indicated that solid/water partitioning was not entirely consistent with predictions based on laboratory studies. Differential PFAA transport was not strongly evident in the subsurface, likely due to remediation-induced conditions. When compared to the surface soil spatial distributions, the relative concentrations of perfluorooctanesulfonate (PFOS) and PFAA precursors in groundwater strongly suggest that remedial activities altered the subsurface PFAS distribution, presumably through significant pumping of groundwater and transformation of precursors to PFAAs. Additional evidence for transformation of PFAA precursors during remediation included elevated ratios of perfluorohexanesulfonate (PFHxS) to PFOS in groundwater near oxygen sparging wells.

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.

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

Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments.

PubMed

Wang, Yanping; Wiatrowski, Heather A; John, Ria; Lin, Chu-Ching; Young, Lily Y; Kerkhof, Lee J; Yee, Nathan; Barkay, Tamar

2013-02-01

The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress. We observed an inverse relationship between Hg concentrations and onset and rates of denitrification in nitrate enrichment cultures containing between 53 and 1.1 μM of inorganic Hg; higher Hg concentrations increasingly extended the time to onset of denitrification and inhibited denitrification rates. Microbial community complexity, as indicated by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA genes, declined with increasing Hg concentrations; at the 312 nM Hg treatment, a single tRFLP peak was detected representing a culture of Bradyrhizobium sp. that possessed the merA gene indicating a potential for Hg reduction. A culture identified as Bradyrhizobium sp. strain FRC01 with an identical 16S rRNA sequence to that of the enriched peak in the tRFLP patterns, reduced Hg(II) to Hg(0) and carried merA whose amino acid sequence has 97 % identity to merA from the Proteobacteria and Firmicutes. This study demonstrates that in subsurface sediment incubations, Hg may inhibit denitrification and that inhibition may be alleviated when Hg resistant denitrifying Bradyrhizobium spp. detoxify Hg by its reduction to the volatile elemental form.

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

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

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane andmore » CO 2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH 4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO 2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems.« less

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

DOE PAGES

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.; ...

2017-02-27

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane andmore » CO 2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH 4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO 2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems.« less

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

PubMed Central

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.; Kellermann, Matthias Y.; Redmond, Molly C.; Andersen, Gary L.; Valentine, David L.

2017-01-01

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane and CO2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems. PMID:28289403

Sedimentological context of the continental sabkhas of Abu Dhabi

NASA Astrophysics Data System (ADS)

Lokier, Stephen; Paul, Andreas; Bixiao, Xin

2017-04-01

For more than half a century, the coastal sabkhas of Abu Dhabi have been the focus of intensive research focusing on deposition, early diagenesis and the role of microbial communities. Given all of this activity, it is somewhat surprising that their continental counterparts have been largely neglected with only a brief mention in larger-scale regional studies. This study redresses this imbalance by documenting the sedimentological, mineralogical and early diagenetic characteristics of continental sabkhas that are hosted in the Rub al Khali desert of the United Arab Emirates. During reconnaissance surveys it has been established that organic-rich microbial mats and evaporite minerals, both similar to those observed in the coastal sabkha, also occur in these continental sabkha settings. Satellite imagery was utilised to identify potential field locations for surface and shallow sub surface investigation; subsequent field reconnaissance established the validity of sites in terms of anthropogenic disruption and accessibility. At each site, surface features were described in detail, particularly with reference to any microbial communities or evaporite crusts; sample pits were dug in order to document sub-surface facies geometries and to recover both sediment and pore water samples for subsequent analysis. In each pit, a range of environmental parameters was measured over a prolonged period, including surface and sub-surface temperatures, ground water salinity and dissolved oxygen. Sediment samples were subjected to a range of analyses in order to establish and quantify primary sediment composition and any early diagenetic mineral phases. The results of this study are used to build an atlas of sedimentary structures and textures that are associated with continental sabkha settings. These observations allow us to establish the defining sedimentological and early diagenetic characteristics that can be employed to identify similar depositional environments in ancient successions. This will, ultimately, enable the development of better reservoir models, in terms of lateral and vertical depositional and petrophysical facies variability, and fluid flow.

Composition and Maturity of Apollo 16 Regolith Core 60013/14

NASA Technical Reports Server (NTRS)

Korotev, Randy T.; Morris, Richard V.

1993-01-01

Samples from every half-centimeter dissection interval of double drive tube 60013/14 (sections 60013 and 60014) were analyzed by magnetic techniques for Fe concentration and surface maturity parameter I(sub s)/ Fe(O), and by neutron activation for concentrations of 25 lithophile and siderophile elements. Core 60013/14 is one of three regolith cores taken in a triangular array 40-50 m apart on the Cayley plains during Apollo 16 mission to the Moon. The core can be divided into three zones based both on I(sub s)/FeO and composition. Unit A (0-44 cm depth) is compositionally similar to other soils from the surface of the central region of the site and is mature throughout, although maturity decreases with depth. Unit B (44-59 cm) is submature and compositionally more feldspathic than Unit A. Regions of lowest maturity in Unit B are characterized by lower Sm/Sc ratios than any soil obtained from the Cayley plains as a result of some unidentified lithologic component with low surface maturity. The component is probably some type of mafic anorthosite that does not occur in such high abundance in any of the other returned soils. Unit C (59-62 cm) is more mature than Unit B and compositionally equivalent to an 87: 13 mixture of soil such as that from Unit A and plagioclase such as found in ferroan anorthosite. Similar soils, but containing greater abundances of anorthosite (plagioclase), are found at depth in the other two cores of the array. These units of immature to submature soil enriched to varying degrees (compared to the mature surface soil) in ferroan anorthosite consisting of approx. 99% plagioclase are the only compositionally distinct subsurface similarities among the three cores. Each of the cores contains other units that are compositionally dissimilar to any soil unit in the other two cores. These compositionally distinct units probably derive from local subsurface blocks deposited by the event(s) that formed the Cayley plains. The ferroan anorthosite with approx. 99% plagioclase, however, must represent some subsurface lithology that is significant on the scale of tens of meters. The compositional uniformity of the surface soil (0-10 cm depth) over distances of kilometers reflects the large-scale uniformity of the plains deposits; the fine- structure reflects small-scale nonuniformity and the inefficiency of the impact-mixing process at depths as shallow as even one meter.

Low-Angle Radar Tracking

DTIC Science & Technology

1976-02-01

Transition from Specular Reflection to Diffuse Scattering. . . 10 Composition of the Electric-Field Vector as Seen at the Radar...r t (16) R • FIGURE P COMPOSITION OF THE ELECTRIC-FIELD VECTOR AS SEEN AT THE RADAR, R, IN FIG. 2. The electric field at the radar, E, is the sum...wavelengths in the VHP and UHF ranges even subsurface characteristics can be important. So in a field experiment one must be careful to measure

[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.

Public perceptions of geology

NASA Astrophysics Data System (ADS)

Gibson, Hazel; Stewart, Iain; Anderson, Mark; Pahl, Sabine; Stokes, Alison

2014-05-01

Geological issues are increasingly intruding on the everyday lives of ordinary people. Whether it be onshore exploration and extraction of oil and gas, deep injection of water for geothermal power or underground storage of carbon dioxide and radioactive waste, many communities across Europe are being faced with potentially contested geological activity under their backyard. As well as being able to communicate the technical aspects of such work, geoscience professionals also need to appreciate that for most people the subsurface is an unfamiliar realm. In order to engage communities and individuals in effective dialogue about geological activities, an appreciation of what 'the public' already know and what they want to know is needed, but this is a subject that is in its infancy. In an attempt to provide insight into these key issues, this study examines the concerns the public have, relating to geology, by constructing 'Mental Models' of people's perceptions of the subsurface. General recommendations for public engagement strategies will be presented based on the results of selected case studies; specifically expert and non-expert mental models for communities in the south-west of England.

Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages

PubMed Central

Durbin, Alan M.; Teske, Andreas

2012-01-01

Examining the patterns of archaeal diversity in little-explored organic-lean marine subsurface sediments presents an opportunity to study the association of phylogenetic affiliation and habitat preference in uncultured marine Archaea. Here we have compiled and re-analyzed published archaeal 16S rRNA clone library datasets across a spectrum of sediment trophic states characterized by a wide range of terminal electron-accepting processes. Our results show that organic-lean marine sediments in deep marine basins and oligotrophic open ocean locations are inhabited by distinct lineages of archaea that are not found in the more frequently studied, organic-rich continental margin sediments. We hypothesize that different combinations of electron donor and acceptor concentrations along the organic-rich/organic-lean spectrum result in distinct archaeal communities, and propose an integrated classification of habitat characteristics and archaeal community structure. PMID:22666218

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

Study of the Martian Subsurface with a Fiber Optics Spectrometer: the Ma_Miss Experiment

NASA Astrophysics Data System (ADS)

Coradini, A.; de Sanctis, M. C.; Ammannito, E.; Boccaccini, A.; Battistelli, E.; Capanni, A.

2009-04-01

In this presentation is described the investigation that we intend to do with a small imaging spectrometer that will be inserted in the drill of the Exomars- Pasteur rover. This spectrometer is named Ma_miss (Mars Multispectral Imager for Subsurface Studies ). The Ma_Miss experiment is located in the drill ,that will be able to make a hole in the Mars soil and rock up to 2 m. Ma_Miss includes the optical head of the spectrometer, a lamp to illuminate the borehole walls, and the optical fiber that brings the signal to the spectrometer. The multispectral images are acquired by means of a sapphire window placed on the lateral wall of the drill tool, as close as possible to the drill head. The images are gathered by means of an optical fibre system and analyzed using the spectrometer. The Ma_Miss gathered light containing the scientific information is transferred to the array detector and electronics of the instrument by means of an optical rotary joint implemented in the roto-translation group of the drill, as shown in the next pictures In the figure is schematically represented the Ma_Miss- Dibs architecture. This experiment will be extremely valuable since it will allow, for the first time, to have an idea of the mineralogical composition of the Martian subsurface and to study freshly cut rocks. The study of surface and subsurface mineralogy of Martian soil and rocks is the key for understanding the chemico-physical processes that led to the formation and evolution of the Red Planet. The history of the water and other volatiles, as well as the signatures of weathering processes are important to understand present and past environmental conditions associated with the possibility of life. Surface samples are highly influenced by exogenous processes (weathering, erosion, sedimentation, impact) that alter their original properties. So, the analyses of uncontaminated samples by means of instrumented drills and in situ analytic stations are the key for unambiguous interpretation of the original environment that leading to the formation of rocks. Analysis of subsurface layers is the only approach that warranties measurements on samples close to their original composition. The upper few meters of the surface materials on Mars play a crucial role in its history, providing important constraints geologic, hydrologic, and climatic to the history of the planet. Drilling into the near-surface crust will provide an opportunity to assess variations in composition, texture, stratification, unconformities, etc. that will help define its lithology and structure, and provide important clues regarding its origin and subsequent evolution. The subsurface material can give information on the evolution of surface sediments (erosion, transport, deposition), on the relation between sediments and bedrock, on the relation between environmental conditions and surface processes permitting to "investigate planetary processes that influence habitability." Investigation of mineralogical composition of near-surface geological materials is needed to fully characterize the geology of the regions that will be visited by the Rover at all appropriate spatial scales, and to interpret the processes that have formed and modified rocks and regolith. Subsurface access, sampling material below the oxidized layer, can be the key to "assess the biological potential of the target environment (past or present)". To date, we have direct observations relative only to the Martian surface. Little is known about the characteristics of the first subsurface layers. The possibility to sample subsurface materials to be delivered to other instruments, and to record the context of the sampled soil doing in situ borehole mineralogical analysis, is fundamental to search for traces of past or present life on Mars. The spectrometer observes a single point target, having 0.1 mm diameter, on the borehole wall surface. Depending on the surface features we are interested in, the observation window can scan the borehole's surface by means of drill tip rotation or translation. When the drill is translated, a "Column Image" is acquired. This translation step can be equal to the observation spot (0.1 mm). The "Ring Image" can be obtained by rotation of the drill tip; a rotation step of about 0.5˚ (corresponding to 720 acquisitions in the ring) is sufficient to assure the full coverage of the ring.

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

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments.

PubMed

Engelhardt, Tim; Kallmeyer, Jens; Cypionka, Heribert; Engelen, Bert

2014-07-01

Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (∼14 Ma old) and the most oligotrophic subsurface sediments of the world's oceans (South Pacific Gyre (SPG)). The numbers of viruses (10(4)-10(9) cm(-3), counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.

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

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.

Antarctic Mirabilite Mounds as Mars Analogs: The Lewis Cliffs Ice Tongue Revisited

NASA Technical Reports Server (NTRS)

Socki, Richard A.; Sun, Tao; Niles, Paul B.; Harvey, Ralph P.; Bish, David L.; Tonui, Eric

2012-01-01

It has been proposed, based on geomorphic and geochemical arguments, that subsurface water has played an important role in the history of water on the planet Mars [1]. Subsurface water, if present, could provide a protected and long lived environment for potential life. Discovery of gullies [2] and recurring slopes [3] on Mars suggest the potential for subsurface liquid water or brines. Recent attention has also focused on small (< approx. 1km dia.) mound-like geomorphic features discovered within the mid to high latitudes on the surface of Mars which may be caused by eruptions of subsurface fluids [4, 5]. We have identified massive but highly localized Na-sulfate deposits (mirabilite mounds, Na2SO4 .10H2O) that may be derived from subsurface fluids and may provide insight into the processes associated with subsurface fluids on Mars. The mounds are found on the end moraine of the Lewis Cliffs Ice Tongue (LCIT) [6] in the Transantarctic Mountains, Antarctica, and are potential terrestrial analogs for mounds observed on the martian surface. The following characteristics distinguish LCIT evaporite mounds from other evaporite mounds found in Antarctic coastal environments and/or the McMurdo Dry Valleys: (1) much greater distance from the open ocean (approx.500 km); (2) higher elevation (approx.2200 meters); and (3) colder average annual temperature (average annual temperature = -30 C for LCIT [7] vs. 20 C at sea level in the McMurdo region [8]. Furthermore, the recent detection of subsurface water ice (inferred as debris-covered glacial ice) by the Mars Reconnaissance Orbiter [9] supports the use of an Antarctic glacial environment, particularly with respect to the mirabilite deposits described in this work, as an ideal terrestrial analog for understanding the geochemistry associated with near-surface martian processes. S and O isotopic compositions.

Effect of recirculation on organic matter removal in a hybrid constructed wetland system.

PubMed

Ayaz, S C; Findik, N; Akça, L; Erdoğan, N; Kinaci, C

2011-01-01

This research project aimed to determine the technologically feasible and applicable wastewater treatment systems which will be constructed to solve environmental problems caused by small communities in Turkey. Pilot-scale treatment of a small community's wastewater was performed over a period of more than 2 years in order to show applicability of these systems. The present study involves removal of organic matter and suspended solids in serially operated horizontal (HFCW) and vertical (VFCW) sub-surface flow constructed wetlands. The pilot-scale wetland was constructed downstream of anaerobic reactors at the campus of TUBITAK-MRC. Anaerobically pretreated wastewater was introduced into this hybrid two-stage sub-surface flow wetland system (TSCW). Wastewater was first introduced into the horizontal sub-surface flow system and then the vertical flow system before being discharged. Recirculation of the effluent was tested in the system. When the recirculation ratio was 100%, average removal efficiencies for TSCW were 91 +/- 4% for COD, 83 +/- 10% for BOD and 96 +/- 3% for suspended solids with average effluent concentrations of 9 +/- 5 mg/L COD, 6 +/- 3 mg/L BOD and 1 mg/L for suspended solids. Comparing non-recirculation and recirculation periods, the lowest effluent concentrations were obtained with a 100% recirculation ratio. The effluent concentrations met the Turkish regulations for discharge limits of COD, BOD and TSS in each case. The study showed that a hybrid constructed wetland system with recirculation is a very effective method of obtaining very low effluent organic matter and suspended solids concentrations downstream of anaerobic pretreatment of domestic wastewaters in small communities.

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.

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.

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

Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification.

PubMed

Theisen, C Harwood; Sumner, D Y; Mackey, T J; Lim, D S S; Brady, A L; Slater, G F

2015-07-01

Modern microbialites in Pavilion Lake, BC, provide an analog for ancient non-stromatolitic microbialites that formed from in situ mineralization. Because Pavilion microbialites are mineralizing under the influence of microbial communities, they provide insights into how biological processes influence microbialite microfabrics and mesostructures. Hemispherical nodules and micrite-microbial crusts are two mesostructures within Pavilion microbialites that are directly associated with photosynthetic communities. Both filamentous cyanobacteria in hemispherical nodules and branching filamentous green algae in micrite-microbial crusts were associated with calcite precipitation at microbialite surfaces and with characteristic microfabrics in the lithified microbialite. Hemispherical nodules formed at microbialite surfaces when calcite precipitated around filamentous cyanobacteria with a radial growth habit. The radial filament pattern was preserved within the microbialite to varying degrees. Some subsurface nodules contained well-defined filaments, whereas others contained only dispersed organic inclusions. Variation in filament preservation is interpreted to reflect differences in timing and amount of carbonate precipitation relative to heterotrophic decay, with more defined filaments reflecting greater lithification prior to degradation than more diffuse filaments. Micrite-microbial crusts produce the second suite of microfabrics and form in association with filamentous green algae oriented perpendicular to the microbialite surface. Some crusts include calcified filaments, whereas others contained voids that reflect the filamentous community in shape, size, and distribution. Pavilion microbialites demonstrate that microfabric variation can reflect differences in lithification processes and microbial metabolisms as well as microbial community morphology and organization. Even when the morphology of individual filaments or cells is not well preserved, the microbial growth habit can be captured in mesoscale microbialite structures. These results suggest that when petrographic preservation is extremely good, ancient microbialite growth structures and microfabrics can be interpreted in the context of variation in community organization, community composition, and lithification history. Even in the absence of distinct microbial microfabrics, mesostructures can capture microbial community morphology. © 2015 John Wiley & Sons Ltd.

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.

Compositional and Textural Analysis of Maar-Diatreme Volcanic Deposits at Hopi Buttes Volcanic Field (AZ) Using GigaPan Panoramic and Thermal Infrared Imagery

NASA Astrophysics Data System (ADS)

Lee, R.; Graettinger, A. H.; Weinell, M.; Hughes, C. G.

2016-12-01

Basaltic maar-diatreme volcanoes are produced when rising magma interacts with groundwater and produces a maar crater at the ground surface. This crater is underlain by a diatreme, a downward-tapering conical structure filled with a mixture of fragments of intruded magma, fractured host rock, and clasts recycled through repeated discrete subsurface explosions. The debris of the diatreme records the mixing processes caused by subsurface explosions and is the source for ejected material that forms maar tephra rings. Determining the variable depths and lateral locations of these explosions and how energy is dissipated in the subsurface is critical to understanding how maar-diatreme eruptions progress. The Hopi Buttes Volcanic Field (HBVF) in the Navajo Nation, Arizona, USA, contains several diatremes and incised tephra rings with heterolithic clasts 10 mm - 10 m in size, and are well-exposed near-vertical to vertical outcrops. Our ability to measure the length scales and distribution of textures produced by subsurface explosions in these diatremes is limited by the physical accessibility of the exposures, due to both the verticality of the outcrops and the cultural sensitivity of the site. Quantifying the number and locations of explosions is dependent on our ability to investigate the full diatreme outcrop, and not just what can be accessed through traditional field observations. We present a novel field and computer-based technique for both quantitatively and qualitatively characterizing the composition and texture of maar-diatreme deposits in vertical outcrops. This technique uses a combination of field-collected multispectral thermal infrared (TIR) image data and visible wavelength GigaPan imagery to characterize the compositional and textural variations over a whole outcrop. To increase the spatial and spectral resolution of the TIR data, a super-resolution technique will be applied. The technique provides a simple and efficient method to augment the study of the maar-diatreme deposits at HBVF. In addition to contributing to a better understanding of the formation processes of maar-diatreme deposits around the world, the technique also shows great promise for studies involving other types of large outcrops and geologic structures.

An assessment of microbial communities associated with surface mining-disturbed overburden.

PubMed

Poncelet, Dominique M; Cavender, Nicole; Cutright, Teresa J; Senko, John M

2014-03-01

To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16 years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16 years and 37 years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37 years of overburden maturation.

Kinetics of conjugative gene transfer on surfaces in granular porous media

NASA Astrophysics Data System (ADS)

Massoudieh, A.; Crain, C.; Lambertini, E.; Nelson, K. E.; Barkouki, T.; L'Amoreaux, P.; Loge, F. J.; Ginn, T. R.

2010-03-01

The transfer of genetic material among bacteria in the environment can occur both in the planktonic and attached state. Given the propensity of organisms to exist in sessile microbial communities in oligotrophic subsurface conditions, and that such conditions typify the subsurface, this study focuses on exploratory modeling of horizontal gene transfer among surface-associated Escherichiacoli in the subsurface. The mathematics so far used to describe the kinetics of conjugation in biofilms are developed largely from experimental observations of planktonic gene transfer, and are absent of lags or plasmid stability that appear experimentally. We develop a model and experimental system to quantify bacterial filtration and gene transfer in the attached state, on granular porous media. We include attachment kinetics described in Nelson et al. (2007) using the filtration theory approach of Nelson and Ginn (2001, 2005) with motility of E. coli described according to Biondi et al. (1998).

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.

Ocean response to typhoons in the western North Pacific: Composite results from Argo data

NASA Astrophysics Data System (ADS)

Lin, Sheng; Zhang, Wen-Zhou; Shang, Shao-Ping; Hong, Hua-Sheng

2017-05-01

Composite structures of ocean temperature and salinity anomalies caused by tropical cyclones (TCs) or typhoons in the western North Pacific Ocean were obtained from Argo data. These structures were used to analyze ocean responses to typhoons and the dynamic mechanisms inherent in those responses with a particular focus on upwelling. TC-induced cooling is often strongly rightward-biased in the surface layer, and shifts toward the typhoon track at depths exceeding roughly 100 m. In the central water column within approximately 75 km of the typhoon track, subsurface warming predicted by vertical mixing is restrained and replaced by cooling due to upwelling. Upwelling contributes 15% on average to temperature cooling in the near surface layer (10-30 m), 84% in the subsurface layer (30-250 m) and 94% in the deep layer (250-600 m) during the period of 0.5-2.5 days after the typhoon's passage. It is suggested that the sea surface cooling effect of vertical mixing can be enhanced by the upwelling. The effect of upwelling is also prominent in the salinity response to typhoons. The composite results from the Argo data clearly reveal basic ocean responses to typhoons and indicate the important role of upwelling therein.

Investigation of off-site airborne transport of lead from a superfund removal action site using lead isotope ratios and concentrations

USGS Publications Warehouse

Pribil, Michael J.; Maddaloni, Mark A.; Staiger, Kimberly; Wilson, Eric; Magriples, Nick; Ali, Mustafa; Santella, Dennis

2014-01-01

Lead (Pb) concentration and Pb isotopic composition of surface and subsurface soil samples were used to investigate the potential for off-site air transport of Pb from a former white Pb processing facility to neighboring residential homes in a six block area on Staten Island, NY. Surface and subsurface soil samples collected on the Jewett White Pb site were found to range from 1.122 to 1.138 for 206Pb/207Pb and 2.393 to 2.411 for 208Pb/207Pb. The off-site surface soil samples collected from residential backyards, train trestle, near site grass patches and background areas varied from 1.144 to 1.196 for 206Pb/207Pb and 2.427 to 2.464 for 208Pb/207Pb. Two soil samples collected along Richmond Terrace, where Jewett site soils accumulated after major rain events, varied from 1.136 to 1.147 for 206Pb/207Pb and 2.407 to 2.419 for 208Pb/207Pb. Lead concentration for on-site surface soil samples ranged from 450 to 8000 ug/g, on-site subsurface soil samples ranged from 90,000 to 240,000 ug/g and off-site samples varied from 380 to 3500 ug/g. Lead concentration and isotopic composition for the Staten Island off-site samples were similar to previously published data for other northeastern US cities and reflect re-suspension and re-mobilization of local accumulated Pb. The considerable differences in both the Pb isotopic composition and Pb concentration of on-site and off-site samples resulted in the ability to geochemically trace the transport of particulate Pb. Data in this study indicate minimal off-site surface transport of Pb from the Jewett site into the neighboring residential area.

Impact-induced compositional variations on Mercury

NASA Astrophysics Data System (ADS)

Rivera-Valentin, E. G.; Barr, A. C.

2013-12-01

The surface of Mercury shows unexpected spectral variations spatially associated with crater and basin ejecta (the so-called 'low-reflectance material' or LRM; [1]). The low reflectance is suggested to be caused by a native darkening agent at depth that has been excavated and redeposited onto the surface [1]. Although LRM is generally associated with crater ejecta, it is not found within the ejecta blankets of many large impact craters, perhaps suggesting that the subsurface source is heterogeneous [2]. We have developed a 3-D Monte Carlo model of impact cratering, excavation, and ejecta blanket deposition. Our simulations of the effect of early impacts onto Mercury show that if the LRM originates from depth to cover ~15% of Mercury's surface [2], its source is ~30 km deep. Considering the estimated mercurian crustal thickness of 50 km [3] this implies the darkening agent is most probably located within a chemically distinct lower crust. Simulations show that repeated and overlapping impacts redistribute the darkening agent away from the basin source and create a weak association between crater size and LRM abundance. Thus subsurface heterogeneity is not required to produce the weak association between crater size and LRM abundance within crater ejecta; this is a natural consequence of overlapping impacts. Our results can elucidate the new high-resolution compositional mapping of Mercury's heavily cratered terrain and provide insight into subsurface composition. Acknowledgements: This work is supported by the Center for Lunar Origin and Evolution through the NASA Lunar Science Institute NNA09DB32A. References: [1] Denevi and Robinson, 2008, Icarus 197, 239-246. [2] Denevi et al., 2009, Science 324, 613-618. [3] Smith et al., 2012, Science 336, 214-217.

Heat transfer through particulated media in stagnant gases model and laboratory measurements: Application to Mars

NASA Astrophysics Data System (ADS)

Piqueux, Sylvain Loic Lucien

The physical characterization of the upper few centimeters to meters of the Martian surface has greatly benefited from remote temperature measurements. Typical grain sizes, rock abundances, subsurface layering, soil cementation, bedrock exposures, and ice compositions have been derived and mapped using temperature data in conjunction with subsurface models of heat conduction. Yet, these models of heat conduction are simplistic, precluding significant advances in the characterization of the physical nature of the Martian surface. A new model of heat conduction for homogeneous particulated media accounting for the grain size, porosity, gas pressure and composition, temperature, and the effect of any cementing phase is presented. The incorporation of the temperature effect on the bulk conductivity results in a distortion of the predicted diurnal and seasonal temperatures when compared to temperatures predicted with a temperature-independent conductivity model. Such distortions have been observed and interpreted to result from subsurface heterogeneities, but they may simply be explained by a temperature-dependency of the thermal inertia, with additional implications on the derived grain sizes. Cements are shown to significantly increase the bulk conductivity of a particulated medium and bond fractions <5% per volume are consistent with Martian thermal inertia data previously hypothesized to correspond to a global duricrust. A laboratory setup has been designed, built, calibrated and used to measure the thermal conductivity of particulated samples in order to test and refine the models mentioned above. Preliminary results confirm the influence of the temperature on the bulk conductivity, as well as the effect of changing the gas composition. Cemented samples are shown to conduct heat more efficiently than their uncemented counterparts.

Effect of chemical environment and rock composition on fracture mechanics properties of reservoir lithologies in context of CO2 sequestration

NASA Astrophysics Data System (ADS)

Major, J. R.; Eichhubl, P.; Callahan, O. A.

2015-12-01

The coupled chemical and mechanical response of reservoir and seal rocks to injection of CO2 have major implications on the short and long term security of sequestered carbon. Many current numerical models evaluating behavior of reservoirs and seals during and after CO2 injection in the subsurface consider chemistry and mechanics separately and use only simple mechanical stability criteria while ignoring time-dependent failure parameters. CO2 injection irreversibly alters the subsurface chemical environment which can then affect geomechanical properties on a range of time scales by altering rock mineralogy and cements through dissolution, remobilization, and precipitation. It has also been documented that geomechanical parameters such as fracture toughness (KIC) and subcritical index (SCI) are sensitive to chemical environment. Double torsion fracture mechanics testing of reservoir lithologies under controlled environmental conditions relevant to CO2 sequestration show that chemical environment can measurably affect KIC and SCI. This coupled chemical-mechanical behavior is also influenced by rock composition, grains, amount and types of cement, and fabric. Fracture mechanics testing of the Aztec Sandstone, a largely silica-cemented, subarkose sandstone demonstrate it is less sensitive to chemical environment than Entrada Sandstone, a silty, clay-rich sandstone. The presence of de-ionized water lowers KIC by approximately 20% and SCI 30% in the Aztec Sandstone relative to tests performed in air, whereas the Entrada Sandstone shows reductions on the order of 70% and 90%, respectively. These results indicate that rock composition influences the chemical-mechanical response to deformation, and that the relative chemical reactivity of target reservoirs should be recognized in context of CO2 sequestration. In general, inert grains and cements such as quartz will be less sensitive to the changing subsurface environment than carbonates and clays.

A TEX86 surface sediment database and extended Bayesian calibration

NASA Astrophysics Data System (ADS)

Tierney, Jessica E.; Tingley, Martin P.

2015-06-01

Quantitative estimates of past temperature changes are a cornerstone of paleoclimatology. For a number of marine sediment-based proxies, the accuracy and precision of past temperature reconstructions depends on a spatial calibration of modern surface sediment measurements to overlying water temperatures. Here, we present a database of 1095 surface sediment measurements of TEX86, a temperature proxy based on the relative cyclization of marine archaeal glycerol dialkyl glycerol tetraether (GDGT) lipids. The dataset is archived in a machine-readable format with geospatial information, fractional abundances of lipids (if available), and metadata. We use this new database to update surface and subsurface temperature calibration models for TEX86 and demonstrate the applicability of the TEX86 proxy to past temperature prediction. The TEX86 database confirms that surface sediment GDGT distribution has a strong relationship to temperature, which accounts for over 70% of the variance in the data. Future efforts, made possible by the data presented here, will seek to identify variables with secondary relationships to GDGT distributions, such as archaeal community composition.

Characterising meso-marine ecosystems of the North Pacific

NASA Astrophysics Data System (ADS)

Batten, Sonia D.; David Hyrenbach, K.; Sydeman, William J.; Morgan, Ken H.; Henry, Michael F.; Yen, Peggy P. Y.; Welch, David W.

2006-02-01

To delineate mesoscale variability in marine ecosystems of the subarctic North Pacific and identify "hotspots" of biological activity, we conducted contemporaneous surveys of plankton and avifaunal communites in 2000-2003. Plankton samples were collected with a continuous plankton recorder (CPR) towed by a commercial vessel while a trained observer recorded marine bird distributions using strip-transect techniques. Near- and sub-surface physical oceanographic properties and productivity patterns were measured using a temperature data logger and satellite-derived chlorophyll a concentrations. We identified 10 distinct biological communities across the North Pacific, which we refer to as 'meso-marine ecosystems' (MME). We examined the characteristics of MME over multiple years to assess temporal persistence. MME were associated with different bathymetric domains and current systems. MME differed in the overall abundance and species composition of their fauna and, therefore, almost certainly in productivity. Regular monitoring of the spatial and temporal variability of MME will enhance our ability to detect and understand coupled climate-ecosystem responses, and, in turn, help guide ecosystem-based fisheries and wildlife management.

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.

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.

Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function. ?? 2006 Springer Science+Business Media, Inc.

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

A New Method and Mass-Spectrometric Instrument for Extraterrestrial Microbial Life Detection Using the Elemental Composition Analyses of Martian Regolith and Permafrost/Ice.

PubMed

Managadze, G G; Safronova, A A; Luchnikov, K A; Vorobyova, E A; Duxbury, N S; Wurz, P; Managadze, N G; Chumikov, A E; Khamizov, R Kh

2017-05-01

We propose a new technique for the detection of microorganisms by elemental composition analyses of a sample extracted from regolith, permafrost, and ice of extraterrestrial bodies. We also describe the design of the ABIMAS instrument, which consists of the onboard time-of-flight laser mass-reflectron (TOF LMR) and the sample preparation unit (SPU) for biomass extraction. This instrument was initially approved to fly on board the ExoMars 2020 lander mission. The instrument can be used to analyze the elemental composition of possible extraterrestrial microbial communities and compare it to that of terrestrial microorganisms. We have conducted numerous laboratory studies to confirm the possibility of biomass identification via the following biomarkers: P/S and Ca/K ratios, and C and N abundances. We underline that only the combination of these factors will allow one to discriminate microbial samples from geological ones. Our technique has been tested experimentally in numerous laboratory trials on cultures of microorganisms and polar permafrost samples as terrestrial analogues for martian polar soils. We discuss various methods of extracting microorganisms and sample preparation. The developed technique can be used to search for and identify microorganisms in different martian samples and in the subsurface of other planets, satellites, comets, and asteroids-in particular, Europa, Ganymede, and Enceladus. Key Words: Mass spectrometry-Life-detection instruments-Biomarkers-Earth Mars-Biomass spectra. Astrobiology 17, 448-458.

Summary of inorganic compositional data for groundwater, soil-water, and surface-water samples collected at the Headgate Draw subsurface drip irrigation site, Johnson County, Wyoming

USGS Publications Warehouse

Geboy, Nicholas J.; Engle, Mark A.; Schroeder, Karl T.; Zupancic, John W.

2011-01-01

As part of a 5-year project on the impact of subsurface drip irrigation (SDI) application of coalbed-methane (CBM) produced waters, water samples were collected from the Headgate Draw SDI site in the Powder River Basin, Wyoming, USA. This research is part of a larger study to understand short- and long-term impacts on both soil and water quality from the beneficial use of CBM waters to grow forage crops through use of SDI. This document provides a summary of the context, sampling methodology, and quality assurance and quality control documentation of samples collected prior to and over the first year of SDI operation at the site (May 2008-October 2009). This report contains an associated database containing inorganic compositional data, water-quality criteria parameters, and calculated geochemical parameters for samples of groundwater, soil water, surface water, treated CBM waters, and as-received CBM waters collected at the Headgate Draw SDI site.

Macrofaunal community structure in Bahía Concepción (Chile) before and after the 8.8 Mw Maule mega-earthquake and tsunami.

PubMed

Cárcamo, Paula J; Hernández-Miranda, Eduardo; Veas, Rodrigo; Quiñones, Renato A

2017-09-01

Faunal assemblages of subtidal sedimentary environments are key components of coastal ecosystems. Benthic communities inhabiting the coastal zone near urban centers in Concepción Bay (Chile) have been described as highly disturbed (i.e. impoverished in diversity and species richness). This is due to the frequent presence of hypoxic conditions at the bottom due to the intrusion of low oxygen Equatorial Subsurface Water, high natural productivity and the high load of organic matter generated by several anthropogenic activities. A mega-earthquake (8.8 Mw) and subsequent tsunami occurred on the coast of south-central Chile on February 27, 2010 (27F), heavily impacting Concepción Bay, which is located 30 km south of the epicenter. The objectives of the present study are: (i) to evaluate the effect produced by the mega-earthquake and tsunami on the benthic community, and (ii) to assess dissimilarity in macrofauna composition and abundance in Concepción Bay at an inter-decadal time scale based on a comparison between our sampling conducted between 2010 and 2013 and information published since 1969. Our results show that the benthic macrofauna of Concepción Bay was disturbed by the 27F (i.e. high community dissimilarity in 2010). Changes in community structure were observed at an inter-annual scale (i.e. diminished community dissimilarity in 2013), suggesting a recovery post-27F. At an inter-decadal scale, community structure post-27F was dissimilar to the structure described for the 1980's and 1990's but more similar to that reported for 1969. The reducing conditions of the sediments due to the high input of organic matter that took place in the 1980's and 1990's may explain this dissimilarity. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Indentation cracking of composite matrix materials.

PubMed

Baran, G; Shin, W; Abbas, A; Wunder, S

1994-08-01

Composite restorative materials wear by a fatigue mechanism in the occlusal contact area. Here, tooth cusps and food debris cyclically indent the restoration. Modeling this phenomenon requires an understanding of material response to indentation. The question in this study was whether material response depends on indenter size and geometry, and also, whether polymers used in restorative materials should be considered elastic and brittle, or plastic and ductile for modeling purposes. Three resins used as matrices in proprietary restorative composites were the experimental materials. To ascertain the influence of glass transition temperature, liquid sorption, and small amounts of filler on indentation response, we prepared materials with various degrees of cure; some samples were soaked in a 50/50 water/ethanol solution, and 3 vol% silica was added in some cases. Indentation experiments revealed that no cracking occurred in any material after indentation by Vickers pyramid or spherical indenters with diameters equal to or smaller than 0.254 mm. Larger spherical indenters induced subsurface median and surface radial and/or ring cracks. Critical loads causing subsurface cracks were measured. Indentation with suitably large spherical indenters provoked an elastoplastic response in polymers, and degree of cure and Tg had less influence on critical load than soaking in solution. Crack morphology was correlated with yield strain. Commonly held assumptions regarding the brittle elastic behavior of composite matrix materials may be incorrect.

Present research results and communicate the modeling results to science community

EPA Science Inventory

Background/Objectives. As a result of subsurface heterogeneity, many field and laboratory studies indicate that the advection-dispersion equation (ADE) model fails to describe the frequently observed long tails of contaminant concentration versus time in a breakthrough curve. T...

Diverse arsenic- and iron-cycling microbial communities in arsenic-contaminated aquifers used for drinking water in Bangladesh.

PubMed

Hassan, Zahid; Sultana, Munawar; van Breukelen, Boris M; Khan, Sirajul I; Röling, Wilfred F M

2015-04-01

Subsurface removal of arsenic by injection with oxygenated groundwater has been proposed as a viable technology for obtaining 'safe' drinking water in Bangladesh. While the oxidation of ferrous iron to solid ferric iron minerals, to which arsenic adsorbs, is assumed to be driven by abiotic reactions, metal-cycling microorganisms may potentially affect arsenic removal. A cultivation-independent survey covering 24 drinking water wells in several geographical regions in Bangladesh was conducted to obtain information on microbial community structure and diversity in general, and on specific functional groups capable of the oxidation or reduction of arsenic or iron. Each functional group, targeted by either group-specific 16S rRNA or functional gene amplification, occurred in at least 79% of investigated samples. Putative arsenate reducers and iron-oxidizing Gallionellaceae were present at low diversity, while more variation in potentially arsenite-oxidizing microorganisms and iron-reducing Desulfuromonadales was revealed within and between samples. Relations between community composition on the one hand and hydrochemistry on the other hand were in general not evident, apart from an impact of salinity on iron-cycling microorganisms. Our data suggest widespread potential for a positive contribution of arsenite and iron oxidizers to arsenic removal upon injection with oxygenated water, but also indicate a potential risk for arsenic re-mobilization by anaerobic arsenate and iron reducers once injection is halted. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Decadal to centennial oscillations in the upper and lower boundaries of the San Diego, California margin Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Myhre, S. E.; Hill, T. M.; Frieder, C.; Grupe, B.

2016-02-01

Here we present two new marine sediment archives from the continental margin of San Diego, California, USA, which record decadal to centennial oscillations in the hydrographic structure of the Eastern Pacific Oxygen Minimum Zone (OMZ). The two cores, located at 528 and 1,180 m water depth, record oceanographic history across overlapping timescales. Biotic communities, including Foraminifera, Echinodermata, Brachiopoda, Mollusca and Ostrocoda, were examined in subsurface (>10 cm sediment core depth) samples. Chronologies for both cores were developed with reservoir-corrected 14C dates of mixed planktonic Foraminifera and linearly interpolated sedimentation rates. Sediment ages for the cores range from 400-1,800 years before present. Indices of foraminiferal community density, diversity and evenness are applied as biotic proxies to track the intensification of the continental margin OMZ. Biotic communities at the shallower site reveal multi-decadal to centennial timescales of OMZ intensification, whereas the deeper site exhibits decadal to multi-decadal scales of hydrographic variability. Hypoxia-associated foraminiferal genera Uvigerina and Bolivina were compositionally dominant during intervals of peak foraminiferal density. Invertebrate assemblages often co-occurred across taxa groups, and thereby provide a broad trophic context for interpreting changes in the margin seafloor. Variability in the advection of Pacific Equatorial Water may mechanistically contribute to this described hydrographic variability. This investigation reconstructs historical timescales of OMZ intensification, seafloor ecological variability, and synchrony between open-ocean processes and regional climate.

Integrated surface/subsurface permafrost thermal hydrology: Model formulation and proof-of-concept simulations

DOE PAGES

Painter, Scott L.; Coon, Ethan T.; Atchley, Adam L.; ...

2016-08-11

The need to understand potential climate impacts and feedbacks in Arctic regions has prompted recent interest in modeling of permafrost dynamics in a warming climate. A new fine-scale integrated surface/subsurface thermal hydrology modeling capability is described and demonstrated in proof-of-concept simulations. The new modeling capability combines a surface energy balance model with recently developed three-dimensional subsurface thermal hydrology models and new models for nonisothermal surface water flows and snow distribution in the microtopography. Surface water flows are modeled using the diffusion wave equation extended to include energy transport and phase change of ponded water. Variation of snow depth in themore » microtopography, physically the result of wind scour, is also modeled heuristically with a diffusion wave equation. The multiple surface and subsurface processes are implemented by leveraging highly parallel community software. Fully integrated thermal hydrology simulations on the tilted open book catchment, an important test case for integrated surface/subsurface flow modeling, are presented. Fine-scale 100-year projections of the integrated permafrost thermal hydrological system on an ice wedge polygon at Barrow Alaska in a warming climate are also presented. Finally, these simulations demonstrate the feasibility of microtopography-resolving, process-rich simulations as a tool to help understand possible future evolution of the carbon-rich Arctic tundra in a warming climate.« less

Subsurface polarimetric migration imaging for full polarimetric ground-penetrating radar

NASA Astrophysics Data System (ADS)

Feng, Xuan; Yu, Yue; Liu, Cai; Fehler, Michael

2015-08-01

Polarization is a property of electromagnetic wave that generally refers to the locus of the electric field vector, which can be used to characterize surface properties by polarimetric radar. However, its use has been less common in the ground-penetrating radar (GPR) community. Full polarimetric GPR data include scattering matrices, by which the polarization properties can be extracted, at each survey point. Different components of the measured scattering matrix are sensitive to different types of subsurface objects, which offers a potential improvement in the detection ability of GPR. This paper develops a polarimetric migration imaging method. By merging the Pauli polarimetric decomposition technique with the Krichhoff migration equation, we develop a polarimetric migration algorithm, which can extract three migrated coefficients that are sensitive to different types of objects. Then fusing the three migrated coefficients, we can obtain subsurface colour-coded reconstructed object images, which can be employed to interpret both the geometrical information and the scattering mechanism of the subsurface objects. A 3-D full polarimetric GPR data set was acquired in a laboratory experiment and was used to test the method. In the laboratory experiment, four objects-a scatterer, a ball, a plate and a dihedral target-were buried in homogeneous dry sand under a flat ground surface. By merging the reconstructed image with polarization properties, we enhanced the subsurface image and improved the classification ability of GPR.

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

STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION

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

Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin

2011-06-15

The objectives of this project 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 at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee, where themore » subsurface is exposed to mixed contamination predominated by uranium and nitrate. A total of 20 publications (16 published or 'in press' and 4 in review), 10 invited talks, and 43 contributed seminars/ meeting presentations were completed during the past four years of the project. PI Kostka served on one proposal review panel each year for the U.S. DOE Office of Science during the four year project period. The PI leveraged funds from the state of Florida to purchase new instrumentation that aided the project. Support was also leveraged by the PI from the Joint Genome Institute in the form of two successful proposals for genome sequencing. Draft genomes are now available for two novel species isolated during our studies and 5 more genomes are in the pipeline. We effectively addressed each of the three project objectives and research highlights are provided. Task I - Isolation and characterization of novel anaerobes: (1) A wide range of pure cultures of metal-reducing bacteria, sulfate-reducing bacteria, and denitrifying bacteria (32 strains) were isolated from subsurface sediments of the Oak Ridge Field Research Center (ORFRC), where the subsurface is exposed to mixed contamination of uranium and nitrate. These isolates which are new to science all show high sequence identity to sequences retrieved from ORFRC subsurface. (2) Based on physiological and phylogenetic characterization, two new species of subsurface bacteria were described: the metal-reducer Geobacter daltonii, and the denitrifier Rhodanobacter denitrificans. (3) Strains isolated from the ORFRC show that Rhodanobacter species are well adapted to the contaminated subsurface. Strains 2APBS1 and 116-2 grow at high salt (3% NaCl), low pH (3.5) and tolerate high concentrations of nitrate (400mM) and nitrite (100mM). Strain 2APBS1 was demonstrated to grow at in situ acidic pHs down to 2.5. (4) R. denitrificans strain 2APBS1 is the first described Rhodanobacter species shown to denitrify. Nitrate is almost entirely converted to N2O, which may account for the large accumulation of N2O in the ORFRC subsurface. (5) G. daltonii, isolated from uranium- and hydrocarbon-contaminated subsurface sediments of the ORFRC, is the first organism from the subsurface clade of the genus Geobacter that is capable of growth on aromatic hydrocarbons. (6) High quality draft genome sequences and a complete eco-physiological description are completed for R. denitrificans strain 2APBS1 and G. daltonii strain FRC-32. (7) Given their demonstrated relevance to DOE remediation efforts and the availability of detailed genotypic/phenotypic characterization, Rhodanobacter denitrificans strain 2APBS1 and Geobacter daltonii strain FRC-32 represent ideal model organisms to provide a predictive understanding of subsurface microbial activity through metabolic modeling. Tasks II and III-Diversity and distribution of active anaerobes and Mechanisms linking electron transport and the fate of radionuclides: (1) Our study showed that members of genus Rhodanobacter and Geobacter are abundant and active in the uranium and nitrate contaminated subsurface. In the contaminant source zone of the Oak Ridge site, Rhodanobacter spp. are the predominant, active organisms detected (comprising 50% to 100% of rRNA detected). (2) We demonstrated for the first time that the function of microbial communities can be quantified in subsurface sediments using messenger RNA assays (molecular proxies) under in situ conditions. (3) Active Geobacteraceae were identified and phylogenetically characterized from the cDNA of messenger RNA extracted from ORFRC subsurface sediment cores. Multiple clone sequences were retrieved from G. uraniireducens, G. daltonii, and G. metallireducens. (4) Results show that Geobacter strain FRC-32 is capable of growth on benzoate, toluene and benzene as the electron donor, thereby providing evidence that this strain is physiologically distinct from other described members of the subsurface Geobacter clade. (5) Fe(III)-reducing bacteria transform structural Fe in clay minerals from their layer edges rather than from their basal surfaces.« less

Respiratory interactions of soil bacteria with (semi)conductive iron-oxide minerals.

PubMed

Kato, Souichiro; Nakamura, Ryuhei; Kai, Fumiyoshi; Watanabe, Kazuya; Hashimoto, Kazuhito

2010-12-01

Pure-culture studies have shown that dissimilatory metal-reducing bacteria are able to utilize iron-oxide nanoparticles as electron conduits for reducing distant terminal acceptors; however, the ecological relevance of such energy metabolism is poorly understood. Here, soil microbial communities were grown in electrochemical cells with acetate as the electron donor and electrodes (poised at 0.2 V versus Ag/AgCl) as the electron acceptors in the presence and absence of iron-oxide nanoparticles, and respiratory current generation and community structures were analysed. Irrespective of the iron-oxide species (hematite, magnetite or ferrihydrite), the supplementation with iron-oxide minerals resulted in large increases (over 30-fold) in current, while only a moderate increase (∼10-fold) was observed in the presence of soluble ferric/ferrous irons. During the current generation, insulative ferrihydrite was transformed into semiconductive goethite. Clone-library analyses of 16S rRNA gene fragments PCR-amplified from the soil microbial communities revealed that iron-oxide supplementation facilitated the occurrence of Geobacter species affiliated with subsurface clades 1 and 2. We suggest that subsurface-clade Geobacter species preferentially thrive in soil by utilizing (semi)conductive iron oxides for their respiration. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

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

Metabolic and Physiological Characteristics of Novel Cultivars from Serpentinite Seep Fluids

NASA Astrophysics Data System (ADS)

Nelson, B.; Chowdhury, S.; Brazelton, W. J.; Schrenk, M. O.

2011-12-01

Subsurface waters associated with the alteration of ultramafic rocks become highly reducing and alkaline through a process known as serpentinization. As habitat, these fluids are in many ways metabolically constraining but can provide sufficient energy for chemolithotrophy. As part of an ongoing effort to characterize these communities, heterotrophic enrichment cultures and anaerobic microcosms were initiated with alkaline waters found at three geographically and geochemically distinct sites of active serpentinization. These include the Northern Apennine ophiolite in the Ligurian region of Italy, the Tablelands ophiolite at Gros Morne National Park, Canada and the Coast Range ophiolite at McLaughlin Natural Reserve, California. Enrichment cultures at pH 11 yielded numerous isolates related to Proteobacteria and Firmicutes, some of which are closely related to other cultivars from high pH and subsurface environments. Anaerobic water samples were amended with combinations of electron donors (hydrogen, complex organics, acetate) and acceptors (ferric iron, sulfate) in a block design. After several weeks of incubation, DNA was extracted from cell concentrations and community differences were compared by TRFLP. Of particular interest is the isolation of a putative iron reducing Firmicute from samples enriched with complex organic compounds and ferric citrate. Ongoing studies are aimed at characterizing the physiology of these isolates. These data provide important insights into the metabolic potential of serpentinite subsurface ecosystems, and are a complement to culture-independent genomic analyses.

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.

Functional microbial diversity explains groundwater chemistry in a pristine aquifer

PubMed Central

2013-01-01

Background The diverse microbial populations that inhabit pristine aquifers are known to catalyze critical in situ biogeochemical reactions, yet little is known about how the structure and diversity of this subsurface community correlates with and impacts upon groundwater chemistry. Herein we examine 8,786 bacterial and 8,166 archaeal 16S rRNA gene sequences from an array of monitoring wells in the Mahomet aquifer of east-central Illinois. Using multivariate statistical analyses we provide a comparative analysis of the relationship between groundwater chemistry and the microbial communities attached to aquifer sediment along with those suspended in groundwater. Results Statistical analyses of 16S rRNA gene sequences showed a clear distinction between attached and suspended communities; with iron-reducing bacteria far more abundant in attached samples than suspended, while archaeal clones related to groups associated with anaerobic methane oxidation and deep subsurface gold mines (ANME-2D and SAGMEG-1, respectively) distinguished the suspended community from the attached. Within the attached bacterial community, cloned sequences most closely related to the sulfate-reducing Desulfobacter and Desulfobulbus genera represented 20% of the bacterial community in wells where the concentration of sulfate in groundwater was high (> 0.2 mM), compared to only 3% in wells with less sulfate. Sequences related to the genus Geobacter, a genus containing ferric-iron reducers, were of nearly equal abundance (15%) to the sulfate reducers under high sulfate conditions, however their relative abundance increased to 34% when sulfate concentrations were < 0.03 mM. Also, in areas where sulfate concentrations were <0.03 mM, archaeal 16S rRNA gene sequences similar to those found in methanogens such as Methanosarcina and Methanosaeta comprised 73–80% of the community, and dissolved CH4 ranged between 220 and 1240 μM in these groundwaters. In contrast, methanogens (and their product, CH4) were nearly absent in samples collected from groundwater samples with > 0.2 mM sulfate. In the suspended fraction of wells where the concentration of sulfate was between 0.03 and 0.2 mM, the archaeal community was dominated by sequences most closely related to the ANME-2D, a group of archaea known for anaerobically oxidizing methane. Based on available energy (∆GA) estimations, results varied little for both sulfate reduction and methanogenesis throughout all wells studied, but could favor anaerobic oxidation of methane (AOM) in wells containing minimal sulfate and dihydrogen, suggesting AOM coupled with H2-oxidizing organisms such as sulfate or iron reducers could be an important pathway occurring in the Mahomet aquifer. Conclusions Overall, the results show several distinct factors control the composition of microbial communities in the Mahomet aquifer. Bacteria that respire insoluble substrates such as iron oxides, i.e. Geobacter, comprise a greater abundance of the attached community than the suspended regardless of groundwater chemistry. Differences in community structure driven by the concentration of sulfate point to a clear link between the availability of substrate and the abundance of certain functional groups, particularly iron reducers, sulfate reducers, methanogens, and methanotrophs. Integrating both geochemical and microbiological observations suggest that the relationships between these functional groups could be driven in part by mutualism, especially between ferric-iron and sulfate reducers. PMID:23800252

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.

Saugus River and Tributaries, Lynn Malden, Revere and Saugus, Massachusetts. Flood Damage Reduction. Volume 8. Appendix K. Environmental

DTIC Science & Technology

1989-06-01

K10 Summary of Soil Analyses for the Salt Marsh Transects K32 KI1 Plant Community Composition Data Along Compartment K33 B Transect K12 Plant...Community Composition Data Along Compartment K33 I Transect K13 Plant Community Composition Data Along Compartment K33 K1 Transect K14 Plant Community... Composition Data Along Compartment K34 K3 Transect K15 Plant Community Composition Data Along Compartment K34 L2 Transect K16 Plant Community Composition

Internal hydrological mechanism of permeable pavement and interaction with subsurface water

EPA Science Inventory

Many communities are implementing green infrastructure stormwater control measures (SCMs) in urban environments across the U.S. to mimic pre-urban, natural hydrology more closely. Permeable pavement is one SCM infrastructure that has been commonly selected for both new and retro...

The Active Bacterial Community in a Pristine Confined Aquifer

EPA Science Inventory

This study of the active bacteria residing in a pristine confined aquifer provides unexpected insights into the ecology of iron-reducing and sulfate-reducing bacteria in the subsurface. At 18 wells in east-central Illinois, we trapped the microbes that attached to aquifer sedimen...

Dynamics of the Genetic Diversity of Subsurface Microbial Communities and Their Applications to Contaminated Site Cleanups

EPA Science Inventory

When compared to traditional approaches, the utilization of molecular and genomic techniques to soil and groundwater cleanup investigations can reduce inherent parameter variability when conducting bench and pilot-scale investigations or carrying out full-scale field applications...

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 ...

Nondestructive evaluation of defects in carbon fiber reinforced polymer (CFRP) composites

NASA Astrophysics Data System (ADS)

Ngo, Andrew C. Y.; Goh, Henry K. H.; Lin, Karen K.; Liew, W. H.

2017-04-01

Carbon fiber reinforced polymer (CFRP) composites are increasingly used in aerospace applications due to its superior mechanical properties and reduced weight. Adhesive bonding is commonly used to join the composite parts since it is capable of joining incompatible or dissimilar components. However, insufficient adhesive or contamination in the adhesive bonds might occur and pose as threats to the integrity of the plane during service. It is thus important to look for suitable nondestructive testing (NDT) techniques to detect and characterize the sub-surface defects within the CFRP composites. Some of the common NDT techniques include ultrasonic techniques and thermography. In this work, we report the use of the abovementioned techniques for improved interpretation of the results.

Effects of cell surface characteristics and manure-application practices on Escherichia coli populations in the subsurface: A three-farm study

NASA Astrophysics Data System (ADS)

Salvucci, A. E.; Elton, M.; Siler, J. D.; Zhang, W.; Richards, B. K.; Geohring, L. D.; Warnick, L. D.; Hay, A. G.; Steenhuis, T.

2010-12-01

The introduction of microbial pathogens into the environment from untreated manure represents a threat to water quality and human health. Thus, understanding the effect of manure management strategies is imperative to effectively mitigate the inadvertent release of pathogens, particularly in subsurface environments where they can be transported through macropores to the groundwater or through agricultural tile line to open water bodies. The production of cell-surface biomolecules is also suspected to play an important role in the environmental survival and transport of enterobacterial pathogens. This study collected Escherichia coli samples from three dairy farms with artificial tile drainage systems and active manure spreading in the Central New York region over a three-month period. Sampling targeted four potential source locations on each farm: (i) cow housing, (ii) manure storage facilities, (iii) field soil, and (iv) subsurface drainage effluent. Over 2800 E. coli isolates were recovered and consequently analyzed for the cell surface components, cellulose and curli, traits associated with increased environmental survival, altered transport and pathogenicity. The E. coli isolates from locations i-iii displayed highly variable curli and cellulose-producing communities, while isolates collected from subsurface runoff on each farm had stable curli and cellulose production communities over all sampling dates. Furthermore, the method of manure application to the fields influenced the population characteristics found in drainage effluent isolates. Incorporation of manure into the soil was correlated to isolate populations largely deficient of curli and cellulose; whereas farms that only surface-applied manure were correlated to isolate populations of high curli and cellulose production. The production of curli and cellulose has previously been shown to be a response to environmental stress on the cell. Therefore, incorporation of manure directly into the soil appears to minimize environmental stresses, like UV radiation, desiccation and temperature fluctuation, typically found on the soil surface. Our findings indicate that E. coli strains above the surface are largely diverse, until they enter subsurface environments where specific extracellular characteristics are likely advantageous for survival and/or transport.

Analysis of Tank 38H (HTF-38-15-119, 127) Surface, Subsurface and Tank 43H (HTF-43-15-116, 117 and 118) Surface, Feed Pump Suction and Jet Suction Subsurface Supernatant Samples in Support of Enrichment, Corrosion Control and Salt Batch Planning Programs

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

Oji, L.

Compositional feed limits have been established to ensure that a nuclear criticality event for the 2H and 3H Evaporators is not possible. The Enrichment Control Program (ECP) requires feed sampling to determine the equivalent enriched uranium content prior to transfer of waste other than recycle transfers (requires sampling to determine the equivalent enriched uranium at two locations in Tanks 38H and 43H every 26 weeks) The Corrosion Control Program (CCP) establishes concentration and temperature limits for key constituents and periodic sampling and analysis to confirm that waste supernate is within these limits. This report provides the results of analyses onmore » Tanks 38H and 43H surface and subsurface supernatant liquid samples in support of the ECP, the CCP, and the Salt Batch 10 Planning Program.« less

Evaluation of 2D ceramic matrix composites in aeroconvective environments

NASA Technical Reports Server (NTRS)

Riccitiello, Salvatore R.; Love, Wendell L.; Balter-Peterson, Aliza

1992-01-01

An evaluation is conducted of a novel ceramic-matrix composite (CMC) material system for use in the aeroconvective-heating environments encountered by the nose caps and wing leading edges of such aerospace vehicles as the Space Shuttle, during orbit-insertion and reentry from LEO. These CMCs are composed of an SiC matrix that is reinforced with Nicalon, Nextel, or carbon refractory fibers in a 2D architecture. The test program conducted for the 2D CMCs gave attention to their subsurface oxidation.

The composition of the lunar crust: Radiative transfer modeling and analysis of lunar visible and near-infrared spectra

NASA Astrophysics Data System (ADS)

Cahill, Joshua T. S.

This dissertation has two focuses: (1) the evaluation and validation of algorithms used for analysis of lunar visible and near-infrared data sets, and (2) the determination of lunar surface and sub-surface crustal composition by virtue of these algorithms. To that end, the results and interpretation reported herein further enhance knowledge of lunar ferroan anorthosite (FAN) and magnesium-suite (Mg-suite) mineralogy, chemistry, and distribution on and in our Moon's crust.

In-Situ Sampling Analysis of a Jupiter Trojan Asteroid by High Resolution Mass Spectrometry in the Solar Power Sail Mission

NASA Astrophysics Data System (ADS)

Kebukawa, Y.; Aoki, J.; Ito, M.; Kawai, Y.; Okada, T.; Matsumoto, J.; Yano, H.; Yurimoto, H.; Terada, K.; Toyoda, M.; Yabuta, H.; Nakamura, R.; Cottin, H.; Grand, N.; Mori, O.

2017-12-01

The Solar Power Sail (SPS) mission is one of candidates for the upcoming strategic middle-class space exploration to demonstrate the first outer Solar System journey of Japan. The mission concept includes in-situ sampling analysis of the surface and subsurface (up to 1 m) materials of a Jupiter Trojan asteroid using high resolution mass spectrometry (HRMS). The candidates for the HRMS are multi-turn time-of-flight mass spectrometer (MULTUM) type and Cosmorbitrap type. We plan to analyze isotopic and elemental compositions of volatile materials from organic matter, hydrated minerals, and ice (if any), in order to understand origin and evolution of the Jupiter Trojan asteroids. It will provide insights into planet formation/migration theories, evolution and distribution of volatiles in the Solar System, and missing link between asteroids and comets on evolutional. The HRMS system allows to measure H, N, C, O isotopic compositions and elemental compositions of molecules prepared by various pre-MS procedures including stepwise heating up to 600ºC, gas chromatography (GC), and high-temperature pyrolysis with catalyst to decompose the samples into simple gaseous molecules (e.g., H2, CO, and N2) for isotopic ratio analysis. The required mass resolution should be at least 30,000 for analyzing isotopic ratios for simple gaseous molecules. For elemental compositions, mass accuracy of 10 ppm is required to determine elemental compositions for molecules with m/z up to 300 (as well as compound specific isotopic compositions for smaller molecules). Our planned analytical sequences consist of three runs for both surface and subsurface samples. In addition, `sniff mode' which simply introduces environmental gaseous molecules into a HRMS will be done by the system.

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

Wrighton, Kelly C.; Castelle, Cindy; Wilkins, Michael J.

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge, and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, Colorado, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via two acetate-based biostimulation treatments. Samples weremore » collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include genomes from a new phylum (ACD20), phylogenetically novel members of the Chloroflexi and Bacteroidetes, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER, and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate, and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen currency in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate, and iron reduction. Thus, fermentation carried out by previously unstudied members of sediment microbial communities may be an important driver of diverse subsurface biogeochemical cycles.« less

Development of stream-subsurface flow module in sub-daily simulation of Escherichia coli using SWAT

NASA Astrophysics Data System (ADS)

Kim, Minjeong; Boithias, Laurie; Cho, Kyung Hwa; Silvera, Norbert; Thammahacksa, Chanthamousone; Latsachack, Keooudone; Rochelle-Newall, Emma; Sengtaheuanghoung, Oloth; Pierret, Alain; Pachepsky, Yakov A.; Ribolzi, Olivier

2017-04-01

Water contaminated with pathogenic bacteria poses a large threat to public health, especially in the rural areas in the tropics where sanitation and drinking water facilities are often lacking. Several studies have used the Soil and Water Assessment Tool (SWAT) to predict the export of in-stream bacteria at a watershed-scale. However, SWAT is limited to in-stream processes, such as die-off, resuspension and, deposition; and it is usually implemented on a daily time step using the SCS Curve Number method, making it difficult to explore the dynamic fate and transport of bacteria during short but intense events such as flash floods in tropical humid montane headwaters. To address these issues, this study implemented SWAT on an hourly time step using the Green-Ampt infiltration method, and tested the effects of subsurface flow (LATQ+GWQ in SWAT) on bacterial dynamics. We applied the modified SWAT model to the 60-ha Houay Pano catchment in Northern Laos, using sub-daily rainfall and discharge measurements, electric conductivity-derived fractions of overland and subsurface flows, suspended sediments concentrations, and the number of fecal indicator organism Escherichia coli monitored at the catchment outlet from 2011 to 2013. We also took into account land use change by delineating the watershed with the 3-year composite land use map. The results show that low subsurface flow of less than 1 mm recovered the underestimation of E. coli numbers during the dry season, while high subsurface flow caused an overestimation during the wet season. We also found that it is more reasonable to apply the stream-subsurface flow interaction to simulate low in-stream bacteria counts. Using fecal bacteria to identify and understand the possible interactions between overland and subsurface flows may well also provide some insight into the fate of other bacteria, such as those involved in biogeochemical fluxes both in-stream and in the adjacent soils and hyporheic zones.

Concentration and characterization of dissolved organic matter in the surface microlayer and subsurface water of the Bohai Sea, China

NASA Astrophysics Data System (ADS)

Chen, Yan; Yang, Gui-Peng; Wu, Guan-Wei; Gao, Xian-Chi; Xia, Qing-Yan

2013-01-01

A total of 19 sea-surface microlayer and corresponding subsurface samples collected from the Bohai Sea, China in April 2010 were analyzed for chlorophyll a, dissolved organic carbon (DOC) and its major compound classes including total dissolved carbohydrates (TDCHO, including monosaccharides, MCHO, and polysaccharides, PCHO) and total hydrolysable amino acids (THAA, including dissolved free, DFAA, and combined fraction, DCAA). The concentrations of DOC in the subsurface water ranged from 130.2 to 407.7 μM C, with an average of 225.9±75.4 μM C, while those in the surface microlayer varied between 140.1 and 330.9 μM C, with an average of 217.8±56.8 μM C. The concentrations of chlorophyll a, DOC, TDCHO and THAA in the microlayer were, respectively correlated with their subsurface water concentrations, implying that there was a strong exchange effect between the microlayer and subsurface water. The concentrations of DOC and TDCHO were negatively correlated with salinity, respectively, indicating that water mixing might play an important role in controlling the distribution of DOC and TDCHO in the water column. Major constituents of DCAA and DFAA present in the study area were glycine, alanine, glutamic acid, serine and histidine. Principal component analysis (PCA) was applied to examine the complex compositional differences that existed among the sampling sites. Our results showed that DFAA had higher mole percentages of glycine, valine and serine in the microlayer than in the subsurface water, while DCAA tended to have higher mole percentages of glutamic acid, aspartic acid, threonine, arginine, alanine, tyrosine, phenylalanine and leucine in the microlayer. The yields of TDCHO and THAA exhibited similar trends between the microlayer and subsurface water. Carbohydrate species displayed significant enrichment in the microlayer, whereas the DFAA and DCAA exhibited non-uniform enrichment in the microlayer.

Río Tinto Faulted Volcanosedimentary Deposits as Analog Habitats for Extant Subsurface Biospheres on Mars: A Synthesis of the MARTE Drilling Project Geobiology Results

NASA Astrophysics Data System (ADS)

Fernández-Remolar, D. C.; Prieto-Ballesteros, O.; Rodríguez, N.; Dávila, F.; Stevens, T.; Amils, R.; Gómez-Elvira, J.; Stoker, C. R.

2005-03-01

Reconstruction of the probable habitats hosting the detected microbial communities through the integration of the geobiological data obtained from the MARTE drilling campaigns, TEM sounding and field surface geological survey

Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay.

PubMed

Goh, Falicia; Allen, Michelle A; Leuko, Stefan; Kawaguchi, Tomohiro; Decho, Alan W; Burns, Brendan P; Neilan, Brett A

2009-04-01

The stromatolites at Shark Bay, Western Australia, are analogues of some of the oldest evidence of life on Earth. The aim of this study was to identify and spatially characterize the specific microbial communities associated with Shark Bay intertidal columnar stromatolites. Conventional culturing methods and construction of 16S rDNA clone libraries from community genomic DNA with both universal and specific PCR primers were employed. The estimated coverage, richness and diversity of stromatolite microbial populations were compared with earlier studies on these ecosystems. The estimated coverage for all clone libraries indicated that population coverage was comprehensive. Phylogenetic analyses of stromatolite and surrounding seawater sequences were performed in ARB with the Greengenes database of full-length non-chimaeric 16S rRNA genes. The communities identified exhibited extensive diversity. The most abundant sequences from the stromatolites were alpha- and gamma-proteobacteria (58%), whereas the cyanobacterial community was characterized by sequences related to the genera Euhalothece, Gloeocapsa, Gloeothece, Chroococcidiopsis, Dermocarpella, Acaryochloris, Geitlerinema and Schizothrix. All clones from the archaeal-specific clone libraries were related to the halophilic archaea; however, no archaeal sequence was identified from the surrounding seawater. Fluorescence in situ hybridization also revealed stromatolite surfaces to be dominated by unicellular cyanobacteria, in contrast to the sub-surface archaea and sulphate-reducing bacteria. This study is the first to compare the microbial composition of morphologically similar stromatolites over time and examine the spatial distribution of specific microorganismic groups in these intertidal structures and the surrounding seawater at Shark Bay. The results provide a platform for identifying the key microbial physiology groups and their potential roles in modern stromatolite morphogenesis and ecology.

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

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

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a six-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments. Frontiers in Earth Science Journal Impact & Description - ResearchGate - Impact Rankings ( 2015 and 2016 ). Available from: https://www.researchgate.net/journal/2296-6463_Frontiers_in_Earth_Science [accessed Jul 25, 2016].« less

Recovery of community genomes to assess subsurface metabolic potential: exploiting the capacity of next generation sequencing-based metagenomics

NASA Astrophysics Data System (ADS)

Wrighton, K. C.; Thomas, B.; Miller, C. S.; Sharon, I.; Wilkins, M. J.; VerBerkmoes, N. C.; Handley, K. M.; Lipton, M. S.; Hettich, R. L.; Williams, K. H.; Long, P. E.; Banfield, J. F.

2011-12-01

With the goal of developing a deterministic understanding of the microbiological and geochemical processes controlling subsurface environments, groundwater bacterial communities were collected from the Rifle Integrated Field Research Challenge (IFRC) site. Biomass from three temporal acetate-stimulated groundwater samples were collected during a period of dominant Fe(III)-reduction, in a region of the aquifer that had previously received acetate amendment the year prior. Phylogenetic analysis revealed a diverse Bacterial community, notably devoid of Archaea with 249 taxa from 9 Bacterial phyla including the dominance of uncultured candidate divisions, BD1-5, OD1, and OP11. We have reconstructed 86 partial to near-complete genomes and have performed a detailed characterization of the underlying metabolic potential of the ecosystem. We assessed the natural variation and redundancy in multi-heme c-type cytochromes, sulfite reductases, and central carbon metabolic pathways. Deep genomic sampling indicated the community contained various metabolic pathways: sulfur oxidation coupled to microaerophilic conditions, nitrate reduction with both acetate and inorganic compounds as donors, carbon and nitrogen fixation, antibiotic warfare, and heavy-metal detoxification. Proteomic investigations using predicted proteins from metagenomics corroborated that acetate oxidation is coupled to reduction of oxygen, sulfur, nitrogen, and iron across the samples. Of particular interest was the detection of acetate oxidizing and sulfate reducing proteins from a Desulfotalea-like bacterium in all three time points, suggesting that aqueous sulfide produced by active sulfate-reducing bacteria could contribute to abiotic iron reduction during the dominant iron reduction phase. Additionally, proteogenomic analysis verified that a large portion of the community, including members of the uncultivated BD1-5, are obligate fermenters, characterized by the presence of hydrogen-evolving hydrogenases, the capacity to oxidize complex organic carbon, as well as lack of membrane bound electron transport chains and an incomplete citric acid cycle. We propose that these organisms grow cryptically on residual biomass from previous biostimulation experiments and thus demonstrate that resource utilization and turnover in the aquifer can be decoupled from existing acetate amendment and external terminal electron accepting processes. In addition to the first recovery of multiple genomes from these novel candidate divisions, our community genomic approach uncovered viral diversity not yet observed at the site, with the reconstruction of six phage genomes and the presence of CRISPR loci detected in bacterial genomes from diverse lineages. These findings have implications for predictive ecosystem modeling, highlighting the importance of integrating the response, adaptation, as well as biological and geochemical feedback mechanisms existing within complex subsurface communities to long term organic carbon amendment.

Clathrate hydrate stability models for Titan: implications for a global subsurface ocean

NASA Astrophysics Data System (ADS)

Basu Sarkar, D.; Elwood Madden, M.

2013-12-01

Titan is the only planetary body in the solar system, apart from the Earth, with liquid at its surface. Titan's changing rotational period suggests that a global subsurface ocean decouples the icy crust from the interior. Several studies predict the existence of such an internal ocean below an Ice I layer, ranging in depth between a few tens of kilometers to a few hundreds of kilometers, depending on the composition of the icy crust and liquid-ocean. While the overall density of Titan is well constrained, the degree of differentiation within the interior is unclear. These uncertainties lead to poor understanding of the volatile content of the moon. However, unlike other similar large icy moons like Ganymede and Callisto, Titan has a thick nitrogen atmosphere, with methane as the second most abundant constituent - 5% near the surface. Titan's atmosphere, surface, and interior are likely home to various compounds such as C2H6, CO2, Ar, N2 and CH4, capable of forming clathrate hydrates. In addition, the moon has low temperature and low-to-high pressure conditions required for clathrate formation. Therefore the occurrence of extensive multicomponent hydrates may effect the composition of near-surface materials, the subsurface ocean, as well as the atmosphere. This work uses models of hydrate stability for a number of plausible hydrate formers including CH4, C2H6, CH4 + C2H6 and CH4 + NH3, and equilibrium geothermal gradients for probable near-surface materials to delineate the lateral and vertical extent of clathrate hydrate stability zones for Titan. By comparing geothermal gradients with clathrate stability fields for these systems we investigate possible compositions of Titan's global subsurface ocean. Preliminary model results indicate that ethane hydrates or compound hydrates of ethane and methane could be destabilized within the proposed depth range of the internal ocean, while methane/ammonia or pure methane hydrates may not be affected. Therefore, ethane or ethane-methane clathrates may be a major component of Titan's icy shell. Modeled geothermal gradients and stability fields of possible clathrate formers with three different scenarios for an internal ocean from the recent literature. Geothermal gradients obtained from thermal conductivity and density representing water ice and pure CH4-C2H6 hydrate. Clathrate stability field determined using HYDOFF and recent publications of NH3 clathrate stability.

The Use of Molecular and Genomic Techniques Applied to Microbial Diversity, Community Structure, and Activities at DNAPL and Metal Contaminated Sites

EPA Science Inventory

A wide variety of in situ subsurface remediation strategies have been developed to mitigate contamination by chlorinated solvent dense non-aqueous phase liquids (DNAPLS) and metals. Geochemical methods include: zerovalent iron emplacement, various electrolytic applications, elec...

Evaluation of the impact of lime softening waste disposal in natural environments

EPA Science Inventory

Drinking water treatment residues (WTR), generated from the lime softening processes, are commonly reused or disposed of in a number of applications; these include use as a soil amendment or a subsurface fill. Recently questions were posed by the Florida regulatory community on w...

Assessing impacts of land-applied manure from concentrated animal feeding operations on fish populations and communities

EPA Science Inventory

Concentrated animal feeding operation (CAFO) waste is a cost effective fertilizer. In the Midwest, networks of subsurface tile-drains expedite transport of animal hormones and nutrients from land-applied CAFO waste to adjacent waterways. The objective of this study was to evaluat...

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.

Bioenergy from coastal bermudagrass receiving subsurface drip irrigation with advance-treated swine wastewater

USDA-ARS?s Scientific Manuscript database

Coastal bermudagrass (Cynodon dactylon L.) may be a potentially important source of bio-based energy in the southern United States due to its vast acreage. It is often produced as part of a waste management plan with varying nutrient composition and energy characteristics on fields irrigated with li...

A 1064 nm dispersive Raman spectral imaging system for food safety and quality evaluation

USDA-ARS?s Scientific Manuscript database

Raman spectral imaging is an effective method to analyze and evaluate chemical composition and structure of a sample, and has many applications for food safety and quality research. This study developed a 1064 nm Raman spectral imaging system for surface and subsurface analysis of food samples. A 10...

Dense Nonaqueous Phase Liquids at Former Manufactured Gas Plants: Challenges to Modeling and Remediation

PubMed Central

Birak, P.S.; Miller, C.T.

2008-01-01

The remediation of dense non-aqueous phase liquids (DNAPLs) in porous media continues to be one of the most challenging problems facing environmental scientists and engineers. Of all the environmentally relevant DNAPLs, tars in the subsurface at former manufactured gas plants (FMGP’s) pose one of the biggest challenges due to their complex chemical composition and tendency to alter wettability. To further our understanding of these complex materials, we consulted historic documentation to evaluate the impact of gas manufacturing on the composition and physicochemical nature of the resulting tars. In the recent literature, most work to date has been focused in a relatively narrow portion of the expected range of tar materials, which has yielded a bias toward samples of relatively low viscosity and density. In this work, we consider the dissolution and movement of tars in the subsurface, models used to predict these phenomena, and approaches used for remediation. We also explore the open issues and detail important gaps in our fundamental understanding of these extraordinarily complex systems that must be resolved to reach a mature level of understanding. PMID:19176266

Experimental Evaluation of Hot Films on Ceramic Substrates for Skin-Friction Measurement

NASA Technical Reports Server (NTRS)

Noffz, Gregory K.; Lavine, Adrienne S.; Hamory, Philip J.

2003-01-01

An investigation has been performed on the use of low-thermal conductivity, ceramic substrates for hot films intended to measure skin friction. Hot films were deposited on two types of ceramic substrates. Four hot films used composite-ceramic substrates with subsurface thermocouples (TCs), and two hot films were deposited on thin Macor(R) substrates. All six sensors were tested side by side in the wall of the NASA Glenn Research Center 8-ft by 6-ft Supersonic Wind Tunnel (SWT). Data were obtained from zero flow to Mach 1.98 in air. Control measurements were made with three Preston tubes and two boundary-layer rakes. The tests were repeated at two different hot film power levels. All hot films and subsurface TCs functioned throughout the three days of testing. At zero flow, the films on the high-thermal conductivity Macor(R) substrates required approximately twice the power as those on the composite-ceramic substrates. Skin-friction results were consistent with the control measurements. Estimates of the conduction heat losses were made using the embedded TCs but were hampered by variability in coating thicknesses and TC locations.

Processes contributing to resilience of coastal wetlands to sea-level rise

USGS Publications Warehouse

Stagg, Camille L.; Krauss, Ken W.; Cahoon, Donald R.; Cormier, Nicole; Conner, William H.; Swarzenski, Christopher M.

2016-01-01

The objectives of this study were to identify processes that contribute to resilience of coastal wetlands subject to rising sea levels and to determine whether the relative contribution of these processes varies across different wetland community types. We assessed the resilience of wetlands to sea-level rise along a transitional gradient from tidal freshwater forested wetland (TFFW) to marsh by measuring processes controlling wetland elevation. We found that, over 5 years of measurement, TFFWs were resilient, although some marginally, and oligohaline marshes exhibited robust resilience to sea-level rise. We identified fundamental differences in how resilience is maintained across wetland community types, which have important implications for management activities that aim to restore or conserve resilient systems. We showed that the relative importance of surface and subsurface processes in controlling wetland surface elevation change differed between TFFWs and oligohaline marshes. The marshes had significantly higher rates of surface accretion than the TFFWs, and in the marshes, surface accretion was the primary contributor to elevation change. In contrast, elevation change in TFFWs was more heavily influenced by subsurface processes, such as root zone expansion or compaction, which played an important role in determining resilience of TFFWs to rising sea level. When root zone contributions were removed statistically from comparisons between relative sea-level rise and surface elevation change, sites that previously had elevation rate deficits showed a surplus. Therefore, assessments of wetland resilience that do not include subsurface processes will likely misjudge vulnerability to sea-level rise.

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

The role of hypoxia in structuring macrobenthos community off the Louisiana shelf

NASA Astrophysics Data System (ADS)

Shivarudrappa, S. K.; Briggs, K.

2013-12-01

Core samples were collected from 24 box cores belonging to four different provinces with varying hypoxia frequency and history in the northern Gulf of Mexico. Macrobenthos from these four provinces were sampled in spring, summer and late-summer seasons. According to historical data of bottom water oxygen concentration since 1985, the control province was exposed to hypoxia <25% of the time, the province 1 was exposed to hypoxia between 50% and 75% of the time, the province 2 was exposed to hypoxia between 25% and 50% of the time, and the province 3 was exposed to hypoxia more than 75% of the time. Samples from the three cruises performed between April 2009 and August 2010 were vertically sectioned to 25 cm sediment depth and analyzed for abundance, biomass, species diversity, and feeding types. Seasonal variability within provinces and between provinces was analyzed in terms of abundance and biomass. The Bray-Curtis dissimilarity indices indicated the four provinces have similar community composition, yet showed the impact of hypoxia in assemblages making up the four communities. Diversity indices were highest for the control province and lowest for province 3 during all three seasons, whereas diversity indices for provinces 1 and 2 showed variable seasonal variations due to hypoxia. Separation of the control province from province 3 at all three samplings by principal component analysis indicated the communities of these two provinces did not change over the period of the study. This difference in assemblages was confirmed by rarefaction curves of expected species diversity. Impact of grain size and organic matter concentration on the community structure was assessed using non-metric multi-dimensional scaling. Different species dominated by their abundance or their biomass at all four provinces, but the effect was magnified in the provinces other than the control. Capitellid, cossurid and spionid polychaetes dominated by abundance, whereas maldanid and nephtyid polychaetes and Nemerteans dominated by biomass. This implies that the fauna responsible for dominance by their abundance were small, opportunistic deposit feeders, and that large carnivores contributed to dominance by their biomass. Although species and abundance changed from province to province and season to season, the functional groups were nevertheless dominated, in order, by subsurface deposit feeders, surface deposit feeders, and carnivores at all provinces in all three seasons. This study provides insight into compositional changes in the macrobenthic community due to hypoxia and subsequent recovery from hypoxia on the northern Gulf of Mexico shelf between the Mississippi and Atchafalaya Rivers.

Fire severity mediates climate-driven shifts in understorey community composition of black spruce stands of interior Alaska

Treesearch

Emily L. Bernhardt; Teresa N. Hollingsworth; F. Stuart Chapin

2011-01-01

Question: How do pre-fire conditions (community composition and environmental characteristics) and climate-driven disturbance characteristics (fire severity) affect post-fire community composition in black spruce stands? Location: Northern boreal forest, interior Alaska. Methods: We compared plant community composition and environmental stand characteristics in 14...

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.

Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil.

PubMed

von der Weid, Irene; Korenblum, Elisa; Jurelevicius, Diogo; Rosado, Alexandre Soares; Dino, Rodolfo; Sebastian, Gina Vasquez; Seldin, Lucy

2008-01-01

The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oilcontamination and very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such deep subsurface environment.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

USGS Publications Warehouse

Waldrop, Mark P.; Holloway, JoAnn M.; Smith, David; Goldhaber, Martin B.; Drenovsky, R.E.; Scow, K.M.; Dick, R.; Howard, Daniel M.; Wylie, Bruce K.; Grace, James B.

2017-01-01

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils.

Color images of Kansas subsurface geology from well logs

USGS Publications Warehouse

Collins, D.R.; Doveton, J.H.

1986-01-01

Modern wireline log combinations give highly diagnostic information that goes beyond the basic shale content, pore volume, and fluid saturation of older logs. Pattern recognition of geology from logs is made conventionally through either the examination of log overlays or log crossplots. Both methods can be combined through the use of color as a medium of information by setting the three color primaries of blue, green, and red light as axes of three dimensional color space. Multiple log readings of zones are rendered as composite color mixtures which, when plotted sequentially with depth, show lithological successions in a striking manner. The method is extremely simple to program and display on a color monitor. Illustrative examples are described from the Kansas subsurface. ?? 1986.

Temporal changes in randomness of bird communities across Central Europe.

PubMed

Renner, Swen C; Gossner, Martin M; Kahl, Tiemo; Kalko, Elisabeth K V; Weisser, Wolfgang W; Fischer, Markus; Allan, Eric

2014-01-01

Many studies have examined whether communities are structured by random or deterministic processes, and both are likely to play a role, but relatively few studies have attempted to quantify the degree of randomness in species composition. We quantified, for the first time, the degree of randomness in forest bird communities based on an analysis of spatial autocorrelation in three regions of Germany. The compositional dissimilarity between pairs of forest patches was regressed against the distance between them. We then calculated the y-intercept of the curve, i.e. the 'nugget', which represents the compositional dissimilarity at zero spatial distance. We therefore assume, following similar work on plant communities, that this represents the degree of randomness in species composition. We then analysed how the degree of randomness in community composition varied over time and with forest management intensity, which we expected to reduce the importance of random processes by increasing the strength of environmental drivers. We found that a high portion of the bird community composition could be explained by chance (overall mean of 0.63), implying that most of the variation in local bird community composition is driven by stochastic processes. Forest management intensity did not consistently affect the mean degree of randomness in community composition, perhaps because the bird communities were relatively insensitive to management intensity. We found a high temporal variation in the degree of randomness, which may indicate temporal variation in assembly processes and in the importance of key environmental drivers. We conclude that the degree of randomness in community composition should be considered in bird community studies, and the high values we find may indicate that bird community composition is relatively hard to predict at the regional scale.

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

Microbial Colonization of Earth's Subsurface: A Thermodynamically Consistent Perspective

NASA Astrophysics Data System (ADS)

Bethke, C. M.; Sanford, R. A.; Jin, Q.; Kirk, M. F.

2014-12-01

The nature of how anaerobic microbes have come to distribute themselves within Earth's crust is an ecologic question that must be posed subject to the laws of thermodynamics, but a question that cannot be understood in light of thermodynamics alone. We use here the results of theory and quantitative modeling, field observations, and long-term laboratory experiments to argue that subsurface communities are composed of groups of microbes that cooperate as well as compete, and whose existence reflects a tight balance between reproduction and cell death. The most significant functional groups colonizing the anoxic crust, classified by electron accepting process, are the methanogens, sulfate reducers, and ferric iron reducers. An anaerobe can harvest the energy it needs to live and reproduce only to the extent that energy available to it in the environment exceeds the cell's internal levels. When methanogens transfer or dismutate electrons, they capture little energy, so as to preserve a thermodynamic drive for their catabolic reaction. In this way, they maximize their environmental range, but grow slowly. Sulfate reducers adopt a different strategy, striving to capture energy quickly and grow rapidly. Iron reduction consumes acid, so the energy available to iron reducers varies sharply with pH. The iron reducers can grow rapidly under acidic conditions, but an alkaline environment may leave them insufficient energy to live. Methane producers are vulnerable to exclusion in the subsurface, as is broadly appreciated, but not because of energetic limitations. Instead, the methanogens require abundant energy substrates in order to reproduce quickly enough to replace cells as they die. Sulfate reducers and iron reducers, instead of working to exclude each other by competing for limited energy sources, as is commonly believed, thrive in mutualistic communities. The three functional groups by necessity compete in their environments for limited sources of energy, but the manner in which the groups have come to colonize the subsurface is richer and more nuanced than can be explained by competition alone.

Finite Element Modeling of the Thermographic Inspection for Composite Materials

NASA Technical Reports Server (NTRS)

Bucinell, Ronald B.

1996-01-01

The performance of composite materials is dependent on the constituent materials selected, material structural geometry, and the fabrication process. Flaws can form in composite materials as a result of the fabrication process, handling in the manufacturing environment, and exposure in the service environment to anomalous activity. Often these flaws show no indication on the surface of the material while having the potential of substantially degrading the integrity of the composite structure. For this reason it is important to have available inspection techniques that can reliably detect sub-surface defects such as inter-ply disbonds, inter-ply cracks, porosity, and density changes caused by variations in fiber volume content. Many non-destructive evaluation techniques (NDE) are capable of detecting sub-surface flaws in composite materials. These include shearography, video image correlation, ultrasonic, acoustic emissions, and X-ray. The difficulty with most of these techniques is that they are time consuming and often difficult to apply to full scale structures. An NDE technique that appears to have the capability to quickly and easily detect flaws in composite structure is thermography. This technique uses heat to detect flaws. Heat is applied to the surface of a structure with the use of a heat lamp or heat gun. A thermographic camera is then pointed at the surface and records the surface temperature as the composite structure cools. Flaws in the material will cause the thermal-mechanical material response to change. Thus, the surface over an area where a flaw is present will cool differently than regions where flaws do not exist. This paper discusses the effort made to thermo-mechanically model the thermography process. First the material properties and physical parameters used in the model will be explained. This will be followed by a detailed discussion of the finite element model used. Finally, the result of the model will be summarized along with recommendations for future work.

Unusual cohabitation and competition between Planktothrix rubescens and Microcystis sp. (cyanobacteria) in a subtropical reservoir (Hammam Debagh) located in Algeria

PubMed Central

Guellati, Fatma Zohra; Touati, Hassen; Tambosco, Kevin; Quiblier, Catherine; Bensouilah, Mourad

2017-01-01

Succession in bloom-forming cyanobacteria belonging to distant functional groups in freshwater ecosystems is currently an undescribed phenomenon. However in the Hammam Debagh reservoir (Algeria), P. rubescens and Microcystis sp. co-occur and sometimes proliferate. With the aim of identifying the main factors and processes involved in this unusual cohabitation, water samples were collected monthly from February 2013 to June 2015 at the subsurface at four sampling stations and along the entire water column at one sampling station. In addition, the composition of the cyanobacterial communities was estimated by Illumina sequencing of a 16S rRNA gene fragment from samples collected over one year (October 2013-November 2014). This molecular approach showed that the Hammam Debagh reservoir displays high species richness (89 species) but very low diversity due to the high dominance of Microcystis in this community. Furthermore, it appears that Planktothrix rubescens and Microcystis sp. coexisted (from September to January) but proliferated alternately (Spring 2015 for P. rubescens and Spring 2014 and Autumn 2014/2015 for Microcystis). The main factors and processes explaining these changes in bloom-forming species seem to be related to the variation in the depth of the lake during the mixing period and to the water temperatures during the winter prior to the bloom season in spring. PMID:28859113

Surge Block Method for Controlling Well Clogging and Sampling Sediment during Bioremediation

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

Wu, Wei-min; Watson, David B; Luo, Jian

2013-01-01

A surge block treatment method (i.e. inserting a solid rod plunger with a flat seal that closely fits the casing interior into a well and stocking it up and down) was performed for the rehabilitation of wells clogged with biomass and for the collection of time series sediment samples during in situ bioremediation tests for U(VI) immobilization at a the U.S. Department of Energy site in Oak Ridge, TN. The clogging caused by biomass growth had been controlled by using routine surge block treatment for18 times over a nearly four year test period. The treatment frequency was dependent of themore » dosage of electron donor injection and microbial community developed in the subsurface. Hydraulic tests showed that the apparent aquifer transmissivity at a clogged well with an inner diameter (ID) of 10.16 cm was increased by 8 13 times after the rehabilitation, indicating the effectiveness of the rehabilitation. Simultaneously with the rehabilitation, the surge block method was successfully used for collecting time series sediment samples composed of fine particles (clay and silt) from wells with ID 1.9 10.16 cm for the analysis of mineralogical and geochemical composition and microbial community during the same period. Our results demonstrated that the surge block method provided a cost-effective approach for both well rehabilitation and frequent solid sampling at the same location.« less

CO2 and CH4 Surface Flux, Soil Profile Concentrations, and Stable Isotope Composition, Barrow, Alaska, 2012-2013

DOE Data Explorer

Curtis, J.B.; Vaughn, L.S.; Torn, M.S.; Conrad, M.S.; Chafe, O.; Bill, M.

2015-12-31

In August-October 2012 and June-October 2013, co-located measurements were made of surface CH4 and CO2 flux, soil pore space concentrations and stable isotope compositions of CH4 and CO2, and subsurface temperature and soil moisture. Measurements were made in intensive study site 1 areas A, B, and C, and from the site 0 and AB transects, from high-centered, flat-centered, and low-centered polygons, from the center, edge, and trough of each polygon.

A petrographic thin sectioning technique for evaluating composite materials

NASA Technical Reports Server (NTRS)

Parker, D. S.; Yee, A. F.

1989-01-01

Petrographic thin sectioning by a low-speed diamond saw has been used in conjunction with transmission polarized light microscopy for the characterization of the microstructure and deformation mechanisms of a variety of polymer systems. It has proven possible by these means to study three types of thermoplastic matrices for composite applications: PEEK, BPA-based polycarbonate (PC), and a rubber-modified PC. The reinforcing fibers for these matrices were in all cases AS4 carbon fibers, unidirectionally arrayed. Superior analyzability of matrix morphology and subsurface fracture processes is achieved by thin sectioning.

Methods of hydrotreating a liquid stream to remove clogging compounds

DOEpatents

Minderhoud, Johannes Kornelis [Amsterdam, NL; Nelson, Richard Gene [Katy, TX; Roes, Augustinus Wilhelmus Maria [Houston, TX; Ryan, Robert Charles [Houston, TX; Nair, Vijay [Katy, TX

2009-09-22

A method includes producing formation fluid from a subsurface in situ heat treatment process. The formation fluid is separated to produce a liquid stream and a gas stream. At least a portion of the liquid stream is provided to a hydrotreating unit. At least a portion of selected in situ heat treatment clogging compositions in the liquid stream are removed to produce a hydrotreated liquid stream by hydrotreating at least a portion of the liquid stream at conditions sufficient to remove the selected in situ heat treatment clogging compositions.

Methane and nitrous oxide cycling microbial communities in soils above septic leach fields: Abundances with depth and correlations with net surface emissions.

PubMed

Fernández-Baca, Cristina P; Truhlar, Allison M; Omar, Amir-Eldin H; Rahm, Brian G; Walter, M Todd; Richardson, Ruth E

2018-05-31

Onsite septic systems use soil microbial communities to treat wastewater, in the process creating potent greenhouse gases (GHGs): methane (CH 4 ) and nitrous oxide (N 2 O). Subsurface soil dispersal systems of septic tank overflow, known as leach fields, are an important part of wastewater treatment and have the potential to contribute significantly to GHG cycling. This study aimed to characterize soil microbial communities associated with leach field systems and quantify the abundance and distribution of microbial populations involved in CH 4 and N 2 O cycling. Functional genes were used to target populations producing and consuming GHGs, specifically methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) for CH 4 and nitric oxide reductase (cnorB) and nitrous oxide reductase (nosZ) for N 2 O. All biomarker genes were found in all soil samples regardless of treatment (leach field, sand filter, or control) or depth (surface or subsurface). In general, biomarker genes were more abundant in surface soils than subsurface soils suggesting the majority of GHG cycling is occurring in near-surface soils. Ratios of production to consumption gene abundances showed a positive relationship with CH 4 emissions (mcrA:pmoA, p < 0.001) but not with N 2 O emission (cnorB:nosZ, p > 0.05). Of the three measured soil parameters (volumetric water content (VWC), temperature, and conductivity), only VWC was significantly correlated to a biomarker gene, mcrA (p = 0.0398) but not pmoA or either of the N 2 O cycling genes (p > 0.05 for cnorB and nosZ). 16S rRNA amplicon library sequencing results revealed soil VWC, CH 4 flux and N 2 O flux together explained 64% of the microbial community diversity between samples. Sequencing of mcrA and pmoA amplicon libraries revealed treatment had little effect on diversity of CH 4 cycling organisms. Overall, these results suggest GHG cycling occurs in all soils regardless of whether or not they are associated with a leach field system. Copyright © 2018 Elsevier B.V. All rights reserved.

Surface Geology of Europa: A Window to Subsurface Composition and Habitability

NASA Astrophysics Data System (ADS)

Dalton, J. Brad; Shirley, James H.; Prockter, Louise M.

2010-05-01

Observations from the Galileo Near-Infrared Mapping Spectrometer (NIMS) provide a wealth of spectral information on the surface composition of Europa. Recent advances in the analysis of spacecraft observations, combined with newly available reference spectra of expected chemical compounds [Dalton et al., 2005], now permit investigation of composition for individual geologic units. Some of these units appear to represent low-viscosity cryovolcanic flows, presenting substantial evidence for subsurface origin. Subsequent processing by radiolysis and photolysis (chemistry driven by high-energy particle and ultraviolet radiation) has altered the composition of these deposits since their emplacement. It has been postulated that hydrated sulfate salts from the interior may have been converted to sulfuric acid hydrate by this exogenic processing [Carlson et al., 1999; McCord et al., 2002]. It has also been postulated that much of the observed sulfuric acid hydrate may be derived entirely from water ice and implanted sulfur ions from Jupiter's magnetosphere [Carlson et al., 2005]. Destruction of large molecules by the same radiation [Loeffler et al., 2010] however suggests that there may be an equilibrium between creation and destruction that varies based on sulfur content and radiation flux. Derivation of compositions for multiple exposures of individual surface units reveals a gradient in sulfuric acid abundance that increases from the leading hemisphere to the trailing hemisphere, which receives a higher radiogenic dose. Certain geologically young cryovolcanic flow surface units exhibit comparatively higher proportions of hydrated salts (with correspondingly lower abundance of sulfuric acid hydrate) than is found for older surface units of the same type, or for surface units of different geologic origin. Taken together these lines of evidence suggest that in at least some of these units, we are observing an intermediate stage of the conversion of endogenically-produced sodium and magnesium sulfate salts into sulfuric acid hydrate by exogenically-driven radiolysis. This is the first step in unraveling the relative influence of exogenic and endogenic processes in determining the composition of Europa's surface deposits. The apparent presence of large quantities of brine and sulfate salts in certain deposits [Shirley et al., 2010] suggests that these deposits may reflect the composition of subsurface liquid reservoirs that produced these deposits. We will report on variations in composition of various surface units and inferences of interior chemistry based on our spectral analysis. This information will be useful for planning of future missions that will have the capability to further discriminate between these materials and provide additional constraints on habitability of the subsurface. References: Carlson, R. W., R. E. Johnson, and M. S. Anderson, 1999. Sulfuric Acid on Europa and the Radiolytic Sulfur Cycle. Science 286, 97-99. Carlson, R. W., M. S. Anderson, R. Mehlman, and R.E. Johnson 2005. Distribution of Hydrate on Europa: Further Evidence for sulfuric acid hydrate, Icarus 177, 461-471. Dalton, J. B., O. Prieto-Ballesteros, J. S. Kargel, C. S. Jamieson, J. Jolivet, & R. Quinn 2005. Spectral comparison of heavily hydrated salts with disrupted terrains on Europa, Icarus 177, 472-490. McCord, T.B., G. Teeter, G.B. Hansen, M.T. Sieger, and T.M. Orlando, 2002. Brines exposed to Europa surface conditions. J. Geophys. Res. 107, doi 10.1029/2000JE001453. Loeffler, M.J., R.L. Hudson, and M.H. Moore, 2010. Ion irradiation of sulfuric acid: Implication for its stability on Europa, Proc. LPSC XLI, #1240. Shirley, J.H., J.B. Dalton, L.M. Prockter, and L.W. Kamp, 2010. Signatures of the Radiolytic Sulfur Cycle on Europa: A New Tool for Integrated Compositional and Stratigraphic Investigations, Proc. LPSC XLI, #2395.

Nanoscale zerovalent iron (nZVI) supported by natural and acid-activated sepiolites: the effect of the nZVI/support ratio on the composite properties and Cd2+ adsorption.

PubMed

Habish, Amal Juma; Lazarević, Slavica; Janković-Častvan, Ivona; Jokić, Bojan; Kovač, Janez; Rogan, Jelena; Janaćković, Đorđe; Petrović, Rada

2017-01-01

Natural (SEP) and partially acid-activated (AAS) sepiolites were used to prepare composites with nanoscale zerovalent iron (nZVI) at different (SEP or AAS)/nZVI ratios in order to achieve the best nZVI dispersibility and the highest adsorption capacity for Cd 2+ . Despite the higher surface area and pore volume of AAS, better nZVI dispersibility was achieved by using SEP as the support. On the other hand, a lower oxidation degree was achieved during the synthesis using AAS. X-ray photoelectron spectroscopy (XPS) analysis of the composite with the best nZVI dispersibility, before and after Cd 2+ adsorption, confirmed that the surface of the nZVI was composed of oxidized iron species. Metallic iron was not present on the surface, but it was detected in the subsurface region after sputtering. The content of zerovalent iron decreased after Cd 2+ adsorption as a result of iron oxidation during Cd 2+ adsorption. The XPS depth profile showed that cadmium was present not only at the surface of the composite but also in the subsurface region. The adsorption isotherms for Cd 2+ confirmed that the presence of SEP and AAS decreased the agglomeration of the nZVI particles in comparison to the pure nZVI, which provided a higher adsorption capacity. The results showed that the prevention of both aggregation and oxidation during the synthesis was necessary for obtaining an SEP/AAS-nZVI composite with a high adsorption capacity, but oxidation during adsorption was beneficial for Cd 2+ removal. The formation of strong bonds between Cd 2+ and the adsorbents sites of different energy until monolayer formation was proposed according to modeling of the adsorption isotherms.

Evolution of light hydrocarbon gases in subsurface processes: Constraints from chemical equilibrium

NASA Astrophysics Data System (ADS)

Sugisaki, Ryuichi; Nagamine, Koichiro

1995-06-01

The behaviour of CH 4, C 2H 6 and C 3H 8 in subsurface processes such as magma intrusion, volcanic gas discharge and natural gas generation have been examined from the viewpoint of chemical equilibrium. It seems that equilibrium among these three hydrocarbons is attainable at about 200°C. When a system at high temperatures is cooled, re-equilibration is continued until a low temperature is reached. The rate at which re-equilibration is achieved, however, steadily diminishes and, below 200°C, the reaction between the hydrocarbons stops and the gas composition at this time is frozen in, and it remains unchanged in a metastable state for a long period of geological time. Natural gas compositions from various fields have shown that, when a hydrocarbon system out of chemical equilibrium is heated, it gradually approaches equilibrium above 150°C. On the way towards equilibration, compositions of thermogenic gases apparently temporarily show a thermodynamic equilibrium constant at a temperature that is higher than the real equilibrium temperature expected from the ambient temperature of the samples; in contrast, biogenic gases indicate a lower temperature. In lower temperature regions, kinetic effects probably control the gas composition; the compositions are essentially subjected to genetic processes operating on the gases (such as pyrolysis of organic material and bacterial activity) and they fluctuate substantially. Examination of volcanic gases and pyrolysis experimental data, however, have suggested that the equilibration rate of these hydrocarbons is sluggish in comparison with that of reactive inorganic species such as H 2S and SO 2. The view presented in this study will be helpful in understanding the genetic processes that create oil and gas and the migration of these hydrocarbons and in interpreting the origins of magmatic gases.

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.

Model-based Analysis of Mixed Uranium(VI) Reduction by Biotic and Abiotic Pathways During in Situ Bioremediation

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

Zhao, Jiao; Scheibe, Timothy D.; Mahadevan, Radhakrishnan

2013-10-24

Uranium bioremediation has emerged as a potential strategy of cleanup of radionuclear contamination worldwide. An integrated geochemical & microbial community model is a promising approach to predict and provide insights into the bioremediation of a complicated natural subsurface. In this study, an integrated column-scale model of uranium bioremediation was developed, taking into account long-term interactions between biotic and abiotic processes. It is also combined with a comprehensive thermodynamic analysis to track the fate and cycling of biogenic species. As compared with other bioremediation models, the model increases the resolution of the connection of microbial community to geochemistry and establishes directmore » quantitative correlation between overall community evolution and geochemical variation, thereby accurately predicting the community dynamics under different sedimentary conditions. The thermodynamic analysis examined a recently identified homogeneous reduction of U(VI) by Fe(II) under dynamic sedimentary conditions across time and space. It shows that the biogenic Fe(II) from Geobacter metabolism can be removed rapidly by the biogenic sulphide from sulfate reducer metabolism, hence constituting one of the reasons that make the abiotic U(VI) reduction thermodynamically infeasible in the subsurface. Further analysis indicates that much higher influent concentrations of both Fe(II) and U(VI) than normal are required to for abiotic U(VI) reduction to be thermodynamically feasible, suggesting that the abiotic reduction cannot be an alternative to the biotic reduction in the remediation of uranium contaminated groundwater.« less

Large-scale variation in subsurface stream biofilms: a cross-regional comparison of metabolic function and community similarity.

PubMed

Findlay, S; Sinsabaugh, R L

2006-10-01

We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r2 approximately 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.

A comparative in situ decomposition study using still born piglets and leaf litter from a deciduous forest.

PubMed

Olakanye, Ayodeji O; Nelson, Andrew; Ralebitso-Senior, T Komang

2017-07-01

A cadaver and dead plant organic matter, or litter, are rich energy sources that undergo a complex decomposition process, which impact the surrounding environmental microbiota. Advances in molecular microbiology techniques, with study of the 16S RNA genes, in particular, have highlighted the application of forensic ecogenomics in addressing key knowledge gaps. To investigate subsurface microbiome shifts as a novel tool to establish "postmortem microbial clock" and augment postmortem interval (PMI) and time-since-burial estimations, an in situ study with triplicate underground burials of piglets as human taphonomic proxies and Quercus robur leaf litter was monitored for 270 days. Changes in microbial community structure and composition were related directly to changes in seasonal temperature, with microbial shifts more pronounced during the summer. For example, Methylococcaceae could be used as seasonal bacterial indicators, from winter to summer, in establishing postmortem microbial clock for this site. Furthermore, Methylophilaceae (Methylophilales order) and Anaerolineaceae would differentiate for the piglet and leaf litter soils, respectively, 180 days after internment. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome-Based Models to Optimize In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Waste Organic Matter

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

Lovley, Derek R

2012-12-28

The goal of this research was to provide computational tools to predictively model the behavior of two microbial communities of direct relevance to Department of Energy interests: 1) the microbial community responsible for in situ bioremediation of uranium in contaminated subsurface environments; and 2) the microbial community capable of harvesting electricity from waste organic matter and renewable biomass. During this project the concept of microbial electrosynthesis, a novel form of artificial photosynthesis for the direct production of fuels and other organic commodities from carbon dioxide and water was also developed and research was expanded into this area as well.

Evaluating runoff simulations from the Community Land Model 4.0 using observations from flux towers and a mountainous watershed

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

Li, Hongyi; Huang, Maoyi; Wigmosta, Mark S.

2011-12-24

Previous studies using the Community Land Model (CLM) focused on simulating landatmosphere interactions and water balance at continental to global scales, with limited attention paid to its capability for hydrologic simulations at watershed or regional scales. This study evaluates the performance of CLM 4.0 (CLM4) for hydrologic simulations, and explores possible directions of improvement. Specifically, it is found that CLM4 tends to produce unrealistically large temporal variation of runoff for applications at a mountainous catchment in the Northwest United States where subsurface runoff is dominant, as well as at a few flux tower sites. We show that runoff simulations frommore » CLM4 can be improved by: (1) increasing spatial resolution of the land surface representations; (2) calibrating parameter values; (3) replacing the subsurface formulation with a more general nonlinear function; (4) implementing the runoff generation schemes from the Variability Infiltration Capacity (VIC) model. This study also highlights the importance of evaluating both the energy and water fluxes application of land surface models across multiple scales.« less

Design, construction and performance of a horizontal subsurface flow wetland system in Australia.

PubMed

Bolton, Lise M W; Bolton, Keith G E

2013-01-01

Malabugilmah is a remote Aboriginal community located in Clarence Valley, Northern NSW, Australia. In 2006, seven horizontal subsurface flow wetland clusters consisting of 3 m × 2 m wetland cells in series were designed and constructed to treat septic tank effluent to a secondary level (Total Suspended Solids (TSS) < 30 mg/L and Biochemical Oxygen Demand (BOD5) <20 mg/L) and achieve >50% Total Nitrogen (TN) reduction, no net Total Phosphorus (TP) export and ≥99.9% Faecal Coliform (FC) reduction. The wetland cell configuration allowed the wetlands to be located on steeper terrain, enabling effluent to be treated to a secondary level without the use of pumps. In addition to the water quality targets, the wetlands were designed and constructed to satisfy environmental, economic and social needs of the community. The wetland systems were planted with a local Australian wetland tree species which has become well established. Two wetland clusters have been monitored over the last 4 years. The wetlands have demonstrated to be robust over time, providing a high level of secondary treatment over an extended period.

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

NASA Astrophysics Data System (ADS)

Beller, H. R.; Han, R.; Karaoz, U.; Lim, H.; Brodie, E. L.

2012-12-01

Pelosinus species are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with Hanford 100H aquifer sediment (constituting 80% of the total bacterial population in the columns). Strain HCF1 ferments lactate to propionate and acetate (a complete fermentation pathway was identified in the genome) and its genome encodes both [NiFe]- and [FeFe]-hydrogenases for H2 cycling. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides. In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of nitrate reductases and hydrogenases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.

Nde of Frp Wrapped Columns Using Infrared Thermography

NASA Astrophysics Data System (ADS)

Halabe, Udaya B.; Dutta, Shasanka Shekhar; GangaRao, Hota V. S.

2008-02-01

This paper investigates the feasibility of using Infrared Thermography (IRT) for detecting debonds in Fiber Reinforced Polymer (FRP) wrapped columns. Laboratory tests were conducted on FRP wrapped concrete cylinders of size 6″×12″ (152.4 mm×304.8 mm) in which air-filled and water-filled debonds of various sizes were placed underneath the FRP wraps. Air-filled debonds were made by cutting plastic sheets into the desired sizes whereas water-filled debonds were made by filling water in custom made polyethylene pouches. Both carbon and glass fiber reinforced wraps were considered in this study. Infrared tests were conducted using a fully radiometric digital infrared camera which was successful in detecting air-filled as well as water-filled subsurface debonds. In addition to the laboratory testing, two field trips were made to Moorefield, West Virginia for detecting subsurface debonds in FRP wrapped timber piles of a railroad bridge using infrared testing. The results revealed that infrared thermography can be used as an effective nondestructive evaluation tool for detecting subsurface debonds in structural components wrapped with carbon or glass reinforced composite fabrics.

Cu-rGO subsurface layer creation on copper substrate and its resistance to oxidation

NASA Astrophysics Data System (ADS)

Pietrzak, Katarzyna; Strojny-Nędza, Agata; Olesińska, Wiesława; Bańkowska, Anna; Gładki, Andrzej

2017-11-01

On the basis of a specially designed experiment, this paper presents a model, which is an attempt to explain the mechanism of formatting and creating oxidation resistance of Cu-rGO subsurface layers. Practically zero chemical affinity of copper to carbon is a fundamental difficulty in creating composite structures of Cu-C, properties which are theoretically possible to estimate. In order to bind the thermally reduced graphene oxide with copper surface, the effect of structural rebuilding of the copper oxide, in the process of annealing in a nitrogen atmosphere, have been used. On intentionally oxidized and anoxic copper substrates the dispersed graphene oxide (GO) and thermally reduced graphene oxide (rGO) were loaded. Annealing processes after the binding effects of both graphene oxide forms to Cu substrates were tested. The methods for high-resolution electron microscopy were found subsurface rGO-Cu layer having a substantially greater resistance to oxidation than pure copper. The mechanism for the effective resistance to oxidation of the Cu-rGO has been presented in a hypothetical form.

Characterizing fish community diversity across Virginia landscapes: Prerequisite for conservation

USGS Publications Warehouse

Angermeier, P.L.; Winston, M.R.

1999-01-01

The number of community types occurring within landscapes is an important, but often unprotected, component of biological diversity. Generally applicable protocols for characterizing community diversity need to be developed to facilitate conservation. We used several multivariate techniques to analyze geographic variation in the composition of fish communities in Virginia streams. We examined relationships between community composition and six landscape variables: drainage basin, physiography, stream order, elevation, channel slope, and map coordinates. We compared patterns at two scales (statewide and subdrainage-specific) to assess sensitivity of community classification to spatial scale. We also compared patterns based on characterizing communities by species composition vs. ecological composition. All landscape variables explained significant proportions of the variance in community composition. Statewide, they explained 32% of the variance in species composition and 48% of the variance in ecological composition. Typical communities in each drainage or physiography were statistically distinctive. Communities in different combinations of drainage, physiography, and stream size were even more distinctive, but composition was strongly spatially autocorrelated. Ecological similarity and species similarity of community pairs were strongly related, but replacement by ecologically similar species was common among drainage-physiography combinations. Landscape variables explained significant proportions of variance in community composition within selected subdrainages, but proportions were less than at the statewide scale, and the explanatory power of individual variables varied considerably among subdrainages. Community variation within subdrainages appeared to be much more closely related to environmental variation than to replacement among ecologically similar species. Our results suggest that taxonomic and ecological characterizations of community composition are complementary; both are useful in a conservation context. Landscape features such as drainage, physiography, and water body size generally may provide a basis for assessing aquatic community diversity, especially in regions where the biota is poorly known. Systematic conservation of community types would be a major advance relative to most current conservation programs, which typically focus narrowly on populations of imperiled species. More effective conservation of aquatic biodiversity will require new approaches that recognize the value of both species and assemblages, and that emphasize protection of key landscape-scale processes.

Estimation of Mars radar backscatter from measured surface rock populations

USGS Publications Warehouse

Baron, J.E.; Simpson, R.A.; Tyler, G.L.; Moore, H.J.; Harmon, J.K.

1998-01-01

Reanalysis of rock population data at the Mars Viking Lander sites has yielded updated values of rock fractional surface coverage (about 0.16 at both sites, including outcrops) and new estimates of rock burial depths and axial ratios. These data are combined with a finite difference time domain (FDTD) numerical scattering model to estimate diffuse backscatter due to rocks at both the Lander l (VL1) and Lander 2 (VL2) sites. We consider single scattering from both surface and subsurface objects of various shapes, ranging from an ideal sphere to an accurate digitized model of a terrestrial rock. The FDTD cross-section calculations explicitly account for the size, shape, composition, orientation, and burial state of the scattering object, the incident wave angle and polarization, and the composition of the surface. We calculate depolarized specific cross sections at 12.6 cm wavelength due to lossless rock-like scatterers of about 0.014 at VL1 and 0.023 at VL2, which are comparable to the measured ranges of 0.019-0.032 and 0.012-0.018, respectively. We also discuss the variation of the diffuse cross section as the local angle of incidence, ??i, changes. Numerical calculations for a limited set of rock shapes indicate a marked difference between the angular backscattering behavior of wavelength-scale surface and subsurface rocks: while subsurface rocks scatter approximately as a cosine power law, surface rocks display a complex variation, often with peak backscattering at high incidence angles (??i = 70??-75??). Copyright 1998 by the American Geophysical Union.

Latitude Variation of the Subsurface Lunar Temperature: Lunar Prospector Thermal Neutrons

NASA Astrophysics Data System (ADS)

Little, R. C.; Feldman, W. C.; Maurice, S.; Genetay, I.; Lawrence, D. J.; Lawson, S. L.; Gasnault, O.; Barraclough, B. L.; Elphic, R. C.; Prettyman, T. H.; Binder, A. B.

2001-05-01

Planetary thermal neutron fluxes provide a sensitive proxy for mafic and feldspathic terranes, and are also necessary for translating measured gamma-ray line strengths to elemental abundances. Both functions require a model for near surface temperatures and a knowledge of the dependence of thermal neutron flux on temperature. We have explored this dependence for a representative sample of lunar soil compositions and surface temperatures using MCNP. For all soil samples, the neutron density is found to be independent of temperature, in accord with neutron moderation theory. The thermal neutron flux, however, does vary with temperature in a way that depends on D, the ratio of macroscopic absorption to energy-loss cross sections of soil compositions. The weakest dependence is for the largest D (which corresponds to the Apollo 17 high Ti basalt in our soil selection), and the largest dependence is for the lowest D (which corresponds to ferroan anorthosite, [FAN] in our selection). For the lunar model simulated, the depth at which the thermal neutron population is most sensitive to temperature is ~30 g/cm**2. These simulations were compared with the flux of thermal neutrons measured using the Lunar Prospector neutron spectrometer over the lunar highlands using a sub-surface temperature profile that varies with latitude, L, as (Cos L)**0.25. The fit is excellent. The best fitting equatorial temperature is determined to be, Teq=224+/-40 K. This temperature range brackets the average temperature measured below the thermal wave at the equator, Tmeas = 252+/-3K [Langseth and Keihm, 1977]. The present result represents the first measurement of subsurface temperature from orbit using neutrons.

The association of hydrogen with sulfur on Mars across latitudes, longitudes, and compositional extremes

NASA Astrophysics Data System (ADS)

Karunatillake, Suniti; Wray, James J.; Gasnault, Olivier; McLennan, Scott M.; Deanne Rogers, A.; Squyres, Steven W.; Boynton, William V.; Skok, J. R.; Button, Nicole E.; Ojha, Lujendra

2016-07-01

Midlatitudinal hydrated sulfates on Mars may influence brine pH, atmospheric humidity, and collectively water activity. These factors affect the habitability of the planetary subsurface and the preservation of relict biomolecules. Regolith at grain sizes smaller than gravel, constituting the bulk of the Martian subsurface at regional scales, may be a primary repository of chemical alteration, mechanical alteration, and biosignatures. The Mars Odyssey Gamma Ray Spectrometer with hundreds of kilometers of lateral resolution and compositional sensitivity to decimeter depth provides unique insight into this component of the regolith, which we call soil. Advancing the globally compelling association between H2O and S established by our previous work, we characterize latitudinal variations in the association between H and S, as well as in the hydration state of soil. Represented by H2O:S molar ratios, the hydration state of candidate sulfates increases with latitude in the northern hemisphere. In contrast, hydration states generally decrease with latitude in the south. Furthermore, we observe that H2O concentration may affect the degree of sulfate hydration more than S concentration. Limited H2O availability in soil-atmosphere exchange and in subsurface recharge could explain such control exerted by H2O on salt hydration. Differences in soil thickness, ground ice table depths, atmospheric circulation, and insolation may contribute to hemispheric differences in the progression of hydration with latitude. Our observations support chemical association of H2O with S in the southern hemisphere as suggested by Karunatillake et al. (2014), including the possibility of Fe sulfates as a key mineral group.

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

Microbiology of Ultrabasic Groundwaters of the Coast Range Ophiolite, California

NASA Astrophysics Data System (ADS)

Schrenk, M. O.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Cardace, D.; Hoehler, T. M.; McCollom, T. M.

2013-12-01

Upon exposure to water, ultramafic rocks characteristic of the Earth's mantle undergo a process known as serpentinization. These water-rock reactions lead to highly reducing conditions and some of the highest pH values reported in nature. In contrast to alkaline soda lakes, actively serpentinizing environments exposed on land are commonly associated with low salinity freshwaters, imparting unique challenges upon their resident microbial communities. These environments are especially prevalent along continental margins, and cover extensive portions of the west coast of North America. Most studies of serpentinizing environments have focused upon springs that emanate from fractures in the subsurface. Here, we present microbiological data from a series of groundwater wells associated with active serpentinization in the California Coast Range, an ophiolite complex near Lower Lake, California. Waters from ultrabasic wells had lower microbial cell concentrations and diversity than were found in moderate pH wells in the same area. Bacteria consistently made up a higher proportion of the microbial communities compared to Archaea as determined by qPCR. High pH wells were dominated by taxa within the Betaproteobacteria and Clostridia, whereas moderate pH wells predominantly contained common soil taxa related to Gammaproteobacteria and Bacilli. Multivariate statistical analyses incorporating key environmental parameters supported these observations and also highlighted correlations between the high-pH taxa and the abundance of hydrogen and methane gas. Similarly, colony forming units of alkaliphilic microorganisms were consistently 1-2 orders of magnitude higher in the ultrabasic wells and were taxonomically distinct from the moderate pH groundwaters. Together, these results show that distinct populations inhabit subsurface environments associated with active serpentinization, consistent with previous observations, and suggest that Betaproteobacteria and Clostridia probably play significant roles in the microbiology of these ecosystems. The low diversity microbial communities of serpentinizing subsurface habitats are likely sustained by the high hydrogen and methane fluxes that emanate from such systems and further investigations will directly test their roles in mediating biogeochemical cycles in these environments.

Aromatic-degrading Sphingomonas isolates from the deep subsurface

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

Fredrickson, J.K.; Romine, M.F.; Balkwill, D.L.

An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1{omega}7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16SrRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequencemore » analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains could also grow on a broad range of aromatic compounds and could mineralize [{sup 14C}]toluene and [{sup 14C}]naphthalene. S. capsulata (ATCC 14666), Sphingomonas paucimobiolis (ATCC 29837), and one of the subsurface isolates were unable to grow on any of the aromatic compounds or mineralize toluene or naphthalene. These results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Sphingomonas species from this environment. 41 refs., 2 figs., 5 tabs.« less

Identification of subsurface structures using electromagnetic data and shape priors

NASA Astrophysics Data System (ADS)

Tveit, Svenn; Bakr, Shaaban A.; Lien, Martha; Mannseth, Trond

2015-03-01

We consider the inverse problem of identifying large-scale subsurface structures using the controlled source electromagnetic method. To identify structures in the subsurface where the contrast in electric conductivity can be small, regularization is needed to bias the solution towards preserving structural information. We propose to combine two approaches for regularization of the inverse problem. In the first approach we utilize a model-based, reduced, composite representation of the electric conductivity that is highly flexible, even for a moderate number of degrees of freedom. With a low number of parameters, the inverse problem is efficiently solved using a standard, second-order gradient-based optimization algorithm. Further regularization is obtained using structural prior information, available, e.g., from interpreted seismic data. The reduced conductivity representation is suitable for incorporation of structural prior information. Such prior information cannot, however, be accurately modeled with a gaussian distribution. To alleviate this, we incorporate the structural information using shape priors. The shape prior technique requires the choice of kernel function, which is application dependent. We argue for using the conditionally positive definite kernel which is shown to have computational advantages over the commonly applied gaussian kernel for our problem. Numerical experiments on various test cases show that the methodology is able to identify fairly complex subsurface electric conductivity distributions while preserving structural prior information during the inversion.

Evaluating the Competitive Use of the Subsurface: The Influence of Energy Storage and Production in Groundwater

NASA Astrophysics Data System (ADS)

Helmig, R.; Becker, B.; Flemisch, B.

2015-12-01

The natural subsurface is gaining in importance for a variety of engineering applications related to energy supply. At the same time it is already utilized in many ways. On the one hand, the subsurface with its groundwater system represents the most important source of drinking water; on the other hand, it contains natural resources such as petroleum, natural gas and coal. In recent years, the subsurface has been gaining importance as a resource of energy and as an energy and waste repository. It can serve as a short-, medium- or long-term storage medium for energy in various forms, e.g. in the form of methane (CH4), hydrogen (H2) or compressed air. The subsurface is also attracting increasing interest as a natural source of energy, regarding, for instance, the extraction of fossil methane by hydraulic fracturing or the utilization of geothermal energy as a renewable energy source. As a result, with increasing exploitation, resource conflicts are becoming more and more common and complex. Modeling concepts for simulating multiphase flow that can reproduce the high complexity of the underlying processes in an efficient way need to be developed. The application of these model concepts is of great importance with respect to feasibility, risk analysis, storage capacity and sensitivity issues. This talk will give an overview on possible utilization conflicts in subsurface systems and how the groundwater is affected. It will focus on presenting fundamental properties and functions of a compositional multiphase system in a porous medium and introduce basic multiscale and multiphysics concepts as well as formulate conser­vation laws for simulating energy storage in the subsurface. Large-scale simulations that show the general applicability of the modeling concepts of such complicated natural systems, especially the impact on the groundwater of simultaneously using geothermal energy and storing chemical and thermal energy, and how such real large-scale systems provide a good environment for balancing the efficiency potential and possible weaknesses of the approaches will be discussed.

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.

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar

PubMed Central

Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T.; Halpern, Malka

2015-01-01

Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness. PMID:26122961

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar.

PubMed

Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T; Halpern, Malka

2015-06-30

Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness.

Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

PubMed Central

Hu, Ziye; Meng, Han; Shi, Jin-Huan; Bu, Nai-Shun; Fang, Chang-Ming; Quan, Zhe-Xue

2014-01-01

Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA) are much higher than that of ammonia oxidizing bacteria (AOB). The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition. PMID:25101072

Salinization Sources Along the Lower Jordan River Under Draught Conditions

NASA Astrophysics Data System (ADS)

Holtzman, R.; Shavit, U.; Segal, M.; Vengosh, A.; Farber, E.; Gavrieli, I.

2003-12-01

The Lower Jordan River, once a flowing freshwater river, is suffering from an ongoing reduction of discharge and water quality. The river flows between the Sea of Galilee and the Dead Sea, an aerial distance of about 105 Km. The severe reduction is caused by an excessive exploitation of its sources and diversion of sewage and agricultural drainage into the river. The extreme low flows and low water quality threaten the natural existence of the river and its potential use for agriculture. In spite of its importance, little research has been done in the river. The objectives of the study were to measure the discharge and water composition along the river and to evaluate the main sources that control its flow and chemical characteristics. The hypothesis of the study was that interaction with subsurface flows significantly affects the river flow and chemical composition. The research is based on a detailed field study, which included flow rate measurements in the river and its tributaries, water sampling and analysis and mass balance calculations of water and solutes. A portable Acoustic Doppler Velocimeter (ADV) was used to measure velocities and bathymetry at different locations across the river sections. Due to accessibility constraints, a floating traverse construction, which enables the ADV's deployment from one bank of the river, was developed. It was found that flow rate ranges between 500-1,100 L/s in northern (upstream) sections and 300-1,650 L/s in the south. This low discharge represents a significant reduction from historical values and is lower than recent published estimations. This research represents base flows only, as the measurements were done during a period of two consecutive draught years. Calculated mass balance of water flows in the northern sections shows that the subsurface source contributes to the river around 200-670 L/s (30-80% of the river flow). Calculations of solute balance show that the subsurface flows add 20-50% of the mass of solutes (e.g. Sulfate) that flows in the river. The assumption of a hydraulic gradient that points at inflows from subsurface flows is encouraged by high water levels measured in nearby piezometers. Possible natural subsurface sources include shallow groundwater or rising of water from deep formations. The existence of adjacent thermal wells strengthens the reasonability of such water rise. Possible anthropogenic sources include return flows and effluents. The results are consistent and agree with the geochemical and isotopic analyses. It is concluded that the impact of the subsurface component on the Jordan River is significant and must be taken into consideration, for future water management schemes and implementation of the Peace Treaty between Israel and Jordan.

Geochemical and iron isotopic insights into hydrothermal iron oxyhydroxide deposit formation at Loihi Seamount

NASA Astrophysics Data System (ADS)

Rouxel, Olivier; Toner, Brandy; Germain, Yoan; Glazer, Brian

2018-01-01

Low-temperature hydrothermal vents, such as those encountered at Loihi Seamount, harbor abundant microbial communities and provide ideal systems to test hypotheses on biotic versus abiotic formation of hydrous ferric oxide (FeOx) deposits at the seafloor. Hydrothermal activity at Loihi Seamount produces abundant microbial mats associated with rust-colored FeOx deposits and variably encrusted with Mn-oxyhydroxides. Here, we applied Fe isotope systematics together with major and trace element geochemistry to study the formation mechanisms and preservation of such mineralized microbial mats. Iron isotope composition of warm (<60 °C), Fe-rich and H2S-depleted hydrothermal fluids yielded δ56Fe values near +0.1‰, indistinguishable from basalt values. Suspended particles in the vent fluids and FeOx deposits recovered nearby active vents yielded systematically positive δ56Fe values. The enrichment in heavy Fe isotopes between +1.05‰ and +1.43‰ relative to Fe(II) in vent fluids suggest partial oxidation of Fe(II) during mixing of the hydrothermal fluid with seawater. By comparing the results with experimentally determined Fe isotope fractionation factors, we determined that less than 20% of Fe(II) is oxidized within active microbial mats, although this number may reach 80% in aged or less active deposits. These results are consistent with Fe(II) oxidation mediated by microbial processes considering the expected slow kinetics of abiotic Fe oxidation in low oxygen bottom water at Loihi Seamount. In contrast, FeOx deposits recovered at extinct sites have distinctly negative Fe-isotope values down to -1.77‰ together with significant enrichment in Mn and occurrence of negative Ce anomalies. These results are best explained by the near-complete oxidation of an isotopically light Fe(II) source produced during the waning stage of hydrothermal activity under more oxidizing conditions. Light Fe isotope values of FeOx are therefore generated by subsurface precipitation of isotopically heavy Fe-oxides rather than by the activity of dissimilatory Fe reduction in the subsurface. Overall, Fe-isotope compositions of microbial mats at Loihi Seamount display a remarkable range between -1.2‰ and +1.6‰ which indicate that Fe isotope compositions of hydrothermal Fe-oxide precipitates are particularly sensitive to local environmental conditions where they form, and are less sensitive to abiotic versus biotic origins. It follows that FeOx deposits at Loihi Seamount provides important modern analogues for ancient seafloor Fe-rich deposits allowing for testing hypotheses about the biogeochemical cycling of Fe isotopes on early Earth.

Development of a Carbon Sequestration Visualization Tool using Google Earth Pro

NASA Astrophysics Data System (ADS)

Keating, G. N.; Greene, M. K.

2008-12-01

The Big Sky Carbon Sequestration Partnership seeks to prepare organizations throughout the western United States for a possible carbon-constrained economy. Through the development of CO2 capture and subsurface sequestration technology, the Partnership is working to enable the region to cleanly utilize its abundant fossil energy resources. The intent of the Los Alamos National Laboratory Big Sky Visualization tool is to allow geochemists, geologists, geophysicists, project managers, and other project members to view, identify, and query the data collected from CO2 injection tests using a single data source platform, a mission to which Google Earth Pro is uniquely and ideally suited . The visualization framework enables fusion of data from disparate sources and allows investigators to fully explore spatial and temporal trends in CO2 fate and transport within a reservoir. 3-D subsurface wells are projected above ground in Google Earth as the KML anchor points for the presentation of various surface subsurface data. This solution is the most integrative and cost-effective possible for the variety of users in the Big Sky community.

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.

A "mental models" approach to the communication of subsurface hydrology and hazards

NASA Astrophysics Data System (ADS)

Gibson, Hazel; Stewart, Iain S.; Pahl, Sabine; Stokes, Alison

2016-05-01

Communicating information about geological and hydrological hazards relies on appropriately worded communications targeted at the needs of the audience. But what are these needs, and how does the geoscientist discern them? This paper adopts a psychological "mental models" approach to assess the public perception of the geological subsurface, presenting the results of attitudinal studies and surveys in three communities in the south-west of England. The findings reveal important preconceptions and misconceptions regarding the impact of hydrological systems and hazards on the geological subsurface, notably in terms of the persistent conceptualisation of underground rivers and the inferred relations between flooding and human activity. The study demonstrates how such mental models can provide geoscientists with empirical, detailed and generalised data of perceptions surrounding an issue, as well reveal unexpected outliers in perception that they may not have considered relevant, but which nevertheless may locally influence communication. Using this approach, geoscientists can develop information messages that more directly engage local concerns and create open engagement pathways based on dialogue, which in turn allow both geoscience "experts" and local "non-experts" to come together and understand each other more effectively.

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

PubMed Central

Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

2014-01-01

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material. PMID:24705618

Field and Lab-Based Microbiological Investigations of the Marcellus Shale

NASA Astrophysics Data System (ADS)

Wishart, J. R.; Neumann, K.; Edenborn, H. M.; Hakala, A.; Yang, J.; Torres, M. E.; Colwell, F. S.

2013-12-01

The recent exploration of shales for natural gas resources has provided the opportunity to study their subsurface geochemistry and microbiology. Evidence indicates that shale environments are marked by extreme conditions such as high temperature and pressure, low porosity, permeability and connectivity, and the presence of heavy metals and radionuclides. It has been postulated that many of these shales are naturally sterile due to the high pressure and temperature conditions under which they were formed. However, it has been shown in the Antrim and New Albany shales that microbial communities do exist in these environments. Here we review geochemical and microbiological evidence for the possible habitation of the Marcellus shale by microorganisms and compare these conditions to other shales in the U.S. Furthermore, we describe the development of sampling and analysis techniques used to evaluate microbial communities present in the Marcellus shale and associated hydraulic fracturing fluid. Sampling techniques thus far have consisted of collecting flowback fluids from wells and water impoundments and collecting core material from previous drilling expeditions. Furthermore, DNA extraction was performed on Marcellus shale sub-core with a MoBio PowerSoil kit to determine its efficiency. Assessment of the Marcellus shale indicates that it has low porosity and permeability that are not conducive to dense microbial populations; however, moderate temperatures and a natural fracture network may support a microbial community especially in zones where the Marcellus intersects more porous geologic formations. Also, hydraulic fracturing extends this fracture network providing more environments where microbial communities can exist. Previous research which collected flowback fluids has revealed a diverse microbial community that may be derived from hydrofrac fluid production or from the subsurface. DNA extraction from 10 g samples of Marcellus shale sub-core were unsuccessful even when samples were spiked with 8x108 cells/g of shale. This indicated that constituents of shale such as high levels of carbonates, humic acids and metals likely inhibited components of the PowerSoil kit. Future research is focused on refining sample collection and analyses to gain a full understanding of the microbiology of the Marcellus shale and associated flowback fluids. This includes the development of an in situ osmosampler, which will collect temporally relevant fluid and colonized substrate samples. The design of the osmosampler for hydraulic fracturing wells is being adapted from those used to sample marine environments. Furthermore, incubation experiments are underway to study interactions between microbial communities associated with hydraulic fracturing fluid and Marcellus shale samples. In conclusion, evidence suggests that the Marcellus shale is a possible component of the subsurface biosphere. Future studies will be valuable in determining the microbial community structure and function in relation to the geochemistry of the Marcellus shale and its future development as a natural gas resource.

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.

Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles

PubMed Central

Huang, Jing; Xi, Jun; Huang, Zhi; Wang, Qi; Zhang, Zhen-Dong

2014-01-01

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure. PMID:24077700

Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

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

Yagi, J.M.; Madsen, E.L.

The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ni Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72: 4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with Rhodococcus and Sphingomonas to 32 previously uncharacterized Rieske gene sequence clone groups. The nag genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized bymore » low (similar to 10{sup 2} ppb; similar to 1 {mu} M) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of nag genes (and archetypal nah genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that nah- and nag-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.« less

Stimulation of Microbially Mediated Arsenic Release in Bangladesh Aquifers by Young Carbon Indicated by Radiocarbon Analysis of Sedimentary Bacterial Lipids.

PubMed

Whaley-Martin, K J; Mailloux, B J; van Geen, A; Bostick, B C; Silvern, R F; Kim, C; Ahmed, K M; Choudhury, I; Slater, G F

2016-07-19

The sources of reduced carbon driving the microbially mediated release of arsenic to shallow groundwater in Bangladesh remain poorly understood. Using radiocarbon analysis of phospholipid fatty acids (PLFAs) and potential carbon pools, the abundance and carbon sources of the active, sediment-associated, in situ bacterial communities inhabiting shallow aquifers (<30 m) at two sites in Araihazar, Bangladesh, were investigated. At both sites, sedimentary organic carbon (SOC) Δ(14)C signatures of -631 ± 54‰ (n = 12) were significantly depleted relative to dissolved inorganic carbon (DIC) of +24 ± 30‰ and dissolved organic carbon (DOC) of -230 ± 100‰. Sediment-associated PLFA Δ(14)C signatures (n = 10) at Site F (-167‰ to +20‰) and Site B (-163‰ to +21‰) were highly consistent and indicated utilization of carbon sources younger than the SOC, likely from the DOC pool. Sediment-associated PLFA Δ(14)C signatures were consistent with previously determined Δ(14)C signatures of microbial DNA sampled from groundwater at Site F indicating that the carbon source for these two components of the subsurface microbial community is consistent and is temporally stable over the two years between studies. These results demonstrate that the utilization of relatively young carbon sources by the subsurface microbial community occurs at sites with varying hydrology. Further they indicate that these young carbon sources drive the metabolism of the more abundant sediment-associated microbial communities that are presumably more capable of Fe reduction and associated release of As. This implies that an introduction of younger carbon to as of yet unaffected sediments (such as those comprising the deeper Pleistocene aquifer) could stimulate microbial communities and result in arsenic release.

Remote sensing capacity of Raman spectroscopy in identification of mineral and organic constituents

NASA Astrophysics Data System (ADS)

Chen, Bin; Stoker, Carol; Cabrol, Nathalie; McKay, Christopher P.

2007-09-01

We present design, integration and test results for a field Raman spectrometer science payload, integrated into the Mars Analog Research and Technology (MARTE) drilling platform. During the drilling operation, the subsurface Raman spectroscopy inspection system has obtained signatures of organic and mineral compositions. We also performed ground truth studies using both this field unit and a laboratory micro Raman spectrometer equipped with multiple laser excitation wavelengths on series of field samples including Mojave rocks, Laguna Verde salty sediment and Rio Tinto topsoil. We have evaluated laser excitation conditions and optical probe designs for further improvement. We have demonstrated promising potential for Raman spectroscopy as a non-destructive in situ, high throughput, subsurface detection technique, as well as a desirable active remote sensing tool for future planetary and space missions.

Microbial community structure in a shallow hydrocarbon-contaminated aquifer associated with high electrical conductivity

NASA Astrophysics Data System (ADS)

Duris, J. W.; Rossbach, S.; Atekwana, E. A.; Werkema, D., Jr.

2003-04-01

Little is known about the complex interactions between microbial communities and electrical properties in contaminated aquifers. In order to investigate possible connections between these parameters a study was undertaken to investigate the hypothesis that the degradation of hydrocarbons by resident microbial communities causes a local increase in organic acid concentrations, which in turn cause an increase in native mineral weathering and a concurrent increase in the bulk electrical conductivity of soil. Microbial community structure was analyzed using a 96-well most probable number (MPN) method and rDNA intergenic spacer region analysis (RISA). Microbial community structure was found to change in the presence of hydrocarbon contaminants and these changes were consistently observed in regions of high electrical conductivity. We infer from this relationship that geophysical methods for monitoring the subsurface are a promising new technology for monitoring changes in microbial community structure and simultaneous changes in geochemistry that are associated with hydrocarbon degradation.

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.

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.

Simulating oil droplet dispersal from the Deepwater Horizon spill with a Lagrangian approach

USGS Publications Warehouse

North, Elizabeth W.; Schlag, Zachary; Adams, E. Eric; Sherwood, Christopher R.; He, Ruoying; Hyun, Hoon; Socolofsky, Scott A.

2011-01-01

An analytical multiphase plume model, combined with time-varying flow and hydrographic fields generated by the 3-D South Atlantic Bight and Gulf of Mexico model (SABGOM) hydrodynamic model, were used as input to a Lagrangian transport model (LTRANS), to simulate transport of oil droplets dispersed at depth from the recent Deepwater Horizon MC 252 oil spill. The plume model predicts a stratification-dominated near field, in which small oil droplets detrain from the central plume containing faster rising large oil droplets and gas bubbles and become trapped by density stratification. Simulated intrusion (trap) heights of ∼ 310–370 m agree well with the midrange of conductivity-temperature-depth observations, though the simulated variation in trap height was lower than observed, presumably in part due to unresolved variability in source composition (percentage oil versus gas) and location (multiple leaks during first half of spill). Simulated droplet trajectories by the SABGOM-LTRANS modeling system showed that droplets with diameters between 10 and 50 μm formed a distinct subsurface plume, which was transported horizontally and remained in the subsurface for >1 month. In contrast, droplets with diameters ≥90 μm rose rapidly to the surface. Simulated trajectories of droplets ≤50 μm in diameter were found to be consistent with field observations of a southwest-tending subsurface plume in late June 2010 reported by Camilli et al. [2010]. Model results suggest that the subsurface plume looped around to the east, with potential subsurface oil transport to the northeast and southeast. Ongoing work is focusing on adding degradation processes to the model to constrain droplet dispersal.

Revealing the Role of Microbes in Controlling Contaminants

ScienceCinema

Williams, Kenneth Hurst

2018-05-11

In Rifle, Colorado, Berkeley Lab earth scientist, Kenneth Hurst Williams, highlights the role subsurface microbial communities can play in controlling the flow of contaminants in groundwater. The DOE Joint Genome Institute is a key collaborator in the research. Williams is Component Lead of Watershed Structure and Controls within Berkeley Lab's Genomes-to-Watershed Scientific Focus Area.

Revealing the Role of Microbes in Controlling Contaminants

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

Williams, Kenneth Hurst

2015-04-02

In Rifle, Colorado, Berkeley Lab earth scientist, Kenneth Hurst Williams, highlights the role subsurface microbial communities can play in controlling the flow of contaminants in groundwater. The DOE Joint Genome Institute is a key collaborator in the research. Williams is Component Lead of Watershed Structure and Controls within Berkeley Lab's Genomes-to-Watershed Scientific Focus Area.

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.

PubMed

Dassen, Sigrid; Cortois, Roeland; Martens, Henk; de Hollander, Mattias; Kowalchuk, George A; van der Putten, Wim H; De Deyn, Gerlinde B

2017-08-01

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting.

PubMed

Huhe; Jiang, Chao; Wu, Yanpei; Cheng, Yunxiang

2017-12-01

During composting, the composition of microbial communities is subject to constant change owing to interactions with fluctuating physicochemical parameters. This study explored the changes in bacterial and fungal communities during cattle farm waste composting and aimed to identify and prioritize the contributing physicochemical factors. Microbial community compositions were determined by high-throughput sequencing. While the predominant phyla in the bacterial and fungal communities were largely consistent during the composting, differences in relative abundances were observed. Bacterial and fungal community diversity and relative abundance varied significantly, and inversely, over time. Relationships between physicochemical factors and microbial community compositions were evaluated by redundancy analysis. The variation in bacterial community composition was significantly related to water-soluble organic carbon (WSOC), and pile temperature and moisture (p < .05), while the largest portions of variation in fungal community composition were explained by pile temperature, WSOC, and C/N (p < .05). These findings indicated that those parameters are the most likely ones to influence, or be influenced by the bacterial and fungal communities. Variation partitioning analyses indicated that WSOC and pile temperature had predominant effects on bacterial and fungal community composition, respectively. Our findings will be useful for improving the quality of cattle farm waste composts. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Subsurface flow and vegetation patterns in tidal environments

NASA Astrophysics Data System (ADS)

Ursino, Nadia; Silvestri, Sonia; Marani, Marco

2004-05-01

Tidal environments are characterized by a complex interplay of hydrological, geomorphic, and biological processes, and their understanding and modeling thus require the explicit description of both their biotic and abiotic components. In particular, the presence and spatial distribution of salt marsh vegetation (a key factor in the stabilization of the surface soil) have been suggested to be related to topographic factors and to soil moisture patterns, but a general, process-based comprehension of this relationship has not yet been achieved. The present paper describes a finite element model of saturated-unsaturated subsurface flow in a schematic salt marsh, driven by tidal fluctuations and evapotranspiration. The conditions leading to the establishment of preferentially aerated subsurface zones are studied, and inferences regarding the development and spatial distribution of salt marsh vegetation are drawn, with important implications for the overall ecogeomorphological dynamics of tidal environments. Our results show that subsurface water flow in the marsh induces complex water table dynamics, even when the tidal forcing has a simple sinusoidal form. The definition of a space-dependent aeration time is then proposed to characterize root aeration. The model shows that salt marsh subsurface flow depends on the distance from the nearest creek or channel and that the subsurface water movement near tidal creeks is both vertical and horizontal, while farther from creeks, it is primarily vertical. Moreover, the study shows that if the soil saturated conductivity is relatively low (10-6 m s-1, values quite common in salt marsh areas), a persistently unsaturated zone is present below the soil surface even after the tide has flooded the marsh; this provides evidence of the presence of an aerated layer allowing a prolonged presence of oxygen for aerobic root respiration. The results further show that plant transpiration increases the extent and persistence of the aerated layer, thereby introducing a strong positive feedback: Pioneer plants on marsh edges have the effect of increasing soil oxygen availability, thus creating the conditions for the further development of other plant communities.

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.

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.

Assessment of the Lunar Surface Layer and in Situ Materials to Sustain Construction-related Applications

NASA Technical Reports Server (NTRS)

Johnson, Stewart W.; Chua, Koon Meng

1992-01-01

Present and future technologies to facilitate lunar composition and resource assessment with applications to lunar surface construction are presented. We are particularly interested in the construction activity associated with lunar-based astronomy. We address, as an example, the use of ground-probing radar to help assess subsurface conditions at sites for observatories and other facilities.

Microbial Communities in Terrestrial CO2 Springs: Insights into the Long-Term Effects of Carbon Sequestration on Subsurface Microorganisms

NASA Astrophysics Data System (ADS)

Santillan, E. F. U.; Major, J. R.; Bennett, P.

2014-12-01

Over long timescales, microbial populations and communities living in environments where CO2 has been sequestered will adapt to this environmental stress. Their presence and activities can have implications for fluid flow, geochemistry, and the fate of the stored CO2. Because of the interplay between microorganisms and environment, many environmental factors beyond CO2 will also contribute to community structure, including groundwater composition and mineralogy. To determine the long-term effect of CO2 on microbial communities, we analyzed terrestrial CO2 springs as analogues to CO2 sequestration in 3 locations in the United States: the Little Grand Wash Fault (LGW), UT; Bravo Dome (BD), NM; and Klickitat Mineral Spring (KMS), WA. These sites differed in multiple aspects such as depth, salinity, Fe content, and mineralogy. LGW and BD were located in the Colorado Plateau in sedimentary locations while KMS was located within the Columbia River Basalt Group. Sites were compared to non-CO2 springs in similar sedimentary formations for comparison. Microbial communities from sedimentary formations were characterized by low diversity and the dominance of the phylotypes Acinetobacter or Burkholderia compared to non-CO2 springs, suggesting community stress and the selection of specific organisms most resilient to CO2. Communities in the basalt formation were more diverse, though diversity is lower than a non-CO2 community sampled from the same formation (Lavalleur and Colwell 2013). Organisms present at the basalt site contained novel lineages, such as the OP candidate phyla. KMS was also the only site containing Archaea, such as Methanoplanus, suggesting CH4 production at depth. Statistical analyses indicate other factors such as depth and nutrient availability may be other factors that can affect diversity in addition to CO2. Growth of a CO2-tolerant organism from LGW also shows organisms in these environments are viable. Results confirm the presence of microbial communities at high PCO2 and suggest that while CO2 is one environmental stress that can lower diversity, many other environmental factors can also influence survival. Lavalleur, H.J., Colwell, F.S., 2013. Microbial characterization of basalt formation waters targeted for geological carbon sequestration. FEMS Microbiology Ecology 85, 62-73.

The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks

PubMed Central

Hawlena, Hadas; Rynkiewicz, Evelyn; Toh, Evelyn; Alfred, Andrew; Durden, Lance A; Hastriter, Michael W; Nelson, David E; Rong, Ruichen; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith

2013-01-01

Bacterial community composition in blood-sucking arthropods can shift dramatically across time and space. We used 16S rRNA gene amplification and pyrosequencing to investigate the relative impact of vertebrate host-related, arthropod-related and environmental factors on bacterial community composition in fleas and ticks collected from rodents in southern Indiana (USA). Bacterial community composition was largely affected by arthropod identity, but not by the rodent host or environmental conditions. Specifically, the arthropod group (fleas vs ticks) determined the community composition of bacteria, where bacterial communities of ticks were less diverse and more dependent on arthropod traits—especially tick species and life stage—than bacterial communities of fleas. Our data suggest that both arthropod life histories and the presence of arthropod-specific endosymbionts may mask the effects of the vertebrate host and its environment. PMID:22739493

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.

Evolving hydrologic connectivity in discontinuous permafrost lowlands: what it means for lake systems

NASA Astrophysics Data System (ADS)

Walvoord, M. A.; Jepsen, S. M.; Rover, J.; Voss, C. I.; Briggs, M. A.

2015-12-01

Permafrost influence on the hydrologic connectivity of surface water bodies in high-latitude lowlands is complicated by subsurface heterogeneity and the propensity of the system to change over time. In general, permafrost limits the subsurface exchange of water, solute, and nutrients between lakes and rivers. It follows that permafrost thaw could enhance subsurface hydrologic connectivity among surface water bodies, but the impact of this process on lake distribution is not well known. Changes in the extent of lakes in interior Alaska have important ecological and societal impacts since lakes provide (1) critical habitat for migratory arctic shorebirds and waterfowl, fish, and wildlife, and (2) provisional, recreational, and cultural resources for local communities. We utilize electromagnetic imaging of the shallow subsurface and remote sensing of lake level dynamics in the Yukon Flats of interior Alaska, USA, together with water balance modeling, to gain insight into the influence of discontinuous permafrost on lowland lake systems. In the study region with relatively low precipitation, observations suggest that lakes that are hydrologically isolated during normal conditions are sustained by periodic river flooding events, including ice-jam floods that occur during river ice break-up. Climatically-influenced alterations in flooding frequency and intensity, as well as depth to permafrost, are quantitatively assessed in the context of lake maintenance. Scenario modeling is used to evaluate lake level evolution under plausible changing conditions. Model results demonstrate how permafrost degradation can reduce the dependence of typical lowland lakes on flooding events. Study results also suggest that river flooding may recharge a more spatially widespread zone of lakes and wetlands under future scenarios of permafrost table deepening and enhanced subsurface hydrologic connectivity.

Workshop to develop deep-life continental scientific drilling projects

DOE PAGES

Kieft, T. L.; Onstott, T. C.; Ahonen, L.; ...

2015-05-29

The International Continental Scientific Drilling Program (ICDP) has long espoused studies of deep subsurface life, and has targeted fundamental questions regarding subsurface life, including the following: "(1) What is the extent and diversity of deep microbial life and what are the factors limiting it? (2) What are the types of metabolism/carbon/energy sources and the rates of subsurface activity? (3) How is deep microbial life adapted to subsurface conditions? (4) How do subsurface microbial communities affect energy resources? And (5) how does the deep biosphere interact with the geosphere and atmosphere?" (Horsfield et al., 2014) Many ICDP-sponsored drilling projects have includedmore » a deep-life component; however, to date, not one project has been driven by deep-life goals, in part because geomicrobiologists have been slow to initiate deep biosphere-driven ICDP projects. Therefore, the Deep Carbon Observatory (DCO) recently partnered with the ICDP to sponsor a workshop with the specific aim of gathering potential proponents for deep-life-driven ICDP projects and ideas for candidate drilling sites. Twenty-two participants from nine countries proposed projects and sites that included compressional and extensional tectonic environments, evaporites, hydrocarbon-rich shales, flood basalts, Precambrian shield rocks, subglacial and subpermafrost environments, active volcano–tectonic systems, megafan deltas, and serpentinizing ultramafic environments. The criteria and requirements for successful ICDP applications were presented. Deep-life-specific technical requirements were discussed and it was concluded that, while these procedures require adequate planning, they are entirely compatible with the sampling needs of other disciplines. As a result of this workshop, one drilling workshop proposal on the Basin and Range Physiographic Province (BRPP) has been submitted to the ICDP, and several other drilling project proponents plan to submit proposals for ICDP-sponsored drilling workshops in 2016.« less

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

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

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

Characterization and Distribution of Lunar Mare Basalt Types Using Remote Sensing Techniques. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Pieters, C.

1977-01-01

The types of basal to be found on the moon were identified using reflectance spectra from a variety of lunar mare surfaces and craters as well as geochemical interpretations of laboratory measurements of reflectance from lunar, terrestrial, and meteoritic samples. Findings indicate that major basaltic units are not represented in lunar sample collections. The existence of late stage high titanium basalts is confirmed. All maria contain lateral variations of compositionally heterogenous basalts; some are vertically inhomogenous with distinctly different subsurface composition. Some basalt types are spectrally gradational, suggesting minor variations in composition. Mineral components of unsampled units can be defined if spectra are obtained with sufficient spectral coverage (.3 to 2.5 micron m) and spatial resolution (approximating .5 km).