Hydro-environmental changes and their influence on the subsurface environment in the context of urban development.

PubMed

Yoshikoshi, Akihisa; Adachi, Itsu; Taniguchi, Tomomasa; Kagawa, Yuichi; Kato, Masahiro; Yamashita, Akio; Todokoro, Taiko; Taniguchi, Makoto

2009-04-15

The relationship between urban development and hydro-environmental change, particularly with regard to the subsurface environment is examined for three coastal cities affected by Asian monsoons (Tokyo and Osaka in Japan, and Bangkok in Thailand). Major differences in subsurface changes among these cities are closely related to city size, urban structure, and the timing, stage and extent of urbanization as well as the natural environment. The work shows that the urban development has not affected the Bangkok subsurface hydro-environment in the same way it has in Tokyo and Osaka. Three reasons for the difference account for this, (1) Bangkok's abundant annual rainfall, (2) Bangkok has the smallest ratio of impervious pavement surface area, meaning that surface water can more easily infiltrate underground., (3) the degree and extent of urbanization. Bangkok's subsurface hydro-environment has not been heavily affected because underground development has not yet reached deep subterranean areas. By researching yet more cities, at different stages of urbanization to that of Tokyo, Osaka and Bangkok, we plan to quantitatively examine urbanization and its influence on subsurface hydro-environments. This research will help limit damage to developing cities that are not yet experiencing subsurface failures but which are expected to confront these problems in the future.

Microeukaryotic diversity in marine environments, an analysis of surface layer sediments from the East Sea.

PubMed

Park, Soo-Je; Park, Byoung-Joon; Pham, Vinh Hoa; Yoon, Dae-No; Kim, Si-Kwan; Rhee, Sung-Keun

2008-06-01

Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.

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 structures in an Alpine Thermal Spring - Microscopic techniques for the examination of Biofilms in a Subsurface Environment

NASA Astrophysics Data System (ADS)

Dornmayr-Pfaffenhuemer, Marion; Pierson, Elisabeth; Janssen, Geert-Jan; Stan-Lotter, Helga

2010-05-01

The research into extreme environments hast important implications for biology and other sciences. Many of the organisms found there provide insights into the history of Earth. Life exists in all niches where water is present in liquid form. Isolated environments such as caves and other subsurface locations are of interest for geomicrobiological studies. And because of their "extra-terrestrial" conditions such as darkness and mostly extreme physicochemical state they are also of astrobiological interest. The slightly radioactive thermal spring at Bad Gastein (Austria) was therefore examined for the occurrence of subsurface microbial communities. The surfaces of the submerged rocks in this warm spring were overgrown by microbial mats. Scanning electron microscopy (SEM) performed by the late Dr. Wolfgang Heinen revealed an interesting morphological diversity in biofilms found in this environment (1, 2). Molecular analysis of the community structure of the radioactive subsurface thermal spring was performed by Weidler et al. (3). The growth of these mats was simulated using sterile glass slides which were exposed to the water stream of the spring. Those mats were analysed microscopically. Staining, using fluorescent dyes such as 4',6-Diamidino-2-phenylindol (DAPI), gave an overview of the microbial diversity of these biofilms. Additional SEM samples were prepared using different fixation protocols. Scanning confocal laser microscopy (SCLM) allowed a three dimensional view of the analysed biofilms. This work presents some electron micrographs of Dr. Heinen and additionally new microscopic studies of the biofilms formed on the glass slides. The appearances of the new SEM micrographs were compared to those of Dr. Heinen that were done several years ago. The morphology and small-scale distribution in the microbial mat was analyzed by fluorescence microscopy. The examination of natural biomats and biofilms grown on glass slides using several microscopical techniques

Contaminated environments in the subsurface and bioremediation: organic contaminants.

PubMed

Holliger, C; Gaspard, S; Glod, G; Heijman, C; Schumacher, W; Schwarzenbach, R P; Vazquez, F

1997-07-01

Due to leakages, spills, improper disposal and accidents during transport, organic compounds have become subsurface contaminants that threaten important drinking water resources. One strategy to remediate such polluted subsurface environments is to make use of the degradative capacity of bacteria. It is often sufficient to supply the subsurface with nutrients such as nitrogen and phosphorus, and aerobic treatments are still dominating. However, anaerobic processes have advantages such as low biomass production and good electron acceptor availability, and they are sometimes the only possible solution. This review will focus on three important groups of environmental organic contaminants: hydrocarbons, chlorinated and nitroaromatic compounds. Whereas hydrocarbons are oxidized and completely mineralized under anaerobic conditions in the presence of electron acceptors such as nitrate, iron, sulfate and carbon dioxide, chlorinated and nitroaromatic compounds are reductively transformed. For the aerobic often persistent polychlorinated compounds, reductive dechlorination leads to harmless products or to compounds that are aerobically degradable. The nitroaromatic compounds are first reductively transformed to the corresponding amines and can subsequently be bound to the humic fraction in an aerobic process. Such new findings and developments give hope that in the near future contaminated aquifers can efficiently be remediated, a prerequisite for a sustainable use of the precious-subsurface drinking water resources.

Electrode Cultivation and Interfacial Electron Transport in Subsurface Microorganisms

NASA Astrophysics Data System (ADS)

Karbelkar, A. A.; Jangir, Y.; Reese, B. K.; Wanger, G.; Anderson, C.; El-Naggar, M.; Amend, J.

2016-12-01

Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Microbes can use extracellular electron transfer (EET) as a metabolic strategy to interact with redox active surfaces. This process can be mimicked on electrode surfaces and hence can lead to enrichment and quantification of subsurface microorganisms A primary bioelectrochemical enrichment with different oxidizing and reducing potentials set up in a single bioreactor was applied in situ to subsurface microorganisms residing in iron oxide rich deposits in the Sanford Underground Research Facility. Secondary enrichment revealed a plethora of classified and unclassified subsurface microbiota on both oxidizing and reducing potentials. From this enrichment, we have isolated a Gram-positive Bacillus along with Gram-negative Cupriavidus and Anaerospora strains (as electrode reducers) and Comamonas (as an electrode oxidizer). The Bacillus and Comamonas isolates were subjected to a detailed electrochemical characterization in half-reactors at anodic and cathodic potentials, respectively. An increase in cathodic current upon inoculation and cyclic voltammetry measurements confirm the hypothesis that Comamonas is capable of electron uptake from electrodes. In addition, measurements of Bacillus on anodes hint towards novel mechanisms that allow EET from Gram-positive bacteria. This study suggests that electrochemical approaches are well positioned to dissect such extracellular interactions that may be prevalent in the subsurface, while using physical electrodes to emulate the microhabitats, redox and geochemical gradients, and the spatially dependent interspecies interactions encountered in the subsurface. Electrochemical

UNDERSTANDING THE FATE OF PETROLEUM HYDROCARBONS IN THE SUBSURFACE ENVIRONMENT

EPA Science Inventory

Sinca a significant number of the two or more million underground storage tank (UST) systems used for petroleum products leak, their cleanup poses a major environmental challenge. Our understnading of the fate of petroleum hydrocarbons in the subsurface environment is critical t...

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.

The Hebrus Valles Exploration Zone: Access to the Martian Surface and Subsurface

NASA Astrophysics Data System (ADS)

Davila, A.; Fairén, A. G.; Rodríguez, A. P.; Schulze-Makuch, D.; Rask, J.; Zavaleta, J.

2015-10-01

The Hebrus Valles EZ represents a diverse setting with multiple geological contacts and layers, possible remnant water ice and protected subsurface environments, which could be critical for the establishment of long-term human settlements.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

Colonization of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focused on the settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associated vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soil types on the surface of the island. Total viable bacterial counts were performed with the plate count method at 22, 30 and 37 °C for all soil samples, and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms and aerobic and anaerobic bacteria. The subsurface biosphere was investigated by collecting liquid subsurface samples from a 181 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between nutrient deficits and the number of microorganisms in surface soil samples. The lowest number of bacteria (1 × 104-1 × 105 cells g-1) was detected in almost pure pumice but the count was significantly higher (1 × 106-1 × 109 cells g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated samples and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 and 172 m depth at 80 and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

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

NASA Astrophysics Data System (ADS)

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

2014-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.

PubMed

Zhuang, Kai; Izallalen, Mounir; Mouser, Paula; Richter, Hanno; Risso, Carla; Mahadevan, Radhakrishnan; Lovley, Derek R

2011-02-01

The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies.

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

PubMed Central

Zhuang, Kai; Izallalen, Mounir; Mouser, Paula; Richter, Hanno; Risso, Carla; Mahadevan, Radhakrishnan; Lovley, Derek R

2011-01-01

The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies. PMID:20668487

Microbial production and oxidation of methane in deep subsurface

NASA Astrophysics Data System (ADS)

Kotelnikova, Svetlana

2002-10-01

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.

Advances in Multiphase Flow and Transport in the Subsurface Environment

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

Shi, Xiaoqing; Finsterle, Stefan; Zhang, Keni

Multiphase flow and transport processes in the subsurface environment are extremely important in a number of industrial and environmental applications at various spatial and temporal scales. Thus, it is necessary to identify, understand, and predict these processes to improve the production of conventional and unconventional oil and gas, to increase the safety of geological sequestration of carbon dioxide and nuclear waste disposal, and to make remediation of contaminated aquifers more effective.

Advances in Multiphase Flow and Transport in the Subsurface Environment

DOE PAGES

Shi, Xiaoqing; Finsterle, Stefan; Zhang, Keni; ...

2018-03-04

Multiphase flow and transport processes in the subsurface environment are extremely important in a number of industrial and environmental applications at various spatial and temporal scales. Thus, it is necessary to identify, understand, and predict these processes to improve the production of conventional and unconventional oil and gas, to increase the safety of geological sequestration of carbon dioxide and nuclear waste disposal, and to make remediation of contaminated aquifers more effective.

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.

Active Serpentinization and the Potential for a Diverse Subsurface Biosphere

NASA Astrophysics Data System (ADS)

Canovas, P. A.; Shock, E.

2013-12-01

The ubiquitous nature of serpentinization and the unique fluids it generates have major consequences for habitat generation, abiotic organic synthesis, and biosynthesis. The production of hydrogen from the anaerobic hydrolysis of ultramafic minerals sets the redox state of serpentinizing fluids to be thermodynamically favorable for these processes. Consequently, a host of specialized microbial populations and metabolisms can be sustained. Active low-temperature serpentinizing systems, such as the Samail ophiolite in Oman, offer an ideal opportunity to investigate biogeochemical processes during the alteration of ultramafic minerals. At the Samail ophiolite in particular, serpentinization may provide the potential for an active subsurface microbial community shielded from potentially unfavorable surface conditions. Support for this assertion comes from geochemical data including Mg, Ca, CH4 (aq), and H2 (aq) abundances indicating that methane is a product of serpentinization. To further investigate viable metabolic strategies, affinity calculations were performed on both the surface waters and the hyperalkaline springs, which may be considered as messengers of processes occurring in the subsurface. Almost all sites yield positive affinities (i.e., are thermodynamically favorable) for a diverse suite of serpentinization metabolisms including methanogenesis, anammox, and carbon monoxide, nitrate, and sulfate reduction with hydrogen, as well as anaerobic methanotrophy coupled to nitrate, nitrite, and sulfate reduction. Reaction path modeling was performed to ascertain the extent to which serpentinization and mixing of surface waters with hyperalkaline spring waters in the subsurface can generate suitable habitats. The serpentinization model simulates the reaction of pristine Oman harzburgite with surface water to quantify the redox state and generation of hyperalkaline spring water. Preliminary results show that water-rock ratios as high as 100 could effectively reduce

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

Anthropogenic effects on the subsurface thermal and groundwater environments in Osaka, Japan and Bangkok, Thailand.

PubMed

Taniguchi, Makoto; Shimada, Jun; Fukuda, Yoichi; Yamano, Makoto; Onodera, Shin-ichi; Kaneko, Shinji; Yoshikoshi, Akihisa

2009-04-15

Anthropogenic effects in both Osaka and Bangkok were evaluated to compare the relationships between subsurface environment and the development stage of both cities. Subsurface thermal anomalies due to heat island effects were found in both cities. The Surface Warming Index (SWI), the departure depth from the steady geothermal gradient, was used as an indicator of the heat island effect. SWI increases (deeper) with the magnitude of heat island effect and the elapsed time starting from the surface warming. Distributions of subsurface thermal anomalies due to the heat island effect agreed well with the distribution of changes in air temperature due to the same process, which is described by the distribution of population density in both Osaka and Bangkok. Different time lags between groundwater depression and subsidence in the two cities was found. This is attributed to differences in hydrogeologic characters, such as porosity and hydraulic conductivity. We find that differences in subsurface degradations in Osaka and Bangkok, including subsurface thermal anomalies, groundwater depression, and land subsidence, depends on the difference of the development stage of urbanization and hydrogeological characters.

Isolation of Geobacter species from diverse sedimentary environments

USGS Publications Warehouse

Coaxes, J.D.; Phillips, E.J.P.; Lonergan, D.J.; Jenter, H.; Lovley, D.R.

1996-01-01

In an attempt to better understand the microorganisms responsible for Fe(III) reduction in sedimentary environments, Fe(III)-reducing microorganisms were enriched for and isolated from freshwater aquatic sediments, a pristine deep aquifer, and a petroleum-contaminated shallow aquifer. Enrichments were initiated with acetate or toluene as the electron donor and Fe(III) as the electron acceptor. Isolations were made with acetate or benzoate. Five new strains which could obtain energy for growth by dissimilatory Fe(III) reduction were isolated. All five isolates are gram- negative strict anaerobes which grow with acetate as the electron donor and Fe(III) as the electron acceptor. Analysis of the 16S rRNA sequence of the isolated organisms demonstrated that they all belonged to the genus Geobacter in the delta subdivision of the Proteobacteria. Unlike the type strain, Geobacter metallireducens, three of the five isolates could use H2 as an electron donor fur Fe(III) reduction. The deep subsurface isolate is the first Fe(III) reducer shown to completely oxidize lactate to carbon dioxide, while one of the freshwater sediment isolates is only the second Fe(III) reducer known that can oxidize toluene. The isolation of these organisms demonstrates that Geobacter species are widely distributed in a diversity of sedimentary environments in which Fe(III) reduction is an important process.

Effect of electrochemical corrosion on the subsurface microstructure evolution of a CoCrMo alloy in albumin containing environment

NASA Astrophysics Data System (ADS)

Wang, Zhongwei; Yan, Yu; Su, Yanjing; Qiao, Lijie

2017-06-01

The subsurface microstructures of metallic implants play a key role in bio-tribocorrosion. Due to wear or change of local environment, the implant surface can have inhomogeneous electrochemical corrosion properties. In this work, the effect of electrochemical corrosion conditions on the subsurface microstructure evolution of CoCrMo alloys for artificial joints was investigated. Transmission electron microscope (TEM) was employed to observe the subsurface microstructures of worn areas at different applied potentials in a simulated physiological solution. The results showed that applied potentials could affect the severity of the subsurface deformation not only by changing the surface passivation but also affecting the adsorption of protein on the alloy surface.

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

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

On the possibility of galactic cosmic ray-induced radiolysis-powered life in subsurface environments in the Universe.

PubMed

Atri, Dimitra

2016-10-01

Photosynthesis is a mechanism developed by terrestrial life to utilize the energy from photons of solar origin for biological use. Subsurface regions are isolated from the photosphere, and consequently are incapable of utilizing this energy. This opens up the opportunity for life to evolve alternative mechanisms for harvesting available energy. Bacterium Candidatus Desulforudis audaxviator, found 2.8 km deep in a South African mine, harvests energy from radiolysis, induced by particles emitted from radioactive U, Th and K present in surrounding rock. Another radiation source in the subsurface environments is secondary particles generated by galactic cosmic rays (GCRs). Using Monte Carlo simulations, it is shown that it is a steady source of energy comparable to that produced by radioactive substances, and the possibility of a slow metabolizing life flourishing on it cannot be ruled out. Two mechanisms are proposed through which GCR-induced secondary particles can be utilized for biological use in subsurface environments: (i) GCRs injecting energy in the environment through particle-induced radiolysis and (ii) organic synthesis from GCR secondaries interacting with the medium. Laboratory experiments to test these hypotheses are also proposed. Implications of these mechanisms on finding life in the Solar System and elsewhere in the Universe are discussed. © 2016 The Author(s).

On the possibility of galactic cosmic ray-induced radiolysis-powered life in subsurface environments in the Universe

PubMed Central

2016-01-01

Photosynthesis is a mechanism developed by terrestrial life to utilize the energy from photons of solar origin for biological use. Subsurface regions are isolated from the photosphere, and consequently are incapable of utilizing this energy. This opens up the opportunity for life to evolve alternative mechanisms for harvesting available energy. Bacterium Candidatus Desulforudis audaxviator, found 2.8 km deep in a South African mine, harvests energy from radiolysis, induced by particles emitted from radioactive U, Th and K present in surrounding rock. Another radiation source in the subsurface environments is secondary particles generated by galactic cosmic rays (GCRs). Using Monte Carlo simulations, it is shown that it is a steady source of energy comparable to that produced by radioactive substances, and the possibility of a slow metabolizing life flourishing on it cannot be ruled out. Two mechanisms are proposed through which GCR-induced secondary particles can be utilized for biological use in subsurface environments: (i) GCRs injecting energy in the environment through particle-induced radiolysis and (ii) organic synthesis from GCR secondaries interacting with the medium. Laboratory experiments to test these hypotheses are also proposed. Implications of these mechanisms on finding life in the Solar System and elsewhere in the Universe are discussed. PMID:27707907

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

BIODEGRADATION OF ATRAZINE IN SUBSURFACE ENVIRONMENTS

EPA Science Inventory

The pesticide atrazine is frequently detected in ground water, including ground water used as drinking water. Little information is available on the fate of atrazine in the subsurface, including its biodegradability. The objectives of this study were to evaluate the biodegradabil...

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

Emerge - A Python environment for the modeling of subsurface transfers

NASA Astrophysics Data System (ADS)

Lopez, S.; Smai, F.; Sochala, P.

2014-12-01

The simulation of subsurface mass and energy transfers often relies on specific codes that were mainly developed using compiled languages which usually ensure computational efficiency at the expense of relatively long development times and relatively rigid software. Even if a very detailed, possibly graphical, user-interface is developed the core numerical aspects are rarely accessible and the smallest modification will always need a compilation step. Thus, user-defined physical laws or alternative numerical schemes may be relatively difficult to use. Over the last decade, Python has emerged as a popular and widely used language in the scientific community. There already exist several libraries for the pre and post-treatment of input and output files for reservoir simulators (e.g. pytough). Development times in Python are considerably reduced compared to compiled languages, and programs can be easily interfaced with libraries written in compiled languages with several comprehensive numerical libraries that provide sequential and parallel solvers (e.g. PETSc, Trilinos…). The core objective of the Emerge project is to explore the possibility to develop a modeling environment in full Python. Consequently, we are developing an open python package with the classes/objects necessary to express, discretize and solve the physical problems encountered in the modeling of subsurface transfers. We heavily relied on Python to have a convenient and concise way of manipulating potentially complex concepts with a few lines of code and a high level of abstraction. Our result aims to be a friendly numerical environment targeting both numerical engineers and physicist or geoscientists with the possibility to quickly specify and handle geometries, arbitrary meshes, spatially or temporally varying properties, PDE formulations, boundary conditions…

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

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

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.

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

Lithological properties of sedimentary environments in the shallow subsurface of the Northern Netherlands

NASA Astrophysics Data System (ADS)

Harting, Ronald; Bosch, Aleid; Gunnink, Jan

2014-05-01

Society has an increasing demand from the subsurface, which in the Dutch shallow subsurface (upper 30 to 40 meters) mainly focuses on natural aggregate resources, groundwater, infrastructure and dike safety. This stimulates the demand for knowledge about the composition and heterogeneity of the subsurface and its physical and chemical properties, including the uncertainties involved. Physical and chemical properties of sediments in the subsurface have been under investigation for decades; however, the usefulness of this data for applied research and the understanding of these properties is limited. This is due to several factors: studies consist mainly of separately collected datasets, targeted at a limited amount of parameters, focused on a small number of geological units, distributed unevenly with depth and usually collected from clustered drillings with limited spatial extent or are analysed with different techniques and methods, often on disturbed samples. These factors result in a heterogeneous and biased dataset not suitable to function as a reference dataset or to statistically determine regional characteristics of geological units. To overcome these shortcomings, the Geological Survey of the Netherlands is establishing a nation-wide reference dataset for physical and chemical properties. In 2006, a drilling campaign was started using cone penetration tests, cored drillings and geophysical well logs, choosing the sites for a good geographical distribution. The lithological properties of the undisturbed cores are visually described and interpreted for lithostratigraphy and inferred sedimentary environment based on lithofacies. The location of the samples in the cores are chosen based on this description and interpretation, resulting in an evenly distributed dataset of in situ samples with respect to geological units as well as an adequate number of samples suitable for statistical analysis. Analyses are uniformly performed for grain size distribution

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

Achieving diversity in nursing through multicontextual learning environments.

PubMed

Giddens, Jean Foret

2008-01-01

Attempts to increase diversity within the nursing profession have resulted in the admission of more ethnically diverse students into nursing education programs. However, traditional curricular and pedagogical practices seen in many nursing programs do not accommodate the learning needs of diverse learners. Nurse educators are encouraged to adopt learner-centered pedagogical approaches and embrace multicontextual learning environments. The purpose of this article is to describe the concept of multicontextuality and to introduce an exemplar of a multicontextual learning environment that has been recently developed and implemented in an undergraduate nursing program. The virtual community, known as The Neighborhood, presents nursing concepts in a rich personal and community context through stories and supplemental multimedia. The perceived benefit is enhancement of conceptual learning in a student-oriented learning environment.

Human utilization of subsurface extraterrestrial environments.

PubMed

Boston, P J; Frederick, R D; Welch, S M; Werker, J; Meyer, T R; Sprungman, B; Hildreth-Werker, V; Thompson, S L; Murphy, D L

2003-06-01

Caves have been used in the ancient past as shelter or habitat by many organisms (including humans). Since antiquity, humans have explored caves for the minerals they contain and sometimes for ceremonial purposes. Over the past century, caves have become the target of increasing exploration, scientific research, and recreation. The use of caves on extraterrestrial bodies for human habitation has been suggested by several investigators. Lunar lava tube bases received early attention because lava tubes were clearly visible in lunar images from the Apollo Era. More recently, Mars Observer Camera data has shown us clear evidence of large tubes visible in a number of volcanic regions on Mars. The budding field of cave geomicrobiology has direct application to questions about subsurface life on other planets. Caves contain many unusual organisms making their living from unlikely materials like manganese, iron, and sulfur. This makes caves and other subsurface habitats prime targets for astrobiological missions to Mars and possibly other bodies. We present the results of a completed Phase I and on-going Phase II NASA Institute for Advanced Concepts (NIAC) study that intensively examines the possibilities of using extraterrestrial caves as both a resource for human explorers and as a highly promising scientific target for both robotic and future human missions to Mars and beyond.

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.

The diversity issue revisited: international students in clinical environment.

PubMed

Pitkäjärvi, Marianne; Eriksson, Elina; Pitkälä, Kaisu

2012-01-01

Background. Globalization within higher education leads to an increase in cultural and linguistic diversity in student populations. The purpose of this study was to explore culturally diverse health care students' experiences in clinical environment in Finland, and to compare them with those of native Finnish students' participating in the same program. Method. A cross-sectional survey was performed at 10 polytechnic faculties of health care in Finland. 283 respondents (148 international and 95 Finnish students) responded to items concerning clinical rotation. The survey included items grouped as dimensions: (1) welcoming clinical environment, (2) unsupportive clinical environment, (3) approach to cultural diversity, (4) communication, and (5) structural arrangements. Results. International students felt as welcome on their placements as Finnish students. Concerning structural arrangements set up to facilitate preceptorship and approach to cultural diversity in the learning environment, the two groups' opinions were similar. However, international students were more likely than Finnish students to experience their clinical learning environment as unsupportive (P < 0.001). In addition, their experiences of communication with the staff was poorer than that of their Finnish peers' (P = 0.04). Conclusions. Awareness of strategies that enhance understanding, acceptance, and appreciation of cultural and linguistic diversity in any health care setting are needed.

Creative work environments in sport organizations: the influence of sexual orientation diversity and commitment to diversity.

PubMed

Cunningham, George B

2011-01-01

Drawing from creative capital theory, the purpose of this study was to examine the degree to which sexual orientation diversity and commitment to diversity were predictive of workplaces that fostered creativity. Data were collected from 653 senior level athletic administrators and aggregated to the athletic department level of analysis (n = 199). Moderated regression indicated that sexual orientation diversity did not influence the presence of a creative work environment. There was however, a significant sexual orientation diversity × commitment to diversity interaction. When commitment to diversity was high, there was a positive association between sexual orientation diversity and a creative work environment; on the other hand, when commitment to diversity was low, the aforementioned relationship was negative. Results provide support for the notion that all diversity forms can be a source of enrichment and understanding, thereby benefiting the workplace.

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.

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars.

PubMed

Mickol, R L; Kral, T A

2017-12-01

The low pressure at the surface of Mars (average: 6 mbar) is one potentially biocidal factor that any extant life on the planet would need to endure. Near subsurface life, while shielded from ultraviolet radiation, would also be exposed to this low pressure environment, as the atmospheric gas-phase pressure increases very gradually with depth. Few studies have focused on low pressure as inhibitory to the growth or survival of organisms. However, recent work has uncovered a potential constraint to bacterial growth below 25 mbar. The study reported here tested the survivability of four methanogen species (Methanothermobacter wolfeii, Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis) under low pressure conditions approaching average martian surface pressure (6 mbar - 143 mbar) in an aqueous environment. Each of the four species survived exposure of varying length (3 days - 21 days) at pressures down to 6 mbar. This research is an important stepping-stone to determining if methanogens can actively metabolize/grow under these low pressures. Additionally, the recently discovered recurring slope lineae suggest that liquid water columns may connect the surface to deeper levels in the subsurface. If that is the case, any organism being transported in the water column would encounter the changing pressures during the transport.

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars

NASA Astrophysics Data System (ADS)

Mickol, R. L.; Kral, T. A.

2017-12-01

The low pressure at the surface of Mars (average: 6 mbar) is one potentially biocidal factor that any extant life on the planet would need to endure. Near subsurface life, while shielded from ultraviolet radiation, would also be exposed to this low pressure environment, as the atmospheric gas-phase pressure increases very gradually with depth. Few studies have focused on low pressure as inhibitory to the growth or survival of organisms. However, recent work has uncovered a potential constraint to bacterial growth below 25 mbar. The study reported here tested the survivability of four methanogen species ( Methanothermobacter wolfeii, Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis) under low pressure conditions approaching average martian surface pressure (6 mbar - 143 mbar) in an aqueous environment. Each of the four species survived exposure of varying length (3 days - 21 days) at pressures down to 6 mbar. This research is an important stepping-stone to determining if methanogens can actively metabolize/grow under these low pressures. Additionally, the recently discovered recurring slope lineae suggest that liquid water columns may connect the surface to deeper levels in the subsurface. If that is the case, any organism being transported in the water column would encounter the changing pressures during the transport.

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

Isolation and Characterization of Electrochemically Active Subsurface Delftia and Azonexus Species

PubMed Central

Jangir, Yamini; French, Sarah; Momper, Lily M.; Moser, Duane P.; Amend, Jan P.; El-Naggar, Mohamed Y.

2016-01-01

Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Extracellular electron transfer (EET) is a metabolic strategy that microorganisms can deploy to meet the challenges of interacting with redox-active surfaces. Though mechanistically characterized in a few metal-reducing bacteria, the role, extent, and diversity of EET in subsurface ecosystems remains unclear. Since this process can be mimicked on electrode surfaces, it opens the door to electrochemical techniques to enrich for and quantify the activities of environmental microorganisms in situ. Here, we report the electrochemical enrichment of microorganisms from a deep fractured-rock aquifer in Death Valley, CA, USA. In experiments performed in mesocosms containing a synthetic medium based on aquifer chemistry, four working electrodes (WEs) were poised at different redox potentials (272, 373, 472, 572 mV vs. SHE) to serve as electron acceptors, resulting in anodic currents coupled to the oxidation of acetate during enrichment. The anodes were dominated by Betaproteobacteria from the families Comamonadaceae and Rhodocyclaceae. A representative of each dominant family was subsequently isolated from electrode-associated biomass. The EET abilities of the isolated Delftia strain (designated WE1-13) and Azonexus strain (designated WE2-4) were confirmed in electrochemical reactors using WEs poised at 522 mV vs. SHE. The rise in anodic current upon inoculation was correlated with a modest increase in total protein content. Both genera have been previously observed in mixed communities of microbial fuel cell enrichments, but this is the first direct measurement of their electrochemical activity. While alternate

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

PubMed Central

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

2015-01-01

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

Subsurface event detection and classification using Wireless Signal Networks.

PubMed

Yoon, Suk-Un; Ghazanfari, Ehsan; Cheng, Liang; Pamukcu, Sibel; Suleiman, Muhannad T

2012-11-05

Subsurface environment sensing and monitoring applications such as detection of water intrusion or a landslide, which could significantly change the physical properties of the host soil, can be accomplished using a novel concept, Wireless Signal Networks (WSiNs). The wireless signal networks take advantage of the variations of radio signal strength on the distributed underground sensor nodes of WSiNs to monitor and characterize the sensed area. To characterize subsurface environments for event detection and classification, this paper provides a detailed list and experimental data of soil properties on how radio propagation is affected by soil properties in subsurface communication environments. Experiments demonstrated that calibrated wireless signal strength variations can be used as indicators to sense changes in the subsurface environment. The concept of WSiNs for the subsurface event detection is evaluated with applications such as detection of water intrusion, relative density change, and relative motion using actual underground sensor nodes. To classify geo-events using the measured signal strength as a main indicator of geo-events, we propose a window-based minimum distance classifier based on Bayesian decision theory. The window-based classifier for wireless signal networks has two steps: event detection and event classification. With the event detection, the window-based classifier classifies geo-events on the event occurring regions that are called a classification window. The proposed window-based classification method is evaluated with a water leakage experiment in which the data has been measured in laboratory experiments. In these experiments, the proposed detection and classification method based on wireless signal network can detect and classify subsurface events.

Efforts to estimate pesticide degradation rates in subsurface ...

EPA Pesticide Factsheets

When pesticides are used in real-world settings, the objective is to be effective in pest eradication at the site of application, but also it is desired that the pesticide have minimal persistence and mobility as it migrates away from the application site. At the site of application, sorption on soil and surface-soil degradation rates both factor into the pesticides' persistence. But once it migrates to the subsurface vadose zone and/or aquifers, subsurface degradation rate is a factor as well. Unfortunately, numerous soil properties that might affect pesticide degradation rate vary by orders of magnitude in the subsurface environment, both spatially and temporally, e.g., organic-carbon concentration, oxygen concentration, redox conditions, pH and soil mineralogy. Consequently, estimation of subsurface pesticide degradation rates and, in tum, pesticide persistence and mobility in the environment, has remained a challenge. To address this intransigent uncertainty, we surveyed peer-reviewed literature to identify > 100 data pairs in which investigators reported pesticide degradation rates in both surface and subsurface soils, using internally consistent experimental methods. These > 100 data pairs represented >30 separate pesticides. When the > 100 subsurface half-lives were plotted against surface half-lives, a limiting line could be defined for which all subsurface half-lives but three fe ll below the line. Of the three data points plotting above the limiting li

Diversity: creating an environment of inclusiveness.

PubMed

Swanson, Jane W

2004-01-01

Diversity is a concept that most organizations espouse but find challenging to put into practice. It is especially critical for healthcare organizations to be responsive in addressing issues of diversity related to not only employees but also clients. This article identifies the following 3 areas that must be addressed if an organization is to succeed in creating an environment where diversity and inclusiveness are honored: (1) organizations and their leaders need to be aware of their reactions "those who are different" in their organization. This awareness is critical in identifying the underlying obstacles that prevent a truly inclusive workplace; (2) organizations and their leaders need to be able to expand their perspectives allowing them to not only understand but appreciate others. These expanded perspectives can provide a potentially powerful tool for both problem solving and conflict resolution; (3) if organizations and their leaders are actively engaged in exploring options and are open to alternatives, they will find that they not only succeed in creating an environment of inclusiveness but also are in a better position to meet the needs of employees, patients, and a multicultural society.

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.

Subsurface Event Detection and Classification Using Wireless Signal Networks

PubMed Central

Yoon, Suk-Un; Ghazanfari, Ehsan; Cheng, Liang; Pamukcu, Sibel; Suleiman, Muhannad T.

2012-01-01

Subsurface environment sensing and monitoring applications such as detection of water intrusion or a landslide, which could significantly change the physical properties of the host soil, can be accomplished using a novel concept, Wireless Signal Networks (WSiNs). The wireless signal networks take advantage of the variations of radio signal strength on the distributed underground sensor nodes of WSiNs to monitor and characterize the sensed area. To characterize subsurface environments for event detection and classification, this paper provides a detailed list and experimental data of soil properties on how radio propagation is affected by soil properties in subsurface communication environments. Experiments demonstrated that calibrated wireless signal strength variations can be used as indicators to sense changes in the subsurface environment. The concept of WSiNs for the subsurface event detection is evaluated with applications such as detection of water intrusion, relative density change, and relative motion using actual underground sensor nodes. To classify geo-events using the measured signal strength as a main indicator of geo-events, we propose a window-based minimum distance classifier based on Bayesian decision theory. The window-based classifier for wireless signal networks has two steps: event detection and event classification. With the event detection, the window-based classifier classifies geo-events on the event occurring regions that are called a classification window. The proposed window-based classification method is evaluated with a water leakage experiment in which the data has been measured in laboratory experiments. In these experiments, the proposed detection and classification method based on wireless signal network can detect and classify subsurface events. PMID:23202191

Environmental and taxonomic bacterial diversity of anaerobic uranium(IV) bio-oxidation.

PubMed

Weber, Karrie A; Thrash, J Cameron; Van Trump, J Ian; Achenbach, Laurie A; Coates, John D

2011-07-01

Microorganisms in diverse terrestrial surface and subsurface environments can anaerobically catalyze the oxidative dissolution of uraninite. While a limited quantity (∼5 to 12 μmol liter(-1)) of uranium is oxidatively dissolved in pure culture studies, the metabolism is coupled to electron transport, providing the potential of uraninite to support indigenous microbial populations and to solubilize uranium.

Subsurface Contamination Control

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

Y. Yuan

There are two objectives of this report, ''Subsurface Contamination Control''. The first is to provide a technical basis for recommending limiting radioactive contamination levels (LRCL) on the external surfaces of waste packages (WP) for acceptance into the subsurface repository. The second is to provide an evaluation of the magnitude of potential releases from a defective WP and the detectability of the released contents. The technical basis for deriving LRCL has been established in ''Retrieval Equipment and Strategy for Wp on Pallet'' (CRWMS M and O 2000g, 6.3.1). This report updates the derivation by incorporating the latest design information of themore » subsurface repository for site recommendation. The derived LRCL on the external surface of WPs, therefore, supercede that described in CRWMS M and O 2000g. The derived LRCL represent the average concentrations of contamination on the external surfaces of each WP that must not be exceeded before the WP is to be transported to the subsurface facility for emplacement. The evaluation of potential releases is necessary to control the potential contamination of the subsurface repository and to detect prematurely failed WPs. The detection of failed WPs is required in order to provide reasonable assurance that the integrity of each WP is intact prior to MGR closure. An emplaced WP may become breached due to manufacturing defects or improper weld combined with failure to detect the defect, by corrosion, or by mechanical penetration due to accidents or rockfall conditions. The breached WP may release its gaseous and volatile radionuclide content to the subsurface environment and result in contaminating the subsurface facility. The scope of this analysis is limited to radioactive contaminants resulting from breached WPs during the preclosure period of the subsurface repository. This report: (1) documents a method for deriving LRCL on the external surfaces of WP for acceptance into the subsurface repository; (2

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

PubMed

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

2010-01-01

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

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

Cyanobacterial diversity and halotolerance in a variable hypersaline environment.

PubMed

Kirkwood, Andrea E; Buchheim, Julie A; Buchheim, Mark A; Henley, William J

2008-04-01

The Great Salt Plains (GSP) in north-central Oklahoma, USA is an expansive salt flat (approximately 65 km(2)) that is part of the federally protected Salt Plains National Wildlife Refuge. The GSP serves as an ideal environment to study the microbial diversity of a terrestrial, hypersaline system that experiences wide fluctuations in freshwater influx and diel temperature. Our study assessed cyanobacterial diversity at the GSP by focusing on the taxonomic and physiological diversity of GSP isolates, and the 16S rRNA phylogenetic diversity of isolates and environmental clones from three sites (north, central, and south). Taxonomic diversity of isolates was limited to a few genera (mostly Phormidium and Geitlerinema), but physiological diversity based on halotolerance ranges was strikingly more diverse, even between strains of the same phylotype. The phylogenetic tree revealed diversity that spanned a number of cyanobacterial lineages, although diversity at each site was dominated by only a few phylotypes. Unlike other hypersaline systems, a number of environmental clones from the GSP were members of the heterocystous lineage. Although a number of cyanobacterial isolates were close matches with prevalent environmental clones, it is not certain if these clones reflect the same halotolerance ranges of their matching isolates. This caveat is based on the notable disparities we found between strains of the same phylotype and their inherent halotolerance. Our findings support the hypothesis that variable or poikilotrophic environments promote diversification, and in particular, select for variation in ecotype more than phylotype.

Mobile user environment and satellite diversity for NGSO S-PCN's

NASA Technical Reports Server (NTRS)

Werner, Markus; Bischl, Hermann; Lutz, Erich

1995-01-01

The performance of satellite diversity under the influence of the mobile user environment is analyzed. To this end, a digital channel model is presented which takes into account the elevation angle as well as the user mobility in a given environment. For different LEO and MEO systems and for varying mobile user environments, some crucial benefits and drawbacks of satellite diversity are discussed. Specifically, the important GW service area concept is introduced. The conclusions are validated by numerical results from computer simulations. Globalstar (LEO) and Inmarsat (MEO) are compared in terms of visibility, service availability and equivalent handover complexity for different environments and user mobility.

Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools.

PubMed

Shabarova, Tanja; Villiger, Jörg; Morenkov, Oleg; Niggemann, Jutta; Dittmar, Thorsten; Pernthaler, Jakob

2014-07-01

Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes. We tested the hypothesis that microorganisms introduced to the pools during floods faced environmental filtering toward a 'typical' karst water community, and we investigated whether DOM composition was related to floodings and the residence time of water in stagnant pools. As predicted, longer water residence consistently led to a decline of bacterial diversity. The microbial assemblages in the influx water harbored more 'exotic' lineages with large distances to known genotypes, yet these initial communities already appeared to be shaped by selective processes. β-Proteobacterial operational taxonomic units (OTUs) closely related to microbes from subsurface or surface aquatic environments were mainly responsible for the clustering of samples according to water residence time in the pools. By contrast, several Cytophagaceae and Flavobacteriaceae OTUs were related to different floodings, which were also the main determinants of DOM composition. A subset of compounds distinguishable by molecular mass and O/C content were characteristic for individual floods. Moreover, there was a transformation of DOM in stagnant pools toward smaller and more aromatic compounds, potentially also reflecting microbial utilization. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Isolation and characterization of metal-reducing thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado.

PubMed

Roh, Yul; Liu, Shi V; Li, Guangshan; Huang, Heshu; Phelps, Tommy J; Zhou, Jizhong

2002-12-01

Five bacterial strains were isolated from anaerobic enrichment cultures that had originated from inoculations with samples collected from the deep subsurface environments of the millions-of-years-old, geologically and hydrologically isolated Piceance Basin in Colorado. Small-subunit rRNA gene-based analyses indicated that all of these bacteria were closely related to Thermoanaerobacter ethanolicus, with similarities of 99.4 to 99.5%. Three isolates (X513, X514, and X561) from the five bacterial strains were used to examine physiological characteristics. These thermophilic bacteria were able to use acetate, glucose, hydrogen, lactate, pyruvate, succinate, and xylose as electron donors while reducing Fe(III), cobalt(III), chromium(VI), manganese(IV), and uranium(VI) at 60 degrees C. One of the isolates (X514) was also able to utilize hydrogen as an electron donor for Fe(III) reduction. These bacteria exhibited diverse mineral precipitation capabilities, including the formation of magnetite (Fe(3)O(4)), siderite (FeCO(3)), rhodochrosite (MnCO(3)), and uraninite (UO(2)). The gas composition of the incubation headspace and the ionic composition of the incubation medium exerted profound influences on the types of minerals formed. The susceptibility of the thermophilic Fe(III)-reducing cultures to metabolic inhibitors specific for ferric reductase, hydrogenase, and electron transport indicated that iron reduction by these bacteria is an enzymatic process.

Lunar and Martian Sub-surface Habitat Structure Technology Development and Application

NASA Technical Reports Server (NTRS)

Boston, Penelope J.; Strong, Janet D.

2005-01-01

NASA's human exploration initiative poses great opportunity and great risk for manned missions to the Moon and Mars. Subsidace structures such as caves and lava tubes offer readily available and existing in-situ habitat options. Sub-surface dwellings can provide complete radiation, micro-meteorite and exhaust plume shielding and a moderate and constant temperature environment; they are, therefore, excellent pre-existing habitat risk mitigation elements. Technical challenges to subsurface habitat structure development include surface penetration (digging and mining equipment), environmental pressurization, and psychological environment enhancement requirements. Lunar and Martian environments and elements have many beneficial similarities. This will allow for lunar testing and design development of subsurface habitat structures for Martian application; however, significant differences between lunar and Martian environments and resource elements will mandate unique application development. Mars is NASA's ultimate exploration goal and is known to have many very large lava tubes. Other cave types are plausible. The Moon has unroofed rilles and lava tubes, but further research will, in the near future, define the extent of Lunar and Martian differences and similarities. This paper will discuss Lunar and Martian subsurface habitation technology development challenges and opportunities.

Subsurface metagenomes uncover a vast repertoire of hypervariable proteins encoded by genetic elements in uncultivated organisms and viruses

NASA Astrophysics Data System (ADS)

Paul, B. G.; Burstein, D.; Castelle, C. J.; Banfield, J. F.; Valentine, D. L.; Miller, J. F.; Ghosh, P.; Handa, S.; Arambula, D.; Czornyj, E.; Thomas, B. C.

2016-12-01

Uncultivated microorganisms primarily account for the remarkable diversity harbored in subsurface environments and represent an expansive subset of the current Tree of Life. Recent metagenomic efforts to investigate subsurface biomes have unveiled an array of bacterial and archaeal candidate phyla, whose members have minimal genomes and an apparent host-dependent existence. Still, little is known about the adaptive strategies that mediate host interactions in these organisms or their viruses. Genomic features known as diversity-generating retroelements (DGRs), which guide variability into targeted genes, were recently discovered in two single-cell genomes of uncultivated nanoarchaea, and independently in the genome of a marine virus from methane seep sediments. These prodigious drivers of protein hypervariability were first identified as the key force behind phage tail fiber diversification for binding different host receptors. Since their discovery, approximately 500 new DGRs have been found across a wide range of bacterial genomes representing various niches. We identified an unexpected 1136 distinct diversifiers from a single groundwater environment in reconstructed microbial genomes and genome fragments. The newly detected DGRs - predominantly linked to members of the candidate phyla radiation (CPR) - appear to target genes associated with cell-cell attachment, signaling, and transcription regulation. These findings suggest that targeted protein diversification may have an important role in regulating symbiotic or parasitic associations in groundwater microbiomes.

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.

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

PubMed

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

2017-01-01

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

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

PubMed Central

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

2017-01-01

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

Prokaryotic phylogenetic diversity of Hungarian deep subsurface geothermal well waters.

PubMed

Németh, Andrea; Szirányi, Barbara; Krett, Gergely; Janurik, Endre; Kosáros, Tünde; Pekár, Ferenc; Márialigeti, Károly; Borsodi, Andrea K

2014-09-01

Geothermal wells characterized by thermal waters warmer than 30°C can be found in more than 65% of the area of Hungary. The examined thermal wells located nearby Szarvas are used for heating industrial and agricultural facilities because of their relatively high hydrocarbon content. The aim of this study was to reveal the prokaryotic community structure of the water of SZR18, K87 and SZR21 geothermal wells using molecular cloning methods and Denaturing Gradient Gel Electrophoresis (DGGE). Water samples from the outflow pipes were collected in 2012 and 2013. The phylogenetic distribution of archaeal molecular clones was very similar in each sample, the most abundant groups belonged to the genera Methanosaeta, Methanothermobacter and Thermofilum. In contrast, the distribution of bacterial molecular clones was very diverse. Many of them showed the closest sequence similarities to uncultured clone sequences from similar thermal environments. From the water of the SZR18 well, phylotypes closely related to genera Fictibacillus and Alicyclobacillus (Firmicutes) were only revealed, while the bacterial diversity of the K87 well water was much higher. Here, the members of the phyla Thermodesulfobacteria, Proteobacteria, Nitrospira, Chlorobi, OP1 and OPB7 were also detected besides Firmicutes.

Exploring the hydraulic fracturing parameter space: a novel high-pressure, high-throughput reactor system for investigating subsurface chemical transformations.

PubMed

Sumner, Andrew J; Plata, Desiree L

2018-02-21

Hydraulic fracturing coupled with horizontal drilling (HDHF) involves the deep-well injection of a fracturing fluid composed of diverse and numerous chemical additives designed to facilitate the release and collection of natural gas from shale plays. Analyses of flowback wastewaters have revealed organic contamination from both geogenic and anthropogenic sources. The additional detections of undisclosed halogenated chemicals suggest unintended in situ transformation of reactive additives, but the formation pathways for these are unclear in subsurface brines. To develop an efficient experimental framework for investigating the complex shale-well parameter space, we have reviewed and synthesized geospatial well data detailing temperature, pressure, pH, and halide ion values as well as industrial chemical disclosure and concentration data. Our findings showed subsurface conditions can reach pressures up to 4500 psi (310 bars) and temperatures up to 95 °C, while at least 588 unique chemicals have been disclosed by industry, including reactive oxidants and acids. Given the extreme conditions necessary to simulate the subsurface, we briefly highlighted existing geochemical reactor systems rated to the necessary pressures and temperatures, identifying throughput as a key limitation. In response, we designed and developed a custom reactor system capable of achieving 5000 psi (345 bars) and 90 °C at low cost with 15 individual reactors that are readily turned over. To demonstrate the system's throughput, we simultaneously tested 12 disclosed HDHF chemicals against a radical initiator compound in simulated subsurface conditions, ruling out a dozen potential transformation pathways in a single experiment. This review outlines the dynamic and diverse parameter range experienced by HDHF chemical additives and provides an optimized framework and novel reactor system for the methodical study of subsurface transformation pathways. Ultimately, enabling such studies will provide

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

Diversity of Ktedonobacteria with Actinomycetes-Like Morphology in Terrestrial Environments

PubMed Central

Yabe, Shuhei; Sakai, Yasuteru; Abe, Keietsu; Yokota, Akira

2017-01-01

Bacteria with an actinomycetes-like morphology have recently been discovered, and the class Ktedonobacteria was created for these bacteria in the phylum Chloroflexi. They may prove to be a valuable resource with the potential to produce unprecedented secondary metabolites. However, our understanding of their diversity, richness, habitat, and ecological significance is very limited. We herein developed a 16S rRNA gene-targeted, Ktedonobacteria-specific primer and analyzed ktedonobacterial amplicons. We investigated abundance, diversity, and community structure in forest and garden soils, sand, bark, geothermal sediment, and compost. Forest soils had the highest diversity among the samples tested (1181–2934 operational taxonomic units [OTUs]; Chao 1 estimate, 2503–5613; Shannon index, 4.21–6.42). A phylogenetic analysis of representative OTUs revealed at least eight groups within unclassified Ktedonobacterales, expanding the known diversity of this order. Ktedonobacterial communities markedly varied among our samples. The common mesic environments (soil, sand, and bark) were dominated by diverse phylotypes within the eight groups. In contrast, compost and geothermal sediment samples were dominated by known ktedonobacterial families (Thermosporotrichaceae and Thermogemmatisporaceae, respectively). The relative abundance of Ktedonobacteria in the communities, based on universal primers, was ≤0.8%, but was 12.9% in the geothermal sediment. These results suggest that unknown diverse Ktedonobacteria inhabit common environments including forests, gardens, and sand at low abundances, as well as extreme environments such as geothermal areas. PMID:28321007

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.

Does the Cave Environment Reduce Functional Diversity?

PubMed Central

Fernandes, Camile Sorbo; Batalha, Marco Antonio; Bichuette, Maria Elina

2016-01-01

Caves are not colonised by all taxa present in the surface species pool, due to absence of light and the tendency to food limitation when compared to surface communities. Under strong species sorting during colonisation and later by the restrictive environmental filter, traits that are not adaptive in subterranean habitats may be filtered out. We tested whether cave communities were assembled by the restrictive regime propitiated by permanent darkness or by competitive exclusion due to resource scarcity. When compared to surface communities, the restrictive subterranean regime would lead to lower functional diversity and phenotypic clustering inside the caves, and the opposite should be expected in the case of competitive exclusion. Using isopods (Oniscidea) as model taxa, we measured several niche descriptors of taxa from surface and cave habitats, used a multivariate measure of functional diversity, and compared their widths. We found phenotypic overdispersion and higher functional diversity in cave taxa when compared to surface taxa. On the one hand, the dry climate outside of caves hampered the survival of several taxa and their ecological strategies, not viable under severe desiccation risk, culminating in the clustering of functional traits. In contrast, this restriction does not occur inside of caves, where isopods find favourable conditions under lower predation pressures and more amenable environmental parameters that allow occupation and subsequent diversification. Our results showed that, at least for some taxa, caves may not be such a harsh environment as previously thought. The high functional diversity we found inside caves adds an additional reason for the conservation of these sensitive environments. PMID:27003837

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

The Mojave vadose zone: a subsurface biosphere analogue for Mars.

PubMed

Abbey, William; Salas, Everett; Bhartia, Rohit; Beegle, Luther W

2013-07-01

If life ever evolved on the surface of Mars, it is unlikely that it would still survive there today, but as Mars evolved from a wet planet to an arid one, the subsurface environment may have presented a refuge from increasingly hostile surface conditions. Since the last glacial maximum, the Mojave Desert has experienced a similar shift from a wet to a dry environment, giving us the opportunity to study here on Earth how subsurface ecosystems in an arid environment adapt to increasingly barren surface conditions. In this paper, we advocate studying the vadose zone ecosystem of the Mojave Desert as an analogue for possible subsurface biospheres on Mars. We also describe several examples of Mars-like terrain found in the Mojave region and discuss ecological insights that might be gained by a thorough examination of the vadose zone in these specific terrains. Examples described include distributary fans (deltas, alluvial fans, etc.), paleosols overlain by basaltic lava flows, and evaporite deposits.

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

Unidimensional games, propitious environments, and maximum diversity

NASA Astrophysics Data System (ADS)

Sales, Tasso R. M.

1993-10-01

Cellular automata have been extensively used in the modeling of complexity. In biological phenomena complexity is directly related to the intuitive concept of diversity, which manifests itself in several forms. Particularly, the game Life [E. R. Berlekamp, J. H. Conway, and R. K. Guy, Winning Ways for Your Mathematical Plays (Academic, New York, 1982), Vol. 2] may be viewed as a picture of nonlinear open biological systems acting cooperatively. However, it has been shown that, in Life, diversity (defined in terms of different clusters) decreases with time. We derive an alternative game introducing the concept of a propitious environment which confers longevity to live sites in time evolution. It is shown that the game self-organizes in a configuration of maximum diversity exhibiting a high geometrical complexity. This game is considered in one dimension and has some connections with the unidimensional Life.

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

NASA Astrophysics Data System (ADS)

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

2007-12-01

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

Energy as a Constraint on Habitability in the Subsurface

NASA Astrophysics Data System (ADS)

Hoehler, T.

2008-12-01

All living things must obtain energy from the environment to grow, to maintain a metabolic steady state, or simply to preserve viability. The availability of energy sources in the environment thus represents a key factor in determining the size, distribution, and activity of biological populations, and ultimately constrains the possibility for life itself. Lacking the abundant energy provided by solar radiation or the products of oxygenic photosynthesis, life in subsurface environments may be limited by energy availability as much as any other factor. The biological requirement for energy is expressed in two dimensions - analogous to the power and voltage requirements of electrical devices - and consideration and quantification of these requirements establishes quantitative boundary conditions on subsurface habitability. The magnitude of these requirements depends significantly on physicochemical environment, as does the provision of biologically-accessible energy from subsurface sources. With this conceptual basis, we are developing an 'energy balance' model that is designed to ultimately predict the habitability of a given environment, with respect to a given metabolism, in quantitative terms (as 'biomass density potential'). The model will develop from conceptual to quantitative as experimental and observational work constrains and quantifies, in natural populations adapted to low energy conditions, the magnitude of the biological energy requirements and the impacts of physicochemical environmental conditions on energy demand and supply.

Microbial physiology-based model of ethanol metabolism in subsurface sediments

NASA Astrophysics Data System (ADS)

Jin, Qusheng; Roden, Eric E.

2011-07-01

A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

Soil Carbon Dioxide Production and Surface Fluxes: Subsurface Physical Controls

NASA Astrophysics Data System (ADS)

Risk, D.; Kellman, L.; Beltrami, H.

Soil respiration is a critical determinant of landscape carbon balance. Variations in soil temperature and moisture patterns are important physical processes controlling soil respiration which need to be better understood. Relationships between soil respi- ration and physical controls are typically addressed using only surface flux data but other methods also exist which permit more rigorous interpretation of soil respira- tion processes. Here we use a combination of subsurface CO_{2} concentrations, surface CO_{2} fluxes and detailed physical monitoring of the subsurface envi- ronment to examine physical controls on soil CO_{2} production at four climate observatories in Eastern Canada. Results indicate that subsurface CO_{2} produc- tion is more strongly correlated to the subsurface thermal environment than the surface CO_{2} flux. Soil moisture was also found to have an important influence on sub- surface CO_{2} production, particularly in relation to the soil moisture - soil profile diffusivity relationship. Non-diffusive profile CO_{2} transport appears to be im- portant at these sites, resulting in a de-coupling of summertime surface fluxes from subsurface processes and violating assumptions that surface CO_{2} emissions are the result solely of diffusion. These results have implications for the study of soil respiration across a broad range of terrestrial environments.

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

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

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

Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

DOE PAGES

Hurt, Jr., Richard A.; Robeson II, Michael S.; Shakya, Migun; ...

2014-07-14

Despite more than three decades of progress, efficient nucleic acid extraction from microbial communities has remained difficult, particularly from clay environments. Lysis with concentrated guanidine followed by concentrated sodium phosphate extraction supported DNA and RNA recovery from high iron, low humus content clay. Alterating the extraction pH or using other ionic solutions (Na 2SO 4 and NH 4H 2PO 4) yielded no detectable nucleic acid. DNA recovered using a lysis solution with 500 mM phosphate buffer (PB) followed by a 1 M PB wash was 15.22±2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25more » g DNA/g clay with the Powerlyzer soil DNA system (MoBio). Increasing [PB] in the lysis reagent coincided with increasing DNA fragment length. Rarefaction plots based on16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more bacterial species recovered using this system. Additionally, some OTU's having more than 100 sequences in these libraries were absent in samples extracted using the PowerLyzer reagents or the previous lysis method.« less

Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

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

Hurt, Jr., Richard A.; Robeson II, Michael S.; Shakya, Migun

Despite more than three decades of progress, efficient nucleic acid extraction from microbial communities has remained difficult, particularly from clay environments. Lysis with concentrated guanidine followed by concentrated sodium phosphate extraction supported DNA and RNA recovery from high iron, low humus content clay. Alterating the extraction pH or using other ionic solutions (Na 2SO 4 and NH 4H 2PO 4) yielded no detectable nucleic acid. DNA recovered using a lysis solution with 500 mM phosphate buffer (PB) followed by a 1 M PB wash was 15.22±2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25more » g DNA/g clay with the Powerlyzer soil DNA system (MoBio). Increasing [PB] in the lysis reagent coincided with increasing DNA fragment length. Rarefaction plots based on16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more bacterial species recovered using this system. Additionally, some OTU's having more than 100 sequences in these libraries were absent in samples extracted using the PowerLyzer reagents or the previous lysis method.« 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.

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

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

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

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

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

DOE PAGES

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

2017-02-07

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

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

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.

Microbial Diversity in Surface Iron-Rich Aqueous Environments: Implications for Seeking Signs of Life on Mars

NASA Technical Reports Server (NTRS)

Brown, I. I.; Allen, C. C.; Tringe, S. G.; Klatt, C. G.; Bryant, D. A.; Sarkisova, S. A.; Garrison, D. H.; McKay, D. S.

2010-01-01

The success of selecting future landing sites on Mars to discover extinct and/or extant extraterrestrial life is dependent on the correct approximation of available knowledge about terrestrial paleogeochemistry and life evolution to Martian (paleo) geology and geochemistry. It is well known that both Earth and Mars are Fe rich. This widespread occurrence suggests that Fe may have played a key role in early life forms, where it probably served as a key constituent in early prosthetic moieties in many proteins of ancient microbes on Earth and likely Mars. The second critical idea is the premise that Life on Mars could most likely have developed when Mars experienced tectonic activity [1] which dramatically decreased around 1 bin years after Martian creation. After that Martian life could have gone extinct or hibernated in the deep subsurface, which would be expensive to reach in contrast to the successful work of Martian surface rovers. Here we analyze the diversity of microbes in several terrestrial Fe rich surface environments in conjunction with the phylogeny and molecular timing of emergence of those microbes on Earth. Anticipated results should help evaluate future landing sites on Mars in searches for biosignatures.

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.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

DOE PAGES

Jungbluth, Sean P.; Glavina del Rio, Tijana; Tringe, Susannah G.; ...

2017-04-06

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “more » Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “ Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Finally, our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.« less

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

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

Jungbluth, Sean P.; Glavina del Rio, Tijana; Tringe, Susannah G.

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “more » Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “ Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Finally, our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.« less

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

PubMed Central

Glavina del Rio, Tijana; Tringe, Susannah G.; Stepanauskas, Ramunas

2017-01-01

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments. PMID:28396823

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

Translucent Radiosity: Efficiently Combining Diffuse Inter-Reflection and Subsurface Scattering.

PubMed

Sheng, Yu; Shi, Yulong; Wang, Lili; Narasimhan, Srinivasa G

2014-07-01

It is hard to efficiently model the light transport in scenes with translucent objects for interactive applications. The inter-reflection between objects and their environments and the subsurface scattering through the materials intertwine to produce visual effects like color bleeding, light glows, and soft shading. Monte-Carlo based approaches have demonstrated impressive results but are computationally expensive, and faster approaches model either only inter-reflection or only subsurface scattering. In this paper, we present a simple analytic model that combines diffuse inter-reflection and isotropic subsurface scattering. Our approach extends the classical work in radiosity by including a subsurface scattering matrix that operates in conjunction with the traditional form factor matrix. This subsurface scattering matrix can be constructed using analytic, measurement-based or simulation-based models and can capture both homogeneous and heterogeneous translucencies. Using a fast iterative solution to radiosity, we demonstrate scene relighting and dynamically varying object translucencies at near interactive rates.

Architectural design influences the diversity and structure of the built environment microbiome

PubMed Central

Kembel, Steven W; Jones, Evan; Kline, Jeff; Northcutt, Dale; Stenson, Jason; Womack, Ann M; Bohannan, Brendan JM; Brown, G Z; Green, Jessica L

2012-01-01

Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome—the community of microorganisms that live indoors—is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors. PMID:22278670

Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere.

PubMed

Fullerton, Heather; Moyer, Craig L

2016-05-15

Chloroflexi small-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylum Chloroflexi is represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurface Chloroflexi Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurface Chloroflexi single amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nine Chloroflexi SAGs (seven of which are from the order Anaerolineales) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of the Chloroflexi SAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the seven Anaerolineales SAGs contains a distinct reductive dehalogenase homologous (rdhA) gene. Through the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, the Chloroflexi These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examined Chloroflexi SAGs, our genomes (several are from the order Anaerolineales) were recovered from a hydrothermally driven system and therefore provide a unique window into

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

PubMed

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

2016-11-01

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

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.

Akuna: An Open Source User Environment for Managing Subsurface Simulation Workflows

NASA Astrophysics Data System (ADS)

Freedman, V. L.; Agarwal, D.; Bensema, K.; Finsterle, S.; Gable, C. W.; Keating, E. H.; Krishnan, H.; Lansing, C.; Moeglein, W.; Pau, G. S. H.; Porter, E.; Scheibe, T. D.

2014-12-01

The U.S. Department of Energy (DOE) is investing in development of a numerical modeling toolset called ASCEM (Advanced Simulation Capability for Environmental Management) to support modeling analyses at legacy waste sites. ASCEM is an open source and modular computing framework that incorporates new advances and tools for predicting contaminant fate and transport in natural and engineered systems. The ASCEM toolset includes both a Platform with Integrated Toolsets (called Akuna) and a High-Performance Computing multi-process simulator (called Amanzi). The focus of this presentation is on Akuna, an open-source user environment that manages subsurface simulation workflows and associated data and metadata. In this presentation, key elements of Akuna are demonstrated, which includes toolsets for model setup, database management, sensitivity analysis, parameter estimation, uncertainty quantification, and visualization of both model setup and simulation results. A key component of the workflow is in the automated job launching and monitoring capabilities, which allow a user to submit and monitor simulation runs on high-performance, parallel computers. Visualization of large outputs can also be performed without moving data back to local resources. These capabilities make high-performance computing accessible to the users who might not be familiar with batch queue systems and usage protocols on different supercomputers and clusters.

Aseptically Sampled Organics in Subsurface Rocks From the Mars Analog Rio Tinto Experiment: An Analog For The Search for Deep Subsurface Life on Mars.}

NASA Astrophysics Data System (ADS)

Bonaccorsi, R.; Stoker, C. R.

2005-12-01

The subsurface is the key environment for searching for life on planets lacking surface life. Subsurface ecosystems are of great relevance to astrobiology including the search for past/present life on Mars. The surface of Mars has conditions preventing current life but the subsurface might preserve organics and even host some life [1]. The Mars-Analog-Rio-Tinto-Experiment (MARTE) is performing a simulation of a Mars drilling experiment. This comprises conventional and robotic drilling of cores in a volcanically-hosted-massive-pyrite deposit [2] from the Iberian Pyritic Belt (IBP) and life detection experiments applying anti-contamination protocols (e.g., ATP Luminometry assay). The RT is considered an important analog of the Sinus Meridiani site on Mars and an ideal model analog for a deep subsurface Martian environment. Former results from MARTE suggest the existence of a relatively complex subsurface life including aerobic and anaerobic chemoautotrophs and strict anaerobic methanogens sustained by Fe and S minerals in anoxic conditions. A key requirement for the analysis of a subsurface sample on Mars is a set of simple tests that can help determine if the sample contains organic material of biological origin, and its potential for retaining definitive biosignatures. We report here on the presence of bulk organic matter Corg (0.03-0.05 Wt%), and Ntot (0.01-0.04 Wt%) and amount of measured ATP (Lightning MVP, Biocontrol) in weathered rocks (tuffs, gossan, pyrite stockwork from Borehole #8; >166m). This provides key insight on the type of trophic system sustaining the subsurface biosphere (i.e., heterotrophs vs. autotrophs) at RT. ATP data (Relative-Luminosity-Units, RLU) provide information on possible contamination and distribution of viable biomass with core depth (BH#8, and BH#7, ~3m). Avg. 153 RLU, i.e., surface vs. center of core, suggest that cleaness/sterility can be maintained when using a simple sterile protocol under field conditions. Results from this

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.

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Biogenic Carbon on Mars: A Subsurface Chauvinistic Viewpoint

NASA Astrophysics Data System (ADS)

Onstott, T. C.; Lau, C. Y. M.; Magnabosco, C.; Harris, R.; Chen, Y.; Slater, G.; Sherwood Lollar, B.; Kieft, T. L.; van Heerden, E.; Borgonie, G.; Dong, H.

2015-12-01

A review of 150 publications on the subsurface microbiology of the continental subsurface provides ~1,400 measurements of cellular abundances down to 4,800 meter depth. These data suggest that the continental subsurface biomass is comprised of ~1016-17 grams of carbon, which is higher than the most recent estimates of ~1015 grams of carbon (1 Gt) for the marine deep biosphere. If life developed early in Martian history and Mars sustained an active hydrological cycle during its first 500 million years, then is it possible that Mars could have developed a subsurface biomass of comparable size to that of Earth? Such a biomass would comprise a much larger fraction of the total known Martian carbon budget than does the subsurface biomass on Earth. More importantly could a remnant of this subsurface biosphere survive to the present day? To determine how sustainable subsurface life could be in isolation from the surface we have been studying subsurface fracture fluids from the Precambrian Shields in South Africa and Canada. In these environments the energetically efficient and deeply rooted acetyl-CoA pathway for carbon fixation plays a central role for chemolithoautotrophic primary producers that form the base of the biomass pyramid. These primary producers appear to be sustained indefinitely by H2 generated through serpentinization and radiolytic reactions. Carbon isotope data suggest that in some subsurface locations a much larger population of secondary consumers are sustained by the primary production of biogenic CH4 from a much smaller population of methanogens. These inverted biomass and energy pyramids sustained by the cycling of CH4 could have been and could still be active on Mars. The C and H isotopic signatures of Martian CH4 remain key tools in identifying potential signatures of an extant Martian biosphere. Based upon our results to date cavity ring-down spectroscopic technologies provide an option for making these measurements on future rover missions.

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

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.

WISDOM, a polarimetric GPR for the shallow subsurface characterization

NASA Astrophysics Data System (ADS)

Ciarletti, V.; Plettemeier, D.; Hassen-Kodja, R.; Clifford, S. M.; Wisdom Team

2011-12-01

WISDOM (Water Ice and Subsurface Deposit Observations on Mars) is a polarimetric Ground Penetrating Radar (GPR) that has been selected to be part of the Pasteur payload onboard the Rover of the 2018 ExoMars mission. It will perform large-scale scientific investigations of the sub-surface of the landing site and provide precise information about the subsurface structure prior to drilling. WISDOM has been designed to provide accurate information on the sub-surface structure down to a depth in excess to 2 meters (commensurate to the drill capacities) with a vertical resolution of a several centimetres. It will give access to the geological structure, electromagnetic nature, and, possibly, to the hydrological state of the shallow subsurface by retrieving the layering and properties of the layers and buried reflectors. The data will also be used to determine the most promising locations to collect underground samples with the drilling system mounted on board the rover. Polarimetric measurements have been recently acquired on perfectly known targets as well as in natural environments. They demonstrated the ability to provide a better understanding of sub-surface structure and significantly reduce the ambiguity associated with identifying the location of off-nadir reflectors, relative to the rover path. This work describes the instrument and its operating modes with particular emphasis on its polarimetric capacities.

Ubiquity and Diversity of Heterotrophic Bacterial nasA Genes in Diverse Marine Environments

PubMed Central

Jiang, Xuexia; Dang, Hongyue; Jiao, Nianzhi

2015-01-01

Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating that NAB may be

Survival in the hot subsurface: Hydrogen stress on hyperthermophilic heterotrophs and methanogens

NASA Astrophysics Data System (ADS)

Topcuoglu, B. D.; Holden, J. F.

2017-12-01

Marine hyperthermophilic heterotrophs and methanogens belonging to the Thermococcales and Methanococcales are often found in hot subsurface environments such as hydrothermal vents, marine sediments, and oil reservoirs. This project aims to make fundamental advances in our understanding of interspecies microbe-microbe interactions in hot subsurface environments by integrating metabolic network modeling, transcriptomic analyses and continuous cultivation of hyperthermophiles and describe how heterotrophs and methanogens eliminate H2 stress. Some subsurface environments may lack alternative electron acceptors (e.g., S°) for the heterotroph and sufficient environmental flux rates to draw in fresh energy sources or remove excess metabolic products. We observed a decrease in growth rates for the H2-producer Thermococcus paralvinellae when grown with an aqueous H2 background of 65 µM relative to no added H2. Metabolite analysis showed increased formate production during H2 inhibition. Differential gene expression analyses coupled with metabolic network modeling showed that T. paralvinellae oxidized H2 and made formate by a formate hydrogenlyase to survive H2 inhibition. Low H2 concentrations (20 µM) also caused a decrease in growth and CH4 production rates for the H2-consuming methanogen Methanocaldococcus jannaschii. H2 stress in both organisms was ameliorated when the organisms were grown together syntrophically. CH4 was produced without any added H2 during syntrophic growth, and there was no formate produced by T. paralvinellae. These organisms may impact the biogeochemistry, especially natural gas production, in saline, organic-rich subsurface environments when both are present.

Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa

PubMed Central

Borgonie, G.; Linage-Alvarez, B.; Ojo, A. O.; Mundle, S.O.C.; Freese, L B.; Van Rooyen, C.; Kuloyo, O.; Albertyn, J.; Pohl, C.; Cason, E. D.; Vermeulen, J.; Pienaar, C.; Litthauer, D.; Van Niekerk, H.; Van Eeden, J.; Lollar, B. Sherwood.; Onstott, T. C.; Van Heerden, E.

2015-01-01

Following the discovery of the first Eukarya in the deep subsurface, intense interest has developed to understand the diversity of eukaryotes living in these extreme environments. We identified that Platyhelminthes, Rotifera, Annelida and Arthropoda are thriving at 1.4 km depths in palaeometeoric fissure water up to 12,300 yr old in South African mines. Protozoa and Fungi have also been identified; however, they are present in low numbers. Characterization of the different species reveals that many are opportunistic organisms with an origin due to recharge from surface waters rather than soil leaching. This is the first known study to demonstrate the in situ distribution of biofilms on fissure rock faces using video documentation. Calculations suggest that food, not dissolved oxygen is the limiting factor for eukaryal population growth. The discovery of a group of Eukarya underground has important implications for the search for life on other planets in our solar system. PMID:26597082

Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa.

PubMed

Borgonie, G; Linage-Alvarez, B; Ojo, A O; Mundle, S O C; Freese, L B; Van Rooyen, C; Kuloyo, O; Albertyn, J; Pohl, C; Cason, E D; Vermeulen, J; Pienaar, C; Litthauer, D; Van Niekerk, H; Van Eeden, J; Sherwood Lollar, B; Onstott, T C; Van Heerden, E

2015-11-24

Following the discovery of the first Eukarya in the deep subsurface, intense interest has developed to understand the diversity of eukaryotes living in these extreme environments. We identified that Platyhelminthes, Rotifera, Annelida and Arthropoda are thriving at 1.4 km depths in palaeometeoric fissure water up to 12,300 yr old in South African mines. Protozoa and Fungi have also been identified; however, they are present in low numbers. Characterization of the different species reveals that many are opportunistic organisms with an origin due to recharge from surface waters rather than soil leaching. This is the first known study to demonstrate the in situ distribution of biofilms on fissure rock faces using video documentation. Calculations suggest that food, not dissolved oxygen is the limiting factor for eukaryal population growth. The discovery of a group of Eukarya underground has important implications for the search for life on other planets in our solar system.

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

Improving diversity in cultures of bacteria from an extreme environment.

PubMed

Vester, Jan Kjølhede; Glaring, Mikkel Andreas; Stougaard, Peter

2013-08-01

The ikaite columns in the Ikka Fjord in Greenland represent one of the few permanently cold and alkaline environments on Earth, and the interior of the columns is home to a bacterial community adapted to these extreme conditions. The community is characterized by low cell numbers imbedded in a calcium carbonate matrix, making extraction of bacterial cells and DNA a challenge and limiting molecular and genomic studies of this environment. To utilize this genetic resource, cultivation at high pH and low temperature was studied as a method for obtaining biomass and DNA from the fraction of this community that would not otherwise be amenable to genetic analyses. The diversity and community dynamics in mixed cultures of bacteria from ikaite columns was investigated using denaturing gradient gel electrophoresis and pyrosequencing of 16S rDNA. Both medium composition and incubation time influenced the diversity of the culture and many hitherto uncharacterized genera could be brought into culture by extended incubation time. Extended incubation time also gave rise to a more diverse community with a significant number of rare species not detected in the initial community.

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

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

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

PubMed Central

Probst, Alexander J; Holman, Hoi-Ying N; DeSantis, Todd Z; Andersen, Gary L; Birarda, Giovanni; Bechtel, Hans A; Piceno, Yvette M; Sonnleitner, Maria; Venkateswaran, Kasthuri; Moissl-Eichinger, Christine

2013-01-01

Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging. PMID:23178669

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

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

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

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

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

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.

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.

Microbial Life in the Deep Subsurface: Deep, Hot and Radioactive

NASA Technical Reports Server (NTRS)

DeStefano, Andrea L.; Ford, Jill C.; Winsor, Seana K.; Allen, Carlton C.; Miller, Judith; McNamara, Karen M.; Gibson, Everett K., Jr.

2000-01-01

Recent studies, motivated in part by the search for extraterrestrial life, continue to expand the recognized limits of Earth's biosphere. This work explored evidence for life a high-temperature, radioactive environment in the deep subsurface.

Evaluation of coarse and fine particles in diverse Indian environments.

PubMed

George, K V; Patil, Dinakar D; Anil, Mulukutla N V; Kamal, Neel; Alappat, Babu J; Kumar, Prashant

2017-02-01

The estimates of airborne fine particle (PM 2.5 ) concentrations are possible through rigorous empirical correlations based on the monitored PM 10 data. However, such correlations change depending on the nature of sources in diverse ambient environments and, therefore, have to be environment specific. Studies presenting such correlations are limited but needed, especially for those areas, where PM 2.5 is not routinely monitored. Moreover, there are a number of studies focusing on urban environments but very limited for coal mines and coastal areas. The aim of this study is to comprehensively analyze the concentrations of both PM 10 and PM 2.5 and develop empirical correlations between them. Data from 26 different sites spread over three distinct environments, which are a relatively clean coastal area, two coal mining areas, and a highly urbanized area in Delhi were used for the study. Distributions of PM in the 0.43-10-μm size range were measured using eight-stage cascade impactors. Regression analysis was used to estimate the percentage of PM 2.5 in PM 10 across distinct environments for source identification. Relatively low percentage of PM 2.5 concentrations (21, 28, and 32%) in PM 10 were found in clean coastal and two mining areas, respectively. Percentage of PM 2.5 concentrations in PM 10 in the highly urbanized area of Delhi was 51%, indicating a presence of a much higher percentage of fine particles due to vehicular combustion in Delhi. The findings of this work are important in estimating concentrations of much harmful fine particles from coarse particles across distinct environments. The results are also useful in source identification of particulates as differences in the percentage of PM 2.5 concentrations in PM 10 can be attributed to characteristics of sources in the diverse ambient environments.

Microbially catalyzed nitrate-dependent metal/radionuclide oxidation in shallow subsurface sediments

NASA Astrophysics Data System (ADS)

Weber, K.; Healy, O.; Spanbauer, T. L.; Snow, D. D.

2011-12-01

enumeration of nitrate-dependent U(IV) oxidizing microorganisms demonstrated an abundant community ranging from 1.61x104 to 2.74x104 cells g-1 sediment. Enrichments initiated verified microbial U reduction and U oxidation coupled to nitrate reduction. Sediment slurries were serially diluted and incubated over a period of eight weeks and compared to uninoculated controls. Oxidation (0-4,554 μg/L) and reduction (0-55 μg/L) of U exceeded uninoculated controls further providing evidence of a U biogeochemical cycling in these subsurface sediments. The oxidation of U(IV) could contribute to U mobilization in the groundwater and result in decreased water quality. Not only could nitrate serve as an oxidant, but Fe(III) could also contribute to U mobilization. Nitrate-dependent Fe(II) oxidation is an environmentally ubiquitous process facilitated by a diversity of microorganisms. Additional research is necessary in order to establish a role of biogenic Fe(III) oxides in U geochemical cycling at this site. These microbially mediated processes could also have a confounding effect on uranium mobility in subsurface environments.

The emergence of hydrogeophysics for improved understanding of subsurface processes over multiple scales

PubMed Central

Hubbard, Susan S.; Huisman, Johan A.; Revil, André; Robinson, David A.; Singha, Kamini; Slater, Lee D.

2015-01-01

Abstract Geophysics provides a multidimensional suite of investigative methods that are transforming our ability to see into the very fabric of the subsurface environment, and monitor the dynamics of its fluids and the biogeochemical reactions that occur within it. Here we document how geophysical methods have emerged as valuable tools for investigating shallow subsurface processes over the past two decades and offer a vision for future developments relevant to hydrology and also ecosystem science. The field of “hydrogeophysics” arose in the late 1990s, prompted, in part, by the wealth of studies on stochastic subsurface hydrology that argued for better field‐based investigative techniques. These new hydrogeophysical approaches benefited from the emergence of practical and robust data inversion techniques, in many cases with a view to quantify shallow subsurface heterogeneity and the associated dynamics of subsurface fluids. Furthermore, the need for quantitative characterization stimulated a wealth of new investigations into petrophysical relationships that link hydrologically relevant properties to measurable geophysical parameters. Development of time‐lapse approaches provided a new suite of tools for hydrological investigation, enhanced further with the realization that some geophysical properties may be sensitive to biogeochemical transformations in the subsurface environment, thus opening up the new field of “biogeophysics.” Early hydrogeophysical studies often concentrated on relatively small “plot‐scale” experiments. More recently, however, the translation to larger‐scale characterization has been the focus of a number of studies. Geophysical technologies continue to develop, driven, in part, by the increasing need to understand and quantify key processes controlling sustainable water resources and ecosystem services. PMID:26900183

Environmental Electrokinetics for a sustainable subsurface.

PubMed

Lima, A T; Hofmann, A; Reynolds, D; Ptacek, C J; Van Cappellen, P; Ottosen, L M; Pamukcu, S; Alshawabekh, A; O'Carroll, D M; Riis, C; Cox, E; Gent, D B; Landis, R; Wang, J; Chowdhury, A I A; Secord, E L; Sanchez-Hachair, A

2017-08-01

Soil and groundwater are key components in the sustainable management of the subsurface environment. Source contamination is one of its main threats and is commonly addressed using established remediation techniques such as in-situ chemical oxidation (ISCO), in-situ chemical reduction (ISCR; most notably using zero-valent iron [ZVI]), enhanced in-situ bioremediation (EISB), phytoremediation, soil-washing, pump-and-treat, soil vapour extraction (SVE), thermal treatment, and excavation and disposal. Decades of field applications have shown that these techniques can successfully treat or control contaminants in higher permeability subsurface materials such as sands, but achieve only limited success at sites where low permeability soils, such as silts and clays, prevail. Electrokinetics (EK), a soil remediation technique mostly recognized in in-situ treatment of low permeability soils, has, for the last decade, been combined with more conventional techniques and can significantly enhance the performance of several of these remediation technologies, including ISCO, ISCR, EISB and phytoremediation. Herein, we discuss the use of emerging EK techniques in tandem with conventional remediation techniques, to achieve improved remediation performance. Furthermore, we highlight new EK applications that may come to play a role in the sustainable treatment of the contaminated subsurface. Copyright © 2017 Elsevier Ltd. All rights reserved.

Scenario simulation based assessment of subsurface energy storage

NASA Astrophysics Data System (ADS)

Beyer, C.; Bauer, S.; Dahmke, A.

2014-12-01

Energy production from renewable sources such as solar or wind power is characterized by temporally varying power supply. The politically intended transition towards renewable energies in Germany („Energiewende") hence requires the installation of energy storage technologies to compensate for the fluctuating production. In this context, subsurface energy storage represents a viable option due to large potential storage capacities and the wide prevalence of suited geological formations. Technologies for subsurface energy storage comprise cavern or deep porous media storage of synthetic hydrogen or methane from electrolysis and methanization, or compressed air, as well as heat storage in shallow or moderately deep porous formations. Pressure build-up, fluid displacement or temperature changes induced by such operations may affect local and regional groundwater flow, geomechanical behavior, groundwater geochemistry and microbiology. Moreover, subsurface energy storage may interact and possibly be in conflict with other "uses" like drinking water abstraction or ecological goods and functions. An utilization of the subsurface for energy storage therefore requires an adequate system and process understanding for the evaluation and assessment of possible impacts of specific storage operations on other types of subsurface use, the affected environment and protected entities. This contribution presents the framework of the ANGUS+ project, in which tools and methods are developed for these types of assessments. Synthetic but still realistic scenarios of geological energy storage are derived and parameterized for representative North German storage sites by data acquisition and evaluation, and experimental work. Coupled numerical hydraulic, thermal, mechanical and reactive transport (THMC) simulation tools are developed and applied to simulate the energy storage and subsurface usage scenarios, which are analyzed for an assessment and generalization of the imposed THMC

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.

Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing.

PubMed

Poza, Margarita; Gayoso, Carmen; Gómez, Manuel J; Rumbo-Feal, Soraya; Tomás, María; Aranda, Jesús; Fernández, Ana; Bou, Germán

2012-01-01

Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.

[Community Characteristics of ANAMMOX Bacteria in Subsurface Flow Constructed Wetland (SSFCW) for Processing of Aquaculture Waster Water].

PubMed

Zeng, Xian-lei; Liu, Xing-guo; Wu, Zong-fan; Shi, Xu; Lu, Shi-min

2016-02-15

Anaerobic ammonium oxidation (ANAMMOX) is one of the important functions in waste water treatment by subsurface flow constructed wetland (SSFCW), however, there are few studies on ANAMMOX in SSFCW environment at present. The community characteristics of ANAMMOX in the SSFCW of processing aquaculture waste water were explored in this study. In order to analyze the structure, diversity and abundance of ANAMMOX bacteria, several 16S rRNA clone libraries were constructed and real-time PCR targeting specific 16S rRNA genes together with diversity analysis was adopted. The obtained results showed that the SSFCW identified a total of three unknown clusters and two known clusters including Candidatus brocadia and Candidatus kuenenia. The dominant cluster was Candidatus brocadia. The highest diversity levels of ANAMMOX bacteria occurred in autumn (H', 1.21), while the lowest in spring (H', 0.64). The abundance of ANAMMOX bacteria in SSFCW environment ranged from 8.0 x 10(4) to 9.4 x 10(6) copies x g(-1) of fresh weight and the copy number of total bacterial 16S rRNA genes ranged from 7.3 x 10(9) to 9.1 x 10(10) copies x g(-1) of fresh weight during culture cycle. There were significant differences in the ANAMMOX bacteria abundances of different stratum and seasons in SSFCW environment, but the differences in total bacterial abundances were not obvious. In addition, the differences in ANAMMOX bacteria abundances in different stratum and seasons in SSFCW environment were irregular in different culture cycle. According to the distribution characteristics of ANAMMOX bacteria in the wetland, the denitrification effect of SSFCW could be improved by changing the supplying manners of aquaculture wastewater and adjusting the structure of wetland. The research results will provide reference for further optimizing the SSFCW and improving the efficiency of purification.

Residues of endosulfan in surface and subsurface agricultural soil and its bioremediation.

PubMed

Odukkathil, Greeshma; Vasudevan, Namasivayam

2016-01-01

The persistence of many hydrophobic pesticides has been reported by various workers in various soil environments and its bioremediation is a major concern due to less bioavailability. In the present study, the pesticide residues in the surface and subsurface soil in an area of intense agricultural activity in Pakkam Village of Thiruvallur District, Tamilnadu, India, and its bioremediation using a novel bacterial consortium was investigated. Surface (0-15 cm) and subsurface soils (15-30 cm and 30-40 cm) were sampled, and pesticides in different layers of the soil were analyzed. Alpha endosulfan and beta endosulfan concentrations ranged from 1.42 to 3.4 mg/g and 1.28-3.1 mg/g in the surface soil, 0.6-1.4 mg/g and 0.3-0.6 mg/g in the subsurface soil (15-30 cm), and 0.9-1.5 mg/g and 0.34-1.3 mg/g in the subsurface soil (30-40 cm) respectively. Residues of other persistent pesticides were also detected in minor concentrations. These soil layers were subjected to bioremediation using a novel bacterial consortium under a simulated soil profile condition in a soil reactor. The complete removal of alpha and beta endosulfan was observed over 25 days. Residues of endosulfate were also detected during bioremediation, which was subsequently degraded on the 30th day. This study revealed the existence of endosulfan in the surface and subsurface soils and also proved that the removal of such a ubiquitous pesticide in the surface and subsurface environment can be achieved in the field by bioaugumenting a biosurfactant-producing bacterial consortium that degrades pesticides. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fractal topography and subsurface water flows from fluvial bedforms to the continental shield

USGS Publications Warehouse

Worman, A.; Packman, A.I.; Marklund, L.; Harvey, J.W.; Stone, S.H.

2007-01-01

Surface-subsurface flow interactions are critical to a wide range of geochemical and ecological processes and to the fate of contaminants in freshwater environments. Fractal scaling relationships have been found in distributions of both land surface topography and solute efflux from watersheds, but the linkage between those observations has not been realized. We show that the fractal nature of the land surface in fluvial and glacial systems produces fractal distributions of recharge, discharge, and associated subsurface flow patterns. Interfacial flux tends to be dominated by small-scale features while the flux through deeper subsurface flow paths tends to be controlled by larger-scale features. This scaling behavior holds at all scales, from small fluvial bedforms (tens of centimeters) to the continental landscape (hundreds of kilometers). The fractal nature of surface-subsurface water fluxes yields a single scale-independent distribution of subsurface water residence times for both near-surface fluvial systems and deeper hydrogeological flows. Copyright 2007 by the American Geophysical Union.

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.

Evaluating a Gender Diversity Workshop to Promote Positive Learning Environments

ERIC Educational Resources Information Center

Burford, James; Lucassen, Mathijs F. G.; Hamilton, Thomas

2017-01-01

Drawing on data from an Aotearoa/New Zealand study of more than 230 secondary students, this article evaluates the potential of a 60-min gender diversity workshop to address bullying and promote positive environments for learning. Students completed pre- and postworkshop questionnaires. The authors used descriptive statistics to summarize results…

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.

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.

Some New Windows into Terrestrial Deep Subsurface Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Moser, D. P.

2011-12-01

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

Identifying future directions for subsurface hydrocarbon migration research

NASA Astrophysics Data System (ADS)

Leifer, I.; Clark, J. F.; Luyendyk, B.; Valentine, D.

Subsurface hydrocarbon migration is important for understanding the input and impacts of natural hydrocarbon seepage on the environment. Great uncertainties remain in most aspects of hydrocarbon migration, including some basic mechanisms of this four-phase flow of tar, oil, water, and gas through the complex fracture-network geometry particularly since the phases span a wide range of properties. Academic, government, and industry representatives recently attended a workshop to identify the areas of greatest need for future research in shallow hydrocarbon migration.Novel approaches such as studying temporal and spatial seepage variations and analogous geofluid systems (e.g., geysers and trickle beds) allow deductions of subsurface processes and structures that remain largely unclear. Unique complexities exist in hydrocarbon migration due to its multiphase flow and complex geometry, including in-situ biological weathering. Furthermore, many aspects of the role of hydrocarbons (positive and negative) in the environment are poorly understood, including how they enter the food chain (respiration, consumption, etc.) and “percolate” to higher trophic levels. But understanding these ecological impacts requires knowledge of the emissions' temporal and spatial variability and trajectories.

The emergence of hydrogeophysics for improved understanding of subsurface processes over multiple scales

DOE PAGES

Binley, Andrew; Hubbard, Susan S.; Huisman, Johan A.; ...

2015-06-15

Geophysics provides a multidimensional suite of investigative methods that are transforming our ability to see into the very fabric of the subsurface environment, and monitor the dynamics of its fluids and the biogeochemical reactions that occur within it. Here we document how geophysical methods have emerged as valuable tools for investigating shallow subsurface processes over the past two decades and offer a vision for future developments relevant to hydrology and also ecosystem science. The field of “hydrogeophysics” arose in the late 1990s, prompted, in part, by the wealth of studies on stochastic subsurface hydrology that argued for better field-based investigativemore » techniques. These new hydrogeophysical approaches benefited from the emergence of practical and robust data inversion techniques, in many cases with a view to quantify shallow subsurface heterogeneity and the associated dynamics of subsurface fluids. Furthermore, the need for quantitative characterization stimulated a wealth of new investigations into petrophysical relationships that link hydrologically relevant properties to measurable geophysical parameters. Development of time-lapse approaches provided a new suite of tools for hydrological investigation, enhanced further with the realization that some geophysical properties may be sensitive to biogeochemical transformations in the subsurface environment, thus opening up the new field of “biogeophysics.” Early hydrogeophysical studies often concentrated on relatively small “plot-scale” experiments. More recently, however, the translation to larger-scale characterization has been the focus of a number of studies. In conclusion, geophysical technologies continue to develop, driven, in part, by the increasing need to understand and quantify key processes controlling sustainable water resources and ecosystem services.« less

The emergence of hydrogeophysics for improved understanding of subsurface processes over multiple scales

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

Binley, Andrew; Hubbard, Susan S.; Huisman, Johan A.

Geophysics provides a multidimensional suite of investigative methods that are transforming our ability to see into the very fabric of the subsurface environment, and monitor the dynamics of its fluids and the biogeochemical reactions that occur within it. Here we document how geophysical methods have emerged as valuable tools for investigating shallow subsurface processes over the past two decades and offer a vision for future developments relevant to hydrology and also ecosystem science. The field of “hydrogeophysics” arose in the late 1990s, prompted, in part, by the wealth of studies on stochastic subsurface hydrology that argued for better field-based investigativemore » techniques. These new hydrogeophysical approaches benefited from the emergence of practical and robust data inversion techniques, in many cases with a view to quantify shallow subsurface heterogeneity and the associated dynamics of subsurface fluids. Furthermore, the need for quantitative characterization stimulated a wealth of new investigations into petrophysical relationships that link hydrologically relevant properties to measurable geophysical parameters. Development of time-lapse approaches provided a new suite of tools for hydrological investigation, enhanced further with the realization that some geophysical properties may be sensitive to biogeochemical transformations in the subsurface environment, thus opening up the new field of “biogeophysics.” Early hydrogeophysical studies often concentrated on relatively small “plot-scale” experiments. More recently, however, the translation to larger-scale characterization has been the focus of a number of studies. In conclusion, geophysical technologies continue to develop, driven, in part, by the increasing need to understand and quantify key processes controlling sustainable water resources and ecosystem services.« less

Complete genome sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment

DOE PAGES

Hwang, C.; Copeland, A.; Lucas, Susan; ...

2015-01-22

We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and uranium-contaminated subsurface sediment of the Oak Ridge Integrated Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN. The bacterium’s genome sequence will elucidate its physiological potential in subsurface sediments undergoing in situ uranium bioremediation and natural attenuation.

Evidence of Late Pliocene-Early Pleistocene marine environments in the deep subsurface of the Lihue Basin, Kauai, Hawaii

USGS Publications Warehouse

Izuka, S.K.; Resig, J.M.

2008-01-01

Cuttings recovered from two deep exploratory wells in the Lihue Basin, Kauai, Hawaii, include fossiliferous marine deposits that offer an uncommon opportunity to study paleoenvironments from the deep subsurface in Hawaii and interpret the paleogeography and geologic history of Kauai. These deposits indicate that two marine incursions gave rise to protected shallow-water, low-energy embayments in the southern part of the Lihue Basin in the late Pliocene-early Pleistocene. During the first marine incursion, the embayment was initially zoned, with a variable-salinity environment nearshore and a normal-marine reef environment offshore. The offshore reef environment eventually evolved to a nearshore, variable-salinity environment as the outer part of the embayment shallowed. During the second marine incursion, the embayment had normal-marine to hypersaline conditions, which constitute a significant departure from the variable-salinity environment present during the first marine incursion. Large streams draining the southern Lihue Basin are a likely source of the freshwater that caused the salinity fluctuations evident in the fossils from the first marine incursion. Subsequent volcanic eruptions produced lava flows that buried the embayment and probably diverted much of the stream flow in the southern Lihue Basin northward, to its present point of discharge north of Kalepa Ridge. As a result, the embayment that formed during the second marine incursion received less freshwater, and a normal-marine to hypersaline environment developed. The shallow-water marine deposits, currently buried between 86 m and 185 m below present sea level, have implications for regional tectonics and global eustasy. Copyright ?? 2008, SEPM (Society for Sedimentary Geology).

The InSight Mars Lander and Its Effect on the Subsurface Thermal Environment

NASA Astrophysics Data System (ADS)

Siegler, Matthew A.; Smrekar, Suzanne E.; Grott, Matthias; Piqueux, Sylvain; Mueller, Nils; Williams, Jean-Pierre; Plesa, Ana-Catalina; Spohn, Tilman

2017-10-01

The 2018 InSight (Interior Exploration using Seismic Investigations, Geodesy and Heat Transport) Mission has the mission goal of providing insitu data for the first measurement of the geothermal heat flow of Mars. The Heat Flow and Physical Properties Package (HP3) will take thermal conductivity and thermal gradient measurements to approximately 5 m depth. By necessity, this measurement will be made within a few meters of the lander. This means that thermal perturbations from the lander will modify local surface and subsurface temperature measurements. For HP3's sensitive thermal gradient measurements, this spacecraft influence will be important to model and parameterize. Here we present a basic 3D model of thermal effects of the lander on its surroundings. Though lander perturbations significantly alter subsurface temperatures, a successful thermal gradient measurement will be possible in all thermal conditions by proper (>3 m depth) placement of the heat flow probe.

Controlling Subsurface Fractures and Fluid Flow: A Basic Research Agenda

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

Pyrak-Nolte, Laura J; DePaolo, Donald J.; Pietraß, Tanja

2015-05-22

From beneath the surface of the earth, we currently obtain about 80-percent of the energy our nation consumes each year. In the future we have the potential to generate billions of watts of electrical power from clean, green, geothermal energy sources. Our planet’s subsurface can also serve as a reservoir for storing energy produced from intermittent sources such as wind and solar, and it could provide safe, long-term storage of excess carbon dioxide, energy waste products and other hazardous materials. However, it is impossible to underestimate the complexities of the subsurface world. These complexities challenge our ability to acquire themore » scientific knowledge needed for the efficient and safe exploitation of its resources. To more effectively harness subsurface resources while mitigating the impacts of developing and using these resources, the U.S. Department of Energy established SubTER – the Subsurface Technology and Engineering RD&D Crosscut team. This DOE multi-office team engaged scientists and engineers from the national laboratories to assess and make recommendations for improving energy-related subsurface engineering. The SubTER team produced a plan with the overall objective of “adaptive control of subsurface fractures and fluid flow.”This plan revolved around four core technological pillars—Intelligent Wellbore Systems that sustain the integrity of the wellbore environment; Subsurface Stress and Induced Seismicity programs that guide and optimize sustainable energy strategies while reducing the risks associated with subsurface injections; Permeability Manipulation studies that improve methods of enhancing, impeding and eliminating fluid flow; and New Subsurface Signals that transform our ability to see into and characterize subsurface systems. The SubTER team developed an extensive R&D plan for advancing technologies within these four core pillars and also identified several areas where new technologies would require additional basic

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.

Insights into the diversity of eukaryotes in acid mine drainage biofilm communities.

PubMed

Baker, Brett J; Tyson, Gene W; Goosherst, Lindsey; Banfield, Jillian F

2009-04-01

Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain (northern California). Phylogenetic analysis revealed that the majority (68%) of the sequences belonged to fungi. Protists falling into the deeply branching lineage named the acidophilic protist clade (APC) and the class Heterolobosea were also present. The APC group represents kingdom-level novelty, with <76% sequence similarity to 18S rRNA gene sequences of organisms from other environments. Fluorescently labeled oligonucleotide rRNA probes were designed to target each of these groups in biofilm samples, enabling abundance and morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.

Engineers' Perceptions of Diversity and the Learning Environment at Work: A Mixed Methods Study

ERIC Educational Resources Information Center

Firestone, Brenda L.

2012-01-01

The purpose of this dissertation research study was to investigate engineers' perceptions of diversity and the workplace learning environment surrounding diversity education efforts in engineering occupations. The study made use of a mixed methods methodology and was theoretically framed using a critical feminist adult education lens and…

Feeding a subsurface biosphere: radiolysis and abiogenic energy sources

NASA Astrophysics Data System (ADS)

Onstott, T.

Noble gas analyses of ground water collected from the deep, fractured, basaltic andesite and quartzite Archean strata in South Africa suggest subsurface residence times ranging from tens to hundreds of millions of years. Hydraulically isolated compartments of highly saline water contain hundreds of μM concentrations of gas comprised primarily of C1-4 hydrocarbons, H2 and He, with minor Ar and N .2 Carbon and hydrogen isotopic analyses of the hydrocarbons suggest an abiogenic origin com atible with surface catalysed reductive assimilation (i.e. Fischer-Tropschp synthesis). H2 and He data suggest that the H2 is generated by subsurface radiolysis of water. One sample of a saline, isolated water/gas pocket agrees exactly with that predicted by radioactive decay of U, Th, K in the host rock and indicates a subsurface H2 production rate of 0.1 to 1 nM/yr. Other samples yielded less H2 than predicted and require a sink for this H2 . Possible sinks include microbial H2 oxidation and abiotic formation of hydrocarbons at rates slightly less than the H2 production rate. Highly diffusive H2 is essential for life in deep subsurface environments where only trace amounts of organic carbon exist. Lithoautotrophic microbes can acquire energy from the redox reactions involving H2 with other electron acceptors (Fe3 +, SO4 2 - or CO2 ), to synthesis organic carbon and can be fully independent of solar-driven photosynthesis. The microbial abundance in many of these ground water samples, however, is below our detection limit (<5000 cells/ml). This contrasts with shallow sedimentary aquifers where H2 levels of tens of nM are regulated by the coexistence of autotrophs/lithotrophs and heterotrophs for maximum efficiency of H2 utilization. The excessive H2 found in deep crustal environments implies that these microbial ecosystems are electron-acceptor and or substrate limited. The oxidants generated by water radiolysis interact with the reduced solid phases in the rock matrix, e.g. pyrite

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

Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals.

PubMed

Dziewit, Lukasz; Pyzik, Adam; Szuplewska, Magdalena; Matlakowska, Renata; Mielnicki, Sebastian; Wibberg, Daniel; Schlüter, Andreas; Pühler, Alfred; Bartosik, Dariusz

2015-01-01

The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m) Lubin mine were taken and 20 bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e., they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface.

Biofilm-induced calcium carbonate precipitation: application in the subsurface

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

PubMed Central

Twing, Katrina I.; Brazelton, William J.; Kubo, Michael D. Y.; Hyer, Alex J.; Cardace, Dawn; Hoehler, Tori M.; McCollom, Tom M.; Schrenk, Matthew O.

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments. PMID:28298908

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

PubMed

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

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

Subsurface Nitrogen-Cycling Microbial Communities at Uranium Contaminated Sites in the Colorado River Basin

NASA Astrophysics Data System (ADS)

Cardarelli, E.; Bargar, J.; Williams, K. H.; Dam, W. L.; Francis, C.

2015-12-01

Throughout the Colorado River Basin (CRB), uranium (U) persists as a relic contaminant of former ore processing activities. Elevated solid-phase U levels exist in fine-grained, naturally-reduced zone (NRZ) sediments intermittently found within the subsurface floodplain alluvium of the following Department of Energy-Legacy Management sites: Rifle, CO; Naturita, CO; and Grand Junction, CO. Coupled with groundwater fluctuations that alter the subsurface redox conditions, previous evidence from Rifle, CO suggests this resupply of U may be controlled by microbially-produced nitrite and nitrate. Nitrification, the two-step process of archaeal and bacterial ammonia-oxidation followed by bacterial nitrite oxidation, generates nitrate under oxic conditions. Our hypothesis is that when elevated groundwater levels recede and the subsurface system becomes anoxic, the nitrate diffuses into the reduced interiors of the NRZ and stimulates denitrification, the stepwise anaerobic reduction of nitrate/nitrite to dinitrogen gas. Denitrification may then be coupled to the oxidation of sediment-bound U(IV) forming mobile U(VI), allowing it to resupply U into local groundwater supplies. A key step in substantiating this hypothesis is to demonstrate the presence of nitrogen-cycling organisms in U-contaminated, NRZ sediments from the upper CRB. Here we investigate how the diversity and abundances of nitrifying and denitrifying microbial populations change throughout the NRZs of the subsurface by using functional gene markers for ammonia-oxidation (amoA, encoding the α-subunit of ammonia monooxygenase) and denitrification (nirK, nirS, encoding nitrite reductase). Microbial diversity has been assessed via clone libraries, while abundances have been determined through quantitative polymerase chain reaction (qPCR), elucidating how relative numbers of nitrifiers (amoA) and denitrifiers (nirK, nirS) vary with depth, vary with location, and relate to uranium release within NRZs in sediment

Subsurface Conditions Controlling Uranium Incorporation in Iron Oxides: A Redox Stable Sink

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

Fendorf, Scott

2016-04-05

Toxic metals and radionuclides throughout the U.S. Department of Energy Complex pose a serious threat to ecosystems and to human health. Of particular concern is the redox-sensitive radionuclide uranium, which is classified as a priority pollutant in soils and groundwaters at most DOE sites owing to its large inventory, its health risks, and its mobility with respect to primary waste sources. The goal of this research was to contribute to the long-term mission of the Subsurface Biogeochemistry Program by determining reactions of uranium with iron (hydr)oxides that lead to long-term stabilization of this pervasive contaminant. The research objectives of thismore » project were thus to (1) identify the (bio)geochemical conditions, including those of the solid-phase, promoting uranium incorporation in Fe (hydr)oxides, (2) determine the magnitude of uranium incorporation under a variety of relevant subsurface conditions in order to quantify the importance of this pathway when in competition with reduction or adsorption; (3) identify the mechanism(s) of U(VI/V) incorporation in Fe (hydr)oxides; and (4) determine the stability of these phases under different biogeochemical (inclusive of redox) conditions. Our research demonstrates that redox transformations are capable of achieving U incorporation into goethite at ambient temperatures, and that this transformation occurs within days at U and Fe(II) concentrations that are common in subsurface geochemical environments with natural ferrihydrites—inclusive of those with natural impurities. Increasing Fe(II) or U concentration, or initial pH, made U(VI) reduction to U(IV) a more competitive sequestration pathway in this system, presumably by increasing the relative rate of U reduction. Uranium concentrations commonly found in contaminated subsurface environments are often on the order of 1-10 μM, and groundwater Fe(II) concentrations can reach exceed 1 mM in reduced zones of the subsurface. The redox-driven U

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

PubMed

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

2017-01-01

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

Biosignature Preservation and Detection in Mars Analog Environments.

PubMed

Hays, Lindsay E; Graham, Heather V; Des Marais, David J; Hausrath, Elisabeth M; Horgan, Briony; McCollom, Thomas M; Parenteau, M Niki; Potter-McIntyre, Sally L; Williams, Amy J; Lynch, Kennda L

2017-04-01

This review of material relevant to the Conference on Biosignature Preservation and Detection in Mars Analog Environments summarizes the meeting materials and discussions and is further expanded upon by detailed references to the published literature. From this diverse source material, there is a detailed discussion on the habitability and biosignature preservation potential of five primary analog environments: hydrothermal spring systems, subaqueous environments, subaerial environments, subsurface environments, and iron-rich systems. Within the context of exploring past habitable environments on Mars, challenges common to all of these key environments are laid out, followed by a focused discussion for each environment regarding challenges to orbital and ground-based observations and sample selection. This leads into a short section on how these challenges could influence our strategies and priorities for the astrobiological exploration of Mars. Finally, a listing of urgent needs and future research highlights key elements such as development of instrumentation as well as continued exploration into how Mars may have evolved differently from Earth and what that might mean for biosignature preservation and detection. Key Words: Biosignature preservation-Biosignature detection-Mars analog environments-Conference report-Astrobiological exploration. Astrobiology 17, 363-400.

Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site

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

Truex, Michael J.; Lee, Brady D.; Johnson, Christian D.

The fate and transport of 129I in the environment and potential remediation technologies are currently being studied as part of environmental remediation activities at the Hanford Site. A conceptual model describing the nature and extent of subsurface contamination, factors that control plume behavior, and factors relevant to potential remediation processes is needed to support environmental remedy decisions. Because 129I is an uncommon contaminant, relevant remediation experience and scientific literature are limited. Thus, the conceptual model also needs to both describe known contaminant and biogeochemical process information and to identify aspects about which additional information needed to effectively support remedy decisions.more » this document summarizes the conceptual model of iodine behavior relevant to iodine in the subsurface environment at the Hanford site.« less

Human impact on genetic diversity of Toxoplasma gondii: example of the anthropized environment from French Guiana.

PubMed

Mercier, A; Ajzenberg, D; Devillard, S; Demar, M P; de Thoisy, B; Bonnabau, H; Collinet, F; Boukhari, R; Blanchet, D; Simon, S; Carme, B; Dardé, M-L

2011-08-01

In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been

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.

Blooms and subsurface phytoplankton layers on the Scotian Shelf: Insights from profiling gliders

NASA Astrophysics Data System (ADS)

Ross, Tetjana; Craig, Susanne E.; Comeau, Adam; Davis, Richard; Dever, Mathieu; Beck, Matthew

2017-08-01

Understanding how phytoplankton respond to their physical environment is key to predicting how bloom dynamics might change under future climate change scenarios. Phytoplankton are at the base of most marine food webs and play an important role in drawing CO2 out of the atmosphere. Using nearly 5 years of simultaneous CTD, irradiance, chlorophyll a fluorescence and optical backscattering observations obtained from Slocum glider missions, we observed the subsurface phytoplankton populations across the Scotian Shelf, near Halifax (Nova Scotia, Canada) along with their physical environment. Bloom conditions were observed in each of the 5 springs, with the average chlorophyll in the upper 60 m of water generally exceeding 3 mg m- 3. These blooms occurred when the upper water column stratification was at its lowest, in apparent contradiction of the critical depth hypothesis. A subsurface chlorophyll layer was observed each summer at about 30 m depth, which was below the base of the mixed layer. This subsurface layer lasted 3-4 months and contained, on average, 1/4 of the integrated water column chlorophyll found during the spring bloom. This suggests that a significant portion of the primary productivity over the Scotian Shelf occurs at depths that cannot be observed by satellites-highlighting the importance of including subsurface observations in the monitoring of future changes to primary productivity in the ocean.

Microbiological Transformations of Radionuclides in the Subsurface

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

Marshall, Matthew J.; Beliaev, Alex S.; Fredrickson, Jim K.

2010-01-04

Microorganisms are ubiquitous in subsurface environments although their populations sizes and metabolic activities can vary considerably depending on energy and nutrient inputs. As a result of their metabolic activities and the chemical properties of their cell surfaces and the exopolymers they produce, microorganisms can directly or indirectly facilitate the biotransformation of radionuclides, thus altering their solubility and overall fate and transport in the environment. Although biosorption to cell surfaces and exopolymers can be an important factor modifying the solubility of some radionuclides under specific conditions, oxidation state is often considered the single most important factor controlling their speciation and, therefore,more » environmental behavior.« less

Communities of archaea and bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing Crenarchaeota.

PubMed

Weidler, Gerhard W; Dornmayr-Pfaffenhuemer, Marion; Gerbl, Friedrich W; Heinen, Wolfgang; Stan-Lotter, Helga

2007-01-01

Scanning electron microscopy revealed great morphological diversity in biofilms from several largely unexplored subterranean thermal Alpine springs, which contain radium 226 and radon 222. A culture-independent molecular analysis of microbial communities on rocks and in the water of one spring, the "Franz-Josef-Quelle" in Bad Gastein, Austria, was performed. Four hundred fifteen clones were analyzed. One hundred thirty-two sequences were affiliated with 14 bacterial operational taxonomic units (OTUs) and 283 with four archaeal OTUs. Rarefaction analysis indicated a high diversity of bacterial sequences, while archaeal sequences were less diverse. The majority of the cloned archaeal 16S rRNA gene sequences belonged to the soil-freshwater-subsurface (1.1b) crenarchaeotic group; other representatives belonged to the freshwater-wastewater-soil (1.3b) group, except one clone, which was related to a group of uncultivated Euryarchaeota. These findings support recent reports that Crenarchaeota are not restricted to high-temperature environments. Most of the bacterial sequences were related to the Proteobacteria (alpha, beta, gamma, and delta), Bacteroidetes, and Planctomycetes. One OTU was allied with Nitrospina sp. (delta-Proteobacteria) and three others grouped with Nitrospira. Statistical analyses suggested high diversity based on 16S rRNA gene analyses; the rarefaction plot of archaeal clones showed a plateau. Since Crenarchaeota have been implicated recently in the nitrogen cycle, the spring environment was probed for the presence of the ammonia monooxygenase subunit A (amoA) gene. Sequences were obtained which were related to crenarchaeotic amoA genes from marine and soil habitats. The data suggested that nitrification processes are occurring in the subterranean environment and that ammonia may possibly be an energy source for the resident communities.

Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

PubMed Central

2014-01-01

Background Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples and only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity ‘tag’ sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations. Results We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97% sequence similarity suggesting this diversity encompasses a range of biologically and ecologically distinct organisms. Conclusions These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally ‘active’ and intact cells. Given the phylogenetic range

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

PubMed

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

2009-03-01

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

Biosignature Preservation and Detection in Mars Analog Environments

PubMed Central

Graham, Heather V.; Des Marais, David J.; Hausrath, Elisabeth M.; Horgan, Briony; McCollom, Thomas M.; Parenteau, M. Niki; Potter-McIntyre, Sally L.; Williams, Amy J.; Lynch, Kennda L.

2017-01-01

Abstract This review of material relevant to the Conference on Biosignature Preservation and Detection in Mars Analog Environments summarizes the meeting materials and discussions and is further expanded upon by detailed references to the published literature. From this diverse source material, there is a detailed discussion on the habitability and biosignature preservation potential of five primary analog environments: hydrothermal spring systems, subaqueous environments, subaerial environments, subsurface environments, and iron-rich systems. Within the context of exploring past habitable environments on Mars, challenges common to all of these key environments are laid out, followed by a focused discussion for each environment regarding challenges to orbital and ground-based observations and sample selection. This leads into a short section on how these challenges could influence our strategies and priorities for the astrobiological exploration of Mars. Finally, a listing of urgent needs and future research highlights key elements such as development of instrumentation as well as continued exploration into how Mars may have evolved differently from Earth and what that might mean for biosignature preservation and detection. Key Words: Biosignature preservation—Biosignature detection—Mars analog environments—Conference report—Astrobiological exploration. Astrobiology 17, 363–400. PMID:28177270

Transformation of zinc-concentrate in surface and subsurface environments: Implications for assessing zinc mobility/toxicity and choosing an optimal remediation strategy.

PubMed

Kwon, Man Jae; Boyanov, Maxim I; Yang, Jung-Seok; Lee, Seunghak; Hwang, Yun Ho; Lee, Ju Yeon; Mishra, Bhoopesh; Kemner, Kenneth M

2017-07-01

Zinc contamination in near- and sub-surface environments is a serious threat to many ecosystems and to public health. Sufficient understanding of Zn speciation and transport mechanisms is therefore critical to evaluating its risk to the environment and to developing remediation strategies. The geochemical and mineralogical characteristics of contaminated soils in the vicinity of a Zn ore transportation route were thoroughly investigated using a variety of analytical techniques (sequential extraction, XRF, XRD, SEM, and XAFS). Imported Zn-concentrate (ZnS) was deposited in a receiving facility and dispersed over time to the surrounding roadside areas and rice-paddy soils. Subsequent physical and chemical weathering resulted in dispersal into the subsurface. The species identified in the contaminated areas included Zn-sulfide, Zn-carbonate, other O-coordinated Zn-minerals, and Zn species bound to Fe/Mn oxides or clays, as confirmed by XAFS spectroscopy and sequential extraction. The observed transformation from S-coordinated Zn to O-coordinated Zn associated with minerals suggests that this contaminant can change into more soluble and labile forms as a result of weathering. For the purpose of developing a soil washing remediation process, the contaminated samples were extracted with dilute acids. The extraction efficiency increased with the increase of O-coordinated Zn relative to S-coordinated Zn in the sediment. This study demonstrates that improved understanding of Zn speciation in contaminated soils is essential for well-informed decision making regarding metal mobility and toxicity, as well as for choosing an appropriate remediation strategy using soil washing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Transformation of zinc-concentrate in surface and subsurface environments: Implications for assessing zinc mobility/toxicity and choosing an optimal remediation strategy

DOE PAGES

Kwon, Man Jae; Boyanov, Maxim I.; Yang, Jung -Seok; ...

2017-03-24

Zinc contamination in near- and sub-surface environments is a serious threat to many ecosystems and to public health. Sufficient understanding of Zn speciation and transport mechanisms is therefore critical to evaluating its risk to the environment and to developing remediation strategies. The geochemical and mineralogical characteristics of contaminated soils in the vicinity of a Zn ore transportation route were thoroughly investigated using a variety of analytical techniques (sequential extraction, XRF, XRD, SEM, and XAFS). Imported Zn-concentrate (ZnS) was deposited in a receiving facility and dispersed over time to the surrounding roadside areas and rice-paddy soils. Subsequent physical and chemical weatheringmore » resulted in dispersal into the subsurface. The species identified in the contaminated areas included Zn-sulfide, Zn-carbonate, other O-coordinated Zn-minerals, and Zn species bound to Fe/Mn oxides or clays, as confirmed by XAFS spectroscopy and sequential extraction. The observed transformation from S-coordinated Zn to O-coordinated Zn associated with minerals suggests that this contaminant can change into more soluble and labile forms as a result of weathering. For the purpose of developing a soil washing remediation process, the contaminated samples were extracted with dilute acids. The extraction efficiency increased with the increase of O-coordinated Zn relative to S-coordinated Zn in the sediment. Furthermore, this study demonstrates that improved understanding of Zn speciation in contaminated soils is essential for well-informed decision making regarding metal mobility and toxicity, as well as for choosing an appropriate remediation strategy using soil washing.« less

Diversity of Listeria Species in Urban and Natural Environments

PubMed Central

Overdevest, Jon; Fortes, Esther; Windham, Katy; Schukken, Ynte; Lembo, Arthur; Wiedmann, Martin

2012-01-01

A total of 442 Listeria isolates, including 234 Listeria seeligeri, 80 L. monocytogenes, 74 L. welshimeri, 50 L. innocua, and 4 L. marthii isolates, were obtained from 1,805 soil, water, and other environmental samples collected over 2 years from four urban areas and four areas representing natural environments. Listeria spp. showed similar prevalences in samples from natural (23.4%) and urban (22.3%) environments. While L. seeligeri and L. welshimeri were significantly associated with natural environments (P ≤ 0.0001), L. innocua and L. monocytogenes were significantly associated with urban environments (P ≤ 0.0001). Sequencing of sigB for all isolates revealed 67 allelic types with a higher level of allelic diversity among isolates from urban environments. Some Listeria spp. and sigB allelic types showed significant associations with specific urban and natural areas. Nearest-neighbor analyses also showed that certain Listeria spp. and sigB allelic types were spatially clustered within both natural and urban environments, and there was evidence that these species and allelic types persisted over time in specific areas. Our data show that members of the genus Listeria not only are common in urban and natural environments but also show species- and subtype-specific associations with different environments and areas. This indicates that Listeria species and subtypes within these species may show distinct ecological preferences, which suggests (i) that molecular source-tracking approaches can be developed for Listeria and (ii) that detection of some Listeria species may not be a good indicator for L. monocytogenes. PMID:22504820

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

PubMed Central

Warren, Lesley A.; Kendra, Kathryn E.

2015-01-01

Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments

PubMed Central

McRose, Darcy L.; Zhang, Xinning; Kraepiel, Anne M. L.; Morel, François M. M.

2017-01-01

The nitrogenase enzyme, which catalyzes the reduction of N2 gas to NH4+, occurs as three separate isozyme that use Mo, Fe-only, or V. The majority of global nitrogen fixation is attributed to the more efficient ‘canonical’ Mo-nitrogenase, whereas Fe-only and V-(‘alternative’) nitrogenases are often considered ‘backup’ enzymes, used when Mo is limiting. Yet, the environmental distribution and diversity of alternative nitrogenases remains largely unknown. We searched for alternative nitrogenase genes in sequenced genomes and used PacBio sequencing to explore the diversity of canonical (nifD) and alternative (anfD and vnfD) nitrogenase amplicons in two coastal environments: the Florida Everglades and Sippewissett Marsh (MA). Genome-based searches identified an additional 25 species and 10 genera not previously known to encode alternative nitrogenases. Alternative nitrogenase amplicons were found in both Sippewissett Marsh and the Florida Everglades and their activity was further confirmed using newly developed isotopic techniques. Conserved amino acid sequences corresponding to cofactor ligands were also analyzed in anfD and vnfD amplicons, offering insight into environmental variants of these motifs. This study increases the number of available anfD and vnfD sequences ∼20-fold and allows for the first comparisons of environmental Mo-, Fe-only, and V-nitrogenase diversity. Our results suggest that alternative nitrogenases are maintained across a range of organisms and environments and that they can make important contributions to nitrogenase diversity and nitrogen fixation. PMID:28293220

Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments.

PubMed

McRose, Darcy L; Zhang, Xinning; Kraepiel, Anne M L; Morel, François M M

2017-01-01

The nitrogenase enzyme, which catalyzes the reduction of N 2 gas to NH 4 + , occurs as three separate isozyme that use Mo, Fe-only, or V. The majority of global nitrogen fixation is attributed to the more efficient 'canonical' Mo-nitrogenase, whereas Fe-only and V-('alternative') nitrogenases are often considered 'backup' enzymes, used when Mo is limiting. Yet, the environmental distribution and diversity of alternative nitrogenases remains largely unknown. We searched for alternative nitrogenase genes in sequenced genomes and used PacBio sequencing to explore the diversity of canonical ( nifD ) and alternative ( anfD and vnfD ) nitrogenase amplicons in two coastal environments: the Florida Everglades and Sippewissett Marsh (MA). Genome-based searches identified an additional 25 species and 10 genera not previously known to encode alternative nitrogenases. Alternative nitrogenase amplicons were found in both Sippewissett Marsh and the Florida Everglades and their activity was further confirmed using newly developed isotopic techniques. Conserved amino acid sequences corresponding to cofactor ligands were also analyzed in anfD and vnfD amplicons, offering insight into environmental variants of these motifs. This study increases the number of available anfD and vnfD sequences ∼20-fold and allows for the first comparisons of environmental Mo-, Fe-only, and V-nitrogenase diversity. Our results suggest that alternative nitrogenases are maintained across a range of organisms and environments and that they can make important contributions to nitrogenase diversity and nitrogen fixation.

Application of AMDS mortar as a treatment agent for arsenic in subsurface environment

NASA Astrophysics Data System (ADS)

Choi, J.; Lee, H.; Choi, U. K.; Yang, I. J.

2014-12-01

Among the treatment technologies available for As in soil and groundwater, adsorption or precipitation using acid mine drainage (AMD) sludge has become a promised technique because of high efficiency, inexpensiveness and simple to handling. The adsorbents were prepared by addition of Cement, Joomoonjin sand, fly ash, and Ca(OH)2 to air dry AMD sludge. In this work, the adsorption of As (III) and As (V) on AMDS mortar has been studied as a function of kinetic, pH, and initial arsenic concentration. Results of batch study showed that 75-90% of both As (III) and As (V) were removed at pH 7. Arsenic adsorption capacities were the highest at neutral pH condition and the adsorption equilibrium time reached in 7 days using AMDS mortar. Additionally, the adsorption kinetic process is expressed well by pseudo-second-order model. The adsorption capacities of AMDS mortar for As(III) and As(V) were found 19.04 and 30.75 mg g-1, respectively. The results of As (III) adsorption isotherms were fitted well to the Freundlich model. Moreover, As (V) adsorption isotherms were fitted well to the Langmuir model rather than Freundlich model. Based on experimental results in this study, we could conclude that AMDS mortar can be effectively used for arsenic removal agent from subsurface environment.

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

Effects of diversity in olfactory environment on children's sense of smell.

PubMed

Martinec Nováková, Lenka; Fialová, Jitka; Havlíček, Jan

2018-02-13

Diversity in children's everyday olfactory environment may affect the development of their olfactory abilities and odor awareness. To test this, we collected data on olfactory abilities using the Sniffin' Sticks and odor awareness with Children's Olfactory Behaviors in Everyday Life Questionnaire in 153 preschool children and retested them one and a half year later. Parents completed an inventory on children's exposure to a variety of odors and on their own odor awareness using the Odor Awareness Scale. We controlled for the effects of age and verbal fluency on the children's performance. We found that the children's odor identification and discrimination scores differed as a function of parental odor awareness. Although these effects were rather small, they were commensurate in size with those of gender and age. To the best of our knowledge, this study is the first to present evidence that diversity in children's olfactory environment affects variation in their olfactory abilities and odor awareness. We suggest that future studies consider the long-term impact of perceptual learning out of the laboratory and its consequences for olfactory development.

Shallow characterization of the subsurface for the 2018 Mission to Mars

NASA Astrophysics Data System (ADS)

Ciarletti, V.; plettemeier, D.; Vieau, A. J.; Hassen-Khodja, R.; Lustrement, B.; Cais, P.; Clifford, S.

2012-04-01

The highest priority scientific objectives of the revised 2018 mission to Mars are (1) to search for evidence of past or present life, (2) to identify the samples that are most likely to preserve potential evidence of life and the nature of the early Martian environment that might have given rise to it and (3) to cache them for later retrieval back to Earth for more detailed analyses than can be performed by the rover's onboard analytical laboratory. WISDOM is a ground penetrating radar that has been designed to investigate the near subsurface of Mars down to a depth of ~2-3 m, with a vertical resolution of several centimeters - commensurate with the sampling capabilities of the ExoMars onboard drill. The ability of WISDOM to investigate the geology of the landing site in 3-dimensions will permit direct correlations between subsurface layers and horizons with those exposed in nearby outcrops and the interior of impact craters. By combining periodic soundings conducted during a Rover traverse with targeted, high density grid-type soundings of areas of potential scientific interest, it will be possible to construct a 3-dimensional map of the local radar stratigraphy. Of all of the Pasteur Payload instruments, only WISDOM has the ability to investigate and characterize the nature of the subsurface remotely. Moreover, the geoelectrical properties of H2O make WISDOM a powerful tool to understand the local distribution and state of subsurface H2O, including the potential presence of segregated ground ice and the persistent or transient occurrence of liquid water/brine. A WISDOM prototype, representative of the final flight model is now being tested. A series of calibrations and verifications have been initiated. The real performance of the instrument is currently assessed for various test environments. Results about the resolution and sensitivity achieved are presented as well as 3D representations of detected subsurface structures. Preliminary estimates of permittivity

Genome-to-Watershed Predictive Understanding of Terrestrial Environments

NASA Astrophysics Data System (ADS)

Hubbard, S. S.; Agarwal, D.; Banfield, J. F.; Beller, H. R.; Brodie, E.; Long, P.; Nico, P. S.; Steefel, C. I.; Tokunaga, T. K.; Williams, K. H.

2014-12-01

Although terrestrial environments play a critical role in cycling water, greenhouse gasses, and other life-critical elements, the complexity of interactions among component microbes, plants, minerals, migrating fluids and dissolved constituents hinders predictive understanding of system behavior. The 'Sustainable Systems 2.0' project is developing genome-to-watershed scale predictive capabilities to quantify how the microbiome affects biogeochemical watershed functioning, how watershed-scale hydro-biogeochemical processes affect microbial functioning, and how these interactions co-evolve with climate and land-use changes. Development of such predictive capabilities is critical for guiding the optimal management of water resources, contaminant remediation, carbon stabilization, and agricultural sustainability - now and with global change. Initial investigations are focused on floodplains in the Colorado River Basin, and include iterative model development, experiments and observations with an early emphasis on subsurface aspects. Field experiments include local-scale experiments at Rifle CO to quantify spatiotemporal metabolic and geochemical responses to O2and nitrate amendments as well as floodplain-scale monitoring to quantify genomic and biogeochemical response to natural hydrological perturbations. Information obtained from such experiments are represented within GEWaSC, a Genome-Enabled Watershed Simulation Capability, which is being developed to allow mechanistic interrogation of how genomic information stored in a subsurface microbiome affects biogeochemical cycling. This presentation will describe the genome-to-watershed scale approach as well as early highlights associated with the project. Highlights include: first insights into the diversity of the subsurface microbiome and metabolic roles of organisms involved in subsurface nitrogen, sulfur and hydrogen and carbon cycling; the extreme variability of subsurface DOC and hydrological controls on carbon and

Probing the critical zone using passive- and active-source estimates of subsurface shear-wave velocities

NASA Astrophysics Data System (ADS)

Callahan, R. P.; Taylor, N. J.; Pasquet, S.; Dueker, K. G.; Riebe, C. S.; Holbrook, W. S.

2016-12-01

Geophysical imaging is rapidly becoming popular for quantifying subsurface critical zone (CZ) architecture. However, a diverse array of measurements and measurement techniques are available, raising the question of which are appropriate for specific study goals. Here we compare two techniques for measuring S-wave velocities (Vs) in the near surface. The first approach quantifies Vs in three dimensions using a passive source and an iterative residual least-squares tomographic inversion. The second approach uses a more traditional active-source seismic survey to quantify Vs in two dimensions via a Monte Carlo surface-wave dispersion inversion. Our analysis focuses on three 0.01 km2 study plots on weathered granitic bedrock in the Southern Sierra Critical Zone Observatory. Preliminary results indicate that depth-averaged velocities from the two methods agree over the scales of resolution of the techniques. While the passive- and active-source techniques both quantify Vs, each method has distinct advantages and disadvantages during data acquisition and analysis. The passive-source method has the advantage of generating a three dimensional distribution of subsurface Vs structure across a broad area. Because this method relies on the ambient seismic field as a source, which varies unpredictably across space and time, data quality and depth of investigation are outside the control of the user. Meanwhile, traditional active-source surveys can be designed around a desired depth of investigation. However, they only generate a two dimensional image of Vs structure. Whereas traditional active-source surveys can be inverted quickly on a personal computer in the field, passive source surveys require significantly more computations, and are best conducted in a high-performance computing environment. We use data from our study sites to compare these methods across different scales and to explore how these methods can be used to better understand subsurface CZ architecture.

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.

Detection of microbes in the subsurface

NASA Technical Reports Server (NTRS)

White, David C.; Tunlid, Anders

1989-01-01

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

RESEARCH ACTIVITIES AT U.S. GOVERNMENT AGENCIES IN SUBSURFACE REACTIVE TRANSPORT MODELING

EPA Science Inventory

The fate of contaminants in the environment is controlled by both chemical reactions and transport phenomena in the subsurface. Our ability to understand the significance of these processes over time requires an accurate conceptual model that incorporates the various mechanisms ...

Estimates of abundance and diversity of Shewanella genus in natural and engineered aqueous environments with newly designed primers.

PubMed

Li, Bing-Bing; Cheng, Yuan-Yuan; Fan, Yang-Yang; Liu, Dong-Feng; Fang, Cai-Yun; Wu, Chao; Li, Wen-Wei; Yang, Zong-Chuang; Yu, Han-Qing

2018-05-12

Shewanella species have a diverse respiratory ability and wide distribution in environments and play an important role in bioremediation and the biogeochemical cycles of elements. Primers with more accuracy and broader coverage are required with consideration of the increasing number of Shewanella species and evaluation of their roles in various environments. In this work, a new primer set of 640F/815R was developed to quantify the abundance of Shewanella species in natural and engineered environments. In silico tools for primer evaluation, quantitative polymerase chain reaction (qPCR) and clone library results showed that 640F/815R had a higher specificity and coverage than the previous primers in quantitative analysis of Shewanella. Another newly developed primer pair of 211F/815cR was also adopted to analyze the Shewanella diversity and demonstrated to be the best candidate in terms of specificity and coverage. We detected more Shewanella-related species in freshwater environments and found them to be substantially different from those in marine environments. Abundance and diversity of Shewanella species in wastewater treatment plants were largely affected by the process and operating conditions. Overall, this study suggests that investigations of abundance and diversity of Shewanella in various environments are of great importance to evaluate their ecophysiology and potential ecological roles. Copyright © 2018 Elsevier B.V. All rights reserved.

Evolution of genomic diversity and sex at extreme environments: Fungal life under hypersaline Dead Sea stress

PubMed Central

Kis-Papo, Tamar; Kirzhner, Valery; Wasser, Solomon P.; Nevo, Eviatar

2003-01-01

We have found that genomic diversity is generally positively correlated with abiotic and biotic stress levels (1–3). However, beyond a high-threshold level of stress, the diversity declines to a few adapted genotypes. The Dead Sea is the harshest planetary hypersaline environment (340 g·liter–1 total dissolved salts, ≈10 times sea water). Hence, the Dead Sea is an excellent natural laboratory for testing the “rise and fall” pattern of genetic diversity with stress proposed in this article. Here, we examined genomic diversity of the ascomycete fungus Aspergillus versicolor from saline, nonsaline, and hypersaline Dead Sea environments. We screened the coding and noncoding genomes of A. versicolor isolates by using >600 AFLP (amplified fragment length polymorphism) markers (equal to loci). Genomic diversity was positively correlated with stress, culminating in the Dead Sea surface but dropped drastically in 50- to 280-m-deep seawater. The genomic diversity pattern paralleled the pattern of sexual reproduction of fungal species across the same southward gradient of increasing stress in Israel. This parallel may suggest that diversity and sex are intertwined intimately according to the rise and fall pattern and adaptively selected by natural selection in fungal genome evolution. Future large-scale verification in micromycetes will define further the trajectories of diversity and sex in the rise and fall pattern. PMID:14645702

Staphylococcus aureus pathogenesis in diverse host environments

PubMed Central

Balasubramanian, Divya; Harper, Lamia; Shopsin, Bo; Torres, Victor J.

2017-01-01

Abstract Staphylococcus aureus is an eminent human pathogen that can colonize the human host and cause severe life-threatening illnesses. This bacterium can reside in and infect a wide range of host tissues, ranging from superficial surfaces like the skin to deeper tissues such as in the gastrointestinal tract, heart and bones. Due to its multifaceted lifestyle, S. aureus uses complex regulatory networks to sense diverse signals that enable it to adapt to different environments and modulate virulence. In this minireview, we explore well-characterized environmental and host cues that S. aureus responds to and describe how this pathogen modulates virulence in response to these signals. Lastly, we highlight therapeutic approaches undertaken by several groups to inhibit both signaling and the cognate regulators that sense and transmit these signals downstream. PMID:28104617

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

PubMed

Fredrickson, J K; Balkwill, D L; Romine, M F; Shi, T

1999-10-01

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteria cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.

Alpine cushion plants inhibit the loss of phylogenetic diversity in severe environments.

PubMed

Butterfield, B J; Cavieres, L A; Callaway, R M; Cook, B J; Kikvidze, Z; Lortie, C J; Michalet, R; Pugnaire, F I; Schöb, C; Xiao, S; Zaitchek, B; Anthelme, F; Björk, R G; Dickinson, K; Gavilán, R; Kanka, R; Maalouf, J-P; Noroozi, J; Parajuli, R; Phoenix, G K; Reid, A; Ridenour, W; Rixen, C; Wipf, S; Zhao, L; Brooker, R W

2013-04-01

Biotic interactions can shape phylogenetic community structure (PCS). However, we do not know how the asymmetric effects of foundation species on communities extend to effects on PCS. We assessed PCS of alpine plant communities around the world, both within cushion plant foundation species and adjacent open ground, and compared the effects of foundation species and climate on alpha (within-microsite), beta (between open and cushion) and gamma (open and cushion combined) PCS. In the open, alpha PCS shifted from highly related to distantly related with increasing potential productivity. However, we found no relationship between gamma PCS and climate, due to divergence in phylogenetic composition between cushion and open sub-communities in severe environments, as demonstrated by increasing phylo-beta diversity. Thus, foundation species functioned as micro-refugia by facilitating less stress-tolerant lineages in severe environments, erasing a global productivity - phylogenetic diversity relationship that would go undetected without accounting for this important biotic interaction. © 2013 Blackwell Publishing Ltd/CNRS.

Mechanisms of Arsenic Mobilization and Attenuation in Subsurface Sediments

NASA Astrophysics Data System (ADS)

O'Day, P. A.; Illera, V.; Root, R.; Choi, S.; Vlassopoulos, D.

2007-12-01

This talk will review molecular mechanisms of As mobilization and attenuation in subsurface sediments using examples from recent field studies that represent a range in oxidation-redox (redox) potential. As a ubiquitous trace element in sediments, As speciation and fate is linked to the abundance and biogeochemical behavior of the generally more abundant redox-active elements Fe, S, and Mn. All four elements are subject to oxidation, reduction, and pH-dependent processes such as sorption, desorption, precipitation, and dissolution, and which may include both biotic and abiotic reaction steps. We have used spectroscopic interrogation and geochemical modeling to characterize As speciation in subsurface sediments in several contrasting environments, including high and low S and Fe settings. Aquifers most at risk for contamination by As include those that are rich in organic matter and nutrients, stimulating high rates of microbial reduction and creating anoxic conditions, but limited in labile or available S and/or Fe that remove As by precipitation or adsorption. In subsurface sediments with low labile S and Fe, laboratory experiments and spectroscopic studies suggest that sediment Mn minerals are important in the oxidation of sorbed As(III) to As(V), but that they have a limited oxidation capacity. Arsenic attenuation and mobilization in the subsurface are affected by seasonal variations when hydraulic conditions are influenced by surface infiltration, which may induce transitions from oxidized to reduced conditions (or vice versa) in porewater.

In-situ Planetary Subsurface Imaging System

NASA Astrophysics Data System (ADS)

Song, W.; Weber, R. C.; Dimech, J. L.; Kedar, S.; Neal, C. R.; Siegler, M.

2017-12-01

Geophysical and seismic instruments are considered the most effective tools for studying the detailed global structures of planetary interiors. A planet's interior bears the geochemical markers of its evolutionary history, as well as its present state of activity, which has direct implications to habitability. On Earth, subsurface imaging often involves massive data collection from hundreds to thousands of geophysical sensors (seismic, acoustic, etc) followed by transfer by hard links or wirelessly to a central location for post processing and computing, which will not be possible in planetary environments due to imposed mission constraints on mass, power, and bandwidth. Emerging opportunities for geophysical exploration of the solar system from Venus to the icy Ocean Worlds of Jupiter and Saturn dictate that subsurface imaging of the deep interior will require substantial data reduction and processing in-situ. The Real-time In-situ Subsurface Imaging (RISI) technology is a mesh network that senses and processes geophysical signals. Instead of data collection then post processing, the mesh network performs the distributed data processing and computing in-situ, and generates an evolving 3D subsurface image in real-time that can be transmitted under bandwidth and resource constraints. Seismic imaging algorithms (including traveltime tomography, ambient noise imaging, and microseismic imaging) have been successfully developed and validated using both synthetic and real-world terrestrial seismic data sets. The prototype hardware system has been implemented and can be extended as a general field instrumentation platform tailored specifically for a wide variety of planetary uses, including crustal mapping, ice and ocean structure, and geothermal systems. The team is applying the RISI technology to real off-world seismic datasets. For example, the Lunar Seismic Profiling Experiment (LSPE) deployed during the Apollo 17 Moon mission consisted of four geophone instruments

The impact of pre-restoration land-use and disturbance on sediment structure, hydrology and the sediment geochemical environment in restored saltmarshes.

PubMed

Spencer, Kate L; Carr, Simon J; Diggens, Lucy M; Tempest, James A; Morris, Michelle A; Harvey, Gemma L

2017-06-01

Saltmarshes are being lost or degraded as a result of human activity resulting in loss of critical ecosystem services including the provision of wild species diversity, water quality regulation and flood regulation. To compensate, saltmarshes are being restored or re-created, usually driven by legislative requirements for increased habitat diversity, flood regulation and sustainable coastal defense. Yet, there is increasing evidence that restoration may not deliver anticipated ecosystem services; this is frequently attributed to poor drainage and sediment anoxia. However, physical sediment characteristics, hydrology and the sediment geochemical environment are rarely examined in restoration schemes, despite such factors being critical for plant succession. This study presents the novel integration of 3D-computed X-ray microtomography to quantify sediment structure and porosity, with water level and geochemical data to understand the impact of pre-restoration land use and disturbance on the structure and functioning of restored saltmarshes. The study combines a broad-scale investigation of physical sediment characteristics in nine de-embanked saltmarshes across SE England, with an intensive study at one site examining water levels, sediment structure and the sediment geochemical environment. De-embankment does not restore the hydrological regime, or the physical/chemical framework in the saltmarshes and evidence of disturbance includes a reduction in microporosity, pore connectivity and water storage capacity, a lack of connectivity between the sub-surface environment and overlying floodwaters, and impeded sub-surface water flow and drainage. This has significant consequences for the sediment geochemical environment. This disturbance is evident for at least two decades following restoration and is likely to be irreversible. It has important implications for plant establishment in particular, ecosystem services including flood regulation, nutrient cycling and wild

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

PubMed

Klier, Christine

2012-03-06

The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments

PubMed Central

Berg, Maureen; Stenuit, Ben; Ho, Joshua; Wang, Andrew; Parke, Caitlin; Knight, Matthew; Alvarez-Cohen, Lisa; Shapira, Michael

2016-01-01

It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota. PMID:26800234

The Next Generation of Space Cells for Diverse Environments

NASA Technical Reports Server (NTRS)

Bailey, Sheila; Landis, Geoffrey; Raffaelle, Ryne

2002-01-01

Future science, military and commercial space missions are incredibly diverse. Military and commercial missions range from large arrays of hundreds of kilowatt to small arrays of ten watts in various Earth orbits. While science missions also have small to very large power needs there are additional unique requirements to provide power for near-sun missions and planetary exploration including orbiters, landers and rovers both to the inner planets and the outer planets with a major emphasis in the near term on Mars. These mission requirements demand cells for low intensity, low temperature applications, high intensity, high temperature applications, dusty environments and often high radiation environments. This paper discusses mission requirements, the current state of the art of space solar cells, and a variety of both evolving thin-film cells as well as new technologies that may impact the future choice of space solar cells for a specific mission application.

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

Tracking fluid-borne odors in diverse and dynamic environments using multiple sensory mechanisms

NASA Astrophysics Data System (ADS)

Taylor, Brian Kyle

The ability to locate odor sources in different types of environments (i.e. diverse) and environments that change radically during the mission (i.e., dynamic) is essential. While many engineered odor tracking systems have been developed, they appear to be designed for a particular environment (e.g., strong or low flow). In field conditions, agents may encounter both. Insect olfactory orientation studies show that several animals can locate odor sources in both high and low flow environments, and environments where the wind vanishes during tracking behavior. Furthermore, animals use multi-modal sensing, including olfaction, vision and touch to localize a source. This work uses simulated and hardware environments to explore how engineered systems can maintain wind-driven tracking behavior in diverse and dynamic environments. The simulation uses olfaction, vision and tactile attributes to track and localize a source in the following environments: high flow, low flow, and transition from high to low flow (i.e., Wind Stop). The hardware platform tests two disparate tracking strategies (including the simulated strategy) in an environment that transitions from strong to low flow. Results indicate that using a remembered wind direction post wind-shutoff is a viable way to maintain wind-driven tracking behavior in a wind stop environment, which can help bridge the gap between high flow and low flow strategies. Also, multi-modal sensing with tactile attributes, vision and olfaction helps a vehicle to localize a source. In addition to engineered systems, the moth Manduca sexta is challenged to track in the following environments: Wind and Odor, Wind Stop, Odor and No Wind, No Odor and No Wind to gain a better understanding of animal behavior in these environments. Results show that contrary to previous studies of different moth species, M. sexta does not generally maintain its wind-driven tracking behavior post-wind shutoff, but instead executes a stereotyped sequence of

Transport of Chemical Vapors from Subsurface Sources to Atmosphere as Affected by Shallow Subsurface and Atmospheric Conditions

NASA Astrophysics Data System (ADS)

Rice, A. K.; Smits, K. M.; Hosken, K.; Schulte, P.; Illangasekare, T. H.

2012-12-01

Understanding the movement and modeling of chemical vapor through unsaturated soil in the shallow subsurface when subjected to natural atmospheric thermal and mass flux boundary conditions at the land surface is of importance to applications such as landmine detection and vapor intrusion into subsurface structures. New, advanced technologies exist to sense chemical signatures at the land/atmosphere interface, but interpretation of these sensor signals to make assessment of source conditions remains a challenge. Chemical signatures are subject to numerous interactions while migrating through the unsaturated soil environment, attenuating signal strength and masking contaminant source conditions. The dominant process governing movement of gases through porous media is often assumed to be Fickian diffusion through the air phase with minimal or no quantification of other processes contributing to vapor migration, such as thermal diffusion, convective gas flow due to the displacement of air, expansion/contraction of air due to temperature changes, temporal and spatial variations of soil moisture and fluctuations in atmospheric pressure. Soil water evaporation and interfacial mass transfer add to the complexity of the system. The goal of this work is to perform controlled experiments under transient conditions of soil moisture, temperature and wind at the land/atmosphere interface and use the resulting dataset to test existing theories on subsurface gas flow and iterate between numerical modeling efforts and experimental data. Ultimately, we aim to update conceptual models of shallow subsurface vapor transport to include conditionally significant transport processes and inform placement of mobile sensors and/or networks. We have developed a two-dimensional tank apparatus equipped with a network of sensors and a flow-through head space for simulation of the atmospheric interface. A detailed matrix of realistic atmospheric boundary conditions was applied in a series of

Non-extremophilic 'extremophiles' - Archaeal dominance in the subsurface and their implication for life

NASA Astrophysics Data System (ADS)

Reitschuler, Christoph; Lins, Philipp; Illmer, Paul

2014-05-01

Archaea - besides bacteria and eukaryota constituting the third big domain of life - were so far regarded as typical inhabitants of extreme environments, as indicated by the name (Archaeon, Greek: 'original', 'primal'). Previous research and cultivation successes were basically carried out in habitats characterized by extreme temperature, pH and salinity regimes. Such extreme conditions, as expected at the beginning of the Earth's evolution, are occasionally also prevalent on extraterrestrial planets and moons and make the Archaeal domain a key group to be studied concerning life's evolution and the most likely pioneer organisms to colonize environments that are regarded as hostile. However, in recent years it became obvious that Archaea, in particular non-extremophilic species, can be found almost ubiquitously in marine, freshwater, terrestrial and also subsurface habitats and occasionally outnumber other microbial domains and hold key positions in globally relevant energy and nutrient cycles. Besides extreme environments - the big question remains how to define a parameter as extreme - subsurface and cave environments present a window to the past, where adaptions to early life's conditions can be studied and how microbiomes may be structured in a habitat that represents a refugium on extraterrestrial celestial bodies, were surface conditions might be at first sight too extreme for life. The lower part of the alpine Hundsalm cave in Tyrol (Austria) offered a unique opportunity to study an almost pristine cave habitat, which is separated from the touristic part of the ice cave. The main focus of our research was laid on the microbial communities that were supposed to be in connection with secondary carbonate precipitations ('moonmilk'). For the ascertainment of these so far poorly evaluated structures a multiple approach assessment was chosen to generate a virtually complete picture of these subsurface microbiomes. Thereby, a combination of different cultivation

Culturally and linguistically diverse healthcare students' experiences of learning in a clinical environment: A systematic review of qualitative studies.

PubMed

Mikkonen, Kristina; Elo, Satu; Kuivila, Heli-Maria; Tuomikoski, Anna-Maria; Kääriäinen, Maria

2016-02-01

Learning in the clinical environment of healthcare students plays a significant part in higher education. The greatest challenges for culturally and linguistically diverse healthcare students were found in clinical placements, where differences in language and culture have been shown to cause learning obstacles for students. There has been no systematic review conducted to examine culturally and linguistically diverse healthcare students' experiences of their learning in the clinical environment. This systematic review aims to identify culturally and linguistically diverse healthcare students' experiences of learning in a clinical environment. The search strategy followed the guidelines of the Centre of Reviews and Dissemination. The original studies were identified from seven databases (CINAHL, Medline Ovid, Scopus, Web of Science, Academic Search Premiere, Eric and Cochrane Library) for the period 2000-2014. Two researchers selected studies based on titles, abstracts and full texts using inclusion criteria and assessed the quality of studies independently. Twelve original studies were chosen for the review. The culturally and linguistically diverse healthcare students' learning experiences were divided into three influential aspects of learning in a clinical environment: experiences with implementation processes and provision; experiences with peers and mentors; and experiences with university support and instructions. The main findings indicate that culturally and linguistically diverse healthcare students embarking on clinical placements initially find integration stressful. Implementing the process of learning in a clinical environment requires additional time, well prepared pedagogical orientation, prior cultural and language education, and support for students and clinical staff. Barriers to learning by culturally and linguistically diverse healthcare students were not being recognized and individuals were not considered motivated; learners experienced the

[Diversity of culturable sulfur-oxidizing bacteria in deep-sea hydrothermal vent environments of the South Atlantic].

PubMed

Xu, Hongxiu; Jiang, Lijing; Li, Shaoneng; Zhong, Tianhua; Lai, Qiliang; Shao, Zongze

2016-01-04

To investigate the diversity of culturable sulfur-oxidizing bacteria in hydrothermal vent environments of the South Atlantic, and analyze their characteristics of sulfur oxidation. We enriched and isolated sulfur-oxidizing bacteria from hydrothermal vent samples collected from the South Atlantic. The microbial diversity in enrichment cultures was analyzed using the Denatural Gradient Gel Electrophoresis method. Sulfur-oxidizing characteristics of the isolates was further studied by using ion chromatography. A total of 48 isolates were obtained from the deep-sea hydrothermal vent samples, which belonged to 23 genera and mainly grouped into alpha-Proteobacteria (58.3%), Actinobacteria (22.9%) and gama-Proteobacteria (18.8%). Among them, the genus Thalassospira, Martelella and Microbacterium were dominant. About 60% of the isolates exibited sulfur-oxidizing ability and strain L6M1-5 had a higher sulfur oxidation rate by comparison analysis. The diversity of sulfur-oxidizing bacteria in hydrothermal environments of the South Atlantic was reported for the first time based on culture-dependent methods. The result will help understand the biogechemical process of sulfur compounds in the deep-sea hydrothermal environments.

Imaging of Subsurface Corrosion Using Gradient-Field Pulsed Eddy Current Probes with Uniform Field Excitation

PubMed Central

Ren, Shuting; Yan, Bei; Zainal Abidin, Ilham Mukriz; Wang, Yi

2017-01-01

A corrosive environment leaves in-service conductive structures prone to subsurface corrosion which poses a severe threat to the structural integrity. It is indispensable to detect and quantitatively evaluate subsurface corrosion via non-destructive evaluation techniques. Although the gradient-field pulsed eddy current technique (GPEC) has been found to be superior in the evaluation of corrosion in conductors, it suffers from a technical drawback resulting from the non-uniform field excited by the conventional pancake coil. In light of this, a new GPEC probe with uniform field excitation for the imaging of subsurface corrosion is proposed in this paper. The excited uniform field makes the GPEC signal correspond only to the field perturbation due to the presence of subsurface corrosion, which benefits the corrosion profiling and sizing. A 3D analytical model of GPEC is established to analyze the characteristics of the uniform field induced within a conductor. Following this, experiments regarding the imaging of subsurface corrosion via GPEC have been carried out. It has been found from the results that the proposed GPEC probe with uniform field excitation not only applies to the imaging of subsurface corrosion in conductive structures, but provides high-sensitivity imaging results regarding the corrosion profile and opening size. PMID:28758985

Imaging of Subsurface Corrosion Using Gradient-Field Pulsed Eddy Current Probes with Uniform Field Excitation.

PubMed

Li, Yong; Ren, Shuting; Yan, Bei; Zainal Abidin, Ilham Mukriz; Wang, Yi

2017-07-31

A corrosive environment leaves in-service conductive structures prone to subsurface corrosion which poses a severe threat to the structural integrity. It is indispensable to detect and quantitatively evaluate subsurface corrosion via non-destructive evaluation techniques. Although the gradient-field pulsed eddy current technique (GPEC) has been found to be superior in the evaluation of corrosion in conductors, it suffers from a technical drawback resulting from the non-uniform field excited by the conventional pancake coil. In light of this, a new GPEC probe with uniform field excitation for the imaging of subsurface corrosion is proposed in this paper. The excited uniform field makes the GPEC signal correspond only to the field perturbation due to the presence of subsurface corrosion, which benefits the corrosion profiling and sizing. A 3D analytical model of GPEC is established to analyze the characteristics of the uniform field induced within a conductor. Following this, experiments regarding the imaging of subsurface corrosion via GPEC have been carried out. It has been found from the results that the proposed GPEC probe with uniform field excitation not only applies to the imaging of subsurface corrosion in conductive structures, but provides high-sensitivity imaging results regarding the corrosion profile and opening size.

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

NASA Astrophysics Data System (ADS)

Geesey, G.

2005-12-01

to remotely measure microbial community parameters that define their key functions at a scale that accurately reflects their role in large scale subsurface system behavior. The practical questions that geomicrobiologist must answer in the short term are: 1) What is known about the activities of the dominant microbial populations or those of their closest relatives? 2) Which of these activities is likely to dominate under in situ conditions? In the process of answering these questions, researchers will obtain answers to questions of a more fundamental nature such as 1) How deep does "active" life extend below the surface of the seafloor and terrestrial subsurface? 2) How are electrons exchanged between microbial cells and solid phase minerals? 3) What is the metabolic state and mechanism of survival of "inactive" life forms in the subsurface? 4) What can genomes of life forms trapped in geological material tell us about evolution of life that current methods cannot? The subsurface environment represents a challenging environment to understand and model. As the need to understand subsurface processes increases and the technologies to characterize them become available, modeling subsurface behavior will approach the level of sophistication of models used today to predict behavior of other large scale systems such as the oceans.

Cotton Flowers: Pollen and Petal Humidity Sensitivities Determine Reproductive Competitiveness in Diverse Environments

USDA-ARS?s Scientific Manuscript database

Genetic diversity in reproductive abiotic stress tolerance has been reported for cotton [Gossypium hirsutum (L.)] based upon the percentage of anther dehiscence of mature pollen in adverse environments. This study investigated the abiotic stress tolerance of mature pollen and identified genetic vari...

ExoMars WISDOM Left-Right-Evaluation of Subsurface Features

NASA Astrophysics Data System (ADS)

Plettemeier, Dirk; Ciarletti, Valerie; Benedix, Wolf-Stefan; Clifford, Stephen; Dorizon, Sophie; Statz, Christoph

2013-04-01

measurements in artificial environment with known material parameters is carried out to estimate the performance for buried objects. Finally, the procedure is applied to measurement data gained from a field test. The data were recorded during a campaign in a cave of the Dachstein mountain area in Austria. Since the echo interpretation of lots of subsurface features at once is not easy, the gray scale data of both polarizations has been set to different color channels and combined. The different colors allow also in a realistic environment the discrimination of subsurface features located on the left from those located on the right hand side of the rover path. This technique is interesting especially for the traverse mode, where the rover is moving long distances from one place of investigation to the next rather that following a grid like pattern necessary to get a real 3D mapping of the subsurface. Even in this case where radar measurements are done on the way one can get a more detailed (3D-like) insight of the subsurface structure.

Diversity of halophilic archaea from six hypersaline environments in Turkey.

PubMed

Ozcan, Birgul; Ozcengiz, Gulay; Coleri, Arzu; Cokmus, Cumhur

2007-06-01

The diversity of archaeal strains from six hypersaline environments in Turkey was analyzed by comparing their phenotypic characteristics and 16S rDNA sequences. Thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16S rDNA gene sequences. The results showed that all isolates belong to the family Halobacteriaceae. Phylogenetic analyses using approximately 1,388 bp comparisions of 16S rDNA sequences demonstrated that all isolates clustered closely to species belonging to 9 genera, namely Halorubrum (8 isolates), Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), Haloterrigena (3 isolates), Halalkalicoccus (1 isolate), and Halomicrobium (1 isolate). The results revealed a high diversity among the isolated halophilic strains and indicated that some of these strains constitute new taxa of extremely halophilic archaea.

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.

Mars penetrator: Subsurface science mission

NASA Technical Reports Server (NTRS)

Lumpkin, C. K.

1974-01-01

A penetrator system to emplace subsurface science on the planet Mars is described. The need for subsurface science is discussed, and the technologies for achieving successful atmospheric entry, Mars penetration, and data retrieval are presented.

Biotransformation at 10 C of di-n-butyl phthalate in subsurface microcosms

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

Chauret, C.; Inniss, W.E.; Mayfield, C.I.

1996-09-01

Di-n-butyl phthalate (DBP) was found to be transformed by microorganisms under aerobic and anaerobic conditions at 10 C in microcosms simulating the Canadian Forces Base (CFB) Borden subsurface environment. Biotransformation of DBP was observed under aerobic, nitrate-reducing, Fe(III)-reducing, and sulfate-reducing conditions. The biotransformation of DBP in the microcosms was significantly decrease3d as the redox potential was lowered, especially under sulfate-reducing conditions. However, other factors such as nutrient depletion and buildup of toxic intermediates could have affected the biotransformation rates. The highest DBP biotransformation rate (0.57 {micro}g DBP{center_dot}g sediment{sup {minus}1}{center_dot}day{sup {minus}1}) was under sulfate-reducing conditions. Biotransformation of DBP at 10 Cmore » was significantly enhanced by the addition of 10 mM NaNO{sub 3} suggesting that both the addition of nitrate and high redox conditions favor its biotransformation in subsurface environments.« less

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

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

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

Fredrickson, Jim K.; Balkwill, David L.; Romine, Margaret F.

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteriamore » cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.« less

Final technical report for project titled Quantitative Characterization of Cell Aggregation/Adhesion as Predictor for Distribution and Transport of Microorganisms in Subsurface Environment

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

Gu, April Z.; Wan, Kai-tak

This project aims to explore and develop enabling methodology and techniques for nano-scale characterization of microbe cell surface contact mechanics, interactions and adhesion quantities that allow for identification and quantification of indicative properties related to microorganism migration and transport behavior in porous media and in subsurface environments. Microbe transport has wide impact and therefore is of great interest in various environmental applications such as in situ or enhanced subsurface bioremediation,filtration processes for water and wastewater treatments and protection of drinking water supplies. Although great progress has been made towards understanding the identities and activities of these microorganisms in the subsurface,more » to date, little is known of the mechanisms that govern the mobility and transport of microorganisms in DOE’s contaminated sites, making the outcomes of in situ natural attenuation or contaminant stability enhancement unpredictable. Conventionally, movement of microorganisms was believed to follows the rules governing solute (particle) transport. However, recent studies revealed that cell surface properties, especially those pertaining to cell attachment/adhesion and aggregation behavior, can cause the microbe behavior to deviate from non-viable particles and hence greatly influence the mobility and distribution of microorganisms in porous media.This complexity highlights the need to obtain detailed information of cell-cell and cell-surface interactions in order to improve and refine the conceptual and quantitative model development for fate and transport of microorganisms and contaminant in subsurface. Traditional cell surface characterization methods are not sufficient to fully predict the deposition rates and transport behaviors of microorganism observed. A breakthrough of methodology that would allow for quantitative and molecular-level description of intrinsic cell surface properties indicative for cell

Cranial biomechanics underpins high sauropod diversity in resource-poor environments

PubMed Central

Button, David J.; Rayfield, Emily J.; Barrett, Paul M.

2014-01-01

High megaherbivore species richness is documented in both fossil and contemporary ecosystems despite their high individual energy requirements. An extreme example of this is the Late Jurassic Morrison Formation, which was dominated by sauropod dinosaurs, the largest known terrestrial vertebrates. High sauropod diversity within the resource-limited Morrison is paradoxical, but might be explicable through sophisticated resource partitioning. This hypothesis was tested through finite-element analysis of the crania of the Morrison taxa Camarasaurus and Diplodocus. Results demonstrate divergent specialization, with Camarasaurus capable of exerting and accommodating greater bite forces than Diplodocus, permitting consumption of harder food items. Analysis of craniodental biomechanical characters taken from 35 sauropod taxa demonstrates a functional dichotomy in terms of bite force, cranial robustness and occlusal relationships yielding two polyphyletic functional ‘grades’. Morrison taxa are widely distributed within and between these two morphotypes, reflecting distinctive foraging specializations that formed a biomechanical basis for niche partitioning between them. This partitioning, coupled with benefits associated with large body size, would have enabled the high sauropod diversities present in the Morrison Formation. Further, this provides insight into the mechanisms responsible for supporting the high diversities of large megaherbivores observed in other Mesozoic and Cenozoic communities, particularly those occurring in resource-limited environments. PMID:25297869

Geomorphic factors related to the persistence of subsurface oil from the Exxon Valdez oil spill

USGS Publications Warehouse

Nixon, Zachary; Michel, Jacqueline; Hayes, Miles O.; Irvine, Gail V.; Short, Jeffrey

2013-01-01

Oil from the 1989 Exxon Valdez oil spill has persisted along shorelines of Prince William Sound, Alaska, for more than two decades as both surface and subsurface oil residues. To better understand the distribution of persistent subsurface oil and assess the potential need for further restoration, a thorough and quantitative understanding of the geomorphic factors controlling the presence or absence of subsurface oil is required. Data on oiling and geomorphic features were collected at 198 sites in Prince William Sound to identify and quantify the relationships among these geomorphic factors and the presence and absence of persistent subsurface oil. Geomorphic factors associated with the presence of subsurface oil were initial oil exposure, substrate permeability, topographic slope, low exposure to waves, armoring on gravel beaches, tombolos, natural breakwaters, and rubble accumulations. Geomorphic factors associated with the absence of subsurface oil were impermeable bedrock; platforms with thin sediment veneer; fine-grained, well-sorted gravel beaches with no armor; and low-permeability, raised bay-bottom beaches. Relationships were found between the geomorphic and physical site characteristics and the likelihood of encountering persistent subsurface oiling at those sites. There is quantitative evidence of more complex interactions between the overall wave energy incident at a site and the presence of fine-scale geomorphic features that may have provided smaller, local wave energy sheltering of oil. Similarly, these data provide evidence for interactions between the shoreline slope and the presence of angular rubble, with decreased likelihood for encountering subsurface oil at steeply sloped sites except at high-angle sheltered rubble shoreline locations. These results reinforce the idea that the interactions of beach permeability, stability, and site-specific wave exposure are key drivers for subsurface oil persistence in exposed and intermittently exposed mixed

Genetic diversity of Escherichia coli isolates from surface water and groundwater in a rural environment.

PubMed

Gambero, Maria Laura; Blarasin, Monica; Bettera, Susana; Giuliano Albo, Jesica

2017-10-01

The genetic characteristics among Escherichia coli strains can be grouped by origin of isolation. Then, it is possible to use the genotypes as a tool to determine the source of water contamination. The aim of this study was to define water aptitude for human consumption in a rural basin and to assess the diversity of E. coli water populations. Thus, it was possible to identify the main sources of fecal contamination and to explore linkages with the hydrogeological environment and land uses. The bacteriological analysis showed that more than 50% of samples were unfit for human consumption. DNA fingerprinting analysis by BOX-PCR indicated low genotypic diversity of E. coli isolates taken from surface water and groundwater. The results suggested the presence of a dominant source of fecal contamination. The relationship between low genotypic diversity and land use would prove that water contamination comes from livestock. The genetic diversity of E. coli isolated from surface water was less than that identified in groundwater because of the different hydraulic features of both environments. Furthermore, each one of the two big strain groups identified in this basin is located in different sub-basins, showing that hydrological dynamics exerts selective pressure on bacteria DNA.

The thermal impact of subsurface building structures on urban groundwater resources - A paradigmatic example.

PubMed

Epting, Jannis; Scheidler, Stefan; Affolter, Annette; Borer, Paul; Mueller, Matthias H; Egli, Lukas; García-Gil, Alejandro; Huggenberger, Peter

2017-10-15

Shallow subsurface thermal regimes in urban areas are increasingly impacted by anthropogenic activities, which include infrastructure development like underground traffic lines as well as industrial and residential subsurface buildings. In combination with the progressive use of shallow geothermal energy systems, this results in the so-called subsurface urban heat island effect. This article emphasizes the importance of considering the thermal impact of subsurface structures, which commonly is underestimated due to missing information and of reliable subsurface temperature data. Based on synthetic heat-transport models different settings of the urban environment were investigated, including: (1) hydraulic gradients and conductivities, which result in different groundwater flow velocities; (2) aquifer properties like groundwater thickness to aquitard and depth to water table; and (3) constructional features, such as building depths and thermal properties of building structures. Our results demonstrate that with rising groundwater flow velocities, the heat-load from building structures increase, whereas down-gradient groundwater temperatures decrease. Thermal impacts on subsurface resources therefore have to be related to the permeability of aquifers and hydraulic boundary conditions. In regard to the urban settings of Basel, Switzerland, flow velocities of around 1 md -1 delineate a marker where either down-gradient temperature deviations or heat-loads into the subsurface are more relevant. Furthermore, no direct thermal influence on groundwater resources should be expected for aquifers with groundwater thicknesses larger 10m and when the distance of the building structure to the groundwater table is higher than around 10m. We demonstrate that measuring temperature changes down-gradient of subsurface structures is insufficient overall to assess thermal impacts, particularly in urban areas. Moreover, in areas which are densely urbanized, and where groundwater flow

Homeostasis of Complementary Pair Theory: Ecological Comparisons in Diverse Universal Design for Learning Environments

ERIC Educational Resources Information Center

Ianneo, Brittany

2014-01-01

Accommodation~assimilation relations were theorized by Kelso and Engstrom (2006) as independent and dependent complementary pairs. This study defined relationships between organisms that experienced complementary interactions of accommodation~assimilation in diverse ecologies designed with universal design for learning environments (UDLE) compared…

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

Numerical simulation of trace element transport on subsurface environment pollution in coal mine spoil.

PubMed

Qiang, Xue; Bing, Liang; Hui-yun, Wang; Lei, Liu

2006-01-01

An understanding of the dynamic behavior of trace elements leaching from coal mine spoil is important in predicting the groundwater quality. The relationship between trace element concentrations and leaching times, pH values of the media is studied. Column leaching tests conducted in the laboratory showed that there was a close correlation between pH value and trace element concentrations. The longer the leaching time, the higher the trace element concentrations. Different trace elements are differently affected by pH values of leaching media. A numerical model for water flow and trace element transport has been developed based on analyzing the characteristics of migration and transformation of trace elements leached from coal mine spoil. Solutions to the coupled model are accomplished by Eulerian-Lagrangian localized adjoint method. Numerical simulation shows that rainfall intensity determined maximum leaching depth. As rainfall intensity is 3.6ml/s, the outflow concentrations indicate a breakthrough of trace elements beyond the column base, with peak concentration at 90cm depth. And the subsurface pollution range has a trend of increase with time. The model simulations are compared to experimental results of trace element concentrations, with reasonable agreement between them. The analysis and modeling of trace elements suggested that the infiltration of rainwater through the mine spoil might lead to potential groundwater pollution. It provides theoretical evidence for quantitative assessment soil-water quality of trace element transport on environment pollution.

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

The Interest of the Diversity of Perspectives and Methodologies in Evaluating the Science Laboratory Learning Environment

ERIC Educational Resources Information Center

Membiela, Pedro; Vidal, Manuel

2017-01-01

The importance of researching the opinions of students and teachers has been pointed out concerning the improvement of teaching and learning in laboratory environments. In this regard, a study of the laboratory environment was carried out from a diversity of perspectives and methodologies. By means of a questionnaire it was learned that the…

Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

NASA Astrophysics Data System (ADS)

Hunter, K. S.; Van Cappellen, P.

2000-01-01

Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

Subsurface injection of liquid waste in Florida, United States of America

USGS Publications Warehouse

Vecchioli, John

1981-01-01

In 1979, liquid waste was injected into the subsurface of Florida by 10 injection systems at an aggregate average rate of 165,000 m3/d. All the systems inject into carbonate rocks that contain salty water. Extensive precautions are taken in the construction of the injection wells and in the monitoring of their operation to provide assurance that overlying and laterally contiguous freshwater resources do not become contaminated with either the injected waste or the saltwater displaced by the waste. Several concerns relating to the effectiveness of the confining bed above the injection zone for containing the injected wastes have arisen over the years. These concerns accentuate the value of a well-planned and implemented monitoring program from which one can evaluate the potential impact of waste injection on the subsurface environment.

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

PubMed Central

2016-01-01

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

The yeast Starmerella bacillaris (synonym Candida zemplinina) shows high genetic diversity in winemaking environments.

PubMed

Masneuf-Pomarede, Isabelle; Juquin, Elodie; Miot-Sertier, Cécile; Renault, Philippe; Laizet, Yec'han; Salin, Franck; Alexandre, Hervé; Capozzi, Vittorio; Cocolin, Luca; Colonna-Ceccaldi, Benoit; Englezos, Vasileios; Girard, Patrick; Gonzalez, Beatriz; Lucas, Patrick; Mas, Albert; Nisiotou, Aspasia; Sipiczki, Matthias; Spano, Giuseppe; Tassou, Chrysoula; Bely, Marina; Albertin, Warren

2015-08-01

The yeast Candida zemplinina (Starmerella bacillaris) is frequently isolated from grape and wine environments. Its enological use in mixed fermentation with Saccharomyces cerevisiae has been extensively investigated these last few years, and several interesting features including low ethanol production, fructophily, glycerol and other metabolites production, have been described. In addition, molecular tools allowing the characterization of yeast populations have been developed, both at the inter- and intraspecific levels. However, most of these fingerprinting methods are not compatible with population genetics or ecological studies. In this work, we developed 10 microsatellite markers for the C. zemplinina species that were used for the genotyping of 163 strains from nature or various enological regions (28 vineyards/wineries from seven countries). We show that the genetic diversity of C. zemplinina is shaped by geographical localization. Populations isolated from winemaking environments are quite diverse at the genetic level: neither clonal-like behaviour nor specific genetic signature were associated with the different vineyards/wineries. Altogether, these results suggest that C. zemplinina is not under selective pressure in winemaking environments. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

On the edge of a deep biosphere: Real animals in extreme environments

NASA Astrophysics Data System (ADS)

Childress, James J.; Fisher, Charles F.; Felbeck, Horst; Girguis, Peter

This paper considers the possibility of animals living in a subsurface environment on the global mid-ocean ridge system. It considers the possible environments and looks at the possibilities of animal inhabitants of the subsurface biosphere based on adaptations of animals to other extreme habitats. We conclude that there are known bridging inhabitants of the subsurface biosphere, that part-time inhabitants are extremely likely, and that there could be full-time inhabitants if conditions are stable within the tolerance limits of metazoans for time periods of months.

Enhanced groundwater recharge rates and altered recharge sensitivity to climate variability through subsurface heterogeneity

PubMed Central

Hartmann, Andreas; Gleeson, Tom; Wagener, Thorsten

2017-01-01

Our environment is heterogeneous. In hydrological sciences, the heterogeneity of subsurface properties, such as hydraulic conductivities or porosities, exerts an important control on water balance. This notably includes groundwater recharge, which is an important variable for efficient and sustainable groundwater resources management. Current large-scale hydrological models do not adequately consider this subsurface heterogeneity. Here we show that regions with strong subsurface heterogeneity have enhanced present and future recharge rates due to a different sensitivity of recharge to climate variability compared with regions with homogeneous subsurface properties. Our study domain comprises the carbonate rock regions of Europe, Northern Africa, and the Middle East, which cover ∼25% of the total land area. We compare the simulations of two large-scale hydrological models, one of them accounting for subsurface heterogeneity. Carbonate rock regions strongly exhibit “karstification,” which is known to produce particularly strong subsurface heterogeneity. Aquifers from these regions contribute up to half of the drinking water supply for some European countries. Our results suggest that water management for these regions cannot rely on most of the presently available projections of groundwater recharge because spatially variable storages and spatial concentration of recharge result in actual recharge rates that are up to four times larger for present conditions and changes up to five times larger for potential future conditions than previously estimated. These differences in recharge rates for strongly heterogeneous regions suggest a need for groundwater management strategies that are adapted to the fast transit of water from the surface to the aquifers. PMID:28242703

Enhanced Groundwater Recharge Rates and Altered Recharge Sensitivity to Climate Variability Through Subsurface Heterogeneity

NASA Technical Reports Server (NTRS)

Hartmann, Andreas; Gleeson, Tom; Wada, Yoshihide; Wagener, Thorsten

2017-01-01

Our environment is heterogeneous. In hydrological sciences, the heterogeneity of subsurface properties, such as hydraulic conductivities or porosities, exerts an important control on water balance. This notably includes groundwater recharge, which is an important variable for efficient and sustainable groundwater resources management. Current large-scale hydrological models do not adequately consider this subsurface heterogeneity. Here we show that regions with strong subsurface heterogeneity have enhanced present and future recharge rates due to a different sensitivity of recharge to climate variability compared with regions with homogeneous subsurface properties. Our study domain comprises the carbonate rock regions of Europe, Northern Africa, and the Middle East, which cover 25 of the total land area. We compare the simulations of two large-scale hydrological models, one of them accounting for subsurface heterogeneity. Carbonate rock regions strongly exhibit karstification, which is known to produce particularly strong subsurface heterogeneity. Aquifers from these regions contribute up to half of the drinking water supply for some European countries. Our results suggest that water management for these regions cannot rely on most of the presently available projections of groundwater recharge because spatially variable storages and spatial concentration of recharge result in actual recharge rates that are up to four times larger for present conditions and changes up to five times larger for potential future conditions than previously estimated. These differences in recharge rates for strongly heterogeneous regions suggest a need for groundwater management strategies that are adapted to the fast transit of water from the surface to the aquifers.

Hints of Habitable Environments on Mars Challenge Our Studies of Mars-Analog Sites on Earth

NASA Technical Reports Server (NTRS)

desMarais, David J

2009-01-01

Life as we know it requires water with a chemical activity (alpha) >or approx.0.6 and sources of nutrients and useful energy. Some biota can survive even if favorable conditions occur only intermittently, but the minimum required frequency of occurrences is poorly understood. Recent discoveries have vindicated the Mars exploration strategy to follow the water. Mars Global Surveyor s Thermal Emission Spectrometer (TES) found coarse-grained hematite at Meridiani Planum. Opportunity rover confirmed this and also found evidence of ancient sulfate-rich playa lakes and near-surface groundwater. Elsewhere, TES found evidence of evaporitic halides in topographic depressions. But alpha might not have approached 0.6 in these evaporitic sulfate- and halide-bearing waters. Mars Express (MEX) and Mars Reconnaissance Orbiter (MRO) found extensive sulfate evaporites in Meridiani and Valles Marineris. MEX found phyllosilicates at several sites, most notably Mawrth Valles and Nili Fossae. MRO's CRISM near-IR mapper extended the known diversity and geographic distribution of phyllosilicates to include numerous Noachian craters. Phyllosilicates typically occur at the base of exposed ancient rock sections or in sediments in early Hesperian craters. It is uncertain whether the phyllosilicates developed in surface or subsurface aqueous environments and how long aqueous conditions persisted. Spirit rover found remarkably pure ferric sulfate, indicating oxidation and transport of Fe and S, perhaps in fumaroles or hot springs. Spirit also found opaline silica, consistent with hydrothermal activity. CRISM mapped extensive silica deposits in the Valles Marineris region, consistent with aqueous weathering and deposition. CRISM also found ultramafic rocks and magnesite at Nili Fossae, consistent with serpentinization, a process that can sustain habitable environments on Earth. The report of atmospheric methane implies subsurface aqueous conditions. A working hypothesis is that aqueous

MA_MISS: Mars Multispectral Imager for Subsurface Studies

NASA Astrophysics Data System (ADS)

De Sanctis, M. C.; Coradini, A.; Ammannito, E.; Boccaccini, A.; Di Iorio, T.; Battistelli, E.; Capanni, A.

2012-04-01

A Drilling system, coupled with an in situ analysis package, is installed on the ExoMars Pasteur Rover to perform in situ investigations up to 2m in the Mars soil. Ma_Miss (Mars Multispectral Imager for Subsurface Studies) is a spectrometer devoted to observe the lateral wall of the borehole generated by the Drilling system. The instrument is fully integrated with the Drill and shares its structure and electronics. For the first time in Mars exploration experiments the water/geochemical environment will be investigated as function of depth in the shallow subsurface. Samples from the subsurface of Martian soil are unaltered by weathering process, oxidation and erosion. Subsurface access can be the key to look for signs of present and past environmental conditions, associated to the possibility for life (water, volatiles and weathering process). The analysis of uncontaminated samples by means of instrumented Drill and in situ observations is the solution for unambiguous interpretation of the original environment that leading to the formation of rocks. Ma_Miss experiment is perfectly suited to perform multispectral imaging of the drilled layers. Ma_Miss is a miniaturized near-infrared imaging spectrometer in the range 0.4-2.2 µm with 20nm spectral sampling. The task of illuminating the borehole wall and collecting the diffused light from the illuminated spot on the target requires a transparent window on the Drill tool, which shall prevent the dust contamination of the optical and mechanical elements inside. Hardness of sapphire is the closest to diamond one, thus avoiding the risk of scratches on its surface. The Sapphire window is cylindrical, and bounded such as to realize a continuous auger profile. Ma_Miss Optical Head performs the double task of illuminating the borehole wall with a spot around 1 mm diameter and of collecting the scattered light coming from a 0.1 mm diameter spot of the target. The signal from the Optical Head to the spectrometer is transferred

Diversity and impact of prokaryotic toxins on aquatic environments: a review.

PubMed

Valério, Elisabete; Chaves, Sandra; Tenreiro, Rogério

2010-10-01

Microorganisms are ubiquitous in all habitats and are recognized by their metabolic versatility and ability to produce many bioactive compounds, including toxins. Some of the most common toxins present in water are produced by several cyanobacterial species. As a result, their blooms create major threats to animal and human health, tourism, recreation and aquaculture. Quite a few cyanobacterial toxins have been described, including hepatotoxins, neurotoxins, cytotoxins and dermatotoxins. These toxins are secondary metabolites, presenting a vast diversity of structures and variants. Most of cyanobacterial secondary metabolites are peptides or have peptidic substructures and are assumed to be synthesized by non-ribosomal peptide synthesis (NRPS), involving peptide synthetases, or NRPS/PKS, involving peptide synthetases and polyketide synthases hybrid pathways. Besides cyanobacteria, other bacteria associated with aquatic environments are recognized as significant toxin producers, representing important issues in food safety, public health, and human and animal well being. Vibrio species are one of the most representative groups of aquatic toxin producers, commonly associated with seafood-born infections. Some enterotoxins and hemolysins have been identified as fundamental for V. cholerae and V. vulnificus pathogenesis, but there is evidence for the existence of other potential toxins. Campylobacter spp. and Escherichia coli are also water contaminants and are able to produce important toxins after infecting their hosts. Other bacteria associated with aquatic environments are emerging as toxin producers, namely Legionella pneumophila and Aeromonas hydrophila, described as responsible for the synthesis of several exotoxins, enterotoxins and cytotoxins. Furthermore, several Clostridium species can produce potent neurotoxins. Although not considered aquatic microorganisms, they are ubiquitous in the environment and can easily contaminate drinking and irrigation water

Diversity and Impact of Prokaryotic Toxins on Aquatic Environments: A Review

PubMed Central

Valério, Elisabete; Chaves, Sandra; Tenreiro, Rogério

2010-01-01

Microorganisms are ubiquitous in all habitats and are recognized by their metabolic versatility and ability to produce many bioactive compounds, including toxins. Some of the most common toxins present in water are produced by several cyanobacterial species. As a result, their blooms create major threats to animal and human health, tourism, recreation and aquaculture. Quite a few cyanobacterial toxins have been described, including hepatotoxins, neurotoxins, cytotoxins and dermatotoxins. These toxins are secondary metabolites, presenting a vast diversity of structures and variants. Most of cyanobacterial secondary metabolites are peptides or have peptidic substructures and are assumed to be synthesized by non-ribosomal peptide synthesis (NRPS), involving peptide synthetases, or NRPS/PKS, involving peptide synthetases and polyketide synthases hybrid pathways. Besides cyanobacteria, other bacteria associated with aquatic environments are recognized as significant toxin producers, representing important issues in food safety, public health, and human and animal well being. Vibrio species are one of the most representative groups of aquatic toxin producers, commonly associated with seafood-born infections. Some enterotoxins and hemolysins have been identified as fundamental for V. cholerae and V. vulnificus pathogenesis, but there is evidence for the existence of other potential toxins. Campylobacter spp. and Escherichia coli are also water contaminants and are able to produce important toxins after infecting their hosts. Other bacteria associated with aquatic environments are emerging as toxin producers, namely Legionella pneumophila and Aeromonas hydrophila, described as responsible for the synthesis of several exotoxins, enterotoxins and cytotoxins. Furthermore, several Clostridium species can produce potent neurotoxins. Although not considered aquatic microorganisms, they are ubiquitous in the environment and can easily contaminate drinking and irrigation water

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.

Subsurface water and clay mineral formation during the early history of Mars.

PubMed

Ehlmann, Bethany L; Mustard, John F; Murchie, Scott L; Bibring, Jean-Pierre; Meunier, Alain; Fraeman, Abigail A; Langevin, Yves

2011-11-02

Clay minerals, recently discovered to be widespread in Mars's Noachian terrains, indicate long-duration interaction between water and rock over 3.7 billion years ago. Analysis of how they formed should indicate what environmental conditions prevailed on early Mars. If clays formed near the surface by weathering, as is common on Earth, their presence would indicate past surface conditions warmer and wetter than at present. However, available data instead indicate substantial Martian clay formation by hydrothermal groundwater circulation and a Noachian rock record dominated by evidence of subsurface waters. Cold, arid conditions with only transient surface water may have characterized Mars's surface for over 4 billion years, since the early-Noachian period, and the longest-duration aqueous, potentially habitable environments may have been in the subsurface.

Modeling subsurface stormflow initiation in low-relief landscapes

NASA Astrophysics Data System (ADS)

Hopp, Luisa; Vaché, Kellie B.; Rhett Jackson, C.; McDonnell, Jeffrey J.

2015-04-01

Shallow lateral subsurface flow as a runoff generating mechanism at the hillslope scale has mostly been studied in steeper terrain with typical hillside angles of 10 - 45 degrees. These studies have shown that subsurface stormflow is often initiated at the interface between a permeable upper soil layer and a lower conductivity impeding layer, e.g. a B horizon or bedrock. Many studies have identified thresholds of event size and soil moisture states that need to be exceeded before subsurface stormflow is initiated. However, subsurface stormflow generation on low-relief hillslopes has been much less studied. Here we present a modeling study that investigates the initiation of subsurface stormflow on low-relief hillslopes in the Upper Coastal Plain of South Carolina, USA. Hillslopes in this region typically have slope angles of 2-5 degrees. Topsoils are sandy, underlain by a low-conductivity sandy clay loam Bt horizon. Subsurface stormflow has only been intercepted occasionally in a 120 m long trench, and often subsurface flow was not well correlated with stream signals, suggesting a disconnect between subsurface flow on the hillslopes and stream flow. We therefore used a hydrologic model to better understand which conditions promote the initiation of subsurface flow in this landscape, addressing following questions: Is there a threshold event size and soil moisture state for producing lateral subsurface flow? What role does the spatial pattern of depth to the impeding clay layer play for subsurface stormflow dynamics? We reproduced a section of a hillslope, for which high-resolution topographic data and depth to clay measurements were available, in the hydrologic model HYDRUS-3D. Soil hydraulic parameters were based on experimentally-derived data. The threshold analysis was first performed using hourly climate data records for 2009-2010 from the study site to drive the simulation. For this period also trench measurements of subsurface flow were available. In addition

Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments.

PubMed

Futagami, Taiki; Morono, Yuki; Terada, Takeshi; Kaksonen, Anna H; Inagaki, Fumio

2009-11-01

Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (rdhA) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem.

Distribution and Diversity of Symbiotic Thermophiles, Symbiobacterium thermophilum and Related Bacteria, in Natural Environments

PubMed Central

Ueda, Kenji; Ohno, Michiyo; Yamamoto, Kaori; Nara, Hanae; Mori, Yujiro; Shimada, Masafumi; Hayashi, Masahiko; Oida, Hanako; Terashima, Yuko; Nagata, Mitsuyo; Beppu, Teruhiko

2001-01-01

Symbiobacterium thermophilum is a tryptophanase-positive thermophile which shows normal growth only in coculture with its supporting bacteria. Analysis of the 16S rRNA gene (rDNA) indicated that the bacterium belongs to a novel phylogenetic branch at the outermost position of the gram-positive bacterial group without clustering to any other known genus. Here we describe the distribution and diversity of S. thermophilum and related bacteria in the environment. Thermostable tryptophanase activity and amplification of the specific 16S rDNA fragment were effectively employed to detect the presence of Symbiobacterium. Enrichment with kanamycin raised detection sensitivity. Mixed cultures of thermophiles containing Symbiobacterium species were frequently obtained from compost, soil, animal feces, and contents in the intestinal tracts, as well as feeds. Phylogenetic analysis and denaturing gradient gel electrophoresis of the specific 16S rDNA amplicons revealed a diversity of this group of bacteria in the environment. PMID:11525967

Subsurface application of poultry litter and its influence on nutrient losses in runoff water from permanent pastures.

PubMed

Watts, D B; Way, T R; Torbert, H A

2011-01-01

Environmental pressure to reduce nutrient losses from agricultural fields has increased in recent years. To abate this nutrient loss to the environment, better management practices and new technologies need to be developed. Thus, research was conducted to evaluate if subsurface banding poultry litter (PL) would reduce nitrogen (N) and phosphorus (P) loss in surface water runoff using a four-row prototype implement. Rainfall simulations were conducted to create a 40-min runoff event in an established bermudagrass (Cynodon dactylon L.) pasture on soil types common to the Coastal Plain and Piedmont regions. The Coastal Plain soil type was a Marvyn loamy sand (fine-loamy, kaolinitic, thermic Typic Kanhapludults) and the Piedmont soil type was a Hard Labor loamy sand (fine, kaolinitic, thermic Oxyaquic Kanhapludults). Treatments consisted of surface- and subsurface-applied PL at a rate of 9 Mg ha(-1), surface broadcast-applied commercial fertilizer (CF; urea and triple superphosphate blend) at the equivalent N (330 kg N ha(-1)) and P (315 kg N ha(-1)) content of PL, and a nonfertilized control. The greatest loss for inorganic N, total N, dissolved reactive P (DRP), and total P occurred with the surface broadcast treatments, with CF contributing to the greatest loss. Nutrient losses from the subsurface banded treatment reduced N and P in surface water runoff to levels of the control. Subsurface banding of PL reduced concentrations of inorganic N 91%, total N 90%, DRP 86%, and total P 86% in runoff water compared with surface broadcasted PL. These results show that subsurface band-applied PL can greatly reduce the impact of N and P loss to the environment compared with conventional surface-applied PL and CF practices.

Stress management skills in the subsurface: H2 stress on thermophilic heterotrophs and methanogens

NASA Astrophysics Data System (ADS)

Topcuoglu, B. D.; Holden, J. F.

2017-12-01

Marine hyperthermophilic heterotrophs and methanogens belonging to the Thermococcales and Methanococcales are often found in subsurface environments such as coal and shale beds, marine sediments, and oil reservoirs where they encounter H2 stress conditions. It is important to study the H2 stress survival strategies of these organisms and their cooperation with one another for survival to better understand their biogeochemical impact in hot subsurface environments. In this study, we have shown that H2 inhibition changed the growth kinetics and the transcriptome of Thermococcus paralvinellae. We observed a significant decrease in batch phase growth rates and cell concentrations with high H2 background. Produced metabolite production measurements, RNA-seq analyses of differentially expressed genes and in silico experiments we performed with the T. paralvinellae metabolic model showed that T. paralvinellae produces formate by a formate hydrogenlyase to survive H2 inhibition. We have also shown that H2 limitation caused a significant decrease in batch phase growth rates and methane production rates of the methanogen, Methanocaldococcus jannaschii. H2 stress of both organisms can be ameliorated by syntrophic growth. H2 syntrophy was demonstrated in microcosm incubations for a natural assemblage of Thermococcus and hyperthermophilic methanogens present in hydrothermal fluid samples. This project aims to describe how a hyperthermophilic heterotroph and a hyperthermophilic methanogen eliminate H2 stress and explore cooperation among thermophiles in the hot subsurface.

Subsurface sounders

NASA Technical Reports Server (NTRS)

1975-01-01

Airborne or spaceborne electromagnetic systems used to detect subsurface features are discussed. Data are given as a function of resistivity of ground material, magnetic permeability of free space, and angular frequency. It was noted that resistivities vary with the water content and temperature.

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.

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.

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

Real rock-microfluidic flow cell: A test bed for real-time in situ analysis of flow, transport, and reaction in a subsurface reactive transport environment.

PubMed

Singh, Rajveer; Sivaguru, Mayandi; Fried, Glenn A; Fouke, Bruce W; Sanford, Robert A; Carrera, Martin; Werth, Charles J

2017-09-01

Physical, chemical, and biological interactions between groundwater and sedimentary rock directly control the fundamental subsurface properties such as porosity, permeability, and flow. This is true for a variety of subsurface scenarios, ranging from shallow groundwater aquifers to deeply buried hydrocarbon reservoirs. Microfluidic flow cells are now commonly being used to study these processes at the pore scale in simplified pore structures meant to mimic subsurface reservoirs. However, these micromodels are typically fabricated from glass, silicon, or polydimethylsiloxane (PDMS), and are therefore incapable of replicating the geochemical reactivity and complex three-dimensional pore networks present in subsurface lithologies. To address these limitations, we developed a new microfluidic experimental test bed, herein called the Real Rock-Microfluidic Flow Cell (RR-MFC). A porous 500μm-thick real rock sample of the Clair Group sandstone from a subsurface hydrocarbon reservoir of the North Sea was prepared and mounted inside a PDMS microfluidic channel, creating a dynamic flow-through experimental platform for real-time tracking of subsurface reactive transport. Transmitted and reflected microscopy, cathodoluminescence microscopy, Raman spectroscopy, and confocal laser microscopy techniques were used to (1) determine the mineralogy, geochemistry, and pore networks within the sandstone inserted in the RR-MFC, (2) analyze non-reactive tracer breakthrough in two- and (depth-limited) three-dimensions, and (3) characterize multiphase flow. The RR-MFC is the first microfluidic experimental platform that allows direct visualization of flow and transport in the pore space of a real subsurface reservoir rock sample, and holds potential to advance our understandings of reactive transport and other subsurface processes relevant to pollutant transport and cleanup in groundwater, as well as energy recovery. Copyright © 2017 Elsevier B.V. All rights reserved.

Biodegradation of crude oil in Arctic subsurface water from the Disko Bay (Greenland) is limited.

PubMed

Scheibye, Katrine; Christensen, Jan H; Johnsen, Anders R

2017-04-01

Biological degradation is the main process for oil degradation in a subsurface oil plume. There is, however, little information on the biodegradation potential of Arctic, marine subsurface environments. We therefore investigated oil biodegradation in microcosms at 2 °C containing Arctic subsurface seawater from the Disko Bay (Greenland) and crude oil at three concentrations of 2.5-10 mg/L. Within 71 days, the total petroleum hydrocarbon concentration decreased only by 18 ± 18% for an initial concentration of 5 mg/L. The saturated alkanes nC13-nC30 and the isoprenoids iC18-iC21 were biodegraded at all concentrations indicating a substantial potential for biodegradation of these compound classes. Polycyclic aromatic compounds (PACs) disappeared from the oil phase, but dissolution was the main process of removal. Analysis of diagnostic ratios indicated almost no PAC biodegradation except for the C1-naphthalenes. To conclude, the marine subsurface microorganisms from the Disko Bay had the potential for biodegradation of n-alkanes and isoprenoids while the metabolically complex and toxic PACs and their alkylated homologs remained almost unchanged. Copyright © 2016 Elsevier Ltd. All rights reserved.

Roadside IED detection using subsurface imaging radar and rotary UAV

NASA Astrophysics Data System (ADS)

Qin, Yexian; Twumasi, Jones O.; Le, Viet Q.; Ren, Yu-Jiun; Lai, C. P.; Yu, Tzuyang

2016-05-01

Modern improvised explosive device (IED) and mine detection sensors using microwave technology are based on ground penetrating radar operated by a ground vehicle. Vehicle size, road conditions, and obstacles along the troop marching direction limit operation of such sensors. This paper presents a new conceptual design using a rotary unmanned aerial vehicle (UAV) to carry subsurface imaging radar for roadside IED detection. We have built a UAV flight simulator with the subsurface imaging radar running in a laboratory environment and tested it with non-metallic and metallic IED-like targets. From the initial lab results, we can detect the IED-like target 10-cm below road surface while carried by a UAV platform. One of the challenges is to design the radar and antenna system for a very small payload (less than 3 lb). The motion compensation algorithm is also critical to the imaging quality. In this paper, we also demonstrated the algorithm simulation and experimental imaging results with different IED target materials, sizes, and clutters.

Hydrogen Isotopic Constraints on the Evolution of Surface and Subsurface Water on Mars

NASA Technical Reports Server (NTRS)

Usui, T.; Kurokawa, H.; Wang, J.; Alexander, C. M. O’D.; Simon, J. I.; Jones, J. H.

2017-01-01

The geology and geomorphology of Mars provide clear evidence for the presence of liquid water on its surface during the Noachian and Hesperien eras (i.e., >3 Ga). In contrast to the ancient watery environment, today the surface of Mars is relatively dry. The current desert-like surface conditions, however, do not necessarily indicate a lack of surface or near-surface water/ice. In fact, massive deposits of ground ice and/or icy sediments have been proposed based on subsurface radar sounder observations. Hence, accurate knowledge of both the evolution of the distribution of water and of the global water inventory is crucial to our understanding of the evolution of the climate and near-surface environments and the potential habitability of Mars. This study presents insights from hydrogen isotopes for the interactive evolution of Martian water reservoirs. In particular, based on our new measurement of the D/H ratio of 4 Ga-old Noachian water, we constrain the atmospheric loss and possible exchange of surface and subsurface water through time.

Subsurface geomicrobiology in a Mars terrestrial analogue, Río Tinto (SW, Spain)

NASA Astrophysics Data System (ADS)

Amils, R.; Fernández-Remolar, D.; Gómez, F.; González-Toril, E.; Rodríguez, N.; Prieto-Ballesteros, O.; Sanz, J. L.; Díaz, E.; Stoker, C.

2008-09-01

Since its discovery, only few years ago, subsurface geomicrobiology is a matter of growing interest [1]. 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 life in other planetary bodies, e.g., Mars, as well as early life on Earth. Río Tinto is an unusual extreme acidic environment due to its size (around 100 km), constant acidic pH (mean pH 2.3), high concentrations of heavy metals and high level of microbial diversity [2]. Río Tinto rises in the core of the Iberian Pyritic Belt, one of the biggest sulfidic ore deposits in the world [3]. Today it is well stablished that the extreme characteristics of Río Tinto are not due to acid mine drainage from mining activity, as has been suggested in the past. To explore the hypothesis that a continuous underground reactor of chemolithotrophic microorganisms thriving in the rich sulfidic minerals of the Iberian Pyritic Belt is responsible for the extreme conditions found in the system, a drilling project has been developed to detect evidence of subsurface microbial activity and potential resources to support these microbial communities in situ (MARTE project) [4]. Here we report a search for subsurface life in volcanically hosted massive sulfidic deposits from the Iberian Pyritic Belt. Aseptic core samples were obtained within and down-gradient from the massive sulfide deposits and formation water was sampled within the resulting bore holes. Microbial activity was detected in un-contaminated samples by culture-dependent and culture-independent methods. Aerobic iron- and sulfide- oxidizing bacteria, and anaerobic denitrifying thiosulfate-oxidizing bacteria, sulfate reducing bacteria and methanogenic archaea have been identified. Potential energy fluxes detected in the system include oxidation of reduced iron and sulfur, or hydrogen gas coupled to nitrite, sulfate, ferric iron, inorganic

Environments. Our Common Home: Earth. A Curriculum Strategy to Affect Student Skills Development and Exposure to Diverse Global Natural/Social Environments.

ERIC Educational Resources Information Center

Peters, Richard

One of a series of global education instructional units, this unit on environments was designed to be infused with existing social studies courses aimed at students in grades 5-12. Concept-based and skills-oriented, the curriculum provides opportunities for students to develop an understanding of the nature and character of diverse global natural…

Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

PubMed Central

Hurt, Richard A.; Robeson, Michael S.; Shakya, Migun; Moberly, James G.; Vishnivetskaya, Tatiana A.; Gu, Baohua; Elias, Dwayne A.

2014-01-01

Despite over three decades of progress, extraction of high molecular weight (HMW) DNA from high clay soils or iron oxide cemented clay has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage. Several DNA extraction procedures were compared from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions offered no improvement in nucleic acid recovery. Lysis by liquid N2 grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides. DNA recovered using 1 M sodium phosphate buffer (PB) as a competitive desorptive wash was 15.22±2.33 µg DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 µg DNA/g clay with the Powerlyzer system (MoBio). Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots of 16S rRNA (V1–V3 region) pyrosequencing from A-horizon and clay soils showed an ∼80% and ∼400% larger accessed diversity compared to the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU) recovered. PMID:25033199

Using Geophysical Signatures to Investigate Temporal Changes Due to Source Reduction in the Subsurface Contaminated with Hydrocarbons

EPA Science Inventory

We investigated the geophysical response to subsurface hydrocarbon contamination source removal. Source removal by natural attenuation or by engineered bioremediation is expected to change the biological, chemical, and physical environment associated with the contaminated matrix....

Archaeal diversity and CO2 fixers in carbonate-/siliciclastic-rock groundwater ecosystems

USGS Publications Warehouse

Lazar, Cassandre Sara; Stoll, Wenke; Lehmann, Robert; Herrmann, Martina; Schwab, Valérie F.; Akob, Denise M.; Nawaz, Ali; Wubet, Tesfaye; Buscot, François; Totsche, Kai-Uwe; Küsel, Kirsten

2017-01-01

Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13CO2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO2, while archaeal autotrophy seems to be limited in the groundwater.

Archaeal Diversity and CO2 Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems.

PubMed

Lazar, Cassandre Sara; Stoll, Wenke; Lehmann, Robert; Herrmann, Martina; Schwab, Valérie F; Akob, Denise M; Nawaz, Ali; Wubet, Tesfaye; Buscot, François; Totsche, Kai-Uwe; Küsel, Kirsten

2017-01-01

Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13 CO 2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO 2 , while archaeal autotrophy seems to be limited in the groundwater.

Archaeal Diversity and CO2 Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems

PubMed Central

Lazar, Cassandre Sara; Stoll, Wenke; Lehmann, Robert; Herrmann, Martina; Schwab, Valérie F.; Akob, Denise M.; Nawaz, Ali; Wubet, Tesfaye; Buscot, François; Totsche, Kai-Uwe

2017-01-01

Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13CO2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO2, while archaeal autotrophy seems to be limited in the groundwater. PMID:28694737

30 CFR 250.801 - Subsurface safety devices.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions, hydrate formation, or paraffins, an alternate setting depth of the subsurface safety device may... conditions such as permafrost, unstable bottom conditions, hydrate formations, and paraffins. (g) Subsurface...

A geological model for the management of subsurface data in the urban environment of Barcelona and surrounding area

NASA Astrophysics Data System (ADS)

Vázquez-Suñé, Enric; Ángel Marazuela, Miguel; Velasco, Violeta; Diviu, Marc; Pérez-Estaún, Andrés; Álvarez-Marrón, Joaquina

2016-09-01

The overdevelopment of cities since the industrial revolution has shown the need to incorporate a sound geological knowledge in the management of required subsurface infrastructures and in the assessment of increasingly needed groundwater resources. Additionally, the scarcity of outcrops and the technical difficulty to conduct underground exploration in urban areas highlights the importance of implementing efficient management plans that deal with the legacy of heterogeneous subsurface information. To deal with these difficulties, a methodology has been proposed to integrate all the available spatio-temporal data into a comprehensive spatial database and a set of tools that facilitates the analysis and processing of the existing and newly added data for the city of Barcelona (NE Spain). Here we present the resulting actual subsurface 3-D geological model that incorporates and articulates all the information stored in the database. The methodology applied to Barcelona benefited from a good collaboration between administrative bodies and researchers that enabled the realization of a comprehensive geological database despite logistic difficulties. Currently, the public administration and also private sectors both benefit from the geological understanding acquired in the city of Barcelona, for example, when preparing the hydrogeological models used in groundwater assessment plans. The methodology further facilitates the continuous incorporation of new data in the implementation and sustainable management of urban groundwater, and also contributes to significantly reducing the costs of new infrastructures.

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.

Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments▿ †

PubMed Central

Futagami, Taiki; Morono, Yuki; Terada, Takeshi; Kaksonen, Anna H.; Inagaki, Fumio

2009-01-01

Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (rdhA) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem. PMID:19749069

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.

Microbial community structure and diversity within hypersaline Keke Salt Lake environments.

PubMed

Han, Rui; Zhang, Xin; Liu, Jing; Long, Qifu; Chen, Laisheng; Liu, Deli; Zhu, Derui

2017-11-01

Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%-58.35% relative abundance), Lactococcus (9.52%-10.51%), and Oceanobacillus (8.82%-9.88%) within the Firmicutes phylum (74.81%-80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai-Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg 2+ , Cl - , Na + , and K + ) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.

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.

Indications of Subsurface Ice: Polygons on the Northern Plains

NASA Technical Reports Server (NTRS)

1999-01-01

Someone's kitchen floor? A stone patio?This picture actually does show a floor--the floor of an old impact crater on the northern plains of Mars. Each 'tile' is somewhat larger than a football field. Polygonal patterns are familiar to Mars geologists because they are also common in arctic and antarctic environments on Earth. Typically, such polygons result from the stresses induced in frozen ground by the freeze-thaw cycles of subsurface ice. This picture was taken by MOC in May 1999 and is illuminated from the lower left.

The Search for Sustainable Subsurface Habitats on Mars, and the Sampling of Impact Ejecta

NASA Astrophysics Data System (ADS)

Ivarsson, Magnus; Lindgren, Paula

2010-07-01

On Earth, the deep subsurface biosphere of both the oceanic and the continental crust is well known for surviving harsh conditions and environments characterized by high temperatures, high pressures, extreme pHs, and the absence of sunlight. The microorganisms of the terrestrial deep biosphere have an excellent capacity for adapting to changing geochemistry, as the alteration of the crust proceeds and the conditions of their habitats slowly change. Despite an almost complete isolation from surface conditions and the surface biosphere, the deep biosphere of the crustal rocks has endured over geologic time. This indicates that the deep biosphere is a self-sufficient system, independent of the global events that occur at the surface, such as impacts, glaciations, sea level fluctuations, and climate changes. With our sustainable terrestrial subsurface biosphere in mind, the subsurface on Mars has often been suggested as the most plausible place to search for fossil Martian life, or even present Martian life. Since the Martian surface is more or less sterile, subsurface settings are the only place on Mars where life could have been sustained over geologic time. To detect a deep biosphere in the Martian basement, drilling is a requirement. However, near future Mars sample return missions are limited by the mission's payload, which excludes heavy drilling equipment and restrict the missions to only dig the topmost meter of the Martian soil. Therefore, the sampling and analysis of Martian impact ejecta has been suggested as a way of accessing the deeper Martian subsurface without using heavy drilling equipment. Impact cratering is a natural geological process capable of excavating and exposing large amounts of rock material from great depths up to the surface. Several studies of terrestrial impact deposits show the preservation of pre-impact biosignatures, such as fossilized organisms and chemical biological markers. Therefore, if the Martian subsurface contains a record

Microbial diversity in hydrothermal surface to subsurface environments of Suiyo Seamount, Izu-Bonin Arc, using a catheter-type in situ growth chamber.

PubMed

Higashi, Yowsuke; Sunamura, Michinari; Kitamura, Keiko; Nakamura, Ko-ichi; Kurusu, Yasurou; Ishibashi, Jun-ichiro; Urabe, Tetsuro; Maruyama, Akihiko

2004-03-01

After excavation using a portable submarine driller near deep-sea hydrothermal vents in the Suiyo Seamount, Izu-Bonin Arc, microbial diversity was examined in samples collected from inside the boreholes using an in situ growth chamber called a vent catheter. This instrument, which we devised for this study, consists of a heat-tolerant pipe tipped with a titanium mesh entrapment capsule that is packed with sterilized inorganic porous grains, which serve as an adhesion substrate. After this instrument was deployed inside each of the boreholes, as well as a natural vent, for 3-10 days in the vicinity of hot vent fluids (maxima: 156-305 degrees C), DNA was extracted from the adhesion grains, 16S rDNA was amplified, and randomly selected clones were sequenced. In phylogenetic analysis of more than 120 clones, several novel phylotypes were detected within the epsilon-Proteobacteria, photosynthetic bacteria (PSB)-related alpha-Proteobacteria, and Euryarchaeota clusters. Members of epsilon-Proteobacteria were frequently encountered. Half of these were classified between two known groups, Corre's B and D. The other half of the clones were assigned to new groups, SSSV-BE1 and SSSV-BE2 (Suiyo Seamount sub-vent origin, Bacteria domain, epsilon-Proteobacteria, groups 1 and 2). From this hydrothermal vent field, we detected a novel lineage within the PSB cluster, SSNV-BA1 (Suiyo Seamount natural vent origin, Bacteria domain, alpha-Proteobacteria, group 1), which is closely related to Rhodopila globiformis isolated from a hot spring. A number of archaeal clones were also detected from the borehole samples. These clones formed a novel monophyletic clade, SSSV-AE1 (Suiyo Seamount sub-vent origin, Archaea domain, Euryarchaeota, group 1), approximately between methanogenic hyperthermophilic members of Methanococcales and environmental clone members of DHVE Group II. Thus, this hydrothermal vent environment appears to be a noteworthy microbial and genetic resource. It is also

Understanding Subsurface Geoelectrical and Structural Constrains for Low Frequency Radar Sounding of Jovian Satellites

NASA Astrophysics Data System (ADS)

Heggy, Essam; Bruzzone, Lorenzo; Beck, Pierre; Doute, Sylvain; Gim, Youngyu; Herique, Alain; Kofman, Wlodek; Orosei, Roberto; Plaut, Jeffery; Rosen, Paul; Seu, Roberto

2010-05-01

Thermally stable Ice sheets on earth are known to be among the most favorable geophysical contexts for deep subsurface sounding radars. Penetrations ranging from few to several hundreds of meters have been observed at 10 to 60 MHz when sounding homogenous and pure ice sheets in Antarctica and in Alaskan glaciers. Unlike the terrestrial case, ice sheets on Jovian satellites are older formations with a more complex matrix of mineral inclusions with an even three dimensional distribution on the surface and subsurface that is yet to be understood in order to quantify its effect on the dielectric attenuation at the experiment sounding frequencies. Moreover, ridges, tectonic and shock features, may results in a complex and heterogeneous subsurface structure that can induce scattering attenuation with different amplitudes depending on the subsurface heterogeneity levels. Such attenuation phenomena's has to be accounted in the instrument design and future data analysis in order to optimize the science return, reduce mission risk and define proper operation modes. In order to address those challenges in the current performance studies and instrument design of the proposed radar sounding experiments, we present an attempt to quantify both the dielectric and scattering losses on both icy satellites, Ganymede and Europa, based on experimental dielectric characterization of relevant icy-dust mixtures samples, field work from analog environment and radar propagation simulations in parametric subsurface geophysical models representing potential geological scenarios of the two Jovian satellites. Our preliminary results suggest that the use of a dual band radar enable to overcome several of these constrains and reduces ambiguities associated subsurface interface mapping. Acknowledgement. This research is carried out by the Jet Propulsion Laboratory/Caltech, under a grant from the National Aeronautics and Space Administration.

Metabolic potential of a Novel Gram-Negative, Spore-forming, and Putatively Sulfate-Reducing Bacterium in the Continental Subsurface

NASA Astrophysics Data System (ADS)

Lau, C. Y. M.; Becraft, E. D.; Cason, E. D.; Borgonie, G.; Kieft, T. L.; Li, L.; van Heerden, E.; Jarett, J.; Woyke, T.; Stepanauskas, R.; Onstott, T. C.

2017-12-01

Anaerobic sulfate reduction is among the most thermodynamically favorable biochemical reactions in the deep subsurface environments. Phylogenetically and functionally diverse sulfate-reducing bacteria (SRB) within Deltaproteobacteria and Firmicutes have been reported. However, only few of them have been isolated in pure cultures for detailed physiological characterization. Previous studies showed that fracture fluid samples from the 1 km-deep borehole DR5IPC (Driefontein gold mine, South Africa) harbored novel SRB, as indicated by the low percentages (84% and 90%) of identity of the 16S ribosomal RNA clone sequences to known SRB. To overcome the challenge of low cultivability, we employed next-generation sequencing to unveil the metabolic potential of these novel SRB. Metagenomic assembly and binning yielded seven >50% complete genomes including a methylotrophic SRB belonging to Deltaproteobacteria (DR5_3) and two draft genomes representing an uncultivated phylum, tentatively "Driefonteinae" (DR5_4 and DR5_5). They accounted for 3%, 2% and 18% of all metagenomic reads. Three single-cell assembled genomes (SAGs) sharing 99% of average nucleotide identity (ANI) with DR5_5 were obtained. Analysis of the protein-coding genes in DR5_5 and related SAGs indicated that "Driefonteinae" possesses dissimilatory sulfite reductase genes (dsrAB), suggesting that sulfate would be the terminal electron acceptor. Whereas it may use diverse electron acceptors such as carbon monoxide, acetate, lactate and formate. A near-complete collection of genes for Wood-Ljungdahl pathway and genes for partial pentose phosphate pathway, glycolysis and tricarboxylic acid cycle further showed that "Driefonteinae" may live a mixotrophic life style. It is evident that archaeal genes related to methanogens were acquired through horizontal gene transfer. Phenotypically, "Driefonteinae" has a Gram-negative cell wall and flagella. The ability of forming spores would enable this microorganism to endure

Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments

NASA Astrophysics Data System (ADS)

Nixon, Sophie L.; Telling, Jon P.; Wadham, Jemma L.; Cockell, Charles S.

2017-03-01

Subglacial environments are known to harbour metabolically diverse microbial communities. These microbial communities drive chemical weathering of underlying bedrock and influence the geochemistry of glacial meltwater. Despite its importance in weathering reactions, the microbial cycling of iron in subglacial environments, in particular the role of microbial iron reduction, is poorly understood. In this study we address the prevalence of viable iron-reducing microorganisms in subglacial sediments from five geographically isolated glaciers. Iron-reducing enrichment cultures were established with sediment from beneath Engabreen (Norway), Finsterwalderbreen (Svalbard), Leverett and Russell glaciers (Greenland), and Lower Wright Glacier (Antarctica). Rates of iron reduction were higher at 4 °C compared with 15 °C in all but one duplicated second-generation enrichment culture, indicative of cold-tolerant and perhaps cold-adapted iron reducers. Analysis of bacterial 16S rRNA genes indicates Desulfosporosinus were the dominant iron-reducing microorganisms in low-temperature Engabreen, Finsterwalderbreen and Lower Wright Glacier enrichments, and Geobacter dominated in Russell and Leverett enrichments. Results from this study suggest microbial iron reduction is widespread in subglacial environments and may have important implications for global biogeochemical iron cycling and export to marine ecosystems.

Subsurface drainage processes and management impacts

Treesearch

Elizabeth T. Keppeler; David Brown

1998-01-01

Storm-induced streamflow in forested upland watersheds is linked to rainfall by transient, variably saturated flow through several different flow paths. In the absence of exposed bedrock, shallow flow-restrictive layers, or compacted soil surfaces, virtually all of the infiltrated rainfall reaches the stream as subsurface flow. Subsurface runoff can occur within...

Crystal structure of laser-induced subsurface modifications in Si

NASA Astrophysics Data System (ADS)

Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; Haberl, B.; Bradby, J. E.; Williams, J. S.; Huis in't Veld, A. J.

2015-08-01

Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this work, we investigate the geometry and crystal structure of laser-induced subsurface modifications in monocrystalline silicon wafers. In addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si -iii/Si -xii occur as a result of the laser irradiation.

75 FR 1276 - Requirements for Subsurface Safety Valve Equipment

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-11

...-0066] RIN 1010-AD45 Requirements for Subsurface Safety Valve Equipment AGENCY: Minerals Management... Edition of the American Petroleum Institute's Specification for Subsurface Safety Valve Equipment (API... 14A, Specification for Subsurface Safety Valve Equipment, Eleventh Edition, October 2005, Effective...

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

Field Simulation of a Drilling Mission to Mars to Search for Subsurface Life

NASA Technical Reports Server (NTRS)

Stoker, C. R.; Lemke, L. G.; Cannon, H.; Glass, B.; Dunagan, S.; Zavaleta, J.; Miller, D.; Gomez-Elvira, J.

2005-01-01

The discovery of near surface ground ice by the Mars Odyssey mission and the abundant evidence for recent Gulley features observed by the Mars Global Surveyor mission support longstanding theoretical arguments for subsurface liquid water on Mars. Thus, implementing the Mars program goal to search for life points to drilling on Mars to reach liquid water, collecting samples and analyzing them with instrumentation to detect in situ organisms and biomarker compounds. Searching for life in the subsurface of Mars will require drilling, sample extraction and handling, and new technologies to find and identify biomarker compounds and search for living organisms. In spite of its obvious advantages, robotic drilling for Mars exploration is in its technological infancy and has yet to be demonstrated in even a terrestrial field environment.

Crystal structure of laser-induced subsurface modifications in Si

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

Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.

2015-06-04

Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystalmore » structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.« less

SEMINAR PUBLICATION: SITE CHARACTERIZATION FOR SUBSURFACE REMEDIATION

EPA Science Inventory

This seminar publication provides a comprehensive approach to site characterization for subsurface remediation. Chapter 1 describes a methodology for integrating site characterization with subsurface remediation. The rest of the handbook is divided into three parts. Part I covers...

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

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

PubMed Central

Kubo, Kyoko; Lloyd, Karen G; F Biddle, Jennifer; Amann, Rudolf; Teske, Andreas; Knittel, Katrin

2012-01-01

Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes. PMID:22551871

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

Potential Physiologies of Deep Branches on the Tree of Life with Deep Subsurface Samples from IODP Leg 347: Baltic Sea Paleoenvironment

NASA Astrophysics Data System (ADS)

Lloyd, K. G.; Bird, J. T.; Shumaker, A.

2014-12-01

Very little is known about how evolutionary branches that are distantly related to cultured microorganisms make a living in the deep subsurface marine environment. Here, sediments are cut-off from surface inputs of organic substrates for tens of thousands of years; yet somehow support a diverse population of microorganisms. We examined the potential metabolic and ecological roles of uncultured archaea and bacteria in IODP Leg 347: Baltic Sea Paleoenvironment samples, using quantitative PCR holes 60B, 63E, 65C, and 59C and single cell genomic analysis for hole 60B. We quantified changes in total archaea and bacteria, as well as deeply-branching archaeal taxa with depth. These sediment cores alternate between high and low salinities, following a glacial cycle. This allows changes in the quantities of these groups to be placed in the context of potentially vastly different organic matter sources. In addition, single cells were isolated, and their genomes were amplified and sequenced to allow a deeper look into potential physiologies of uncultured deeply-branching organisms found up to 86 meters deep in marine sediments. Together, these data provide deeper insight into the relationship between microorganisms and their organic matter substrates in this extreme environments.

Improved measurement of extracellular enzymatic activities in subsurface sediments using competitive desorption treatment

NASA Astrophysics Data System (ADS)

Hoarfrost, Adrienne; Snider, Rachel; Arnosti, Carol

2017-02-01

Extracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments.

Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE)

PubMed Central

Knapp, Emily A.; Nau, Claudia; Brandau, Sy; DeWalle, Joseph; Hirsch, Annemarie G.; Bailey-Davis, Lisa; Schwartz, Brian S.; Glass, Thomas A.

2017-01-01

There are currently no direct observation environmental audit tools that measure diverse aspects of the obesity-related environment efficiently and reliably in a variety of geographical settings. The goal was to develop a new instrument to reliably characterize the overall properties and features of rural, suburban, and urban settings along multiple dimensions. The Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE) is an iPad-based instrument that incorporates global positioning system coordinates and photography and is comprised of 214 items yielding 7 summary indices. A comprehensive spatial sampling strategy, training manual, and supporting data analysis code were also developed. Random geospatial sampling using GIS was used to captured features of the community as a whole. A single auditor collected 510 observation points in 30 communities (2013–2015). This analysis was done in 2015–2016. Correlation coefficients were used to compare items and indices to each other and to standard measures. Multilevel unconditional means models were used to calculate intraclass correlation coefficients (ICC) to determine if there was significant variation between communities. Results suggest that CASCADDE measures aspects of communities not previously captured by secondary data sources. Additionally, 7 summary indices capture meaningful differences between communities based on 15 observations per community. Community audit tools such as CASCADDE complement secondary data sources and have the potential to offer new insights about the mechanisms through which communities affect obesity and other health outcomes. PMID:28209283

Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE).

PubMed

Knapp, Emily A; Nau, Claudia; Brandau, Sy; DeWalle, Joseph; Hirsch, Annemarie G; Bailey-Davis, Lisa; Schwartz, Brian S; Glass, Thomas A

2017-04-01

There are currently no direct observation environmental audit tools that measure diverse aspects of the obesity-related environment efficiently and reliably in a variety of geographic settings. The goal was to develop a new instrument to reliably characterize the overall properties and features of rural, suburban, and urban settings along multiple dimensions. The Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE) is an iPad-based instrument that incorporates GPS coordinates and photography and comprises 214 items yielding seven summary indices. A comprehensive spatial sampling strategy, training manual, and supporting data analysis code were also developed. Random geospatial sampling using GIS was used to capture features of the community as a whole. A single auditor collected 510 observation points in 30 communities (2013-2015). This analysis was done in 2015-2016. Correlation coefficients were used to compare items and indices to each other and to standard measures. Multilevel unconditional means models were used to calculate intraclass correlation coefficients to determine if there was significant variation between communities. Results suggest that CASCADDE measures aspects of communities not previously captured by secondary data sources. Additionally, seven summary indices capture meaningful differences between communities based on 15 observations per community. Community audit tools such as CASCADDE complement secondary data sources and have the potential to offer new insights about the mechanisms through which communities affect obesity and other health outcomes. Copyright © 2017 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

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.

Environment degeneration affects habitat diversity of Tamarix spp. in arid zone

NASA Astrophysics Data System (ADS)

Li, Tiejun; Yang, Weikang

2003-07-01

There are 18 species of Tamarix spp. in China and 16 of them in Xinjiang. As a group of bushes which widespread in salty and sandy land in arid zone, Tamarix spp. had gotten more and more attention by ecologists because of their unique bio-ecological characteristics, ecological and social economy functions. Wide Distribution of Tamarix spp. affects ecological environment stabilization of arid zone in western China. The modern distribution and habitat of Tamarix spp. diversity in Xinjiang were studied in this paper. Result revealed that water (surface water and high groundwater ) is the critical environment factor which determines the modern distribution of Tamarix spp.. Depend on analyzing groundwater lever and salt content of soil(two environment factors), author divided the habitat of Tamarix spp. into six type groups (low salt type with high groundwater, middle salt type with high groundwater, high salt type with high groundwater, low salt type with low groundwater and middle salt type with low groundwater etc.) which consisting of ten habitat types. Habitat of Tamarix spp. in Xinjiang never exists in isolation, but associate with each other. The groundwater lever and salt content of soil varies with the lapse of time, then habitats transform from one type into another and species of Tamarix spp. in habitats transforms accordingly.

Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site

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

Truex, Michael J.; Lee, Brady D.; Johnson, Christian D.

Isotopes of iodine were generated during plutonium production within the nine production reactors at the U.S. Department of Energy Hanford Site. The short half-life 131I that was released from the fuel into the atmosphere during the dissolution process (when the fuel was dissolved) in the Hanford Site 200 Area is no longer present at concentrations of concern in the environment. The long half-life 129I generated at the Hanford Site during reactor operations was (1) stored in single-shell and double-shell tanks, (2) discharged to liquid disposal sites (e.g., cribs and trenches), (3) released to the atmosphere during fuel reprocessing operations, ormore » (4) captured by off-gas absorbent devices (silver reactors) at chemical separations plants (PUREX, B-Plant, T-Plant, and REDOX). Releases of 129I to the subsurface have resulted in several large, though dilute, plumes in the groundwater. There is also 129I remaining in the vadose zone beneath disposal or leak locations. The fate and transport of 129I in the environment and potential remediation technologies are currently being studied as part of environmental remediation activities at the Hanford Site. A conceptual model describing the nature and extent of subsurface contamination, factors that control plume behavior, and factors relevant to potential remediation processes is needed to support environmental remedy decisions. Because 129I is an uncommon contaminant, relevant remediation experience and scientific literature are limited. In addition, its behavior in subsurface is different from that of other more common and important contaminants (e.g., U, Cr and Tc) in terms of sorption (adsorption and precipitation), and aqueous phase species transformation via redox reactions. Thus, the conceptual model also needs to both describe known contaminant and biogeochemical process information and identify aspects about which additional information is needed to effectively support remedy decisions.« less

Subsurface characterization by the ground penetrating radar WISDOM/ExoMars 2020

NASA Astrophysics Data System (ADS)

Hervé, Y.; Ciarletti, V.; Le Gall, A. A.; Oudart, N.; Loizeau, D.; Guiffaut, C.; Dorizon, S.

2017-12-01

The main objective of the ExoMars 2020 mission is to search for signs of past and/or present life on Mars. Toward this goal, a rover was designed to investigate the shallow subsurface which is the most likely place where signs of life may be preserved, beneath the hostile surface of Mars. The rover of the ExoMars 2020 mission has on board a polarimetric ground penetrating radar called WISDOM (Water Ice Subsurface Deposits Observation on Mars). Thanks to its large frequency bandwidth of 2.5 GHz, WISDOM is able to probe down to a depth of approximately 3 m on sedimentary rock with a vertical resolution of a few centimeters.The main scientific objectives of WISDOM are to characterize the shallow subsurface of Mars, to help understand the local geological context and to identify the most promising location for drilling. The WISDOM team is currently working on the preparation of the scientific return of the ExoMars 2020 mission. In particular, tools are developed to interpret WISDOM experimental data and, more specifically, to extract information from the radar signatures of expected buried reflectors. Insights into the composition of the ground (through the retrieval of its permittivity) and the geological context of the site can be inferred from the radar signature of buried rocks since the shape and the density of rocks in the subsurface is related to the geological processes that have shaped and placed them there (impact, fluvial processes, volcanism). This paper presents results obtained by automatic detection of structures of interest on a radargram, especially radar signature of buried rocks. The algorithm we developed uses a neural network to identify the position of buried rocks/blocs and then a Hough transform to characterize each signature and to estimate the local permittivity of the medium. Firstly, we will test the performances of the algorithm on simulated data constructed with a 3D FDTD code. This code allows us to simulate radar operation in realistic

Subsurface high resolution definition of subsurface heterogeneity for understanding the biodynamics of natural field systems: Advancing the ability for scaling to field conditions. 1998 annual progress report

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

Majer, E.L.; Brockman, F.J.

1998-06-01

'This research is an integrated physical (geophysical and hydrologic) and microbial study using innovative geophysical imaging and microbial characterization methods to identify key scales of physical heterogeneities that affect the biodynamics of natural subsurface environments. Data from controlled laboratory and in-situ experiments at the INEEL Test Area North (TAN) site are being used to determine the dominant physical characteristics (lithologic, structural, and hydrologic) that can be imaged in-situ and correlated with microbial properties. The overall goal of this research is to contribute to the understanding of the interrelationships between transport properties and spatially varying physical, chemical, and microbiological heterogeneity. Themore » outcome will be an improved understanding of the relationship between physical and microbial heterogeneity, thus facilitating the design of bioremediation strategies in similar environments. This report summarizes work as of May 1998, the second year of the project. This work is an extension of basic research on natural heterogeneity first initiated within the DOE/OHER Subsurface Science Program (SSP) and is intended to be one of the building blocks of an integrated and collaborative approach with an INEEL/PNNL effort aimed at understanding the effect of physical heterogeneity on transport properties and biodynamics in natural systems. The work is closely integrated with other EMSP projects at INEEL (Rick Colwell et al.) and PNNL (Fred Brockman and Jim Fredrickson).'« less

10 CFR 39.45 - Subsurface tracer studies.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Subsurface tracer studies. 39.45 Section 39.45 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.45 Subsurface tracer studies. (a) The licensee shall require all personnel handling radioactive...

10 CFR 39.45 - Subsurface tracer studies.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Subsurface tracer studies. 39.45 Section 39.45 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.45 Subsurface tracer studies. (a) The licensee shall require all personnel handling radioactive...

Sorption and oxic degradation of the explosive CL-20 during transport in subsurface sediments.

PubMed

Szecsody, J E; Girvin, D C; Devary, B J; Campbell, J A

2004-08-01

The abiotic sorption and oxic degradation processes that control the fate of the explosive CL-20, Hexanitrohexaazaisowurtzitane, in the subsurface environment were investigated to determine the potential for vadose and groundwater contamination. Sorption of aqueous CL-20 is relatively small (K(d) = 0.02-3.83 cm3 g(-1) for 7 sediments and 12 minerals), which results in only slight retardation relative to water movement. Thus, CL-20 could move quickly through unsaturated and saturated sediments of comparable composition to groundwater, similar to the subsurface behavior of RDX. CL-20 sorption was mainly to mineral surfaces of the sediments, and the resulting isotherm was nonlinear. CL-20 abiotically degrades in oxic environments at slow rates (i.e., 10s to 100s of hours) with a wide variety of minerals, but at fast rates (i.e., minutes) in the presence of 2:1 phyllosilicate clays (hectorite, montmorillonite, nontronite), micas (biotite, illite), and specific oxides (MnO2 and the ferrous-ferric iron oxide magnetite). High concentrations of surface ferrous iron in a dithionite reduced sediment degraded CL-20 the fastest (half-life < 0.05 h), but 2:1 clays containing no structural or adsorbed ferrous iron (hectorite) could also quickly degrade CL-20 (half-life < 0.2 h). CL-20 degradation rates were slower in natural sediments (half-life 3-800 h) compared to minerals. Sediments with slow degradation rates and small sorption would exhibit the highest potential for deep subsurface migration. Products of CL-20 oxic degradation included three high molecular weight compounds and anions (nitrite and formate). The 2-3.5 moles of nitrite produced suggest CL-20 nitro-groups are degraded, and the amount of formate produced (0.2-1.2 moles) suggests the CL-20 cage structure is broken in some sediments. Identification of further degradation products and CL-20 mineralization rates is needed to fully assess the impact of these CL-20 transformation rates on the risk of CL-20 (and

Microbial-sized, carboxylate-modified microspheres as surrogate tracers in a variety of subsurface environments: An overview

USGS Publications Warehouse

Harvey, Ronald W.; Metge, David W.; LeBlanc, Denis R.

2017-01-01

Since 1986, fluorescent carboxylate-modified polystyrene/latex microspheres (FCM) have been co-injected into aquifers along with conservative tracers and viruses, bacteria, and (or) protozoa. Use of FCM has resulted in new information about subsurface transport behaviors of microorganisms in fractured crystalline rock, karst limestone, soils, and granular aquifers. FCM have been used as surrogates for oocysts of the pathogenic protist Cryptosporidium parvum in karst limestone and granular drinking-water aquifers. The advantages of FCM in subsurface transport studies are that they are safe in tracer applications, negatively charged, easy to detect, chemically inert, and available in wide range of sizes. The limitations of FCM are that the quantities needed for some field transport studies can be prohibitively expensive and that their surface characteristics may not match the microorganisms of interest. These limitations may be ameliorated, in part by using chemically modified FCM so that their surface characteristics are a better match to that of the organisms. Also, more sensitive methods of detection may allow using smaller quantities of FCM. To assess how the transport behaviors of FCM and pathogens might compare at the field scale, it is helpful to conduct side-by-side comparisons of their transport behaviors using the geologic media and site-specific conditions that characterize the field site.

BioDiversity.

ERIC Educational Resources Information Center

Wilson, E. O., Ed.; Peter, Frances M., Ed.

The diversity of life forms is one of the greatest wonders of the planet earth. The biosphere is an intricate tapestry of interwoven life forms. This book offers an overall view of this biological diversity and carries an urgent warning about the rapid alteration and destruction of the environments that have fostered the diversity of life forms…

Phytoplankton diversity in the Upper Paraná River floodplain during two years of drought (2000 and 2001).

PubMed

Borges, P A F; Train, S

2009-06-01

Floodplain lakes and lotic environments of the High Paraná River floodplain present notable biodiversity, especially in relation to phytoplanktonic community. The goal of this work was to evaluate phytoplankton diversity (alpha, beta and gamma) in three subsystems during two years of drought (2000 and 2001). We sampled 33 habitats at the pelagic zone subsurface during February and August. Due to low hydrometric levels of the Paraná and Ivinhema Rivers, there was no clear distinction between the potamophase and limnophase periods for the two hydrosedimentological cycles analysed. We recorded 366 taxa. The values obtained for gamma diversity estimators ranged from 55.5-87.8%. DCA and variance analyses revealed only spatial differences in the phytoplankton composition. The mean values of species richness, evenness and Shannon diversity were low, especially when compared to those obtained in previous periods for Baía subsystem. The highest mean values of species richness were verified in the connected floodplain lakes. The highest beta diversity was obtained from the Paraná subsystem and lotic environments in 2001. In general, we observed that the Upper Paraná River floodplain has the highest values of species richness, evenness and H' during the potamophase period, when the flood facilitates dispersion. However, this pattern was not observed in 2000 and 2001, years influenced by La Niña. Besides the low precipitation observed during that period, we must consider the influence of the Porto Primavera impoundment, which also altered the discharge regime of the Paraná River by decreasing the degree of connectivity between fluvial channels and the lentic environments of the floodplain. Thus, the prevalence of conditions characterising the limnophase during 2000 and 2001 explains the lack of significant variability registered for most components of phytoplankton diversity over the study period. We conclude that variations in phytoplankton diversity during the study

10 CFR 39.45 - Subsurface tracer studies.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Subsurface tracer studies. 39.45 Section 39.45 Energy....45 Subsurface tracer studies. (a) The licensee shall require all personnel handling radioactive tracer material to use protective gloves and, if required by the license, other protective clothing and...

10 CFR 39.45 - Subsurface tracer studies.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Subsurface tracer studies. 39.45 Section 39.45 Energy....45 Subsurface tracer studies. (a) The licensee shall require all personnel handling radioactive tracer material to use protective gloves and, if required by the license, other protective clothing and...

10 CFR 39.45 - Subsurface tracer studies.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Subsurface tracer studies. 39.45 Section 39.45 Energy....45 Subsurface tracer studies. (a) The licensee shall require all personnel handling radioactive tracer material to use protective gloves and, if required by the license, other protective clothing and...

Holocene evolution of the North Atlantic subsurface transport

NASA Astrophysics Data System (ADS)

Repschläger, Janne; Garbe-Schönberg, Dieter; Weinelt, Mara; Schneider, Ralph

2017-04-01

Previous studies suggested that short-term freshening events in the subpolar gyre can be counterbalanced by advection of saline waters from the subtropical gyre and thus stabilize the Atlantic Meridional Overturning Circulation (AMOC). However, little is known about the inter-gyre transport pathways. Here, we infer changes in surface and subsurface transport between the subtropical and polar North Atlantic during the last 11 000 years, by combining new temperature and salinity reconstructions obtained from combined δ18O and Mg / Ca measurements on surface and subsurface dwelling foraminifera with published foraminiferal abundance data from the subtropical North Atlantic, and with salinity and temperature data from the tropical and subpolar North Atlantic. This compilation implies an overall stable subtropical warm surface water transport since 10 ka BP. In contrast, subsurface warm water transport started at about 8 ka but still with subsurface heat storage in the subtropical gyre. The full strength of intergyre exchange was probably reached only after the onset of northward transport of warm saline subsurface waters at about 7 ka BP, associated with the onset of the modern AMOC mode. A critical evaluation of different potential forcing mechanisms leads to the assumption that freshwater supply from the Laurentide Ice Sheet was the main control on subtropical to subpolar ocean transport at surface and subsurface levels.

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

Age, environment, object recognition and morphological diversity of GFAP-immunolabeled astrocytes.

PubMed

Diniz, Daniel Guerreiro; de Oliveira, Marcus Augusto; de Lima, Camila Mendes; Fôro, César Augusto Raiol; Sosthenes, Marcia Consentino Kronka; Bento-Torres, João; da Costa Vasconcelos, Pedro Fernando; Anthony, Daniel Clive; Diniz, Cristovam Wanderley Picanço

2016-10-10

and that the detrimental effects of aging on memory in mice from a standard environment may be associated with a reduction of astrocytes morphological diversity.

The Design and Implementation of Instruments for Low-Frequency Electromagnetic Sounding of the Martian Subsurface

NASA Technical Reports Server (NTRS)

Delory, G. T.; Grimm, R. E.

2003-01-01

Low-frequency electromagnetic soundings of the subsurface can identify liquid water at depths ranging from hundreds of meters to approx. 10 km in an environment such as Mars. Among the tools necessary to perform these soundings are low-frequency electric and magnetic field sensors capable of being deployed from a lander or rover such that horizontal and vertical components of the fields can be measured free of structural or electrical interference. Under a NASA Planetary Instrument Definition and Development Program (PIDDP), we are currently engaged in the prototype stages of low frequency sensor implementations that will enable this technique to be performed autonomously within the constraints of a lander platform. Once developed, this technique will represent both a complementary and alternative method to orbital radar sounding investigations, as the latter may not be able to identify subsurface water without significant ambiguities. Low frequency EM methods can play a crucial role as a ground truth measurement, performing deep soundings at sites identified as high priority areas by orbital radars. Alternatively, the penetration depth and conductivity discrimination of low-frequency methods may enable detection of subsurface water in areas that render radar methods ineffective. In either case, the sensitivity and depth of penetration inherent in low frequency EM exploration makes this tool a compelling candidate method to identify subsurface liquid water from a landed platform on Mars or other targets of interest.

Comparative isolation and genetic diversity of Arcobacter sp. from fish and the coastal environment.

PubMed

Rathlavath, S; Kumar, S; Nayak, B B

2017-07-01

Arcobacter species are emerging food-borne and water-borne human pathogens associated mostly with food animals and their environment. The present study was aimed to isolate Arcobacter species from fish, shellfish and coastal water samples using two methods and to determine their genetic diversity. Of 201 samples of fish, shellfish and water samples analysed, 66 (32·8%) samples showed the presence of Arcobacter DNA from both Arcobacter enrichment broth and Bolton broth. Arcobacters were isolated from 58 (87·8%) and 38 (57·5%) of Arcobacter DNA-positive samples using Arcobacter blood agar and Preston blood agar, respectively. Arcobacter sp. identified by biochemical tests were further analysed by a genus-specific PCR, followed by a multiplex-PCR and 16S rRNA-RFLP. From both the methods, four different Arcobacter species namely Arcobacter butzleri, Arcobacter skirrowii, Arcobacter mytili and Arcobacter defluvii were isolated, of which A. butzleri was the predominant species. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprint analysis revealed that the arcobacters isolated in this study were genetically very diverse and no specific genotype was found associated with a specific source (seafood or water). Since pathogenic arcobacters are not known to be natural inhabitants of coastal marine environment, identifying the sources of contamination will be crucial for effective management of this problem. Arcobacter sp. are emerging food- and water-borne human pathogens. In this study, comparison of two selective media suggested Arcobacter blood agar to be more efficient in yielding Arcobacter sp. from seafood. Furthermore, the isolation of Arcobacter sp. such as Arcobacter butzleri, A. skirrowii, A. mytili and A. defluvii from seafood suggests diverse sources of contamination of seafood by Arcobacter sp. Analysis of enterobacterial repetitive intergenic consensus sequence-PCR patterns of A. butzleri showed high genetic diversity and lack of clonality

Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines)

PubMed Central

Woycheese, Kristin M.; Meyer-Dombard, D'Arcy R.; Cardace, Dawn; Argayosa, Anacleto M.; Arcilla, Carlo A.

2015-01-01

In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca2+-OH−-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO2) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep's source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes. PMID:25745416

Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines).

PubMed

Woycheese, Kristin M; Meyer-Dombard, D'Arcy R; Cardace, Dawn; Argayosa, Anacleto M; Arcilla, Carlo A

2015-01-01

In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca(2+)-OH(-)-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO2) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep's source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes.

Predictability of Subsurface Temperature and the AMOC

NASA Astrophysics Data System (ADS)

Chang, Y.; Schubert, S. D.

2013-12-01

GEOS 5 coupled model is extensively used for experimental decadal climate prediction. Understanding the limits of decadal ocean predictability is critical for making progress in these efforts. Using this model, we study the subsurface temperature initial value predictability, the variability of the Atlantic meridional overturning circulation (AMOC) and its impacts on the global climate. Our approach is to utilize the idealized data assimilation technology developed at the GMAO. The technique 'replay' allows us to assess, for example, the impact of the surface wind stresses and/or precipitation on the ocean in a very well controlled environment. By running the coupled model in replay mode we can in fact constrain the model using any existing reanalysis data set. We replay the model constraining (nudging) it to the MERRA reanalysis in various fields from 1948-2012. The fields, u,v,T,q,ps, are adjusted towards the 6-hourly analyzed fields in atmosphere. The simulated AMOC variability is studied with a 400-year-long segment of replay integration. The 84 cases of 10-year hindcasts are initialized from 4 different replay cycles. Here, the variability and predictability are examined further by a measure to quantify how much the subsurface temperature and AMOC variability has been influenced by atmospheric forcing and by ocean internal variability. The simulated impact of the AMOC on the multi-decadal variability of the SST, sea surface height (SSH) and sea ice extent is also studied.

Defining the Post-Machined Sub-surface in Austenitic Stainless Steels

NASA Astrophysics Data System (ADS)

Srinivasan, N.; Sunil Kumar, B.; Kain, V.; Birbilis, N.; Joshi, S. S.; Sivaprasad, P. V.; Chai, G.; Durgaprasad, A.; Bhattacharya, S.; Samajdar, I.

2018-04-01

Austenitic stainless steels grades, with differences in chemistry, stacking fault energy, and thermal conductivity, were subjected to vertical milling. Anodic potentiodynamic polarization was able to differentiate (with machining speed/strain rate) between different post-machined sub-surfaces in SS 316L and Alloy A (a Cu containing austenitic stainless steel: Sanicroe 28™), but not in SS 304L. However, such differences (in the post-machined sub-surfaces) were revealed in surface roughness, sub-surface residual stresses and misorientations, and in the relative presence of sub-surface Cr2O3 films. It was shown, quantitatively, that higher machining speed reduced surface roughness and also reduced the effective depths of the affected sub-surface layers. A qualitative explanation on the sub-surface microstructural developments was provided based on the temperature-dependent thermal conductivity values. The results herein represent a mechanistic understanding to rationalize the corrosion performance of widely adopted engineering alloys.

Defining the Post-Machined Sub-surface in Austenitic Stainless Steels

NASA Astrophysics Data System (ADS)

Srinivasan, N.; Sunil Kumar, B.; Kain, V.; Birbilis, N.; Joshi, S. S.; Sivaprasad, P. V.; Chai, G.; Durgaprasad, A.; Bhattacharya, S.; Samajdar, I.

2018-06-01

Austenitic stainless steels grades, with differences in chemistry, stacking fault energy, and thermal conductivity, were subjected to vertical milling. Anodic potentiodynamic polarization was able to differentiate (with machining speed/strain rate) between different post-machined sub-surfaces in SS 316L and Alloy A (a Cu containing austenitic stainless steel: Sanicroe 28™), but not in SS 304L. However, such differences (in the post-machined sub-surfaces) were revealed in surface roughness, sub-surface residual stresses and misorientations, and in the relative presence of sub-surface Cr2O3 films. It was shown, quantitatively, that higher machining speed reduced surface roughness and also reduced the effective depths of the affected sub-surface layers. A qualitative explanation on the sub-surface microstructural developments was provided based on the temperature-dependent thermal conductivity values. The results herein represent a mechanistic understanding to rationalize the corrosion performance of widely adopted engineering alloys.

Temporally variable environments maintain more beta-diversity in Mediterranean landscapes

NASA Astrophysics Data System (ADS)

Martin, Beatriz; Ferrer, Miguel

2015-10-01

We examined the relationships between different environmental factors and the alpha and beta-diversity of terrestrial vertebrates (birds, mammals, amphibians and reptiles) in a Mediterranean region at the landscape level. We investigated whether the mechanisms underlying alpha and beta-diversity patterns are influenced by energy availability, habitat heterogeneity and temporal variability and if the drivers of the diversity patterns differed between both components of diversity. We defined alpha-diversity as synonym of species richness whereas beta-diversity was measured as distinctiveness. We evaluated a total of 13 different predictors using generalized linear mixed model (GLMM) analysis. Habitat spatial heterogeneity increased alpha-diversity, but contrastingly, it did not significantly affect beta-diversity among sites. Disturbed landscapes may show higher habitat spatial variation and higher alpha-diversity due to the contribution of highly generalist species that are wide-distributed and do not differ in composition (beta-diversity) among different sites within the region. Contrastingly, higher beta-diversity levels were negatively related to more stable sites in terms of temporal environmental variation. This negative relationship between environmental stability and beta-diversity levels is explained in terms of species adaptation to the local environmental conditions. Our study highlights the importance of temporal environmental variability in maintaining beta-diversity patterns under highly variable environmental conditions.

Subsurface Ice Probe

NASA Technical Reports Server (NTRS)

Hecht, Michael; Carsey, Frank

2005-01-01

The subsurface ice probe (SIPR) is a proposed apparatus that would bore into ice to depths as great as hundreds of meters by melting the ice and pumping the samples of meltwater to the surface. Originally intended for use in exploration of subsurface ice on Mars and other remote planets, the SIPR could also be used on Earth as an alternative to coring, drilling, and melting apparatuses heretofore used to sample Arctic and Antarctic ice sheets. The SIPR would include an assembly of instrumentation and electronic control equipment at the surface, connected via a tether to a compact assembly of boring, sampling, and sensor equipment in the borehole (see figure). Placing as much equipment as possible at the surface would help to attain primary objectives of minimizing power consumption, sampling with high depth resolution, and unobstructed imaging of the borehole wall. To the degree to which these requirements would be satisfied, the SIPR would offer advantages over the aforementioned ice-probing systems.

Method for Implementing Subsurface Solid Derived Concentration Guideline Levels (DCGL) - 12331

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

Lively, J.W.

2012-07-01

The U.S. Nuclear Regulatory Commission (NRC) and other federal agencies currently approve the Multi-Agency Radiation Site Survey and Investigation Manual (MARSSIM) as guidance for licensees who are conducting final radiological status surveys in support of decommissioning. MARSSIM provides a method to demonstrate compliance with the applicable regulation by comparing residual radioactivity in surface soils with derived concentration guideline levels (DCGLs), but specifically discounts its applicability to subsurface soils. Many sites and facilities undergoing decommissioning contain subsurface soils that are potentially impacted by radiological constituents. In the absence of specific guidance designed to address the derivation of subsurface soil DCGLs andmore » compliance demonstration, decommissioning facilities have attempted to apply DCGLs and final status survey techniques designed specifically for surface soils to subsurface soils. The decision to apply surface soil limits and surface soil compliance metrics to subsurface soils typically results in significant over-excavation with associated cost escalation. MACTEC, Inc. has developed the overarching concepts and principles found in recent NRC decommissioning guidance in NUREG 1757 to establish a functional method to derive dose-based subsurface soil DCGLs. The subsurface soil method developed by MACTEC also establishes a rigorous set of criterion-based data evaluation metrics (with analogs to the MARSSIM methodology) that can be used to demonstrate compliance with the developed subsurface soil DCGLs. The method establishes a continuum of volume factors that relate the size and depth of a volume of subsurface soil having elevated concentrations of residual radioactivity with its ability to produce dose. The method integrates the subsurface soil sampling regime with the derivation of the subsurface soil DCGL such that a self-regulating optimization is naturally sought by both the responsible party and

Evidence for biological activity in mineralization of secondary sulphate deposits in a basaltic environment: implications for the search for life in the Martian subsurface

NASA Astrophysics Data System (ADS)

Richardson, C. Doc; Hinman, Nancy W.; Scott, Jill R.

2013-10-01

Evidence of microbial activity associated with mineralization of secondary Na-sulphate minerals (thenardite, mirabilite) in the basaltic subsurface of Craters of the Moon National Monument (COM), Idaho were examined by scanning electron microscopy, X-ray diffraction, laser desorption Fourier transform ion cyclotron resonance mass spectrometry (LD-FTICR-MS), Fourier transform infrared spectroscopy (FTIR) and isotope ratio mass spectrometry. Peaks suggestive of bio/organic compounds were observed in the secondary Na-sulphate deposits by LD-FTICR-MS. FTIR provided additional evidence for the presence of bio/organic compounds. Sulphur fractionation was explored to assist in determining if microbes may play a role in oxidizing sulphur. The presence of bio/organic compounds associated with Na-sulphate deposits, along with the necessity of oxidizing reduced sulphur to sulphate, suggests that biological activity may be involved in the formation of these secondary minerals. The secondary Na-sulphate minerals probably form from the overlying basalt through leached sodium ions and sulphate ions produced by bio-oxidation of Fe-sulphide minerals. Since the COM basalts are one of the most comparable terrestrial analogues for their Martian counterparts, the occurrence of biological activity in the formation of sulphate minerals at COM has direct implications for the search for life on Mars. In addition, the presence of caves on Mars suggests the importance of these environments as possible locations for growth and preservation of microbial activity. Therefore, understanding the physiochemical pathways of abiotic and biotic mineralization in the COM subsurface and similar basaltic settings has direct implications for the search for extinct or extant life on Mars.

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.

Mineralogical Control on Microbial Diversity in a Weathered Granite?

NASA Astrophysics Data System (ADS)

Gleeson, D.; Clipson, N.; McDermott, F.

2003-12-01

Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that

Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

PubMed Central

Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

2016-01-01

Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea’s genetic data sources. PMID:27446038

A Search for Life in the Subsurface At Rio Tinto Spain, An Analog To Searching For Life On Mars.

NASA Astrophysics Data System (ADS)

Stoker, C. R.

2003-12-01

Most familiar life forms on Earth live in the surface biosphere where liquid water, sunlight, and the essential chemical elements for life are abundant. However, such environments are not found on Mars or anywhere else in the solar system. On Mars, the surface environmental conditions of pressure and temperature prevent formation of liquid water. Furthermore, conditions at the Martian surface are unfavorable to life due to intense ultraviolet radiation and strong oxidizing compounds that destroy organic compounds. However, subsurface liquid water on Mars has been predicted on theoretical grounds. The recent discovery of near surface ground ice by the Mars Odyssey mission, and the abundant evidence for recent Gully features observed by the Mars Global Surveyor mission strengthen the case for subsurface liquid water on Mars. Thus, the strategy for searching for life on Mars points to drilling to the depth of liquid water, bringing samples to the surface and analyzing them with instrumentation to detect in situ organisms and biomarker compounds. The MARTE (Mars Astrobiology Research and Technology Experiment) project is a field experiment focused on searching for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Rio Tinto, a river in southwestern Spain while also demonstrating technology relevant to searching for a subsurface biosphere on Mars. The Tinto river is located in the Iberian Pyrite belt, one of the largest deposits of sulfide minerals in the world. The surface (river) system is an acidic extreme environment produced and maintained by microbes that metabolize sulfide minerals and produce sulfuric acid as a byproduct. Evidence suggests that the river is a surface manifestation of an underground biochemical reactor. Organisms found in the river are capable of chemoautotrophic metabolism using sulfide and ferric iron mineral substrates, suggesting these organisms could thrive in groundwater which is the source of the Rio Tinto

DNA barcoding reveals diversity of Hymenoptera and the dominance of parasitoids in a sub-arctic environment

PubMed Central

2013-01-01

Background Insect diversity typically declines with increasing latitude, but previous studies have shown conflicting latitude-richness gradients for some hymenopteran parasitoids. However, historical estimates of insect diversity and species richness can be difficult to confirm or compare, because they may be based upon dissimilar methods. As a proxy for species identification, we used DNA barcoding to identify molecular operational taxonomic units (MOTUs) for 7870 Hymenoptera specimens collected near Churchill, Manitoba, from 2004 through 2010. Results We resolved 1630 MOTUs for this collection, of which 75% (1228) were ichneumonoids (Ichneumonidae + Braconidae) and 91% (1484) were parasitoids. We estimate the total number of Hymenoptera MOTUs in this region at 2624-2840. Conclusions The diversity of parasitoids in this sub-Arctic environment implies a high diversity of potential host species throughout the same range. We discuss these results in the contexts of resolving interspecific interactions that may include cryptic species, and developing reproducible methods to estimate and compare species richness across sites and between surveys, especially when morphological specialists are not available to identify every specimen. PMID:23351160

Analysis of a PAH-degrading bacterial population in subsurface sediments on the Mid-Atlantic Ridge

NASA Astrophysics Data System (ADS)

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

2010-05-01

Little is known about the types and concentrations of polycyclic aromatic hydrocarbons (PAHs) existing in the deep-sea subsurface environment, which is believed to be cold, oligothrophic and of high static pressure. PAHs in the upper layers of the water column are unavoidably subjected to degradation while they are deposited to the sea floor and become embedded in the deep-sea sediment. In this report, a high concentration of PAHs was discovered in the sediment 2.7 m beneath the bottom surface at a water depth of 3962 m on the Mid-Atlantic Ridge (MAR). The total concentration of PAHs was 445 ng (g dry wt sediment) -1. Among the seven detected PAHs, the concentrations of phenanthrene (222 ng g -1) and fluorene (79 ng g -1) were relatively high. In addition, PAH-degrading bacteria were found within the sediments. As in a previously detected site on the MAR, in the PAH-enriched region of this site, a bacterium of the genus Cycloclasticus was found to be the predominant isolate detected by PCR-DGGE analysis. In addition, bacteria of the Halomonas, Marinobacter, Alcanivorax, Thalassospira and Maricaulis genera, were also included in the PAH-degrading community. In summary, a high concentration of PAHs was detected in the subsurface of the deep-sea sediment, and once again, the Cycloclasticus bacterium was confirmed to be a ubiquitous marine PAH degrader even in the subsurface marine environment. Considering the abundance of PAHs therein, biodegradation is thus thought to be inactive, probably because of the low temperature, limited oxygen and/or limited nutrients.

Experimental validation of a sub-surface model of solar power for distributed marine sensor systems

NASA Astrophysics Data System (ADS)

Hahn, Gregory G.; Cantin, Heather P.; Shafer, Michael W.

2016-04-01

The capabilities of distributed sensor systems such as marine wildlife telemetry tags could be significantly enhanced through the integration of photovoltaic modules. Photovoltaic cells could be used to supplement the primary batteries for wildlife telemetry tags to allow for extended tag deployments, wherein larger amounts of data could be collected and transmitted in near real time. In this article, we present experimental results used to validate and improve key aspects of our original model for sub-surface solar power. We discuss the test methods and results, comparing analytic predictions to experimental results. In a previous work, we introduced a model for sub-surface solar power that used analytic models and empirical data to predict the solar irradiance available for harvest at any depth under the ocean's surface over the course of a year. This model presented underwater photovoltaic transduction as a viable means of supplementing energy for marine wildlife telemetry tags. The additional data provided by improvements in daily energy budgets would enhance the temporal and spatial comprehension of the host's activities and/or environments. Photovoltaic transduction is one method that has not been widely deployed in the sub-surface marine environments despite widespread use on terrestrial and avian species wildlife tag systems. Until now, the use of photovoltaic cells for underwater energy harvesting has generally been disregarded as a viable energy source in this arena. In addition to marine telemetry systems, photovoltaic energy harvesting systems could also serve as a means of energy supply for autonomous underwater vehicles (AUVs), as well as submersible buoys for oceanographic data collection.

Iron-based subsurface arsenic removal technologies by aeration: A review of the current state and future prospects.

PubMed

Luong, Vu T; Cañas Kurz, Edgardo E; Hellriegel, Ulrich; Luu, Tran L; Hoinkis, Jan; Bundschuh, Jochen

2018-04-15

Arsenic contamination in groundwater is a critical issue and one that raises great concern around the world as the cause of many negative health impacts on the human body, including internal and external cancers. There are many ways to remove or immobilize arsenic, including membrane technologies, adsorption, sand filtration, ion exchange, and capacitive deionization. These exhibit many different advantages and disadvantages. Among these methods, in-situ subsurface arsenic immobilization by aeration and the subsequent removal of arsenic from the aqueous phase has shown to be very a promising, convenient technology with high treatment efficiency. In contrast to most of other As remediation technologies, in-situ subsurface immobilization offers the advantage of negligible waste production and hence has the potential of being a sustainable treatment option. This paper reviews the application of subsurface arsenic removal (SAR) technologies as well as current modeling approaches. Unlike subsurface iron removal (SIR), which has proven to be technically feasible in a variety of hydrogeochemical settings for many years, SAR is not yet an established solution since it shows vulnerability to diverse geochemical conditions such as pH, Fe:As ratio, and the presence of co-ions. In some situations, this makes it difficult to comply with the stringent guideline value for drinking water recommended by the WHO (10 μg L -1 ). In order to overcome its limitations, more theoretical and experimental studies are needed to show long-term application achievements and help the development of SAR processes into state-of-the-art technology. Copyright © 2018 Elsevier Ltd. All rights reserved.

Subsurface Microbiology and Biogeochemistry

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

Fredrickson, Jim K.; Fletcher, Madilyn

2001-05-01

Jim contributed a chapter to this book, in addition to co-editing it with Madilyn Fletcher. Fredrickson, J. K., and M. Fletcher. (eds.) 2001 Subsurface Microbiology and Biogeochemistry. Wiley-Liss, Inc., New York.

Maize diversity and ethnolinguistic diversity in Chiapas, Mexico

PubMed Central

Perales, Hugo R.; Benz, Bruce F.; Brush, Stephen B.

2005-01-01

The objective of this study is to investigate whether ethnolinguistic diversity influences crop diversity. Factors suggest a correlation between biological diversity of crops and cultural diversity. Although this correlation has been noted, little systematic research has focused on the role of culture in shaping crop diversity. This paper reports on research in the Maya highlands (altitude > 1,800 m) of central Chiapas in southern Mexico that examined the distribution of maize (Zea mays) types among communities of two groups, the Tzeltal and Tzotzil. The findings suggest that maize populations are distinct according to ethnolinguistic group. However, a study of isozymes indicates no clear separation of the region's maize into two distinct populations based on ethnolin-guistic origin. A reciprocal garden experiment shows that there is adaptation of maize to its environment but that Tzeltal maize sometimes out-yields Tzotzil maize in Tzotzil environments. Because of the proximity of the two groups and selection for yield, we would expect that the superior maize would dominate both groups' maize populations, but we find that such domination is not the case. The role of ethnolinguistic identity in shaping social networks and information exchange is discussed in relation to landrace differentiation. PMID:15640353

Maize diversity and ethnolinguistic diversity in Chiapas, Mexico.

PubMed

Perales, Hugo R; Benz, Bruce F; Brush, Stephen B

2005-01-18

The objective of this study is to investigate whether ethnolinguistic diversity influences crop diversity. Factors suggest a correlation between biological diversity of crops and cultural diversity. Although this correlation has been noted, little systematic research has focused on the role of culture in shaping crop diversity. This paper reports on research in the Maya highlands (altitude >1,800 m) of central Chiapas in southern Mexico that examined the distribution of maize (Zea mays) types among communities of two groups, the Tzeltal and Tzotzil. The findings suggest that maize populations are distinct according to ethnolinguistic group. However, a study of isozymes indicates no clear separation of the region's maize into two distinct populations based on ethnolinguistic origin. A reciprocal garden experiment shows that there is adaptation of maize to its environment but that Tzeltal maize sometimes out-yields Tzotzil maize in Tzotzil environments. Because of the proximity of the two groups and selection for yield, we would expect that the superior maize would dominate both groups' maize populations, but we find that such domination is not the case. The role of ethnolinguistic identity in shaping social networks and information exchange is discussed in relation to landrace differentiation.

Method of imaging the electrical conductivity distribution of a subsurface

DOEpatents

Johnson, Timothy C.

2017-09-26

A method of imaging electrical conductivity distribution of a subsurface containing metallic structures with known locations and dimensions is disclosed. Current is injected into the subsurface to measure electrical potentials using multiple sets of electrodes, thus generating electrical resistivity tomography measurements. A numeric code is applied to simulate the measured potentials in the presence of the metallic structures. An inversion code is applied that utilizes the electrical resistivity tomography measurements and the simulated measured potentials to image the subsurface electrical conductivity distribution and remove effects of the subsurface metallic structures with known locations and dimensions.

Developing methanogenic microbial consortia from diverse coal sources and environments

DOE PAGES

Fuertez, John; Boakye, Richard; McLennan, John; ...

2017-08-18

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor

Developing methanogenic microbial consortia from diverse coal sources and environments

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

Fuertez, John; Boakye, Richard; McLennan, John

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor

Survivability and growth kinetics of methanogenic archaea at various pHs and pressures: Implications for deep subsurface life on Mars

NASA Astrophysics Data System (ADS)

Sinha, Navita; Nepal, Sudip; Kral, Timothy; Kumar, Pradeep

2017-02-01

Life as we know it requires liquid water and sufficient liquid water is highly unlikely on the surface of present-day Mars. However, according to thermal models there is a possibility of liquid water in the deep subsurface of Mars. Thus, the martian subsurface, where the pressure and temperature is higher, could potentially provide a hospitable environment for a biosphere. Also, methane has been detected in the Mars' atmosphere. Analogous to Earth's atmospheric methane, martian methane could also be biological in origin. The carbon and energy sources for methanogenesis in the subsurface of Mars could be available by downwelling of atmospheric CO2 into the regolith and water-rock reactions such as serpentinization, respectively. Corresponding analogs of the martian subsurface on Earth might be the active sites of serpentinization at depths where methanogenic thermophilic archaea are the dominant species. Methanogens residing in Earth's hydrothermal environments are usually exposed to a variety of physiological stresses including a wide range of pressures, temperatures, and pHs. Martian geochemical models imply that the pH of probable groundwater varies from 4.96 to 9.13. In this work, we used the thermophilic methanogen, Methanothermobacter wolfeii, which grows optimally at 55oC. Therefore, a temperature of 55oC was chosen for these experiments, possibly simulating Mars' subsurface temperature. A martian geophysical model suggests depth and pressure corresponding to a temperature of 55 °C would be between 1-30 km and 100-3,000 atm respectively. Here, we have simulated Mars deep subsurface pH, pressure, and temperature conditions and have investigated the survivability, growth rate, and morphology of M. wolfeii after exposure to a wide range of pH 5-9) and pressure (1-1200 atm) at a temperature of 55 °C. Interestingly, in this study we have found that M. wolfeii was able to survive at all the pressures and pHs tested at 55 °C. In order to understand the effect of

Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments.

PubMed

Lai, Qiliang; Liu, Yang; Yuan, Jun; Du, Juan; Wang, Liping; Sun, Fengqin; Shao, Zongze

2014-01-01

Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16-97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76-97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments.

Multilocus Sequence Analysis for Assessment of Phylogenetic Diversity and Biogeography in Thalassospira Bacteria from Diverse Marine Environments

PubMed Central

Yuan, Jun; Du, Juan; Wang, Liping; Sun, Fengqin; Shao, Zongze

2014-01-01

Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16–97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76–97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments. PMID:25198177

Preparing the Future STEM Workforce for Diverse Environments

ERIC Educational Resources Information Center

Daily, Shaundra Bryant; Eugene, Wanda

2013-01-01

Following the belief that diversity breeds innovation in scientific endeavors, there is a national push for more diversity in the science, technology, engineering, and mathematics (STEM) workforce in order to maintain national economic competitiveness. Currently, STEM-related employment is only 28% non-White; however, greater efforts to recruit…

Mars Analog Rio Tinto Experiment (MARTE): 2003 Drilling Campaign to Search for a Subsurface Biosphere at Rio Tinto Spain

NASA Technical Reports Server (NTRS)

Stoker, Carol; Dunagan, Stephen; Stevens, Todd; Amils, Ricardo; Gomez-Elvira, Javier; Fernandez, David; Hall, James; Lynch, Kennda; Cannon, Howard; Zavaleta, Jhony

2004-01-01

The MARTE (Mars Astrobiology Research and Technology Experiment) project, an ASTEP field experiment, is exploring for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Tinto River- or Rio Tinto- in southwestern Spain. It is also demonstrating technology needed to search for a subsurface biosphere on Mars. The project has three primary objectives: (1) search for and characterize subsurface life at Rio Tinto along with the physical and chemical properties and sustaining energy sources of its environment, (2) perform a high fidelity simulation of a robotic Mars drilling mission to search for life, and (3) demonstrate the drilling, sample handling, and instrument technologies relevant to searching for life on Mars. The simulation of the robotic drilling mission is guided by the results of the aseptic drilling campaign to search for life at Rio Tinto. This paper describes results of the first phase of the aseptic drilling campaign.

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

Groundwater Salinity Simulation of a Subsurface Reservoir in Taiwan

NASA Astrophysics Data System (ADS)

Fang, H. T.

2015-12-01

The subsurface reservoir is located in Chi-Ken Basin, Pescadores (a group islands located at western part of Taiwan). There is no river in these remote islands and thus the freshwater supply is relied on the subsurface reservoir. The basin area of the subsurface reservoir is 2.14 km2 , discharge of groundwater is 1.27×106m3 , annual planning water supplies is 7.9×105m3 , which include for domestic agricultural usage. The annual average temperature is 23.3oC, average moisture is 80~85%, annual average rainfall is 913 mm, but ET rate is 1975mm. As there is no single river in the basin; the major recharge of groundwater is by infiltration. Chi-Ken reservoir is the first subsurface reservoir in Taiwan. Originally, the water quality of the reservoir is good. The reservoir has had the salinity problem since 1991 and it became more and more serious from 1992 until 1994. Possible reason of the salinity problem was the shortage of rainfall or the leakage of the subsurface barrier which caused the seawater intrusion. The present study aimed to determine the leakage position of subsurface barrier that caused the salinity problem. In order to perform the simulation for different possible leakage position of the subsurface reservoir, a Groundwater Modeling System (GMS) is used to define soils layer data, hydro-geological parameters, initial conditions, boundary conditions and the generation of three dimension meshes. A three dimension FEMWATER(Yeh , 1996) numerical model was adopted to find the possible leakage position of the subsurface barrier and location of seawater intrusion by comparing the simulation of different possible leakage with the observations. 1.By assuming the leakage position in the bottom of barrier, the simulated numerical result matched the observation better than the other assumed leakage positions. It showed that the most possible leakage position was at the bottom of the barrier. 2.The research applied three dimension FEMWATER and GMS as an interface

Bacterial diversity in a nonsaline alkaline environment: heterotrophic aerobic populations.

PubMed

Tiago, Igor; Chung, Ana Paula; Veríssimo, António

2004-12-01

Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)2-enriched, extremely diluted groundwater with pH 11.4. One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods. To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis. Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates. Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species Dietzia natrolimnae (32% of the isolates), to Frigoribacterium/Clavibacter lineages (29% of the isolates), and to the type strain of Microbacterium kitamiense (20% of the isolates). Other isolates were phylogenetically related to strains of the genera Agrococcus, Leifsonia, Kytococcus, Janibacter, Kocuria, Rothia, Nesterenkonia, Citrococcus, Micrococcus, Actinomyces, Rhodococcus, Bacillus, and Staphylococcus. Only five isolates were gram negative: one was related to the Sphingobacteria lineage and the other four were related to the alpha-Proteobacteria lineage. Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11.

Subsurface banding poultry litter impacts greenhouse gas emissions

USDA-ARS?s Scientific Manuscript database

The impact subsurface banding poultry litter (PL) has on greenhouse gas emissions is limited. Thus, a study was conducted in established bermudagrass pastures located in Coastal Plain and Piedmont regions to determine the effects subsurface applying PL has on soil flux using two different band spaci...

Facilitated strontium transport by remobilization of strontium-containing secondary precipitates in Hanford Site subsurface.

PubMed

Wang, Guohui; Um, Wooyong

2013-03-15

Significantly enhanced immobilization of radionuclides (such as (90)Sr and (137)Cs) due to adsorption and coprecipitation with neo-formed colloid-sized secondary precipitates has been reported at the U.S. Department of Energy's Hanford Site. However, the stability of these secondary precipitates containing radionuclides in the subsurface under changeable field conditions is not clear. Here, the authors tested the remobilization possibility of Sr-containing secondary precipitates (nitrate-cancrinite) in the subsurface using saturated column experiments under different geochemical and flow conditions. The columns were packed with quartz sand that contained secondary precipitates (nitrate-cancrinite containing Sr), and leached using colloid-free solutions under different flow rates, varying pH, and ionic strength conditions. The results indicate remobilization of the neo-formed secondary precipitates could be possible given a change of pH of ionic strength and flow rate conditions. The remobility of the neo-formed precipitates increased with the rise in the leaching solution flow rate and pH (in a range of pH 4-11), as well as with decreasing solution ionic strength. The increased mobility of Sr-containing secondary precipitates with changing background conditions can be a potential source for additional radionuclide transport in Hanford Site subsurface environments. Published by Elsevier B.V.

Tidal Response of Europa's Subsurface Ocean

NASA Astrophysics Data System (ADS)

Karatekin, O.; Comblen, R.; Deleersnijder, E.; Dehant, V. M.

2010-12-01

Time-variable tides in the subsurface oceans of icy satellites cause large periodic surface displacements and tidal dissipation can become a major energy source that can affect long-term orbital and internal evolution. In the present study, we investigate the response of the subsurface ocean of Europa to a time-varibale tidal potential. Two-dimensional nonlinear shallow water equations are solved on a sphere by means of a finite element code. The resulting ocean tidal flow velocities,dissipation and surface displacements will be presented.

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

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.

Intrinsic Anaerobic Bioremediation of Hydrocarbons in Contaminated Subsurface Plumes and Marine Sediments

NASA Astrophysics Data System (ADS)

Nanny, M. A.; Nanny, M. A.; Suflita, J. M.; Suflita, J. M.; Davidova, I.; Kropp, K.; Caldwell, M.; Philp, R.; Gieg, L.; Rios-Hernandez, L. A.

2001-05-01

In recent years, several classes of petroleum hydrocarbons contaminating subsurface and marine environments have been found susceptible to anaerobic biodegradation using novel mechanisms entirely distinct from aerobic metabolic pathways. For example, the anaerobic decay of toluene can be initiated by the addition of the aryl methyl group to the double bond of fumarate, resulting in a benzylsuccinic acid metabolite. Our work has shown that an analogous mechanism also occurs with ethylbenzene and the xylene isomers, yielding 3-phenyl-1,2-butane dicarboxylic acid and methylbenzylsuccinic acid, respectively. Moreover, these metabolites have been detected in contaminated environments. Most recently, we have identified metabolites resulting from the initial attack of H26- or D26-n-dodecane during degradation by a sulfate-reducing bacterial culture. Using GC-MS, these metabolites were identified as fatty acids that result from C-H or C-D addition across the double bond of fumarate to give dodecylsuccinic acids in which all 26 protons or deuteriums of the parent alkane were retained. Further, when this enrichment culture was challenged with hexane or decane, hexylsuccinic acid or decylsuccinic acid were identified as resulting metabolites. Similarly, the study of an ethylcyclopentane-degrading sulfate-reducing enrichment produced a metabolite, which is consistent with the addition of fumarate to the parent substrate. These novel anaerobic addition products are characterized by similar, distinctive mass spectral (MS) features (ions specific to the succinic acid portion of the molecule) that can potentially be used to probe contaminated environments for evidence of intrinsic remediation of hydrocarbons. Indeed, analyses of water extracts from two gas condensate-contaminated sites resulted in the tentative detection of alkyl- and cycloalkylsuccinic acids ranging from C3 to C9, including ethylcyclopentyl-succinic acid. In water extracts collected from an area underlying a

Technical geothermal potential of urban subsurface influenced by land surface effects

NASA Astrophysics Data System (ADS)

Rivera, Jaime A.; Blum, Philipp; Bayer, Peter

2016-04-01

Changes in land use are probably one of the most notorious anthropogenic perturbations in urban environments. They significantly change the coupled thermal regime at the ground surface leading in most cases to increased ground surface temperatures (GST). The associated elevated vertical heat fluxes act at different scales and can influence the thermal conditions in several tens of meters in the subsurface. Urban subsurface thus often stores a higher amount of heat than less affected rural surroundings. The stored heat is regarded as a potential source of low-enthalpy geothermal energy to supply the heating energy demands in urban areas. In this work, we explore the technical geothermal potential of urban subsurface via ground coupled heat pumps with borehole heat exchangers (BHE). This is tackled by semi-analytical line-source equations. The commonly used response factors or g-functions are modified to include transient land surface effects. By including this additional source of heat, the new formulation allows to analyse the effect of pre-existing urban warming as well as different exploitation schemes fulfilling standard renewable and sustainable criteria. In our generalized reference scenario, it is demonstrated that energy gains for a single BHE may be up to 40 % when compared to non-urbanized conditions. For a scenario including the interaction of multiple BHEs, results indicate that it would be possible to supply between 6 % and 27 % of the heating demands in Central European urban settlements in a renewable way. The methodology is also applied to a study case of the city of Zurich, Switzerland, where the detailed evolution of land use is available.

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

Reactive transport codes for subsurface environmental simulation

DOE PAGES

Steefel, C. I.; Appelo, C. A. J.; Arora, B.; ...

2014-09-26

A general description of the mathematical and numerical formulations used in modern numerical reactive transport codes relevant for subsurface environmental simulations is presented. The formulations are followed by short descriptions of commonly used and available subsurface simulators that consider continuum representations of flow, transport, and reactions in porous media. These formulations are applicable to most of the subsurface environmental benchmark problems included in this special issue. The list of codes described briefly here includes PHREEQC, HPx, PHT3D, OpenGeoSys (OGS), HYTEC, ORCHESTRA, TOUGHREACT, eSTOMP, HYDROGEOCHEM, CrunchFlow, MIN3P, and PFLOTRAN. The descriptions include a high-level list of capabilities for each of themore » codes, along with a selective list of applications that highlight their capabilities and historical development.« less

Combined Geothermal Potential of Subsurface Urban Heat Islands

NASA Astrophysics Data System (ADS)

Benz, Susanne; Bayer, Peter; Menberg, Kathrin; Blum, Philipp

2016-04-01

The subsurface urban heat island (SUHI) can be seen as a geothermal potential in form of elevated groundwater temperatures caused by anthropogenic heat fluxes into the subsurface. In this study, these fluxes are quantified for an annual timeframe in two German cities, Karlsruhe and Cologne. Our two-dimensional (2D) statistical analytical model determines the renewable and sustainable geothermal potential caused by six vertical anthropogenic heat fluxes into the subsurface: from (1) elevated ground surface temperatures, (2) basements, (3) sewage systems, (4) sewage leakage, (5) subway tunnels, and (6) district heating networks. The results show that at present 2.15 ± 1.42 PJ and 0.99 ± 0.32 PJ of heat are annually transported into the shallow groundwater of Karlsruhe and Cologne, respectively, due to anthropogenic heat fluxes into the subsurface. This is sufficient to sustainably cover 32% and 9% of the annual residential space heating demand of Karlsruhe and Cologne, respectively. However, most of the discussed anthropogenic fluxes into the subsurface are conductive heat fluxes and therefore dependent on the groundwater temperature itself. Accordingly, a decrease in groundwater temperature back to its natural (rural) state, achieved through the use of geothermal heat pumps, will increase these fluxes and with them the sustainable potential. Hence, we propose the introduction of a combined geothermal potential that maximizes the sustainability of urban shallow geothermal energy use and the efficiency of shallow geothermal systems by balancing groundwater temperature with anthropogenic heat fluxes into the subsurface. This will be a key element in the development of a demand-oriented, cost-efficient geothermal management tool with an additional focus on the sustainability of the urban heat sources.

Evidence for biological activity in mineralization of secondary sulphate deposits in a basaltic environment: implications for the search for life in the Martian subsurface

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

C. Doc Richardson; Nancy W. Hinman; Jill R. Scott

Evidence of microbial activity associated with mineralization of secondary Na-sulphate minerals (thenardite, mirabilite) in the basaltic subsurface of Craters of the Moon National Monument (COM), Idaho were examined by scanning electron microscopy, X-ray diffraction, laser desorption Fourier transform ion cyclotron resonance mass spectrometry (LD-FTICR-MS), Fourier transform infrared spectroscopy (FTIR) and isotope ratio mass spectrometry. Peaks suggestive of bio/organic compounds were observed in the secondary Na-sulphate deposits by LD-FTICR-MS. FTIR provided additional evidence for the presence of bio/organic compounds. Sulphur fractionation was explored to assist in determining if microbes may play a role in oxidizing sulphur. The presence of bio/organic compoundsmore » associated with Na-sulphate deposits, along with the necessity of oxidizing reduced sulphur to sulphate, suggests that biological activity may be involved in the formation of these secondary minerals. The secondary Na-sulphate minerals probably form from the overlying basalt through leached sodium ions and sulphate ions produced by bio-oxidation of Fe-sulphide minerals. Since the COM basalts are one of the most comparable terrestrial analogues for their Martian counterparts, the occurrence of biological activity in the formation of sulphate minerals at COM has direct implications for the search for life on Mars. In addition, the presence of caves on Mars suggests the importance of these environments as possible locations for growth and preservation of microbial activity. Therefore, understanding the physiochemical pathways of abiotic and biotic mineralization in the COM subsurface and similar basaltic settings has direct implications for the search for extinct or extant life on Mars.« less

Time series analysis of contaminant transport in the subsurface: applications to conservative tracer and engineered nanomaterials.

PubMed

Bai, Chunmei; Li, Yusong

2014-08-01

Accurately predicting the transport of contaminants in the field is subject to multiple sources of uncertainty due to the variability of geological settings, the complexity of field measurements, and the scarcity of data. Such uncertainties can be amplified when modeling some emerging contaminants, such as engineered nanomaterials, when a fundamental understanding of their fate and transport is lacking. Typical field work includes collecting concentration at a certain location for an extended period of time, or measuring the movement of plume for an extended period time, which would result in a time series of observation data. This work presents an effort to evaluate the possibility of applying time series analysis, particularly, autoregressive integrated moving average (ARIMA) models, to forecast contaminant transport and distribution in the subsurface environment. ARIMA modeling was first assessed in terms of its capability to forecast tracer transport at two field sites, which had different levels of heterogeneity. After that, this study evaluated the applicability of ARIMA modeling to predict the transport of engineered nanomaterials at field sites, including field measured data of nanoscale zero valent iron and (nZVI) and numerically generated data for the transport of nano-fullerene aggregates (nC60). This proof-of-concept effort demonstrates the possibility of applying ARIMA to predict the contaminant transport in the subsurface environment. Like many other statistical models, ARIMA modeling is only descriptive and not explanatory. The limitation and the challenge associated with applying ARIMA modeling to contaminant transport in the subsurface are also discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

Time series analysis of contaminant transport in the subsurface: Applications to conservative tracer and engineered nanomaterials

NASA Astrophysics Data System (ADS)

Bai, Chunmei; Li, Yusong

2014-08-01

Accurately predicting the transport of contaminants in the field is subject to multiple sources of uncertainty due to the variability of geological settings, the complexity of field measurements, and the scarcity of data. Such uncertainties can be amplified when modeling some emerging contaminants, such as engineered nanomaterials, when a fundamental understanding of their fate and transport is lacking. Typical field work includes collecting concentration at a certain location for an extended period of time, or measuring the movement of plume for an extended period time, which would result in a time series of observation data. This work presents an effort to evaluate the possibility of applying time series analysis, particularly, autoregressive integrated moving average (ARIMA) models, to forecast contaminant transport and distribution in the subsurface environment. ARIMA modeling was first assessed in terms of its capability to forecast tracer transport at two field sites, which had different levels of heterogeneity. After that, this study evaluated the applicability of ARIMA modeling to predict the transport of engineered nanomaterials at field sites, including field measured data of nanoscale zero valent iron and (nZVI) and numerically generated data for the transport of nano-fullerene aggregates (nC60). This proof-of-concept effort demonstrates the possibility of applying ARIMA to predict the contaminant transport in the subsurface environment. Like many other statistical models, ARIMA modeling is only descriptive and not explanatory. The limitation and the challenge associated with applying ARIMA modeling to contaminant transport in the subsurface are also discussed.

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments.

PubMed

Bouskill, Nicholas J; Eveillard, Damien; Chien, Diana; Jayakumar, Amal; Ward, Bess B

2012-03-01

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Armored Enzyme Nanoparticles for Remediation of Subsurface

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

Grate, Jay W.

2005-09-01

The remediation of subsurface contaminants is a critical problem for the Department of Energy, other government agencies, and our nation. Severe contamination of soil and groundwater exists at several DOE sites due to various methods of intentional and unintentional release. Given the difficulties involved in conventional removal or separation processes, it is vital to develop methods to transform contaminants and contaminated earth/water to reduce risks to human health and the environment. Transformation of the contaminants themselves may involve conversion to other immobile species that do not migrate into well water or surface waters, as is proposed for metals and radionuclides;more » or degradation to harmless molecules, as is desired for organic contaminants. Transformation of contaminated earth (as opposed to the contaminants themselves) may entail reductions in volume or release of bound contaminants for remediation.« less

Subsurface Mapping: A Question of Position and Interpretation

ERIC Educational Resources Information Center

Kellie, Andrew C.

2009-01-01

This paper discusses the character and challenges inherent in the graphical portrayal of features in subsurface mapping. Subsurface structures are, by their nature, hidden and must be mapped based on drilling and/or geophysical data. Efficient use of graphical techniques is central to effectively communicating the results of expensive exploration…

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

Heating systems for heating subsurface formations

DOEpatents

Nguyen, Scott Vinh [Houston, TX; Vinegar, Harold J [Bellaire, TX

2011-04-26

Methods and systems for heating a subsurface formation are described herein. A heating system for a subsurface formation includes a sealed conduit positioned in an opening in the formation and a heat source. The sealed conduit includes a heat transfer fluid. The heat source provides heat to a portion of the sealed conduit to change phase of the heat transfer fluid from a liquid to a vapor. The vapor in the sealed conduit rises in the sealed conduit, condenses to transfer heat to the formation and returns to the conduit portion as a liquid.

Plasmid incidence in bacteria from deep subsurface sediments

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

Fredrickson, J.K.; Hicks, R.J.; Li, S.W.

Bacteria were isolated from deep terrestrial subsurface sediments underlying the coastal plain of South Carolina. A total of 163 isolates from deep sediments, surface soil, and return drill muds were examined for plasmid DNA content and resistance to the antibiotics penicillin, ampicillin, carbenicillin, streptomycin, kanamycin, and tetracycline. MICs of Cu{sup 2+}, Cr{sup 3+}, and Hg{sup 2+} for each isolate were also determined. The overall frequency of plasmid occurrence in the subsurface bacteria was 33%. Resistance was most frequent to penicillin (70% of all isolates), ampicillin (49%), and carbenicillin (32%) and was concluded to be related to the concentrations of themore » individual antibiotics in the disks used for assaying resistance and to the production of low levels of {beta}-lactamase. The frequencies of resistance to penicillin and ampicillin were significantly greater for isolates bearing plasmids than for plasmidless isolates; however, resistance was not transferable to penicillin-sensitive Escherichia coli. Hybridization of subsurface bacterial plasmids and chromosomal DNA with a whole-TOL-plasmid (pWWO) probe revealed some homology of subsurface bacterial plasmid and chromosomal DNAs, indicating a potential for those bacterial to harbor catabolic genes on plasmids or chromosomes. The incidences of antibiotic resistance and MICs of metals for subsurface bacteria were significantly different from those drill mud bacteria, ruling out the possibility that bacteria from sediments were derived from drill muds.« less

The Impact of the Built Environment on Children's School Conduct Grades: The Role of Diversity of Use in a Hispanic Neighborhood

PubMed Central

Szapocznik, José; Lombard, Joanna; Martinez, Frank; Mason, Craig A.; Gorman-Smith, Deborah; Plater-Zyberk, Elizabeth; Brown, Scott C.; Spokane, Arnold

2013-01-01

A population-based study examined the relationship between diversity of use of the built environment and teacher reports of children's grades. Diversity of use of the built environment (i.e., proportion of a block that is residential, institutional, commercial and vacant) was assessed for all 403 city blocks in East Little Havana, Miami—a Hispanic neighborhood. Cluster analysis identified three block-types, based on diversity of use: Residential, Mixed-Use, and Commercial. Cross-classified hierarchical linear modeling was used to examine the impact of diversity of use, school, gender, and year-in-school on academic and conduct grades for 2857 public school children who lived in these blocks. Contrary to popular belief, mixed-use blocks were associated with optimal outcomes. Specifically, follow-up analyses found that a youth living on a residential block had a 74% greater odds of being in the lowest 10% of conduct grades (conduct GPA <2.17) than a youth living on a mixed-use block. In fact, an analysis of the population attributable fraction suggests that if the risk associated with residential blocks could be reduced to the level of risk associated with mixed-use blocks, a 38% reduction in Conduct GPAs <2.17 could be achieved in the total population. These findings suggest that public policy targeting the built environment may be a mechanism for community-based interventions to enhance children's classroom conduct, and potentially related sequelae. PMID:16967342

GIS based 3D visualization of subsurface and surface lineaments / faults and their geological significance, northern tamil nadu, India

NASA Astrophysics Data System (ADS)

Saravanavel, J.; Ramasamy, S. M.

2014-11-01

The study area falls in the southern part of the Indian Peninsular comprising hard crystalline rocks of Archaeozoic and Proterozoic Era. In the present study, the GIS based 3D visualizations of gravity, magnetic, resistivity and topographic datasets were made and therefrom the basement lineaments, shallow subsurface lineaments and surface lineaments/faults were interpreted. These lineaments were classified as category-1 i.e. exclusively surface lineaments, category-2 i.e. surface lineaments having connectivity with shallow subsurface lineaments and category-3 i.e. surface lineaments having connectivity with shallow subsurface lineaments and basement lineaments. These three classified lineaments were analyzed in conjunction with known mineral occurrences and historical seismicity of the study area in GIS environment. The study revealed that the category-3 NNE-SSW to NE-SW lineaments have greater control over the mineral occurrences and the N-S, NNE-SSW and NE-SW, faults/lineaments control the seismicities in the study area.

Diversity and feeding strategies of soil microfauna along elevation gradients in Himalayan cold deserts

PubMed Central

Háněl, Ladislav; Řeháková, Klára; Doležal, Jiří

2017-01-01

High-elevation cold deserts in Tibet and Himalaya are one of the most extreme environments. One consequence is that the diversity of macrofauna in this environment is often limited, and soil microorganisms have a more influential role in governing key surface and subsurface bioprocesses. High-elevation soil microfauna represent important components of cold ecosystems and dominant consumers of microbial communities. Still little is known about their diversity and distribution on the edge of their reproductive and metabolic abilities. In this study, we disentangle the impact of elevation and soil chemistry on diversity and distribution of rotifers, nematodes and tardigrades and their most frequent feeding strategies (microbial filter-feeders, bacterivores, fungivores, root-fungal feeders, omnivores) along two contrasting altitudinal gradients in Indian NW Himalaya (Zanskar transect from 3805 to 4714 m a.s.l.) and southwestern Tibet (Tso Moriri transect from 4477 to 6176 m a.s.l.), using a combination of multivariate analysis, variation partitioning and generalized additive models. Zanskar transect had higher precipitation, soil moisture, organic matter and available nutrients than dry Tso Moriri transect. In total, 40 species of nematodes, 19 rotifers and 1 tardigrade were discovered. Species richness and total abundance of rotifers and nematodes showed mid-elevation peaks in both investigated transects. The optimum for rotifers was found at higher elevation than for nematodes. Diversity and distribution of soil microfauna was best explained by soil nitrogen, phosphorus and organic matter. More fertile soils hosted more diverse and abundant faunal communities. In Tso Moriri, bacterivores represented 60% of all nematodes, fungivores 35%, root-fungal feeders 1% and omnivores 3%. For Zanskar the respective proportions were 21%, 13%, 56% and 9%. Elevational optima of different feeding strategies occurred in Zanskar in one elevation zone (4400–4500 m), while in Tso

Remarkable morphological diversity of viruses and virus-like particles in hot terrestrial environments.

PubMed

Rachel, R; Bettstetter, M; Hedlund, B P; Häring, M; Kessler, A; Stetter, K O; Prangishvili, D

2002-12-01

Electron microscopic studies of the viruses in two hot springs (85 degrees C, pH 1.5-2.0, and 75-93 degrees C, pH 6.5) in Yellowstone National Park revealed particles with twelve different morphotypes. This diversity encompassed known viruses of hyperthermophilic archaea, filamentous Lipothrixviridae, rod-shaped Rudiviridae, and spindle-shaped Fuselloviridae, and novel morphotypes previously not observed in nature. Two virus types resembled head-and-tail bacteriophages from the families Siphoviridae and Podoviridae, and constituted the first observation of these viruses in a hydrothermal environment. Viral hosts in the acidic spring were members of the hyperthermophilic archaeal genus Acidianus.

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

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.

Autonomous microexplosives subsurface tracing system final report.

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

Engler, Bruce Phillip; Nogan, John; Melof, Brian Matthew

The objective of the autonomous micro-explosive subsurface tracing system is to image the location and geometry of hydraulically induced fractures in subsurface petroleum reservoirs. This system is based on the insertion of a swarm of autonomous micro-explosive packages during the fracturing process, with subsequent triggering of the energetic material to create an array of micro-seismic sources that can be detected and analyzed using existing seismic receiver arrays and analysis software. The project included investigations of energetic mixtures, triggering systems, package size and shape, and seismic output. Given the current absence of any technology capable of such high resolution mapping ofmore » subsurface structures, this technology has the potential for major impact on petroleum industry, which spends approximately $1 billion dollar per year on hydraulic fracturing operations in the United States alone.« less

Phytosiderophore effects on subsurface actinide contaminants: potential for phytostabilization and phytoextraction.

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

Ruggiero, C. E.; Twary, S. N.; Deladurantaye, E.

2003-01-01

In recognition of the need for a safe, effective technology for long term Pu/Th/Actinide stabilization or removal from soils, we have begun an investigation of the potential for phytoremediation (phytostabilization and/or phytoextraction) of Pu and other actinide soil contaminants at DOE sites using phytosiderophore producing plants, and are investigating the contribution of phytosiderophores to actinide mobility in the subsurface environment. Phytoremediation and Phytostabilization have been proven to be a cost-effective, safe, efficient, and publicly acceptable technology for clean up and/or stabilization of contaminant metals . However, no phyto-based technologies have been developed for stabilization or removal of plutonium from soilsmore » and groundwater, and very few have been investigated for other actinides . Current metal-phytostabilization and phytoremediation techniques, predominately based around lead, nickel, and other soft-metal phytoextraction, will almost certainly be inadequate for plutonium due its distinct chemical properties . Phytosiderophore-based phytoremediation may provide technically and financially practical methods for remediation and long-term stewardship of soils that have low to moderate, near surface actinide contamination . We plan to demonstrate potential benefits of phytosiderophore-producing plants for long-term actinide contaminant stabilization by the plant's prevention of soil erosion and actinide migration through hydraulic control and/or through actinide removal through phytoextraction . We may also show possible harm caused by these plants through increased presence of actinide chelators that could increase actinide mobilization and migration in the subsurface environment. This information can then be directly applied by either removal of harmful plants, or be used to develop plant-based soil stabilization/remediation technologies .« less

[Correlative analysis of the diversity patterns of regional surface water, NDVI and thermal environment].

PubMed

Duan, Jin-Long; Zhang, Xue-Lei

2012-10-01

Taking Zhengzhou City, the capital of Henan Province in Central China, as the study area, and by using the theories and methodologies of diversity, a discreteness evaluation on the regional surface water, normalized difference vegetation index (NDVI), and land surface temperature (LST) distribution was conducted in a 2 km x 2 km grid scale. Both the NDVI and the LST were divided into 4 levels, their spatial distribution diversity indices were calculated, and their connections were explored. The results showed that it was of operability and practical significance to use the theories and methodologies of diversity in the discreteness evaluation of the spatial distribution of regional thermal environment. There was a higher overlap of location between the distributions of surface water and the lowest temperature region, and the high vegetation coverage was often accompanied by low land surface temperature. In 1988-2009, the discreteness of the surface water distribution in the City had an obvious decreasing trend. The discreteness of the surface water distribution had a close correlation with the discreteness of the temperature region distribution, while the discreteness of the NDVI classification distribution had a more complicated correlation with the discreteness of the temperature region distribution. Therefore, more environmental factors were needed to be included for a better evaluation.

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

Polymer-Enhanced Subsurface Delivery and Distribution of Permanganate

DTIC Science & Technology

2013-02-01

Subsurface Delivery and Distribution of Permanganate February 2013 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for...SUBTITLE Polymer-Enhanced Subsurface Delivery and Distribution of Permanganate 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...SAMPLING RESULTS ........................................................................................ 28 5.6.1 Permanganate Distribution and Sweep

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.

Anaerobic decomposition of humic substances by Clostridium from the deep subsurface

PubMed Central

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

2016-01-01

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

Influence of Si wafer thinning processes on (sub)surface defects

NASA Astrophysics Data System (ADS)

Inoue, Fumihiro; Jourdain, Anne; Peng, Lan; Phommahaxay, Alain; De Vos, Joeri; Rebibis, Kenneth June; Miller, Andy; Sleeckx, Erik; Beyne, Eric; Uedono, Akira

2017-05-01

Wafer-to-wafer three-dimensional (3D) integration with minimal Si thickness can produce interacting multiple devices with significantly scaled vertical interconnections. Realizing such a thin 3D structure, however, depends critically on the surface and subsurface of the remaining backside Si after the thinning processes. The Si (sub)surface after mechanical grinding has already been characterized fruitfully for a range of few dozen of μm. Here, we expand the characterization of Si (sub)surface to 5 μm thickness after thinning process on dielectric bonded wafers. The subsurface defects and damage layer were investigated after grinding, chemical mechanical polishing (CMP), wet etching and plasma dry etching. The (sub)surface defects were characterized using transmission microscopy, atomic force microscopy, and positron annihilation spectroscopy. Although grinding provides the fastest removal rate of Si, the surface roughness was not compatible with subsequent processing. Furthermore, mechanical damage such as dislocations and amorphous Si cannot be reduced regardless of Si thickness and thin wafer handling systems. The CMP after grinding showed excellent performance to remove this grinding damage, even though the removal amount is 1 μm. For the case of Si thinning towards 5 μm using grinding and CMP, the (sub)surface is atomic scale of roughness without vacancy. For the case of grinding + dry etch, vacancy defects were detected in subsurface around 0.5-2 μm. The finished surface after wet etch remains in the nm scale in the strain region. By inserting a CMP step in between grinding and dry etch it is possible to significantly reduce not only the roughness, but also the remaining vacancies at the subsurface. The surface of grinding + CMP + dry etching gives an equivalent mono vacancy result as to that of grinding + CMP. This combination of thinning processes allows development of extremely thin 3D integration devices with minimal roughness and vacancy surface.

Robotic astrobiology - the need for sub-surface penetration of Mars

NASA Astrophysics Data System (ADS)

Ellery, A.; Ball, A.; Cockell, C.; Coste, P.; Dickensheets, D.; Edwards, H.; Hu, H.; Kolb, C.; Lammer, H.; Lorenz, R.; McKee, G.; Richter, L.; Winfield, A.; Welch, C.

2002-11-01

Recent interest in the astrobiological investigation of Mars has culminated in the only planned astrobiology-focussed robotic mission to Mars - the Beagle2 mission to be carried to Mars by the Mars Express spacecraft in 2003. Beagle2 will be primarily investigating the surface and near-surface environment of Mars. However, the results from the Viking Mars lander indicated that the Martian surface is saturated in peroxides and super-oxides which would rapidly degrade any organic material. Furthermore, recent models of gardening due to meteoritic impacts on the Martian surface suggest that the depth of this oxidising layer could extend to depths of 2-3m. Given that the discovery of organic fossilised residues will be the primary target for astrobiological investigation, this implies that future robotic astrobiology missions to Mars must penetrate to below these depths. The need to penetrate into the sub-surface of Mars has recently been given greater urgency with the discovery of extensive water ice-fields as little as 1m from the surface. We review the different technologies that make this penetration into the sub-surface a practical possibility on robotic missions. We further briefly present one such implementation of these technologies through the use of ground-penetrating moles - The Vanguard Mars mission proposal.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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.

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

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico).

PubMed

Medrano-Santillana, Miguel; Souza-Brito, Elcia Margaret; Duran, Robert; Gutierrez-Corona, Felix; Reyna-López, Georgina Elena

2017-05-01

Active volcanoes are among the most extreme environments on Earth. The extreme temperatures, presence of toxic heavy metals and low nutrient bioavailability favor the development of extremophiles. We characterized the physical-chemical parameters of and bacterial communities (T-RFLP and 16S rRNA gene libraries) inhabiting fumarole niches of the Paricutín volcano located in Michoacán (Mexico). This volcano, which surged in 1943, is one of the youngest volcanoes on Earth and the microbial diversity in this area is yet to be characterized. The sampling stations were characterized in a pH range from 5.34 to 7.89 and showed different temperatures (soil, 27-87 °C; air, 13.6-56 °C) with high concentrations of metals such as iron and arsenic. The most abundant bacterial populations, confirmed by T-RFLP and 16S rRNA gene libraries, were related to members of Firmicutes and Proteobacteria phyla including sequences associated with thermophiles and sulfate reducing bacteria. Overall, the Paricutín volcano showed low bacterial diversity and its prokaryotic diversity was characterized by the impossibility of amplifying Archaea-related sequences.

The Mojave Subsurface Bio-Geochemistry Explorer (MOSBE)

NASA Technical Reports Server (NTRS)

Guerrero, J.; Beegle, L.; Abbey, W.; Bhartia, R.; Kounaves, S.; Russell, M.; Towles, D.

2012-01-01

The MOSBE Team has developed a terrestrial field campaign to explore two subsurface biological habitats under the Mojave Desert. This field campaign will not only help us understand terrestrial desert biology, but also will develop methodologies and strategies for potential future Mars missions that would seek to explore the Martian subsurface. We have proposed to the ASTEP program to integrate a suite of field demonstrated instruments with a 20 m subsurface drill as a coherent unit, the Mojave Subsurface Bio-geochemistry Explorer. The ATK Space Modular Planetary Drill System (MPDS) requires no drilling fluid, which allows aseptic sampling, can penetrate lithic ground up to 20 meters of depth, and utilizes less than 100 Watts throughout the entire depth. The drill has been developed and demonstrated in field testing to a depth of 10 meters in Arizona, December 2002. In addition to caching a continuous core throughout the drilling depth, it also generates and caches cuttings and fines that are strata-graphically correlated with the core. As a core segment is brought to the surface, it will be analyzed for texture and structure by a color microscopic imager and for relevant chemistry and mineralogy with a UV fluorescence/Raman spectrometer. Organic and soluble ionic species will be identified through two instruments -- a microcapillary electrophoresis, and an ion trap mass spectrometer that have been developed under PIDDP, ASTID and MIDP funding.

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Chemistry and Environments of Dolomitization —A Reappraisal

NASA Astrophysics Data System (ADS)

Machel, Hans-G.; Mountjoy, Eric W.

1986-05-01

Dolomitization of calcium carbonate can best be expressed by mass transfer reactions that allow for volume gain, preservation, or loss during the replacement process. Experimental data, as well as textures and porosities of natural dolomites, indicate that these reactions must include CO 32- and/or HCO 3- supplied by the solution to the reaction site. Since dolomite formation is thermodynamically favoured in solutions of (a) low Ca 2+/Mg 2+ ratios, (b) low Ca 2+/CO 32- (or Ca 2+/HCO 3-) ratios, and (c) high temperatures, the thermodynamic stability for the system calcite-dolomite-water is best represented in a diagram with these three parameters as axes. Kinetic considerations favour dolomitization under the same conditions, and additionally at low as well as at high salinities. If thermodynamic and kinetic considerations are combined, the following conditions and environments are considered chemically conducive to dolomitization: (1) environments of any salinity above thermodynamic and kinetic saturation with respect to dolomite (i.e. freshwater/seawater mixing zones, normal saline to hypersaline subtidal environments, hypersaline supratidal environments, schizohaline environments); (2) alkaline environments (i.e. those under the influence of bacterial reduction and/or fermentation processes, or with high input of alkaline continental groundwaters); and (3) many environments with temperatures greater than about 50°C (subsurface and hydrothermal environments). Whether or not massive, replacive dolostones are formed in these environments depends on a sufficient supply of magnesium, and thus on hydrologic parameters. Most massive dolostones, particularly those consisting of shallowing-upward cycles and capped by regional unconformities, have been interpreted to be formed according to either the freshwater/seawater mixing model or the sabkha with reflux model. However, close examination of natural mixing zones and exposed evaporitic environments reveals that the

Peeking Beneath the Caldera: Communicating Subsurface Knowledge of Newberry Volcano

NASA Astrophysics Data System (ADS)

Mark-Moser, M.; Rose, K.; Schultz, J.; Cameron, E.

2016-12-01

"Imaging the Subsurface: Enhanced Geothermal Systems and Exploring Beneath Newberry Volcano" is an interactive website that presents a three-dimensional subsurface model of Newberry Volcano developed at National Energy Technology Laboratory (NETL). Created using the Story Maps application by ArcGIS Online, this format's dynamic capabilities provide the user the opportunity for multimedia engagement with the datasets and information used to build the subsurface model. This website allows for an interactive experience that the user dictates, including interactive maps, instructive videos and video capture of the subsurface model, and linked information throughout the text. This Story Map offers a general background on the technology of enhanced geothermal systems and the geologic and development history of Newberry Volcano before presenting NETL's modeling efforts that support the installation of enhanced geothermal systems. The model is driven by multiple geologic and geophysical datasets to compare and contrast results which allow for the targeting of potential EGS sites and the reduction of subsurface uncertainty. This Story Map aims to communicate to a broad audience, and provides a platform to effectively introduce the model to researchers and stakeholders.

Ecology and distribution of a new biomarker linked to 1,2-dichloropropane dechlorination in subsurface environments

NASA Astrophysics Data System (ADS)

Padilla-Crespo, E.; Loeffler, F. E.

2011-12-01

of dehalospiring populations in subsurface environments.

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.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-08-01

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

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

NASA Astrophysics Data System (ADS)

Rose, K.

2016-12-01

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

Robust Representation of Integrated Surface-subsurface Hydrology at Watershed Scales

NASA Astrophysics Data System (ADS)

Painter, S. L.; Tang, G.; Collier, N.; Jan, A.; Karra, S.

2015-12-01

A representation of integrated surface-subsurface hydrology is the central component to process-rich watershed models that are emerging as alternatives to traditional reduced complexity models. These physically based systems are important for assessing potential impacts of climate change and human activities on groundwater-dependent ecosystems and water supply and quality. Integrated surface-subsurface models typically couple three-dimensional solutions for variably saturated flow in the subsurface with the kinematic- or diffusion-wave equation for surface flows. The computational scheme for coupling the surface and subsurface systems is key to the robustness, computational performance, and ease-of-implementation of the integrated system. A new, robust approach for coupling the subsurface and surface systems is developed from the assumption that the vertical gradient in head is negligible at the surface. This tight-coupling assumption allows the surface flow system to be incorporated directly into the subsurface system; effects of surface flow and surface water accumulation are represented as modifications to the subsurface flow and accumulation terms but are not triggered until the subsurface pressure reaches a threshold value corresponding to the appearance of water on the surface. The new approach has been implemented in the highly parallel PFLOTRAN (www.pflotran.org) code. Several synthetic examples and three-dimensional examples from the Walker Branch Watershed in Oak Ridge TN demonstrate the utility and robustness of the new approach using unstructured computational meshes. Representation of solute transport in the new approach is also discussed. Notice: This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC0500OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid

Agriculture and wildlife: ecological implications of subsurface irrigation drainage

Treesearch

A. Dennis Lemly

1994-01-01

Subsurface agricultural irrigation drainage is a wastewater with the potential to severely impact wetlands and wildlife populations. Widespread poisoning of migratory birds by drainwater contaminants has occurred in the western United States and waterfowl populations are threatened in the Pacific and Central flyways. Irrigated agriculture could produce subsurface...

Enamel subsurface damage due to tooth preparation with diamonds.

PubMed

Xu, H H; Kelly, J R; Jahanmir, S; Thompson, V P; Rekow, E D

1997-10-01

In clinical tooth preparation with diamond burs, sharp diamond particles indent and scratch the enamel, causing material removal. Such operations may produce subsurface damage in enamel. However, little information is available on the mechanisms and the extent of subsurface damage in enamel produced during clinical tooth preparation. The aim of this study, therefore, was to investigate the mechanisms of subsurface damage produced in enamel during tooth preparation by means of diamond burs, and to examine the dependence of such damage on enamel rod orientation, diamond particle size, and removal rate. Subsurface damage was evaluated by a bonded-interface technique. Tooth preparation was carried out on two enamel rod orientations, with four clinical diamond burs (coarse, medium, fine, and superfine) used in a dental handpiece. The results of this study showed that subsurface damage in enamel took the form of median-type cracks and distributed microcracks, extending preferentially along the boundaries between the enamel rods. Microcracks within individual enamel rods were also observed. The median-type cracks were significantly longer in the direction parallel to the enamel rods than perpendicular to the rods. Preparation with the coarse diamond bur produced cracks as deep as 84 +/- 30 microns in enamel. Finishing with fine diamond burs was effective in crack removal. The crack lengths in enamel were not significantly different when the removal rate was varied. Based on these results, it is concluded that subsurface damage in enamel induced by tooth preparation takes the form of median-type cracks as well as inter- and intra-rod microcracks, and that the lengths of these cracks are sensitive to diamond particle size and enamel rod orientation, but insensitive to removal rate.

Influence of hydrological, biogeochemical and temperature transients on subsurface carbon fluxes in a flood plain environment

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

Arora, Bhavna; Spycher, Nicolas F.; Steefel, Carl I.

2016-02-01

Flood plains play a potentially important role in the global carbon cycle. The accumulation of organic matter in flood plains often induces the formation of chemically reduced groundwater and sediments along riverbanks. In this study, our objective is to evaluate the cumulative impact of such reduced zones, water table fluctuations, and temperature gradients on subsurface carbon fluxes in a flood plain at Rifle, Colorado located along the Colorado River. 2-D coupled variably-saturated, non-isothermal flow and biogeochemical reactive transport modeling was applied to improve our understanding of the abiotic and microbially mediated reactions controlling carbon dynamics at the Rifle site. Modelmore » simulations considering only abiotic reactions (thus ignoring microbial reactions) underestimated CO2 partial pressures observed in the unsaturated zone and severely underestimated inorganic (and overestimated organic) carbon fluxes to the river compared to simulations with biotic pathways. Both model simulations and field observations highlighted the need to include microbial contributions from chemolithoautotrophic processes (e.g., Fe?2 and S-2 oxidation) to match locally-observed high CO2 concentrations above reduced zones. Observed seasonal variations in CO2 concentrations in the unsaturated zone could not be reproduced without incorporating temperature gradients in the simulations. Incorporating temperature fluctuations resulted in an increase in the annual groundwater carbon fluxes to the river by 170 % to 3.3 g m-2 d-1, while including water table variations resulted in an overall decrease in the simulated fluxes. We conclude that spatial microbial and redox zonation as well as temporal fluctuations of temperature and water table depth contribute significantly to subsurface carbon fluxes in flood plains and need to be represented appropriately in model simulations.« less

History and anatomy of subsurface ice on Mars

NASA Astrophysics Data System (ADS)

Schorghofer, Norbert; Forget, Francois

2012-08-01

Ice buried beneath a thin layer of soil has been revealed by neutron spectroscopy and explored by the Phoenix Mars Lander. It has also been exposed by recent impacts. This subsurface ice is thought to lose and gain volume in response to orbital variations (Milankovitch cycles). We use a powerful numerical model to follow the growth and retreat of near-surface ice as a result of regolith-atmosphere exchange continuously over millions of years. If a thick layer of almost pure ice has been deposited recently, it has not yet reached equilibrium with the atmospheric water vapor and may still remain as far equatorward as 43°N, where ice has been revealed by recent impacts. A potentially observable consequence is present-day humidity output from the still retreating ice. We also demonstrate that in a sublimation environment, subsurface pore ice can accumulate in two ways. The first mode, widely known, is the progressive filling of pores by ice over a range of depths. The second mode occurs on top of an already impermeable ice layer; subsequent ice accumulates in the form of pasted on horizontal layers such that beneath the ice table, the pores are completely full with ice. Most or all of the pore ice on Mars today may be of the second type. At the Phoenix landing site, where such a layer is also expected to exist above an underlying ice sheet, it may be extremely thin, due to exceptionally small variations in ice stability over time.

Induction heaters used to heat subsurface formations

DOEpatents

Nguyen, Scott Vinh [Houston, TX; Bass, Ronald M [Houston, TX

2012-04-24

A heating system for a subsurface formation includes an elongated electrical conductor located in the subsurface formation. The electrical conductor extends between at least a first electrical contact and a second electrical contact. A ferromagnetic conductor at least partially surrounds and at least partially extends lengthwise around the electrical conductor. The electrical conductor, when energized with time-varying electrical current, induces sufficient electrical current flow in the ferromagnetic conductor such that the ferromagnetic conductor resistively heats to a temperature of at least about 300.degree. C.

May cause environmental damage the diversion of the Danube in the Szigetköz area, Hungary?

NASA Astrophysics Data System (ADS)

Novak, Brigitta

2009-04-01

has no connection, and these sections of river bed already turned muddy, and organic material accumulated in the sediment, which further increase the rate of reduction and decrease the flow rate. The extreme values, and values not following the trend in the time series of chemical parameters can be explained only by further detailed examination. On the whole, it is unambiguously clear, since the diversion of Danube the water replenishment of the meandering sub-branch system is poorer, causing unfavourable changes in water chemistry both in surface and subsurface water. Other research teams of the monitoring system, studying ecology, have found that the water regulation has major adverse effects on the biology as well. The typical floodplain vegetation is changing toward species tolerating dryness. In the water flora and fauna alters gradually as well, due to the changing chemical characteristic of water and the decreasing flow. Considering that the abiotic environment react slower than the biotic to the anthropologic influence, we do not have a clear view how the water quality will deteriorate on the long run. Furthermore, the changes in flora and fauna have already caused changes in water chemistry, and these changes will persist causing a slow but continuous diversion from the original, natural values. In Szigetköz area, the decreased flow and the deteriorating quality of surface water will endanger the important subsurface drinking water aquifer on the long-term.

Diversity of squalene-hopene cyclases in a tropical carbonate-rich environment

NASA Astrophysics Data System (ADS)

Leavitt, W. D.; Pearson, A.

2007-12-01

Hopanoids are isoprenoid lipids which derive primarily from bacteria and are ubiquitous in contemporary Earth surface environments. In the geologic record, hopanes found in sedimentary rocks are used as proxies to help decipher ancient biological communities. However, in contrast to the ubiquity of these lipid products, biosynthesis of hopanoids appears to be a relatively rare physiological trait among bacteria in complex environmental communities. We have recently estimated that fewer than one in ten bacterial cells in soils and fewer than one in twenty bacterial cells in the ocean contains the gene squalene-hopene cyclase (sqhC) [1]. Biosynthesis of hopanoids is rarer in natural communities than it is among species that have been propagated in pure culture [2]. Here we continue our previous work to survey the phylogeny and diversity of hopanoid producers using culture-independent methods. In particular, genes affiliated with known cyanobacterial sequences were not detected in the contemporary environments analyzed previously [1]. One possible explanation is that hopanoid-producing strains of cyanobacteria are regionally localized. It has been suggested that throughout the long-term sedimentary record there is a correlation between 2-methylhopanoid index (a putative indicator of cyanobacterial biomass) and the global prevalence of shallow carbonate platform environments [3], and in previous work we did not analyze any such environments. To address this question we surveyed a land-sea gradient across the Bahamian island of San Salvador. Samples were taken from upland soil, a hypersaline lake, a tidal creek, and the shallow open ocean. The data are remarkably similar to our previous results: environmental sqhCs average < 65% translated amino acid identity to their closest relatives in public databases, and non- cyanobacterial sequences continue to dominate. We will discuss the challenges these results pose for deciphering the global distribution of microbially

Lack of correlation of desiccation and radiation tolerance in microorganisms from diverse extreme environments tested under anoxic conditions

PubMed Central

Bohmeier, Maria; Perras, Alexandra K; Schwendner, Petra; Rabbow, Elke; Moissl-Eichinger, Christine; Cockell, Charles S; Vannier, Pauline; Marteinsson, Viggo T; Monaghan, Euan P; Ehrenfreund, Pascale; Garcia-Descalzo, Laura; Gómez, Felipe; Malki, Moustafa; Amils, Ricardo; Gaboyer, Frédéric; Westall, Frances; Cabezas, Patricia; Walter, Nicolas; Rettberg, Petra

2018-01-01

Abstract Four facultative anaerobic and two obligate anaerobic bacteria were isolated from extreme environments (deep subsurface halite mine, sulfidic anoxic spring, mineral-rich river) in the frame MASE (Mars Analogues for Space Exploration) project. The isolates were investigated under anoxic conditions for their survivability after desiccation up to 6 months and their tolerance to ionizing radiation up to 3000 Gy. The results indicated that tolerances to both stresses are strain-specific features. Yersinia intermedia MASE-LG-1 showed a high desiccation tolerance but its radiation tolerance was very low. The most radiation-tolerant strains were Buttiauxella sp. MASE-IM-9 and Halanaerobium sp. MASE-BB-1. In both cases, cultivable cells were detectable after an exposure to 3 kGy of ionizing radiation, but cells only survived desiccation for 90 and 30 days, respectively. Although a correlation between desiccation and ionizing radiation resistance has been hypothesized for some aerobic microorganisms, our data showed that there was no correlation between tolerance to desiccation and ionizing radiation, suggesting that the physiological basis of both forms of tolerances is not necessarily linked. In addition, these results indicated that facultative and obligate anaerobic organisms living in extreme environments possess varied species-specific tolerances to extremes. PMID:29474542

Water and nitrogen requirements of subsurface drip irrigated pomegranate

USDA-ARS?s Scientific Manuscript database

Surface drip irrigation is a well-developed practice for both annual and perennial crops. The use of subsurface drip is a well-established practice in many annual row crops, e.g. tomatoes, strawberries, lettuce. However, the use of subsurface drip on perennial crops has been slow to develop. With th...

Evaluating roadway subsurface drainage practices - phase II : [tech transfer summary].

DOT National Transportation Integrated Search

2015-04-01

The presence of subsurface drainage systems (e.g., granular bases or : outlets) is generally believed to be beneficial to the performance of : various pavement types. Well-performing subsurface drainage systems : form an important aspect of pavement ...

Urban heat fluxes in the subsurface of Cologne, Germany

NASA Astrophysics Data System (ADS)

Zhu, K.; Bayer, P.; Blum, P.

2012-04-01

Urbanization during the last hundred years has led to both environmental and thermal impacts on the subsurface. The urban heat island (UHI) effect is mostly described as an atmospheric phenomenon, where the measured aboveground temperatures in cities are elevated in comparison to undisturbed rural regions. However, UHIs can be found below, as well as above ground. A large amount of anthropogenic heat migrates into the urban subsurface, which also raises the ground temperature and permanently changes the thermal conditions in shallow aquifers. The main objective of our work is to study and determine the urban heat fluxes in Cologne, Germany, and to improve our understanding of the dynamics of subsurface energy fluxes in UHIs. Ideally, our findings will contribute to strategic and more sustainable geothermal use in cities. For a quantitative analysis of the energy fluxes within the subsurface and across the atmospheric boundary, two and three-dimensional coupled numerical flow and heat transport models were developed. The simulation results indicate that during the past hundred years, an average vertical urban heat flux that ranges between 80 and 375 mW m-2 can be deduced. Thermal anomalies have migrated into the local urban aquifer system and they reach a depth of about 150 m. In this context, the influence of the regional groundwater flow on the subsurface heat transport and temperature development is comprehensively discussed.

Nematoda from the terrestrial deep subsurface of South Africa.

PubMed

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

2011-06-02

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

Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation

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

Williams, Kenneth H.; Kemna, Andreas; Wilkins, Michael J.

2009-08-05

Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1more » Hz) andwasdependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous phase response were enriched in Fe(II), dissolved sulfide, and cell-associated FeS nanoparticles. The accumulation of mineral precipitates and electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the anomalous IP response and revealing the usefulness of multifrequency IP measurements for monitoring mineralogical and geochemical changes accompanying stimulated subsurface bioremediation.« less

Modified Lipid Extraction Methods for Deep Subsurface Shale

PubMed Central

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

2017-01-01

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

Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments.

PubMed

Sharp, Christine E; Brady, Allyson L; Sharp, Glen H; Grasby, Stephen E; Stott, Matthew B; Dunfield, Peter F

2014-06-01

Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable temperatures in the tropics. Studies to date suggest that this temperature-diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R(2) values up to 0.62 for neutral-alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13-20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible.

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.

Radar Soundings of the Subsurface of Mars

NASA Technical Reports Server (NTRS)

Picardi, Giovanni; Plaut, Jeffrey J.; Biccari, Daniela; Bombaci, Ornella; Calabrese, Diego; Cartacci, Marco; Cicchetti, Andrea; Clifford, Stephen M.; Edenhofer, Peter; Farrell, William M.;

Impact of transgenic Cry1Ac + CpTI cotton on diversity and dynamics of rhizosphere bacterial community of different root environments.

PubMed

Li, Peng; Li, Yongchun; Shi, Jialiang; Yu, Zhibo; Pan, Aihu; Tang, Xueming; Ming, Feng

2018-05-08

The objective of this study was to characterize the diversity and dynamics of rhizosphere bacterial community, especially the response of dominant and rare bacterial taxa to the cultivation of Bt cotton for different root environments at different growth stages. qPCR analyses indicated that bacterial abundances of the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different at seedling and bolling stages. But no significant differences were detected between the same root zones from Bt and the conventional cotton varieties. Total bacterial genera had similar pattern with dominant genera in abundance, and with rare genera in richness to the changes of bacterial community, respectively. Although the rhizosphere bacterial diversity of the three cotton varieties changed in taproot and lateral root, no significant differences were detected in the same root environments between Bt and conventional cotton. Moreover, Soil pH was more correlated with variations in the bacterial community composition than Bt proteins. In conclusion, these results revealed no indication that rhizosphere bacterial community of Bt cotton had different response to increased Bt protein regarding the same root environment. In particular, dominant and rare bacterial taxa showed the variation in diversity and community composition in different root microhabitats. Copyright © 2018. Published by Elsevier B.V.

Five willow varieties cultivated across diverse field environments reveal stem density variation associated with high tension wood abundance

PubMed Central

Berthod, Nicolas; Brereton, Nicholas J. B.; Pitre, Frédéric E.; Labrecque, Michel

2015-01-01

Sustainable and inexpensive production of biomass is necessary to make biofuel production feasible, but represents a challenge. Five short rotation coppice willow cultivars, selected for high biomass yield, were cultivated on sites at four diverse regions of Quebec in contrasting environments. Wood composition and anatomical traits were characterized. Tree height and stem diameter were measured to evaluate growth performance of the cultivars according to the diverse pedoclimatic conditions. Each cultivar showed very specific responses to its environment. While no significant variation in lignin content was observed between sites, there was variation between cultivars. Surprisingly, the pattern of substantial genotype variability in stem density was maintained across all sites. However, wood anatomy did differ between sites in a cultivar (producing high and low density wood), suggesting a probable response to an abiotic stress. Furthermore, twice as many cellulose-rich G-fibers, comprising over 50% of secondary xylem, were also found in the high density wood, a finding with potential to bring higher value to the lignocellulosic bioethanol industry. PMID:26583024

Cultivation of Hard-To-Culture Subsurface Mercury-Resistant Bacteria and Discovery of New merA Gene Sequences▿

PubMed Central

Rasmussen, L. D.; Zawadsky, C.; Binnerup, S. J.; Øregaard, G.; Sørensen, S. J.; Kroer, N.

2008-01-01

Mercury-resistant bacteria may be important players in mercury biogeochemistry. To assess the potential for mercury reduction by two subsurface microbial communities, resistant subpopulations and their merA genes were characterized by a combined molecular and cultivation-dependent approach. The cultivation method simulated natural conditions by using polycarbonate membranes as a growth support and a nonsterile soil slurry as a culture medium. Resistant bacteria were pregrown to microcolony-forming units (mCFU) before being plated on standard medium. Compared to direct plating, culturability was increased up to 2,800 times and numbers of mCFU were similar to the total number of mercury-resistant bacteria in the soils. Denaturing gradient gel electrophoresis analysis of DNA extracted from membranes suggested stimulation of growth of hard-to-culture bacteria during the preincubation. A total of 25 different 16S rRNA gene sequences were observed, including Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. The diversity of isolates obtained by direct plating included eight different 16S rRNA gene sequences (Alpha- and Betaproteobacteria and Actinobacteria). Partial sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One of the sequences did not result in a match in the BLAST search. The results illustrate the power of integrating advanced cultivation methodology with molecular techniques for the characterization of the diversity of mercury-resistant populations and assessing the potential for mercury reduction in contaminated environments. PMID:18441111

Yucca Mountain Project Subsurface Facilities Design

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

A. Linden; R.S. Saunders; R.J. Boutin

2002-11-19

Four units of the Topopah Springs formation (volcanic tuff) are considered for the proposed repository: the upper lithophysal, the middle non-lithophysal, the lower lithophysal, and the lower non-lithophysal. Yucca Mountain was recently designated the site for a proposed repository to dispose of spent nuclear fuel and high-level radioactive waste. Work is proceeding to advance the design of subsurface facilities to accommodate emplacing waste packages in the proposed repository. This paper summarized recent progress in the design of subsurface layout of the proposed repository. The original Site Recommendation (SR) concept for the subsurface design located the repository largely within the lowermore » lithophysal zone (approximately 73%) of the Topopah The Site Recommendation characterized area suitable for emplacement consisted of the primary upper block, the lower block and the southern upper block extension. The primary upper block accommodated the mandated 70,000 metric tons of heavy metal (MTHM) at a 1.45 kW/m hear heat load. Based on further study of the Site Recommendation concept, the proposed repository siting area footprint was modified to make maximum use of available site characterization data, and thus, reduce uncertainties associated with performance assessment. As a result of this study, a modified repository footprint has been proposed and is presently being review for acceptance by the DOE. A panel design concept was developed to reduce overall costs and reduce the overall emplacement schedule. This concept provides flexibility to adjust the proposed repository subsurface layout with time, as it makes it unnecessary to ''commit'' to development of a large single panel at the earliest stages of construction. A description of the underground layout configuration and influencing factors that affect the layout configuration are discussed in the report.« less

Molecular Analysis of the In Situ Growth Rates of Subsurface Geobacter Species

PubMed Central

Giloteaux, Ludovic; Barlett, Melissa; Chavan, Milind A.; Smith, Jessica A.; Williams, Kenneth H.; Wilkins, Michael; Long, Philip; Lovley, Derek R.

2013-01-01

Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole-genome microarray analyses of a subsurface isolate of Geobacter uraniireducens, grown under a variety of conditions, identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, was further evaluated with quantitative reverse transcription-PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r2 = 0.90) with specific growth rates. Therefore, expression patterns of rpsC were used to estimate specific growth rates of Geobacter species during an in situ uranium bioremediation field experiment in which acetate was added to the groundwater to promote dissimilatory metal reduction. Initially, increased availability of acetate in the groundwater resulted in higher expression of Geobacter rpsC, and the increase in the number of Geobacter cells estimated with fluorescent in situ hybridization compared well with specific growth rates estimated from levels of in situ rpsC expression. However, in later phases, cell number increases were substantially lower than predicted from rpsC transcript abundance. This change coincided with a bloom of protozoa and increased attachment of Geobacter species to solid phases. These results suggest that monitoring rpsC expression may better reflect the actual rate that Geobacter species are metabolizing and growing during in situ uranium bioremediation than changes in cell abundance. PMID:23275510

Distribution, Numbers, and Diversity of ESBL-Producing E. coli in the Poultry Farm Environment

PubMed Central

Blaak, Hetty; van Hoek, Angela H. A. M.; Hamidjaja, Raditijo A.; van der Plaats, Rozemarijn Q. J.; Kerkhof-de Heer, Lianne; de Roda Husman, Ana Maria; Schets, Franciska M.

2015-01-01

This study aimed to discern the contribution of poultry farms to the contamination of the environment with ESBL-producing Escherichia coli and therewith, potentially to the spread of these bacteria to humans and other animals. ESBL-producing E. coli were detected at all investigated laying hen farms (n = 5) and broiler farms (n = 3) in 65% (46/71) and 81% (57/70) of poultry faeces samples, respectively. They were detected in rinse water and run-off water (21/26; 81%), other farm animals (11/14; 79%), dust (21/35; 60%), surface water adjacent to farms (20/35; 57%), soil (48/87; 55%), on flies (11/73; 15%), and in barn air (2/33; 6%). The highest prevalence and concentrations in the outdoor environment were observed in soil of free-range areas at laying hen farms (100% of samples positive, geometric mean concentration 2.4×104 cfu/kg), and surface waters adjacent to broiler farms during, or shortly after, cleaning between production rounds (91% of samples positive, geometric mean concentration 1.9×102 cfu/l). The diversity of ESBL-producing E. coli variants with respect to sequence type, phylogenetic group, ESBL-genotype and antibiotic resistance profile was high, especially on broiler farms where on average 16 different variants were detected, and the average Simpson’s Indices of diversity (SID; 1–D) were 0.93 and 0.94 among flock and environmental isolates respectively. At laying hen farms on average nine variants were detected, with SIDs of 0.63 (flock isolates) and 0.77 (environmental isolates). Sixty percent of environmental isolates were identical to flock isolates at the same farm. The highest proportions of ‘flock variants’ were observed in dust (94%), run-off gullies (82%), and barn air (67%), followed by surface water (57%), soil (56%), flies (50%) and other farm animals (35%).The introduction of ESBL-producing E. coli from poultry farms to the environment may pose a health risk if these bacteria reach places where people may become exposed. PMID

Diversity in the Workplace. Symposium.

ERIC Educational Resources Information Center

2002

Three papers comprise this symposium on diversity in the workplace. "Factors That Assist and Barriers That Hinder the Success of Diversity Initiatives in Multinational Corporations" (Rose Mary Wentling) reports that factors that assisted in the success were classified under diversity department, human, and work environment; barriers were…

Diffusion and aggregation of subsurface radiation defects in lithium fluoride nanocrystals

NASA Astrophysics Data System (ADS)

Voitovich, A. P.; Kalinov, V. S.; Martynovich, E. F.; Stupak, A. P.; Runets, L. P.

2015-09-01

Lithium fluoride nanocrystals were irradiated by gamma rays at a temperature below the temperature corresponding to the mobility of anion vacancies. The kinetics of the aggregation of radiation-induced defects in subsurface layers of nanocrystals during annealing after irradiation was elucidated. The processes that could be used to determine the activation energy of the diffusion of anion vacancies were revealed. The value of this energy in subsurface layers was obtained. For subsurface layers, the concentrations ratio of vacancies and defects consisting of one vacancy and two electrons was found. The factors responsible for the differences in the values of the activation energies and concentration ratios in subsurface layers and in the bulk of the crystals were discussed.

Subsurface Hydrology: Data Integration for Properties and Processes

NASA Astrophysics Data System (ADS)

Hyndman, David W.; Day-Lewis, Frederick D.; Singha, Kamini

Groundwater is a critical resource and the PrinciPal source of drinking water for over 1.5 billion people. In 2001, the National Research Council cited as a "grand challenge" our need to understand the processes that control water movement in the subsurface. This volume faces that challenge in terms of data integration between complex, multi-scale hydrologie processes, and their links to other physical, chemical, and biological processes at multiple scales. Subsurface Hydrology: Data Integration for Properties and Processes presents the current state of the science in four aspects: • Approaches to hydrologie data integration • Data integration for characterization of hydrologie properties • Data integration for understanding hydrologie processes • Meta-analysis of current interpretations Scientists and researchers in the field, the laboratory, and the classroom will find this work an important resource in advancing our understanding of subsurface water movement.

Quantitative subsurface analysis using frequency modulated thermal wave imaging

NASA Astrophysics Data System (ADS)

Subhani, S. K.; Suresh, B.; Ghali, V. S.

2018-01-01

Quantitative depth analysis of the anomaly with an enhanced depth resolution is a challenging task towards the estimation of depth of the subsurface anomaly using thermography. Frequency modulated thermal wave imaging introduced earlier provides a complete depth scanning of the object by stimulating it with a suitable band of frequencies and further analyzing the subsequent thermal response using a suitable post processing approach to resolve subsurface details. But conventional Fourier transform based methods used for post processing unscramble the frequencies with a limited frequency resolution and contribute for a finite depth resolution. Spectral zooming provided by chirp z transform facilitates enhanced frequency resolution which can further improves the depth resolution to axially explore finest subsurface features. Quantitative depth analysis with this augmented depth resolution is proposed to provide a closest estimate to the actual depth of subsurface anomaly. This manuscript experimentally validates this enhanced depth resolution using non stationary thermal wave imaging and offers an ever first and unique solution for quantitative depth estimation in frequency modulated thermal wave imaging.

Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Hibbett, David

2018-05-18

David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

The Subsurface Flow and Transport Laboratory: A New Department of Energy User's Facility for Intermediate-Scale Experimentation

NASA Astrophysics Data System (ADS)

Wietsma, T. W.; Oostrom, M.; Foster, N. S.

2003-12-01

Intermediate-scale experiments (ISEs) for flow and transport are a valuable tool for simulating subsurface features and conditions encountered in the field at government and private sites. ISEs offer the ability to study, under controlled laboratory conditions, complicated processes characteristic of mixed wastes and heterogeneous subsurface environments, in multiple dimensions and at different scales. ISEs may, therefore, result in major cost savings if employed prior to field studies. A distinct advantage of ISEs is that researchers can design physical and/or chemical heterogeneities in the porous media matrix that better approximate natural field conditions and therefore address research questions that contain the additional complexity of processes often encountered in the natural environment. A new Subsurface Flow and Transport Laboratory (SFTL) has been developed for ISE users in the Environmental Spectroscopy & Biogeochemistry Facility in the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). The SFTL offers a variety of columns and flow cells, a new state-of-the-art dual-energy gamma system, a fully automated saturation-pressure apparatus, and analytical equipment for sample processing. The new facility, including qualified staff, is available for scientists interested in collaboration on conducting high-quality flow and transport experiments, including contaminant remediation. Close linkages exist between the SFTL and numerical modelers to aid in experimental design and interpretation. This presentation will discuss the facility and outline the procedures required to submit a proposal to use this unique facility for research purposes. The W. R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility, is sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments

PubMed Central

Sharp, Christine E; Brady, Allyson L; Sharp, Glen H; Grasby, Stephen E; Stott, Matthew B; Dunfield, Peter F

2014-01-01

Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable temperatures in the tropics. Studies to date suggest that this temperature–diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5–99 °C and a pH range of 1.8–9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R2 values up to 0.62 for neutral–alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13–20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible. PMID:24430481

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.

The Updated AGU Ethics Policy: Supporting Inclusive and Diverse Field and Lab Environments within the Geosciences.

NASA Astrophysics Data System (ADS)

Williams, B. M.; McPhaden, M. J.; Gundersen, L. C.

2017-12-01

The American Geophysical Union (AGU), a scientific society of >60,000 members worldwide, has established a set of scientific integrity and professional ethics guidelines for the actions of its members, for the governance of the union in its internal activities, and for the operations and participation in its publications and scientific meetings. More recently AGU has undertaken actions to help address the issue of harassment in the sciences and other work climate issues; and, where applied more broadly as a code of standard behavior, will help address tangential issues of diversity and inclusion. This presentation will highlight the proposed policy changes and additional resources now in place, as they apply to field and lab environments. Progress to date and remaining challenges of this effort will be discussed, including AGU's work to provide additional program strength in the areas of Ethics, Diversity and Inclusion.

WISDOM GPR aboard the ExoMars rover : a powerful instrument to investigate the state and distribution of water in the Martian shallow subsurface

NASA Astrophysics Data System (ADS)

Dorizon, S.; Ciarletti, V.; Clifford, S. M.; Plettemeier, D.

2013-12-01

The Water Ice Subsurface Deposits Observation on Mars (WISDOM) Ground Penetrating Radar (GPR) has been selected as part of the Pasteur payload for the European Space Agency (ESA) ExoMars 2018 mission. The main scientific objectives of the mission are to search for evidence of past or present life and to characterize the water/geochemical environment as a function of depth in the shallow subsurface. A rover equipped with a 2 meters capacity drill and a suite of instruments will land on Mars in 2018, collect and analyze samples from outcrops and at depth. The WISDOM GPR will support these activities by sounding the subsurface and provide understanding of the geologic context and evolution of the local environment. When operated on the ExoMars rover, WISDOM will offer the possibility to understand the 3D geology in terms of stratigraphy and structure, spatial heterogeneities as well as the compositional and electromagnetic properties of the subsurface. According to these scientific objectives, this radar has been designed as a polarimetric step frequency GPR, operating from 0.5 GHz to 3GHz, which allows the sounding of the first 3 meters of the subsurface with a vertical resolution of a few centimeters. The importance of this GPR is particularly enhanced by its ability to investigate the water content, state (ice or liquid) and distribution in the subsurface, which are crucial clues to constrain the possibility of life traces evidence. In addition, WISDOM will be operated at a distance of 30 cm above the ground. This configuration allows the monitoring of potential transient liquid water that could appear on Mars surface. Results from several laboratory tests and a campaign in alpine ice caves in Austria are consistent with the expected performances of WISDOM regarding the question of water characterization. The specific configuration of the antennas allows the retrieval of the first layer permittivity value from the surface echo, which is related to the water content

25 CFR 211.22 - Leases for subsurface storage of oil or gas.

Code of Federal Regulations, 2011 CFR

2011-04-01

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25 CFR 211.22 - Leases for subsurface storage of oil or gas.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 25 Indians 1 2012-04-01 2011-04-01 true Leases for subsurface storage of oil or gas. 211.22... TRIBAL LANDS FOR MINERAL DEVELOPMENT How To Acquire Leases § 211.22 Leases for subsurface storage of oil... subsurface storage of oil or gas, irrespective of the lands from which production is initially obtained. The...

25 CFR 211.22 - Leases for subsurface storage of oil or gas.

Code of Federal Regulations, 2010 CFR

2010-04-01

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25 CFR 211.22 - Leases for subsurface storage of oil or gas.

Code of Federal Regulations, 2014 CFR

2014-04-01

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25 CFR 211.22 - Leases for subsurface storage of oil or gas.

Code of Federal Regulations, 2013 CFR

2013-04-01

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

PubMed

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

2013-01-01

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

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

PubMed Central

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

2013-01-01

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

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

Patterns in coupled water and energy cycle: Modeling, synthesis with observations, and assessing the subsurface-landsurface interactions

NASA Astrophysics Data System (ADS)

Rahman, A.; Kollet, S. J.; Sulis, M.

2013-12-01

In the terrestrial hydrological cycle, the atmosphere and the free groundwater table act as the upper and lower boundary condition, respectively, in the non-linear two-way exchange of mass and energy across the land surface. Identifying and quantifying the interactions among various atmospheric-subsurface-landsurface processes is complicated due to the diverse spatiotemporal scales associated with these processes. In this study, the coupled subsurface-landsurface model ParFlow.CLM was applied over a ~28,000 km2 model domain encompassing the Rur catchment, Germany, to simulate the fluxes of the coupled water and energy cycle. The model was forced by hourly atmospheric data from the COSMO-DE model (numerical weather prediction system of the German Weather Service) over one year. Following a spinup period, the model results were synthesized with observed river discharge, soil moisture, groundwater table depth, temperature, and landsurface energy flux data at different sites in the Rur catchment. It was shown that the model is able to reproduce reasonably the dynamics and also absolute values in observed fluxes and state variables without calibration. The spatiotemporal patterns in simulated water and energy fluxes as well as the interactions were studied using statistical, geostatistical and wavelet transform methods. While spatial patterns in the mass and energy fluxes can be predicted from atmospheric forcing and power law scaling in the transition and winter months, it appears that, in the summer months, the spatial patterns are determined by the spatially correlated variability in groundwater table depth. Continuous wavelet transform techniques were applied to study the variability of the catchment average mass and energy fluxes at varying time scales. From this analysis, the time scales associated with significant interactions among different mass and energy balance components were identified. The memory of precipitation variability in subsurface hydrodynamics

Metabolic Strategies in Energy-Limited Microbial Communities in the Anoxic Subsurface (Frasassi Cave System, Italy)

NASA Astrophysics Data System (ADS)

McCauley, R. L.; Jones, D. S.; Schaperdoth, I.; Steinberg, L.; Macalady, J. L.

2010-12-01

Two major sources of energy, light and chemical potential, are available to microorganisms. However, energy is not always abundant and is often a limiting factor in microbial survival and replication. The anoxic, terrestrial subsurface offers a unique opportunity to study microorganisms and their potentially novel metabolic strategies that are relevant for understanding biogeochemistry and biosignatures as related to the non-photosynthetic, energy-limited environments on the modern and ancient Earth and elsewhere in the solar system. Geochemical data collected in a remote stratified lake 600 m below ground surface in the sulfidic Frasassi cave system (Italy) suggest that little redox energy is available for life, consistent with low signal from domain-specific FISH probes. The carbon isotope signatures of biofilms (-33‰) and DIC (-9‰) in the anoxic water suggest in situ production by lithoautotrophs using RuBisCO. 16S rDNA libraries constructed from the biofilm are dominated by diverse sulfate reducing bacteria. The remaining bacterial and archaeal clones affiliate with more than 11 major uncultivated or novel prokaryotic lineages. Diverse dsrAB gene sequences are consistent with high sulfate concentrations and undetectable or extremely low oxygen, nitrate, and iron concentrations. However, the electron donor for sulfate reduction is unclear. Methane is detectable in the anoxic water although no 16S rDNA sequences associated with known methanogens or anaerobic methane oxidizers were retrieved. mcrA gene sequences retrieved from the biofilm by cloning are not related to cultivated methanogens or to known anaerobic methane oxidizers. Non-purgable organic carbon (NPOC) is below detection limits (i.e. <42 μM acetate) suggesting that alternative electron donors or novel metabolisms may be important. A sample collected by cave divers in October 2009 was pyrosequenced at the Pennsylvania State University Genomics Core Facility using Titanium chemistry (454 Life

Influence of hydrological, biogeochemical and temperature transients on subsurface carbon fluxes in a flood plain environment

DOE PAGES

Arora, Bhavna; Spycher, Nicolas F.; Steefel, Carl I.; ...

2016-02-12

Flood plains play a potentially important role in the global carbon cycle. The accumulation of organic matter in flood plains often induces the formation of chemically reduced groundwater and sediments along riverbanks. In this study, our objective is to evaluate the cumulative impact of such reduced zones, water table fluctuations, and temperature gradients on subsurface carbon fluxes in a flood plain at Rifle, Colorado located along the Colorado River. 2-D coupled variably-saturated, non-isothermal flow and biogeochemical reactive transport modeling was applied to improve our understanding of the abiotic and microbially mediated reactions controlling carbon dynamics at the Rifle site. Modelmore » simulations considering only abiotic reactions (thus ignoring microbial reactions) underestimated CO 2 partial pressures observed in the unsaturated zone and severely underestimated inorganic (and overestimated organic) carbon fluxes to the river compared to simulations with biotic pathways. Both model simulations and field observations highlighted the need to include microbial contributions from chemolithoautotrophic processes (e.g., Fe +2 and S -2 oxidation) to match locally-observed high CO 2 concentrations above reduced zones. Observed seasonal variations in CO 2 concentrations in the unsaturated zone could not be reproduced without incorporating temperature gradients in the simulations. Incorporating temperature fluctuations resulted in an increase in the annual groundwater carbon fluxes to the river by 170 % to 3.3 g m -2 d -1, while including water table variations resulted in an overall decrease in the simulated fluxes. We thus conclude that spatial microbial and redox zonation as well as temporal fluctuations of temperature and water table depth contribute significantly to subsurface carbon fluxes in flood plains and need to be represented appropriately in model simulations.« less

Clonal plasticity and diversity facilitates the adaptation of Rhododendron aureum Georgi to alpine environment

PubMed Central

Wang, Xiaolong; Zhao, Wei; Li, Lin; You, Jian; Ni, Biao

2018-01-01

Four small oval populations and five large intensive populations of Rhododendron aureum growing at the alpine in Changbai Mountain (China) were studied in two types of habitat (in the tundra and in Betula ermanii forest). Identification and delimitation of genets were inferred from excavation in small populations and from amplified fragment length polymorphism (AFLP) markers by the standardized sampling design in large populations. Clonal architecture and clonal diversity were then estimated. For the four small populations, they were monoclonal, the spacer length (18.6 ± 5.6 in tundra, 29.7 ± 9.7 in Betula ermanii forest, P < 0.05) was shorter and branching intensity (136.7 ± 32.9 in tundra, 43.4 ± 12.3 in Betula ermanii forest, P < 0.05) was higher in the tundra than that in Betula ermanii forest. For the five large populations, they were composed of multiple genets with high level of clonal diversity (Simpson’s index D = 0.84, clonal richness R = 0.25, Fager's evenness E = 0.85); the spatial distribution of genets showed that the clonal growth strategy of R. aureum exhibits both guerilla and phalanx. Our results indicate that the clonal plasticity of R. aureum could enhance exploitation of resource heterogeneity and in turn greatly contribute to maintenance or improvement of fitness and the high clonal diversity of R. aureum increase the evolutionary rates to adapt the harsh alpine environment in Changbai Mountain. PMID:29746526

Characterization of active members in C and N cycles in the subsurface environment of the Witwatersrand Basin

NASA Astrophysics Data System (ADS)

Lindsay, M. R.; Lau, C. M.; Tetteh, G.; Snyder, L.; Kieft, T. L.; Lollar, B. S.; Li, L.; Maphanga, S.; van Heerden, E.; Onstott, T. C.

2012-12-01

Fracture fluid from various depths and locations in Beatrix gold mine (Gold Fields Ltd.), located in the Welkom region on the 2.9 Ga Witwatersrand Basin of South Africa has been previously studied. Research has shown differential geochemistry data and distinctive community structure which varies from the dominance of different Proteobacterial classes in waters with paleometeoric 18O and 2H signatures including methanotrophs to one dominated by Firmicutes including Candidatus Desulforudis audaxviator-like taxa, which are associated with more saline waters with high concentrations of dissolved H2, hydrocarbons from water-rock reaction and 18O and 2H signatures above the Global Meteoric Water Line. Archaea seem to be a minority and all are euryarchaeota including methanogenic genera. The question is:Which of them are actively driving the subsurface C and N cycles? At shaft 3 on level 26, 1.3 kmbls, fracture water from 42 m behind the tunnel wall located in the Main quartzite formation was collected and analyzed. The temperature, pH, Eh, dissolved O2 and salinity of this hydrocarbon-containing fracture water ranged from 35 to 38°C, 8.2 to 8.8, -30 to -100 mV, 0.3 to 30 μM and 4.2 to 4.3 ppt, respectively. Gas comprised 60% CH4 and 20% N2. The same fracture formerly yielded Halicephalobus mephisto, the first reported subsurface nematode. Microorganisms were captured on filters in two field seasons. Defined by 16S rDNA, 2011 January sample contains β-Proteobacteria (50%), Firmicutes (39%) and α- and γ-Proteobacteria (7%). Of the Firmicutes, 90% were represented by Ca. D. audaxviator. All archaea detected are closestly related to sequences also reported from South African gold mines, with Crenarchaeota accounting for 77% of the clones. Prospective methane-oxidation and production were assessed by amplifying genes encoding for particulate methane monooxygenase alpha subunit (pmoA) and methyl-coenzyme M reductase alpha subunit (mcrA). PmoA genes of Type II

Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site