Science.gov

Sample records for subsurface environments diversity

  1. Microbial Diversity of Groundwater from Deep Subsurface Environment

    NASA Astrophysics Data System (ADS)

    Lin, L.; Onstott, T. C.; Hall, J.

    2002-12-01

    The subsurface environment harbors one of the most abundant reservoirs of biomass on Earth. The distribution of microbial ecosystems and the diversity of microbial metabolisms there remained poorly understood due to lack of detailed sampling over three-dimensional space with extremely heterogeneous characteristics. South African Au mines, however, provide the best access in the world to various types of groundwater and rocks at depths up to 4 km below surface. In this study, we present our recent analyses of microbial community structure of groundwater (with residence time of several million years) collected from depths between 850 to 1500 mbsl of Beatrix Au mine, South Africa. Five groundwater samples were collected anaerobically from freshly drilling boreholes with flow rates of 1 to 38 L/min. Cells were concentrated through filtration and total DNA were extracted from filters and PCR-amplified with primers targeting 16S rDNA gene. The amplicons were cloned and digested with restriction enzymes to identify the unique clone type. Sequences were obtained through direct sequencing of representative clones and compared with the closest matching sequences deposited in the gene bank for the construction of phylogenetic tree. The archaeal signatures were only found in one sample and close to the lineage of methanosarcina. The most predominant ribotype was similar to the environmental clone found in the same mine under the species level while the rest of ribotypes were either close to those capable of methanogenesis from long-chain alkanes or found in rice field or were distant from other environmental clones reported in previous study (Takai et al., 2001). The bacterial community exhibited a wide range of diversity among samples. Most samples were dominated by sequences close to alpha proteobacteria with various proportions of beta, gamma proteobacteria and environmental clones. A significant proportion of sequences close to thermophilic delta proteobacteria and

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

    USGS Publications Warehouse

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

    2007-01-01

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

  3. Bacterial diversity in a deep-subsurface clay environment.

    PubMed Central

    Boivin-Jahns, V; Ruimy, R; Bianchi, A; Daumas, S; Christen, R

    1996-01-01

    The presence of bacteria in a deep clay sediment was analyzed in a 20-m-long core horizontally drilled from a mine gallery at a depth of 224 m in the Boom clay formation (Mol, Belgium). This clay deposit is the result of a marine sedimentary process that occurred 35 million years ago. Bacterial activities were estimated by measuring respiration on [14C]glucose. Using the same samples, universal primers for the genes coding for eubacterial 16S rRNA were used to amplify extracted DNA. PCR products were then cloned, sequenced, and analyzed by molecular phylogeny. Our data showed a decrease in bacterial densities as a function of distance from the gallery, with few bacteria detectable by culture at more than 80 cm from the gallery wall. PCR experiments showed the presence of bacteria in all samples, and phylogenetic analyses were then used to tentatively identify these organisms. Because of low bacterial densities in deep clay samples, direct counts and enumeration of viable bacteria on diverse culture media remained negative. All experiments, both cultures and PCR, demonstrated the difficulty of analyzing samples that contain only a few poorly active bacteria as it is difficult to avoid a small contamination by active bacteria during sampling. Since the porosity of the Boom clay formation is less than the expected size of bacteria, it is possible that some of the bacteria present in this 35-million-year-old deep clay deposit derive from cells initially trapped during the sedimentation process. PMID:8795233

  4. Physiological and phylogenetic study of microbes from geochemically and hydrogeologically diverse subsurface environments

    SciTech Connect

    Balkwill, D.L.; Reeves, R.H.

    1992-10-01

    An important aspect of our ongoing research effort in the DOE Deep Microbiology Program has been the characterization of certain microorganisms in samples of subsurface materials from various DOE production sites. Recently, it was our responsibility to determine the numbers, diversity, morphological characteristics, and physiological traits (including the potential metabolic capabilities) of the viable, aerobic, chemoheterotrophic micro-organisms in samples that were obtained from the Idaho National Engineering Laboratory (INEL) and the Hanford Reservation (HR) in 1990. It was decided that the physiological characteristics of the INEL and HR subsurface microbial isolates would be analyzed during the current project. We describe here the research on physiological characteristics that has been completed during the eleven-month period covered by the present technical report. Approximately 750 microbial strains were isolated by our laboratory from the INEL and HR samples in 1990 and 1991. During the portion of the current project covered by this interim report, all of these strains were tested for their ability to utilize each of 95 different organic compounds as sole sources of carbon. Identifications are based on how well the carbon utilization patterns of the isolates match those of 659 species and subspecies (i.e., established taxa).

  5. Physiological and phylogenetic study of microbes from geochemically and hydrogeologically diverse subsurface environments

    SciTech Connect

    Balkwill, D.L.; Reeves, R.H.

    1991-01-01

    The present document is an interim technical report in which we describe the research which has been completed during the seven-month period since the start of the grant. Progress is summarized in two main areas. The first is microbiological characterization of subsurface materials from the Hanford reservation and the Idaho National Engineering Laboratory, and the second is phylogenetic characterization of these microorganisms. The major tools used for phylogenetic characterization are RFLP analysis of PCR derived material and 16S rRNA sequencing. A description of manuscripts ready for publication is also provided. 4 refs. (MHB)

  6. Diversity and distribution of anaeromyxobacter strains in a uranium-contaminated subsurface environment with a nonuniform groundwater flow.

    PubMed

    Thomas, Sara H; Padilla-Crespo, Elizabeth; Jardine, Phillip M; Sanford, Robert A; Löffler, Frank E

    2009-06-01

    Versaphilic Anaeromyxobacter dehalogenans strains implicated in hexavalent uranium reduction and immobilization are present in the fractured saprolite subsurface environment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge (IFC) site near Oak Ridge, TN. To provide insight into the in situ distribution of Anaeromyxobacter strains in this system with a nonuniform groundwater flow, 16S rRNA gene-targeted primers and linear hybridization (TaqMan) probes were designed for Oak Ridge IFC Anaeromyxobacter isolates FRC-D1 and FRC-W, along with an Anaeromyxobacter genus-targeted probe and primer set. Multiplex quantitative real-time PCR (mqPCR) was applied to samples collected from Oak Ridge IFC site areas 1 and 3, which are not connected by the primary groundwater flow paths; however, transport between them through cross-plane fractures is hypothesized. Strain FRC-W accounted for more than 10% of the total quantifiable Anaeromyxobacter community in area 1 soils, while strain FRC-D1 was not detected. In FeOOH-amended enrichment cultures derived from area 1 site materials, strain FRC-D1 accounted for 30 to 90% of the total Anaeromyxobacter community, demonstrating that this strain was present in situ in area 1. The area 3 total Anaeromyxobacter abundance exceeded that of area 1 by 3 to 5 orders of magnitude, but neither strain FRC-W- nor FRC-D1-like sequences were quantifiable in any of the 33 area 3 groundwater or sediment samples tested. The Anaeromyxobacter community in area 3 increased from <10(5) cells/g sediment outside the ethanol biostimulation treatment zone to 10(8) cells/g sediment near the injection well, and 16S rRNA gene clone library analysis revealed that representatives of a novel phylogenetic cluster dominated the area 3 Anaeromyxobacter community inside the treatment loop. The combined applications of genus- and strain-level mqPCR approaches along with clone libraries provided novel information on patterns of microbial

  7. Microbial communities in subsurface environments: Diversity, origin, and evolution. Project technical progress report, September 1, 1993--August 31, 1996

    SciTech Connect

    Nierzwicki-Bauer, S.A.

    1994-05-02

    This report summarizes the progress made from 9-1-93 to 5-1-94 on this DOE grant. As participants in the subsurface science program, the authors are assessing the influence of environmental conditions on the distribution and evolution of subsurface microorganisms employing molecular techniques. The approach utilizes 16S rRNA targeted oligonucleotide probes, polymerase chain reaction (PCR) amplification of gene sequences, and sequencing techniques. Continued progress towards identifying target sequences for selected microbial types and groups is being made by analysis of rRNA sequence data for subsurface microorganisms and other microorganisms in the rRNA databases. Hybridization probes for these target sequences are being produced and used to classify isolated strains of subsurface microbes into focus clades useful for testing origins hypotheses.

  8. Physiological and phylogenetic study of microbes from geochemically and hydrogeologically diverse subsurface environments. Interim technical report, November 1, 1991--September 30, 1992

    SciTech Connect

    Balkwill, D.L.; Reeves, R.H.

    1992-10-01

    An important aspect of our ongoing research effort in the DOE Deep Microbiology Program has been the characterization of certain microorganisms in samples of subsurface materials from various DOE production sites. Recently, it was our responsibility to determine the numbers, diversity, morphological characteristics, and physiological traits (including the potential metabolic capabilities) of the viable, aerobic, chemoheterotrophic micro-organisms in samples that were obtained from the Idaho National Engineering Laboratory (INEL) and the Hanford Reservation (HR) in 1990. It was decided that the physiological characteristics of the INEL and HR subsurface microbial isolates would be analyzed during the current project. We describe here the research on physiological characteristics that has been completed during the eleven-month period covered by the present technical report. Approximately 750 microbial strains were isolated by our laboratory from the INEL and HR samples in 1990 and 1991. During the portion of the current project covered by this interim report, all of these strains were tested for their ability to utilize each of 95 different organic compounds as sole sources of carbon. Identifications are based on how well the carbon utilization patterns of the isolates match those of 659 species and subspecies (i.e., established taxa).

  9. In situ detection of anaerobic alkane metabolites in subsurface environments.

    PubMed

    Agrawal, Akhil; Gieg, Lisa M

    2013-01-01

    Alkanes comprise a substantial fraction of crude oil and refined fuels. As such, they are prevalent within deep subsurface fossil fuel deposits and in shallow subsurface environments such as aquifers that are contaminated with hydrocarbons. These environments are typically anaerobic, and host diverse microbial communities that can potentially use alkanes as substrates. Anaerobic alkane biodegradation has been reported to occur under nitrate-reducing, sulfate-reducing, and methanogenic conditions. Elucidating the pathways of anaerobic alkane metabolism has been of interest in order to understand how microbes can be used to remediate contaminated sites. Alkane activation primarily occurs by addition to fumarate, yielding alkylsuccinates, unique anaerobic metabolites that can be used to indicate in situ anaerobic alkane metabolism. These metabolites have been detected in hydrocarbon-contaminated shallow aquifers, offering strong evidence for intrinsic anaerobic bioremediation. Recently, studies have also revealed that alkylsuccinates are present in oil and coal seam production waters, indicating that anaerobic microbial communities can utilize alkanes in these deeper subsurface environments. In many crude oil reservoirs, the in situ anaerobic metabolism of hydrocarbons such as alkanes may be contributing to modern-day detrimental effects such as oilfield souring, or may lead to more beneficial technologies such as enhanced energy recovery from mature oilfields. In this review, we briefly describe the key metabolic pathways for anaerobic alkane (including n-alkanes, isoalkanes, and cyclic alkanes) metabolism and highlight several field reports wherein alkylsuccinates have provided evidence for anaerobic in situ alkane metabolism in shallow and deep subsurface environments.

  10. In situ detection of anaerobic alkane metabolites in subsurface environments

    PubMed Central

    Agrawal, Akhil; Gieg, Lisa M.

    2013-01-01

    Alkanes comprise a substantial fraction of crude oil and refined fuels. As such, they are prevalent within deep subsurface fossil fuel deposits and in shallow subsurface environments such as aquifers that are contaminated with hydrocarbons. These environments are typically anaerobic, and host diverse microbial communities that can potentially use alkanes as substrates. Anaerobic alkane biodegradation has been reported to occur under nitrate-reducing, sulfate-reducing, and methanogenic conditions. Elucidating the pathways of anaerobic alkane metabolism has been of interest in order to understand how microbes can be used to remediate contaminated sites. Alkane activation primarily occurs by addition to fumarate, yielding alkylsuccinates, unique anaerobic metabolites that can be used to indicate in situ anaerobic alkane metabolism. These metabolites have been detected in hydrocarbon-contaminated shallow aquifers, offering strong evidence for intrinsic anaerobic bioremediation. Recently, studies have also revealed that alkylsuccinates are present in oil and coal seam production waters, indicating that anaerobic microbial communities can utilize alkanes in these deeper subsurface environments. In many crude oil reservoirs, the in situ anaerobic metabolism of hydrocarbons such as alkanes may be contributing to modern-day detrimental effects such as oilfield souring, or may lead to more beneficial technologies such as enhanced energy recovery from mature oilfields. In this review, we briefly describe the key metabolic pathways for anaerobic alkane (including n-alkanes, isoalkanes, and cyclic alkanes) metabolism and highlight several field reports wherein alkylsuccinates have provided evidence for anaerobic in situ alkane metabolism in shallow and deep subsurface environments. PMID:23761789

  11. Accessing Surface and Subsurface Habitable Environments of Ancient Mars

    NASA Astrophysics Data System (ADS)

    Mustard, J. F.

    2014-12-01

    The martian Curiosity rover has characterized the Yellowknife Bay region as habitable based on the presence of sedimentary rocks, the array of elements essential to supporting life (CHNOPS), and indications of hydrologic activity either as a shallow stream bed or intermittently wet lake bed. However as an ancient site this surface was challenging for sustained habitability due to the radiation environment and unknown persistence of water. In contrast the shallow subsurface was potentially a longer lived environment sheltered from the harsh surface conditions. Yet our knowledge of subsurface environments is limited. Did the ancient subsurface of Mars encompass the full range of factors needed for habitability, what is the evidence for this, and was this preserved in the geologic record? Syntheses of global 0.4-5.0 μm spectroscopic observations from high (19 m/pixel CRISM) to moderate (1 km/pixel OMEGA) resolution VNIR data show diverse assemblages of aqueous minerals. The most common environment observed from orbit is a subsurface hydrothermal-type environment accounting for more than 70% of observed sites with hydrated silicates. The dominant hydrated mineral phase is smectite clay, implying a moderate pH environment and a thermal environmental <350°C. The heat source to drive hydrothermal systems could be crustal cooling following planet formation, conductive heat flow from the mantle, impact generated heat pulses, deuteric alteration and magmatism. Evidence of relatively rapid cooling of the crust after formation perhaps by hydrothermal circulation is provided by ancient topography preserved by a rigid crust. Exhumation of Noachian-aged phyllosilicate-rich terrains reveal abundant linear ridges resistant to erosion interpreted to be mineralized fraction zones in regional hydrothermal systems. The proposed landing site in Northeast Syrtis provides excellent access to both surface (Late Noachian fluvial systems with standing bodies of water) and subsurface

  12. 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 (Na2SO4 and NH4H2PO4) 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±0.25 g DNA/g clay with themore » 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

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

    SciTech Connect

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

    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 (Na2SO4 and NH4H2PO4) 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±0.25 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.

  14. RADIOIODINE GEOCHEMISTRY IN THE SRS SUBSURFACE ENVIRONMENT

    SciTech Connect

    Kaplan, D.; Emerson, H.; Powell, B.; Roberts, K.; Zhang, S.; Xu, C.; Schwer, K.; Li, H.; Ho, Y.; Denham, M.; Yeager, C.; Santschi, P.

    2013-05-16

    Iodine-129 is one of the key risk drivers for several Savannah River Site (SRS) performance assessments (PA), including that for the Low-Level Waste Disposal Facility in E-Area. In an effort to reduce the uncertainty associated with the conceptual model and the input values used in PA, several studies have recently been conducted dealing with radioiodine geochemistry at the SRS. The objective of this report was to review these recent studies and evaluate their implications on SRS PA calculations. For the first time, these studies measured iodine speciation in SRS groundwater and provided technical justification for assuming the presence of more strongly sorbing species (iodate and organo-iodine), and measured greater iodine sediment sorption when experiments included these newly identified species; specifically they measured greater sorption coefficients (K{sub d} values: the concentration ratio of iodine on the solid phase divided by the concentration in the aqueous phase). Based on these recent studies, new best estimates were proposed for future PA calculations. The new K{sub d} values are greater than previous recommended values. These proposed K{sub d} values reflect a better understanding of iodine geochemistry in the SRS subsurface environment, which permits reducing the associated conservatism included in the original estimates to account for uncertainty. Among the key contributing discoveries supporting the contention that the K{sub d} values should be increased are that: 1) not only iodide (I{sup -}), but also the more strongly sorbing iodate (IO{sub 3}{sup -}) species exists in SRS groundwater (average total iodine = 15% iodide, 42% iodate, and 43% organoiodine), 2) when iodine was added as iodate, the measured K{sub d} values were 2 to 6 times greater than when the iodine was added as iodide, and perhaps most importantly, 3) higher desorption (10 to 20 mL/g) than (ad)sorption (all previous studies) K{sub d} values were measured. The implications of this

  15. 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

  16. Microbial Diversity and Heterogeneity in Sandy Subsurface Soils

    PubMed Central

    Zhou, Jizhong; Xia, Beicheng; Huang, Heshu; Palumbo, Anthony V.; Tiedje, James M.

    2004-01-01

    Microbial community diversity and heterogeneity in saturated and unsaturated subsurface soils from Abbott's Pit in Virginia (1.57, 3.25, and 4.05 m below surface) and Dover Air Force Base in Delaware (6.00 and 7.50 m below surface) were analyzed using a culture-independent small-subunit (SSU) rRNA gene (rDNA)-based cloning approach. Four to six dominant operational taxonomic units (OTUs) were identified in 33 to 100 unique SSU rDNA clones (constituting about 40 to 50% of the total number of SSU rDNA clones in the clone library) from the saturated subsurface samples, whereas no dominant OTUs were observed in the unsaturated subsurface sample. Less than 10% of the clones among samples from different depths at the same location were identical, and the proportion of overlapping OTUs was lower for the samples that were vertically far apart than for adjacent samples. In addition, no OTUs were shared between the Abbott's Pit and Dover samples. The majority of the clones (80%) had sequences that were less than 5% different from those in the current databases. Phylogenetic analysis indicated that most of the bacterial clones were affiliated with members of the Proteobacteria family (90%), gram-positive bacteria (3%), and members of the Acidobacteria family (3%). Principal component analysis revealed that samples from different geographic locations were well separated and that samples from the same location were closely grouped together. In addition, the nonsaturated subsurface samples from Abbott's Pit clustered together and were well separated from the saturated subsurface soil sample. Finally, the overall diversity of the subsurface samples was much lower than that of the corresponding surface soil samples. PMID:15006798

  17. Microbial activities in deep subsurface environments

    SciTech Connect

    Phelps, T.J.; Raione, E.G.; White, D.C. |; Fliermans, C.B.

    1988-12-31

    Activities of microorganisms residing in terrestrial deep subsurface sediments were examined in forty-six sediment samples from three aseptically sampled boreholes. Radiolabeled time course experiments assessing in situ microbial activities were initiated within 30 minutes of core recovery. [{sup 14}C-1-] Acetate incorporation into lipids. [methyl-{sup 3}H-]thymidine incorporation into DNA, [{sup 14}C-2-]acetate and [{sup 14}C-U-]glucose mineralization in addition to microbial enrichment and enumeration studies were examined in surface and subsurface sediments. Surface soils contained the greatest biomass and activities followed by the shallow aquifer zones. Water saturated subsurface sediments exhibited three to four orders of magnitude greater activity and culturable microorganisms than the dense clay zones. Regardless of depth, sediments which contained more than 20% clays exhibited the lowest activities and culturable microorganisms.

  18. 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...

  19. Subsurface heat flow in an urban environment

    NASA Astrophysics Data System (ADS)

    Ferguson, Grant; Woodbury, Allan D.

    2004-02-01

    The subsurface temperature field beneath Winnipeg, Canada, is significantly different from that of the surrounding rural areas. Downward heat flow to depths as great as 130 m has been noted in some areas beneath the city and groundwater temperatures in a regional aquifer have risen by as much as 5°C in some areas. Numerical simulation of heat transport supports the conjecture that these temperature changes can be largely attributed to heat loss from buildings and the temperature at any given point is sensitive to the distance from and the age of any buildings. The effect is most noticable when buildings are closely spaced, which is typical of urban areas. Temperature measurements in areas more than a few hundred meters away from any heated structure were only a few tenths of a degree Celsius greater than those observed outside the city, suggesting that other reasons for increases in subsurface temperature, such as changes in surface cover or climate change, may be responsible for some of the some of the observed increase in temperatures. These sources of additional heat to the subsurface make it difficult to resolve information on past climates from temperatures measured in boreholes and monitoring wells. In some areas, the temperature increases may also have an impact on geothermal energy resources. This impact might be in the form of an increase in heat pump efficiency or in the case of the Winnipeg area, a decrease in the efficiency of direct use of groundwater for cooling.

  20. 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.

  1. Microbial iron-redox cycling in subsurface environments.

    PubMed

    Roden, Eric E

    2012-12-01

    In addition to its central role in mediating electron-transfer reactions within all living cells, iron undergoes extracellular redox transformations linked to microbial energy generation through utilization of Fe(II) as a source of chemical energy or Fe(III) as an electron acceptor for anaerobic respiration. These processes permit microbial populations and communities to engage in cyclic coupled iron oxidation and reduction within redox transition zones in subsurface environments. In the present paper, I review and synthesize a few case studies of iron-redox cycling in subsurface environments, highlighting key biochemical aspects of the extracellular iron-redox metabolisms involved. Of specific interest are the coupling of iron oxidation and reduction in field and experimental systems that model redox gradients and fluctuations in the subsurface, and novel pathways and organisms involved in the redox cycling of insoluble iron-bearing minerals. These findings set the stage for rapid expansion in our knowledge of the range of extracellular electron-transfer mechanisms utilized by subsurface micro-organisms. The observation that closely coupled oxidation and reduction of iron can take place under conditions common to the subsurface motivates this expansion in pursuit of molecular tools for studying iron-redox cycling communities in situ.

  2. Identifying Heterogeneities in Subsurface Environment using the Level Set Method

    SciTech Connect

    Lei, Hongzhuan; Lu, Zhiming; Vesselinov, Velimir Valentinov

    2016-08-25

    These are slides from a presentation on identifying heterogeneities in subsurface environment using the level set method. The slides start with the motivation, then explain Level Set Method (LSM), the algorithms, some examples are given, and finally future work is explained.

  3. 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...

  4. High CO2 subsurface environment enriches for novel microbial lineages capable of autotrophic carbon fixation

    NASA Astrophysics Data System (ADS)

    Probst, A. J.; Jerett, J.; Castelle, C. J.; Thomas, B. C.; Sharon, I.; Brown, C. T.; Anantharaman, K.; Emerson, J. B.; Hernsdorf, A. W.; Amano, Y.; Suzuki, Y.; Tringe, S. G.; Woyke, T.; Banfield, J. F.

    2015-12-01

    Subsurface environments span the planet but remain little understood from the perspective of the capacity of the resident organisms to fix CO2. Here we investigated the autotrophic capacity of microbial communities in range of a high-CO2 subsurface environments via analysis of 250 near-complete microbial genomes (151 of them from distinct species) that represent the most abundant organisms over a subsurface depth transect. More than one third of the genomes belonged to the so-called candidate phyla radiation (CPR), which have limited metabolic capabilities. Approximately 30% of the community members are autotrophs that comprise 70% of the microbiome with metabolism likely supported by sulfur and nitrogen respiration. Of the carbon fixation pathways, the Calvin Benson Basham Cycle was most common, but the Wood-Ljungdhal pathway was present in the greatest phylogenetic diversity of organisms. Unexpectedly, one organism from a novel phylum sibling to the CPR is predicted to fix carbon by the reverse TCA cycle. The genome of the most abundant organism, an archaeon designated "Candidatus Altiarchaeum hamiconexum", was also found in subsurface samples from other continents including Europe and Asia. The archaeon was proven to be a carbon fixer using a novel reductive acetyl-CoA pathway. These results provide evidence that carbon dioxide is the major carbon source in these environments and suggest that autotrophy in the subsurface represents a substantial carbon dioxide sink affecting the global carbon cycle.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  6. Microbial Diversity in the Columbia River Basalt Group and the Context for Life in Subsurface Basalts

    NASA Astrophysics Data System (ADS)

    Lavalleur, H. J.; Smith, A.; Fisk, M. R.; Colwell, F. S.

    2012-12-01

    Large igneous provinces constitute a sizable volume of porous and fractured materials in the Earth's crust and many of these environments exist within the boundaries of survival for subsurface life. The results of microbiological studies of basalts and other igneous materials in subsurface settings hint at the types of microbes that dwell in these environments. We investigated the microbes in aquifers in the Columbia River Basalt Group (CRBG) and also considered the microbial communities in subsurface basalts more broadly to determine if there are recurrent themes in the types of microbes and the nature of diversity present in these geological systems. Bacteria and Archaea collected from five intervals in the CRBG were examined using high-throughput DNA sequencing directed at the 16S rRNA genes. The highest bacterial biomass and the highest bacterial diversity were observed in the deepest samples (>1018 meters below land surface) whereas the highest archaeal diversity was detected in the shallowest samples (<449 mbls). Microbes classified as Proteobacteria, Firmicutes, and Actinobacteria dominated the aquifers. These findings are generally consistent with earlier cultivation- and clone library-based studies performed on microbes from the CRBG and the Snake River Plain aquifer. Microbes associated with marine basalts are similar to those found in terrestrial settings and include Proteobacteria, Firmicutes, candidate division bacterium OP1, Euryarchaeota, and Crenarchaeota. Based on 16S rRNA sequence similarities to known microbes, both basaltic regions have taxa with representative physiologies likely to include hydrogen oxidation, iron and sulfur metabolism, acetogenesis, and hydrocarbon metabolism. Research on the microbiology of basalt rich provinces on the planet has informed our understanding of biogeochemical cycling where igneous rocks dominate. The knowledge gained in these investigations also promotes our ability to verify the remediation of contaminants

  7. Bacterial growth in a simulated Martian subsurface environment

    NASA Astrophysics Data System (ADS)

    Kronyak, R. E.; Pavlov, A.; House, C. H.

    2013-12-01

    The ability of microorganisms to grow under Martian conditions has implications in both the search for life and habitability of Mars as well as the potential contamination of Mars by landing spacecraft. Factors that inhibit the growth of organisms on Mars include UV radiation, low pressure and temperature, CO2 atmosphere, lack of liquid water, and extreme desiccation. Yet a possible biozone capable of supporting microbial life on Mars exists in the shallow subsurface where there is protection from harsh UV rays. In addition, the presence of widespread subsurface ice, confirmed by the Phoenix Lander, offers a water source as the ice sublimates through the upper soil. Here we will determine the ability of the organism Halomonas desiderata strain SP1 to grow in the simulated Martian subsurface environment. Halomonas was chosen as the bacteria of interest due to its tolerance to extreme environments, including carrying salt concentrations and pH. Experiments were carried out in the Mars Simulation Chamber, where temperatures, pressures, and atmospheric composition can be closely monitored to simulate Martian conditions. A series of stress experiments were conducted to observe Halomonas's ability to withstand exposure to a Mars analog soil, freezing temperatures, anoxic conditions, and low pressures. We have determined that Halomonas is able to survive exposures to low temperatures, pressures, and anoxic conditions. We will report on the survival and growth of Halomonas in the simulated Martian permafrost under low (6-10 mbar) atmospheric pressures.

  8. Salinity constraints on subsurface archaeal diversity and methanogenesis in sedimentary rock rich in organic matter.

    PubMed

    Waldron, Patricia J; Petsch, Steven T; Martini, Anna M; Nüsslein, Klaus; Nüslein, Klaus

    2007-07-01

    The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. In particular, biodegradation of organic matter in sedimentary rocks contributes to the biogeochemical cycling of carbon and other elements and strongly impacts the recovery and quality of fossil fuel resources. In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl(-) in a subsurface shale rich in CH(4) derived from biodegradation of sedimentary hydrocarbons. Shale pore waters collected from wells in the main CH(4)-producing zone lacked electron acceptors such as O(2), NO(3)(-), Fe(3+), or SO(4)(2-). Acetate was detected only in high-salinity waters, suggesting that acetoclastic methanogenesis is inhibited at Cl(-) concentrations above approximately 1,000 mM. Most-probable-number series revealed differences in methanogen substrate utilization (acetate, trimethylamine, or H(2)/CO(2)) associated with chlorinity. The greatest methane production in enrichment cultures was observed for incubations with salinity at or close to the native pore water salinity of the inoculum. Restriction fragment length polymorphism analyses of archaeal 16S rRNA genes from seven wells indicated that there were links between archaeal communities and pore water salinity. Archaeal clone libraries constructed from sequences from 16S rRNA genes isolated from two wells revealed phylotypes similar to a halophilic methylotrophic Methanohalophilus species and a hydrogenotrophic Methanoplanus species at high salinity and a single phylotype closely related to Methanocorpusculum bavaricum at low salinity. These results show that several distinct communities of methanogens persist in this subsurface, CH(4)-producing environment and that each community is adapted to particular conditions of salinity and preferential substrate use and each community induces distinct geochemical signatures in shale formation waters.

  9. Salinity Constraints on Subsurface Archaeal Diversity and Methanogenesis in Sedimentary Rock Rich in Organic Matter▿

    PubMed Central

    Waldron, Patricia J.; Petsch, Steven T.; Martini, Anna M.; Nüslein, Klaus

    2007-01-01

    The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. In particular, biodegradation of organic matter in sedimentary rocks contributes to the biogeochemical cycling of carbon and other elements and strongly impacts the recovery and quality of fossil fuel resources. In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl− in a subsurface shale rich in CH4 derived from biodegradation of sedimentary hydrocarbons. Shale pore waters collected from wells in the main CH4-producing zone lacked electron acceptors such as O2, NO3−, Fe3+, or SO42−. Acetate was detected only in high-salinity waters, suggesting that acetoclastic methanogenesis is inhibited at Cl− concentrations above ∼1,000 mM. Most-probable-number series revealed differences in methanogen substrate utilization (acetate, trimethylamine, or H2/CO2) associated with chlorinity. The greatest methane production in enrichment cultures was observed for incubations with salinity at or close to the native pore water salinity of the inoculum. Restriction fragment length polymorphism analyses of archaeal 16S rRNA genes from seven wells indicated that there were links between archaeal communities and pore water salinity. Archaeal clone libraries constructed from sequences from 16S rRNA genes isolated from two wells revealed phylotypes similar to a halophilic methylotrophic Methanohalophilus species and a hydrogenotrophic Methanoplanus species at high salinity and a single phylotype closely related to Methanocorpusculum bavaricum at low salinity. These results show that several distinct communities of methanogens persist in this subsurface, CH4-producing environment and that each community is adapted to particular conditions of salinity and preferential substrate use and each community induces distinct geochemical signatures in shale formation waters. PMID:17468287

  10. 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.

  11. 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.

  12. Change in ocean subsurface environment to suppress tropical cyclone intensification under global warming.

    PubMed

    Huang, Ping; Lin, I-I; Chou, Chia; Huang, Rong-Hui

    2015-05-18

    Tropical cyclones (TCs) are hazardous natural disasters. Because TC intensification is significantly controlled by atmosphere and ocean environments, changes in these environments may cause changes in TC intensity. Changes in surface and subsurface ocean conditions can both influence a TC's intensification. Regarding global warming, minimal exploration of the subsurface ocean has been undertaken. Here we investigate future subsurface ocean environment changes projected by 22 state-of-the-art climate models and suggest a suppressive effect of subsurface oceans on the intensification of future TCs. Under global warming, the subsurface vertical temperature profile can be sharpened in important TC regions, which may contribute to a stronger ocean coupling (cooling) effect during the intensification of future TCs. Regarding a TC, future subsurface ocean environments may be more suppressive than the existing subsurface ocean environments. This suppressive effect is not spatially uniform and may be weak in certain local areas.

  13. Biogeography and diversity of methane and sulfur-cycling ecotypes in deep subsurface sediments

    NASA Astrophysics Data System (ADS)

    Adams, M. M.; Biddle, J.; Girguis, P. R.

    2013-12-01

    The microbially mediated anaerobic oxidation of methane (AOM) is critical for regulating the flux of methane from the ocean. AOM is coupled to sulfate availability in many anoxic marine environments, which has been extensively studied at cold seeps, hydrothermal vents, and the sulfate-methane transition zone at the seafloor. The microbes known to catalyze AOM form phylogenetically distinct anaerobic methanotroph (ANME) clusters and sometimes live in concert with sulfate-reducing bacteria (SRB). Strikingly, certain ANME groups and subgroups have been shown to occupy different ecological niches in both hydrocarbon seep and hydrothermal vent sediments. However, the environmental parameters that select for certain phylogenetic variants or 'ecotypes' in a wide range of marine systems are still unknown. A marine environment that remains elusive to characterization of potential ANME and SRB ecotype diversity is methane hydrate formations in the deep subsurface. Current estimates indicate that seafloor hydrates may exceed 10,000 GtC at standard temperature and pressure conditions. However, only a handful of studies have investigated the potential for AOM in the deep subsurface associated with methane hydrates. To gain a better understanding of the distribution of methane- and sulfur- cycling ecotypes in biogeochemically distinct marine subsurface ecosystems, we generated a substantial library of 16S rRNA gene sequences for these uncultivable deep sea microorganisms using Illumina sequencing. Sediment strata were collected from the methane-hydrate associated deep subsurface of Hydrate Ridge (30 - 100 mbsf), hydrocarbon cold seeps of Monterey Bay, metalliferous sedimented hydrothermal vents of Juan de Fuca Ridge, and organic-rich hydrothermally influenced sediments of Guaymas Basin. We used the Illumina MiSeq sequencing platform to assess Archaeal and Bacterial richness in a total of 36 deep sea sediment samples followed by qPCR for quantification of ANME and SRB phylotype

  14. 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.

  15. Introduction to special section on Colloid Transport in Subsurface Environments

    NASA Astrophysics Data System (ADS)

    Saiers, James E.; Ryan, Joseph N.

    2006-12-01

    The Water Resources Research special section on Colloid Transport in Subsurface Environments presents new knowledge that is critical to solving problems related to groundwater pollution by microbial pathogens and hazardous chemicals. This introduction to the special section surveys fourteen manuscripts that advance current understanding of the transport of biocolloids (e.g., bacteria, viruses, and protozoa), mineral colloids, and colloid-associated contaminants in the vadose zone and in groundwater. These papers present new techniques for elucidating mechanisms that govern colloid mobility, propose mathematical models appropriate for quantifying colloid and colloid-associated contaminant transport, and report pore-scale and column-scale observations requisite for evaluating these models. Together, the papers of this special section illuminate the complexity of the colloid transport problem and describe progress toward understanding this complexity.

  16. 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…

  17. Anaerobic microbial transformations of radioactive wastes in subsurface environments

    SciTech Connect

    Francis, A.J.

    1984-01-01

    Radioactive wastes disposed of in subsurface environments contain a variety of radionuclides and organic compounds. Microorganisms play a major role in the transformation of organic and inorganic constituents of the waste and are partly responsible for the problems encountered at the waste disposal sites. These include microbial degradation of waste forms resulting in trench cover subsidence, migration of radionuclides, and production of radioactive gases such as /sup 14/CO/sub 2/, /sup 14/CH/sub 4/, HT, and CH/sub 3/T. Microbial processes involved in solubilization, mobilization, and immobilization of toxic metals under aerobic and anaerobic conditions are reviewed. Complexing agents and several organic acids produced by microbial action affect mobilization of radionuclides and heavy metals from the wastes. Microorganisms play a significant role in the transformation and cycling of tritium in the environment by (i) oxidation of tritium and tritiated methane under aerobic conditions and (ii) production of tritium and tritiated methane from wastes containing tritiated water and organic compounds under anaerobic conditions. 23 references, 2 figures, 2 tables.

  18. ACID GASES IN CO2-RICH SUBSURFACE GEOLOGIC ENVIRONMENTS

    SciTech Connect

    Chialvo, Ariel A; Vlcek, Lukas; Cole, David

    2013-01-01

    The analysis of species behavior involving dilute fluid environments has been crucial for the advance of modern solvation thermodynamics through molecular-based formalisms to guide the development of macroscopic regression tools in the description of fluid behavior and correlation of experimental data (Chialvo 2013). Dilute fluid environments involving geologic formations are of great theoretical and practical relevance regardless of the thermodynamic state conditions. The most challenging systems are those involving highly compressible and reactive confined environments, i.e., where small perturbations of pressure and/or temperature can trigger considerable density changes. This in turn can alter significantly the species solvation, their preferential solvation, and consequently, their reactivity with one another and with the surrounding mineral surfaces whose outcome is the modification of the substrate porosity and permeability, and ultimately, the integrity of the mineral substrates. Considering that changes in porosity and permeability resulting from dissolution and precipitation phenomena in confined environments are at the core of the aqueous CO2-mineral interactions, and that caprock integrity (e.g., sealing capacity) depends on these key parameters, it is imperative to gain fundamental understanding of the mineral-fluid interfacial phenomena and fluid-fluid equilibria under mineral confinement at subsurface conditions. In order to undertand the potential effects of acid gases as contaminants of supercritical CO2 streams, in the next section we will discuss the thermodynamic behavior of CO2 fluid systems by addressing two crucial issues in the context of carbon capture, utilization and sequestration (CCUS) technologies: (i) Why should we consider (acid gas) CO2 impurities? and (ii) Why are CO2 fluid - mineral interactions of paramount relevance?

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  20. Diversity and community structure of archaea in deep subsurface sediments from the tropical Western pacific.

    PubMed

    Zhang, Wei; Saren, Gaowa; Li, Tiegang; Yu, Xinke; Zhang, Linbao

    2010-06-01

    Archaeal 16S rRNA gene clone libraries using PCR amplicons from eight different layers of the MD06-3051 core were obtained from the tropical Western Pacific sediments. A total of 768 clones were randomly selected, and 264 representative clones were sequenced by restriction fragment length polymorphism. Finally, 719 valid clones and 104 operational taxonomic units were identified after chimera-check and > or =97% similarity analysis. The phylogenetic analysis of 16S rDNA sequences obtained from sediment samples were very diverse and showed stratification with depth. Majority of the members were most closely related to uncultivated groups and physiologically uncharacterized assemblages. All phylotypes were affiliated with Crenarchaeota (76%) and Euryarchaeota (24%), respectively. Deep-sea archaeal group (DSAG, 41% of total clones) and miscellaneous crenarchaeotic group (MCG, 29% of total clones) belonging to Crenarchaeota were the most predominant archaeal 16S rDNA phylotypes in clone libraries. Phylotypes in this study shared high similarity with those in subsurface sediments from Peru Margin sites, which indicated that different geographical zones might host similar members of archaeal populations based on similar sedimentary environments. In our study, members of DSAG and MCG seemed to dominate certain layers of the nonhydrate sediments, suggesting a wide ecophysiological adaptation than previously appreciated. The spatial distribution and community structure of these groups might vary with the different geochemical gradients of the environment.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  3. Characterization by culture and molecular analysis of the microbial diversity of a deep subsurface gas storage aquifer.

    PubMed

    Basso, Odile; Lascourreges, Jean-François; Le Borgne, François; Le Goff, Cyril; Magot, Michel

    2009-03-01

    The bacterial diversity of a subsurface water sample collected from a gas storage aquifer in an Upper Jurassic calcareous formation was investigated by culture of microorganisms and construction of a 16S rRNA gene library. Both culture and molecular techniques showed that members of the phyla Firmicutes and class delta-proteobacteria dominated the bacterial community. The presence of hydrogen-utilizing autotrophic bacteria including sulfate reducers (e.g. Desulfovibrio aespoeensis) and homoacetogens (e.g. Acetobacterium carbinolicum) suggested that CO(2) and H(2) are the main carbon and energy sources sustaining a nutrient-limited subsurface lithoautotrophic microbial ecosystem (SLiME). Gram-positive SRB belonging to the genus Desulfotomaculum, frequently observed in subsurface environments, represented 25% of the clone library and 4 distinct phylotypes. No Archaea were detected by both experimental approaches. Water samples were collected in an area of the rauracian geological formation located outside the maximum seasonal extension of underground gas storage. Considering the observed microbial diversity, there is no evidence of any influence on the microbial ecology of the aquifer in the surroundings of maximum extension reached by the gas bubble of the underground storage, which should have resulted from the introduction of exogenous carbon and energy sources in a nutrient-limited ecosystem.

  4. Applicability of MICP in Subsurface and Fractured Environments (Invited)

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    Subsurface leakage mitigation strategies using ureolytic biofilm- or microbially-induced calcium carbonate (CaCO3) precipitation (MICP) have been investigated for sealing high permeability regions, like fractures under subsurface relevant conditions. This technology may help in the deep subsurface to improve security of geologically stored carbon dioxide, seal subsurface hydraulic fractures, or enhance oil recovery. Sealing technologies using low-viscosity fluids, such as those used to promote MICP are advantageous since they may penetrate small aperture fractures not reachable by cement-based sealing technologies. MICP has also been researched by others for applications such as: consolidating porous materials, improving or repairing construction materials and remediating environmental concerns. Firstly, injection strategies to control saturation conditions and region-specific precipitation were developed in two-foot long sand-filled columns. Sporosarcina pasteurii biofilms were promoted and calcium and urea solutions were injected to stimulate mineralization. These injection strategies resulted in: 1) promoting homogeneous CaCO3 distribution along the flow path; 2) minimizing near-injection point plugging; and 3) enhancing precipitation efficiency by periodically reviving ureolytic activity. Secondly, the developed injection strategies were used to reduce permeability and ultimately twice seal a hydraulically fractured, 74 cm diameter (meso-scale) Boyles Sandstone core under ambient pressures. Thirdly, a novel high pressure test vessel was developed to study MICP at subsurface relevant pressures (up to 96 bar) (Figure 1). The fractured core's permeability was reduced by more than two orders of magnitude after promoting MICP under 44 bar of confining pressure. In a recent high pressure meso- scale MICP experiment, non-homogeneous, preferential flow paths were observed as cemented regions in a porous media sand pack. The preferential cementation was hypothesized to

  5. Microbial Transport and Fate in the Subsurface Environment: Introduction to the Special Section.

    PubMed

    Bradford, Scott A; Schijven, Jack; Harter, Thomas

    2015-09-01

    Microorganisms constitute an almost exclusive form of life in the earth's subsurface environment (not including caves), particularly at depths exceeding the soil horizon. While of broad interest to ecology and geology, scientific interest in the fate and transport of microorganisms, particularly those introduced through the anthropogenic environment, has focused on understanding the subsurface environment as a pathway for human pathogens and on optimizing the use of microbial organisms for remediation of potable groundwater. This special section, inspired by the 2014 Ninth International Symposium for Subsurface Microbiology, brings together recent efforts to better understand the spatiotemporal occurrence of anthropogenic microbial groundwater contamination and the fate and transport of microbes in the subsurface environment: in soils, deep unsaturated zones, and within aquifer systems. Work includes field reconnaissance, controlled laboratory studies to improve our understanding of specific fate and transport processes, and the development and application of improved mechanistic understanding of microbial fate and transport processes in the subsurface environment. The findings confirm and also challenge the limitations of our current understanding of highly complex microbial fate and transport processes across spatiotemporal scales in the subsurface environment; they also add to the increasing knowledge base to improve our ability to protect drinking water resources and perform in situ environmental remediation.

  6. 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.

  7. Microbial Adaptations to Biosustainabilitiy in Deep-Subsurface Environments on Earth

    NASA Astrophysics Data System (ADS)

    Pratt, L. M.; Onstott, T. C.

    2005-12-01

    Exploration for life on Mars and icy moons in our solar system necessitates development of innovative techniques for life-detection followed by field testing in analogue environments on Earth. A collaborative international effort is underway to drill and sample within regions of persistent permafrost in northern Canada for the purpose of characterizing microbial ecosystems adapted to long-term cold conditions. In 2001 and 2002, Finnish and Canadian scientists installed an instrumented borehole array in a commercial gold mine with sampling valves at 890 and 1130 meters below the surface. Numerous water and gas samples from the Lupin borehole array have been analyzed for molecular and isotopic compositions of organic and inorganic chemical constituents. Boreholes with the lowest concentration of methane and largest 34S fractionation between dissolved sulfate and sulfide are the focus of microbiological sampling. Microbial diversity at Lupin is being assessed by culturing, sequencing, and direct detection of microbial reactions. Cell counts indicate a low biodensity, ranging from 100 to100,000 cells/ml. Phylogenetic analysis using 16S rDNA indicates low biodiversity with the planktonic biota dominated by a distinctive new phlyotype having 95-97% similarity to Thiohalobaccili. Similarly, the subsurface brines sampled at depths of 1500 to 3500 meters in the Witwatersrand basin of South Africa yield low biodensity and biodiversity with the dominant phylotype being a Desulfotomaculum-like organism that appears to represent a new species and new family. Microbes sampled in fracture water at kilometer depths below the surface are significantly different from surface extremophiles and show specific genetic adaptations to biosustainability in deep-subsurface environments.

  8. 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.

  9. Adaptive Mesh Refinement in Reactive Transport Modeling of Subsurface Environments

    NASA Astrophysics Data System (ADS)

    Molins, S.; Day, M.; Trebotich, D.; Graves, D. T.

    2015-12-01

    Adaptive mesh refinement (AMR) is a numerical technique for locally adjusting the resolution of computational grids. AMR makes it possible to superimpose levels of finer grids on the global computational grid in an adaptive manner allowing for more accurate calculations locally. AMR codes rely on the fundamental concept that the solution can be computed in different regions of the domain with different spatial resolutions. AMR codes have been applied to a wide range of problem including (but not limited to): fully compressible hydrodynamics, astrophysical flows, cosmological applications, combustion, blood flow, heat transfer in nuclear reactors, and land ice and atmospheric models for climate. In subsurface applications, in particular, reactive transport modeling, AMR may be particularly useful in accurately capturing concentration gradients (hence, reaction rates) that develop in localized areas of the simulation domain. Accurate evaluation of reaction rates is critical in many subsurface applications. In this contribution, we will discuss recent applications that bring to bear AMR capabilities on reactive transport problems from the pore scale to the flood plain scale.

  10. [Microbial diversity of deep-sea extremophiles--Piezophiles, Hyperthermophiles, and subsurface microorganisms].

    PubMed

    Kato, C; Takai, K

    2000-12-01

    Knowledge of our Planet's biosphere has increased tremendously during the last 10 to 20 years. In the field of Microbiology in particular, scientists have discovered novel "extremophiles", microorganisms capable of living in extreme environments such as highly acidic or alkaline conditions, at high salt concentration, with no oxygen, extreme temperatures (as low as -20 degrees C and as high as 300 degrees C), at high concentrations of heavy metals and in high pressure environments such as the deep-sea. It is apparent that microorganisms can exist in any extreme environment of the Earth, yet already scientists have started to look for life on other planets; the so-called "Exobiology" project. But as yet we have little knowledge of the deep-sea and subsurface biosphere of our own planet. We believe that we should elucidate the Biodiversity of Earth more thoroughly before exploring life on other planets, and these attempts would provide deeper insight into clarifying the existence of extraterrestrial life. We focused on two deep-sea extremophiles in this article; one is "Piezophiles", and another is "Hyperthermophiles". Piezophiles are typical microorganisms adapted to high-pressure and cold temperature environments, and located in deep-sea bottom. Otherwise, hyperthermophiles are living in high temperature environment, and located at around the hydrothermal vent systems in deep-sea. They are not typical deep-sea microorganisms, but they can grow well at high-pressure condition, just like piezophiles. Deming and Baross mentioned that most of the hyperthermophilic archaea isolated from deep-sea hydrothermal vents are able to grow under conditions of high temperature and pressure, and in most cases their optimal pressure for growth was greater than the environmental pressure they were isolated from. It is possible that originally their native environment may have been deeper than the sea floor and that there had to be a deeper biosphere. This implication suggests that

  11. 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.

  12. Continental subsurface waters support unique but diverse C-acquisition strategies

    NASA Astrophysics Data System (ADS)

    Lau, C. M.; Magnabosco, C.; Brown, C. T.; Grim, S. L.; Lacrampe Couloume, G.; Wilkie, K. M.; Sherwood Lollar, B.; Simkus, D.; Slater, G. F.; Hendrickson, S.; Pullin, M. J.; Kieft, T. L.; Li, L.; Snyder, L.; Kuloyo, O.; Linage, B.; Borgonie, G.; Vermeulen, J.; Maleke, M.; Tlalajoe, N.; Moloantoa, K.; van Heerden, E.; Vermeulen, F.; Pienaar, M.; Munro, A.; Joubert, L.; Ackerman, J.; van Jaarsveld, C.; Onstott, T. C.

    2013-12-01

    Terrestrial subsurface environments generally support two orders of magnitude fewer microorganisms than submarine environments where energy and C sources are more abundant. However, our research on the geochemistry and stable isotopes has suggested that the microbial communities residing in the continental subsurface waters, aged more than thousands of years, do not live by a monotypic metabolic network across sites. We evaluated the taxonomic and functional diversity of microbial communities from three localities in South Africa and their relationship to the environmental parameters associated with each fracture water. The borehole at Tau Tona Au mine (TT107; 3,100 mbls), Masimong Au mine (MM5; 1,900 mbls) and Zondereinde Pt mine (NO14; 2,100 mbls) contain saline fracture water of paleometeroic origin but the anaerobic ecosystems were driven by distinctive C-assimilation strategies. Archaea and Bacteria are present in all samples with the latter being dominant (>75%). The similarity between the Δ14C and δ13C-PLFA with those of the DIC indicates that the majority of cellular C in the TT107 sample was derived from the DIC (0.6 mM), even though dissolved CH4 (8.8 mM) is more available. The DIC may have supported a wide variety of chemoautotrophs including the predominant firmicutes, e.g. Thermincola sp. and Ca. Desulforudis audaxviator. Interestingly, a considerable percentage of sequences related to oligotrophic α-proteobacteria Caulobacter sp. was detected, which warrants further investigation as the aerobic heterotrophic microorganism has a unique dimorphic life cycle. For the MM5 sample, the δ13C and δ2H of the CH4 indicate it was produced via CO2 reduction from DIC, which is consistent with the relatively high abundance of hydrogenotrophic methanogen Methanothermobacter sp. that scavenged the abiogenic H2 and utilized the DIC (0.43 mM) leading to its enriched δ13C signature. In contrast to the TT107 sample, the much-depleted δ13C-CH4 indicates that the

  13. Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

    PubMed Central

    Jasrotia, Puja; Green, Stefan J.; Canion, Andy; Overholt, Will A.; Prakash, Om; Wafula, Denis; Hubbard, Daniela; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

    2014-01-01

    The objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genus Coniochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylum Ascomycota and within a single genus of the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions. PMID:24389927

  14. Watershed-scale fungal community characterization along a pH gradient in a subsurface environment cocontaminated with uranium and nitrate.

    PubMed

    Jasrotia, Puja; Green, Stefan J; Canion, Andy; Overholt, Will A; Prakash, Om; Wafula, Denis; Hubbard, Daniela; Watson, David B; Schadt, Christopher W; Brooks, Scott C; Kostka, Joel E

    2014-03-01

    The objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genus Coniochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylum Ascomycota and within a single genus of the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions.

  15. Watershed scale fungal community characterization along a pH gradient in a subsurface environment co-contaminated with uranium and nitrate

    SciTech Connect

    Jasrotia, Puja; Green, Stefan; Canion, Andy; Overholt, Will; Prakash, Om; Wafula, Dennis; Hubbard, Daniela; Watson, David B; Schadt, Christopher Warren; Brooks, Scott C; Kostka,

    2014-01-01

    The objective of this study was to characterize fungal communities in a subsurface environment co-contaminated with uranium and nitrate at the watershed scale, and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution and diversity of fungi in subsurface groundwater samples were determined using quantitative and semi-quantitative molecular techniques, including quantitative PCR of eukaryotic SSU rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH < 4.5) conditions. Fungal isolates recovered from subsurface sediments were shown to reduce nitrate to nitrous oxide, including cultures of the genus Coniochaeta that were detected in abundance in pyrosequence libraries of site groundwater samples. Denitrifying fungal isolates recovered from the site were classified, and found to be distributed broadly within the phylum Ascomycota, and within a single genus within the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions.

  16. Effective sensing approach for assessment and monitoring of in-situ biodegradation in a subsurface environment

    NASA Astrophysics Data System (ADS)

    Li, Dong X.

    1999-02-01

    Rapid assessment and monitoring of biological conditions in a subsurface environment is becoming more and more important as bioremediation approaches become widely used in environmental cleanup. Remediation monitoring is also more challenging for in-situ remedial approaches, such as bioventing, biosparging, or passive bioremediation, where conventional 'inlet' and 'outlet' monitoring can no longer be applied. A sensing approach using subsurface chemical sensors offers a cost- effective alternative for remediation monitoring. Additional benefits of deploying subsurface sensors include continuous and unattended measurement with minimum disturbance to the subsurface condition. In a series of field studies, an electrochemical oxygen sensor, a non-dispersive infrared (NDIR) carbon dioxide sensor, and two hydrocarbons sensors were employed for monitoring in-situ bioremediation of petroleum hydrocarbon contaminated soils. Biodegradation rates were effectively measured through an in-situ respiration measurement using subsurface oxygen and carbon dioxide sensors. The high sensitivity of the carbon dioxide sensor to small change in the concentration enables rapid respiration measurements. Subsurface hydrocarbon sensors offer a means to monitor the progress of remediation and the migration of contaminant vapors during the remediation. The chemical sensors tested are clearly cost effective for remediation monitoring. The strengths of oxygen and carbon dioxide sensors are complimentary to each other. Strengths and limitations of different hydrocarbon sensors were also noted. Balancing cost and performance of sensors is crucial for environmental remediation application.

  17. Microbial transformations of natural organic compounds and radionuclides in subsurface environments

    SciTech Connect

    Francis, A.J.

    1985-10-01

    A major national concern in the subsurface disposal of energy wastes is the contamination of ground and surface waters by waste leachates containing radionuclides, toxic metals, and organic compounds. Microorganisms play an important role in the transformation of organic compounds, radionuclides, and toxic metals present in the waste and affect their mobility in subsurface environments. Microbial processes involved in dissolution, mobilization, and immobilization of toxic metals under aerobic and anaerobic conditions are briefly reviewed. Metal complexing agents and several organic acids produced by microbial action affect mobilization of radionuclides and toxic metals in subsurface environments. Information on the persistence of and biodegradation rates of synthetic as well as microbiologically produced complexing agents is scarce but important in determining the mobility of metal organic complexes in subsoils. Several gaps in knowledge in the area of microbial transformation of naturally occurring organics, radionuclides, and toxic metals have been identified, and further basic research has been suggested. 31 refs., 1 fig., 3 tabs.

  18. Microbial functional gene diversity with a shift of subsurface redox conditions during In Situ uranium reduction.

    PubMed

    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; Zhou, Jizhong

    2012-04-01

    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 (E(h)) 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.

  19. 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

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

    PubMed Central

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

    2015-01-01

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

  1. 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

  2. The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments

    SciTech Connect

    Aklujkar, Muktak; Young, Nelson D; Holmes, Dawn; Chavan, Milind; Risso, Carla; Kiss, Hajnalka; Han, Cliff; Land, Miriam L; Lovley, Derek

    2010-01-01

    Background. Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species. Results. Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced non-subsurface Geobacteraceae, which will be useful for in silico metabolic modeling of subsurface bioremediation processes involving Geobacter species. Pathways can now be predicted for the use of various carbon sources such as propionate by G. bemidjiensis. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in G. bemidjiensis may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that G. bemidjiensis is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which makes it the first Geobacter species identified as having a vitamin requirement. Several features of the genome indicated that G. bemidjiensis has enhanced abilities to respire, detoxify and avoid oxygen. Conclusion. Overall, the genome sequence of G. bemidjiensis offers surprising insights into the metabolism and physiology of Geobacteraceae in

  3. 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.

  4. Biogenic smectite clay formation in subsurface granitic environments

    NASA Astrophysics Data System (ADS)

    Tuck, V.; Edyvean, R.; West, J.; Bateman, K.; Coombs, P.; Milodowski, A.

    2003-04-01

    Many bacteria and biofilms in groundwater environments are able to adsorb and accumulate soluble components from an aqueous environment and exert a strong influence on the attenuation and transport of a significant range of dissolved species including many pollutants. They can also act as catalysts or nucleation sites for authigenic mineral phases such as metal sulphides or complex silicates. The processes involved are not well defined, but appear to range from large-scale interactions altering bulk groundwater chemistry to very small-scale interactions involving geochemical and physical alterations within biofilms and at the mineral surface. The purpose of this research program is to investigate biologically-induced and unusually rapid formation of smectite and chlorite clays. The work expands on experiments conducted by the British Geological Survey designed to simulate rock-water/microbial interactions, radionuclide mobility and groundwater redox-buffering capacity in the vicinity of the Äspö Underground Research Laboratory (URL) in Sweden. Packed-columns were set up containing crushed Äspö granodiorite, saline groundwater (simulating Äspö’s) and either single or combined inoculations of two bacteria species isolated from the Äspö URL, an iron-reducer Shewanella putrefaciens and a sulphate-reducer Desulfovibrio aespoeensis. Flow was maintained at 12ml/day to mimic that in the Äspö region, and strict anaerobic/reducing conditions were maintained throughout the experiments. Results showed that the iron-reducing bacteria S. putrefaciens quickly attached to surfaces and formed extensive filamentous biofilm meshes across porespaces. Neoformed smectite and chlorite clays also appeared on or near the biofilaments along with a calcium sulphate precipitate. Both of these processes (clay formation and the production of a mesh-like biofilm) served to cause total blockage of the pores, rendering the aggregate impermeable and thus cutting off the flow of

  5. Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water.

    PubMed

    Wouters, Katinka; Moors, Hugo; Boven, Patrick; Leys, Natalie

    2013-12-01

    The Boom Clay in Belgium is investigated in the context of geological nuclear waste disposal, making use of the High Activity Disposal Experimental Site (HADES) underground research facility. This facility, located in the Boom Clay at a depth of 225 m below the surface, offers a unique access to a microbial community in an environment, of which all geological and geochemical characteristics are being thoroughly studied. This study presents the first elaborate description of a microbial community in water samples retrieved from a Boom Clay piezometer (borehole water). Using an integrated approach of microscopy, metagenomics, activity screening and cultivation, the presence and activity of this community are disclosed. Despite the presumed low-energy environment, microscopy and molecular analyses show a large bacterial diversity and richness, tending to correlate positively with the organic matter content of the environment. Among 10 borehole water samples, a core bacterial community comprising seven bacterial phyla is defined, including both aerobic and anaerobic genera with a range of metabolic preferences. In addition, a corresponding large fraction of this community is found cultivable and active. In conclusion, this study shows the possibility of a microbial community of relative complexity to persist in subsurface Boom Clay borehole water.

  6. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments.

    PubMed

    Nesbø, Camilla L; S Swithers, Kristen; Dahle, Håkon; Haverkamp, Thomas H A; Birkeland, Nils-Kåre; Sokolova, Tatiana; Kublanov, Ilya; Zhaxybayeva, Olga

    2015-07-01

    Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the 'burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development.

  7. Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge.

    PubMed

    Zhang, Xinxu; Feng, Xiaoyuan; Wang, Fengping

    2016-01-01

    Deep-sea oceanic crust constitutes the largest region of the earth's surface. Accumulating evidence suggests that unique microbial communities are supported by iron cycling processes, particularly in the young (<10 million-year old), cool (<25°C) subsurface oceanic crust. To test this hypothesis, we investigated the microbial abundance, diversity, and metabolic potentials in the sediment-buried crust from "North Pond" on western flank of the Mid-Atlantic Ridge. Three lithologic units along basement Hole U1383C were found, which typically hosted ∼10(4) cells cm(-3) of basaltic rock, with higher cell densities occurring between 115 and 145 m below seafloor. Similar bacterial community structures, which are dominated by Gammaproteobacterial and Sphingobacterial species closely related to iron oxidizers, were detected regardless of variations in sampling depth. The metabolic potentials of the crust microbiota were assayed by metagenomic analysis of two basalt enrichments which showed similar bacterial structure with the original sample. Genes coding for energy metabolism involved in hydrocarbon degradation, dissimilatory nitrate reduction to ammonium, denitrification and hydrogen oxidation were identified. Compared with other marine environments, the metagenomes from the basalt-hosted environments were enriched in pathways for Fe(3+) uptake, siderophore synthesis and uptake, and Fe transport, suggesting that iron metabolism is an important energy production and conservation mechanism in this system. Overall, we provide evidence that the North Pond crustal biosphere is dominated by unique bacterial groups with the potential for iron-related biogeochemical cycles.

  8. Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge

    PubMed Central

    Zhang, Xinxu; Feng, Xiaoyuan; Wang, Fengping

    2016-01-01

    Deep-sea oceanic crust constitutes the largest region of the earth’s surface. Accumulating evidence suggests that unique microbial communities are supported by iron cycling processes, particularly in the young (<10 million-year old), cool (<25°C) subsurface oceanic crust. To test this hypothesis, we investigated the microbial abundance, diversity, and metabolic potentials in the sediment-buried crust from “North Pond” on western flank of the Mid-Atlantic Ridge. Three lithologic units along basement Hole U1383C were found, which typically hosted ∼104 cells cm-3 of basaltic rock, with higher cell densities occurring between 115 and 145 m below seafloor. Similar bacterial community structures, which are dominated by Gammaproteobacterial and Sphingobacterial species closely related to iron oxidizers, were detected regardless of variations in sampling depth. The metabolic potentials of the crust microbiota were assayed by metagenomic analysis of two basalt enrichments which showed similar bacterial structure with the original sample. Genes coding for energy metabolism involved in hydrocarbon degradation, dissimilatory nitrate reduction to ammonium, denitrification and hydrogen oxidation were identified. Compared with other marine environments, the metagenomes from the basalt-hosted environments were enriched in pathways for Fe3+ uptake, siderophore synthesis and uptake, and Fe transport, suggesting that iron metabolism is an important energy production and conservation mechanism in this system. Overall, we provide evidence that the North Pond crustal biosphere is dominated by unique bacterial groups with the potential for iron-related biogeochemical cycles. PMID:27047476

  9. 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

  10. Does the Cave Environment Reduce Functional Diversity?

    PubMed

    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.

  11. [Microbial activity and functional diversity in rhizosphere of cucumber under different subsurface drip irrigation scheduling].

    PubMed

    Li, Hua; He, Hong-Jun; Li, Teng-Fei; Zhang, Zi-Kun

    2014-08-01

    The effects of subsurface drip irrigation scheduling on microbial activity and functional diversity in rhizosphere of cucumber in solar greenhouse were studied in this paper. The results showed that the soil microbial biomass C and N, basal respiration, metabolic quotient and values of AWCD, Shannon and McIntosh indexes were increased at first and then decreased with the increase of irrigation water amount. The values of microbial C and N, basal respiration and metabolic quotient in I2 treatments were significantly higher than those in I1 treatments at the 0.8E(p) irrigation level. The numbers of bacteria, actinomyces and nitrogen-fixing bacteria, and the activities of urease, phosphatase, sucrase, catalase and polyhenoloxidase were significantly higher in the 0.8E(p) treatment than in the other treatments. The numbers of bacteria and nitrogen-fixing bacteria, the activities of urease, phosphatase and sucrase in I2 treatments were significantly higher than in I1 treatment, the actinomyces number and activities of catalase and polyhenoloxidase had no significant difference between I1 and I2 treatments, however, the fungi number in I2 treatments were significantly lower than in I2 treaments at the 0.8E(p) irrigation level. The microbial activity and functional diversity in rhizosphere of cucumber were strengthened in the I20.8E(p) treatment, meanwhile, the soil microflora was improved and the soil enzymes activities were enhanced, therefore, the cucumber growth was promoted as well.

  12. Role of iron in controlling speciation and mobilization of arsenic in subsurface environment.

    PubMed

    Bose, Purnendu; Sharma, Archana

    2002-11-01

    Widespread arsenic contamination of groundwater has been reported of late in Bangladesh and West Bengal state of India. On the basis of arsenic geochemistry, three probable mechanisms have been cited for arsenic mobility in aquifers of West Bengal and Bangladesh. First, mobilization of arsenic due to the oxidation of arsenic-bearing pyrite minerals. Second, dissolution of arsenic-contaminated iron oxy-hydroxides (FeOOH) due to onset of reducing conditions in the subsurface. Third, due to the release of arsenic sorbed to aquifer minerals by competitive exchange with phosphate ions, that migrates into aquifers due to application of fertilizer to surface soil. Based on the review of field data from the affected region, it appears that the second mechanism described above is the most probable. Two reduction processes associated with this mechanism were investigated, viz., reduction of iron oxy-hydroxide to iron (II), which results in the mobilization of arsenic, and reduction of arsenic (V) to arsenic (III), which may enhance mobility of arsenic under certain conditions. These reactions, in the opinion of some researchers, are possible in subsurface environments mainly through microbial intervention. However, through the data presented in this paper, it has been demonstrated that above red-ox reactions involving iron and arsenic are also possible through predominantly abiotic pathways. While these results do not necessarily imply that abiotic red-ox processes are dominant in all subsurface environments containing iron and arsenic, it is entirely possible that abiotic interactions as described here may be responsible for a substantial amount of transformations involving iron and arsenic in anoxic subsurface environments.

  13. 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.

  14. Thin film subsurface environments; Advanced X-ray spectroscopies and a novel Bayesian inference modeling algorithm

    NASA Astrophysics Data System (ADS)

    Church, Jonathan R.

    New condensed matter metrologies are being used to probe ever smaller length scales. In support of the diverse field of materials research synchrotron based spectroscopies provide sub-micron spatial resolutions and a breadth of photon wavelengths for scientific studies. For electronic materials the thinnest layers in a complementary metal-oxide-semiconductor (CMOS) device have been reduced to just a few nanometers. This raises concerns for layer uniformity, complete surface coverage, and interfacial quality. Deposition processes like chemical vapor deposition (CVD) and atomic layer deposition (ALD) have been shown to deposit the needed high-quality films for the requisite thicknesses. However, new materials beget new chemistries and, unfortunately, unwanted side-reactions and by-products. CVD/ALD tools and chemical precursors provided by our collaborators at Air Liquide utilized these new chemistries and films were deposited for which novel spectroscopic characterization methods were used. The second portion of the thesis focuses on fading and decomposing paint pigments in iconic artworks. Efforts have been directed towards understanding the micro-environments causing degradation. Hard X-ray photoelectron spectroscopy (HAXPES) and variable kinetic energy X-ray photoelectron spectroscopy (VKE-XPS) are advanced XPS techniques capable of elucidating both chemical environments and electronic band structures in sub-surface regions of electronic materials. HAXPES has been used to study the electronic band structure in a typical CMOS structure; it will be shown that unexpected band alignments are associated with the presence of electronic charges near a buried interface. Additionally, a computational modeling algorithm, Bayes-Sim, was developed to reconstruct compositional depth profiles (CDP) using VKE-XPS data sets; a subset algorithm also reconstructs CDP from angle-resolved XPS data. Reconstructed CDP produced by Bayes-Sim were most strongly correlated to the real

  15. 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.

  16. 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).

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

    PubMed Central

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

    2016-01-01

    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. PMID:27022994

  18. Adsorption Behavior of Black Carbon for Radioactive Iodine Species in Subsurface Environments

    NASA Astrophysics Data System (ADS)

    Choung, S.; Kim, M.; Um, W.

    2012-12-01

    Releases of radioactive iodines (125/129/131I) into subsurface environments occur during nuclear power plant operations, nuclear weapons tests, and nuclear accidents such as Chernobyl and Fukushima. Environmental concern is mostly for 129I due to high toxicity and long-half life, t1/2=1,600,000 years. The fate and transport of radioactive iodines depend on the speciation in the environments. Sorption of iodate (IO3-) is strongly affected by natural organic matter (NOM) in soil/sediments, while iodide (I-) sorption is less. Although there are numerous forms and compositions of NOM in soil/sediments, previous studies were mostly focused on general organic matter such as humic and fulvic acids. The objective of this study is addressed to evaluate the impact of black carbon as different NOM forms in subsurface environments. Laboratory-produced wood char was used as a representative of black carbon for sorption batch experiments. Commercial humic acid was added to experiments for comparison of iodine sorption behavior to black carbon material. Stable iodine isotope, 127I, was used as a surrogate of radioactive iodine. The 13C-NMR analyses indicated that the wood char consisted of dominantly aromatic chemical structures, while the humic acid exhibited relatively more aliphatic structures than aromaticity. The char and humic acid significantly increased iodide and iodate sorption, respectively. However, iodate sorption on char and iodide sorption on humic acid were negligible in this study. These observations implied different sorption mechanisms between black carbon and humic acid due to different pore structures and chemical compositions. Both of sorption isotherms are dependent on aqueous concentrations, following Freundlich isotherm with n~0.7. The sorption behavior and mechanism of iodine is significantly influenced by the NOM types in soils and sediments, which can enhance iodine retardation in the subsurface environment.

  19. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments

    PubMed Central

    Nesbø, Camilla L; S Swithers, Kristen; Dahle, Håkon; Haverkamp, Thomas HA; Birkeland, Nils-Kåre; Sokolova, Tatiana; Kublanov, Ilya; Zhaxybayeva, Olga

    2015-01-01

    Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the ‘burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development. PMID:25500512

  20. Experimental investigations of the entrapment and persistence of organic liquid contaminants in the subsurface environment.

    PubMed Central

    Abriola, L M; Bradford, S A

    1998-01-01

    Organic liquids are common polluters of the subsurface environment. Once released, these nonaqueous phase liquids (NAPLs) tend to become entrapped within soils and geologic formations where they may serve as long-term contaminant reservoirs. The interphase mass transfer from such entrapped residuals will ultimately control environmental exposure levels as well as the persistence and/or remedial recovery of these contaminants in the subsurface. This paper summarizes National Institute of Environmental Health Sciences-sponsored research designed to investigate and quantify NAPL entrapment and interphase mass transfer in natural porous media. Results of soil column and batch experiments are presented that highlight research findings over the past several years. These experiments explore dissolution and volatilization of hydrocarbons and chlorinated solvents in sandy porous media. Initial concentration levels and long-term recovery rates are shown to depend on fluid flow rate, soil structure, NAPL composition, and soil wetting characteristics. These observations are explained in the context of conceptual models that describe entrapped NAPL morphology and boundary layer transport. The implications of these laboratory findings on the subsurface persistence and recovery of entrapped NAPLs are discussed. Images Figure 1 Figure 3 Figure 9 PMID:9703497

  1. Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico.

    PubMed

    Ragon, Marie; Van Driessche, Alexander E S; García-Ruíz, Juan M; Moreira, David; López-García, Purificación

    2013-01-01

    The Naica Mine in northern Mexico is famous for its giant gypsum crystals, which may reach up to 11 m long and contain fluid inclusions that might have captured microorganisms during their formation. These crystals formed under particularly stable geochemical conditions in cavities filled by low salinity hydrothermal water at 54-58°C. We have explored the microbial diversity associated to these deep, saline hydrothermal waters collected in the deepest (ca. 700-760 m) mineshafts by amplifying, cloning and sequencing small-subunit ribosomal RNA genes using primers specific for archaea, bacteria, and eukaryotes. Eukaryotes were not detectable in the samples and the prokaryotic diversity identified was very low. Two archaeal operational taxonomic units (OTUs) were detected in one sample. They clustered with, respectively, basal Thaumarchaeota lineages and with a large clade of environmental sequences branching at the base of the Thermoplasmatales within the Euryarchaeota. Bacterial sequences belonged to the Candidate Division OP3, Firmicutes and the Alpha- and Beta-proteobacteria. Most of the lineages detected appear autochthonous to the Naica system, since they had as closest representatives environmental sequences retrieved from deep sediments or the deep subsurface. In addition, the high GC content of 16S rRNA gene sequences belonging to the archaea and to some OP3 OTUs suggests that at least these lineages are thermophilic. Attempts to amplify diagnostic functional genes for methanogenesis (mcrA) and sulfate reduction (dsrAB) were unsuccessful, suggesting that those activities, if present, are not important in the aquifer. By contrast, genes encoding archaeal ammonium monooxygenase (AamoA) were amplified, suggesting that Naica Thaumarchaeota are involved in nitrification. These organisms are likely thermophilic chemolithoautotrophs adapted to thrive in an extremely energy-limited environment.

  2. Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico

    PubMed Central

    Ragon, Marie; Van Driessche, Alexander E. S.; García-Ruíz, Juan M.; Moreira, David; López-García, Purificación

    2013-01-01

    The Naica Mine in northern Mexico is famous for its giant gypsum crystals, which may reach up to 11 m long and contain fluid inclusions that might have captured microorganisms during their formation. These crystals formed under particularly stable geochemical conditions in cavities filled by low salinity hydrothermal water at 54–58°C. We have explored the microbial diversity associated to these deep, saline hydrothermal waters collected in the deepest (ca. 700–760 m) mineshafts by amplifying, cloning and sequencing small-subunit ribosomal RNA genes using primers specific for archaea, bacteria, and eukaryotes. Eukaryotes were not detectable in the samples and the prokaryotic diversity identified was very low. Two archaeal operational taxonomic units (OTUs) were detected in one sample. They clustered with, respectively, basal Thaumarchaeota lineages and with a large clade of environmental sequences branching at the base of the Thermoplasmatales within the Euryarchaeota. Bacterial sequences belonged to the Candidate Division OP3, Firmicutes and the Alpha- and Beta-proteobacteria. Most of the lineages detected appear autochthonous to the Naica system, since they had as closest representatives environmental sequences retrieved from deep sediments or the deep subsurface. In addition, the high GC content of 16S rRNA gene sequences belonging to the archaea and to some OP3 OTUs suggests that at least these lineages are thermophilic. Attempts to amplify diagnostic functional genes for methanogenesis (mcrA) and sulfate reduction (dsrAB) were unsuccessful, suggesting that those activities, if present, are not important in the aquifer. By contrast, genes encoding archaeal ammonium monooxygenase (AamoA) were amplified, suggesting that Naica Thaumarchaeota are involved in nitrification. These organisms are likely thermophilic chemolithoautotrophs adapted to thrive in an extremely energy-limited environment. PMID:23508882

  3. Laboratory and Field Evidence for Long-Term Starvation Survival of Microorganisms in Subsurface Terrestrial Environments

    SciTech Connect

    Kieft, T.L.; Murphy, E.M.; Amy, P.S.; Haldeman, D.L.; Ringelberg, D. B. |

    1997-12-31

    BIOGEOCHEMICAL MODELING OF GROUNDWATER FLOW AND NUTRIENT FLUX IN SUBSURFACE ENVIRONMENTS INDICATES THAT INHABITANT MICROORGANISMS EXPERIENCE SEVERE NUTRIENT LIMITATION. USING LABORATORY AND FIELD METHODS, WE HAVE BEEN TESTING STARVATION SURVIVAL IN SUBSURFACE MICROORGANISMS. IN MICROCOSM EXPERIMENTS, WE HAVE SHOWN THAT STRAINS OF TWO COMMONLY ISOLATED SUBSURFACE GENERA, ARTHROBACTER AND PSEUDOMONAS, ARE ABLE TO MAINTAIN VIABILITY IN LOW-NUTRIENT, NATURAL SUBSURFACE SEDIMENTS FOR OVER ONE YEAR. THESE NON-SPORE-FORMING BACTERIA UNDERGO RAPID INITIAL MINIATURIZATION FOLLOWED BY A STABILIZATION OF CELL SIZE. MEMBRANE LIPID PHOSPHOLIPID FATTY ACID (PLFA) PROFILES OF THE PSEUDOMONAS ARE CONSISTENT WITH ADAPTATION TO NUTRIENT STRESS; ARTHROBACTER APPARENTLY RESPONDS TO NUTRIENT DEPRIVATION WITHOUT ALTERING MEMBRANE PLFA. TO TEST SURVIVABILITY OF MICROORGANISMS OVER A GEOLOGIC TIME SCALE, WE CHARACTERIZED MICROBIAL COMMUNITIES IN A SEQUENCE OF UNSATURATED SEDIMENTS RANGING IN AGE FROM MODEM TO {gt}780,000 years. Sediments were relatively uniform silts in Eastern Washington State. Porewater ages at depth (measured by the chloride mass-balance approach) were as old as 3,600 years. Microbial abundance, biomass, and activities (measured by direct counts, culture counts, total PLFAs, and radiorespirometry) declined with sediment age. The pattern is consistent with laboratory microcosm studies of Microbial survival: rapid short-term change followed by long-term survival of a proportion of cells. Even the oldest sediments evinced a small but viable Microbial community. Microbial survival appeared to be a function of sediment age. Porewater age appeared to influence the markup of surviving communities, as indicated by PLFA profiles. Sites with different Porewater recharge rates and patterns of Pleistocene flooding had different communities.

  4. Diversity, abundance, and distribution of NO-forming nitrite reductase-encoding genes in deep-sea subsurface sediments of the South China Sea.

    PubMed

    Li, M; Hong, Y; Cao, H; Klotz, M G; Gu, J-D

    2013-03-01

    In marine ecosystems, both nitrite-reducing bacteria and anaerobic ammonium-oxidizing (anammox) bacteria, containing different types of NO-forming nitrite reductase-encoding genes, contribute to the nitrogen cycle. The objectives of study were to reveal the diversity, abundance, and distribution of NO-forming nitrite reductase-encoding genes in deep-sea subsurface environments. Results showed that higher diversity and abundance of nirS gene than nirK and Scalindua-nirS genes were evident in the sediments of the South China Sea (SCS), indicating bacteria containing nirS gene dominated the NO-forming nitrite-reducing microbial community in this ecosystem. Similar diversity and abundance distribution patterns of both nirS and Scalindua-nirS genes were detected in this study sites, but different from nirK gene. Further statistical analyses also showed both nirS and Scalindua-nirS genes respond similarly to environmental factors, but differed from nirK gene. These results suggest that bacteria containing nirS and Scalindua-nirS genes share similar niche in deep-sea subsurface sediments of the SCS, but differed from those containing nirK gene, indicating that community structures of nitrite-reducing bacteria are segregated by the functional modules (NirS vs. NirK) rather than the competing processes (anammox vs. classical denitrification).

  5. Reconstruction of the thermal environment evolution from subsurface temperature distribution in large cities in East Asia

    NASA Astrophysics Data System (ADS)

    Hamamoto, H.; Goto, S.; Vuthy, M.; Nishijima, J.; Yamano, M.; Taniguchi, M.; Miyakoshi, A.; Hachinohe, S.; Sasaka, K.; Shiraishi, H.

    2009-12-01

    Temperature changes at the ground surface propagate into the underground and disturb the subsurface temperature structure. Analyzing disturbances in the subsurface temperature structure, we can reconstruct the past ground surface temperature (GST) change, which is closely related to the past surface air temperature change. This method can be applied to studies of thermal environment evolution in urban areas such as the development of “heat islands”. As part of an international multidisciplinary research project “Human Impacts on Urban Subsurface Environments”, we have been investigating GST histories in and around several large cities in East Asia, including Bangkok and Tokyo. We have also started a study on the subsurface thermal environment in Saitama prefecture, located on the north of Tokyo, as a research project of CESS (Center for Environmental Science in Saitama). The eastern part of Saitama prefecture is densely populated and considered to be a part of Tokyo Metropolitan area. In this presentation, we show the results of GST history reconstruction in the both areas. In Bangkok area, we conducted measurements of temperature profiles in groundwater monitoring wells at 45 sites in 2004, 2006, and 2008. In Saitama, we measured temperature profiles at 15 sites in 2009. We examined the shapes of the temperature profiles and selected ones that are not significantly disturbed by groundwater flow. Reconstruction of GST history for the last several hundred years was made at six sites in the Bangkok area and at two sites in the Saitama area. We used a multi-layer model that allows layers with different thermal properties, determining layer boundaries based on lithology of the formations around the wells. All of the reconstructed GST histories show surface warming in the last century. In the Bangkok area, the amount of the temperature increase ranges from 0.4 to 2.6 K and is larger in the city than in the area to the west of Bangkok and in the northern rural

  6. 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.

  7. Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments

    PubMed Central

    Aüllo, Thomas; Ranchou-Peyruse, Anthony; Ollivier, Bernard; Magot, Michel

    2013-01-01

    Gram-positive spore-forming sulfate reducers and particularly members of the genus Desulfotomaculum are commonly found in the subsurface biosphere by culture based and molecular approaches. Due to their metabolic versatility and their ability to persist as endospores. Desulfotomaculum spp. are well-adapted for colonizing environments through a slow sedimentation process. Because of their ability to grow autotrophically (H2/CO2) and produce sulfide or acetate, these microorganisms may play key roles in deep lithoautotrophic microbial communities. Available data about Desulfotomaculum spp. and related species from studies carried out from deep freshwater lakes, marine sediments, oligotrophic and organic rich deep geological settings are discussed in this review. PMID:24348471

  8. Trace elements affect methanogenic activity and diversity in enrichments from subsurface coal bed produced water.

    PubMed

    Unal, 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 (R(2) = 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.

  9. 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

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

    PubMed

    Mickol, R L; Kral, T A

    2016-09-23

    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.

  11. Multi-dimensional Modeling of Fullerene (C60) Nanoparticle Transport in the Subsurface Environment

    NASA Astrophysics Data System (ADS)

    Bai, C.; Li, Y.

    2011-12-01

    The escalating production and consumption of engineered nanomaterials may lead to increased release into groundwater. A number of studies have revealed the potential human health effects and aquatic toxicity of nanomaterials. Understanding the fate and transport of engineered nanomaterials is very important for evaluating their potential risks to human and ecological health. While a lot of efforts have been put forward in this area, limited work has been conducted to evaluate engineered nanomaterial transport in multi-dimension and at field scale. In this work, we simulate the transport of fullerene aggregates (nC60), a widely used engineered nanomaterial, in a multi-dimensional environment. A Modular Three-Dimensional Multispecies Transport Model (MT3DMS) was modified to incorporate the transport and retention of nC60. The modified MT3DMS was validated by comparing with analytical solutions and one-dimensional numerical simulation results. The validated simulator was then used to simulate nC60 transport in two- and three-dimensional field sites. Hypothetical scenarios for nanomaterial entering the subsurface environment, including entering from an injection well and releasing from a waste site were investigated. Influences of injection rate, groundwater velocity, ground water recharge rate, subsurface heterogeneity, and nanomaterial size and surface property were evaluated. Insights gained from this work will be discussed.

  12. 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.

    2016-09-01

    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.

  13. Deep subsurface microbial processes

    USGS Publications Warehouse

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

    1995-01-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

  14. On using rational enzyme redesign to improve enzyme-mediated microbial dehalogenation of recalcitrant substances in deep-subsurface environments

    SciTech Connect

    Ornstein, R.L.

    1993-06-01

    Heavily halogenated hydrocarbons are one of the most prevalent classes of man-made recalcitrant environmental contaminants and often make their way into subsurface environments. Biodegradation of heavily chlorinated compounds in the deep subsurface often occurs at extremely slow rates because native enzymes of indigenous microbes are unable to efficiently metabolize such synthetic substances. Cost-effective engineering solutions do not exist for dealing with disperse and recalcitrant pollutants in the deep subsurface (i.e., ground water, soils, and sediments). Timely biodegradation of heavily chlorinated compounds in the deep subsurface may be best accomplished by rational redesign of appropriate enzymes that enhance the ability of indigenous microbes to metabolize these substances. The isozyme family cytochromes P450 are catalytically very robust and are found in all aerobic life forms and may be active in may anaerobes as well. The author is attempting to demonstrate proof-of-principle rational enzyme redesign of cytochromes P450 to enhance biodehalogenation.

  15. Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction.

    PubMed

    Herrera, Aude; Cockell, Charles S

    2007-07-01

    The last decade has been marked by a large number of studies focused on understanding the distribution of microorganisms in volcanic environments. These studies are motivated by the desire to elucidate how the geochemically extreme conditions of such environments can influence microbial diversity both on the surface and in the subsurface of the Earth. The exploration of microbial community diversity has generally not relied on culture-dependent methods, but has been carried out using environmental DNA extraction. Because of the large diversity of chemically and physically complex samples, extracting DNA from volcanic environments is technically challenging. In view of the emerging literature, and our own experience in the optimisation of methods for DNA extraction from volcanic materials, it is timely to provide a methodological comparison. This review highlights and discusses new insights and methods published on DNA extraction methods from volcanic samples, considering the different volcanic environments. A description of a recent method for DNA extraction from basalt and obsidian glass rock samples from Iceland is included. Finally, we discuss these approaches in the wider context of modern work to understand the microbial diversity of volcanic environments.

  16. Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine.

    PubMed

    Inagaki, Fumio; Takai, Ken; Hirayama, Hisako; Yamato, Yu; Nealson, Kenneth H; Horikoshi, Koki

    2003-08-01

    Distribution and phylogenetic diversity of microbial communities in hot, deep underground environments in the Hishikari epithermal gold mine, southern part of Kyushu, Japan, were evaluated using molecular phylogenetic analyses. Samples included drilled cores such as andesitic volcanic rock (0.95-1.78 Ma) and the oceanic sedimentary basement rock of Shimanto-Supergroup (100 Ma), as well as geothermal hot aquifer waters directly collected from two different sites: AW-site (71.5 degrees C, pH 6.19) and XW-site (85.0 degrees C, pH 6.80) at a depth of 350 mbls (meters below land surface). Based on PCR-amplified 16S rRNA gene clone analysis, the microbial communities in the drilled cores and the hot aquifer water from the XW-site consisted largely of the 16S rRNA gene sequences, closely related to the sequences often found in marine environments, while the aquifer water from the AW-site contained 16S rRNA gene sequences representing members of Aquificales, thermophilic methanotrophs within the gamma-subdivision of the Proteobacteria and uncultivated strains within the beta-subdivision of Proteobacteria. The cultivable microbial community detected by enrichment cultivation analysis largely matched that detected by the culture-independent molecular analysis.

  17. 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.

  18. Isolation and Characterization of Metal-Reducing Thermoanaerobacter Strains from Deep Subsurface Environments of the Piceance Basin, Colorado

    PubMed Central

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

    2002-01-01

    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°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 (Fe3O4), siderite (FeCO3), rhodochrosite (MnCO3), and uraninite (UO2). 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. PMID:12450823

  19. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin.

    PubMed

    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.

  20. 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

  1. Terrestrial Subsurface Ecosystem

    SciTech Connect

    Wilkins, Michael J.; Fredrickson, Jim K.

    2015-10-15

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

  2. Modeling and interpreting bioavailability of organic contaminant mixtures in subsurface environments

    NASA Astrophysics Data System (ADS)

    Haws, Nathan W.; Ball, William P.; Bouwer, Edward J.

    2006-01-01

    Bioavailability often controls the fate of organic contaminants in surface and subsurface aquatic environments. Bioavailability can be limited by sorption, mass transfer, and intrinsic biodegradation potential and can be further altered by the presence of other compounds. This paper reviews current perspectives on the processes influencing subsurface contaminant bioavailability, how these processes are modeled, and how the relative role of the various processes can be assessed through bioavailability indices. Although these processes are increasingly well understood, the use of sophisticated models and indices often are precluded by an inability to estimate the many parameters that are associated with complex models. Nonetheless, the proper representation of sorption, mass transfer, biodegradation, and co-solute effects can be critical in predicting bio-attenuation. The influence of these processes on contaminant fate is illustrated with numerical simulations for the simultaneous degradation of toluene (growth substrate) and trichloroethylene (nongrowth cometabolite) in hypothetical, aerobic, solid-water systems. The results show how the relative impacts on contaminant fate of the model's various component processes depends upon system conditions, including co-solute concentrations. Slow biodegradation rates increase the inhibition effects of a cometabolite and suppress the rate enhancement effects of a growth substrate. Irrespective of co-solute effects, contaminant fate is less sensitive to biodegradation processes in systems with strong sorption and slow desorption rates. Bioavailability indices can be used to relate these findings and to help identify appropriate modeling simplifications. In general, however, there remains a need to redefine such indices in order that bioavailability concepts can be better incorporated into site characterization, remediation design, and regulatory oversight.

  3. Planning Literacy Environments for Diverse Preschoolers

    ERIC Educational Resources Information Center

    Dennis, Lindsay R.; Lynch, Sharon A.; Stockall, Nancy

    2012-01-01

    "Emergent literacy" is defined as the developmental process beginning at birth in which children acquire the foundation for reading and writing, including language, listening comprehension, concepts of print, alphabetic knowledge, and phonological awareness. The environment within which emergent literacy skills develop is also an important…

  4. 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.

  5. 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.

  6. Depositional controls and environments of the upper Frio Formation: Southeastern Louisiana subsurface

    SciTech Connect

    Marlin, D.J. )

    1991-03-01

    The subsurface upper Frio Formation (late Oligocene) consists of interbedded carbonate and siliciclastic facies. Synthesis of induction-electric logs and fragmented conventional core data show that resistive, low porosity carbonates are key to understanding environment of deposition, sandstone facies geometry, and hydrocarbon distribution. The southeastern Louisiana Oligocene shelf received little clastic influx during Frio Formation time. Periodically, the resistive, carbonate facies formed a semi-continuous lineation of banks at the paleo shelf-edge at or about 30N latitude. The banks acted as barriers to siliciclastic deposition with sediments being deflected westward behind the banks and funnelled basinward through breaks in the banks at the shelf edge. Petrographic study of the carbonates commonly reveals lepidocyclinid-nummulitid biomicrites that show signs of early porosity occlusion and minor burial diagenesis. They range in composition from pure limestone to impure, iron-rich dolomitic sandstones. Several cycles of carbonate-shale-sandstone are noted in the upper Frio Formation driven by relative sea-level change. Carbonate banks grew during transgressive periods and were periodically inhibited during early regressive siltation events or water-deepening below the photic range. Subsequent lowering of sea-level initiating progradational pulses of fine- to medium-grained sands that were funnelled around carbonate banks. Sandstone distribution patterns imply funnelling aspects and paleo-bathymetric bank relief while sand lenses within shales imply progradation. The nex sea-level rise initiated conditions advocating renewed bank growth as depicted by carbonate facies overlying sandstones.

  7. Reconstruction of the thermal environment evolution from subsurface temperature distribution in Japan and Thailand

    NASA Astrophysics Data System (ADS)

    Hamamoto, H.; Yamano, M.; Goto, S.; Hachinohe, S.; Shiraishi, H.; Ishiyama, T.; Miyakoshi, A.; Taniguchi, M.; Arimoto, H.; Kitaoka, K.

    2012-12-01

    Temperature changes at the ground surface propagate into the underground and disturb the subsurface temperature structure. Analyzing disturbances in the subsurface temperature structure, we can reconstruct the past ground surface temperature (GST) change, which is closely related to the past surface air temperature change. This method can be applied to studies of thermal environment evolution in urban areas such as the development of "heat islands". We have been investigating GST histories in three areas, which are located in Japan and Thailand. The three areas are the northern part of Kanto area, Osaka area, and Bangkok area. Kanto area and Osaka area have the greatest and second greatest population in Japan, each other. Bangkok area has the greatest population in Thailand. In the northern part of Kanto area, we conducted measurements of temperature profiles in groundwater monitoring wells at 25 sites in 2009, 2010, and 2011. In Osaka area, temperature profiles were measured at 31 sites in 2011 as the project of the Sumitomo Foundation (M. Taniguchi). In Bangkok area, we measured temperature profiles at 45 sites in 2004, 2006, 2008, and 2010. We examined the shapes of the temperature profiles and selected ones that are not significantly disturbed by groundwater flow. Reconstruction of GST history for the last about 300 hundred years was made at two sites in the northern part of Kanto area, at six sites in Osaka area, and at six sites in Bangkok area. We used a multi-layer model that allows layers with different thermal properties, determining layer boundaries based on lithology of the formations around the wells. All of the reconstructed GST histories show surface warming in the last century. In the northern part of Kanto area, the amount of the temperature increase from 1700 to 2010 is about 2.5 K at both sites. In Osaka area, the amount of the temperature increase from 1700 to 2010 ranges from 2.5 K to 5.0 K and is larger in the city center and the southern part

  8. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    SciTech Connect

    WANG,YIFENG; PAPENGUTH,HANS W.

    2000-05-04

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

  9. 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

  10. 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.

  11. DPM — efficient storage in diverse environments

    NASA Astrophysics Data System (ADS)

    Hellmich, Martin; Furano, Fabrizio; Smith, David; Brito da Rocha, Ricardo; Álvarez Ayllón, Alejandro; Manzi, Andrea; Keeble, Oliver; Calvet, Ivan; Regala, Miguel Antonio

    2014-06-01

    Recent developments, including low power devices, cluster file systems and cloud storage, represent an explosion in the possibilities for deploying and managing grid storage. In this paper we present how different technologies can be leveraged to build a storage service with differing cost, power, performance, scalability and reliability profiles, using the popular storage solution Disk Pool Manager (DPM/dmlite) as the enabling technology. The storage manager DPM is designed for these new environments, allowing users to scale up and down as they need it, and optimizing their computing centers energy efficiency and costs. DPM runs on high-performance machines, profiting from multi-core and multi-CPU setups. It supports separating the database from the metadata server, the head node, largely reducing its hard disk requirements. Since version 1.8.6, DPM is released in EPEL and Fedora, simplifying distribution and maintenance, but also supporting the ARM architecture beside i386 and x86_64, allowing it to run the smallest low-power machines such as the Raspberry Pi or the CuBox. This usage is facilitated by the possibility to scale horizontally using a main database and a distributed memcached-powered namespace cache. Additionally, DPM supports a variety of storage pools in the backend, most importantly HDFS, S3-enabled storage, and cluster file systems, allowing users to fit their DPM installation exactly to their needs. In this paper, we investigate the power-efficiency and total cost of ownership of various DPM configurations. We develop metrics to evaluate the expected performance of a setup both in terms of namespace and disk access considering the overall cost including equipment, power consumptions, or data/storage fees. The setups tested range from the lowest scale using Raspberry Pis with only 700MHz single cores and a 100Mbps network connections, over conventional multi-core servers to typical virtual machine instances in cloud settings. We evaluate the

  12. 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

  13. 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.

  14. Environmental Barcoding Reveals Massive Dinoflagellate Diversity in Marine Environments

    PubMed Central

    Stern, Rowena F.; Horak, Ales; Andrew, Rose L.; Coffroth, Mary-Alice; Andersen, Robert A.; Küpper, Frithjof C.; Jameson, Ian; Hoppenrath, Mona; Véron, Benoît; Kasai, Fumai; Brand, Jerry; James, Erick R.; Keeling, Patrick J.

    2010-01-01

    Background Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known “species”, as a reference to measure the natural diversity in three marine environments. Methodology/Principal Findings In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. Conclusions/Significance COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of

  15. A Low T, High RH, and Potentially Life-Friendly Environment Within the Martian Salt-Rich Subsurface in Equatorial Regions

    NASA Astrophysics Data System (ADS)

    Wang, A.; Zheng, M. P.; Kong, F. J.; Ling, Z. C.; Kong, W. G.; Sobron, P.; Jolliff, B. L.

    2011-03-01

    Hydrated sulfates found in the subsurface at Gusev and at saline playa on the Tibet Plateau imply a high RH environment, supported by lab studies. A high-RH, salt-rich subsurface can accommodate organisms, e.g., halophiles in the Tibet saline playa.

  16. 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.

  17. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190.

    PubMed

    Newberry, Carole J; Webster, Gordon; Cragg, Barry A; Parkes, R John; Weightman, Andrew J; Fry, John C

    2004-03-01

    Diversity of Bacteria and Archaea was studied in deep marine sediments by PCR amplification and sequence analysis of 16S rRNA and methyl co-enzyme M reductase (mcrA) genes. Samples analysed were from Ocean Drilling Program (ODP) Leg 190 deep subsurface sediments at three sites spanning the Nankai Trough in the Pacific Ocean off Shikoku Island, Japan. DNA was amplified, from three depths at site 1173 (4.15, 98.29 and 193.29 mbsf; metres below the sea floor), and phylogenetic analysis of clone libraries showed a wide variety of uncultured Bacteria and Archaea. Sequences of Bacteria were dominated by an uncultured and deeply branching 'deep sediment group' (53% of sequences). Archaeal 16S rRNA gene sequences were mainly within the uncultured clades of the Crenarchaeota. There was good agreement between sequences obtained independently by cloning and by denaturing gradient gel electrophoresis. These sequences were similar to others retrieved from marine sediment and other anoxic habitats, and so probably represent important indigenous bacteria. The mcrA gene analysis suggested limited methanogen diversity with only three gene clusters identified within the Methanosarcinales and Methanobacteriales. The cultivated members of the Methanobacteriales and some of the Methanosarcinales can use CO2 and H2 for methanogenesis. These substrates also gave the highest rates in 14C-radiotracer estimates of methanogenic activity, with rates comparable to those from other deep marine sediments. Thus, this research demonstrates the importance of the 'deep sediment group' of uncultured Bacteria and links limited diversity of methanogens to the dominance of CO2/H2 based methanogenesis in deep sub-seafloor sediments.

  18. [Effect of free surface flow wetland and subsurface flow wetland on bacterial diversity in Beijing Cuihu Wetland Park].

    PubMed

    Wang, Xiao-dan; Zhai, Zhen-hua; Zhao, Shuang; Li, Rong-qi; Ma, Wen-lin; Li, Yan-hong

    2009-01-01

    To achieve the effects of artificial wetland on the bacterial diversity, the culturable bacteria and total cell counts of three wetland cells, including sewage pond (SP), free surface wetland (SF) and subsurface flow wetland (SSF), were investigated using the traditional culture-dependent approach and flow cytometry method, based on the detecting the water quality. The bacterial diversity and dominant groups were also compared by PCR-DGGE profiles and 16S rDNA library technique based on its V3 region. Results show that SF and SSF cells can remove the nutrients effectively, the highest removal ratio of COD, total nitrogen, and total phosphorus reach to 42.33%, 52.92% and 41.4%, respectively; The total microbes are increased continuously with the treatment by SF and SSF, and the culturable bacteria clones are decreased after treatment by SF, and increased after further train by SSF. The Shannon-Weaver index is increased to 3.2850 from 3.0819 while the water flowing through SF, but decreased to 3.0181 after flowing through SSF; The dominant groups in SP include Actinobacteria, Cyanobacteria and alpha-Proteobacteria, reach to 38%, 18% and 18%, respectively; but the most dominant bacteria is changed to beta-Proteobacteria with the ratio of 32% and 44%, after treatment by SF and SSF, respectively. Cytophagal Flexibacter/Bacteroides (CFB) phylum is also increased to 24% finally. Therefore, while the Cuihu Wetland removing the nutrients,the bacterial counts, diversity and dominant groups are also changed,some beneficial bacteria in beta-Proteobacteria and CFB phylum increased, and part of those deleterious bacteria in Actinobacteria and Cyanobacteria decreased.

  19. 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…

  20. Variability of Near-stream, Sub-surface Major-ion and Tracer Concentrations in an Acid Mine Drainage Environment

    NASA Astrophysics Data System (ADS)

    Bencala, K. E.; Kimball, B. A.; Runkel, R. L.

    2006-12-01

    In acid mine drainage environments, tracer-injection and synoptic sampling approaches provide tools for making operational estimates of solute loading within a stream segment. Identifying sub-surface contaminant sources remains a challenge both for characterization of in-stream metal loading and hydrological process research. There is a need to quantitatively define the character and source of contaminants entering streams from ground-water pathways, as well as the potential for changes in water chemistry and contaminant concentrations along these flow paths crossing the sediment-water interface. Complicating the identification of inflows is the mixing of solute sources which may occur in the `near-stream' subsurface areas and specifically along hyporheic exchange flows (HEFs). In Mineral Creek (Silverton, Colorado), major-ion (SO42-, Cl-, Na+, Ca2+, Mg2+) meter-scale sampling shows that subsurface inflows and likely HEFs occur in a hydro- geochemical setting of significant, one order-of-magnitude, spatial variation in the solute concentrations. Transient Storage Models (TSMs) are a tool for interpreting the in-stream responses of solute transport in streams influenced by hyporheic exchange flows. Simulations using the USGS TSM code OTIS are interpreted as suggesting that in Mineral Creek the strong concentration `tailing' of bromide following the tracer injection occurred, at least in part, from HEFs in a hydro - solute transport setting of likely multiple, dispersed and mixed sources of water along a 64 m sub-reach of the nominally gaining stream. In acid mine drainage environments, the ability to distinguish between local and deep solute sources is critical in modeling reactive transport along the stream, as well as in identifying the geochemical evolution of dispersed, subsurface inflows thorough the catchment.

  1. Distribution and diversity of halophilic bacteria in a subsurface salt formation.

    PubMed

    Vreeland, R H; Piselli, A F; McDonnough, S; Meyers, S S

    1998-08-01

    The Waste Isolation Pilot Plant (WIPP) is a salt mine constructed 650 meters below the ground surface by the United States Department of Energy. The facility will be used for permanent disposal of transuranic wastes. This underground repository has been constructed in the geologically stable Permian age Salado salt formation. Of the wastes to be placed into the facility, 85% will be biodegradable cellulose. A 3-year survey of the bacterial populations existing within the facility was conducted. Bacterial populations were found to be heterogeneously distributed throughout the mine. Populations in some mine areas reached as high as 1.0 x 10(4) colony-forming units per gram of NaCl. The heterogeneous distribution of bacteria within the mine did not follow any recognizable pattern related to either age of the workings or to human activity. A biochemical comparison between ten known species of halophilic bacteria, and strains isolated from both the mine and nearby surface hypersaline lakes, showed the presence of extreme halophiles with wide biochemical diversity, some of which could prove to represent previously undescribed groups. The halophilic bacteria isolated from the mine were found to degrade cellulose and a wide variety of other carbon compounds. When exposed to two types of common laboratory paper, the cellulose-degrading halophiles attached to the substrate within 30 minutes of inoculation. Cultures enriched directly from a brine seep in the mine easily destroyed both papers and produced detectable amounts of oxalacetic and pyruvic acids. The combination of heterogeneity in the distribution of organisms, the presence of a physiologically diverse community, and the relatively slow metabolism of cellulose may explain several long-standing debates about the existence of microorganisms in ancient underground salt formations.

  2. Contrasting "Fish" Diversity Dynamics between Marine and Freshwater Environments.

    PubMed

    Guinot, Guillaume; Cavin, Lionel

    2015-08-31

    Two theoretical models have been proposed to describe long-term dynamics of diversification: the equilibrium model considers the Earth as a closed system with a fixed maximum biological carrying capacity, whereas the expansion model hypothesizes a continuously increasing diversification of life. Based on the analysis of the fossil record of all organisms, Benton suggested contrasting models of diversity dynamics between marine and continental realms. Diversity in marine environments is characterized by phases of rapid diversification followed by plateaux, i.e., an equilibrium model directly derived from insular biogeography theories, whereas diversity in continental environments is characterized by exponential growth. Previous studies that aimed at testing these models with empirical data were based on datasets extracted directly from the reading of the vagaries of the raw fossil record, without correcting for common fossil record biases (preservation and sampling). Although correction of datasets for the incompleteness of the fossil record is now commonly performed for addressing long-term biodiversity variations, only a few attempts have been made to produce diversity curves corrected by phylogenetic data from extant and extinct taxa. Here we show that phylogenetically corrected diversity curves for "fish" (actinopterygians and elasmobranchs) during the last 200 million years fit an equilibrium model in the marine realm and an expansion model in the freshwater realm. These findings demonstrate that the rate of diversification has decreased for marine fish over the Cenozoic but is in sharp expansion for freshwater fish.

  3. 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

    2017-02-01

    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.

  4. The possible origin of the first cell biosystem in the thermal subsurface environment of the earth.

    PubMed

    Trevors, Jack T

    2004-01-01

    Bacteria are the simplest living biosystems or organisms that exhibit all the characteristics of life. As such, they are excellent models to examine the cell as the basic unit of life and the cell theory which states that all organisms are composed of one or more similar cells. In this article I examine the hypothesis that the primordial soup so often referred to in science was possibly an oil/water interface and/or emulsion in the Earth's, warm, anaerobic subsurface. This warm subsurface location, protected from surface radiation, could have been a favourable location for the assembly of the first bacterial cells on the Earth capable of growth and controlled division or the first biosystem.

  5. Biodegradation and Sorption of Organic Solvents and Hydrocarbon Fuel Constituents in Subsurface Environments

    DTIC Science & Technology

    1988-03-01

    event, and it was not considered necessary to acquire aseptic subsurface samples. The redox potential (Eh) of the aquifer material was measured in a... plated mild steel core barrels. Cores were taken by pressing the length of the core k50 cm) into the ground, extracting the core, redrilling the hole to...ether (EGME) technique (References 42, 43). b. Determination of Partition Coefficients and Sorption Isotherms The compounds used in this study were o

  6. Spatial distribution of microbial populations and carbon cycle in the subsurface environment of the Horonobe area, Hokkaido, Japan

    NASA Astrophysics Data System (ADS)

    Amano, Y.; Ise, K.; Terashima, M.; Sasaki, Y.; Amamiya, H.; Yoshikawa, H.

    2014-12-01

    Microorganisms are widely distributed in the subsurface environments. However, the distribution, role and rate of metabolisms, and the source of their activity are not well known. In this study, we investigated deep groundwater samples from sedimentary rocks, containing saturated methane and CO2, using boreholes at the Horonobe Underground Research Laboratory (URL), northern Hokkaido, Japan. The hydrochemical conditions of groundwaters, such as in-situ water pressure, temperature, electric conductivity, pH, redox potential, were monitored without degassing at multiple intervals along the borehole. Groundwater samples were taken periodically and chemical composition was analyzed using ICP-MS, etc. Cell counts were in the range of 103 to 105 cells ml-1. Molecular analyses revealed the spatial distribution and heterogeneity of the microbial population. Abundant methanogens were detected in the groundwater, and 80% of them were related to either Methanoregula boonei or Methanobacterium flexile that can utilize H2/CO2 by methanogenesis. Phylotypes clustered within the phylum Firmicutes, beta-Proteobacteria, delta-Proteobacteria and candidate division TM7 were dominant in the groundwater samples. Laboratory experiments using a culture technique showed that humic substances purified from the groundwater at Horonobe area appear to be degraded by microorganisms. Our results suggest that microbial spatial distributions in the subsurface environment were correlated closely with geochemical conditions, such as redox condition and carbon sources. In addition, it is inferred that humic substances are one of the important carbon sources for the subsurface microbial redox processes in the environment. This study was partly funded by the Ministry of Economy, Trade and Industry of Japan.

  7. Measuring family food environments in diverse families with young children.

    PubMed

    McCurdy, Karen; Gorman, Kathleen S

    2010-06-01

    This study reports the development and validation of the 20 item Family Food Behavior Survey, a measure designed to assess broad components of the family food environment that may contribute to child overweight. In a diverse sample of 38 parents, factor analyses verified 4 domains: (1) maternal control of child eating behavior; (2) maternal presence during eating; (3) child choice, and (4) organization of eating environment. All domains achieved acceptable internal reliability (alphas= .73, -.83), and test-retest reliability. Mothers of overweight children scored significantly lower on maternal presence and somewhat higher on maternal control than mothers of normal weight children.

  8. Depositional environments and sedimentary tectonics of subsurface Cotton Valley group (upper Jurassic), west-central Mississippi

    SciTech Connect

    Sydboten, B.D. Jr.; Bowen, R.L.

    1987-09-01

    Study of data from 65 selected wells in a 6-county area (about 60 by 60 mi) north and west of Jackson, Mississippi, discloses that Cotton Valley strata, now within the axial trough of the Mississippi embayment, display thickness variations which demonstrate that Late Jurassic sedimentation was strongly controlled by maximum subsidence along the same trough axis. Examination of well logs, other records, and cutting sets from 38 wells has resulted in preparation of dip and strike cross sections that permit information definition of lower, middle, and upper parts of the Cotton Valley Group throughout the area evaluated. Within these lithostratigraphic diversions, lithofacies are discriminable that represent alluvial, upper delta plain, lower delta plain, and prodeltaic environments. These facies display a general variation from coarse, commonly red, oxidized sediments on the north and east, to mudrocks, locally calcareous and carbonaceous, on the southwest. Within the Cotton Valley Group examined, two persistent clastic lobes demonstrate relative environmental stability while deposits ranging in thickness from 1500 ft (northwestern corner of study area) to 4500 ft (axial depocenter on the south) accumulated. During Cotton Valley deposition, west-central Mississippi was the site of a two-toed birdfoot delta within which lignites were deposited. Major sediment supply was from the east and north; a minor source was to the northwest (Ouachita-Ozarks). Irregulatories in both rates of supply of clastics and of shelf subsidence permitted intermittent shallow, clear-water, marine incursions from the south during which thin carbonate beds were deposited, interfingering with the clastics. Thus, potential source and host rocks for hydrocarbon traps are closely associated, for thick, organic-rich, interlobate mudrocks pass laterally and vertically into fluvial sands of the delta lobes.

  9. More noise, please: How cultural overprinting in the urban environment can be exploited for improved subsurface imaging (Invited)

    NASA Astrophysics Data System (ADS)

    Weiss, C. J.

    2009-12-01

    A long standing issue for geophysical imaging methods revolves around the proper treatment of "noise": Defining what noise is; separating "noise" for "signal"; filtering and suppressing noise; and recently, challenging the prevailing view that noise is a nuisance to see if, instead, it may contribute favorably toward improving subsurface imaging fidelity. This last point is particularly relevant to geophysical imaging in the urban environment where noise sources are abundant, complex, and logistical constraints on geophysical field procedures prohibit a crude "turning up the volume" approach to simply drown out the noise with powerful sources of electromagnetic and seismic energy. In this contribution I explore the concept passive geophysical imaging which uses uncorrelated ambient noise as the source of geophysical imaging energy to be used in the urban environment. Examples will be presented from seismic and ground penetrating radar methods, in addition to new theoretical results bearing on the feasibility of low-frequency electromagnetic induction techniques.

  10. 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

  11. Development of Microarrays-Based Metagenomics Technology for Monitoring Sulfate-Reducing Bacteria in Subsurface Environments

    SciTech Connect

    Cindy, Shi

    2015-07-17

    At the contaminated DOE sites, sulfate-reducing bacteria (SRB) are a significant population and play an important role in the microbial community during biostimulation for metal reduction. However, the diversity, structure and dynamics of SRB communities are poorly understood. Therefore, this project aims to use high throughput sequencing-based metagenomics technologies for characterizing the diversity, structure, functions, and activities of SRB communities by developing genomic and bioinformatics tools to link the SRB biodiversity with ecosystem functioning.

  12. Soil microbial diversity patterns of a lowland spring environment.

    PubMed

    Vasileiadis, Sotirios; Puglisi, Edoardo; Arena, Maria; Cappa, Fabrizio; van Veen, Johannes A; Cocconcelli, Pier S; Trevisan, Marco

    2013-11-01

    The Po river plain lowland springs represent unique paradigms of managed environments. Their current locations used to be swamps that were drained 6-7 centuries ago, and they have been in constant use ever since. Our aims were to identify the effects of land use on the microbial communities of these soils, look for associated diversity drivers, and assess the applicability of ecology theories with respect to identified patterns. We screened the microbial diversity across a land use transect via high-throughput sequencing of partial 16S rrRNA gene amplicons. Land use had a major effect on soil properties and microbial community structures. Total organic carbon and pH were major diversity drivers for Bacteria, and pH was important for Archaea. We identified the potential contribution of soil amendments to the indigenous microbial communities, and also gained insights into potential roles of taxa in the organic carbon turnover. Verrucomicrobia coincided with the higher values of the recalcitrant organic carbon. Actinobacteria and Acidobacteria correlated with the more labile organic carbon. Finally, the higher diversity found in the soils less enzymatically active and relatively poorer in nutrients, may be explained to an extent by niche-based theories such as the resource heterogeneity hypothesis and Connell's intermediate disturbance hypothesis.

  13. Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environment.

    PubMed

    Kovacik, William P; Takai, Ken; Mormile, Melanie R; McKinley, James P; Brockman, Fred J; Fredrickson, James K; Holben, William E

    2006-01-01

    A multilevel sampler (MLS) was emplaced in a borehole straddling anaerobic, sulfate-rich Cretaceous-era shale and sandstone rock formations approximately 200 m below ground surface at Cerro Negro, New Mexico. Sterile quartzite sand contained in chambers in the sampler allowed in situ colonization and recovery of nucleic acids for molecular analyses. Denaturing gradient gel electrophoresis and 16S rRNA gene cloning results indicated a homogeneously distributed bacterial community across the shale-sandstone interface. delta-Proteobacteria sequences were common at all depths, and were dominated by members of the Geobacteraceae family (Pelobacter, Desulphuromonas and Geobacter). Other members of this group are capable of dissimilatory Fe(III) and/or S degrees reduction, but not sulfate reduction. RNA hybridization data also suggested that Fe(III)-/S degrees -reducing bacteria were predominant. These findings are striking considering the lack of significant concentrations of these electron acceptors in this environment. The next most abundant bacterial group indicated was the sulfate reducers, including Desulfobacterium, Desulfocapsa and Desulfobulbus. Sequences related to fermenters, denitrifiers and acetogens were also recovered. The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale.

  14. Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S°-reducing bacteria in a sulfate-rich environment

    SciTech Connect

    Kovacik, William P.; Takai, Ken; Mormile, Melanie R.; McKinley, James P.; Brockman, Fred J.; Fredrickson, Jim K.; Holben, William E.

    2006-01-01

    A multi-level sampler (MLS) was emplaced in a borehole straddling anaerobic, sulfate-rich Cretaceous-era shale and sandstone rock formations {approx}200 m below ground surface at Cerro Negro, New Mexico. Sterile quartzite sand contained in chambers in the sampler allowed in situ colonization and recovery of nucleic acids for molecular analyses. DGGE and 16S rRNA gene cloning results indicated a homogeneously distributed bacterial community across the shale/sandstone interface. ?-Proteobacteria sequences were common at all depths, and were dominated by members of the Geobacteraceae family (Pelobacter, Desulfuromonas, and Geobacter). Other members of this group are capable of dissimilatory Fe(III) and/or S0 reduction, but not sulfate reduction. RNA hybridization data also suggested that Fe(III)/S0 reducing bacteria were predominant. These findings are striking considering the lack of significant concentrations of these electron acceptors in this environment. The next most abundant bacterial group indicated was the sulfate reducers, including Desulfobacterium, Desulfocapsa and Desulfobulbus. Sequences related to fermenters, denitrifiers and acetogens were also recovered. The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale.

  15. A parallelization scheme to simulate reactive transport in the subsurface environment with OGS#IPhreeqc

    NASA Astrophysics Data System (ADS)

    He, W.; Beyer, C.; Fleckenstein, J. H.; Jang, E.; Kolditz, O.; Naumov, D.; Kalbacher, T.

    2015-03-01

    This technical paper presents an efficient and performance-oriented method to model reactive mass transport processes in environmental and geotechnical subsurface systems. The open source scientific software packages OpenGeoSys and IPhreeqc have been coupled, to combine their individual strengths and features to simulate thermo-hydro-mechanical-chemical coupled processes in porous and fractured media with simultaneous consideration of aqueous geochemical reactions. Furthermore, a flexible parallelization scheme using MPI (Message Passing Interface) grouping techniques has been implemented, which allows an optimized allocation of computer resources for the node-wise calculation of chemical reactions on the one hand, and the underlying processes such as for groundwater flow or solute transport on the other hand. The coupling interface and parallelization scheme have been tested and verified in terms of precision and performance.

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

    SciTech Connect

    Arora, Bhavna; Spycher, Nicolas F.; Steefel, Carl I.; Molins, Sergi; Bill, Markus; Conrad, Mark E.; Dong, Wenming; Faybishenko, Boris; Tokunaga, Tetsu K.; Wan, Jiamin; Williams, Kenneth H.; Yabusaki, Steven B.

    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. Model 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.

  17. Diversity of Listeria species in urban and natural environments.

    PubMed

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

    2012-06-01

    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.

  18. Geochemical investigations of polychlorinated dibenzo-p-dioxins in the subsurface environment at an abandoned wood-treatment facility

    USGS Publications Warehouse

    Pereira, W.E.; Rostad, C.E.; Sisak, M.E.

    1985-01-01

    The discharge of effluents containing creosote and pentachlorophenol into two unlined surface impoundments at a wood-treatment facility in Pensacola, Florida, resulted in contamination of the underlying sand and gravel aquifer. These wastes contained significant amounts of chlorinated dioxins, such as isomers of hexa- and heptachlorodibenzo-p-dioxins and octachlorodibenzo-p-dioxin, probably derived from commercial pentachlorophenol. Geochemical investigations of pond sludge, groundwater and porous media from the unsaturated and saturated zones indicated that these geologic materials were contaminated by chlorinated dioxins. The fate and movement of these compounds in the subsurface environment were studied using the technique of GC-MS-MS. Chlorinated dioxins migrated both vertically and horizontally in the subsurface and were present at considerable distances from the source of contamination. Concentrations of chlorinated dioxins in groundwater were several orders of magnitude lower than in porous media from the unsaturated and saturated zones. Ratios of the various isomers remained relatively constant in highly contaminated areas. However, in less contaminated areas, isomer ratios changed dramatically; at certain locations, one hexachlorodibenzo-p-dioxin isomer predominated. The environmental significance of these compounds is discussed. ?? 1985.

  19. An electric and electromagnetic geophysical approach for subsurface investigation of anthropogenic mounds in an urban environment

    NASA Astrophysics Data System (ADS)

    Pazzi, Veronica; Tapete, Deodato; Cappuccini, Luca; Fanti, Riccardo

    2016-11-01

    Scientific interest in mounds as geomorphological features that currently represent topographic anomalies in flat urban landscapes mainly lies on the understanding of their origin, either purely natural or anthropogenic. In this second circumstance, another question is whether traces of lost buildings are preserved within the mound subsurface and can be mapped as remnants testifying past settlement. When these landforms have been modified in centuries for civilian use, structural stability is a further element of concern. To address these issues we applied a geophysical approach based on a very low frequency electromagnetic (VLF-EM) technique and two-dimensional electrical resistivity tomography (2D-ERT) and integrated it with well-established surface survey methods within a diagnostic workflow of structural assessment. We demonstrate the practical benefits of this method in the English Cemetery of Florence, Italy, whose mixed nature and history of morphological changes are suggested by archival records. The combination of the two selected geophysical techniques allowed us to overcome the physical obstacles caused by tomb density and to prevent interference from the urban vehicular traffic on the geophysical signals. Eighty-two VLF-EM profiles and five 2D-ERTs were collected to maximise the spatial coverage of the subsurface prospection, while surface indicators of instability (e.g., tomb tilt, location, and direction of ground fractures and wall cracks) were mapped by standard metric survey. High resistive anomalies (> 300 and 400 Ωm) observed in VLF-EM tomographies are attributed to remnants of the ancient perimeter wall that are still buried along the southern side of the mound. While no apparent correlation is found between the causes of tomb and ground movements, the crack pattern map supplements the overall structural assessment. The main outcome is that the northern portion of the retaining wall is classed with the highest hazard rate. The impact of this

  20. 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.

  1. 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

  2. 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.

  3. 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).

  4. Connecting diverse molecular cloud environments with nascent protostars in Orion

    NASA Astrophysics Data System (ADS)

    Stutz, Amelia M.; Megeath, S.; Fischer, W. J.; Ali, B.; Furlan, E.; Tobin, J. J.; Stanke, T.; Henning, T.; Krause, O.; Manoj, P.; Osorio, M.; Robitaille, T.; HOPS Team

    2014-01-01

    Understanding how the gas environment within molecular clouds influences the properties of protostars is a key step towards understanding the physical factors that control star formation. We report on an analysis of the connection between molecular cloud environment and protostellar properties using the Herschel Orion Protostar Survey (HOPS), a large multi-observatory survey of protostars in the Orion molecular clouds. HOPS has produced well sampled 1 um to 870 um SEDs of over 300 protostars in the Orion molecular clouds using images and spectra from 2MASS, Spitzer, Herschel and APEX. Furthermore, the combination of APEX 870 um continuum observations with the HOPS/PACS 160 um data over the same area allows for a determination of the temperatures and column densities in the often filamentary dense gas surrounding the Orion protostars. Based on these data, we link the protostellar properties with their environmental properties. Utilizing the diverse environments present within the Orion molecular clouds, we show how the luminosity and spacing of protostars in Orion depends on the local gas column density. Furthermore, we report an unusual concentration of the youngest known protostars (the Herschel identified PBRS, PACS Bright Red Sources) in the Orion B cloud, and we discuss possible reasons for this concentration.

  5. Diverse alkane hydroxylase genes in microorganisms and environments

    PubMed Central

    Nie, Yong; Chi, Chang-Qiao; Fang, Hui; Liang, Jie-Liang; Lu, She-Lian; Lai, Guo-Li; Tang, Yue-Qin; Wu, Xiao-Lei

    2014-01-01

    AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature. PMID:24829093

  6. RANGE AND DISTRIBUTION OF TECHNETIUM KD VALUES IN THE SRS SUBSURFACE ENVIRONMENT

    SciTech Connect

    Kaplan, D

    2008-10-28

    L/g. The E-Area subsurface is subdivided into three hydrostratigraphic layers: Upper Vadose Zone (11 to 30 ft depth), Lower Vadose Zone (30 to 51 ft depth), and aquifer (51 to 95 ft depth). The Upper Vadose Zone generally contains more clay than the Lower Vadose Zone, and the Aquifer tends to be made up of mostly sand layers with clay strata. The mean K{sub d} values of each of these zones did not differ significantly and the K{sub d} values from each zone were not from the Normal distribution. The ranges of values were greatest in the Upper Vadose Zone and least in the Lower Vadose Zone. Previous Best Estimate Tc K{sub d} values for Sandy Sediment and Clayey Sediment were 0.1 and 0.2 mL/g, respectively (Kaplan 2007a). A more thorough review indicates that the Best Estimates for Sandy Sediment is 0.1 mL/g and for Clayey Sediment is 0.8 mL/g (Kaplan 2007b). This current dataset greatly increases the number of Tc K{sub d} values measured with SRS sediments, but perhaps more importantly, provides a better estimate for E-Area sediments, and provides a measure of Tc K{sub d} distributions. Based on this dataset, the best overall Tc K{sub d} value for E-Area is the mean, 3.4 mL/g, with a log-normal distribution between the 95 percentile values of 2.4 to 4.4 mL/g. This document version differs from the earlier version, SRNS-STI-2008-00286, in that it includes some editorial corrections. This version does not contain any technical changes or changes to the conclusions presented in the earlier version.

  7. Bacterial Diversity in a Nonsaline Alkaline Environment: Heterotrophic Aerobic Populations

    PubMed Central

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

    2004-01-01

    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 α-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. PMID:15574939

  8. Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments.

    PubMed

    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

  9. Stabilization of Plutonium in Subsurface Environments via Microbial Reduction and Biofilm Formation

    SciTech Connect

    Hakim Boukhalfa; Gary A. Icopini; Sean D. Reilly; Mary P. Neu

    2007-04-19

    Plutonium has a long half-life (2.4 x 104 years) and is of concern because of its chemical and radiological toxicity, high-energy alpha radioactive decay. A full understanding of its speciation and interactions with environmental processes is required in order to predict, contain, or remediate contaminated sites. Under aerobic conditions Pu is sparingly soluble, existing primarily in its tetravalent oxidation state. To the extent that pentavalent and hexavalent complexes and small colloidal species form they will increase the solubility and resultant mobility from contamination sources. There is evidence that in both marine environments and brines substantial fractions of the plutonium in solution is present as hexavalent plutonyl, PuO2 2+.

  10. Microbial pathways for the mobilization of mercury as Hg(O) in anoxic subsurface environments

    SciTech Connect

    Barkay, Tamar

    2005-06-01

    The goal of our project which was initiated in June 2005 is focused on the presence of merA in microbial communities of anoxic environments and the effect of anaerobic respiratory pathways on MR expression and activities. The following progress has been made to date: PCR primers were designed to span the known phylogenetic range of merA genes of Gram-negative bacteria. In control experiments, these primers successfully amplified a 288 bp region at the 3? end of previously characterized merA genes from Shewanella putrefaciens pMERPH, Acidithiobacillus ferrooxidans, Pseudomonas stutzeri pPB, Tn5041, Pseudomonas sp. K-62, and Serratia marcescens pDU1358.

  11. Diversity and distribution of pigmented heterotrophic bacteria in marine environments.

    PubMed

    Du, Hailian; Jiao, Nianzhi; Hu, Yaohua; Zeng, Yonghui

    2006-07-01

    A systematic investigation of marine pigmented heterotrophic bacteria (PHB) based on the cultivation method and sequencing analysis of 16S rRNA genes was conducted in Chinese coastal and shelf waters and the Pacific Ocean. Both the abundance of PHB and the ratio of PHB to CFU decreased along trophic gradients from coastal to oceanic waters, with the highest values of 9.9 x 10(3) cell mL(-1) and 39.6%, respectively, in the Yangtze River Estuary. In contrast to the total heterotrophic bacteria (TB) and CFU, which were present in the whole water column, PHB were primarily confined to the euphotic zone, with the highest abundance of PHB and ratio of PHB to CFU occurring in surface water. In total, 247 pigmented isolates were obtained during this study, and the phylogenetic analysis showed a wide genetic diversity covering 25 genera of six phylogenetic classes: Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacilli, Flavobacteria and Sphingobacteria. PHB belonging to Alphaproteobacteria, Flavobacteria and Sphingobacteria were obtained mainly from the South China Sea and East China Sea; PHB from the Pacific Ocean water were predominantly affiliated with Gammaproteobacteria, and most isolates from the Yangtze River Estuary fell into the classes Actinobacteria and Bacilli. The isolates exhibited various colours (e.g. golden, yellow, red, pink and orange), with genus or species specificity. Furthermore, the pigment of PHB cells absorbed light mainly in the wavelength range between 450 and 550 nm. In conclusion, our work has revealed that PHB with broad genetic diversity are widely distributed in the marine environment, and may account for up to 39.6% of culturable bacteria, equivalent to 1.4% of the total microbial community. This value might even be underestimated because it is probable that not all pigmented bacteria were isolated. Their abundance and genetic distribution are heavily influenced by environmental properties, such as light and nutrition

  12. Enzyme-Cascade Analysis of the Rio Tinto Subsurface Environment: A Biosensor Experiment

    NASA Technical Reports Server (NTRS)

    McKay, David S.; Lynch, Kennda; Wainwright, Norman; Child, Alice; Williams, Kendra; McKay, David; Amils, Ricardo; Gonzalez, Elena; Stoker, Carol

    2004-01-01

    The Portable Test System (PTS), designed & developed by Charles Rivers Laboratories, Inc. (Charleston, SC) is a portable instrument that was designed to perform analysis of enzymatic assays related to rapid assessment of microbial contamination (Wainwright, 2003). The enzymatic cascade of Limulus Amebocyte Lysate (LAL) is known to be one of the most sensitive techniques available for microbial detection, enabling the PTS to be evaluated as a potential life detection instrument for in situ Astrobiology missions. In the summer of 2003 the system was tested as a part of the Mars Astrobiology Research and Technology Experiment (MARTE) ground truth science campaign in the Rio Tinto Analogue environment near Nerva, Spain. The preliminary results show that the PTS analysis correlates well with the contamination control tests and the more traditional lab-based biological assays performed during the MARTE field mission. Further work will be conducted on this research during a second field campaign in 2004 and a technology demonstration of a prototype instrument that includes autonomous sample preparation will occur in 2005.

  13. 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

  14. Process studies in modern glacial environments: An innovative method and tool for subsurface site characterization at U.S. Army Alaska installations

    NASA Astrophysics Data System (ADS)

    Evenson, E. B.; Lawson, D. E.; Kopczynski, S. E.; Finnegan, D. C.; Bigl, S. R.; Fosbrook, C.

    2002-12-01

    Subsurface stratigraphy in previously glaciated terrain is complex and difficult to interpret. Textbook models illustrating glacial and periglacial environments are often too idealized to serve as adequate analogs to interpret site-specific subsurface data. Models of emplacement generally provide the perspective of glacial and periglacial processes at synoptic scales. While these models are useful to understand general principles, these models are insufficient to provide geologic information at resolutions necessary for quantitative environmental remediation efforts. Contaminated sites on U.S. Army Alaska Installations are characterized by glacially driven complex subsurface stratigraphy. These subsurface conditions cannot entirely be defined through boreholes, nor can geophysical data (ground penetrating radar, shallow seismics, etc.) be readily interpreted through existing conceptual models, especially in areas of discontinuous permafrost (Fort Wainwright, central Alaska) or formerly glaciated terrains (Fort Richardson, South Central Alaska; Haines Fuel Terminal, Southeast Alaska). Process studies at modern glacier locales, such as the Matanuska Glacier and Glacier Bay, allow us to apply actual field-process observations at a variety of scales to characterize site-specific stratigraphy. This work has led us to refine our geophysical approaches to detect the presence of buried ice, permafrost and sediment layers in active terrestrial and tidewater glacial environments, which has greatly enhanced our ability to map the vertical and lateral distribution of confining layers in our investigative areas (i.e. permafrost and sediments). These data and process observations are synthesized as three-dimensional models allowing us to predict the probable spatial distribution and relationships that exist among aquifers and their confining units. This approach allows us the ability to accurately develop subsurface models that are essential in developing groundwater models to

  15. 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.

  16. 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…

  17. Drivers of carabid functional diversity: abiotic environment, plant functional traits, or plant functional diversity?

    PubMed

    Pakeman, Robin J; Stockan, Jenni A

    2014-05-01

    Understanding how community assembly is controlled by the balance of abiotic drivers (environment or management) and biotic drivers (community composition of other groups) is important in predicting the response of ecosystems to environmental change. If there are strong links between plant assemblage structure and carabid beetle functional traits and functional diversity, then it is possible to predict the impact of environmental change propagating through different functional and trophic groups. Vegetation and pitfall trap beetle surveys were carried out across twenty four sites contrasting in land use, and hence productivity and disturbance regime. Plant functional traits were very successful at explaining the distribution of carabid functional traits across the habitats studied. Key carabid response traits appeared to be body length and wing type. Carabid functional richness was significantly smaller than expected, indicating strong environmental filtering, modulated by management, soil characteristics, and by plant response traits. Carabid functional divergence was negatively related to plant functional evenness, while carabid functional evenness was positively correlated to plant functional evenness and richness. The study shows that there are clear trait linkages between the plant and the carabid assemblage that act not only through the mean traits displayed, but also via their distribution in trait space; powerful evidence that both the mean and variance of traits in one trophic group structure the assemblage of another.

  18. Laboratory controls of precursor and temperature on the kinetics and isotopic fractionations of microbial methane for deep subsurface environments

    NASA Astrophysics Data System (ADS)

    Ling, Y.; Lin, L.; Wang, P.; Sun, C.

    2009-12-01

    In subsurface environments, the mineralization of organic carbon involves complex interactions among geological and microbial processes. As the most reduced form and the shortest hydrocarbon chain, methane, is the final product of both microbial degradation and thermal-cracking of organic matter, it serves as the connection of carbon cycles between different reservoirs. Of various mechanisms for methane formation, microbial methane constitutes 85% of the total methane inventory investigated by far. However, the mechanisms and resultant carbon isotope fingerprints of methanogenesis in environments still remained largely unknown. The types of precursors and temperature might be the most critical factors governing methanogenesis. Lots of studies have been investigating the mechanisms responsible for methanogenesis by pure cultures, but it still remains obscure with regard to which precursors are predominantly utilized by methanogens in natural settings. The effect of temperature is especially prominent for anoxic sediments within which the temperature increases with depth in accordance with the local geotherm. Commonly observed temperatures for methanogenesis span from ambient temperature to 90OC, a temperature range for most diagenetic reactions. In order to address how different precursors would be activated for microbially catalytic methane formation upon different temperatures, we incubated the sediments collected from Kuan-Tzu-Ling hot spring at temperatures up to 90OC. Five precursors including acetate, formate, methanol, methylamine, and hydrogen were added with the inocula to stimulate methanogenesis and inhibit fermentation, and were monitored together with methane production through time. Results of this experiments indicated that methanogenesis was positive at temperatures from room temperature to 80OC and precursors investigated despite substantial variations in the maximum rates and yields. In the experiment supplied with hydrogen and formate

  19. Integrated subsurface water solutions for coastal environments through integrated pump&treat and aquifer storage and recovery (ASR) schemes

    NASA Astrophysics Data System (ADS)

    Perdikaki, Martha; Kallioras, Andreas; Christoforidis, Christophoros; Iossifidis, Dimitris; Zafeiropoulos, Anastasios; Dimitriadis, Klisthenis; Makropoulos, Christos; Raat, Klaasjan; van den Berg, Gerard

    2016-04-01

    Coastal wetlands in semi-arid regions, as in Circum-Mediterranean, are considered important ecosystems that provide valuable services to human population and the environment, such as: flood protection, erosion control, wildlife habitat, water quality, recreation and carbon sequestration. Un-managed surface and groundwater exploitation in these areas usually leads to deterioration of such sensitive ecosystems by means of water resources degradation and/or increased salinity. Groundwater usually plays a vital role for the sustainability of these hydrological systems, as the underlying aquifers operate as regulators for both quantity and quality of their waters. Multi-layer and multi-objective Managed Aquifer Recharge (MAR) systems can be proved effective groundwater engineered solutions for the restoration of deteriorated coastal wetlands in semi- and arid regions. The plain of Marathon is a typical Mediterranean environment that hosts a naturally occurring -and today degraded- coastal wetland with the characteristics of a distinct ecosystem linked to a typical coastal hydrogeological system of a semi-arid region; and therefore can serve as a model for similar systems world-wide. The geo-hydrological setting of the area involves a multi-layer aquifer system consisting of (i) an upper un-consolidated formation of depositional unit dominated mostly by fluvial sediments and (ii) the surrounding and underlying karstified marbles; both being linked to the investigated wetland and also subjected to seawater encroachment. A smart engineered MAR system via an optimised Pump & Treat system integrated with an Aquifer Storage and Recovery (ASR) scheme in this area would include the abstraction of brackish groundwater from the deeper karst aquifer at a location close to the shoreline and direct treatment with Reverse Osmosis (RO). for desalination. Two-fold re-use scheme of the purified effluent can then be engineered for (i) the restoration of the coastal wetland; and (ii

  20. Improving the biodegradative capacity of subsurface bacteria

    SciTech Connect

    Romine, M.F.; Brockman, F.J.

    1993-04-01

    The continual release of large volumes of synthetic materials into the environment by agricultural and industrial sources over the last few decades has resulted in pollution of the subsurface environment. Cleanup has been difficult because of the relative inaccessibility of the contaminants caused by their wide dispersal in the deep subsurface, often at low concentrations and in large volumes. As a possible solution for these problems, interest in the introduction of biodegradative bacteria for in situ remediation of these sites has increased greatly in recent years (Timmis et al. 1988). Selection of biodegradative microbes to apply in such cleanup is limited to those strains that can survive among the native bacterial and predator community members at the particular pH, temperature, and moisture status of the site (Alexander, 1984). The use of microorganisms isolated from subsurface environments would be advantageous because the organisms are already adapted to the subsurface conditions. The options are further narrowed to strains that are able to degrade the contaminant rapidly, even in the presence of highly recalcitrant anthropogenic waste mixtures, and in conditions that do not require addition of further toxic compounds for the expression of the biodegradative capacity (Sayler et al. 1990). These obstacles can be overcome by placing the genes of well-characterized biodegradative enzymes under the control of promoters that can be regulated by inexpensive and nontoxic external factors and then moving the new genetic constructs into diverse groups of subsurface microbes. ne objective of this research is to test this hypothesis by comparing expression of two different toluene biodegradative enzymatic pathways from two different regulatable promoters in a variety of subsurface isolates.

  1. Structural diversity of the 3-micron absorption band in Enceladus’ plume from Cassini VIMS: Insights into subsurface environmental conditions

    NASA Astrophysics Data System (ADS)

    Dhingra, Deepak; Hedman, Matthew M.; Clark, Roger N.

    2015-11-01

    Water ice particles in Enceladus’ plume display their diagnostic 3-micron absorption band in Cassini VIMS data. These near infrared measurements of the plume also exhibit noticeable variations in the character of this band. Mie theory calculations reveal that the shape and location of the 3-micron band are controlled by a number of environmental and structural parameters. Hence, this band provides important insights into the properties of the water ice grains and about the subsurface environmental conditions under which they formed. For example, the position of the 3-micron absorption band minimum can be used to distinguish between crystalline and amorphous forms of water ice and to constrain the formation temperature of the ice grains. VIMS data indicates that the water ice grains in the plume are dominantly crystalline which could indicate formation temperatures above 113 K [e.g. 1, 2]. However, there are slight (but observable) variations in the band minimum position and band shape that may hint at the possibility of varying abundance of amorphous ice particles within the plume. The modeling results further indicate that there are systematic shifts in band minimum position with temperature for any given form of ice but the crystalline and amorphous forms of water ice are still distinguishable at VIMS spectral resolution. Analysis of the eruptions from individual source fissures (tiger stripes) using selected VIMS observations reveal differences in the 3-micron band shape that may reflect differences in the size distributions of the water ice particles along individual fissures. Mie theory models suggest that big ice particles (>3 micron) may be an important component of the plume.[1] Kouchi, A., T. Yamamoto, T. Kozasa, T. Kuroda, and J. M. Greenberg (1994) A&A, 290, 1009-1018 [2] Mastrapa, R. M. E., W. M. Grundy, and M. S. Gudipati (2013) in M. S. Gudipati and J. Castillo-Rogez (Eds.), The Science of Solar System Ices, pp. 371.

  2. Redefining Diversity: Political Responses to the Post-PICS Environment

    ERIC Educational Resources Information Center

    Siegel-Hawley, Genevieve; Frankenberg, Erica

    2011-01-01

    This article examines the federal and local political response to the "Parents Involved" decision. At the federal level, developments suggest a reaction to "Parents Involved" that, since President Obama has taken office, has been largely supportive of voluntary efforts to promote racial diversity. The administration has also…

  3. Population genetic diversity and fitness in multiple environments

    EPA Science Inventory

    When a large number of alleles are lost from a population, increases in homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations t...

  4. Population Genetic Diversity and Fitness in Multiple Environments(BMCEB)

    EPA Science Inventory

    When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of p...

  5. Microbial methanogenesis in subsurface oil and coal.

    PubMed

    Meslé, Margaux; Dromart, Gilles; Oger, Philippe

    2013-11-01

    It is now clear that active methanogens are present in the deep-subsurface. This paper reviews microbial population structures and the biodegradation of organic compounds to methane in situ within oil reservoirs and coal deposits. It summarizes our current knowledge of methanogenes and methanogenesis, fermenters, synthrophs and microbial metabolism of complex organic compounds in these two widely occurring organic-rich subsurface environments. This review is not intended to be an exhaustive report of microbial diversity. Rather, it illustrates the similarities and differences between the two environments with specific examples, from the nature of the organic molecules to the methanogenic metabolic pathways and the structure of the microbial populations to demonstrate that widely diverging microbial populations show surprisingly similar metabolic capabilities.

  6. Quantifying and relating land-surface and subsurface variability in permafrost environments using lidar and surface geophsical datasets

    SciTech Connect

    Hubbard, Susan S; Gangodagmage, C; Dafflon, B; Wainwright, H; Peterson, J; Gusmeroli, A; Ulrich, Craig; Wu, Yuxin; Wilson, Cathy; Rowland, J; Tweedie, Craig; Wullschleger, Stan D

    2013-01-01

    The complexity of permafrost dynamics and its critical impact on climate feedbacks warrant continued development of advanced high-latitude terrestrial ecosystem characterization and monitoring approaches. In this study, we explore the value of remote sensing and surface geophysical data for characterizing land surface and subsurface properties and their linkages in an Alaskan Coastal Plain ecosystem. We base our study on data collected at the end of the 2011 growing season in the Barrow Environmental Observatory, where a nested suite of measurements were collected within a polygon-dominated region including: surface ground penetrating radar, electromagnetic, and electrical resistance tomography data; thaw depth, soil temperature and moisture content, soil texture, soil carbon and nitrogen content, and major and trace cations. Previously-collected lidar data were also available for the study. Analysis of the datasets, individually and in combination, revealed the utility of the methods for characterizing critical land-surface and subsurface properties and associated spatial zonation. Lidar analysis was performed to extract geomorphic metrics (such as slope, curvature, and directed distance of polygons), which potentially indicate drainage potential and permafrost deformation state. Cluster analysis of these lidar-obtained attributes suggested that the land surface can be grouped into three spatially coherent zones, each having a dominant geomorphic expression including: a high centered polygon zone, a low centered polygon zone and a transitional zone. Comparison of the geophysical attributes from radar, electrical resistance tomography, and electromagnetic data with point measurements suggests that the surface geophysical data can provide very high-resolution information about subsurface properties that affect ecosystem feedbacks to climate, such as thaw depth and moisture content. Cluster analysis suggested that the geophysical attributes also varied spatially in a

  7. High diversity of bacterial mercuric reductase genes from surface and sub-surface floodplain soil (Oak Ridge, USA).

    PubMed

    Oregaard, Gunnar; Sørensen, Søren J

    2007-09-01

    DNA was extracted from different depth soils (0-5, 45-55 and 90-100 cm below surface) sampled at Lower East Fork Poplar Creek floodplain (LEFPCF), Oak Ridge (TN, USA). The presence of merA genes, encoding the mercuric reductase, the key enzyme in detoxification of mercury in bacteria, was examined by PCR targeting Actinobacteria, Firmicutes or beta/gamma-Proteobacteria. beta/gamma-Proteobacteria merA genes were successfully amplified from all soils, whereas Actinobacteria were amplified only from surface soil. merA clone libraries were constructed and sequenced. beta/gamma-Proteobacteria sequences revealed high diversity in all soils, but limited vertical similarity. Less than 20% of the operational taxonomic units (OTU) (DNA sequences > or = 95% identical) were shared between the different soils. Only one of the 62 OTU was > or = 95% identical to a GenBank sequence, highlighting that cultivated bacteria are not representative of what is found in nature. Fewer merA sequences were obtained from the Actinobacteria, but these were also diverse, and all were different from GenBank sequences. A single clone was most closely related to merA of alpha-Proteobacteria. An alignment of putative merA genes of genome sequenced mainly marine alpha-Proteobacteria was used for design of merA primers. PCR amplification of soil alpha-Proteobacteria isolates and sequencing revealed that they were very different from the genome-sequenced bacteria (only 62%-66% identical at the amino-acid level), although internally similar. In light of the high functional diversity of mercury resistance genes and the limited vertical distribution of shared OTU, we discuss the role of horizontal gene transfer as a mechanism of bacterial adaptation to mercury.

  8. Analysis of the metabolic utilization of carbon sources and potential functional diversity of the bacterial community in lab-scale horizontal subsurface-flow constructed wetlands.

    PubMed

    Deng, Huanhuan; Ge, Liyun; Xu, Tan; Zhang, Minghua; Wang, Xuedong; Zhang, Yalei; Peng, Hong

    2011-01-01

    Microorganisms are an integral part of the biogeochemical processes in wetlands. To improve the performance of constructed wetlands, it is very important to know the metabolic properties and functional diversity of the microbial communities. The purpose of this study is to analyze the metabolic properties and functional diversity of the microbial community in a horizontal subsurface-flow constructed wetland (CW) in a laboratory study through the sole-carbon-source utilization profiles using Biolog-ECO microplates. The technique has advantages over traditional cell culture techniques, such as molecular-level techniques-RNA amplification, which are time-consuming, expensive, and only applicable to the small number of species that may be cultured. This CW was designed to treat rural eutrophic water in China, using the plant L. This study showed that the metabolic activities of upper front substrate microorganisms (UF) were greater than those of the lower back substrate microorganisms (LB) in the CW. Integrated areas under average well color development (AWCD) curves of substrate microorganisms in the UF were 131.9, 4.8, and 99.3% higher than in the lower front part (LF), the upper back part (UB), and the LB part of the CW, respectively. Principal components analysis showed significant differences in both community structure and metabolic utilization of carbon sources between substrate microorganisms from different sampling sites. Carbon source utilization of polymers, carbohydrates, carboxylic acids, and amino acids was higher in UF than in LF, but that of amines and phenolic compounds was very similar in UF and LF. The richness, evenness, and diversity of upper substrate microbial communities were significantly higher than those of lower substrate. The LF substrate microbial communities had lower evenness than the other sampling plots, and the lowest richness of substrate microbial community was found in the LB part of the CW.

  9. 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.

  10. Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.

    PubMed

    Miller, Christopher S; Handley, Kim M; Wrighton, Kelly C; Frischkorn, Kyle R; Thomas, Brian C; Banfield, Jillian F

    2013-01-01

    In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the "long tail" of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.

  11. 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…

  12. Aram Chaos: a Long Lived Subsurface Aqueous Environment with Strong Water Resources Potential for Human Missions on Mars

    NASA Technical Reports Server (NTRS)

    Sibille, L.; Mueller, R.; Niles, P. B.; Glotch, T.; Archer, P. D.; Bell, M. S.

    2015-01-01

    Aram Chaos, Mars is a crater 280 kilometers in diameter with elevations circa. minus 2 to minus 3 kilometers below datum that provides a compelling landing site for future human explorers as it features multiple scientific regions of interest (ROI) paired with a rich extensible Resource ROI that features poly-hydrated sulfates [1]. The geologic history of Aram Chaos suggests several past episodes of groundwater recharge and infilling by liquid water, ice, and other materials [1-3]. The creation of the fractured region with no known terrestrial equivalent may have been caused by melting of deep ice reservoirs that triggered the collapse of terrain followed by catastrophic water outflows over the region. Aram Chaos is of particular scientific interest because it is hypothesized that the chaotic terrain may be the source of water that contributed to the creation of nearby valleys such as Ares Vallis flowing toward Chryse Planitia. The liquid water was likely sourced as groundwater and therefore represents water derived from a protected subsurface environment making it a compelling astrobiological site [2]. The past history of water is also represented by high concentrations of hematite, Fe-oxyhydroxides, mono-hydrated and poly-hydrated sulfates [1, 2]. Poly-hydrated sulfates are likely to contain abundant water that evolves at temperatures below 500 degrees Centigrade thus conferring Aram Chaos a potentially high value for early in-situ resource utilization (ISRU) [4]. The geologic history also calls for future prospecting of deep ice deposits and possibly liquid water via deep drilling. The most recent stratigraphic units in the central part of Aram Chaos are not fractured, and are part of a dome-shaped formation that features bright, poorly-consolidated material that contains both hydrated sulfates and ferric oxides according to OMEGA (Observatoire pour la Minéralogie, l'Eau, les Glaces et l'Activité) data [5]. These surface material characteristics are

  13. Techniques for assessing the performance of in situ bioreduction and immobilization of metals and radionuclides in contaminated subsurface environments

    SciTech Connect

    Jardine, P.M.; Watson, D.B.; Blake, D.A.; Beard, L.P.; Brooks, S.C.; Carley, J.M.; Criddle, C.S.; Doll, W.E.; Fields, M.W.; Fendorf, S.E.; Geesey, G.G.; Ginder-Vogel, M.; Hubbard, S.S.; Istok, J.D.; Kelly, S.; Kemner, K.M.; Peacock, A.D.; Spalding, B.P.; White, D.C.; Wolf, A.; Wu, W.; Zhou, J.

    2004-11-14

    Department of Energy (DOE) facilities within the weapons complex face a daunting challenge of remediating huge below inventories of legacy radioactive and toxic metal waste. More often than not, the scope of the problem is massive, particularly in the high recharge, humid regions east of the Mississippi river, where the off-site migration of contaminants continues to plague soil water, groundwater, and surface water sources. As of 2002, contaminated sites are closing rapidly and many remediation strategies have chosen to leave contaminants in-place. In situ barriers, surface caps, and bioremediation are often the remedial strategies of chose. By choosing to leave contaminants in-place, we must accept the fact that the contaminants will continue to interact with subsurface and surface media. Contaminant interactions with the geosphere are complex and investigating long term changes and interactive processes is imperative to verifying risks. We must be able to understand the consequences of our action or inaction. The focus of this manuscript is to describe recent technical developments for assessing the performance of in situ bioremediation and immobilization of subsurface metals and radionuclides. Research within DOE's NABIR and EMSP programs has been investigating the possibility of using subsurface microorganisms to convert redox sensitive toxic metals and radionuclides (e.g. Cr, U, Tc, Co) into a less soluble, less mobile forms. Much of the research is motivated by the likelihood that subsurface metal-reducing bacteria can be stimulated to effectively alter the redox state of metals and radionuclides so that they are immobilized in situ for long time periods. The approach is difficult, however, since subsurface media and waste constituents are complex with competing electron acceptors and hydrogeological conditions making biostimulation a challenge. Performance assessment of in situ biostimulation strategies is also difficult and typically requires detailed

  14. Turtle Carapace Anomalies: The Roles of Genetic Diversity and Environment

    PubMed Central

    Velo-Antón, Guillermo; Becker, C. Guilherme; Cordero-Rivera, Adolfo

    2011-01-01

    Background Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales. Methodology/Principal Findings In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3% to 69% in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium. Conclusions/Significance Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants and heritability of anomalies would be useful to better understand the complex origin of anomalies in natural populations. PMID:21533278

  15. Embracing Diversity: Toolkit for Creating Inclusive Learning-Friendly Environments

    ERIC Educational Resources Information Center

    Harris, Ray; Miske, Shirley; Attig, George

    2004-01-01

    An inclusive, learning-friendly environment (ILFE) welcomes, nurtures, and educates all children regardless of their gender, physical, intellectual, socio-economic, emotional, linguistic and other characteristics. "Inclusive" in the school setting generally refers to the inclusion or children with disabilities into regular classrooms designed for…

  16. Protostellar Luminosity Functions in 11 Diverse Star Forming Environments

    NASA Astrophysics Data System (ADS)

    Kryukova, Erin; Megeath, S. T.; Gutermuth, R.; Pipher, J.; Allen, T. S.; Allen, L. E.; Myers, P. C.; Muzerolle, J.; Cygnus-X Legacy Team

    2012-01-01

    Protostars exist in a variety of environments, ranging from clouds with dispersed low-mass stars, such as Taurus, to clustered regions in clouds forming high-mass stars, like Orion. The effect these different environments have on protostar properties such as mass or luminosity is uncertain. One way to probe the effects of cloud environment on the observable property, protostar luminosity is to compare protostellar luminosity functions of clouds hosting varied populations of protostars. In this dissertation talk I will discuss the protostellar luminosity functions from 11 star forming clouds including Lupus, Chamaeleon, Ophiuchus, Perseus, Serpens, Orion, Cep OB3, Mon R2, Cygnus-X, and Maddalena's Cloud, which encompass a wide range of star forming environments. The luminosity functions are constructed from Spitzer surveys of these molecular clouds. I employ a new technique for estimating the bolometric luminosity from near and mid-IR fluxes alone and for subtracting contamination from galaxies, reddened pre-main sequence stars with disks, and edge-on disk systems. The clouds which are forming massive stars show a significant peak at low luminosity and a tail extending toward luminosities above 10 solar luminosities, while the luminosity functions of clouds which are not forming massive stars have no significant peak down to the sensitivity limit and do not exhibit the tail. I compare these luminosity functions to existing models of protostellar evolution. I also compare the luminosity functions of protostars in distributed and clustered environments, as determined using nearest-neighbor distances. In Orion and Cygnus-X, the clouds which contain the largest populations of protostars there is a clear difference in luminosity functions between protostars incrowded and distributed regions, with the luminosity function biased towards higher luminosities in more luminous regions. I will discuss the implications of these variations and the possibility that the IMF is

  17. A palette of fluorescent proteins optimized for diverse cellular environments

    PubMed Central

    Costantini, Lindsey M.; Baloban, Mikhail; Markwardt, Michele L.; Rizzo, Mark; Guo, Feng; Verkhusha, Vladislav V.; Snapp, Erik L.

    2015-01-01

    To perform quantitative live cell imaging, investigators require fluorescent reporters that accurately report protein localization and levels, while minimally perturbing the cell. Yet, within the biochemically distinct environments of cellular organelles, popular fluorescent proteins (FPs), including EGFP, can be unreliable for quantitative imaging, resulting in underestimation of protein levels and incorrect localization. Specifically, within the secretory pathway, significant populations of FPs misfold and fail to fluoresce due to non-native disulphide bond formation. Furthermore, transmembrane FP fusion constructs can disrupt organelle architecture due to oligomerizing tendencies of numerous common FPs. Here, we describe a powerful set of bright and inert FPs optimized for use in multiple cellular compartments, especially oxidizing environments and biological membranes. Also, we provide new insights into use of red FPs in the secretory pathway. Our monomeric "oxFPs" finally resolve long standing, underappreciated, and important problems of cell biology and should be useful for a number of applications. PMID:26158227

  18. Influence of biofilms on the movement of colloids in porous media. Implications for colloid facilitated transport in subsurface environments.

    PubMed

    Leon Morales, Carlos Felipe; Strathmann, Martin; Flemming, Hans-Curt

    2007-05-01

    Colloid transport through porous media can be influenced by the presence of biofilms. Sterile and non-sterile sand columns were investigated using Laponite RD as model colloid and a highly mucoid strain of Pseudomonas aeruginosa as model biofilm former. Laponite RD was marked specifically by fluorescent complexes with rhodamine 6G. Breakthrough curves (BTCs) were used as parameters for determination of colloid transport characteristics. In the sterile columns, the colloid was mobile (collision efficiencies from 0.05 to 0.08) both after the presence of Na(+) and Ca(2+) ions followed by deionised water influent. In the biofilm-grown column, the same treatment did not result in colloid retention in the case of Na(+) exposure, but in altered or enhanced colloid transport. In the case of Ca(2+) ions exposure, colloid retention increased with biofilm age. After 3 weeks, almost complete retention was observed. Similar observations were made in columns packed with material from slow sand filtration units. These data reveal the complex interactions between biofilms, cations and colloid transport. Changes in the electrolyte composition of water percolating the subsurface can frequently occur and will result in different colloid transport characteristics with regard to the dominating species of ions and the relative abundance of microbial biofilms. This has to be considered when modelling colloid transport through the subsurface.

  19. The role of the dental school environment in promoting greater student diversity.

    PubMed

    Pendleton, Darryl D; Graham, Bruce S

    2010-10-01

    This chapter describes the strategies implemented by one dental school during the past decade to establish an environment that supports a culture of diversity. The school audited its initial diversity milieu, authored a strategic plan for diversity, fully participated in university-wide diversity initiatives, and created an administrative infrastructure for underrepresented minority (URM) student support. Mentoring and counseling programs were established for URM students, and a schoolwide diversity committee was formed to make cultural competence a high priority for all students, faculty, and staff. URM faculty members were recruited and retained through a minority faculty development program. Student professional organizations were established and supported by mentoring partnerships with members of the corresponding organizations in the practicing community. The school's diversity culture is continuously evaluated and nurtured within the context of evolving human interactions in society, dental education, and dental practice.

  20. Intraspecific diversity of Aureobasidium pullulans strains from different marine environments

    NASA Astrophysics Data System (ADS)

    Liu, Jia; Liu, Zhiqiang; Chi, Zhenming; Zhang, Liang; Zhang, Dechao

    2009-09-01

    Totally more than 500 yeast strains were isolated from seawater, sea sediments, mud of sea salterns, marine fish guts and marine algae. The results of routine and molecular biology identification methods show that nine strains among these marine yeasts belong to Aureobasidium pullulans, although the morphologies of their colonies are very different. The marine yeasts isolated from different marine environments indicate that A. pullulans is widely distributed in different environmental conditions. These Aureobasidium pullulans strains include A. pullulans 4#2, A. pullulans N13d, A. pullulans HN3-11, A. pullulans HN2-3, A. pullulans JHSc, A. pullulans HN4.7, A. pullulans HN5.3, A. pullulans HN6.2 and A. pullulans W13a. A. pullulans 4#2 could produce cellulase and single cell protein. A. pullulans N13d could produce protease, lipase, amylase and cellulase. Both A. pullulans HN3-11 and A. pullulans HN2-3 were able to produce protease, lipase and cellulase. A. pullulans JHSc could secrete cellulase and killer toxin. Both A. pullulans HN4.7 and A. pullulans HN5.3 could yield lipase and cellulase. A. pullulans W13a was able to secrete extracellular amylase and cellulase while A. pullulans HN4.7 and A. pullulans N13d could produce siderophores. This means that different A. pullulans strains from different marine environments have different physiological characteristics, which may be applied in many different biotechnological industries.

  1. 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.

  2. Exploratory data analysis on data generated in the DOE subsurface microbiology program

    SciTech Connect

    Meglen, R.R.

    1990-06-01

    The preliminary results from the innovative subsurface microbiology research program indicate that new data on the nature of the link between the geosphere and biosphere have been generated. The diversity of scientific disciplines represented in the subsurface microbiology program reflects the complexity of the system under study. The research carried out by national laboratory and university research scientists is addressing fundamental questions about the abundance of microorganisms and factors controlling microbial activity in the complex subsurface hydrologic and geochemical environment. Long-term implications of this research for mitigating contamination are clear and researchers share the broader objective of linking the basic science with applied work.

  3. 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

  4. Subsurface Contamination Control

    SciTech Connect

    Y. Yuan

    2001-12-12

    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 the 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) provides a

  5. Subsurface Contamination Control

    SciTech Connect

    Y. Yuan

    2001-11-16

    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 the 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) provides a

  6. 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.

  7. Subsurface Samples: Collection and Processing

    SciTech Connect

    Long, Philip E.; Griffin, W. Timothy; Phelps, Tommy J.

    2002-12-01

    Microbiological data, interpretation, and conclusions from subsurface samples ultimately depend on the quality and representative character of the samples. Subsurface samples for environmental microbiology ideally contain only the microbial community and geochemical properties that are representative of the subsurface environment from which the sample was taken. To that end, sample contamination by exogenous microorganisms or chemical constituents must be eliminated or minimized, and sample analyses need to begin before changes in the microbial community or geochemical characteristics occur. This article presents sampling methods and sample processing techniques for collecting representative samples from a range of subsurface environments. Factors that should be considered when developing a subsurface sampling program are discussed, including potential benefits, costs, and limitations enabling researchers to evaluate the techniques that are presented and match them to their project requirements. Methods and protocols to address coring, sampling, processing and quality assessment issues are presented.

  8. SEISMIC SOURCE SCALING AND DISCRIMINATION IN DIVERSE TECTONIC ENVIRONMENTS

    SciTech Connect

    Abercrombie, R E; Mayeda, K; Walter, W R; Viegas, G M; Murphy, K

    2008-07-08

    The objectives of this study are to improve low-magnitude (concentrating on M2.5-5) regional seismic discrimination by performing a thorough investigation of earthquake source scaling using diverse, high-quality datasets from varied tectonic regions. Local-to-regional high-frequency discrimination requires an estimate of how earthquakes scale with size. Walter and Taylor (2002) developed the MDAC (Magnitude and Distance Amplitude Corrections) method to empirically account for these effects through regional calibration. The accuracy of these corrections has a direct impact on our ability to identify clandestine explosions in the broad regional areas characterized by low seismicity. Unfortunately our knowledge at small magnitudes (i.e., m{sub b} < {approx} 4.0) is poorly resolved, and source scaling remains a subject of on-going debate in the earthquake seismology community. Recently there have been a number of empirical studies suggesting scaling of micro-earthquakes is non-self-similar, yet there are an equal number of compelling studies that would suggest otherwise. It is not clear whether different studies obtain different results because they analyze different earthquakes, or because they use different methods. Even in regions that are well studied, such as test sites or areas of high seismicity, we still rely on empirical scaling relations derived from studies taken from half-way around the world at inter-plate regions. We investigate earthquake sources and scaling from different tectonic settings, comparing direct and coda wave analysis methods that both make use of empirical Green's function (EGF) earthquakes to remove path effects. Analysis of locally recorded, direct waves from events is intuitively the simplest way of obtaining accurate source parameters, as these waves have been least affected by travel through the earth. But finding well recorded earthquakes with 'perfect' EGF events for direct wave analysis is difficult, limits the number of earthquakes

  9. SEISMIC SOURCE SCALING AND DISCRIMINATION IN DIVERSE TECTONIC ENVIRONMENTS

    SciTech Connect

    Abercrombie, R E; Mayeda, K; Walter, W R; Viegas, G M; Murphy, K

    2007-07-10

    The objectives of this study are to improve low-magnitude regional seismic discrimination by performing a thorough investigation of earthquake source scaling using diverse, high-quality datasets from varied tectonic regions. Local-to-regional high-frequency discrimination requires an estimate of how earthquakes scale with size. Walter and Taylor (2002) developed the MDAC (Magnitude and Distance Amplitude Corrections) method to empirically account for these effects through regional calibration. The accuracy of these corrections has a direct impact on our ability to identify clandestine explosions in the broad regional areas characterized by low seismicity. Unfortunately our knowledge of source scaling at small magnitudes (i.e., m{sub b} < {approx}4.0) is poorly resolved. It is not clear whether different studies obtain contradictory results because they analyze different earthquakes, or because they use different methods. Even in regions that are well studied, such as test sites or areas of high seismicity, we still rely on empirical scaling relations derived from studies taken from half-way around the world at inter-plate regions. We investigate earthquake sources and scaling from different tectonic settings, comparing direct and coda wave analysis methods. We begin by developing and improving the two different methods, and then in future years we will apply them both to each set of earthquakes. Analysis of locally recorded, direct waves from events is intuitively the simplest way of obtaining accurate source parameters, as these waves have been least affected by travel through the earth. But there are only a limited number of earthquakes that are recorded locally, by sufficient stations to give good azimuthal coverage, and have very closely located smaller earthquakes that can be used as an empirical Green's function (EGF) to remove path effects. In contrast, coda waves average radiation from all directions so single-station records should be adequate, and

  10. Subsurface characterization of an oxidation-induced phase transformation and twinning in nickel-based superalloy exposed to oxy-combustion environments

    SciTech Connect

    Zhu, Jingxi; Holcomb, Gordon R.; Jablonski, Paul D.; Wise, Adam; Li, Jia; Laughlin, David E.; Sridhar, Seetharaman

    2012-07-30

    In the integration of oxy-fuel combustion to turbine power generation system, turbine alloys are exposed to high temperature and an atmosphere comprised of steam, CO{sub 2} and O{sub 2}. While surface and internal oxidation of the alloy takes place, the microstructure in the subsurface region also changes due to oxidation. In this study, bare metal coupons of Ni-base superalloys were exposed in oxy-fuel combustion environment for up to 1000 h and the oxidation-related microstructures were examined. Phase transformation occurred in the subsurface region in Ni-based superalloy and led to twinning. The transformation product phases were analyzed through thermodynamic equilibrium calculations and various electron microscopy techniques, including scanning electron microscopy (SEM), orientation imaging microscopy (OIM) and transmission electron microscopy (TEM). The mechanism by which the phase transformation and the formation of the microstructure occurred was also discussed. The possible effects of the product phases on the performance of the alloy in service were discussed.

  11. Gamma-irradiation aggravates stress concentration along subsurface grain boundary of ultra-high molecular weight polyethylene (UHMWPE) under sliding fatigue environment.

    PubMed

    Shibata, Nobuyuki; Tomita, Naohide; Ikeuchi, Ken

    2003-01-01

    Numerical simulations were carried out using a DEM-based model under a sliding fatigue environment to investigate the influences of differences of mechanical properties between intra-granular portions and inter-granular portions on local stress-strain fields and to determine the effect of gamma-irradiative degradation of UHMWPE components on delamination. The predicted stress fields in the gamma-irradiated UHMWPE component were highly nonuniform and were quite different from those predicted in the non-irradiated UHMWPE component. The stress distributions were intensely affected by the structural inhomogeneousness of networked grain boundaries. Marked stress concentrations were observed along subsurface grain boundaries in the gamma-irradiated UHMWPE. The gamma-irradiated UHMWPE showed a steep increase in the maximum equivalent stresses for an increase in the number of sliding. As the number of sliding increased, moreover, the region where the maximum equivalent stress was observed, moved deep into the specimen. These findings suggest that fatigue damage with plastic deformation proceeds mainly at a subsurface region in the gamma-irradiated UHMWPE and at a superficial region in the non-irradiated one. Therefore, gamma-irradiation is an important factor in accelerating fatigue crack initiation resulting in delamination.

  12. 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.

  13. 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.

  14. 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

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

    SciTech Connect

    Gu, April Z.; Wan, Kai-tak

    2014-09-02

    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, 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

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

    PubMed

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

    2012-08-01

    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.

  17. 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.

  18. 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

  19. Modeling total phosphorus removal in an aquatic environment restoring horizontal subsurface flow constructed wetland based on artificial neural networks.

    PubMed

    Li, Wei; Zhang, Yan; Cui, Lijuan; Zhang, Manyin; Wang, Yifei

    2015-08-01

    A horizontal subsurface flow constructed wetland (HSSF-CW) was designed to improve the water quality of an artificial lake in Beijing Wildlife Rescue and Rehabilitation Center, Beijing, China. Artificial neural networks (ANNs), including multilayer perceptron (MLP) and radial basis function (RBF), were used to model the removal of total phosphorus (TP). Four variables were selected as the input parameters based on the principal component analysis: the influent TP concentration, water temperature, flow rate, and porosity. In order to improve model accuracy, alternative ANNs were developed by incorporating meteorological variables, including precipitation, air humidity, evapotranspiration, solar heat flux, and barometric pressure. A genetic algorithm and cross-validation were used to find the optimal network architectures for the ANNs. Comparison of the observed data and the model predictions indicated that, with careful variable selection, ANNs appeared to be an efficient and robust tool for predicting TP removal in the HSSF-CW. Comparison of the accuracy and efficiency of MLP and RBF for predicting TP removal showed that the RBF with additional meteorological variables produced the most accurate results, indicating a high potentiality for modeling TP removal in the HSSF-CW.

  20. Relationship between the adhesive properties of bacteria and their transport and colonization in the subsurface environment. Final report for period September 15, 1996 - September 30, 1999

    SciTech Connect

    Madilyn Fletcher

    2000-04-06

    This research has focused on the attachment of bacteria to solid surfaces and the significance of their adhesion properties in their transport through porous media. Our work has focused on strains of Pseudomonas and a related species Burkholderia cepacia. Most of our experimental strains were isolated from subsurface environments at USDOE experimental field sites. The first portion of this project was conducted at the University of Maryland during 1994-1996, during which two graduates and one graduate student were supported by the award. The project was then continued under contract number DE-FG02-96ER62302 at the University of South Carolina, where one postdoctoral associate has been supported by the award.

  1. 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

  2. Field-scale investigations on the biodegradation of chlorinated aromatic compounds and HCH in the subsurface environment

    NASA Astrophysics Data System (ADS)

    Feidieker, Doris; Kämpfer, Peter; Dott, Wolfgang

    1995-08-01

    The biological in situ remediation of a former pesticide production site, highly contaminated with chlorobenzenes, chlorophenols and hexachlorocyclohexanes, was studied for a period of one year. Field experiments testing the remediation technology were carried out in the subsurface to a depth of 5.5 m. Detailed monitoring of several chemical and microbiological parameters was made in order to evaluate the remediation success. The initial pollution of this site ranged from 0.03-0.30 g EOX (extractable halogenated organic compounds)/kg soil in the saturated layer to 1-20 g kg -1 EOX in the unsaturated layer, whereas the impounded water was polluted with 8-13 mg L -1 AOX (adsorbable halogenated organic compounds). No significant decrease of the pollutants in the subsoil was observed, although oxygen and nutrients were supplied in sufficient concentrations. In contrast, several of the chlorinated organic compounds were eliminated from the water treatment plant, either by physical or biological processes. Based on measurements of AOX in different parts of the plant, 26% of the pollutants was found adsorbed on the activated carbon and 3% was found in the sludge of the filter back-wash. Dependent on these measurements, elimination of ˜ 70% of the pollutants was attributed to microbial degradation. The latter fact is supported by oxygen consumption data, by increase in the microbial counts and by changes in the distribution of the pollutants in the plant effluent. Among the chlorobenzenes, 1,2,4-trichlorobenzene, and among the hexachlorocyclohexanes, a-hexachlorocyclohexane were eliminated preferentially. The results suggest that an in situ remediation of a site polluted with chlorinated organic compounds cannot be recommended; however, an on site circulation water treatment is possible by a combination of physical and biological processes.

  3. 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…

  4. Creating a School Environment for the Effective Management of Cultural Diversity

    ERIC Educational Resources Information Center

    Grobler, B. R.; Moloi, K. C.; Loock, C. F.; Bisschoff, T. C.; Mestry, R. J.

    2006-01-01

    This article examines the factors which impact upon the creation of a school environment for the effective management of cultural diversity as legislated for in the directive principles of the South African Schools Act of 1996 and the Schools Education Act of 1995. The two Acts determine that every person shall have the right to basic education…

  5. The microbial diversity of Polar environments is a fertile ground for bioprospecting.

    PubMed

    de Pascale, Donatella; De Santi, Concetta; Fu, Juan; Landfald, Bjarne

    2012-12-01

    The term bioprospecting has been adopted for systematic searches in nature for new bioactive compounds, genes, proteins, microorganisms and other products with potential for commercial use. Much effort has been focused on microorganisms able to thrive under harsh conditions, including the Polar environments. Both the lipid and protein cellular building blocks of Polar microorganisms are shaped by their adaptation to the permanently low temperatures. In addition, strongly differing environments, such as permafrost, glaciers and sea ice, have contributed to additional functional diversity. Emerging massive-parallel sequencing technologies have revealed the existence of a huge, hitherto unseen diversity of low-abundance phylotypes--the rare biosphere--even in the Polar environments. This realization has further strengthened the need to employ cultivation-independent approaches, including metagenomics and single-cell genomic sequencing, to get comprehensive access to the genetic diversity of microbial communities for bioprospecting purposes. In this review, we present an updated snapshot of recent findings on the molecular basis for adaptation to the cold and the phylogenetic diversities of different Polar environments. Novel approaches in bioprospecting are presented and we conclude by showing recent bioprospecting outcomes in terms of new molecules patented or applied by some biotech companies.

  6. Canada: A Regionally Diverse and Northern Environment. Understanding the Canadian Environment.

    ERIC Educational Resources Information Center

    Brown, Rex B.; And Others

    One of a series of student booklets on the Canadian environment, this unit presents Canada from a geomorphological perspective of the six major regions: the Western Cordillera, the Interior Plains, the Canadian Shield, the Far North, the Great Lakes-St. Lawrence Lowlands, and Appalachian Canada. Intended to help secondary students understand the…

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

    SciTech Connect

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

    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.

  8. Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments

    PubMed Central

    Yang, Desirée C.; Blair, Kris M.

    2016-01-01

    SUMMARY Bacteria display an abundance of cellular forms and can change shape during their life cycle. Many plausible models regarding the functional significance of cell morphology have emerged. A greater understanding of the genetic programs underpinning morphological variation in diverse bacterial groups, combined with assays of bacteria under conditions that mimic their varied natural environments, from flowing freshwater streams to diverse human body sites, provides new opportunities to probe the functional significance of cell shape. Here we explore shape diversity among bacteria, at the levels of cell geometry, size, and surface appendages (both placement and number), as it relates to survival in diverse environments. Cell shape in most bacteria is determined by the cell wall. A major challenge in this field has been deconvoluting the effects of differences in the chemical properties of the cell wall and the resulting cell shape perturbations on observed fitness changes. Still, such studies have begun to reveal the selective pressures that drive the diverse forms (or cell wall compositions) observed in mammalian pathogens and bacteria more generally, including efficient adherence to biotic and abiotic surfaces, survival under low-nutrient or stressful conditions, evasion of mammalian complement deposition, efficient dispersal through mucous barriers and tissues, and efficient nutrient acquisition. PMID:26864431

  9. Microbiome interplay: plants alter microbial abundance and diversity within the built environment.

    PubMed

    Mahnert, Alexander; Moissl-Eichinger, Christine; Berg, Gabriele

    2015-01-01

    The built indoor microbiome has importance for human health. Residents leave their microbial fingerprint but nothing is known about the transfer from plants. Our hypothesis that indoor plants contribute substantially to the microbial abundance and diversity in the built environment was experimentally confirmed as proof of principle by analyzing the microbiome of the spider plant Chlorophytum comosum in relation to their surroundings. The abundance of Archaea, Bacteria, and Eukaryota (fungi) increased on surrounding floor and wall surfaces within 6 months of plant isolation in a cleaned indoor environment, whereas the microbial abundance on plant leaves and indoor air remained stable. We observed a microbiome shift: the bacterial diversity on surfaces increased significantly but fungal diversity decreased. The majority of cells were intact at the time of samplings and thus most probably alive including diverse Archaea as yet unknown phyllosphere inhabitants. LEfSe and network analysis showed that most microbes were dispersed from plant leaves to the surrounding surfaces. This led to an increase of specific taxa including spore-forming fungi with potential allergic potential but also beneficial plant-associated bacteria, e.g., Paenibacillus. This study demonstrates for the first time that plants can alter the microbiome of a built environment, which supports the significance of plants and provides insights into the complex interplay of plants, microbiomes and human beings.

  10. Diversity of Chromobacterium violaceum isolates from aquatic environments of state of Pará, Brazilian Amazon.

    PubMed

    Dall'Agnol, L T; Martins, R N; Vallinoto, A C R; Ribeiro, K T S

    2008-11-01

    The present study intended to characterize the phenotypic and genetic diversity of Brazilian isolates of Chromobacterium violaceum from aquatic environments within the Amazon region. Nineteen isolates showed morphological properties of C. violaceum and the majority grew at 44 degrees C. Low temperatures, in contrast, showed to be inhibitory to their growth, as eleven isolates did not grow at 10 degrees C and nine did not produce pigmentation, clearly indicating an inhibition of their metabolism. The largest variation among isolates was observed in the citrate test (Simmons), in which 12 isolates were positive, and in the oxidation/fermentation of sucrose, with six positives isolates. Chloramphenicol, gentamicin and sulfonamides efficiently inhibited bacterial growth. Amplified products of the recA gene were digested with HindII or PstI, which produced three or four restriction fragments patterns, respectively. The combined analysis arranged the isolates into six genospecies. The higher diversity observed in Belém (genotypes C, D, E and F) may be a consequence of intense human occupation, pollution of the aquatic environment or due to the higher diversity of the environments sampled in that region. In conclusion, a high level of genetic and phenotypic diversity was observed, and four new genospecies were described.

  11. Hydrogen Utilization Potential in Subsurface Sediments.

    PubMed

    Adhikari, Rishi R; Glombitza, Clemens; Nickel, Julia C; Anderson, Chloe H; Dunlea, Ann G; Spivack, Arthur J; Murray, Richard W; D'Hondt, Steven; Kallmeyer, Jens

    2016-01-01

    Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H2ases to successively higher concentrations of H2 in successively deeper zones.

  12. Hydrogen Utilization Potential in Subsurface Sediments

    PubMed Central

    Adhikari, Rishi R.; Glombitza, Clemens; Nickel, Julia C.; Anderson, Chloe H.; Dunlea, Ann G.; Spivack, Arthur J.; Murray, Richard W.; D'Hondt, Steven; Kallmeyer, Jens

    2016-01-01

    Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H2ases to successively higher concentrations of H2 in successively deeper zones. PMID:26858697

  13. Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

    SciTech Connect

    Daly, Michael J.

    2005-06-01

    Natural selection in highly radioactive waste sites may yield bacteria with favorable bioremediating characteristics. However, until recently the microbial ecology of such environments has remained unexplored because of the high costs and technical complexities associated with extracting and characterizing samples from such sites. We have examined the bacterial ecology within radioactive sediments from a high-level nuclear waste plume in the vadose zone on the DOE?s Hanford Site in south-central Washington state (Fredrickson et al, 2004). Manganese-dependent, radiation resistant bacteria have been isolated from this contaminated site including the highly Mn-dependent Deinococcus and Arthrobacter spp.

  14. 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

  15. INTEGRATED OUTCROP AND SUBSURFACE STUDIES OF THE INTERWELL ENVIRONMENT OF CARBONATE RESERVOIRS: CLEAR FORK (LEONARDIAN-AGE) RESERVOIRS, WEST TEXAS AND NEW MEXICO

    SciTech Connect

    F. Jerry Lucia

    2002-01-31

    This is the final report of the project ''Integrated Outcrop and Subsurface Studies of the Interwell Environment of Carbonate Reservoirs: Clear Fork (Leonardian-Age) Reservoirs, West Texas and New Mexico'', Department of Energy contract no. DE-AC26-98BC15105 and is the third in a series of similar projects funded jointly by the U.S. Department of Energy and The University of Texas at Austin, Bureau of Economic Geology, Reservoir Characterization Research Laboratory for Carbonates. All three projects focus on the integration of outcrop and subsurface data for the purpose of developing improved methods for modeling petrophysical properties in the interwell environment. The first project, funded by contract no. DE-AC22-89BC14470, was a study of San Andres outcrops in the Algerita Escarpment, Guadalupe Mountains, Texas and New Mexico, and the Seminole San Andres reservoir, Permian Basin. This study established the basic concepts for constructing a reservoir model using sequence-stratigraphic principles and rock-fabric, petrophysical relationships. The second project, funded by contract no. DE-AC22-93BC14895, was a study of Grayburg outcrops in the Brokeoff Mountains, New Mexico, and the South Cowden Grayburg reservoir, Permian Basin. This study developed a sequence-stratigraphic succession for the Grayburg and improved methods for locating remaining hydrocarbons in carbonate ramp reservoirs. The current study is of the Clear Fork Group in Apache Canyon, Sierra Diablo Mountains, West Texas, and the South Wasson Clear Fork reservoir, Permian Basin. The focus was on scales of heterogeneity, imaging high- and low-permeability layers, and the impact of fractures on reservoir performance. In this study (1) the Clear Fork cycle stratigraphy is defined, (2) important scales of petrophysical variability are confirmed, (3) a unique rock-fabric, petrophysical relationship is defined, (4) a porosity method for correlating high-frequency cycles and defining rock-fabric flow layers

  16. 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

  17. The West African Mauritanid metamorphic suite of Proterozoic age in the subsurface of peninsular Florida and environs

    SciTech Connect

    Winston, G.O.

    1993-03-01

    A high and low-grade Gondwanan metamorphic terrane is revealed by 14 wells in Florida and environs. Two high-grade metamorphics (gneiss and schist) are located in central Florida and are probably Early Proterozoic in age. The 12 other wells contain low-grade metamorphic suites, principally composed of inter-bedded argillites, acid volcanics and quartzites belonging to the Mauritanid sequence of West Africa. These suites are present in south Georgia, north Florida and offshore; a 3,975-foot section was penetrated in one well. These widespread metamorphic rocks are probably the terrane into which the Cambrian Osceola granite of central Florida was intruded. The two grades of metamorphics represent Early and Late Proterozoic episodes of sedimentation, each followed by metamorphism and erosion. Lower Ordovician to Devonian sediments were deposited on this terrane in southern Georgia and northern Florida. In the Early Jurassic, volcanics completely covered southern Florida, concealing the nature of the old underlying surface. Younger Mesozoic sediments eventually buried the entire Pre-Cambrian-Lower Jurassic terrane.

  18. Genetic diversity of archaea in deep-sea hydrothermal vent environments.

    PubMed

    Takai, K; Horikoshi, K

    1999-08-01

    Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.

  19. 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.

  20. [Alpha and beta arthropods diversity from the different environments of Parque Nacional Los Cardones, Salta, Argentina].

    PubMed

    Belén Cava, Maria; Antonio Corronca, José; José Echeverría, Alejandro

    2013-12-01

    The essential role of the National Parks is to protect nature, in order to prevent the deterioration and loss of the ecosystem under protection. Very few records about the diversity of arthropods are known from Los Cardones National Park, where three eco-regions are protected: Puna and Monte eco-regions and the High Andean Grassland of the Yungas. Here, we aimed to compare the alpha and beta diversity of arthropods in these eco-regions, and to prove if sites from the same ecoregion, show greater similarity between them in their assemblages, than with sites of the other eco-regions. We also identified arthropod orders with higher species richness, and indicated the families that contribute the most to the registered beta diversity. Three sampling sites were established on each eco-region and the arthropods were sampled using pitfall traps and suction samples. We evaluated the obtained inventory through nonparametric estimators of species richness, and compared diversity among eco-regions through "diversity profiles" and "effective number of species". Beta diversity was assessed by different methods such as the Morisita Index, nonmetric multidimentional scaling analysis, a multiple permutation procedure, and a Similarity Percentage analysis. We recorded 469 spp/morphospecies and recognized three arthropod orders (spiders, dipterans and hymenopterans) that are diverse and abundant in the Park. Besides, the diversity in Los Cardones National Park was found to be high, but it was observed higher in the High Andean Grassland of the Yungas, and lower in the Puna. The inventory obtained was good, reached up to the 81% of the species richness estimated by nonparametric estimators. Each eco-region of the park showed a very particular arthropod community that was tested by a multi-response permutation procedure. The species turnover between eco-regions was high, so that the different environments of the protected area are contributing to the maintenance of the regional

  1. Genetically Diverse Clostridium difficile Strains Harboring Abundant Prophages in an Estuarine Environment

    PubMed Central

    Hargreaves, K. R.; Colvin, H. V.; Patel, K. V.; Clokie, J. J. P.

    2013-01-01

    Clostridium difficile is the leading cause of antibiotic-associated diarrheal disease in health care settings across the world. Despite its pathogenic capacity, it can be carried asymptomatically and has been found in terrestrial and marine ecosystems outside hospital environments. Little is known about these environmental strains, and few studies have been conducted on estuarine systems. Although prophage abundance and diversity are known to occur within clinical strains, prophage carriage within environmental strains of C. difficile has not previously been explored. In this study, we isolated C. difficile from sites sampled in two consecutive years in an English estuarine system. Isolates were characterized by PCR ribotype, antibiotic resistance, and motility. The prevalence and diversity of prophages were detected by transmission electron microscopy (TEM) and a phage-specific PCR assay. We show that a dynamic and diverse population of C. difficile exists within these sediments and that it includes isolates of ribotypes which are associated with severe clinical infections and those which are more frequently isolated from outside the hospital environment. Prophage carriage was found to be high (75%), demonstrating that phages play a role in the biology of these strains. PMID:23913427

  2. Plant diversity effects on ecosystem evapotranspiration and carbon uptake: a controlled environment (Ecotron) and modeling approach

    NASA Astrophysics Data System (ADS)

    Milcu, Alexandru; Roy, Jacques

    2016-04-01

    Effects of species and functional diversity of plants on ecosystem evapotranspiration and carbon fluxes have been rarely assessed simultaneously. Here we present the results from an experiment that combined a lysimeter setup in a controlled environment facility (Ecotron) with large ecosystem samples/ monoliths originating from a long-term biodiversity experiment ("The Jena Experiment") and a modelling approach. We aimed at (1) quantifying the impact of plant species richness (4 vs. 16 species) on day- and night-time ecosystem water vapor fluxes and carbon uptake, (2) partitioning ecosystem evapotranspiration into evaporation and plant transpiration using the Shuttleworth and Wallace (SW) energy partitioning model, and (3) identifying the most parsimonious predictors of water vapor vapor and CO2 fluxes using plant functional trait-based metrics such as functional diversity and community weighted means. The SW model indicated that at low plant species richness, a higher proportion of the available energy was diverted to evaporation (a non-productive flux), while at higher species richness the proportion of ecosystem transpiration (a production-related water flux) increased. This led to an increased carbon gain per amount of water vapor loss (i.e. increased water use efficiency). While the LAI controlled the carbon and water fluxes, we also found that the diversity of plant functional traits, and in particular of leaf nitrogen concentration are potential important predictors of ecosystem transpiration and carbon uptake and consequently significantly contributed to increase in water use efficiency in communities with higher plant diversity.

  3. Applications of subsurface microscopy.

    PubMed

    Tetard, Laurene; Passian, Ali; Farahi, Rubye H; Voy, Brynn H; Thundat, Thomas

    2012-01-01

    Exploring the interior of a cell is of tremendous importance in order to assess the effects of nanomaterials on biological systems. Outside of a controlled laboratory environment, nanomaterials will most likely not be conveniently labeled or tagged so that their translocation within a biological system cannot be easily identified and quantified. Ideally, the characterization of nanomaterials within a cell requires a nondestructive, label-free, and subsurface approach. Subsurface nanoscale imaging represents a real challenge for instrumentation. Indeed the tools available for high resolution characterization, including optical, electron or scanning probe microscopies, mainly provide topography images or require taggants that fluoresce. Although the intercellular environment holds a great deal of information, subsurface visualization remains a poorly explored area. Recently, it was discovered that by mechanically perturbing a sample, it was possible to observe its response in time with nanoscale resolution by probing the surface with a micro-resonator such as a microcantilever probe. Microcantilevers are used as the force-sensing probes in atomic force microscopy (AFM), where the nanometer-scale probe tip on the microcantilever interacts with the sample in a highly controlled manner to produce high-resolution raster-scanned information of the sample surface. Taking advantage of the existing capabilities of AFM, we present a novel technique, mode synthesizing atomic force microscopy (MSAFM), which has the ability to probe subsurface structures such as non-labeled nanoparticles embedded in a cell. In MSAFM mechanical actuators (PZTs) excite the probe and the sample at different frequencies as depicted in the first figure of this chapter. The nonlinear nature of the tip-sample interaction, at the point of contact of the probe and the surface of the sample, in the contact mode AFM configuration permits the mixing of the elastic waves. The new dynamic system comprises new

  4. 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

  5. Subsurface Biogeochemistry of Actinides

    SciTech Connect

    Kersting, Annie B.; Zavarin, Mavrik

    2016-06-29

    A major scientific challenge in environmental sciences is to identify the dominant processes controlling actinide transport in the environment. It is estimated that currently, over 2200 metric tons of plutonium (Pu) have been deposited in the subsurface worldwide, a number that increases yearly with additional spent nuclear fuel (Ewing et al., 2010). Plutonium has been shown to migrate on the scale of kilometers, giving way to a critical concern that the fundamental biogeochemical processes that control its behavior in the subsurface are not well understood (Kersting et al., 1999; Novikov et al., 2006; Santschi et al., 2002). Neptunium (Np) is less prevalent in the environment; however, it is predicted to be a significant long-term dose contributor in high-level nuclear waste. Our focus on Np chemistry in this Science Plan is intended to help formulate a better understanding of Pu redox transformations in the environment and clarify the differences between the two long-lived actinides. The research approach of our Science Plan combines (1) Fundamental Mechanistic Studies that identify and quantify biogeochemical processes that control actinide behavior in solution and on solids, (2) Field Integration Studies that investigate the transport characteristics of Pu and test our conceptual understanding of actinide transport, and (3) Actinide Research Capabilities that allow us to achieve the objectives of this Scientific Focus Area (SFA and provide new opportunities for advancing actinide environmental chemistry. These three Research Thrusts form the basis of our SFA Science Program (Figure 1).

  6. Mobility of arsenic in the sub-surface environment: An integrated hydrogeochemical study and sorption model of the sandy aquifer materials

    NASA Astrophysics Data System (ADS)

    Nath, Bibhash; Chakraborty, Sudipta; Burnol, André; Stüben, Doris; Chatterjee, Debashis; Charlet, Laurent

    2009-01-01

    SummaryGroundwater and aquifer materials have been characterized geochemically at a field site located in the Chakdaha municipality of West Bengal, India. Sorption experiments were also carried out on a sandy aquifer material to understand the mobility of arsenic (As) in the sub-surface environments. The result shows that the areas associated with high groundwater As (mean: 1.8 μM) is typically associated with low Eh (mean: -129 mV), and high Fe (mean: 0.11 mM), where Fe 2+/Fe(OH) 3 couple is controlling groundwater redox potential. Analysis of the aquifer material total concentrations showed the dominance of As (range: 8.9-22 mg kg -1), Fe (range: 3.0-9.7% as Fe 2O 3) and Mn (range: 0.05-0.18% as MnO) in the silt-/clay-rich sediments; whereas fine-/medium-sand rich sediment contains considerably lower amount of As (<8.1 mg kg -1), Fe (range: 1.6-3.9% as Fe 2O 3) and Mn (range: 0.02-0.08% as MnO). The acid extractable As do not correlate with ascorbate extractable Fe-oxyhydroxide, however Fe-oxyhydroxide is generally high in the sediments from low groundwater As areas. Chemical speciation computations indicated Fe(II), Ca(II), Mg(II) and Mn(II) to be at equilibrium (with respect to calcite, dolomite and rhodochrosite) or slightly over-saturated (with respect to siderite). These carbonate minerals may therefore participate to the As immobilization. The measured total organic carbon (˜1%) and groundwater temperature (26-32 °C) coupled with sorption studies strongly favors microbially mediated Fe(III)-oxyhydroxide reduction as the dominant mechanism for the release of As in the groundwater. Oscillations of As, Mn and Fe concentrations with depth reflected pCO 2 oscillations consecutive to microbial respiration intensity.

  7. Use of CAH-degrading bacteria as test-organisms for evaluating the impact of fine zerovalent iron particles on the anaerobic subsurface environment.

    PubMed

    Velimirovic, Milica; Simons, Queenie; Bastiaens, Leen

    2015-09-01

    The release of fine zerovalent iron (ZVI) particles in the environment after being introduced for in-situ treatment of compounds like chlorinated aliphatic hydrocarbons (CAHs) may raise questions toward environmental safety, especially for nanoscale materials. Classical single-species ecotoxicity tests do focus on aerobic conditions and are only relevant for the scenario when ZVI-particles reach surface water. Herein, we present an alternative approach where a CAH-degrading mixed bacterial culture was used as test-organisms relevant for the anaerobic subsurface. The impact of different ZVI particles on the bacterial culture was evaluated mainly by quantifying ATP, a reporter molecule giving a general indication of the microbial activity. These lab-scale batch tests were performed in liquid medium, without protecting and buffering aquifer material, as such representing worst-case scenario. The activity of the bacterial culture was negatively influenced by nanoscale zerovalent iron at doses as low as 0.05 g L(-1). On the other hand, concentrations up to 2 g L(-1) of several different types of microscale zerovalent iron (mZVI) particles stimulated the activity. However, very high doses of 15-30 g L(-1) of mZVI showed an inhibiting effect on the bacterial community. Negative effects of ZVIs were confirmed by H2 accumulation in the batch reactors and the absence of lactate consumption. Observed inhibition also corresponded to a pH increase above 7.5, explicable by ZVI corrosion that was found to be dose-dependent. The obtained results suggest that low doses of mZVIs will not show severe inhibition effects on the microbial community once used for in-situ treatment of CAHs.

  8. Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface.

    PubMed

    Coombs, Jonna M

    2009-01-01

    The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse communities of viable organisms, which have provided evidence of low but detectable metabolic activity. Although much of the terrestrial subsurface may be considered to be distant and isolated, the concept of horizontal gene transfer (HGT) in this environment has far-reaching implications for bioremediation efforts and groundwater quality, industrial harvesting of subsurface natural resources such as petroleum, and accurate assessment of the risks associated with DNA release and transport from genetically modified organisms. This chapter will explore what is known about some of the major mechanisms of HGT, and how the information gained from surface organisms might apply to conditions in the terrestrial subsurface. Evidence for the presence of mobile elements in subsurface bacteria and limited retrospective studies examining genetic signatures of potential past gene transfer events will be discussed.

  9. Microbial Diversity of Carbonate Chimneys at the Lost City Hydrothermal Field: Implications for Life-Sustaining Systems in Peridotite Seafloor Environments

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; Cimino, P.; Kelley, D. S.; Baross, J. A.

    2002-12-01

    Eubacterial DNA show that diverse microbial communities, including autotrophic microorganisms and animal symbionts, are contained within the vent structures. In concert, these results indicate that abundant and varied microbial communities inhabit different regions of the chimney structure and may be specifically adapted to the reducing, volatile-rich fluids percolating through the chimneys. In addition to expanding the range of known deep-sea ecosystems, the microbial ecology of carbonate structures associated with hydrothermal venting at the LCHF may provide key insights into the microbiology of subsurface environments near this site. Studying the microbial communities within these systems will enable us to better understand geo-microbial processes associated with serpentinite environments and perhaps allow us to expand our search for life elsewhere in the universe.

  10. Lipids biomarkers of the deep terrestrial subsurface biosphere

    NASA Astrophysics Data System (ADS)

    Osburn, M. R.; Momper, L.; Schubotz, F.; Summons, R. E.; Amend, J.

    2014-12-01

    Lipid biomarkers are key tools for the interpretation of past and present environments, and specifically, intact polar lipids (IPLs) reflect contributions from the living biosphere. While several studies have documented intact polar lipid (IPL) distributions in the marine subsurface, the organic geochemistry of terrestrial subsurface communities remains poorly characterized. Here we present IPL distributions from a portal into deep terrestrial biosphere, the former Homestake Mine, SD USA. Interpretation of IPL distributions can be hampered by a lack of comparative pure culture information or comparative molecular and geochemical data, thus we performed IPL analysis in conjunction with detailed geochemistry and DNA sequencing. A large diversity of lipid structures is observed including phospholipids, aminolipids, glycolipids, GDGTs, and a number of unidentified compounds. Variability in lipid distributions is not random with individual samples clustering based on physical and geochemical parameters. For instance, biofilm samples contain abundant aminolipids relative to filtered subsurface fluid samples. Does this difference reflect phosphorus scarcity in the biofilms, or production of aminolipids by specific microbial phyla? Using comparative analysis between the IPL, molecular, and geochemical datasets we address this, and similar questions, as well as identify potential microbial sources of unknown biomarkers. In the case of the aminolipids, we observe strong covariation between the lipid distribution and that of the bacteroidetes, epsilonproteobacteria, and spirochaetes, but no correlation with P concentration. We can also extend this comparison globally; asking how similar IPL distributions of the deep terrestrial subsurface are previously studied sites. A surprising finding from this work is the total lack of similarity between deep marine and terrestrial subsurface sites. This contribution will help to define the phylogenetic and geochemical mechanisms driving

  11. [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.

  12. 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

  13. 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

    2017-02-10

    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.

  14. 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

  15. 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.

  16. Identity and Metabolic Potential of the Serpentinite Subsurface Microbiome

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    Serpentinization is a widespread geochemical process involving the alteration of ultramafic rocks in the presence of water, resulting in a highly reducing environment containing large quantities of dissolved hydrogen and potentially abiogenic organic molecules, which can serve as energy sources for microbes in the subsurface. Habitability models predict that these environments can sustain microbial life, however little work has been done directly characterize the microbial communities utilizing the energy generated from this process. A recent drilling project at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California has supplied rock cores from up to 30 m below the surface and provided a window into an actively serpentinizing system. Microbial communities in rock cores and fluid samples were analyzed by pyrotag sequencing of V4-V6 region of bacterial 16S rRNA genes. These studies found low diversity communities and a predominance of Betaproteobacterial sequences related to the genus Hydrogenophaga, a hydrogen-oxidizing autotroph, in subsurface drill cores. Interestingly, closely-related isolates of Hydrogenophaga were obtained from the same samples. Concerted analyses of the physiology and metabolism of these new isolates, and quantitative PCR of protein-coding genes from the CROMO drill cores is being used to assess the potential of microbes in the serpentinite subsurface to utilize the geochemical products of serpentinization in this harsh environment.

  17. Unraveling the Evolution of Protostars in Diverse Environments: The Herschel Orion Protostar Survey

    NASA Astrophysics Data System (ADS)

    Megeath, S. Thomas; the Herschel Orion Protostar Survey Team

    2014-01-01

    The Herschel Orion Protostar Survey (HOPS), a 200 hour PACS imaging and spectroscopy OTKP, is the cornerstone of a large multi-observatory campaign combining Herschel data with observations from Spitzer,Hubble, APEX, and other facilities. HOPS has produced well sampled 1-870 micron SEDs of over 300 protostars in the Orion molecular clouds, the most extensive such survey of a single cloud complex to date, and has obtained PACS spectra of 36 protostars to observe line emission from CO, OH, and H2O. We will present the major HOPS discoveries that demonstrate Herschel's contributions to an emerging picture of protostellar evolution within the diverse environments of the Orion A & B molecular clouds. Among these, the HOPS team has discovered protostars undetected by Spitzer that appear to be the youngest protostars in Orion (Stutz et al. 2013). We have found that the luminosities of high-J CO lines are correlated with protostellar luminosities, but the excitation temperatures are not, indicating that these lines form in high-temperature gas within outflows (Manoj et al. 2013). We have also constructed and modeled the first 1-70 um SED of a protostellar FU Ori object before and after its outburst, finding an atypically low post-outburst luminosity (Fischer et al. 2012). Finally, we have identified systematic variations in the spacing and luminosity of protostars between the different environments found in Orion (Megeath, Stanke, in prep.). More generally, the HOPS team is now determining the fundamental protostellar properties (envelope mass and density, system luminosity, and outflow cavity geometry) of the 300 Orion protostars by a comparison of the SEDs to radiative transfer models. We will summarize the prospects of using these fundamental properties to construct a detailed sequence for the physical evolution of protostars as they dissipate their envelopes, accounting for the influence of the diverse environments found within Orion.

  18. Studying the deep subsurface biosphere: Emerging technologies and applications

    NASA Astrophysics Data System (ADS)

    Craig Cary, S.; Campbell, Barbara J.; DeLong, Edward F.

    Discoveries from seafloor hydrothermal vent environments continue to challenge accepted notions about microbial metabolism and survivability, geochemical and biochemical interactions, and the limits to and origins of life itself. Recent evidence suggests that a significant and extensive subsurface biosphere exists associated with these vent systems that may support bacteria of unique and unknown lineages using as yet uncharacterized metabolic pathways. With restricted access to the subsurface environment and availability of an extremely limited biomass, microbiologists have resorted to powerful molecular approaches to survey, characterize, and even assist in the later cultivation of these novel subsurface bacteria. Advances in molecular phylogenetic techniques (molecular microbial systematics) based on the small subunit rRNA (16S rRNA) and a knowledge of certain diagnostic metabolic genes have provided an alternative and more comprehensive framework to study microbial populations and communities without the necessity of cultivation. These approaches have been used by a number of investigators in deep-sea hydrothermal vents and terrestrial hot springs with astonishing results. In this paper we introduce some of these current and emerging molecular techniques and demonstrate their efficacy in the context of the subsurface biosphere. Simple gene amplification methods coupled with more sophisticated genomic approaches and fine resolution in situ geochemical tools (see Luther et al., this volume) provides a new-found capability to more fully characterize the diversity of metabolic strategies used by these complex subsurface microbial communities. Understanding these unique microbial communities is not only important from the basic biological perspective but has ramifications for possible industrial applications.

  19. Subsurface Controls on Habitability of Hydrothermal Waters

    NASA Astrophysics Data System (ADS)

    Fristad, K. E.; Som, S. M.; Hoehler, T. M.

    2014-12-01

    Liquid water alone does not make an environment habitable. Environmental settings dominated by water-rock reactions such as in hydrothermal vents and springs are natural targets for astrobiological investigation of waterworlds because the rich geochemical diversity at these locales provides abundant energy in solvent to support microbial life. Hydrogen oxidizers are of particular interest because H2-based metabolisms are widespread and deeply rooted throughout the phylogenetic tree of life, implying they may have emerged extremely early in the evolution, and possibly even the origin, of life on Earth and potentially any other rocky bodies bearing liquid water. Dihydrogen (H2) can be lithogenically produced by the hydrolytic oxidation of the ferrous iron component in Fe-bearing minerals as well as by radiolytic cleavage of water by α, β, or γ radiation produced during the decay of radioactive isotopes. Lithogenic H2 production mechanisms operate across a range of rock types, but the concentration of dissolved H2 available to life is controlled by a number of subsurface factors such as surface geometry, water to rock ratio, production rate, and fluid flux. These factors are often controlled by the larger geologic and structural context of a particular site. We present results of an ongoing project that surveys H2 concentrations from terrestrial hydrothermal waters in diverse chemical and physical settings. Aqueous H2 concentrations and potential subsurface controls are presented for sites across the western U.S. including Yellowstone National Park, Lassen Volcanic National Park, and Iceland. In coordination with field data, we also investigate the habitability of various sites numerically by coupling a geochemical model of water-rock interaction with that of single-cell methanogenesis and compute a habitability index for the given environment. In particular, we investigate the control that temperature, rock composition, water composition, and water to rock ratio

  20. 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.

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

    PubMed Central

    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. PMID:26074880

  2. 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.

  3. Evaluating green infrastructure in urban environments using a multi-taxa and functional diversity approach.

    PubMed

    Pinho, Pedro; Correia, Otília; Lecoq, Miguel; Munzi, Silvana; Vasconcelos, Sasha; Gonçalves, Paula; Rebelo, Rui; Antunes, Cristina; Silva, Patrícia; Freitas, Catarina; Lopes, Nuno; Santos-Reis, Margarida; Branquinho, Cristina

    2016-05-01

    Forested areas within cities host a large number of species, responsible for many ecosystem services in urban areas. The biodiversity in these areas is influenced by human disturbances such as atmospheric pollution and urban heat island effect. To ameliorate the effects of these factors, an increase in urban green areas is often considered sufficient. However, this approach assumes that all types of green cover have the same importance for species. Our aim was to show that not all forested green areas are equal in importance for species, but that based on a multi-taxa and functional diversity approach it is possible to value green infrastructure in urban environments. After evaluating the diversity of lichens, butterflies and other-arthropods, birds and mammals in 31 Mediterranean urban forests in south-west Europe (Almada, Portugal), bird and lichen functional groups responsive to urbanization were found. A community shift (tolerant species replacing sensitive ones) along the urbanization gradient was found, and this must be considered when using these groups as indicators of the effect of urbanization. Bird and lichen functional groups were then analyzed together with the characteristics of the forests and their surroundings. Our results showed that, contrary to previous assumptions, vegetation density and more importantly the amount of urban areas around the forest (matrix), are more important for biodiversity than forest quantity alone. This indicated that not all types of forested green areas have the same importance for biodiversity. An index of forest functional diversity was then calculated for all sampled forests of the area. This could help decision-makers to improve the management of urban green infrastructures with the goal of increasing functionality and ultimately ecosystem services in urban areas.

  4. Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs.

    PubMed

    Ransom-Jones, Emma; Jones, David L; Edwards, Arwyn; McDonald, James E

    2014-10-01

    The Fibrobacteres phylum contains two described species, Fibrobacter succinogenes and Fibrobacter intestinalis, both of which are prolific degraders of cellulosic plant biomass in the herbivore gut. However, recent 16S rRNA gene sequencing studies have identified novel Fibrobacteres in landfill sites, freshwater lakes and the termite hindgut, suggesting that members of the Fibrobacteres occupy a broader ecological range than previously appreciated. In this study, the ecology and diversity of Fibrobacteres was evaluated in 64 samples from contrasting environments where cellulose degradation occurred. Fibrobacters were detected in 23 of the 64 samples using Fibrobacter genus-specific 16S rRNA gene PCR, which provided their first targeted detection in marine and estuarine sediments, cryoconite from Arctic glaciers, as well as a broader range of environmental samples. To determine the phylogenetic diversity of the Fibrobacteres phylum, Fibrobacter-specific 16S rRNA gene clone libraries derived from 17 samples were sequenced (384 clones) and compared with all available Fibrobacteres sequences in the Ribosomal Database Project repository. Phylogenetic analysis revealed 63 lineages of Fibrobacteres (95% OTUs), with many representing as yet unclassified species. Of these, 24 OTUs were exclusively comprised of fibrobacters derived from environmental (non-gut) samples, 17 were exclusive to the mammalian gut, 15 to the termite hindgut, and 7 comprised both environmental and mammalian strains, thus establishing Fibrobacter spp. as indigenous members of microbial communities beyond the gut ecosystem. The data highlighted significant taxonomic and ecological diversity within the Fibrobacteres, a phylum circumscribed by potent cellulolytic activity, suggesting considerable functional importance in the conversion of lignocellulosic biomass in the biosphere.

  5. The Dynamic Arctic Snow Pack: An Unexplored Environment for Microbial Diversity and Activity

    PubMed Central

    Larose, Catherine; Dommergue, Aurélien; Vogel, Timothy M.

    2013-01-01

    The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems. PMID:24832663

  6. 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

  7. 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.

  8. Prevalence and genetic diversity of Salmonella spp. in a river in a tropical environment in Mexico.

    PubMed

    Jiménez, Maribel; Martinez-Urtaza, Jaime; Rodriguez-Alvarez, Maria Xose; Leon-Felix, Josefina; Chaidez, Cristobal

    2014-12-01

    The capability of Salmonella to survive outside a host is especially relevant in tropical regions, where the environmental conditions could be more suitable for its long-term persistence. This study investigated the prevalence and genetic diversity of salmonellae within rivers of the Culiacan Valley in the northwestern region of Mexico. From July 2008 to June 2009, a total of 138 water samples were evaluated for the presence of Salmonella spp.; additionally, its association with environmental parameters was determined using Generalized Additive Models (GAMs). Salmonella spp. were isolated from 111 (80.4%) samples without any statistical influence on the environmental parameters investigated, according to the GAM analysis. Twenty-four serotypes were identified; the most frequently isolated serotypes were Salmonella Oranienburg (25%), Salmonella Saintpaul (9%) and Salmonella Minnesota (6%). Diverse genetic variants of Salmonella Oranienburg were found distributed across the valley with no distinctive geographical or temporal patterns. The high persistence of Salmonella spp. and the lack of differentiation of types found along the river basins suggest the existence of non-point source contamination. Furthermore, the discrepancy between the prevailing serotypes in human infections and those identified in this study denotes a limited influence of these aquatic environments in bacterial dissemination and disease transmission.

  9. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

    PubMed Central

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-01-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. PMID

  10. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.

    PubMed

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-06-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.

  11. The subsurface biosphere at Mid-Ocean Ridges: Issues and challenges

    NASA Astrophysics Data System (ADS)

    Baross, John A.; Wilcock, William S. D.; Kelley, Deborah S.; DeLong, Edward F.; Craig Cary, S.

    A recent growth of interest in subsurface microbiology has been fueled by the recognition that the subsurface may have played an important role in the origin and early evolution of life, and may presently sustain a substantial fraction of Earth's biomass. The uppermost igneous oceanic crust is likely to be one of the most habitable subsurface environments because it is porous and the locus of extensive hydrothermal circulation. This circulation is most vigorous at spreading centers where it is driven by the volcanic accretion of oceanic crust. Hot reduced hydrothermal fluids created by water-rock reactions above magma bodies mix with cold seawater in the subsurface and the resulting chemical disequilibria provide energy and carbon sources that support diverse microbial communities. These communities can be sampled in chronic low-temperature hydrothermal vents and in the hydrothermal fluids released following volcanic eruptions. Investigations of the subseafloor environment at mid-ocean ridges integrate biological and geological approaches to understand the characteristics of hydrothermal circulation and how they are modulated by geological events; the sources of carbon, nutrients and energy; and the types and functions of subsurface organisms. They also utilize analogies with accessible sulfide edifices and comparisons with similar subsurface environments elsewhere. Future studies will combine increasingly sophisticated shore-based studies with data from long-term observatories comprising networks of instruments for measuring key physical, chemical and microbial parameters. They will require the development of technology to drill bare rock mid-ocean ridge sites, collect uncontaminated subsurface samples and deploy instruments at different depths in the crust.

  12. Detection of microbial Life in the Subsurface

    NASA Astrophysics Data System (ADS)

    Stan-Lotter, H.; Fendrihan, S.; Dornmayr-Pfaffenhuemer, M.; Legat, A.; Gruber, C.; Weidler, G.; Gerbl, F.

    2007-08-01

    In recent years microbial communities were detected, which dwell in rocks, soil and caves deep below the surface of the Earth. This has led to a new view of the diversity of the terrestrial biosphere and of the physico-chemical boundaries for life. Two types of subterranean environments are Permo-Triassic salt sediments and thermal radioactive springs from igneous rocks in the Alps. Viable extremely halophilic archaea were isolated from ancient salt sediments which are estimated to be about 250 million years old (1). Chemotaxonomic and molecular characterization showed that they represent novel species, e. g. Halococcus salifodinae, Hcc. dombrowskiiand Halobacterium noricense. Simulation experiments with artificial halite suggested that these microorganisms probably survived while embedded in fluid inclusions. In the thermal springs, evidence for numerous novel microorganisms was found by 16S rDNA sequencing and probing for some metabolic genes; in addition, scanning electron microscopy of biofilms on the rock surfaces revealed great diversity of morphotypes (2). These communities appear to be active and growing, although their energy and carbon sources are entirely unknown. The characterization of subsurface inhabitants is of astrobiological relevance since extraterrestrial halite has been detected (3) and since microbial life on Mars, if existent, may have retreated into the subsurface. As a long-term goal, a thorough census of terrestrial microorganisms should be taken and their survival potential be determined in view of future missions for the search for extraterrestrial life, including planning precautions against possible forward contamination by space probes. (1) Fendrihan, S., Legat, A., Gruber, C., Pfaffenhuemer, M., Weidler, G., Gerbl, F., Stan-Lotter, H. (2006) Extremely halophilic archaea and the issue of long term microbial survival. Reviews in Environmental Science and Bio/technology 5, 1569-1605. (2) Weidler, G.W., Dornmayr-Pfaffenhuemer, M., Gerbl

  13. 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

  14. Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water-saturated environment.

    PubMed

    Costello, Elizabeth K; Schmidt, Steven K

    2006-08-01

    Cold, water-saturated soils play important biogeochemical roles, yet almost nothing is known about the identity and habitat of microbes active under such conditions. We investigated the year-round microenvironment of an alpine tundra wet meadow soil in the Colorado Rocky Mountains, focusing on the biogeochemistry and microbial diversity of spring snowmelt--a dynamic time for alpine ecosystems. In situ measurements revealed spring and autumn periods of long-term temperature stability near 0 degrees C, and that deeper soil (30 cm) was more stable than surface soil, with more moderate summers and winters, and longer isothermal phases. The soil was saturated and water availability was limited by freezing rather than drying. Analyses of bioavailable redox species showed a shift from Mn reduction to net Fe reduction at 2-3 cm depth, elevated SO4(2-) and decreased soluble Zn at spring snowmelt. Terminal restriction fragment length polymorphism profiles detected a correlated shift in bacterial community composition at the surface to subsurface transition. Bacterial and archaeal small-subunit rRNA genes were amplified from saturated spring soil DNA pooled along a depth profile. The most remarkable feature of these subsurface-biased libraries was the high relative abundance of novel, uncultivated Chloroflexi-related sequences comprising the third largest bacterial division sampled, and representing seven new Chloroflexi subdivisions, thereby dramatically expanding the known diversity of this bacterial division. We suggest that these novel Chloroflexi are active at near -0 degrees C temperatures, under likely anoxic conditions, and utilize geochemical inputs such as sulfide from upslope weathering.

  15. Stability of fruit quality traits in diverse watermelon cultivars tested in multiple environments

    PubMed Central

    Dia, Mahendra; Wehner, Todd C; Perkins-Veazie, Penelope; Hassell, Richard; Price, Daniel S; Boyhan, George E; Olson, Stephen M; King, Stephen R; Davis, Angela R; Tolla, Gregory E; Bernier, Jerome; Juarez, Benito

    2016-01-01

    Lycopene is a naturally occurring red carotenoid compound that is found in watermelon. Lycopene has antioxidant properties. Lycopene content, sugar content and hollowheart resistance are subject to significant genotype×environment interaction (G×E), which makes breeding for these fruit quality traits difficult. The objectives of this study were to (i) evaluate the influence of years and locations on lycopene content, sugar content and hollowheart resistance for a set of watermelon genotypes, and (ii) identify genotypes with high stability for lycopene, sugar, and hollowheart resistance. A diverse set of 40 genotypes was tested over 3 years and 8 locations across the southern United States in replicated, multi-harvest trials. Lycopene was tested in a subset of 10 genotypes. Data were analyzed using univariate and multivariate stability statistics (BLUP-GGE biplot) using SASGxE and RGxE programs. There were strong effects of environment as well as G×E interaction on watermelon quality traits. On the basis of stability measures, genotypes were classified as stable or unstable for each quality trait. 'Crimson Sweet' is an inbred line with high quality trait performance as well as trait stability. 'Stone Mountain', 'Tom Watson', 'Crimson Sweet' and 'Minilee' were among the best genotypes for lycopene content, sugar content and hollowheart resistance. We developed a stability chart based on marketable yield and average ranking generated from different stability measures for yield attributes and quality traits. The chart will assist in choosing parents for improvement of watermelon cultivars. See http://cuke.hort.ncsu.edu/cucurbit/wmelon/wmelonmain.html. PMID:28066557

  16. Stability of fruit quality traits in diverse watermelon cultivars tested in multiple environments.

    PubMed

    Dia, Mahendra; Wehner, Todd C; Perkins-Veazie, Penelope; Hassell, Richard; Price, Daniel S; Boyhan, George E; Olson, Stephen M; King, Stephen R; Davis, Angela R; Tolla, Gregory E; Bernier, Jerome; Juarez, Benito

    2016-01-01

    Lycopene is a naturally occurring red carotenoid compound that is found in watermelon. Lycopene has antioxidant properties. Lycopene content, sugar content and hollowheart resistance are subject to significant genotype×environment interaction (G×E), which makes breeding for these fruit quality traits difficult. The objectives of this study were to (i) evaluate the influence of years and locations on lycopene content, sugar content and hollowheart resistance for a set of watermelon genotypes, and (ii) identify genotypes with high stability for lycopene, sugar, and hollowheart resistance. A diverse set of 40 genotypes was tested over 3 years and 8 locations across the southern United States in replicated, multi-harvest trials. Lycopene was tested in a subset of 10 genotypes. Data were analyzed using univariate and multivariate stability statistics (BLUP-GGE biplot) using SASGxE and RGxE programs. There were strong effects of environment as well as G×E interaction on watermelon quality traits. On the basis of stability measures, genotypes were classified as stable or unstable for each quality trait. 'Crimson Sweet' is an inbred line with high quality trait performance as well as trait stability. 'Stone Mountain', 'Tom Watson', 'Crimson Sweet' and 'Minilee' were among the best genotypes for lycopene content, sugar content and hollowheart resistance. We developed a stability chart based on marketable yield and average ranking generated from different stability measures for yield attributes and quality traits. The chart will assist in choosing parents for improvement of watermelon cultivars. See http://cuke.hort.ncsu.edu/cucurbit/wmelon/wmelonmain.html.

  17. Oligonucleotide Microarray for the Study of Functional Gene Diversity in the Nitrogen Cycle in the Environment

    PubMed Central

    Taroncher-Oldenburg, Gaspar; Griner, Erin M.; Francis, Chris A.; Ward, Bess B.

    2003-01-01

    The analysis of functional diversity and its dynamics in the environment is essential for understanding the microbial ecology and biogeochemistry of aquatic systems. Here we describe the development and optimization of a DNA microarray method for the detection and quantification of functional genes in the environment and report on their preliminary application to the study of the denitrification gene nirS in the Choptank River-Chesapeake Bay system. Intergenic and intragenic resolution constraints were determined by an oligonucleotide (70-mer) microarray approach. Complete signal separation was achieved when comparing unrelated genes within the nitrogen cycle (amoA, nifH, nirK, and nirS) and detecting different variants of the same gene, nirK, corresponding to organisms with two different physiological modes, ammonia oxidizers and denitrifying halobenzoate degraders. The limits of intragenic resolution were investigated with a microarray containing 64 nirS sequences comprising 14 cultured organisms and 50 clones obtained from the Choptank River in Maryland. The nirS oligonucleotides covered a range of sequence identities from approximately 40 to 100%. The threshold values for specificity were determined to be 87% sequence identity and a target-to-probe perfect match-to-mismatch binding free-energy ratio of 0.56. The lower detection limit was 10 pg of DNA (equivalent to approximately 107 copies) per target per microarray. Hybridization patterns on the microarray differed between sediment samples from two stations in the Choptank River, implying important differences in the composition of the denitirifer community along an environmental gradient of salinity, inorganic nitrogen, and dissolved organic carbon. This work establishes a useful set of design constraints (independent of the target gene) for the implementation of functional gene microarrays for environmental applications. PMID:12571043

  18. Growth phenology of coast Douglas-fir seed sources planted in diverse environments.

    PubMed

    Gould, Peter J; Harrington, Constance A; St Clair, J Bradley

    2012-12-01

    The timing of periodic life cycle events in plants (phenology) is an important factor determining how species and populations will react to climate change. We evaluated annual patterns of basal-area and height growth of coast Douglas-fir (Pseudotusga menziesii var. menziesii (Mirb.) Franco) seedlings from four seed sources that were planted in four diverse environments as part of the Douglas-fir Seed-Source Movement Trial. Stem diameters and heights were measured periodically during the 2010 growing season on 16 open-pollinated families at each study installation. Stem diameters were measured on a subset of trees with electronic dendrometers during the 2010 and 2011 growing seasons. Trees from the four seed sources differed in phenology metrics that described the timing of basal-area and height-growth initiation, growth cessation and growth rates. Differences in the height-growth metrics were generally larger than differences in the basal-area growth metrics and differences among installations were larger than differences among seed sources, highlighting the importance of environmental signals on growth phenology. Variations in the height- and basal-area growth metrics were correlated with different aspects of the seed-source environments: precipitation in the case of height growth and minimum temperature in the case of basal-area growth. The detailed dendrometer measurements revealed differences in growth patterns between seed sources during distinct periods in the growing season. Our results indicate that multiple aspects of growth phenology should be considered along with other traits when evaluating adaptation of populations to future climates.

  19. Occurrence and Diversity of Clinically Important Vibrio Species in the Aquatic Environment of Georgia

    PubMed Central

    Kokashvili, Tamar; Whitehouse, Chris A.; Tskhvediani, Ana; Grim, Christopher J.; Elbakidze, Tinatin; Mitaishvili, Nino; Janelidze, Nino; Jaiani, Ekaterine; Haley, Bradd J.; Lashkhi, Nino; Huq, Anwar; Colwell, Rita R.; Tediashvili, Marina

    2015-01-01

    Among the more than 70 different Vibrio species inhabiting marine, estuarine, and freshwater ecosystems, 12 are recognized as human pathogens. The warm subtropical climate of the Black Sea coastal area and inland regions of Georgia likely provides a favorable environment for various Vibrio species. From 2006 to 2009, the abundance, ecology, and diversity of clinically important Vibrio species were studied in different locations in Georgia and across seasons. Over a 33-month period, 1,595 presumptive Vibrio isolates were collected from the Black Sea (n = 657) and freshwater lakes around Tbilisi (n = 938). Screening of a subset of 440 concentrated and enriched water samples by PCR-electrospray ionization/mass spectrometry (PCR-ESI/MS) detected the presence of DNA from eight clinically important Vibrio species: V. cholerae, V. parahaemolyticus, V. vulnificus, V. mimicus, V. alginolyticus, V. harveyi, V. metschnikovii, and V. cincinnatiensis. Almost 90% of PCR/ESI-MS samples positive for Vibrio species were collected from June through November. Three important human-pathogenic Vibrio species (V. cholerae, V. parahaemolyticus, and V. vulnificus) were detected in 62.8, 37.8, and 21.4% of samples testing positive for Vibrios, respectively. The results of these activities suggest that natural reservoirs for human-pathogenic Vibrios exist in Georgian aquatic environments. Water temperature at all sampling sites was positively correlated with the abundance of clinically important Vibrio spp. (except V. metschnikovii), and salinity was correlated with species composition at particular Black Sea sites as well as inland reservoirs. PMID:26528464

  20. Stability of Cell Wall Composition and Saccharification Efficiency in Miscanthus across Diverse Environments

    PubMed Central

    van der Weijde, Tim; Dolstra, Oene; Visser, Richard G. F.; Trindade, Luisa M.

    2017-01-01

    To investigate the potential effects of differences between growth locations on the cell wall composition and saccharification efficiency of the bioenergy crop miscanthus, a diverse set of 15 accessions were evaluated in six locations across Europe for the first 3 years following establishment. High-throughput quantification of cellulose, hemicellulose and lignin contents, as well as cellulose and hemicellulose conversion rates was achieved by combining near-infrared reflectance spectroscopy (NIRS) and biochemical analysis. Prediction models were developed and found to predict biomass quality characteristics with high accuracy. Location significantly affected biomass quality characteristics in all three cultivation years, but location-based differences decreased toward the third year as the plants reached maturity and the effect of location-dependent differences in the rate of establishment reduced. In all locations extensive variation in accession performance was observed for quality traits. The performance of the different accessions in the second and third cultivation year was strongly correlated, while accession performance in the first cultivation year did not correlate well with performance in later years. Significant genotype-by-environment (G × E) interactions were observed for most traits, revealing differences between accessions in environmental sensitivity. Stability analysis of accession performance for calculated ethanol yields suggested that selection for good and stable performance is a viable approach. Environmental influence on biomass quality is substantial and should be taken into account in order to match genotype, location and end-use of miscanthus as a lignocellulose feedstock. PMID:28111583

  1. Stability of Cell Wall Composition and Saccharification Efficiency in Miscanthus across Diverse Environments.

    PubMed

    van der Weijde, Tim; Dolstra, Oene; Visser, Richard G F; Trindade, Luisa M

    2016-01-01

    To investigate the potential effects of differences between growth locations on the cell wall composition and saccharification efficiency of the bioenergy crop miscanthus, a diverse set of 15 accessions were evaluated in six locations across Europe for the first 3 years following establishment. High-throughput quantification of cellulose, hemicellulose and lignin contents, as well as cellulose and hemicellulose conversion rates was achieved by combining near-infrared reflectance spectroscopy (NIRS) and biochemical analysis. Prediction models were developed and found to predict biomass quality characteristics with high accuracy. Location significantly affected biomass quality characteristics in all three cultivation years, but location-based differences decreased toward the third year as the plants reached maturity and the effect of location-dependent differences in the rate of establishment reduced. In all locations extensive variation in accession performance was observed for quality traits. The performance of the different accessions in the second and third cultivation year was strongly correlated, while accession performance in the first cultivation year did not correlate well with performance in later years. Significant genotype-by-environment (G × E) interactions were observed for most traits, revealing differences between accessions in environmental sensitivity. Stability analysis of accession performance for calculated ethanol yields suggested that selection for good and stable performance is a viable approach. Environmental influence on biomass quality is substantial and should be taken into account in order to match genotype, location and end-use of miscanthus as a lignocellulose feedstock.

  2. Microbiology of sugar-rich environments: diversity, ecology and system constraints.

    PubMed

    Lievens, Bart; Hallsworth, John E; Pozo, Maria I; Belgacem, Zouhaier Ben; Stevenson, Andrew; Willems, Kris A; Jacquemyn, Hans

    2015-02-01

    Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar-rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high-sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water-activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species-poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high-sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity-mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature, pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high-sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions.

  3. Microbial life in the deep terrestrial subsurface

    SciTech Connect

    Fliermans, C.B.; Balkwill, D.L.; Beeman, R.E.

    1988-12-31

    The distribution and function of microorganisms is a vital issue in microbial ecology. The US Department of Energy`s Program, ``Microbiology of the Deep Subsurface,`` concentrates on establishing fundamental scientific information about organisms at depth, and the use of these organisms for remediation of contaminants in deep vadose zone and groundwater environments. This investigation effectively extends the Biosphere hundreds of meters into the Geosphere and has implications to a variety of subsurface activities.

  4. The Potential Effect of Cultural Differences in a Culturally Diverse Work Environment

    DTIC Science & Technology

    1999-10-01

    for organizational renewal, finding strategic advantage, maintaining high standards of ethics and social responsibility , supporting diversity, and managing the new employee relationships that emphasize empowerment and team.

  5. SUBSURFACE REPOSITORY INTEGRATED CONTROL SYSTEM DESIGN

    SciTech Connect

    D.C. Randle

    2000-01-07

    The primary purpose of this document is to develop a preliminary high-level functional and physical control system architecture for the potential repository at Yucca Mountain. This document outlines an overall control system concept that encompasses and integrates the many diverse process and communication systems being developed for the subsurface repository design. This document presents integrated design concepts for monitoring and controlling the diverse set of subsurface operations. The Subsurface Repository Integrated Control System design will be composed of a series of diverse process systems and communication networks. The subsurface repository design contains many systems related to instrumentation and control (I&C) for both repository development and waste emplacement operations. These systems include waste emplacement, waste retrieval, ventilation, radiological and air monitoring, rail transportation, construction development, utility systems (electrical, lighting, water, compressed air, etc.), fire protection, backfill emplacement, and performance confirmation. Each of these systems involves some level of I&C and will typically be integrated over a data communications network throughout the subsurface facility. The subsurface I&C systems will also interface with multiple surface-based systems such as site operations, rail transportation, security and safeguards, and electrical/piped utilities. In addition to the I&C systems, the subsurface repository design also contains systems related to voice and video communications. The components for each of these systems will be distributed and linked over voice and video communication networks throughout the subsurface facility. The scope and primary objectives of this design analysis are to: (1) Identify preliminary system-level functions and interfaces (Section 6.2). (2) Examine the overall system complexity and determine how and on what levels the engineered process systems will be monitored, controlled, and

  6. 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.

  7. 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

  8. Integrated Outcrop and Subsurface Studies of the Interwell Environment of Carbonate Reservoirs: Clear Fork (Leonaradian Age) Reservoirs, West Texas and New Mexico

    SciTech Connect

    Lucia, F.J.; Ruppel, S.C.

    2001-02-01

    Characterization of cycle and facies architecture on lower Clear Fork and lowermost upper Clear Fork equivalent outcrops in Apache Canyon of Sierra Diablo was complete. The focus of detailed study in Apache Canyon has been the upper Clear Fork section because this interval contains the productive interval in South Wasson field, the preliminary subsurface study area. Parts of three high-frequency sequences (HFS), each 60 to 100 ft thick, are present on the south wall of Apache Canyon. HFS's display an upper-deepening or backstepping pattern associated with longer-term sea level rise. Each HFS is composed of upward-shallowing cycles whose thickness, facies composition, and continuity vary within and between HFS's.

  9. Early environments drive diversity and floristic composition in Mediterranean old fields: Insights from a long-term experiment

    NASA Astrophysics Data System (ADS)

    Cayuela, Luis; Rey Benayas, José María; Maestre, Fernando T.; Escudero, Adrián

    2008-11-01

    While many studies have explored how previous and current environmental conditions affect the performance of individual organisms, their relative importance as drivers of current diversity and composition of communities is virtually unknown. We evaluated the response of herbaceous communities to previous (experienced during early establishment) and current environmental conditions by comparing their composition and diversity in an abandoned Mediterranean cropland planted with Quercus ilex subsp. ballota L. seedlings. These seedlings received different experimental treatments (summer irrigation and artificial shading) during the first three years after planting, and were interrupted from then on. We tested two complementary hypotheses: (i) the previous environments experienced by the herbaceous communities during their establishment have a long-term carry-over effect on diversity and composition of species assemblages and (ii) these communities are influenced by their current environment, particularly by the woody layer and the soil conditions. Overall, we observed an important contribution of initial environmental conditions in determining the current diversity and composition of herbaceous communities. Amelioration of environmental conditions, particularly water stress, during community establishment resulted in a decrease in alpha and beta diversity, possibly as a consequence of decreasing environmental heterogeneity. Previous environments accounted for 26.3% of the explained variance in current community composition. Annuals, legumes and forbs also responded significantly to previous environments, which explained 27.9%, 36.2% and 30.1%, respectively, of the variance in their composition. Our results suggest that those species present at a particular site early in succession pre-empt the site and influence vegetation dynamics on that site for a long time. This study provides important insights for understanding the mechanisms underlying the ecological effects of

  10. Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments

    PubMed Central

    Kimura, Hiroyuki; Sugihara, Maki; Kato, Kenji; Hanada, Satoshi

    2006-01-01

    Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76°C) and river water (14°C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82°C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84°C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84°C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained. PMID:16391020

  11. Selective phylogenetic analysis targeted at 16S rRNA genes of thermophiles and hyperthermophiles in deep-subsurface geothermal environments.

    PubMed

    Kimura, Hiroyuki; Sugihara, Maki; Kato, Kenji; Hanada, Satoshi

    2006-01-01

    Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76 degrees C) and river water (14 degrees C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82 degrees C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84 degrees C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84 degrees C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained.

  12. The Changing Academic Environment and Diversity in Students' Study Philosophy, Beliefs and Attitudes in Higher Education

    ERIC Educational Resources Information Center

    Alauddin, Mohammad; Ashman, Adrian

    2014-01-01

    Student populations in higher education in Australia and elsewhere in the developed world have experienced significant diversity over the past two decades. The existing literature has provided limited clarity about the effects of this diversity on the dimensions underpinning students' study philosophy domain. Based on a large data set from a…

  13. A Female Urinary Diversion Device for Military Women in the Deployed Environment

    DTIC Science & Technology

    2016-10-27

    self- care measure. 15. SUBJECT TERMS female urinary diversion device, deployed military women’s health , genitourinary health in deployed women...study was 1) to explore the utility of a female urinary diversion device (FUDD) as a self- care measure for female urination in the deployment

  14. 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

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

    PubMed

    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.

  16. Convergence in relationships between leaf traits, spectra and age across diverse canopy environments and two contrasting tropical forests.

    PubMed

    Wu, Jin; Chavana-Bryant, Cecilia; Prohaska, Neill; Serbin, Shawn P; Guan, Kaiyu; Albert, Loren P; Yang, Xi; van Leeuwen, Willem J D; Garnello, Anthony John; Martins, Giordane; Malhi, Yadvinder; Gerard, France; Oliviera, Raimundo Cosme; Saleska, Scott R

    2017-05-01

    Leaf age structures the phenology and development of plants, as well as the evolution of leaf traits over life histories. However, a general method for efficiently estimating leaf age across forests and canopy environments is lacking. Here, we explored the potential for a statistical model, previously developed for Peruvian sunlit leaves, to consistently predict leaf ages from leaf reflectance spectra across two contrasting forests in Peru and Brazil and across diverse canopy environments. The model performed well for independent Brazilian sunlit and shade canopy leaves (R(2)  = 0.75-0.78), suggesting that canopy leaves (and their associated spectra) follow constrained developmental trajectories even in contrasting forests. The model did not perform as well for mid-canopy and understory leaves (R(2)  = 0.27-0.29), because leaves in different environments have distinct traits and trait developmental trajectories. When we accounted for distinct environment-trait linkages - either by explicitly including traits and environments in the model, or, even better, by re-parameterizing the spectra-only model to implicitly capture distinct trait-trajectories in different environments - we achieved a more general model that well-predicted leaf age across forests and environments (R(2)  = 0.79). Fundamental rules, linked to leaf environments, constrain the development of leaf traits and allow for general prediction of leaf age from spectra across species, sites and canopy environments.

  17. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla.

    PubMed

    Emerson, Joanne B; Thomas, Brian C; Alvarez, Walter; Banfield, Jillian F

    2016-06-01

    Research on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high-CO2 systems are poorly biologically characterized, partly because of difficulty accessing high-volume, uncontaminated samples. CO2 -driven Crystal Geyser (CG, Utah, USA), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200-500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high-CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron-oxidizing bacteria, including 'marine' Mariprofundus (Zetaproteobacteria) and 'freshwater' Gallionellales, sulfur-oxidizing Thiomicrospira crunogena and Thiobacillus-like Hydrogenophilales. Near-complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as-yet undefined lineages. Many bacteria affiliate with OD1, OP3, OP9, PER, ACD58, WWE3, BD1-5, OP11, TM7 and ZB2. The recovery of nearly 100 genes encoding ribulose-1,5 bisphosphate carboxylase-oxygenase subunit proteins of the Calvin cycle and AMP salvage pathways suggests a strong biological role in high-CO2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration.

  18. Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments

    PubMed Central

    Li, Guizhen; Liu, Yang; Sun, Fengqin; Shao, Zongze

    2014-01-01

    Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus. PMID:25019154

  19. Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove (Kandelia obovata) Rhizosphere Environment.

    PubMed

    Ma, Zhi P; Lao, Yong M; Jin, Hui; Lin, Guang H; Cai, Zhong H; Zhou, Jin

    2016-01-01

    Mangrove rhizosphere environment harbors diverse populations of microbes, and some evidence showed that rhizobacteria behavior was regulated by quorum sensing (QS). Investigating the diverse profiles of QS molecules in mangrove ecosystems may shed light on the bacterial roles and lead to a better understanding of the symbiotic interactions between plants and microbes. The aims of the current study focus on identifying AI-1 type QS signals, i.e., acyl homoserine lactones (AHLs), in Kandelia obovata rhizosphere environment. Approximately 1200 rhizobacteria were screened and 184 strains (15.3%) tested were positive. Subsequent 16s rRNA gene sequencing and dereplication analyses identified 24 species from the positive isolates, which were affiliated to three different phyla, including Proteobacteria, Firmicutes, and Actinobacteria. Thin-layer chromatography separation of extracts revealed diverse AHL profiles and detected at least one active compound in the supernatant of these 24 cultivable AHL-producers. The active extracts from these bacterial isolates were further evaluated by ultra performance liquid chromatography-mass spectrometry, and the carbon side chain length ranged from C4 to C14. This is the first report on the diversity of AI-1 type auto-inducers in the mangrove plant K. obovata, and it is imperative to expand our knowledge of plant-bacteria interactions with respect to the maintenance of wetland ecosystem health.

  20. Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove (Kandelia obovata) Rhizosphere Environment

    PubMed Central

    Ma, Zhi P.; Lao, Yong M.; Jin, Hui; Lin, Guang H.; Cai, Zhong H.; Zhou, Jin

    2016-01-01

    Mangrove rhizosphere environment harbors diverse populations of microbes, and some evidence showed that rhizobacteria behavior was regulated by quorum sensing (QS). Investigating the diverse profiles of QS molecules in mangrove ecosystems may shed light on the bacterial roles and lead to a better understanding of the symbiotic interactions between plants and microbes. The aims of the current study focus on identifying AI-1 type QS signals, i.e., acyl homoserine lactones (AHLs), in Kandelia obovata rhizosphere environment. Approximately 1200 rhizobacteria were screened and 184 strains (15.3%) tested were positive. Subsequent 16s rRNA gene sequencing and dereplication analyses identified 24 species from the positive isolates, which were affiliated to three different phyla, including Proteobacteria, Firmicutes, and Actinobacteria. Thin-layer chromatography separation of extracts revealed diverse AHL profiles and detected at least one active compound in the supernatant of these 24 cultivable AHL-producers. The active extracts from these bacterial isolates were further evaluated by ultra performance liquid chromatography-mass spectrometry, and the carbon side chain length ranged from C4 to C14. This is the first report on the diversity of AI-1 type auto-inducers in the mangrove plant K. obovata, and it is imperative to expand our knowledge of plant-bacteria interactions with respect to the maintenance of wetland ecosystem health. PMID:27994584

  1. Unraveling the Diversity of Early Aqueous Environments and Climate on Mars Through the Phyllosilicate Record

    NASA Technical Reports Server (NTRS)

    Bishop, J. L.; Baker, L. L.; Fairén, A. G.; Gross, C.; Velbel, M. A.; Rampe, E. B.; Michalski, J. R.

    2017-01-01

    Were Martian phyllosilicates formed on the surface or subsurface? Was early Mars warm or cold? How long was liquid water present on the surface of Mars? These are some of the many open questions about our neighboring planet. We propose that the mineralogy of the clay-bearing outcrops on Mars can help address these questions. Abundant phyllosilicates and aqueous minerals are observed nearly everywhere we can see the ancient rocks on Mars. Most bountiful among these is Fe/Mg-smectite. In this study we evaluate the nature and stratigraphy of clay outcrops observed on Mars and the presence of mixtures of other clays or other minerals with the ubiquitous Fe/Mg-smectite.

  2. An appraisal of subsurface geology and groundwater resources of Owerri and environs based on electrical resistivity survey and borehole data evaluation.

    PubMed

    Ibe, K M; Uzoukwu, S C

    2001-09-01

    The research was aimed at determining the depth to the water table, aquifer thickness and subsurface geology of the study area thus revealing its groundwater distribution as well as its potential as a substitute to the surface water resources. Vertical electrical soundings were carried out in the study area with maximum electrode spread. The Schlumberger electrode configuration technique was adopted. VES data were processed using Schlumberger analysis package. Lithologic logs of already existing boreholes in the study area were collected, evaluated and comparison were carried out. The results reveal alternating layers of sands, sandstones, gravel and clay. The lithologic logs revealed that the study area is underlain by coastal sands (Benin formation). The water table varies from 10-64 m and thickness of the aquifer ranges from 20-80 m. Results show that the study area is underlain by a thick extensive aquifer that has a transmissivity of 2.8 x 10(-2) m2 s(-1) to 3.3 x 10(-1) m2 s(-1) and storativity 1.44 x 10(-4) to 1.68 x 10(-3) m s(-1) values. The specific yield is about 0.31. The sandy component of the study area forms more than 90% of the sequence, therefore the permeability, the transmissivity and the storage coefficient are high with an excellent source of groundwater resources.

  3. Quantifying silica reactivity in subsurface environments: Reaction affinity and solute matrix controls on quartz and SiO{sub 2} glass. 1997 annual progress report

    SciTech Connect

    Dove, P.M.

    1997-10-15

    'The author reports the preliminary results of the experiments on the dissolution behavior of vitreous silica (v-SiO{sub 2}) into aqueous solutions of variable pH and ionic strength. The experiments are being conducted in mixed flow reactors with a high circulation rate that simulates constant-stirred conditions, the efficacy of which the authors discuss below. The preliminary results indicate that v-SiO{sub 2} dissolves into aqueous solutions approximately two orders of magnitude more quickly than crystalline silica (e.g., quartz). With additional experiments, they will utilize the dissolution rate data as a framework for understanding the behavior of waste glass compositions in the subsurface. In other work related to the studies of glass reactivity, the author has written one book chapter that will be published as part of a proceedings for the CEA/VALRHO international nuclear waste disposal conference held in Mejannes le Clap, France. In separate work, she is presently writing a second book chapter for the volume entitled Adsorption on Silica Surfaces.'

  4. The subsurface origin of microbial life on the Earth.

    PubMed

    Trevors, J T

    2002-10-01

    Life on Earth can be divided into life on the surface made possible by photosynthesis and subsurface life with chemical energy as the driving force. An understanding of both environments is central to our understanding of the origin of life, the search for novel microbial species in the subsurface and for extraterrestrial life or life signatures. In this manuscript, the surface and subsurface worlds are examined with a focus on the origin or assembly of bacterial life.

  5. Geomicrobial Processes and Biodiversity in the Deep Terrestrial Subsurface

    SciTech Connect

    Fredrickson, Jim K.; Balkwill, David L.

    2005-09-01

    The concept of a deep microbial biosphere has advanced over the past several decades from a hypothesis viewed with considerable skepticism to being widely accepted. Phylogenetically diverse prokaryotes have been cultured from or detected via characterization of directly-extracted nucleic acids from a wide range of deep terrestrial environments. Recent advances have linked the metabolic potential of these microorganisms, determined directly or inferred from phylogeny, to biogeochemical reactions determined via geochemical measurements and modeling. Buried organic matter or kerogen is an important source of energy for sustaining anaerobic heterotrophic microbial communities in deep sediments and sedimentary rock although rates of respiration are among the slowest rates measured on the planet. In contrast, Subsurface Lithoautotrophic Microbial Ecosystems based on H2 as the primary energy source appear to dominate in many crystalline rock environments. These photosynthesis-independent ecosystems remain an enigma due to the difficulty in accessing and characterizing appropriate samples. Deep mines and dedicated rock laboratories, however, may offer unprecedented opportunities for investigating subsurface microbial communities and their interactions with the geosphere.

  6. Workforce diversity in a research and development environment -- a model that works

    SciTech Connect

    McDavid, S.

    1993-11-17

    The Lawrence Livermore National Laboratory (LLNL) Engineering Directorate is in the third year of a diversity process that has changed the culture of the organization in many ways. This work outlines progress toward realizing the LLNL Engineering Diversity Model. Currently recommendations are being implemented that have been formulated through a problem resolution process, described in this work, in which employees helped identify problems, recommend solutions, and work with managers in focus groups. The process of arriving at the recommendations and the lessons learned through the problem resolution process are discussed. Ongoing actions, short-term goals, and long-term goals of the program are described.

  7. Electrical Subsurface Grounding Analysis

    SciTech Connect

    J.M. Calle

    2000-11-01

    The purpose and objective of this analysis is to determine the present grounding requirements of the Exploratory Studies Facility (ESF) subsurface electrical system and to verify that the actual grounding system and devices satisfy the requirements.

  8. Subsurface Microbiology and Biogeochemistry

    SciTech Connect

    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.

  9. Ceramic subsurface marker prototypes

    SciTech Connect

    Lukens, C.E.

    1985-05-02

    The client submitted 5 sets of porcelain and stoneware subsurface (radioactive site) marker prototypes (31 markers each set). The following were determined: compressive strength, thermal shock resistance, thermal crazing resistance, alkali resistance, color retention, and chemical resistance.

  10. Site Recommendation Subsurface Layout

    SciTech Connect

    C.L. Linden

    2000-06-28

    The purpose of this analysis is to develop a Subsurface Facility layout that is capable of accommodating the statutory capacity of 70,000 metric tons of uranium (MTU), as well as an option to expand the inventory capacity, if authorized, to 97,000 MTU. The layout configuration also requires a degree of flexibility to accommodate potential changes in site conditions or program requirements. The objective of this analysis is to provide a conceptual design of the Subsurface Facility sufficient to support the development of the Subsurface Facility System Description Document (CRWMS M&O 2000e) and the ''Emplacement Drift System Description Document'' (CRWMS M&O 2000i). As well, this analysis provides input to the Site Recommendation Consideration Report. The scope of this analysis includes: (1) Evaluation of the existing facilities and their integration into the Subsurface Facility design. (2) Identification and incorporation of factors influencing Subsurface Facility design, such as geological constraints, thermal loading, constructibility, subsurface ventilation, drainage control, radiological considerations, and the Test and Evaluation Facilities. (3) Development of a layout showing an available area in the primary area sufficient to support both the waste inventories and individual layouts showing the emplacement area required for 70,000 MTU and, if authorized, 97,000 MTU.

  11. Creating Culturally Responsive Environments: Ethnic Minority Teachers' Constructs of Cultural Diversity in Hong Kong Secondary Schools

    ERIC Educational Resources Information Center

    Hue, Ming-tak; Kennedy, Kerry John

    2014-01-01

    One of the challenges facing Hong Kong schools is the growing cultural diversity of the student population that is a result of the growing number of ethnic minority students in the schools. This study uses semi-structured interviews with 12 American, Canadian, Indian, Nepalese and Pakistani teachers working in three secondary schools in the public…

  12. Twelve Commandments of Human Relations for the Diverse Academic Environment of Colleges and Universities

    ERIC Educational Resources Information Center

    Davis, William Young; Swartz, Caroline

    2008-01-01

    This paper focuses on applying proven industrial relations approaches and sound management practice to address a range of diversity issues in higher education. Issues addressed include the need to set a clear and consistent direction, the importance of effective policy setting and enforcement, the value of positive reinforcement, and the…

  13. Habitats as Complex Odour Environments: How Does Plant Diversity Affect Herbivore and Parasitoid Orientation?

    PubMed Central

    Wäschke, Nicole; Hardge, Kristin; Hancock, Christine; Hilker, Monika; Obermaier, Elisabeth; Meiners, Torsten

    2014-01-01

    Plant diversity is known to affect success of host location by pest insects, but its effect on olfactory orientation of non-pest insect species has hardly been addressed. First, we tested in laboratory experiments the hypothesis that non-host plants, which increase odour complexity in habitats, affect the host location ability of herbivores and parasitoids. Furthermore, we recorded field data of plant diversity in addition to herbivore and parasitoid abundance at 77 grassland sites in three different regions in Germany in order to elucidate whether our laboratory results reflect the field situation. As a model system we used the herb Plantago lanceolata, the herbivorous weevil Mecinus pascuorum, and its larval parasitoid Mesopolobus incultus. The laboratory bioassays revealed that both the herbivorous weevil and its larval parasitoid can locate their host plant and host via olfactory cues even in the presence of non-host odour. In a newly established two-circle olfactometer, the weeviĺs capability to detect host plant odour was not affected by odours from non-host plants. However, addition of non-host plant odours to host plant odour enhanced the weeviĺs foraging activity. The parasitoid was attracted by a combination of host plant and host volatiles in both the absence and presence of non-host plant volatiles in a Y-tube olfactometer. In dual choice tests the parasitoid preferred the blend of host plant and host volatiles over its combination with non-host plant volatiles. In the field, no indication was found that high plant diversity disturbs host (plant) location by the weevil and its parasitoid. In contrast, plant diversity was positively correlated with weevil abundance, whereas parasitoid abundance was independent of plant diversity. Therefore, we conclude that weevils and parasitoids showed the sensory capacity to successfully cope with complex vegetation odours when searching for hosts. PMID:24416354

  14. Ecosystems in the Backyard: Preparing a Diverse Outdoor Environment for Primary (Ages Three to Six) Children.

    ERIC Educational Resources Information Center

    Verschuur, Mary B.

    2003-01-01

    Chronicles the outdoor work of Lincoln Montessori School in Nebraska in prairie, forest, and indoor greenhouse environments, highlighting the application of prepared environment principles to the natural world. Highlights how implicit to the design are opportunities for caring, including practical life exercises with outdoor tools. Shows how…

  15. Ecosystems in the Backyard: Preparing a Diverse Outdoor Environment for Primary (Ages Three to Six) Children

    ERIC Educational Resources Information Center

    Verschuur, Mary B.

    2013-01-01

    Mary Verschuur chronicles the outdoor work of Lincoln Montessori School in prairie, forest, and indoor greenhouse environments, pointing out the application of the prepared environment principles to the natural world. Implicit to the design are opportunities for caring, including various practical life exercises with outdoor tools blended into…

  16. Interaction Network Estimation: Predicting Problem-Solving Diversity in Interactive Environments

    ERIC Educational Resources Information Center

    Eagle, Michael; Hicks, Drew; Barnes, Tiffany

    2015-01-01

    Intelligent tutoring systems and computer aided learning environments aimed at developing problem solving produce large amounts of transactional data which make it a challenge for both researchers and educators to understand how students work within the environment. Researchers have modeled student-tutor interactions using complex networks in…

  17. Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments

    PubMed Central

    Fusi, Marco; Cherif, Ameur; Abou-Hadid, Ayman; El-Bahairy, Usama; Sorlini, Claudia; Daffonchio, Daniele

    2013-01-01

    Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP) potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches. According to 16S rRNA gene PCR-DGGE, the structure of endosphere and rhizosphere bacterial communities was highly diverse (P = 0.03) and was associated with a cultivar/latitudinal/climatic effect. Despite being diverse, the bacterial communities associated with Egyptian grapevines shared a higher similarity with the Tunisian grapevines than those cultivated in North Italy. A similar distribution, according to the cultivar/latitude/aridity gradients, was observed for the cultivable bacteria. Many isolates (23%) presented in vitro multiple stress resistance capabilities and PGP activities, the most frequent being auxin synthesis (82%), insoluble phosphate solubilisation (61%), and ammonia production (70%). The comparable numbers and types of potential PGP traits among the three different environmental settings indicate a strong functional homeostasis of beneficial bacteria associated with grape root. PMID:23878810

  18. Urban heat island in the subsurface

    NASA Astrophysics Data System (ADS)

    Ferguson, Grant; Woodbury, Allan D.

    2007-12-01

    The urban heat island effect has received significant attention in recent years due to the possible effect on long-term meteorological records. Recent studies of this phenomenon have suggested that this may not be important to estimates of regional climate change once data are properly corrected. However, surface air temperatures within urban environments have significant variation, making correction difficult. In the current study, we examine subsurface temperatures in an urban environment and the surrounding rural area to help characterize the nature of this variability. The results of our study indicate that subsurface temperatures are linked to land-use and supports previous work indicating that the urban heat island effect has significant and complex spatial variability. In most situations, the relationship between subsurface and surface processes cannot be easily determined, indicating that previous studies that relying on such a linkage may require further examination.

  19. The home environment and family asthma management among ethnically diverse urban youth with asthma.

    PubMed

    Sato, Amy F; Kopel, Sheryl J; McQuaid, Elizabeth L; Seifer, Ronald; Esteban, Cynthia; Coutinho, Maria Teresa; Klein, Robert; Fritz, Gregory K; Koinis-Mitchell, Daphne

    2013-06-01

    Although the pediatric psychology literature underscores the importance of illness-related aspects of the home environment for optimal family asthma management, little is known about the contribution of more global aspects of the home environment (e.g., family routines/schedule, quality of stimulation provided to child) to asthma management in ethnic minority and urban families. The goals of this study were to (a) explore ethnic/racial group differences in global and specific dimensions of home environment quality among Latino, non-Latino White (NLW), and African American urban children with asthma; and (b) examine associations between the quality and quantity of support and stimulation within the home environment, as measured by the HOME Inventory, and family asthma management. Urban, low-income children (N = 131) between the ages of 6 and 13 with asthma and a primary caregiver participated in a multimodal assessment, including an in-home observation and semistructured interviews to assess aspects of home environment quality and family asthma management practices. While controlling for poverty, no ethnic group differences were found in the global home environment; however, there were significant differences in specific dimensions (e.g., Family Participation in Developmentally Stimulating Experiences, and Aspects of the Physical Environment) of home environment quality. Across the whole sample, home environment quality predicted family asthma management. When examining this association for specific ethnic groups, this finding did not hold for the Latino subsample. The results highlight the need to consider ethnic group differences in non-illness-specific aspects of the home environment when addressing families' asthma management strategies.

  20. 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.

  1. Global gradients in vertebrate diversity predicted by historical area-productivity dynamics and contemporary environment.

    PubMed

    Jetz, Walter; Fine, Paul V A

    2012-01-01

    Broad-scale geographic gradients in species richness have now been extensively documented, but their historical underpinning is still not well understood. While the importance of productivity, temperature, and a scale dependence of the determinants of diversity is broadly acknowledged, we argue here that limitation to a single analysis scale and data pseudo-replication have impeded an integrated evolutionary and ecological understanding of diversity gradients. We develop and apply a hierarchical analysis framework for global diversity gradients that incorporates an explicit accounting of past environmental variation and provides an appropriate measurement of richness. Due to environmental niche conservatism, organisms generally reside in climatically defined bioregions, or "evolutionary arenas," characterized by in situ speciation and extinction. These bioregions differ in age and their total productivity and have varied over time in area and energy available for diversification. We show that, consistently across the four major terrestrial vertebrate groups, current-day species richness of the world's main 32 bioregions is best explained by a model that integrates area and productivity over geological time together with temperature. Adding finer scale variation in energy availability as an ecological predictor of within-bioregional patterns of richness explains much of the remaining global variation in richness at the 110 km grain. These results highlight the separate evolutionary and ecological effects of energy availability and provide a first conceptual and empirical integration of the key drivers of broad-scale richness gradients. Avoiding the pseudo-replication that hampers the evolutionary interpretation of non-hierarchical macroecological analyses, our findings integrate evolutionary and ecological mechanisms at their most relevant scales and offer a new synthesis regarding global diversity gradients.

  2. The Origins of Diverse Domains of Mathematics: Generalist Genes but Specialist Environments

    ERIC Educational Resources Information Center

    Kovas, Y.; Petrill, S. A.; Plomin, R.

    2007-01-01

    The authors assessed 2,502 ten-year-old children, members of 1,251 pairs of twins, on a Web-based battery of problems from 5 diverse aspects of mathematics assessed as part of the U.K. national curriculum. This 1st genetic study into the etiology of variation in different domains of mathematics showed that the heritability estimates were moderate…

  3. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment

    SciTech Connect

    Barns, S.M.; Fundyga, R.E.; Jeffries, M.W.; Pace, N.R.

    1994-03-01

    Of the three primary phylogenetic domains - Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes) - Archaea is the least understood in terms of its diversity, physiologies, and ecological panorama. Although many species of Crenarchaeota have been isolated, they constitute a relatively tight-knit cluster of lineages in phylogenetic analyses of rRNA sequences. It seemed possible that this limited diversity is merely apparent and reflects only a failure to culture organisms, not their absence. The authors reported here phylogenetic characterization of many archaeal small subunit rRNA gene sequences obtained by polymerase chain reaction amplification of mixed population DNA extracted directly from sediment of a hot spring in Yellowstone National Park. This approach obviates the need for cultivation to identify organisms. The analyses document the existence not only of species belonging to well-characterized crenarchaeal genera or families but also of crenarchaeal species for which no close relatives have so far been found. The large number of distinct archaeal sequence types retrieved from this single hot spring was unexpected and demonstrates that Crenarchaeota is a much more diverse group than was previously suspected. The results have impact on concepts of the phylogenetic organization of Archaea.

  4. Population diversity and adaptive evolution in keratinization genes: impact of environment in shaping skin phenotypes.

    PubMed

    Gautam, Pramod; Chaurasia, Amit; Bhattacharya, Aniket; Grover, Ritika; Mukerji, Mitali; Natarajan, Vivek T

    2015-03-01

    Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.

  5. Characterization of Diazotrophs Containing Mo-Independent Nitrogenases, Isolated from Diverse Natural Environments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molybdenum-independent nitrogenases were first described in the nitrogen-fixing bacterium Azotobacter vinelandii and have since been described in other diazotrophic bacteria. Previously, we reported the isolation of seven diazotrophs with Molybdenum-independent nitrogenases from aquatic environments...

  6. Life history diversity of Snake River finespotted cutthroat trout: managing for persistence in a rapidly changing environment

    USGS Publications Warehouse

    Homel, Kristen M.; Gresswell, Robert E.; Kershner, Jeffrey L.

    2015-01-01

    Over the last century, native trout have experienced dramatic population declines, particularly in larger river systems where habitats associated with different spawning life history forms have been lost through habitat degradation and fragmentation. The resulting decrease in life history diversity has affected the capacity of populations to respond to environmental variability and disturbance. Unfortunately, because few large rivers are intact enough to permit full expression of life history diversity, it is unclear what patterns of diversity should be a conservation target. In this study, radiotelemetry was used to identify spawning and migration patterns of Snake River Finespotted Cutthroat Trout Oncorhynchus clarkii behnkei in the upper Snake River. Individuals were implanted with radio tags in October 2007 and 2008, and monitored through October 2009. Radio-tagged cutthroat trout in the upper Snake River exhibited variation in spawning habitat type and location, migration distance, spawn timing, postspawning behavior, and susceptibility to mortality sources. Between May and July, Cutthroat Trout spawned in runoff-dominated tributaries, groundwater-dominated spring creeks, and side channels of the Snake River. Individuals migrated up to 101 km from tagging locations in the upper Snake River to access spawning habitats, indicating that the upper Snake River provided seasonal habitat for spawners originating throughout the watershed. Postspawning behavior also varied; by August each year, 28% of spring-creek spawners remained in their spawning location, compared with 0% of side-channel spawners and 7% of tributary spawners. These spawning and migration patterns reflect the connectivity, habitat diversity, and dynamic template of the Snake River. Ultimately, promoting life history diversity through restoration of complex habitats may provide the most opportunities for cutthroat trout persistence in an environment likely to experience increased variability from

  7. Effects of different on-farm management on yield and water use efficiency of Potato crop cultivated in semiarid environments under subsurface drip irrigation

    NASA Astrophysics Data System (ADS)

    Ghazouani, Hiba; Provenzano, Giuseppe; Rallo, Giovanni; Mguidiche, Amel; Douh, Boutheina; Boujelben, Abdelhamid

    2016-04-01

    In Tunisia the amount of water for irrigated agriculture is higher than about 80% of the total resource.The increasing population and the rising food demand, associated to the negative effects of climate change,make it crucial to adopt strategies aiming to improve water use efficiency (WUE). Moreover, the absence of an effective public policy for water management amplifies the imbalance between water supply and its demand. Despite improved irrigation technologies can enhance the efficiency of water distribution systems, to achieve environmental goals it is also necessaryto identify on-farm management strategies accounting for actual crop water requirement. The main objective of the paper was to assess the effects of different on-farm managementstrategies (irrigation scheduling and planting date) on yield and water use efficiency of Potato crop (Solanumtuberosum L.) irrigated with a subsurface drip system, under the semi-arid climate of central Tunisia. Experiments were carried out during three growing seasons (2012, 2014 and 2015) at the High Agronomic Institute of ChottMariem in Sousse, by considering different planting dates and irrigation depths, the latter scheduled according to the climate observed during the season. All the considered treatments received the same pesticide and fertilizer management. Experiments evidenced that the climatic variability characterizing the examined seasons (photoperiod, solar radiation and average temperature) affects considerably the crop phenological stages, and the late sowing shortens the crop cycle.It has also been demonstrated that Leaf Area Index (LAI) and crop yield resulted relatively higher for those treatments receiving larger amounts of seasonal water. Crop yield varied between 16.3 t/ha and 39.1 t/ha, with a trend linearly related to the ratio between the seasonal amount of water supplied (Irrigation, I and Precipitation, P) and the maximum crop evapotranspiration (ETm). The maximum crop yield was in particular

  8. Structure and function of subsurface microbial communities affecting radionuclide transport and bioimmobilization

    SciTech Connect

    Kostka, Joel E.; Prakash, Om; Green, Stefan J.; Akob, Denise; Jasrotia, Puja; Kerkhof, Lee; Chin, Kuk-Jeong; Sheth, Mili; Keller, Martin; Venkateswaran, Amudhan; Elkins, James G.; Stucki, Joseph W.

    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. The 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).

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

    ScienceCinema

    Hibbett, David [Clark University

    2016-07-12

    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.

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

    SciTech Connect

    Hibbett, David

    2012-03-21

    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.

  11. Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Gordon, Sean

    2013-03-01

    Sean Gordon of the USDA on "Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  12. Physical, consumer, and social aspects of measuring the food environment among diverse low-income populations.

    PubMed

    Gittelsohn, Joel; Sharma, Sangita

    2009-04-01

    Obesity and other diet-related chronic diseases are directly related to the food environment. We describe how to better assess the food environment in specific ethnic minority settings for designing and implementing interventions, based on a review of our previous work on the food environment in American Indian reservations, Canadian First Nations reserves, the Republic of the Marshall Islands, and inner-city Baltimore. The types of food stores available within each setting and the range of healthy foods available varied greatly across these geographic regions. In all settings, proximity to food stores/supermarkets, cost, and limited availability of healthful foods were common features, which limited access to health-promoting food options. Features specific to each population should be considered in an assessment of the food environment, including physical (e.g., openness of stores, mix of types of food sources); consumer (e.g., adequacy of the food supply, seasonal factors); and social (e.g., inter-household food sharing, perceptions of food quality, language differences) aspects. The food environments common in low-income ethnic subpopulations require special focus and consideration due to the vulnerability of the populations and to specific and unique aspects of each setting.

  13. Morphological and molecular characterization of Calothrix isolates obtained from diverse environments in India.

    PubMed

    Singh, S; Dhar, D W; Gupta, R K

    2011-01-01

    Abstract-Thirty cyanobacterial strains of Calothrix (family Rivulariaceae) isolated from diverse geographical regions of India were analyzed using morphological and molecular approaches. Most of the isolates were planktonic while some grew benthically. Significant differences were observed with regard to the shape and size of the vegetative cells, heterocysts, and akinetes. Analyses of molecular polymorphisms using Restriction Fragment Length Polymorphisms (RFLP) of 16S rRNA genes with the reference strain led to unambiguous differentiation of the isolates as well as understanding of their genetic relationships.

  14. The Origins of Diverse Domains of Mathematics: Generalist Genes but Specialist Environments.

    PubMed

    Kovas, Y; Petrill, S A; Plomin, R

    2007-02-01

    The authors assessed 2,502 ten-year-old children, members of 1,251 pairs of twins, on a Web-based battery of problems from 5 diverse aspects of mathematics assessed as part of the U.K. national curriculum. This 1st genetic study into the etiology of variation in different domains of mathematics showed that the heritability estimates were moderate and highly similar across domains and that these genetic influences were mostly general. Environmental factors unique to each twin in a family (rather than shared by the 2 twins) explained most of the remaining variance, and these factors were mostly specific to each domain.

  15. MSTS - Multiphase Subsurface Transport Simulator theory manual

    SciTech Connect

    White, M.D.; Nichols, W.E.

    1993-05-01

    The US Department of Energy, through the Yucca Mountain Site Characterization Project Office, has designated the Yucca Mountain site in Nevada for detailed study as the candidate US geologic repository for spent nuclear fuel and high-level radioactive waste. Site characterization will determine the suitability of the Yucca Mountain site for the potential waste repository. If the site is determined suitable, subsequent studies and characterization will be conducted to obtain authorization from the Nuclear Regulatory Commission to construct the potential waste repository. A principal component of the characterization and licensing processes involves numerically predicting the thermal and hydrologic response of the subsurface environment of the Yucca Mountain site to the potential repository over a 10,000-year period. The thermal and hydrologic response of the subsurface environment to the repository is anticipated to include complex processes of countercurrent vapor and liquid migration, multiple-phase heat transfer, multiple-phase transport, and geochemical reactions. Numerical simulators based on mathematical descriptions of these subsurface phenomena are required to make numerical predictions of the thermal and hydrologic response of the Yucca Mountain subsurface environment The engineering simulator called the Multiphase Subsurface Transport Simulator (MSTS) was developed at the request of the Yucca Mountain Site Characterization Project Office to produce numerical predictions of subsurface flow and transport phenomena at the potential Yucca Mountain site. This document delineates the design architecture and describes the specific computational algorithms that compose MSTS. Details for using MSTS and sample problems are given in the {open_quotes}User`s Guide and Reference{close_quotes} companion document.

  16. Best Practice -- Subsurface Investigations

    SciTech Connect

    Clark Scott

    2010-03-01

    These best practices for Subsurface Survey processes were developed at the Idaho National Laboratory (INL) and later shared and formalized by a sub-committee, under the Electrical Safety Committee of EFCOG. The developed best practice is best characterized as a Tier II (enhanced) survey process for subsurface investigations. A result of this process has been an increase in the safety and lowering of overall cost, when utility hits and their related costs are factored in. The process involves improving the methodology and thoroughness of the survey and reporting processes; or improvement in tool use rather than in the tools themselves. It is hoped that the process described here can be implemented at other sites seeking to improve their Subsurface Investigation results with little upheaval to their existing system.

  17. 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

  18. Experiences of using the Theoretical Domains Framework across diverse clinical environments: a qualitative study

    PubMed Central

    Phillips, Cameron J; Marshall, Andrea P; Chaves, Nadia J; Jankelowitz, Stacey K; Lin, Ivan B; Loy, Clement T; Rees, Gwyneth; Sakzewski, Leanne; Thomas, Susie; To, The-Phung; Wilkinson, Shelley A; Michie, Susan

    2015-01-01

    Background The Theoretical Domains Framework (TDF) is an integrative framework developed from a synthesis of psychological theories as a vehicle to help apply theoretical approaches to interventions aimed at behavior change. Purpose This study explores experiences of TDF use by professionals from multiple disciplines across diverse clinical settings. Methods Mixed methods were used to examine experiences, attitudes, and perspectives of health professionals in using the TDF in health care implementation projects. Individual interviews were conducted with ten health care professionals from six disciplines who used the TDF in implementation projects. Deductive content and thematic analysis were used. Results Three main themes and associated subthemes were identified including: 1) reasons for use of the TDF (increased confidence, broader perspective, and theoretical underpinnings); 2) challenges using the TDF (time and resources, operationalization of the TDF) and; 3) future use of the TDF. Conclusion The TDF provided a useful, flexible framework for a diverse group of health professionals working across different clinical settings for the assessment of barriers and targeting resources to influence behavior change for implementation projects. The development of practical tools and training or support is likely to aid the utility of TDF. PMID:25834455

  19. Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments.

    PubMed

    Nercessian, Olivier; Bienvenu, Nadège; Moreira, David; Prieur, Daniel; Jeanthon, Christian

    2005-01-01

    To contribute to the identification of methanogens, methanotrophs and sulfate-reducing bacteria (SRB) in microbial communities from the 13 degrees N (East Pacific Rise) and Rainbow (Mid-Atlantic Ridge) hydrothermal vent fields, we investigated the diversity of mcrA, pmoA and dsrAB genes sequences. Clone libraries were obtained using DNA isolated from fragments of diffuse vents, sediment and in situ samplers. The clones were categorized by restriction fragment length polymorphism, and representatives of each group were sequenced. Sequences were related to that of hyperthermophilic (order Methanopyrales and family Methanocaldococcaceae), thermophilic and mesophilic (family Methanococcaceae) methanogens, thermophilic (proposed genus 'Methylothermus') and mesophilic type I methanotrophs, and hyperthermophilic (order Archaeoglobales), thermophilic (order Thermodesulfobacteriales) and mesophilic (family Desulfobulbaceae) SRB. Several of the obtained sequences were distantly related to the genes of cultivated organisms, providing evidence of the existence of novel lineages in the three functional groups. This study provides for the first time an insight into the diversity of several functional genes of deep-sea hydrothermal system microorganisms.

  20. Approach to determine the diversity of Legionella species by nested PCR-DGGE in aquatic environments

    PubMed Central

    Huang, Wen-Chien; Tsai, Hsin-Chi; Tao, Chi-Wei; Chen, Jung-Sheng; Shih, Yi-Jia; Kao, Po-Min; Huang, Tung-Yi; Hsu, Bing-Mu

    2017-01-01

    In this study, we describe a nested PCR-DGGE strategy to detect Legionella communities from river water samples. The nearly full-length 16S rRNA gene was amplified using bacterial primer in the first step. After, the amplicons were employed as DNA templates in the second PCR using Legionella specific primer. The third round of gene amplification was conducted to gain PCR fragments apposite for DGGE analysis. Then the total numbers of amplified genes were observed in DGGE bands of products gained with primers specific for the diversity of Legionella species. The DGGE patterns are thus potential for a high-throughput preliminary determination of aquatic environmental Legionella species before sequencing. Comparative DNA sequence analysis of excised DGGE unique band patterns showed the identity of the Legionella community members, including a reference profile with two pathogenic species of Legionella strains. In addition, only members of Legionella pneumophila and uncultured Legionella sp. were detected. Development of three step nested PCR-DGGE tactic is seen as a useful method for studying the diversity of Legionella community. The method is rapid and provided sequence information for phylogenetic analysis. PMID:28166249

  1. 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

    2017-03-13

    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.

  2. Genetic and physiological diversity of Tetragenococcus halophilus strains isolated from sugar- and salt-rich environments.

    PubMed

    Justé, Annelies; Lievens, Bart; Frans, Ingeborg; Marsh, Terence L; Klingeberg, Michael; Michiels, Chris W; Willems, Kris A

    2008-09-01

    Tetragenococcus halophilus is known to flourish in extreme salt environments. Recently, this halophilic bacterium also appeared as the dominant microflora during storage of sugar thick juice, an intermediate product of beet sugar production. Although T. halophilus can cause degradation of thick juice, dominance of this bacterium does not always result in degradation. In this study T. halophilus strains from high-salt and high-sugar environments, and in particular from degraded and non-degraded thick juice, were compared in detail. Both physiological and genetic characterization using Biolog, repetitive PCR fingerprinting (rep-PCR) and random amplified polymorphic DNA (RAPD) technology, revealed clear differences between T. halophilus strains isolated from salt- and sugar-rich environments. However, no strain pattern could be specifically and systematically associated with degraded or non-degraded thick juice. Remarkably, halophilic T. halophilus strains were not able to grow in sugar thick juice. Irrespective of the differences between the strains from high-salt or high-sugar environments, DNA-DNA hybridization grouped all strains within the species T. halophilus, except one isolate from sugar thick juice that showed different physiological and genetic characteristics, and that may represent a new species of Tetragenococcus.

  3. The Home Smoking Environment: Influence on Behaviors and Attitudes in a Racially Diverse Adolescent Population

    ERIC Educational Resources Information Center

    Muilenburg, Jessica Legge; Latham, Teaniese; Annang, Lucy; Johnson, William D.; Burdell, Alexandra C.; West, Sabra J.; Clayton, Dixie L.

    2009-01-01

    Although studies indicate that public policy can influence the decrease in smoking behaviors, these policies have not necessarily transferred to home environments at the same rate. The authors surveyed 4,296 students in a southern urban area. African American students were 76.3% of the respondents and Caucasians accounted for 23.7%. African…

  4. Detailed composition analyses of diverse oat genotype kernels grown in different environments in North Dakota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nutritional composition of oat kernels from 18 genotypes grown in 6 environments in North Dakota (USA) was analyzed by chemical means. Of the macro-nutrients, mean starch concentration was 56.5%, protein was 18.1%, oil was 7.9%, neutral detergent fiber (insoluble fiber) was 6.0%, beta-glucan (solubl...

  5. Trapping of sediment along the Amazon tidal river in diverse floodplain environments

    NASA Astrophysics Data System (ADS)

    Fricke, A. T.; Nittrouer, C. A.; Ogston, A. S.; Nowacki, D. J.; Souza Filho, P. W.; Silveira, O.; Asp, N. E.

    2013-12-01

    The Amazon tidal river, the freshwater reach that is influenced by tides, extends roughly 800 kilometers upstream of the river mouth. Previous studies suggest that up to one third of the sediment measured at the upstream limit of tides does not reach the ocean, and is likely trapped along the tidal river. Here we present data from a variety of depositional environments along this reach, including intertidal vegetated floodplains, floodplain lakes, and drowned tributary confluences. Sediment delivery to each of these environments is temporally variable as a result of changing tides and river stage, and spatially variable along the continuum from the purely fluvial upstream condition to the strongly tidal downstream environment. Short-term instrument records and direct observations are paired with sedimentological and radiochemical techniques to identify mechanisms of sediment exchange between river and floodplain and associated patterns of sediment accumulation. Sediments in vegetated intertidal floodplains exhibit tidal laminations and incised channel networks similar to muddy marine intertidal areas. Floodplain lakes experience dramatic seasonal changes in size, and during high flows of the river skim water and sediment from the Amazon River by providing a shortcut relative to the meandering mainstem. Amazon sediment is fluxed into the drowned tributary confluences (rías) of the Xingu and Tapajos Rivers by density-driven underflows. In the Tapajos Ría, sediment from the Amazon River has built a 25-km long birdfoot delta, suggesting these tributaries may be net sinks of sediment, rather than sources. These findings help define the importance of each tidal environment in trapping Amazon sediment before it reaches the marine environment.

  6. Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition1[OPEN

    PubMed Central

    Connolly, Erin L.

    2016-01-01

    Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement. PMID:26896393

  7. Molecular Detection and Environment-Specific Diversity of Glycosyl Hydrolase Family 1 β-Glucosidase in Different Habitats

    PubMed Central

    Tiwari, Rameshwar; Kumar, Kanika; Singh, Surender; Nain, Lata; Shukla, Pratyoosh

    2016-01-01

    β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. Therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, Himalayan soil, cow dung and compost by metagenomic approach. Preliminary evaluation through metabolic profiling using BIOLOG based utilization patterns of carbon, nitrogen, phosphorus and sulfur revealed the environment and substrate specific nature of the indigenous microbial population. Furthermore, clonal library selection, screening and sequence analysis revealed that most of the GH1 β-glucosidase proteins had low identities with the available database. Analysis of the distribution of GH1 β-glucosidase gene fragments and β-glucosidase producing microbial community revealed the environment specific nature. The OTUs obtained from Himalayan soil and compost metagenomic libraries were grouped into 19 different genera comprising 6 groups. The cow dung sample displayed the least diversity of GH1 β-glucosidase sequences, with only 14 genera, distributed among three groups- Bacteroidetes, Firmicutes, and Actinobacteria. The metagenomic study coupled with metabolic profiling of GH1 β-glucosidase illustrated the existence of intricate relationship between the geochemical environmental factors and inherent microbial community. PMID:27790196

  8. 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

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

    PubMed

    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.

  10. Early subtropical forest growth is driven by community mean trait values and functional diversity rather than the abiotic environment

    PubMed Central

    Kröber, Wenzel; Li, Ying; Härdtle, Werner; Ma, Keping; Schmid, Bernhard; Schmidt, Karsten; Scholten, Thomas; Seidler, Gunnar; von Oheimb, Goddert; Welk, Erik; Wirth, Christian; Bruelheide, Helge

    2015-01-01

    While functional diversity (FD) has been shown to be positively related to a number of ecosystem functions including biomass production, it may have a much less pronounced effect than that of environmental factors or species-specific properties. Leaf and wood traits can be considered particularly relevant to tree growth, as they reflect a trade-off between resources invested into growth and persistence. Our study focussed on the degree to which early forest growth was driven by FD, the environment (11 variables characterizing abiotic habitat conditions), and community-weighted mean (CWM) values of species traits in the context of a large-scale tree diversity experiment (BEF-China). Growth rates of trees with respect to crown diameter were aggregated across 231 plots (hosting between one and 23 tree species) and related to environmental variables, FD, and CWM, the latter two of which were based on 41 plant functional traits. The effects of each of the three predictor groups were analyzed separately by mixed model optimization and jointly by variance partitioning. Numerous single traits predicted plot-level tree growth, both in the models based on CWMs and FD, but none of the environmental variables was able to predict tree growth. In the best models, environment and FD explained only 4 and 31% of variation in crown growth rates, respectively, while CWM trait values explained 42%. In total, the best models accounted for 51% of crown growth. The marginal role of the selected environmental variables was unexpected, given the high topographic heterogeneity and large size of the experiment, as was the significant impact of FD, demonstrating that positive diversity effects already occur during the early stages in tree plantations. PMID:26380685

  11. Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment

    PubMed Central

    Carré, Claire; Cellamare, Maria; Duval, Charlotte; Intertaglia, Laurent; Lavergne, Céline; Roques, Cécile

    2017-01-01

    This study describes, for the first time, the water chemistry and microbial diversity in Dziani Dzaha, a tropical crater lake located on Mayotte Island (Comoros archipelago, Western Indian Ocean). The lake water had a high level of dissolved matter and high alkalinity (10.6–14.5 g L-1 eq. CO32-, i.e. 160–220 mM compare to around 2–2.5 in seawater), with salinity up to 52 psu, 1.5 higher than seawater. Hierarchical clustering discriminated Dziani Dzaha water from other alkaline, saline lakes, highlighting its thalassohaline nature. The phytoplankton biomass was very high, with a total chlorophyll a concentration of 524 to 875 μg chl a L-1 depending on the survey, homogeneously distributed from surface to bottom (4 m). Throughout the whole water column the photosynthetic biomass was dominated (>97% of total biovolume) by the filamentous cyanobacteria Arthrospira sp. with a straight morphotype. In situ daily photosynthetic oxygen production ranged from 17.3 to 22.2 g O2 m-2 d-1, consistent with experimental production / irradiance measurements and modeling. Heterotrophic bacterioplankton was extremely abundant, with cell densities up to 1.5 108 cells mL-1 in the whole water column. Isolation and culture of 59 Eubacteria strains revealed the prevalence of alkaliphilic and halophilic organisms together with taxa unknown to date, based on 16S rRNA gene analysis. A single cloning-sequencing approach using archaeal 16S rDNA gene primers unveiled the presence of diverse extremophilic Euryarchaeota. The water chemistry of Dziani Dzaha Lake supports the hypothesis that it was derived from seawater and strongly modified by geological conditions and microbial activities that increased the alkalinity. Dziani Dzaha has a unique consortium of cyanobacteria, phytoplankton, heterotrophic Eubacteria and Archaea, with very few unicellular protozoa, that will deserve further deep analysis to unravel its uncommon diversity. A single taxon, belonging to the genus Arthrospira, was

  12. Genetic diversity analysis reveals that geographical environment plays a more important role than rice cultivar in Villosiclava virens population selection.

    PubMed

    Wang, Fei; Zhang, Shu; Liu, Mei-Gang; Lin, Xian-Song; Liu, Hui-Jiang; Peng, You-Liang; Lin, Yang; Huang, Jun-Bin; Luo, Chao-Xi

    2014-05-01

    Rice false smut caused by Villosiclava virens is an economically important disease of grains worldwide. The genetic diversity of 153 isolates from six fields located in Wuhan (WH), Yichang Wangjia (YCW), Yichang Yaohe (YCY), Huanggang (HG), Yangxin (YX), and Jingzhou (JZ) in Hubei province of China were phylogenetically analyzed to evaluate the influence of environments and rice cultivars on the V. virens populations. Isolates (43) from Wuhan were from two rice cultivars, Wanxian 98 and Huajing 952, while most of the other isolates from fields YCW, YCY, HG, YX, and JZ originated from different rice cultivars with different genetic backgrounds. Genetic diversity of isolates was analyzed using random amplified polymorphic DNA (RAPD) and single-nucleotide polymorphisms (SNP). The isolates from the same cultivars in Wuhan tended to group together, indicating that the cultivars had an important impact on the fungal population. The 110 isolates from individual fields tended to cluster according to geographical origin. The values of Nei's gene diversity (H) and Shannon's information index (I) showed that the genetic diversity among isolates was higher between than within geographical populations. Furthermore, mean genetic distance between groups (0.006) was higher than mean genetic distance within groups (0.0048) according to MEGA 5.2. The pairwise population fixation index (FST) values also showed significant genetic differentiation between most populations. Higher genetic similarity of isolates from individual fields but different rice cultivars suggested that the geographical factor played a more important role in the selection of V. virens isolates than rice cultivars. This information could be used to improve the management strategy for rice false smut by adjusting the cultivation measures, such as controlling fertilizer, water, and planting density, in the rice field to change the microenvironment.

  13. Resistome diversity in cattle and the environment decreases during beef production.

    PubMed

    Noyes, Noelle R; Yang, Xiang; Linke, Lyndsey M; Magnuson, Roberta J; Dettenwanger, Adam; Cook, Shaun; Geornaras, Ifigenia; Woerner, Dale E; Gow, Sheryl P; McAllister, Tim A; Yang, Hua; Ruiz, Jaime; Jones, Kenneth L; Boucher, Christina A; Morley, Paul S; Belk, Keith E

    2016-03-08

    Antimicrobial resistant determinants (ARDs) can be transmitted from livestock systems through meat products or environmental effluents. The public health risk posed by these two routes is not well understood, particularly in non-pathogenic bacteria. We collected pooled samples from 8 groups of 1741 commercial cattle as they moved through the process of beef production from feedlot entry through slaughter. We recorded antimicrobial drug exposures and interrogated the resistome at points in production when management procedures could potentially influence ARD abundance and/or transmission. Over 300 unique ARDs were identified. Resistome diversity decreased while cattle were in the feedlot, indicating selective pressure. ARDs were not identified in beef products, suggesting that slaughter interventions may reduce the risk of transmission of ARDs to beef consumers. This report highlights the utility and limitations of metagenomics for assessing public health risks regarding antimicrobial resistance, and demonstrates that environmental pathways may represent a greater risk than the food supply.

  14. In vitro evolution of distinct self-cleaving ribozymes in diverse environments

    PubMed Central

    Popović, Milena; Fliss, Palmer S.; Ditzler, Mark A.

    2015-01-01

    In vitro evolution experiments have long been used to evaluate the roles of RNA in both modern and ancient biology, and as a tool for biotechnology applications. The conditions under which these experiments have been conducted, however, do not reflect the range of cellular environments in modern biology or our understanding of chemical environments on the early earth, when the atmosphere and oceans were largely anoxic and soluble Fe2+ was abundant. To test the impact of environmental factors relevant to RNA's potential role in the earliest forms of life, we evolved populations of self-cleaving ribozymes in an anoxic atmosphere with varying pH in the presence of either Fe2+ or Mg2+. Populations evolved under these different conditions are dominated by different sequences and secondary structures, demonstrating global differences in the underlying fitness landscapes. Comparisons between evolutionary outcomes and catalytic activities also indicate that Mg2+ can readily take the place of Fe2+ in supporting the catalysis of RNA cleavage at neutral pH, but not at lower pH. These results highlight the importance of considering the specific environments in which functional biopolymers evolve when evaluating their potential roles in the origin of life, extant biology, or biotechnology. PMID:26130717

  15. Subsurface connection methods for subsurface heaters

    DOEpatents

    Vinegar, Harold J.; Bass, Ronald Marshall; Kim, Dong Sub; Mason, Stanley Leroy; Stegemeier, George Leo; Keltner, Thomas Joseph; Carl, Jr., Frederick Gordon

    2010-12-28

    A system for heating a subsurface formation is described. The system includes a first elongated heater in a first opening in the formation. The first elongated heater includes an exposed metal section in a portion of the first opening. The portion is below a layer of the formation to be heated. The exposed metal section is exposed to the formation. A second elongated heater is in a second opening in the formation. The second opening connects to the first opening at or near the portion of the first opening below the layer to be heated. At least a portion of an exposed metal section of the second elongated heater is electrically coupled to at least a portion of the exposed metal section of the first elongated heater in the portion of the first opening below the layer to be heated.

  16. 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.

  17. Wave-Based Subsurface Guide Star

    SciTech Connect

    Lehman, S K

    2011-07-26

    Astronomical or optical guide stars are either natural or artificial point sources located above the Earth's atmosphere. When imaged from ground-based telescopes, they are distorted by atmospheric effects. Knowing the guide star is a point source, the atmospheric distortions may be estimated and, deconvolved or mitigated in subsequent imagery. Extending the guide star concept to wave-based measurement systems to include acoustic, seismo-acoustic, ultrasonic, and radar, a strong artificial scatterer (either acoustic or electromagnetic) may be buried or inserted, or a pre-existing or natural sub-surface point scatterer may be identified, imaged, and used as a guide star to determine properties of the sub-surface volume. That is, a data collection is performed on the guide star and the sub-surface environment reconstructed or imaged using an optimizer assuming the guide star is a point scatterer. The optimization parameters are the transceiver height and bulk sub-surface background refractive index. Once identified, the refractive index may be used in subsequent reconstructions of sub-surface measurements. The wave-base guide star description presented in this document is for a multimonostatic ground penetrating radar (GPR) but is applicable to acoustic, seismo-acoustic, and ultrasonic measurement systems operating in multimonostatic, multistatic, multibistatic, etc., modes.

  18. Quantifying Silica Reactivity in Subsurface Environments: Reaction Affinity and Solute Matrix Controls on Quartz and SiO2 Glass Dissolution Kinetics

    SciTech Connect

    Patricia M. Dove

    2000-12-13

    During the three years of this project, Professor Dove's laboratory made tremendous progress in understanding controls on amorphous silica dissolution kinetics in aqueous solutions. Our findings have already received considerable attention. In hydrothermal and low temperature studies, the work focused on determining quantitative and mechanistic controls on the most abundant silica polymorphs in Earth environments--quartz and amorphous silica. Our studies achieved goals set forth in the original proposal to establish a new quantitative understanding of amorphous silica dissolution. This support has resulted in 10 journal, 12 abstracts and 2 thesis publications. The PI and students were also recognized with 6 awards during this period. The 1998 EMSP conference in Chicago was an important meeting for our project. The symposium, enabled P.I. Dove to establish valuable contacts with ''users'' having specific needs for the findings of our EMSP project related to the urgency of problems in the Tanks Focus Area (TFA). Since that time, our working relations developed as Dove interacted with TFA scientists and engineers on the problems of waste glass properties. These interactions refined our experimental objectives to better meet their needs. Dove presented the results of EMSP research findings to a TFA subgroup at a Product Acceptance Workshop held in Salt Lake City during December 1998. The travel costs to attend this unanticipated opportunity were paid from EMSP project funds. In January 2000, Dove also attended a similar meeting in Atlanta with PNNL, SRL and BNF scientists/engineers to discuss new issues and make another level of decisions on the Product Acceptance goals. Our EMSP-funded research interfaced very well with the ongoing studies of Dr. Pete McGrail and colleagues in the Applied Geochemistry Group at PNNL. The value of our work to ''users'' was further demonstrated when Dove's EMSP-funded Postdoc, Dr. Jonathan Icenhower was hired by the same PNNL group. With

  19. Bacterial Diversity, Sediment Age and Organic Respiration in the Marine Sedimentary Environment

    NASA Astrophysics Data System (ADS)

    Walsh, E. A.; Kirkpatrick, J. B.; Pockalny, R. A.; Sauvage, J.; Sogin, M. L.; D'Hondt, S.

    2014-12-01

    Subseafloor sediment hosts to a large1, taxonomically rich2 and metabolically diverse3 microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show that subseafloor bacterial richness varies directly with sediment age and net rate of organic-fueled respiration. We examined three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), with sediment depths to 404 meters below seafloor. At all locations, taxonomic richness decreases exponentially with increasing sediment age. Richness declines most rapidly for a few hundred thousand years after sediment deposition. This profile generally matches the canonical relationship between rates of organic oxidation and sediment age 4. To examine the potential link between organic oxidation and taxonomic richness we used pore-water chemical profiles to quantify net rates of organic respiration at the three open-ocean sites (the chemical profiles of the ocean-margin site are not in diffusive steady state). Taxonomic richness and total rate of organic-fueled respiration are highest at the high productivity Bering Sea site and lower at the moderate productivity equatorial Pacific sites. At each of these sites, organic-fueled respiration rate and taxonomic richness are highest at the surface and decline together as sediment depth and age increase. To our knowledge, this is the first evidence that taxonomic richness is closely linked to organic-fueled respiration rate and sediment age in subseafloor sediment. References1. Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C. & D'Hondt, S. Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1203849109 (2012). 2. Inagaki, F. et al. Proceedings of the National Academy of Sciences 103, 2815-2820 (2006). 3. D'Hondt, S. et al. Science 306, 2216-2221, doi:10.1126/science.1101155 (2004). 4. Middelburg, J. J. Geochimica et Cosmochimica Acta 53

  20. Fluxes of carbon dioxide and methane from diverse aquatic environments in an agricultural landscape

    NASA Astrophysics Data System (ADS)

    Stanley, E. H.; Crawford, J. T.; Loken, L. C.; Casson, N. J.; Gubbins, N. J.; Oliver, S. K.

    2014-12-01

    The contribution of aquatic environments to landscape carbon cycling is particularly apparent in carbon- and water-rich regions. Such areas arguably represent an end member in terms of the relative significance of aquatic carbon cycling, while dry, carbon-poor zones are the likely opposing end member. Not surprisingly, most limnological attention has focused on these former regions, leaving open questions as to how aquatic systems in other locales influence larger-scale carbon dynamics. This includes human-dominated landscapes where agricultural and urban land uses can fundamentally alter carbon dynamics. Surveys of streams, ponds, and lakes in a southern Wisconsin landscape highlight three findings relevant to understanding the role of these aquatic systems in larger-scale carbon dynamics. First, streams and ponds had unexpectedly high summertime concentrations in and fluxes of CO2 and CH4. These values were approximately an order of magnitude greater than for less disturbed, forest and wetland-dominated landscapes in northern Wisconsin. Second, while mean C gas concentrations in lakes were lower than in streams and ponds, detailed spatial measurements demonstrate variability in surface water CO2 (43-1090 ppm pCO2) and CH4 (6-839 ppm pCH4) within a lake on a single day is similar to that observed among 25 streams included in our survey (260-6000 ppm pCO2; 50-600 ppm pCH4). This small-scale heterogeneity highlights a basic challenge for upscaling site-specific data collected at one or a few points to the whole lake and across lakes. Third, while agricultural and urban ecosystems are not necessarily carbon-rich environments, area-specific carbon storage in streams and ponds is substantial (up to 3000-5000 g C per m2). Further, carbon storage was strongly related to CH4 concentrations in streams, as C-rich sediments provided both an environment and substrate to fuel methanogenesis. The picture that emerges of C processing in aquatic environments throughout this human

  1. Amplification of Diverse Catalytic Properties of Evolving Molecules in a Simulated Hydrothermal Environment

    NASA Astrophysics Data System (ADS)

    Yokoyama, Shinnosuke; Koyama, Akihiro; Nemoto, Atsushi; Honda, Hajime; Imai, Ei-Ichi; Hatori, Kuniyuki; Matsuno, Koichiro

    2003-12-01

    We observed chemical evolution in a mixture of four amino acids, glycine, L-alanine, L-valine and L-aspartic acid, circulated through a flow reactor simulating the thermodynamic conditions of a hydrothermal environment. These monomers form peptides with tertiary structures and potential catalytic functions. The HPLC profile of synthesized oligomers varied with each particular run, but the products were found to separate into distinct clusters when more than one hundred runs were compared statistically. This observation suggests that chemical evolution on the early Earth had stochastic aspects that must be understood in order to develop useful models of prebiotic evolution.

  2. 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.

  3. Resistome diversity in cattle and the environment decreases during beef production

    PubMed Central

    Noyes, Noelle R; Yang, Xiang; Linke, Lyndsey M; Magnuson, Roberta J; Dettenwanger, Adam; Cook, Shaun; Geornaras, Ifigenia; Woerner, Dale E; Gow, Sheryl P; McAllister, Tim A; Yang, Hua; Ruiz, Jaime; Jones, Kenneth L; Boucher, Christina A; Morley, Paul S; Belk, Keith E

    2016-01-01

    Antimicrobial resistant determinants (ARDs) can be transmitted from livestock systems through meat products or environmental effluents. The public health risk posed by these two routes is not well understood, particularly in non-pathogenic bacteria. We collected pooled samples from 8 groups of 1741 commercial cattle as they moved through the process of beef production from feedlot entry through slaughter. We recorded antimicrobial drug exposures and interrogated the resistome at points in production when management procedures could potentially influence ARD abundance and/or transmission. Over 300 unique ARDs were identified. Resistome diversity decreased while cattle were in the feedlot, indicating selective pressure. ARDs were not identified in beef products, suggesting that slaughter interventions may reduce the risk of transmission of ARDs to beef consumers. This report highlights the utility and limitations of metagenomics for assessing public health risks regarding antimicrobial resistance, and demonstrates that environmental pathways may represent a greater risk than the food supply. DOI: http://dx.doi.org/10.7554/eLife.13195.001 PMID:26952213

  4. Bark functional ecology: evidence for tradeoffs, functional coordination, and environment producing bark diversity.

    PubMed

    Rosell, Julieta A; Gleason, Sean; Méndez-Alonzo, Rodrigo; Chang, Yvonne; Westoby, Mark

    2014-01-01

    The causes underlying bark diversity are unclear. Variation has been frequently attributed to environmental differences across sites. However, variation may also result from tradeoffs and coordination between bark's multiple functions. Bark traits may also covary with wood and leaf traits as part of major dimensions of plant variation. To assess hypotheses regarding tradeoffs and functional coordination, we measured bark traits reflecting protection, storage, mechanics, and photosynthesis in branches of 90 species spanning a wide phylogenetic and environmental range. We also tested associations between bark, wood, and leaf traits. We partitioned trait variation within species, and within and across communities to quantify variation associated with across-site differences. We observed associations between bark mechanics and storage, density and thickness, and thickness and photosynthetic activity. Increasing bark thickness contributed significantly to stiffer stems and greater water storage. Bark density, water content, and mechanics covaried strongly with the equivalent wood traits, and to a lesser degree with leaf size, xylem conductivity, and vessel diameter. Most variation was observed within sites and had low phylogenetic signal. Compared with relatively minor across-site differences, tradeoffs and coordination among functions of bark, leaves, and wood are likely to be major and overlooked factors shaping bark ecology and evolution.

  5. A study of diverse clinical decision support rule authoring environments and requirements for integration

    PubMed Central

    2012-01-01

    Background Efficient rule authoring tools are critical to allow clinical Knowledge Engineers (KEs), Software Engineers (SEs), and Subject Matter Experts (SMEs) to convert medical knowledge into machine executable clinical decision support rules. The goal of this analysis was to identify the critical success factors and challenges of a fully functioning Rule Authoring Environment (RAE) in order to define requirements for a scalable, comprehensive tool to manage enterprise level rules. Methods The authors evaluated RAEs in active use across Partners Healthcare, including enterprise wide, ambulatory only, and system specific tools, with a focus on rule editors for reminder and medication rules. We conducted meetings with users of these RAEs to discuss their general experience and perceived advantages and limitations of these tools. Results While the overall rule authoring process is similar across the 10 separate RAEs, the system capabilities and architecture vary widely. Most current RAEs limit the ability of the clinical decision support (CDS) interventions to be standardized, sharable, interoperable, and extensible. No existing system meets all requirements defined by knowledge management users. Conclusions A successful, scalable, integrated rule authoring environment will need to support a number of key requirements and functions in the areas of knowledge representation, metadata, terminology, authoring collaboration, user interface, integration with electronic health record (EHR) systems, testing, and reporting. PMID:23145874

  6. Diversity of Leptospira spp. in Rats and Environment from Urban Areas of Sarawak, Malaysia

    PubMed Central

    Pui, Chai Fung; Apun, Kasing; Su'ut, Lela

    2017-01-01

    Various prevalence studies on Leptospira in animals and humans, as well as environmental samples, had been conducted worldwide, including Malaysia. However, limited studies have been documented on the presence of pathogenic, intermediate, and saprophytic Leptospira in selected animals and environments. This study was therefore conducted to detect Leptospira spp. in rats, soil, and water from urban areas of Sarawak using the polymerase chain reaction (PCR) method. A total of 107 rats, 292 soil samples, and 324 water samples were collected from April 2014 to February 2015. Pathogenic Leptospira was present in 5.6% (6/107) of rats, 11.6% (34/292) of soil samples, and 1.9% (6/324) of water samples. Intermediate Leptospira was present in 2.7% (8/292) of soil samples and 1.9% (6/324) of water samples. Saprophytic Leptospira was present in 10.3% (11/107) of rats, 1.4% (4/292) of soil samples, and 0.3% (1/324) of water samples. From this study, 76 Leptospira spp. were isolated. Based on DNA sequencing, the dominant Leptospira spp. circulating in urban areas of Sarawak are pathogenic Leptospira noguchii, intermediate Leptospira wolffii serovar Khorat, and saprophytic Leptospira meyeri, respectively. Overall, this study provided important surveillance data on the prevalence of Leptospira spp. from rats and the environment, with dominant local serovars in urban areas of Sarawak. PMID:28348601

  7. Virtual Environments, Online Racial Discrimination, and Adjustment among a Diverse, School-Based Sample of Adolescents

    PubMed Central

    Tynes, Brendesha M.; Rose, Chad A.; Hiss, Sophia; Umaña-Taylor, Adriana J.; Mitchell, Kimberly; Williams, David

    2015-01-01

    Given the recent rise in online hate activity and the increased amount of time adolescents spend with media, more research is needed on their experiences with racial discrimination in virtual environments. This cross-sectional study examines the association between amount of time spent online, traditional and online racial discrimination and adolescent adjustment, including depressive symptoms, anxiety and externalizing behaviors. The study also explores the role that social identities, including race and gender, play in these associations. Online surveys were administered to 627 sixth through twelfth graders in K-8, middle and high schools. Multiple regression results revealed that discrimination online was associated with all three outcome variables. Additionally, a significant interaction between online discrimination by time online was found for externalizing behaviors indicating that increased time online and higher levels of online discrimination are associated with more problem behavior. This study highlights the need for clinicians, educational professionals and researchers to attend to race-related experiences online as well as in traditional environments. PMID:27134698

  8. The rule for a subdiffusive particle in an extremely diverse environment

    NASA Astrophysics Data System (ADS)

    Flomenbom, Ophir

    2009-04-01

    We consider a subdiffusive continuous time random walker in an inhomogeneous environment. Each microscopic random time is drawn from a waiting time probability density function (WT-PDF) of the form: φ(t;k)∼k/(1, 0<β⩽1. The parameter k is a random quantity also, and is drawn from a PDF, p(k)={1-γk˜(, 0⩽γ<1, for a cutoff parameter k˜. We show that the effective WT-PDF, ψ(t), obtained by averaging φ(t;k) with p(k), exhibits a transition in the rule that governs the power of ψ(t). ψ(t) obeys, ψ(t)∼1/t, and μ is given by two different formula. When, 1-γ>β, μ=β, but otherwise, μ=1-γ. The rule for the scaling of ψ(t) reflects the competition between two different mechanisms for subdiffusion: subdiffusion due to the heavily tailed φ(t;k) for individual jumps, and subdiffusion due to the collective effect of an environment made of many slow local regions. These two different mechanisms for subdiffusion are not additive, and compete each other. The reported transition is dimension independent, and disappears when the power β is also distributed, in the range, 0<β⩽1. Simulations exemplified the transition, and implications are discussed.

  9. Bioprospecting thermotolerant ethanologenic yeasts for simultaneous saccharification and fermentation from diverse environments.

    PubMed

    Choudhary, Jairam; Singh, Surender; Nain, Lata

    2017-03-01

    Lignocellulosic biomass, a promising renewable energy source, can be used for the production of second generation bioethanol. Simultaneous saccharification and fermentation (SSF), the process which alleviates the problem of separate hydrolysis and fermentation (SHF), requires thermotolerant ethanologenic yeast for bioethanol production. Therefore, ten yeast strains isolated from diverse sources, belonging to various genera like Saccharomyces, Candida, Pichia and Wickerhamomyces were evaluated for their thermotolerance, sugar utilization pattern, inhibitor tolerance and ethanol production potential with glucose, xylose and alkali pretreated paddy straw. All the tested strains were found to be thermotolerant, capable of significant growth at 40°C. Candida tropicalis Y6 was capable of utilizing a wide range of sugars as compared with other yeast isolates. Strains of Candida showed better inhibitor tolerance as compared to Saccharomyces and Pichia strains and exhibited only 5.1-18.8% and 4.7-7.9% reduction in growth with furfural and 5-hydroxymethyl furfural, respectively. Saccharomyces cerevisiae JRC6, isolated from distillery waste, produced ethanol with 88.3% and 89.1% theoretical efficiency at 40°C and 42°C, respectively, from glucose. This strain also produced significantly higher amount of ethanol (3.8 g/L) with better fermentation efficiency (87.9%) from alkali pretreated paddy straw at 40°C, as compared with the other yeast strains. Therefore, S. cerevisiae JRC6, based on its ability to ferment sugars at a higher temperature, can be a promising candidate for production of ethanol from lignocellulosic biomass via SSF process.

  10. [Escherichia coli: diversity of biochemical phenotypes in aquatic environments (Santa, Fe, Argentina)].

    PubMed

    Emiliani, F; Lajmanovich, R; González, S M

    2001-01-01

    During certain environmental conditions, the floating aquatic vegetation, mainly represented by Eichhornia crassipes (water hyacinth) invade and even cover water courses assigned to recreational activities or to the supply of drinkable water. The rhizosphere of these plants constitutes an unknown biotope of bacteria of sanitary interest, possibly different from waters without vegetation and of the sediment of the same aquatic system. To verify such possibility, 206 isolated strains in MacConkey Agar (Difco) were typified and identified (78 from water, 65 from sediment and 63 from rhizosphere) using the API 20 E system (v. 4.0) and Apilab plus software (v 3.3.3), both of bioMérieux (Marcy-l'Etoile, France, 1998). Nineteen different biochemical phenotypes from E. coli were found. The 79% of the population belonged to only 7 phenotypes; the 21% remaining, to the other 12 phenotypes. Twelve phenotypes did not share the biotopes, while only 4 were in the three. These results (and those obtained by other authors who used the API 20 E system in other biotopes) suggest that it would be possible to characterize the rhizosphere using those phenotypes that are found in smaller proportion. The greatest index of diversity (H) and evenness (E) were found in the rhizosphere (H = 2.903; E = 0.874). The dendrogram (average distances and UPGMA method) reaffirms the dissimilarity in biochemical phenotypes of E. coli populations of the rhizosphere with regard to the other biotopes. The most abundant bacterial species in the three biotopes were E. coli, Klebsiella terrigena and K. pneumoniae, corresponding to 75.2% of the community. The rhizosphere differed from Serratia odorifera and from Klebsiella spp. because of its higher rate of isolation.

  11. Distribution and diversity of Verrucomicrobia methanotrophs in geothermal and acidic environments.

    PubMed

    Sharp, Christine E; Smirnova, Angela V; Graham, Jaime M; Stott, Matthew B; Khadka, Roshan; Moore, Tim R; Grasby, Stephen E; Strack, Maria; Dunfield, Peter F

    2014-06-01

    Recently, methanotrophic members of the phylum Verrucomicrobia have been described, but little is known about their distribution in nature. We surveyed methanotrophic bacteria in geothermal springs and acidic wetlands via pyrosequencing of 16S rRNA gene amplicons. Putative methanotrophic Verrucomicrobia were found in samples covering a broad temperature range (22.5-81.6°C), but only in acidic conditions (pH 1.8-5.0) and only in geothermal environments, not in acidic bogs or fens. Phylogenetically, three 16S rRNA gene sequence clusters of putative methanotrophic Verrucomicrobia were observed. Those detected in high-temperature geothermal samples (44.1-81.6°C) grouped with known thermoacidiphilic 'Methylacidiphilum' isolates. A second group dominated in moderate-temperature geothermal samples (22.5-40.1°C) and a representative mesophilic methanotroph from this group was isolated (strain LP2A). Genome sequencing verified that strain LP2A possessed particulate methane monooxygenase, but its 16S rRNA gene sequence identity to 'Methylacidiphilum infernorum' strain V4 was only 90.6%. A third group clustered distantly with known methanotrophic Verrucomicrobia. Using pmoA-gene targeted quantitative polymerase chain reaction, two geothermal soil profiles showed a dominance of LP2A-like pmoA sequences in the cooler surface layers and 'Methylacidiphilum'-like pmoA sequences in deeper, hotter layers. Based on these results, there appears to be a thermophilic group and a mesophilic group of methanotrophic Verrucomicrobia. However, both were detected only in acidic geothermal environments.

  12. Lateral gene transfer in the subsurface

    SciTech Connect

    Barkay, Tamar; Sobecky, Patricia

    2007-08-27

    Lateral gene transfer (LGT) is an important adaptive mechanism among prokaryotic organisms. This mechanism is particularly important for the response of microorganisms to changing environmental conditions because it facilitates the transfer of a large number of genes and their rapid expression. Together the transferred genes promote rapid genetic and metabolic changes that may enhance survival to newly established and sometimes hostile environmental conditions. The goal of our project was to examine if and how LGT enhances microbial adaptation to toxic heavy metals in subsurface environments that had been contaminated by mixed wastes due to activities associated with the production of nuclear energy and weapons. This task has been accomplished by dividing the project to several sub-tasks. Thus, we: (1) Determined the level of resistance of subsurface bacterial isolates to several toxic metals, all identified as pollutants of concern in subsurface environments; (2) Designed, tested, and applied, a molecular approach that determined whether metal resistance genes had evolved by LGT among subsurface bacteria; and (3) Developed a DNA hybridization array for the identification of broad host range plasmids and of metal resistance plasmids. The results are briefly summarized below with references to published papers and manuscripts in preparation where details about our research can be found. Additional information may be found in copies of our published manuscripts and conference proceedings, and our yearly reports that were submitted through the RIMS system.

  13. The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park.

    PubMed

    Jay, Zackary J; Beam, Jacob P; Kozubal, Mark A; Jennings, Ryan deM; Rusch, Douglas B; Inskeep, William P

    2016-12-01

    High-temperature environments (> 70°C) contain diverse and abundant members of the crenarchaeal order Thermoproteales. However, a comprehensive study of the distribution and function of diverse members of this group across different habitat types has not been conducted. Consequently, the goals of this study were to determine the distribution of different Thermoproteales genera across geochemically distinct geothermal habitats of Yellowstone National Park, and to identify key functional attributes of major genera that correlate with environmental parameters. Curated sequence assemblies belonging to five genera were characterized in replicate samples of 11 high-temperature communities ranging in pH from 3 to 9. Thermocladium, Vulcanisaeta and Caldivirga spp. were the primary Thermoproteales populations present in low pH (pH < 5) habitats, whereas Thermoproteus populations were found in mildly-acidic (pH 5-6) sulfur sediments, and Pyrobaculum populations were confined to higher pH (pH > 6) sulfur sediments and/or filamentous 'streamer' communities. Metabolic reconstruction and comparative genomics among assemblies show that these populations are primarily chemoorganotrophs that utilize different electron acceptors depending on geochemical conditions. The presence of potential CO2 fixation pathways in some Thermoproteales populations appears to be linked with NiFe hydrogenases, which combined with high levels of H2 in many sulfidic systems, may provide the energy required to fix inorganic C.

  14. Air Quality Impacts of Atmospheric Particles & Trace Gases: Field Studies in Diverse Environments

    NASA Astrophysics Data System (ADS)

    Mwaniki, George R.

    Air pollution impacts occur at all scales, meaning that policies and air quality management practices must be implemented and coordinated at the local, regional, national, and global scales. This dissertation is part of a continuing effort to improve our understanding of various air quality related issues in different environments. The dissertation consists of four studies. In the first study, wintertime chemical composition of water-soluble particulate matter with aerodynamic diameter less than 2.5 microm (PM2.5) was monitored in the Treasure Valley region near Boise, Idaho. This study was aimed at understanding the major drivers of wintertime PM2.5 within the locality of Boise and its suburbs. From this study, organics and particulate nitrate were the dominant contributors to the PM2.5 mass during wintertime. In the second study, particle size distribution, light scattering coefficient, speciated water soluble PM2.5, and cloud condensation nuclei (CCN) concentration were monitored in a mixed deciduous forest in Northern Michigan during the Community Atmosphere-Biosphere Interactions Experiment (CABINEX-2009). The overall goal of this study was to understand on how emissions of biogenic volatile organic compounds (BVOC) affect the gas-phase and particle-phase chemistry in the near-canopy environment, and the implications on local and regional air quality. From this study aerosol derived from the oxidation of BVOCs exhibited reduced hygroscopicity and CCN activation potential compared to aerosols derived from anthropogenic activities. The third study employed the eddy covariance (EC) technique to understand source-sink interactions of carbon dioxide (CO2), methane (CH 4), carbon monoxide (CO) and nitrous oxide (N2O) in Xi'an, China. In this study urban vegetation were found to play a major role in regulating CO2 emissions within the city while vehicular activities were a major driver for CO and CH4 fluxes. In the fourth study, visibility degradation effects of

  15. High Prevalence, Genetic Diversity and Intracellular Growth Ability of Legionella in Hot Spring Environments

    PubMed Central

    Zhou, Haijian; Wang, Huanxin; Xu, Ying; Zhao, Mingqiang; Guan, Hong; Li, Machao; Shao, Zhujun

    2013-01-01

    Background Legionella is the causative agent of Legionnaires' disease, and hot springs are a major source of outbreaks of this disease. It is important from a public health perspective to survey hot spring environments for the presence of Legionella. Methods Prospective surveillance of the extent of Legionella pollution was conducted at three hot spring recreational areas in Beijing, China in 2011. Pulsed-field gel electrophoresis (PFGE) and sequence-based typing (SBT) were used to describe the genetic polymorphism of isolates. The intracellular growth ability of the isolates was determined by interacting with J774 cells and plating the dilutions onto BCYE agar plates. Results Overall, 51.9% of spring water samples showed Legionella-positive, and their concentrations ranged from 1 CFU/liter to 2,218 CFU/liter. The positive rates of Legionella were significantly associated with a free chlorine concentration of ≥0.2 mg/L, urea concentration of ≥0.05 mg/L, total microbial counts of ≥400 CFU/ml and total coliform of ≥3 MPN/L (p<0.01). The Legionella concentrations were significantly associated with sample temperature, pH, total microbial counts and total coliform (p<0.01). Legionella pneumophila was the most frequently isolated species (98.9%), and the isolated serogroups included serogroups 3 (25.3%), 6 (23.4%), 5 (19.2%), 1 (18.5%), 2 (10.2%), 8 (0.4%), 10 (0.8%), 9 (1.9%) and 12 (0.4%). Two hundred and twenty-eight isolates were analyzed by PFGE and 62 different patterns were obtained. Fifty-seven L. pneumophila isolates were selected for SBT analysis and divided into 35 different sequence types with 5 main clonal groups. All the 57 isolates had high intracellular growth ability. Conclusions Our results demonstrated high prevalence and genetic polymorphism of Legionella in springs in Beijing, China, and the SBT and intracellular growth assay results suggested that the Legionella isolates of hot spring environments were pathogenic. Improved control and

  16. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation

    PubMed Central

    Honigberg, Saul M.

    2016-01-01

    Diploid budding yeast (Saccharomyces cerevisiae) can adopt one of several alternative differentiation fates in response to nutrient limitation, and each of these fates provides distinct biological functions. When different strain backgrounds are taken into account, these various fates occur in response to similar environmental cues, are regulated by the same signal transduction pathways, and share many of the same master regulators. I propose that the relationships between fate choice, environmental cues and signaling pathways are not Boolean, but involve graded levels of signals, pathway activation and master-regulator activity. In the absence of large differences between environmental cues, small differences in the concentration of cues may be reinforced by cell-to-cell signals. These signals are particularly essential for fate determination within communities, such as colonies and biofilms, where fate choice varies dramatically from one region of the community to another. The lack of Boolean relationships between cues, signaling pathways, master regulators and cell fates may allow yeast communities to respond appropriately to the wide range of environments they encounter in nature. PMID:27917388

  17. Effects of environment and genotype on phenolic acids in wheat in the HEALTHGRAIN diversity screen.

    PubMed

    Fernandez-Orozco, Rebeca; Li, Li; Harflett, Claudia; Shewry, Peter R; Ward, Jane L

    2010-09-08

    Phenolic acid content and composition have been determined in 26 wheat genotypes grown in Hungary over three consecutive years and at three additional locations (France, United Kingdom, and Poland) during the third year. Fractions comprising free, soluble conjugated, and bound phenolic acids were analyzed using HPLC with measurements being made for individual phenolic acids in each fraction. Statistically significant differences in phenolic acid content occurred across the different growing locations with the average total phenolic acid content being highest in the genotypes grown in Hungary. The growth year in Hungary also had a large impact, especially on the free and conjugated phenolic acid contents. Certain genotypes were more resistant to environmental impacts than others. Of the genotypes with high levels of total phenolic acids, Lynx, Riband, Tommi, and Cadenza were most stable with respect to their total contents, whereas Valoris, Herzog, and Malacca, also high in phenolic acid content, were least stable. Of the three fractions analyzed, the free and conjugated phenolic acids were most variable and were also susceptible to the effect of environment, whereas bound phenolic acids, which comprised the greatest proportion of the total phenolic acids, were the most stable.

  18. Toward Lower Organic Environments in Astromaterial Sample Curation for Diverse Collections

    NASA Technical Reports Server (NTRS)

    Allton, J. H.; Allen, C. C.; Burkett, P. J.; Calaway, M. J.; Oehler, D. Z.

    2012-01-01

    Great interest was taken during the frenzied pace of the Apollo lunar sample return to achieve and monitor organic cleanliness. Yet, the first mission resulted in higher organic contamination to samples than desired. But improvements were accomplished by Apollo 12 [1]. Quarantine complicated the goal of achieving organic cleanliness by requiring negative pressure glovebox containment environments, proximity of animal, plant and microbial organic sources, and use of organic sterilants in protocols. A special low organic laboratory was set up at University of California Berkeley (UCB) to cleanly subdivide a subset of samples [2, 3, 4]. Nevertheless, the basic approach of handling rocks and regolith inside of a positive pressure stainless steel glovebox and restrict-ing the tool and container materials allowed in the gloveboxes was established by the last Apollo sample re-turn. In the last 40 years, the collections have grown to encompass Antarctic meteorites, Cosmic Dust, Genesis solar wind, Stardust comet grains and Hayabusa asteroid grains. Each of these collections have unique curation requirements for organic contamination monitor-ing and control. Here is described some changes allowed by improved technology or driven by changes in environmental regulations and economy, concluding with comments on organic witness wafers. Future sample return missions (OSIRIS-Rex; Mars; comets) will require extremely low levels of organic contamination in spacecraft collection and thus similarly low levels in curation. JSC Curation is undertaking a program to document organic baseline levels in current operations and devise ways to reduce those levels.

  19. 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.

  20. Subsurface contaminants focus area

    SciTech Connect

    1996-08-01

    The US Department of Enregy (DOE) Subsurface Contaminants Focus Area is developing technologies to address environmental problems associated with hazardous and radioactive contaminants in soil and groundwater that exist throughout the DOE complex, including radionuclides, heavy metals; and dense non-aqueous phase liquids (DNAPLs). More than 5,700 known DOE groundwater plumes have contaminated over 600 billion gallons of water and 200 million cubic meters of soil. Migration of these plumes threatens local and regional water sources, and in some cases has already adversely impacted off-site rsources. In addition, the Subsurface Contaminants Focus Area is responsible for supplying technologies for the remediation of numerous landfills at DOE facilities. These landfills are estimated to contain over 3 million cubic meters of radioactive and hazardous buried Technology developed within this specialty area will provide efective methods to contain contaminant plumes and new or alternative technologies for development of in situ technologies to minimize waste disposal costs and potential worker exposure by treating plumes in place. While addressing contaminant plumes emanating from DOE landfills, the Subsurface Contaminants Focus Area is also working to develop new or alternative technologies for the in situ stabilization, and nonintrusive characterization of these disposal sites.

  1. The biochemical diversity of life near and above 100°C in marine environments.

    PubMed

    Adams, M W

    1998-12-01

    Hyperthermophilic micro-organisms grow at temperatures above 90 °C with a current upper limit of 113 °C. They are a recent discovery in the microbial world and have been isolated mainly from marine geothermal environments, which include both shallow and deep sea hydrothermal vents. By 16S rRNA analyses they are the most slowly evolving of all extant life forms, and all but two of the nearly 20 known genera are classified as Archaea (formerly Archaebacteria). Almost all hyperthermophiles are strict anaerobes. They include species of methanogens, iron-oxidizers and sulphate reducers, but the majority are obligate heterotrophs that depend upon the reduction of elemental sulphur (S°) to hydrogen sulphide for significant growth. The heterotrophs utilize proteinaceous materials as carbon and energy sources, although a few species are also saccharolytic. A scheme for electron flow during the oxidation of carbohydrates and peptides and the reduction of S° has been proposed. Two S°-reducing enzymes have been purified from the cytoplasm of one hyperthermophile (T(opt) 100 °C) that is able to grow either with and without S°. However, the mechanisms by which S° reduction is coupled to energy conservation in this organism and in obligate S°-reducing hyperthermophiles is not known. In the heterotrophs, sugar fermentation is achieved by a novel glycolytic pathway involving unusual ADP-dependent kinases and ATP synthetases, and novel oxidoreductases that are ferredoxin- rather than NAD(P)-linked. Similarly, peptide fermentation involves several unusual ferredoxin-linked oxidoreductases not found in mesophilic organisms. Several of these oxido-reductases contain tungsten, an element that is rarely used in biological systems. Tungsten is present in exceedingly low concentrations in normal sea water, but hydrothermal systems contain much higher tungsten concentrations, more than sufficient to support hyperthermophilic life.

  2. Denitrifying bacteria from the terrestrial subsurface exposed to mixed waste contamination

    SciTech Connect

    Green, Stefan; Prakash, Om; Gihring, Thomas; Akob, Denise M.; Jasrotia, Puja; Jardine, Philip M; Watson, David B; Brown, Steven D; Palumbo, Anthony Vito; Kostka, Joel

    2010-01-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available with which to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy s Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria) and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were confirmed as complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. Ribosomal RNA gene analyses reveal that bacteria from the genus Rhodanobacter comprise a diverse population of circumneutral to moderately acidophilic denitrifiers at the ORIFRC site, with a high relative abundance in areas of the acidic source zone. Rhodanobacter species do not contain a periplasmic nitrite reductase and have not been previously detected in functional gene surveys of denitrifying bacteria at the OR-IFRC site. Sequences of nitrite and nitrous oxide reductase genes were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation, genomic and metagenomic data are essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifying microorganisms. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

  3. Microbial Diversity in Maras Salterns, a Hypersaline Environment in the Peruvian Andes

    PubMed Central

    Maturrano, Lenin; Santos, Fernando; Rosselló-Mora, Ramon; Antón, Josefa

    2006-01-01

    Maras salterns are located 3,380 m above sea level in the Peruvian Andes. These salterns consist of more than 3,000 little ponds which are not interconnected and act as crystallizers where salt precipitates. These ponds are fed by hypersaline spring water rich in sodium and chloride. The microbiota inhabiting these salterns was examined by fluorescence in situ hybridization (FISH), 16S rRNA gene clone library analysis, and cultivation techniques. The total counts per milliliter in the ponds were around 2 × 106 to 3 × 106 cells/ml, while the spring water contained less than 100 cells/ml and did not yield any detectable FISH signal. The microbiota inhabiting the ponds was dominated (80 to 86% of the total counts) by Archaea, while Bacteria accounted for 10 to 13% of the 4′,6′-diamidino-2-phenylindole (DAPI) counts. A total of 239 16S rRNA gene clones were analyzed (132 Archaea clones and 107 Bacteria clones). According to the clone libraries, the archaeal assemblage was dominated by microorganisms related to the cosmopolitan square archaeon “Haloquadra walsbyi,” although a substantial number of the sequences in the libraries (31% of the 16S rRNA gene archaeal clones) were related to Halobacterium sp., which is not normally found in clone libraries from solar salterns. All the bacterial clones were closely related to each other and to the γ-proteobacterium “Pseudomonas halophila” DSM 3050. FISH analysis with a probe specific for this bacterial assemblage revealed that it accounted for 69 to 76% of the total bacterial counts detected with a Bacteria-specific probe. When pond water was used to inoculate solid media containing 25% total salts, both extremely halophilic Archaea and Bacteria were isolated. Archaeal isolates were not related to the isolates in clone libraries, although several bacterial isolates were very closely related to the “P. halophila” cluster found in the libraries. As observed for other hypersaline environments, extremely

  4. Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments.

    PubMed

    Sliwinski, Marek K; Goodman, Robert M

    2004-03-01

    To explore whether the crenarchaeal consortium found in the rhizosphere is distinct from the assemblage of crenarchaeotes inhabiting bulk soil, PCR-single-stranded-conformation polymorphism (PCR-SSCP) profiles were generated for 76 plant samples collected from native environments. Divergent terrestrial plant groups including bryophytes (mosses), lycopods (club mosses), pteridophytes (ferns), gymnosperms (conifers), and angiosperms (seed plants) were collected for this study. Statistical analysis revealed significant differences between rhizosphere and bulk soil PCR-SSCP profiles (Hotelling paired T(2) test, P < 0.0001), suggesting that a distinct crenarchaeal consortium is associated with plants. In general, phylotype richness increased in the rhizosphere compared to the corresponding bulk soil, although the range of this increase was variable. Examples of a major change in rhizosphere (versus bulk soil) PCR-SSCP profiles were detected for all plant groups, suggesting that crenarchaeotes form associations with phylogenetically diverse plants in native environments. In addition, examples of minor to no detectable difference were found for all terrestrial plant groups, suggesting that crenarchaeal associations with plants are mediated by environmental conditions.

  5. Comparison of Crenarchaeal Consortia Inhabiting the Rhizosphere of Diverse Terrestrial Plants with Those in Bulk Soil in Native Environments

    PubMed Central

    Sliwinski, Marek K.; Goodman, Robert M.

    2004-01-01

    To explore whether the crenarchaeal consortium found in the rhizosphere is distinct from the assemblage of crenarchaeotes inhabiting bulk soil, PCR-single-stranded-conformation polymorphism (PCR-SSCP) profiles were generated for 76 plant samples collected from native environments. Divergent terrestrial plant groups including bryophytes (mosses), lycopods (club mosses), pteridophytes (ferns), gymnosperms (conifers), and angiosperms (seed plants) were collected for this study. Statistical analysis revealed significant differences between rhizosphere and bulk soil PCR-SSCP profiles (Hotelling paired T2 test, P < 0.0001), suggesting that a distinct crenarchaeal consortium is associated with plants. In general, phylotype richness increased in the rhizosphere compared to the corresponding bulk soil, although the range of this increase was variable. Examples of a major change in rhizosphere (versus bulk soil) PCR-SSCP profiles were detected for all plant groups, suggesting that crenarchaeotes form associations with phylogenetically diverse plants in native environments. In addition, examples of minor to no detectable difference were found for all terrestrial plant groups, suggesting that crenarchaeal associations with plants are mediated by environmental conditions. PMID:15006809

  6. Microbial diversity and biogeochemistry in glacier forefields: assessment of ecological stability in high alpine environments

    NASA Astrophysics Data System (ADS)

    Meola, M.; Lazzaro, A.; Zeyer, J.

    2012-04-01

    Microbial communities inhabiting recently deglaciated, unvegetated, high alpine soils (e.g. glacier forefields) need to be adapted to fluctuating environmental conditions, such as strong daily and seasonal humidity and temperature variations. Soil-related characteristics (e.g. oligotrophy, pH, water holding capacity, nutrient concentration) may in addition determine the presence of locally adapted microbial communities. Currently little is known on the ecological stability (resistance and resilience) of such an environment. In this project, we aim at understanding ecological stability of microbial communities of alpine glacier forefields through a reciprocal soil transplantation experiment. The study consists in i) determining bacterial phylotypes that may respond to environmental changes and ii) relating biological, chemical and physical data to observed microbial responses. We selected two different glacier forefields located in the Swiss Alps (approximately at 2500 m.a.s.l.) The Griessen forefield (Canton Obwalden) is characterized by a calcareous bedrock, while the Tiefen forefield (Canton Uri) is of siliceous composition. The sites are well characterized in terms of their geography (e.g. exposure, slope) and climatic fluctuations (Lazzaro et al. 2009, Lazzaro et al. 2011). At each site, we incubated stainless steel pots with four different soil treatments (autochthonous untreated, autochthonous sterilized, allochthonous untreated and allochthonous sterilized). The setup was repeated in quadruplicate. Soil temperature and soil moisture at 10 cm depth were measured every hour by Decagon EM 50 sensors (Decagon Devices Inc.). In July (D0), August (D1) and September (D2) 2011, soil aliquots were sampled from the pots for analysis. We plan to further extend the sampling for at least three snow-free seasons (2011-2013). Chemical analysis of the soil encompassed soluble ions, pH and DOC. Bacterial community analysis included microbial biomass (DAPI cell counts), basal

  7. Sex and racial differences in preference for a caring morality in a corporate environment that promotes diversity and equal opportunity.

    PubMed

    Jones, Nona J

    2002-10-01

    This study investigated the caring moral perspective of managers in a corporation recognized as being a champion of promoting diversity and equal opportunity. Caring is described as a morality of responsibility and relationship, a sensitivity to the needs of persons. The study was based on the prediction that the attachment and caring shown elsewhere to be characteristic of the morality of females would be characteristic of all managers, regardless of sex or race in this kind of corporate environment. 121 male and female, African-American and Euro-American managers responded to a survey using three subscales of a Caring Morality Inventory: caring orientation, use of intuition and feeling to make a judgment, and concern with others in decision-making. Analysis showed female managers, regardless of race, scored significantly higher on the Caring Morality scale than the male managers, supporting other findings of sex differences in caring moral perspective and suggesting that working for a company actively promoting diversity and equal opportunity does not cancel out these differences. In addition, for this study it was assumed that, although African Americans, in general, may have been sensitized to lean more toward a caring morality, any racial differences in caring morality would be cancelled out by the fact that all of the managers work for the same prodiversity and, by assumption, more sensitive company. The Euro-American managers, regardless of sex, actually scored higher on the Caring Morality scale than did the African-American managers, with the difference being attributable solely to the greater tendency of the Euro-American managers to use intuition and feeling to make a judgment.

  8. 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

  9. Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments.

    PubMed

    Hamamura, N; Macur, R E; Korf, S; Ackerman, G; Taylor, W P; Kozubal, M; Reysenbach, A-L; Inskeep, W P

    2009-02-01

    The identification and characterization of genes involved in the microbial oxidation of arsenite will contribute to our understanding of factors controlling As cycling in natural systems. Towards this goal, we recently characterized the widespread occurrence of aerobic arsenite oxidase genes (aroA-like) from pure-culture bacterial isolates, soils, sediments and geothermal mats, but were unable to detect these genes in all geothermal systems where we have observed microbial arsenite oxidation. Consequently, the objectives of the current study were to measure arsenite-oxidation rates in geochemically diverse thermal habitats in Yellowstone National Park (YNP) ranging in pH from 2.6 to 8, and to identify corresponding 16S rRNA and aroA genotypes associated with these arsenite-oxidizing environments. Geochemical analyses, including measurement of arsenite-oxidation rates within geothermal outflow channels, were combined with 16S rRNA gene and aroA functional gene analysis using newly designed primers to capture previously undescribed aroA-like arsenite oxidase gene diversity. The majority of bacterial 16S rRNA gene sequences found in acidic (pH 2.6-3.6) Fe-oxyhydroxide microbial mats were closely related to Hydrogenobaculum spp. (members of the bacterial order Aquificales), while the predominant sequences from near-neutral (pH 6.2-8) springs were affiliated with other Aquificales including Sulfurihydrogenibium spp., Thermocrinis spp. and Hydrogenobacter spp., as well as members of the Deinococci, Thermodesulfobacteria and beta-Proteobacteria. Modified primers designed around previously characterized and newly identified aroA-like genes successfully amplified new lineages of aroA-like genes associated with members of the Aquificales across all geothermal systems examined. The expression of Aquificales aroA-like genes was also confirmed in situ, and the resultant cDNA sequences were consistent with aroA genotypes identified in the same environments. The aroA sequences

  10. Enhanced bioremediation of subsurface contamination: Enzyme recruitment and redesign

    SciTech Connect

    Brockman, F.J.; Ornstein, R.L.

    1991-12-01

    Subsurface systems containing radionuclide, heavy metal, and organic wastes must be carefully attended to avoid further impacts to the environment or exposures to human populations. It is appropriate, therefore, to invest in basic research to develop the requisite tools and methods for addressing complex cleanup problems. The rational modification of subsurface microoganisms by enzyme recruitment and enzyme design, in concert with engineered systems for delivery of microorganisms and nutrients to the contaminated zone, are potentially useful tools in the spectrum of approaches that will be required for successful remediation of deep subsurface contamination.

  11. Seasonal variations in the subsurface ultraviolet-B on an inshore Pacific coral reef ecosystem.

    PubMed

    Downs, Nathan J; Schouten, Peter W; Parisi, Alfio V

    2013-01-01

    Fringing coral reefs provide a unique opportunity to study shallow aquatic ecosystems. A fringing coral reef system located in close proximity to a developed region was considered in this study. In such an environment, the rate of decay of dissolved organic matter is high and the penetration of higher energy ultraviolet-B (UVB) extends a greater influence on species diversity, particularly upon shallow benthic communities. Results from a 9 month subsurface UVB exposure measurement campaign performed at a site located on the southern Queensland coast (Hervey Bay, 25°S) are presented in this research. For this, a novel dosimetric technique was utilized to measure long-term subsurface UVB exposures. The resultant data set includes exposure measurements made during the significant La Niña event of late 2010 which resulted in unprecedented high sea surface temperatures and severe flooding across eastern Australia, impacting upon the lagoon regions of the Great Barrier Reef and Queensland's southern estuaries, including the study site. The influence of season, diurnal tidal variation, cloud cover and solar zenith angle were analyzed over the campaign period. Mean minimum daylight water depth was found to be the most significant factor influencing subsurface UVB.

  12. 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.

  13. A Systems Engineering Framework for Implementing a Security and Critical Patch Management Process in Diverse Environments (Academic Departments' Workstations)

    NASA Astrophysics Data System (ADS)

    Mohammadi, Hadi

    Use of the Patch Vulnerability Management (PVM) process should be seriously considered for any networked computing system. The PVM process prevents the operating system (OS) and software applications from being attacked due to security vulnerabilities, which lead to system failures and critical data leakage. The purpose of this research is to create and design a Security and Critical Patch Management Process (SCPMP) framework based on Systems Engineering (SE) principles. This framework will assist Information Technology Department Staff (ITDS) to reduce IT operating time and costs and mitigate the risk of security and vulnerability attacks. Further, this study evaluates implementation of the SCPMP in the networked computing systems of an academic environment in order to: 1. Meet patch management requirements by applying SE principles. 2. Reduce the cost of IT operations and PVM cycles. 3. Improve the current PVM methodologies to prevent networked computing systems from becoming the targets of security vulnerability attacks. 4. Embed a Maintenance Optimization Tool (MOT) in the proposed framework. The MOT allows IT managers to make the most practicable choice of methods for deploying and installing released patches and vulnerability remediation. In recent years, there has been a variety of frameworks for security practices in every networked computing system to protect computer workstations from becoming compromised or vulnerable to security attacks, which can expose important information and critical data. I have developed a new mechanism for implementing PVM for maximizing security-vulnerability maintenance, protecting OS and software packages, and minimizing SCPMP cost. To increase computing system security in any diverse environment, particularly in academia, one must apply SCPMP. I propose an optimal maintenance policy that will allow ITDS to measure and estimate the variation of PVM cycles based on their department's requirements. My results demonstrate that

  14. Microbial Oxidation of Arsenite in a Subarctic Environment: Diversity of Arsenite Oxidase Genes and Identification of a Psychrotolerant Arsenite Oxidiser

    SciTech Connect

    Osborne, T.; Jamieson, H; Hudson-Edwards, K; Nordstrom, D; Walker, S; Ward, S; Santini, J

    2010-01-01

    Arsenic is toxic to most living cells. The two soluble inorganic forms of arsenic are arsenite (+3) and arsenate (+5), with arsenite the more toxic. Prokaryotic metabolism of arsenic has been reported in both thermal and moderate environments and has been shown to be involved in the redox cycling of arsenic. No arsenic metabolism (either dissimilatory arsenate reduction or arsenite oxidation) has ever been reported in cold environments (i.e. < 10 C). Our study site is located 512 kilometres south of the Arctic Circle in the Northwest Territories, Canada in an inactive gold mine which contains mine waste water in excess of 50 mM arsenic. Several thousand tonnes of arsenic trioxide dust are stored in underground chambers and microbial biofilms grow on the chamber walls below seepage points rich in arsenite-containing solutions. We compared the arsenite oxidisers in two subsamples (which differed in arsenite concentration) collected from one biofilm. 'Species' (sequence) richness did not differ between subsamples, but the relative importance of the three identifiable clades did. An arsenite-oxidizing bacterium (designated GM1) was isolated, and was shown to oxidise arsenite in the early exponential growth phase and to grow at a broad range of temperatures (4-25 C). Its arsenite oxidase was constitutively expressed and functioned over a broad temperature range. The diversity of arsenite oxidisers does not significantly differ from two subsamples of a microbial biofilm that vary in arsenite concentrations. GM1 is the first psychrotolerant arsenite oxidiser to be isolated with the ability to grow below 10 C. This ability to grow at low temperatures could be harnessed for arsenic bioremediation in moderate to cold climates.

  15. Molecular diversity of class 2 integrons in antibiotic-resistant gram-negative bacteria found in wastewater environments in China.

    PubMed

    Xia, Ruirui; Ren, Ye; Guo, Xianhu; Xu, Hai

    2013-03-01

    The molecular architecture of class 2 integrons among gram-negative bacteria from wastewater environments was investigated in Jinan, China. Out of the 391 antibiotic-resistant bacteria found, 38 isolates harboring class 2 integrons encoding potentially transferrable genes that could confer antibiotic resistance were found. These isolates were classified into 19 REP-PCR types. These strains were identified using 16S rRNA gene sequencing and found to be as follows: Proteus mirabilis (16), Escherichia coli (7), Providencia spp. (7), Proteus spp. (2), P. vulgaris (3), Shigella sp. (1), Citrobacter freundii (1), and Acinetobacter sp. (1). Their class 2 integron cassette arrays were amplified and then either analyzed using PCR-RFLP or sequenced. The typical array dfrA1-sat2-aadA1 was detected in 27 isolates. Six atypical arrays were observed, including three kinds of novel arrangements (linF2(∆attC1)-dfrA1(∆attC2)-aadA1-orf441 or linF2(∆attC1)-dfrA1(∆attC2)-aadA1, dfrA1-catB2-sat2-aadA1, and estX(Vr)-sat2-aadA1) and a hybrid with the 3'CS of class 1 integrons (dfrA1-sat2-aadA1-qacH), and dfrA1-sat1. Twenty-four isolates were also found to carry class 1 integrons with 10 types of gene cassette arrays. Several non-integron-associated antibiotic resistance genes were found, and their transferability was investigated. Results showed that water sources in the Jinan region harbored a diverse community of both typical and atypical class 2 integrons, raising concerns about the overuse of antibiotics and their careless disposal into the environment.

  16. Subsurface fracture spacing

    SciTech Connect

    Lorenz, J.C. ); Hill, R.E. )

    1991-01-01

    This study was undertaken in order to document and analyze the unique set of data on subsurface fracture characteristics, especially spacing, provided by the US Department of Energy's Slant Hole Completion Test well (SHCT-1) in the Piceance Basin, Colorado. Two hundred thirty-six (236) ft (71.9 m) of slant core and 115 ft (35.1 m) of horizontal core show irregular, but remarkably close, spacings for 72 natural fractures cored in sandstone reservoirs of the Mesaverde Group. Over 4200 ft (1280 m) of vertical core (containing 275 fractures) from the vertical Multiwell Experiment wells at the same location provide valuable information on fracture orientation, termination, and height, but only data from the SHCT-1 core allow calculations of relative fracture spacing. Within the 162-ft (49-m) thick zone of overlapping core from the vertical and deviated wellbores, only one fracture is present in vertical core whereas 52 fractures occur in the equivalent SHCT-1 core. The irregular distribution of regional-type fractures in these heterogeneous reservoirs suggests that measurements of average fracture spacing'' are of questionable value as direct input parameters into reservoir engineering models. Rather, deviated core provides data on the relative degree of fracturing, and confirms that cross fractures can be rare in the subsurface. 13 refs., 11 figs.

  17. Isolation and Characterization of Electrochemically Active Subsurface Delftia and Azonexus Species.

    PubMed

    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

  18. Water-related environments: a multistep procedure to assess the diversity and enzymatic properties of cultivable bacteria.

    PubMed

    Grivalský, Tomáš; Bučková, Maria; Puškárová, Andrea; Kraková, Lucia; Pangallo, Domenico

    2016-03-01

    Studying the culturable portion of environmental bacterial populations is valuable for understanding the ecology, for discovering taxonomically interesting isolates and for exploiting their enzymatic abilities. In this study, diverse water-related samples, iced water (3 °C) from river, the sediment (29 °C) and water (55 °C) of a hot-spring, were investigated by two cultivation strategies, Dry and novel Wet approach. The isolates were clustered by fluorescent internal transcribed spacer PCR and identified by 16S rRNA sequencing. Several bacterial groups were also sub-typed through the application of Random Amplified Microsatellite Polymorphisms method. A broad enzymatic screening of all bacterial isolates was performed in order to assess the proteolytic, cellulolytic, lipolytic, esterolytic, amylolytic properties, as well as catalase and peroxidase activities. The Wet cultivation demonstrated to be suitable for the isolation of potential new species belonging to genera Massilia, Algoriphagus, Rheinheimera and Pandoraea. Valuable microbial resources with extensive enzymatic activities were recognized among the psychrophilic (Pantoea brenneri and Serratia sp.), mesophilic (Pandoraea, Massilia, Pseudomonas, Stenotrophomonas, Bacillus and Aeromonas) and thermophilic bacteria (Aeribacullus pallidus and Geobacillus kaustophilus). The experimental strategy developed in this study includes simple investigation tools able to reveal the genetic and enzymatic peculiarities of isolated microorganisms. It can be applied to different kinds of aquatic samples and extreme environments similar to those described in this study.

  19. High diversity of airborne fungi in the hospital environment as revealed by meta-sequencing-based microbiome analysis

    PubMed Central

    Tong, Xunliang; Xu, Hongtao; Zou, Lihui; Cai, Meng; Xu, Xuefeng; Zhao, Zuotao; Xiao, Fei; Li, Yanming

    2017-01-01

    Invasive fungal infections acquired in the hospital have progressively emerged as an important cause of life-threatening infection. In particular, airborne fungi in hospitals are considered critical pathogens of hospital-associated infections. To identify the causative airborne microorganisms, high-volume air samplers were utilized for collection, and species identification was performed using a culture-based method and DNA sequencing analysis with the Illumina MiSeq and HiSeq 2000 sequencing systems. Few bacteria were grown after cultivation in blood agar. However, using microbiome sequencing, the relative abundance of fungi, Archaea species, bacteria and viruses was determined. The distribution characteristics of fungi were investigated using heat map analysis of four departments, including the Respiratory Intensive Care Unit, Intensive Care Unit, Emergency Room and Outpatient Department. The prevalence of Aspergillus among fungi was the highest at the species level, approximately 17% to 61%, and the prevalence of Aspergillus fumigatus among Aspergillus species was from 34% to 50% in the four departments. Draft genomes of microorganisms isolated from the hospital environment were obtained by sequence analysis, indicating that investigation into the diversity of airborne fungi may provide reliable results for hospital infection control and surveillance. PMID:28045065

  20. Phylogeny and expression pattern of starch branching enzyme family genes in cassava (Manihot esculenta Crantz) under diverse environments.

    PubMed

    Pei, Jinli; Wang, Huijun; Xia, Zhiqiang; Liu, Chen; Chen, Xin; Ma, Pingan; Lu, Cheng; Wang, Wenquan

    2015-08-01

    Starch branching enzyme (SBE) is one of the key enzymes involved in starch biosynthetic metabolism. In this study, six SBE family genes were identified from the cassava genome. Phylogenetic analysis divided the MeSBE family genes into dicot family A, B, C, and the new group. Tissue-specific analysis showed that MeSBE2.2 was strongly expressed in leaves, stems cortex, and root stele, and MeSBE3 had high expression levels in stem cortex and root stele of plants in the rapid growth stage under field condition, whereas the expression levels of MeSBE2.1, MeSBE4, and MeSBE5 were low except for in stems cortex. The transcriptional activity of MeSBE2.2 and MeSBE3 was higher compared with other members and gradually increased in the storage roots during root growth process, while the other MeSBE members normally remained low expression levels. Expression of MeSBE2.2 could be induced by salt, drought, exogenous abscisic acid, jasmonic acid, and salicylic acid signals, while MeSBE3 had positive response to drought, salt, exogenous abscisic acid, and salicylic acid in leaves but not in storage root, indicating that they might be more important in starch biosynthesis pathway under diverse environments.

  1. Handling the Diversity in the Coming Flood of InSAR Data with the InSAR Scientific Computing Environment

    NASA Astrophysics Data System (ADS)

    Rosen, P. A.; Gurrola, E. M.; Sacco, G. F.; Agram, P. S.; Lavalle, M.; Zebker, H. A.

    2014-12-01

    The NASA ESTO-developed InSAR Scientific Computing Environment (ISCE) provides acomputing framework for geodetic image processing for InSAR sensors that ismodular, flexible, and extensible, enabling scientists to reduce measurementsdirectly from a diverse array of radar satellites and aircraft to newgeophysical products. ISCE can serve as the core of a centralized processingcenter to bring Level-0 raw radar data up to Level-3 data products, but isadaptable to alternative processing approaches for science users interested innew and different ways to exploit mission data. This is accomplished throughrigorous componentization of processing codes, abstraction and generalization ofdata models, and a xml-based input interface with multi-level prioritizedcontrol of the component configurations depending on the science processingcontext. The proposed NASA-ISRO SAR (NISAR) Mission would deliver data ofunprecedented quantity and quality, making possible global-scale studies inclimate research, natural hazards, and Earth's ecosystems. ISCE is planned tobecome a key element in processing projected NISAR data into higher level dataproducts, enabling a new class of analyses that take greater advantage of thelong time and large spatial scales of these new data than current approaches.NISAR would be but one mission in a constellation of radar satellites in thefuture delivering such data. ISCE has been incorporated into two prototypecloud-based systems that have demonstrated its elasticity to addressing largerdata processing problems in a "production" context and its ability to becontrolled by individual science users on the cloud for large data problems.

  2. Physiologically anaerobic microorganisms of the deep subsurface

    SciTech Connect

    Stevens, S.E. Jr.; Chung, K.T.

    1991-06-01

    This study seeks to determine numbers, diversity, and morphology of anaerobic microorganisms in 15 samples of subsurface material from the Idaho National Engineering Laboratory, in 18 samples from the Hanford Reservation and in 1 rock sample from the Nevada Test Site; set up long term experiments on the chemical activities of anaerobic microorganisms based on these same samples; work to improve methods for the micro-scale determination of in situ anaerobic microbial activity;and to begin to isolate anaerobes from these samples into axenic culture with identification of the axenic isolates.

  3. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Shih, Patrick [Kerfeld Lab, UC Berkeley and JGI

    2016-07-12

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  4. Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants.

    PubMed

    Arnan, Xavier; Cerdá, Xim; Retana, Javier

    2015-01-01

    We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a

  5. Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants

    PubMed Central

    Cerdá, Xim; Retana, Javier

    2015-01-01

    We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait’s phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a

  6. Genotypic Variation in Grain P Loading across Diverse Rice Growing Environments and Implications for Field P Balances.

    PubMed

    Vandamme, Elke; Wissuwa, Matthias; Rose, Terry; Dieng, Ibnou; Drame, Khady N; Fofana, Mamadou; Senthilkumar, Kalimuthu; Venuprasad, Ramaiah; Jallow, Demba; Segda, Zacharie; Suriyagoda, Lalith; Sirisena, Dinarathna; Kato, Yoichiro; Saito, Kazuki

    2016-01-01

    More than 60% of phosphorus (P) taken up by rice (Oryza spp.) is accumulated in the grains at harvest and hence exported from fields, leading to a continuous removal of P. If P removed from fields is not replaced by P inputs then soil P stocks decline, with consequences for subsequent crops. Breeding rice genotypes with a low concentration of P in the grains could be a strategy to reduce maintenance fertilizer needs and slow soil P depletion in low input systems. This study aimed to assess variation in grain P concentrations among rice genotypes across diverse environments and evaluate the implications for field P balances at various grain yield levels. Multi-location screening experiments were conducted at different sites across Africa and Asia and yield components and grain P concentrations were determined at harvest. Genotypic variation in grain P concentration was evaluated while considering differences in P supply and grain yield using cluster analysis to group environments and boundary line analysis to determine minimum grain P concentrations at various yield levels. Average grain P concentrations across genotypes varied almost 3-fold among environments, from 1.4 to 3.9 mg g(-1). Minimum grain P concentrations associated with grain yields of 150, 300, and 500 g m(-2) varied between 1.2 and 1.7, 1.3 and 1.8, and 1.7 and 2.2 mg g(-1) among genotypes respectively. Two genotypes, Santhi Sufaid and DJ123, were identified as potential donors for breeding for low grain P concentration. Improvements in P balances that could be achieved by exploiting this genotypic variation are in the range of less than 0.10 g P m(-2) (1 kg P ha(-1)) in low yielding systems, and 0.15-0.50 g P m(-2) (1.5-5.0 kg P ha(-1)) in higher yielding systems. Improved crop management and alternative breeding approaches may be required to achieve larger reductions in grain P concentrations in rice.

  7. Genotypic Variation in Grain P Loading across Diverse Rice Growing Environments and Implications for Field P Balances

    PubMed Central

    Vandamme, Elke; Wissuwa, Matthias; Rose, Terry; Dieng, Ibnou; Drame, Khady N.; Fofana, Mamadou; Senthilkumar, Kalimuthu; Venuprasad, Ramaiah; Jallow, Demba; Segda, Zacharie; Suriyagoda, Lalith; Sirisena, Dinarathna; Kato, Yoichiro; Saito, Kazuki

    2016-01-01

    More than 60% of phosphorus (P) taken up by rice (Oryza spp.) is accumulated in the grains at harvest and hence exported from fields, leading to a continuous removal of P. If P removed from fields is not replaced by P inputs then soil P stocks decline, with consequences for subsequent crops. Breeding rice genotypes with a low concentration of P in the grains could be a strategy to reduce maintenance fertilizer needs and slow soil P depletion in low input systems. This study aimed to assess variation in grain P concentrations among rice genotypes across diverse environments and evaluate the implications for field P balances at various grain yield levels. Multi-location screening experiments were conducted at different sites across Africa and Asia and yield components and grain P concentrations were determined at harvest. Genotypic variation in grain P concentration was evaluated while considering differences in P supply and grain yield using cluster analysis to group environments and boundary line analysis to determine minimum grain P concentrations at various yield levels. Average grain P concentrations across genotypes varied almost 3-fold among environments, from 1.4 to 3.9 mg g−1. Minimum grain P concentrations associated with grain yields of 150, 300, and 500 g m−2 varied between 1.2 and 1.7, 1.3 and 1.8, and 1.7 and 2.2 mg g−1 among genotypes respectively. Two genotypes, Santhi Sufaid and DJ123, were identified as potential donors for breeding for low grain P concentration. Improvements in P balances that could be achieved by exploiting this genotypic variation are in the range of less than 0.10 g P m−2 (1 kg P ha−1) in low yielding systems, and 0.15–0.50 g P m−2 (1.5–5.0 kg P ha−1) in higher yielding systems. Improved crop management and alternative breeding approaches may be required to achieve larger reductions in grain P concentrations in rice. PMID:27729916

  8. Origins of Cell-to-Cell Bioprocessing Diversity and Implications of the Extracellular Environment Revealed at the Single-Cell Level

    PubMed Central

    Vasdekis, A. E.; Silverman, A. M.; Stephanopoulos, G.

    2015-01-01

    Bioprocess limitations imposed by microbial cell-to-cell phenotypic diversity remain poorly understood. To address this, we investigated the origins of such culture diversity during lipid production and assessed the impact of the fermentation microenvironment. We measured the single-cell lipid production dynamics in a time-invariant microfluidic environment and discovered that production is not monotonic, but rather sporadic with time. To characterize this, we introduce bioprocessing noise and identify its epigenetic origins. We linked such intracellular production fluctuations with cell-to-cell productivity diversity in culture. This unmasked the phenotypic diversity amplification by the culture microenvironment, a critical parameter in strain engineering as well as metabolic disease treatment. PMID:26657999

  9. Comparative microbial diversity and redox environments of black shale and stromatolite facies in the Mesoproterozoic Xiamaling Formation

    NASA Astrophysics Data System (ADS)

    Luo, Genming; Hallmann, Christian; Xie, Shucheng; Ruan, Xiaoyan; Summons, Roger E.

    2015-02-01

    The composition of microbial communities and their relationship to ocean redox structure in the Precambrian are topics of continuing interest in geobiology. Our knowledge of organismic diversity and environmental conditions during this time are mostly based on fragmentary paleontological and geochemical records and might be skewed accordingly. In North China the Xiamaling Formation (∼1.37 Ga) is characterized by black shales of relatively low thermal maturity (Tmax is ∼445 °C) and has been identified as a potential petroleum source rock. To date, however, the biological sources of the organic matter and the environmental conditions prevalent during the deposition of these sediments remain unclear. In this study we analyzed the hydrocarbon biomarker compositions of the Xiamaling Formation shales and a superjacent stromatolitic carbonate in order to shed light on the microbial diversity in the sedimentary environments they represent. The hydrocarbons extracted from both sediments are dominated by low-molecular-weight n-alkanes with a maximum at C15-18, suggesting that bacteria and/or algae were primary biotic precursors. Our inability to detect steranes in bitumen I, and only traces of rearranged steranes in bitumen II of black shales, indicates that modern eukaryotic algae were either ecologically insignificant or not preserved due to a taphonomic bias. The high relative concentration of hopanes and diahopanes ranging from C27 to C35, as well as monomethylalkanes, suggests that cyanobacteria may have been the dominant primary producers and could have contributed to the biologically available nitrogen pool through N2-fixation. This observation is supported by the low nitrogen isotopic composition of the kerogens. Even though all facies zones appear to have been anoxic but not sulfidic on the basis of biomarker ratios and trace metals, subtle but distinct molecular differences are observed between the stromatolite and the black shales, which can be attributed to

  10. Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water

    PubMed Central

    Magnabosco, Cara; Tekere, Memory; Lau, Maggie C. Y.; Linage, Borja; Kuloyo, Olukayode; Erasmus, Mariana; Cason, Errol; van Heerden, Esta; Borgonie, Gaetan; Kieft, Thomas L.; Olivier, Jana; Onstott, Tullis C.

    2014-01-01

    South Africa has numerous thermal springs that represent topographically driven meteoric water migrating along major fracture zones. The temperature (40–70°C) and pH (8–9) of the thermal springs in the Limpopo Province are very similar to those of the low salinity fracture water encountered in the South African mines at depths ranging from 1.0 to 3.1 km. The major cation and anion composition of these thermal springs are very similar to that of the deep fracture water with the exception of the dissolved inorganic carbon and dissolved O2, both of which are typically higher in the springs than in the deep fracture water. The in situ biological relatedness of such thermal springs and the subsurface fracture fluids that feed them has not previously been evaluated. In this study, we evaluated the microbial diversity of six thermal spring and six subsurface sites in South Africa using high-throughput sequencing of 16S rRNA gene hypervariable regions. Proteobacteria were identified as the dominant phylum within both subsurface and thermal spring environments, but only one genera, Rheinheimera, was identified among all samples. Using Morisita similarity indices as a metric for pairwise comparisons between sites, we found that the communities of thermal springs are highly distinct from subsurface datasets. Although the Limpopo thermal springs do not appear to provide a new window for viewing subsurface bacterial communities, we report that the taxonomic compositions of the subsurface sites studied are more similar than previous results would indicate and provide evidence that the microbial communities sampled at depth are more correlated to subsurface conditions than geographical distance. PMID:25566203

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

    SciTech Connect

    Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin; Martin Keller; Joseph W. Stucki

    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 the subsurface is exposed to mixed contamination predominated by uranium and nitrate. A total of 20 publications (16 published or 'in press' and 4 in review), 10 invited talks, and 43 contributed seminars/ meeting presentations were completed during the past four years of the project. PI Kostka served on one proposal review panel each year for the U.S. DOE Office of Science during the four year project period. The PI leveraged funds from the state of Florida to purchase new instrumentation that aided the project. Support was also leveraged by the PI from the Joint Genome Institute in the form of two successful proposals for genome sequencing. Draft genomes are now available for two novel species isolated during our studies and 5 more genomes are in the pipeline. We effectively addressed each of the three project objectives and research highlights are provided. Task I - Isolation and characterization of novel anaerobes: (1) A wide range of pure cultures of metal-reducing bacteria, sulfate-reducing bacteria, and denitrifying bacteria (32 strains) were isolated from subsurface sediments of the Oak Ridge Field Research Center (ORFRC), where the subsurface is exposed to mixed contamination of uranium and nitrate. These isolates which are new

  12. Nonintrusive subsurface surveying capability

    SciTech Connect

    Tunnell, T.W.; Cave, S.P.

    1994-06-01

    This presentation describes the capabilities of a ground-pentrating radar (GPR) system developed by EG&G Energy Measurements (EM), a prime contractor to the Department of Energy (DOE). The focus of the presentation will be on the subsurface survey of DOE site TA-21 in Los Alamos, New Mexico. EG&G EM developed the system for the Department of Defense. The system is owned by the Department of the Army and currently resides at KO in Albuquerque. EM is pursuing efforts to transfer this technology to environmental applications such as waste-site characterization with DOE encouragement. The Army has already granted permission to use the system for the waste-site characterization activities.

  13. Containment of subsurface contaminants

    DOEpatents

    Corey, J.C.

    1994-09-06

    A barrier is disclosed for reducing the spread of a plume of subsurface contaminants. The apparatus includes a well system for injecting a fluid, such as air, just outside and below the periphery of the plume. The fluid is injected at a pressure sufficient to lower the hydraulic conductivity of the soil from the point of injection to the surface thus establishing a curtain-like barrier to groundwater movement. The barrier is established upgradient of the plume to divert groundwater away, or preferably completely around the plume to reduce the flow of groundwater into or out of the plume. The barrier enables the remediation of the confined contamination and then, when the injection of the fluid is halted, the barrier quickly dissipates. 5 figs.

  14. Containment of subsurface contaminants

    DOEpatents

    Corey, John C.

    1994-01-01

    A barrier for reducing the spread of a plume of subsurface contaminants. The apparatus includes a well system for injecting a fluid, such as air, just outside and below the periphery of the plume. The fluid is injected at a pressure sufficient to lower the hydraulic conductivity of the soil from the point of injection to the surface thus establishing a curtain-like barrier to groundwater movement. The barrier is established upgradient of the plume to divert groundwater away, or preferably completely around the plume to reduce the flow of groundwater into or out of the plume. The barrier enables the remediation of the confined contamination and then, when the injection of the fluid is halted, the barrier quickly dissipates.

  15. Metalliferous Biosignatures for Deep Subsurface Microbial Activity

    NASA Astrophysics Data System (ADS)

    Parnell, John; Brolly, Connor; Spinks, Sam; Bowden, Stephen

    2016-03-01

    The interaction of microbes and metals is widely assumed to have occurred in surface or very shallow subsurface environments. However new evidence suggests that much microbial activity occurs in the deep subsurface. Fluvial, lacustrine and aeolian `red beds' contain widespread centimetre-scale reduction spheroids in which a pale reduced spheroid in otherwise red rocks contains a metalliferous core. Most of the reduction of Fe (III) in sediments is caused by Fe (III) reducing bacteria. They have the potential to reduce a range of metals and metalloids, including V, Cu, Mo, U and Se, by substituting them for Fe (III) as electron acceptors, which are all elements common in reduction spheroids. The spheroidal morphology indicates that they were formed at depth, after compaction, which is consistent with a microbial formation. Given that the consequences of Fe (III) reduction have a visual expression, they are potential biosignatures during exploration of the terrestrial and extraterrestrial geological record. There is debate about the energy available from Fe (III) reduction on Mars, but the abundance of iron in Martian soils makes it one of the most valuable prospects for life there. Entrapment of the microbes themselves as fossils is possible, but a more realistic target during the exploration of Mars would be the colour contrasts reflecting selective reduction or oxidation. This can be achieved by analysing quartz grains across a reduction spheroid using Raman spectroscopy, which demonstrates its suitability for life detection in subsurface environments. Microbial action is the most suitable explanation for the formation of reduction spheroids and may act as metalliferous biosignatures for deep subsurface microbial activity.

  16. The DOE subsurface microbial culture collection at Florida State University. Final technical report, January 16, 1996--February 15, 1997

    SciTech Connect

    Balkwill, D.L.

    1998-05-25

    This report describes the research that supports the Subsurface Science Program by maintaining a culture collection of microorganisms isolated from deep terrestrial subsurface environments (the Subsurface Microbial Culture Collection, or SMCC). The general distribution of cultures and data was identified as an important function of the SMCC. The accomplishments related to this function of the culture collection are described.

  17. Aβ and Inflammatory Stimulus Activate Diverse Signaling Pathways in Monocytic Cells: Implications in Retaining Phagocytosis in Aβ-Laden Environment

    PubMed Central

    Savchenko, Ekaterina; Malm, Tarja; Konttinen, Henna; Hämäläinen, Riikka H.; Guerrero-Toro, Cindy; Wojciechowski, Sara; Giniatullin, Rashid; Koistinaho, Jari; Magga, Johanna

    2016-01-01

    Background: Accumulation of amyloid β (Aβ) is one of the main hallmarks of Alzheimer’s disease (AD). The enhancement of Aβ clearance may provide therapeutic means to restrict AD pathology. The cellular responses to different forms of Aβ in monocytic cells are poorly known. We aimed to study whether different forms of Aβ induce inflammatory responses in monocytic phagocytes and how Aβ may affect monocytic cell survival and function to retain phagocytosis in Aβ-laden environment. Methods: Monocytic cells were differentiated from bone marrow hematopoietic stem cells (HSC) in the presence of macrophage-colony stimulating factor. Monocytic cells were stimulated with synthetic Aβ42 and intracellular calcium responses were recorded with calcium imaging. The formation of reactive oxygen species (ROS), secretion of cytokines and cell viability were also assessed. Finally, monocytic cells were introduced to native Aβ deposits ex vivo and the cellular responses in terms of cell viability, pro-inflammatory activation and phagocytosis were determined. The ability of monocytic cells to phagocytose Aβ plaques was determined after intrahippocampal transplantation in vivo. Results: Freshly solubilized Aβ induced calcium oscillations, which persisted after removal of the stimulus. After few hours of aggregation, Aβ was not able to induce oscillations in monocytic cells. Instead, lipopolysaccharide (LPS) induced calcium responses divergent from Aβ-induced response. Furthermore, while LPS induced massive production of pro-inflammatory cytokines, neither synthetic Aβ species nor native Aβ deposits were able to induce pro-inflammatory activation of monocytic cells, contrary to primary microglia. Finally, monocytic cells retained their viability in the presence of Aβ and exhibited phagocytic activity towards native fibrillar Aβ deposits and congophilic Aβ plaques. Conclusion: Monocytic cells carry diverse cellular responses to Aβ and inflammatory stimulus LPS. Even

  18. Microbial diversity in anaerobic sediments at Rio Tinto, a naturally acidic environment with a high heavy metal content.

    PubMed

    Sánchez-Andrea, Irene; Rodríguez, Nuria; Amils, Ricardo; Sanz, José Luis

    2011-09-01

    The Tinto River is an extreme environment located at the core of the Iberian Pyritic Belt (IPB). It is an unusual ecosystem due to its size (100 km long), constant acidic pH (mean pH, 2.3), and high concentration of heavy metals, iron, and sulfate in its waters, characteristics that make the Tinto River Basin comparable to acidic mine drainage (AMD) systems. In this paper we present an extensive survey of the Tinto River sediment microbiota using two culture-independent approaches: denaturing gradient gel electrophoresis and cloning of 16S rRNA genes. The taxonomic affiliation of the Bacteria showed a high degree of biodiversity, falling into 5 different phyla: Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria; meanwhile, all the Archaea were affiliated with the order Thermoplasmatales. Microorganisms involved in the iron (Acidithiobacillus ferrooxidans, Sulfobacillus spp., Ferroplasma spp., etc.), sulfur (Desulfurella spp., Desulfosporosinus spp., Thermodesulfobium spp., etc.), and carbon (Acidiphilium spp., Bacillus spp., Clostridium spp., Acidobacterium spp., etc.) cycles were identified, and their distribution was correlated with physicochemical parameters of the sediments. Ferric iron was the main electron acceptor for the oxidation of organic matter in the most acid and oxidizing layers, so acidophilic facultative Fe(III)-reducing bacteria appeared widely in the clone libraries. With increasing pH, the solubility of iron decreases and sulfate-reducing bacteria become dominant, with the ecological role of methanogens being insignificant. Considering the identified microorganisms-which, according to the rarefaction curves and Good's coverage values, cover almost all of the diversity-and their corresponding metabolism, we suggest a model of the iron, sulfur, and organic matter cycles in AMD-related sediments.

  19. 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.

  20. 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

  1. Among Friends: The Role of Academic-Preparedness Diversity in Individual Performance within a Small-Group STEM Learning Environment

    ERIC Educational Resources Information Center

    Micari, Marina; Van Winkle, Zachary; Pazos, Pilar

    2016-01-01

    In this study, we investigate the relationship between academic-preparedness diversity within small learning groups and individual academic performance in science, technology, engineering, and mathematics (STEM) university courses. We further examine whether academic-preparedness diversity impacts academically more- and less-prepared students…

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

    PubMed Central

    Fullerton, Heather

    2016-01-01

    ABSTRACT 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. IMPORTANCE 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

  3. 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.

  4. 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.

  5. Inferring deep biosphere function and diversity through (near) surface biosphere portals (Invited)

    NASA Astrophysics Data System (ADS)

    Meyer-Dombard, D. R.; Cardace, D.; Woycheese, K. M.; Swingley, W.; Schubotz, F.; Shock, E.

    2013-12-01

    The consideration of surface expressions of the deep subsurface- such as springs- remains one of the most economically viable means to query the deep biosphere's diversity and function. Hot spring source pools are ideal portals for accessing and inferring the taxonomic and functional diversity of related deep subsurface microbial communities. Consideration of the geochemical composition of deep vs. surface fluids provides context for interpretation of community function. Further, parallel assessment of 16S rRNA data, metagenomic sequencing, and isotopic compositions of biomass in surface springs allows inference of the functional capacities of subsurface ecosystems. Springs in Yellowstone National Park (YNP), the Philippines, and Turkey are considered here, incorporating near-surface, transition, and surface ecosystems to identify 'legacy' taxa and functions of the deep biosphere. We find that source pools often support functional capacity suited to subsurface ecosystems. For example, in hot ecosystems, source pools are strictly chemosynthetic, and surface environments with measureable dissolved oxygen may contain evidence of community functions more favorable under anaerobic conditions. Metagenomic reads from a YNP ecosystem indicate the genetic capacity for sulfate reduction at high temperature. However, inorganic sulfate reduction is only minimally energy-yielding in these surface environments suggesting the potential that sulfate reduction is a 'legacy' function of deeper biosphere ecosystems. Carbon fixation tactics shift with increased surface exposure of the thermal fluids. Genes related to the rTCA cycle and the acetyl co-A pathway are most prevalent in highest temperature, anaerobic sites. At lower temperature sites, fewer total carbon fixation genes were observed, perhaps indicating an increase in heterotrophic metabolism with increased surface exposure. In hydrogen and methane rich springs in the Philippines and Turkey, methanogenic taxa dominate source

  6. Among friends: the role of academic-preparedness diversity in individual performance within a small-group STEM learning environment

    NASA Astrophysics Data System (ADS)

    Micari, Marina; Van Winkle, Zachary; Pazos, Pilar

    2016-08-01

    In this study, we investigate the relationship between academic-preparedness diversity within small learning groups and individual academic performance in science, technology, engineering, and mathematics (STEM) university courses. We further examine whether academic-preparedness diversity impacts academically more- and less-prepared students differently. We use data from 5367 university students nested within 1141 science, engineering, and mathematics learning groups and use a regression analysis to estimate the effect of group diversity, measured in two ways, on course performance. Our results indicate that academic-preparedness diversity is generally associated with positive learning outcomes, that academically less-prepared students derive greater benefit, and that less-prepared students fare best when they are not alone in a group of highly prepared students. Implications for teaching and small-group facilitation are addressed.

  7. Local diversity hot spots in the Middle Miocene of the Central Paratethys: influence of environment and sampling

    NASA Astrophysics Data System (ADS)

    Nawrot, Rafal; Zuschin, Martin; Harzhauser, Mathias; Kroh, Andreas; Mandic, Oleg

    2015-04-01

    Species richness captured by historical fossil inventories is a complex function of true local diversity, degree of outcrop-scale heterogeneity in species composition and sampling intensity. Disentangling these factors is hindered by the fact that the 'systematists follow the fossils' (Raup, 1977) and thus non-uniform research effort may both drive apparent diversity patterns and follow the actual presence of highly fossiliferous strata. The molluscan fauna of Lapugiu de Sus (Hunedoara District, Romania) constitutes one of the most diverse Early Badenian (Langhian) assemblages of the Paratethys Sea, with almost one thousand species reported during 170 years of extensive studies. We evaluate whether this exceptional richness reflects the actual diversity hot spot or just a long history of fossil-collecting by comparing the fauna of Lapugiu with other Paratethyan molluscan lagerstätten of similar age. The literature-derived species lists for each section were contrasted with independent abundance data based on a standardized sampling protocol (42 samples, 24,000 specimens, and 530 species from six localities). Although individual samples from other localities can exhibit comparable diversity levels, richness estimates for samples from Lapugiu are all consistently high, reflecting increasing evenness in more offshore depositional settings. This translates to the highest diversity at the outcrop scale when all samples are pooled. In contrast to other localities, however, for which data from historical inventories corresponds well to our quantitative estimates of total richness, the number of species described from Lapugiu is much higher than expected. This excessive richness likely reflects the 'Bonanza Effect' (sensu Dunhill et al., 2012), where uniformly species-rich deposits were attracting intensive taxonomic studies. The strong positive feedback between palaeontological sampling effort and fossil diversity may thus greatly overestimate the true differences in

  8. Microbial Transport in the Subsurface

    SciTech Connect

    Ginn, Timothy R.; Camesano, Terri; Scheibe, Timothy D.; Nelson, Kirk B.; Clement, T. P.; Wood, Brian D.

    2005-12-01

    In this article we focus on the physical, chemical, and biological processes involved in the transport of bacteria in the saturated subsurface. We will first review conceptual models of bacterial phases in the subsurface, and then the processes controlling fate and transport on short (e.g., bioremediation) time scales. Finally we briefly review field bacterial transport experiments and discuss a number of issues that impact the application of current process descriptions and models at the field scale.

  9. 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.

  10. The number of limiting resources in the environment controls the temporal diversity patterns in the algal benthos.

    PubMed

    Larson, Chad A; Adumatioge, Larry; Passy, Sophia I

    2016-07-01

    The role of the number of limiting resources (NLR) on species richness has been the subject of much theoretical and experimental work. However, how the NLR controls temporal beta diversity and the processes of community assembly is not well understood. To address this knowledge gap, we initiated a series of laboratory microcosm experiments, exposing periphyton communities to a gradient of NLR from 0 to 3, generated by supplementation with nitrogen, phosphorus, iron, and all their combinations. We hypothesized that similarly to alpha diversity, shown to decrease with the NLR in benthic algae, temporal beta diversity would also decline due to filtering. Additionally, we predicted that the NLR would also affect turnover and community nestedness, which would show opposing responses. Indeed, as the NLR increased, temporal beta diversity decreased; turnover, indicative of competition, decreased; and nestedness, suggestive of complementarity, increased. Finally, the NLR determined the role of deterministic versus stochastic processes in community assembly, showing respectively an increasing and a decreasing trend. These results imply that the NLR has a much greater, yet still unappreciated influence on producer communities, constraining not only alpha diversity but also temporal dynamics and community assembly.

  11. Yeast and bacterial diversity along a transect in an acidic, As-Fe rich environment revealed by cultural approaches.

    PubMed

    Delavat, François; Lett, Marie-Claire; Lièvremont, Didier

    2013-10-01

    Acid mine drainages (AMDs) are often thought to harbour low biodiversity, yet little is known about the diversity distribution along the drainages. Using culture-dependent approaches, the microbial diversity from the Carnoulès AMD sediment was investigated for the first time along a transect showing progressive environmental stringency decrease. In total, 20 bacterial genera were detected, highlighting a higher bacterial diversity than previously thought. Moreover, this approach led to the discovery of 16 yeast species, demonstrating for the first time the presence of this important phylogenetic group in this AMD. All in all, the location of the microbes along the transect helps to better understand their distribution in a pollution gradient.

  12. Subsurface Geotechnical Parameters Report

    SciTech Connect

    D. Rigby; M. Mrugala; G. Shideler; T. Davidsavor; J. Leem; D. Buesch; Y. Sun; D. Potyondy; M. Christianson

    2003-12-17

    The Yucca Mountain Project is entering a the license application (LA) stage in its mission to develop the nation's first underground nuclear waste repository. After a number of years of gathering data related to site characterization, including activities ranging from laboratory and site investigations, to numerical modeling of processes associated with conditions to be encountered in the future repository, the Project is realigning its activities towards the License Application preparation. At the current stage, the major efforts are directed at translating the results of scientific investigations into sets of data needed to support the design, and to fulfill the licensing requirements and the repository design activities. This document addresses the program need to address specific technical questions so that an assessment can be made about the suitability and adequacy of data to license and construct a repository at the Yucca Mountain Site. In July 2002, the U.S. Nuclear Regulatory Commission (NRC) published an Integrated Issue Resolution Status Report (NRC 2002). Included in this report were the Repository Design and Thermal-Mechanical Effects (RDTME) Key Technical Issues (KTI). Geotechnical agreements were formulated to resolve a number of KTI subissues, in particular, RDTME KTIs 3.04, 3.05, 3.07, and 3.19 relate to the physical, thermal and mechanical properties of the host rock (NRC 2002, pp. 2.1.1-28, 2.1.7-10 to 2.1.7-21, A-17, A-18, and A-20). The purpose of the Subsurface Geotechnical Parameters Report is to present an accounting of current geotechnical information that will help resolve KTI subissues and some other project needs. The report analyzes and summarizes available qualified geotechnical data. It evaluates the sufficiency and quality of existing data to support engineering design and performance assessment. In addition, the corroborative data obtained from tests performed by a number of research organizations is presented to reinforce

  13. 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

  14. Urbanization and subsurface environmental issues: an attempt at DPSIR model application in Asian cities.

    PubMed

    Jago-on, Karen Ann Bianet; Kaneko, Shinji; Fujikura, Ryo; Fujiwara, Akimasa; Imai, Tsuyoshi; Matsumoto, Toru; Zhang, Junyi; Tanikawa, Hiroki; Tanaka, Katsuya; Lee, Backjin; Taniguchi, Makoto

    2009-04-15

    This paper synthesizes existing information and knowledge on subsurface environments to understand the major cause and effect relationships of subsurface environmental issues by using the DPSIR (Driving force-Pressure-Status-Impact-Response) approach as the framework of analysis. Description is given to the major subsurface environmental issues common among the selected Asian cities (Bangkok, Jakarta, Manila, Osaka, Seoul, Taipei and Tokyo), such as excessive groundwater abstraction, land subsidence and groundwater contamination. The DPSIR framework is used to analyze the issues and problems of subsurface in key stages and suggestions are made for additional indicators to improve our description of the stages of urban development for the future.

  15. Disability and Diversity in Canada: Problems and Opportunities in Creating Accessible and Inclusive Learning and Service Delivery Environments

    ERIC Educational Resources Information Center

    Matanga, Zephania; Freeze, Rick; Duchesne, Hermann; Nyachoti, Martin

    2008-01-01

    A novel participatory workshop methodology was adopted in this qualitative study of the intersection of disability and diversity in the lives of individuals. Social service recipients, parents, educators, service providers, and policy makers in three Canadian cities were conjoined in daylong discussions designed to investigate if the realities of…

  16. Tangible Exploration of Subsurface Data

    NASA Astrophysics Data System (ADS)

    Petrasova, A.; Harmon, B.; Mitasova, H.; White, J.

    2014-12-01

    Since traditional subsurface visualizations using 2D maps, profiles or charts can be difficult to interpret and often do not convey information in an engaging form, scientists are interested in developing alternative visualization techniques which would help them communicate the subsurface volume data with students and general public. We would like to present new technique for interactive visualization of subsurface using Tangible geospatial modeling and visualization system (Tangeoms). It couples a physical, three-dimensional model with geospatial modeling and analysis through a cycle of scanning and projection. Previous applications of Tangeoms were exploring the impact of terrain modifications on surface-based geophysical processes, such as overland water flow, sediment transport, and also on viewsheds, cast shadows or solar energy potential. However, Tangeoms can serve as a tool for exploring subsurface as well. By creating a physical sand model of a study area, removing the sand from different parts of the model and projecting the computed cross-sections, we can look under the ground as if we were at an excavation site, and see the actual data represented as a 3D raster in that particular part of the model. Depending on data availability, we can also incorporate temporal dimension. Our method is an intuitive and natural way of exploring subsurface data and for users, it represents an alternative to more abstract 3D computer visualization tools, by offering direct, tangible interface.

  17. 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.

  18. 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

  19. 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

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

    PubMed

    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.

  1. Endoscopic subsurface imaging in tissues

    SciTech Connect

    Demos, S G; Staggs, M; Radousky, H B

    2001-02-12

    The objective of this work is to develop endoscopic subsurface optical imaging technology that will be able to image different tissue components located underneath the surface of the tissue at an imaging depth of up to 1 centimeter. This effort is based on the utilization of existing technology and components developed for medical endoscopes with the incorporation of the appropriate modifications to implement the spectral and polarization difference imaging technique. This subsurface imaging technique employs polarization and spectral light discrimination in combination with image processing to remove a large portion of the image information from the outer layers of the tissue which leads to enhancement of the contrast and image quality of subsurface tissue structures.

  2. Measuring isotropic subsurface light transport.

    PubMed

    Happel, Kathrin; Dörsam, Edgar; Urban, Philipp

    2014-04-21

    Subsurface light transport can affect the visual appearance of materials significantly. Measuring and modeling this phenomenon is crucial for accurately reproducing colors in printing or for rendering translucent objects on displays. In this paper, we propose an apparatus to measure subsurface light transport employing a reference material to cancel out adverse signals that may bias the results. In contrast to other approaches, the setup enables improved focusing on rough surfaces (e.g. uncoated paper). We derive a measurement equation that may be used to deduce the point spread function (PSF) of subsurface light transport. Main contributions are the usage of spectrally-narrowband exchangeable LEDs allowing spectrally-resolved measurements and an approach based on quadratic programming for reconstructing PSFs in the case of isotropic light transport.

  3. 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.

  4. Reactive transport benchmarks for subsurface environmental simulation

    SciTech Connect

    Steefel, Carl I.; Yabusaki, Steven B.; Mayer, K. U.

    2015-06-01

    Over the last 20 years, we have seen firsthand the evolution of multicomponent reactive transport modeling and the expanding range and increasing complexity of subsurface applications it is being used to address. There is a growing reliance on reactive transport modeling (RTM) to address some of the most compelling issues facing our planet: climate change, nuclear waste management, contaminant remediation, and pollution prevention. While these issues are motivating the development of new and improved capabilities for subsurface environmental modeling using RTM (e.g., biogeochemistry from cell-scale physiology to continental-scale terrestrial ecosystems, nonisothermal multiphase conditions, coupled geomechanics), there remain longstanding challenges in characterizing the natural variability of hydrological, biological, and geochemical properties in subsurface environments and limited success in transferring models between sites and across scales. An equally important trend over the last 20 years is the evolution of modeling from a service sought out after data has been collected to a multifaceted research approach that provides (1) an organizing principle for characterization and monitoring activities; (2) a systematic framework for identifying knowledge gaps, developing and integrating new knowledge; and (3) a mechanistic understanding that represents the collective wisdom of the participating scientists and engineers. There are now large multidisciplinary projects where the research approach is model-driven, and the principal product is a holistic predictive simulation capability that can be used as a test bed for alternative conceptualizations of processes, properties, and conditions. Much of the future growth and expanded role for RTM will depend on its continued ability to exploit technological advancements in the earth and environmental sciences. Advances in measurement technology, particularly in molecular biology (genomics), isotope fractionation, and high

  5. Species diversity of sandflies (Diptera: Psychodidae) during different seasons and in different environments in the district of Taquaruçú, state of Tocantins, Brazil.

    PubMed

    Machado, Tâmara Oliveira; Bragança, Marcos Antônio Lima; Carvalho, Muzenilha Lima; Andrade Filho, José Dilermando

    2012-11-01

    Phlebotomine sandflies are the vectors for the protozoan parasites that cause leishmaniasis. The present study investigated the species composition of sandfly fauna in the rural district of Taquaruçú, municipality of Palmas, state of Tocantins, Brazil and compared the diversity of species among intradomicile, peridomicile and forest environments during the dry and rainy seasons. Sandflies were collected using CDC light traps over the course of three months during the dry and rainy seasons. A total of 767 specimens were captured, belonging to different 32 species. The most abundant species were Micropygomyia goiana (Martins, Falcão & Silva), Sciopemyia sordellii (Shannon & Del Ponte), Evandromyia carmelinoi (Ryan Fraiha, Lainson & Shaw), Evandromyia termitophila (Martins, Falcão & Silva), Nyssomyia whitmani (Antunes & Coutinho) and Lutzomyia longipalpis (Lutz & Neiva). The highest species diversity (30) and the greatest percentage of specimens (78.3%) were obtained during the rainy season. During the dry season, the species richness and abundance were greater in domestic environments. However, during the rainy season, the forest displayed the highest species richness and the domestic environment exhibited the greatest species abundance. Several important vector species are reported in this study.

  6. Low symbiont diversity as a potential adaptive strategy in a marginal non-reefal environment: a case study of corals in Hong Kong

    NASA Astrophysics Data System (ADS)

    Ng, Tsz Yan; Ang, Put

    2016-09-01

    Symbiosis with genetically diverse Symbiodinium has been shown to affect host coral physiological responses to environmental stresses. Hong Kong, located in a subtropical region, is a marginal environment for coral growth largely due to its wide annual temperature fluctuation with low mean winter sea water temperature (~16 °C) and variable salinity conditions. The symbiont diversity in Hong Kong corals is therefore worth investigating to enrich our understanding on symbioses in marginal and fluctuating environments. Examination of 56 scleractinian coral species and five soft coral species using denaturing gel gradient electrophoresis of the internal transcribed spacer region 2 found only five distinct subclades of Symbiodinium with C1 the dominant type occurring in all but one scleractinian coral and all soft coral species investigated. C15 and C21 Symbiodinium were found in Porites spp. and Montipora peltiformis, respectively, both of which are vertical transmitters. D8-12 was found in Oulastrea crispata, a stress-tolerant species, and D1 in a single sample of Goniastrea aspera. No spatial differences in Symbiodinium composition were found among different regions of Hong Kong. Seasonal monitoring of tagged Platygyra acuta and Porites spp. colonies also revealed no changes in their symbiont types despite wide ranges of in situ temperature fluctuation. Hong Kong scleractinian corals hosted a remarkably low symbiont diversity compared with corals in the surrounding regions. The predominance of a single subclade, C1 Symbiodinium, suggests that this subclade is best acclimatized to local fluctuating conditions and/or low winter temperature. Forming symbiosis with the best acclimatized symbiont, instead of with a diverse group of symbionts with different physiological performances, either sequentially or simultaneously, may be a strategy used by Hong Kong corals to cope with stressful conditions.

  7. Convergence in relationships between leaf traits, spectra and age across diverse canopy environments and two contrasting tropical forests

    SciTech Connect

    Wu, Jin; Chavana-Bryant, Cecilia; Prohaska, Neill; Serbin, Shawn P.; Guan, Kaiyu; Albert, Loren P.; Yang, Xi; van Leeuwen, Willem J. D.; Garnello, Anthony John; Martins, Giordane; Malhi, Yadvinder; Gerard, France; Oliviera, Raimundo Cosme; Saleska, Scott R.

    2016-07-06

    Leaf age structures the phenology and development of plants, as well as the evolution of leaf traits over life histories. Furthermore, a general method for efficiently estimating leaf age across forests and canopy environments is lacking.

  8. Towed Subsurface Optical Communications Buoy

    NASA Technical Reports Server (NTRS)

    Stirbl, Robert C.; Farr, William H.

    2013-01-01

    The innovation allows critical, high-bandwidth submarine communications at speed and depth. This reported innovation is a subsurface optical communications buoy, with active neutral buoyancy and streamlined flow surface veins for depth control. This novel subsurface positioning for the towed communications buoy enables substantial reduction in water-absorption and increased optical transmission by eliminating the intervening water absorption and dispersion, as well as by reducing or eliminating the beam spread and the pulse spreading that is associated with submarine-launched optical beams.

  9. [Correlation between aquatic plant diversity and water environment in the typical sites of Hangzhou section of the Beijing-Hangzhou Grand Canal].

    PubMed

    Lu, Yin; Xu, Xiao-Lu; Zhang, De-Yong; Wang, Li; Zhu, Xu-Ni; Feng, Feng; Zhou, Qiao-Jun; Xie, Peng

    2014-05-01

    Community characteristics of aquatic plant are important indicators for water quality. In order to understand the distribution characteristics of aquatic plants in aquatic ecosystem of the Beijing-Hangzhou Grand Canal ( Hangzhou section) , and to analyze the relationship between water quality and plant community, an investigation of the aquatic plants in five typical sites was made in this study. Species composition, biological diversity, quantity distribution and dominant species of aquatic plants in five sites were studied for ecological changes. Physicochemical factors such as temperature, pH value, transparency, dissolved oxygen and main elements of living were also analyzed. Based on the results, the distribution of phytoplankton diversity and environment factor correlations by multivariate statistical analysis were discussed. The trophic levels of these sites were assessed by using related biological standards. Results indicated that the diversity of aquatic plant mainly depends on the diversity of phytoplankton in the typical sites of the Beijing-Hangzhou Grand Canal. We observed and identified 35 genus algae, including advantage community of Hyalodiscus Ehrenberg and Melosira Agardh, which belonged to Bacillariophyta. According to the impact on the phytoplankton diversity and distribution, factors such as dissolved oxygen, transparency, water temperature, etc. had an obvious influence on the distribution of phytoplankton in the existing 6 environmental factors, while the influence of pH value was the highest. In terms of water quality eutrophication, site Tangxi Bridge and Maiyu Bridge showed a relatively lighter pollution, while site Yiqiao Bridge, Gujia Bridge and Gongchen Bridge showed a higher pollution, and the pollution of site Yiqiao Bridge was the most serious.

  10. 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

  11. Metabolic promiscuity from the deep subsurface: a story of survival or superiority

    NASA Astrophysics Data System (ADS)

    van Heerden, E.; Opperman, D. J.; Bester, A. P.; Van Marwijk, J.; Cason, E. D.; Litthauer, D.; Piater, L. A.; Onstott, T. C.

    2008-08-01

    The Witwatersrand Supergroup is a 2.9-billion-year-old formation of low permeability sandstone and shale with minor volcanic units and conglomerates with an ambient rock temperature of approximately 60°C. Thermus scotoductus SA-01 was isolated from fissure water at a depth of 3.2 kmbls in a South African gold mine and it shows the ability to reduce a variety of heavy metals under anaerobic conditions. It has been postulated that such microorganisms could play an important role in nutrient and metal cycling within the subsurface. Recently, our studies indicate that the cycling of metals could also occur under aerobic conditions and not only by the action of redox active enzymes, but other diverse metabolic proteins as well. In this study the capability of specific proteins to interact with metals is elucidated. Using Thermus SA-01 and its now completed genome sequence, metal reduction is studied through classic proteomic- and genomic methods. Finally we identify thermostable enzymes responsible for the transformation of various metals (Iron, Chrome, Uranium, Gold, etc) and discuss that reduction occurs via the serendipitous action of enzymes with other primary physiological functions, some of which are classical catabolic enzymes and anabolic proteins. This paper discusses the use of a ubiquitous enzyme/protein performing more than one function, possibly detoxifying the environment and using moonlighting as resource to decrease cellular energy requirements rather than elaborate metabolism in the subsurface.

  12. 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

  13. A qualitative analysis of parents' perceptions of weight talk and weight teasing in the home environments of diverse low-income children.

    PubMed

    Berge, Jerica M; Trofholz, Amanda; Fong, Sherri; Blue, Laura; Neumark-Sztainer, Dianne

    2015-09-01

    Research has shown that family weight talk and teasing are associated with child overweight status and unhealthy weight control behaviors. However, little is known about how weight talk and teasing are experienced in the home, how parents respond, and what factors influence whether weight talk and teasing occur. The main objective of this study is to qualitatively examine weight talk and teasing in the home environments of diverse low-income children. Parents (N=118) from a mixed-methods cross-sectional study were interviewed in their home. The majority of parents (90% female; mean age=35 years.) were from minority (65% African American) and low income (<$25,000/year) households. A grounded theory analysis found the following themes: weight talk contradictions, overt and covert weight talk/teasing, reciprocal teasing, and cultural factors related to weight talk/teasing. These themes should be addressed when developing family-based interventions to reduce weight talk and teasing in the home environment.

  14. 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 ...

  15. Integrated Surface/subsurface flow modeling in PFLOTRAN

    SciTech Connect

    Painter, Scott L

    2016-10-01

    Understanding soil water, groundwater, and shallow surface water dynamics as an integrated hydrological system is critical for understanding the Earth’s critical zone, the thin outer layer at our planet’s surface where vegetation, soil, rock, and gases interact to regulate the environment. Computational tools that take this view of soil moisture and shallow surface flows as a single integrated system are typically referred to as integrated surface/subsurface hydrology models. We extend the open-source, highly parallel, subsurface flow and reactive transport simulator PFLOTRAN to accommodate surface flows. In contrast to most previous implementations, we do not represent a distinct surface system. Instead, the vertical gradient in hydraulic head at the land surface is neglected, which allows the surface flow system to be eliminated and incorporated directly into the subsurface system. This tight coupling approach leads to a robust capability and also greatly simplifies implementation in existing subsurface simulators such as PFLOTRAN. Successful comparisons to independent numerical solutions build confidence in the approximation and implementation. Example simulations of the Walker Branch and East Fork Poplar Creek watersheds near Oak Ridge, Tennessee demonstrate the robustness of the approach in geometrically complex applications. The lack of a robust integrated surface/subsurface hydrology capability had been a barrier to PFLOTRAN’s use in critical zone studies. This work addresses that capability gap, thus enabling PFLOTRAN as a community platform for building integrated models of the critical zone.

  16. Diversity of the Genetic Environment of the blaKPC-2 Gene Among Klebsiella pneumoniae Clinical Isolates in a Chinese Hospital.

    PubMed

    Wang, Lian-Hui; Wei, Dan-Dan; Wan, La-Gen; Yu, Yang; Deng, Qiong; Liu, Yang

    2016-01-01

    KPC-producing Klebsiella pneumoniae (KPC-Kp) has been frequently reported worldwide and constitutes a major healthcare threat, given their extensively drug-resistant phenotypes. In this study, we report the characterization of the genetic environment of blaKPC-2 gene in KPC-Kp clinical strains from China belonging to diverse genotypes. Thirty-five nonduplicated KPC-Kp isolates collected in a Chinese hospital during 2012 were analyzed. All were multidrug resistant due to the presence of other resistance determinants, including metallo-β-lactamases (IMP-4, NDM-1), extended-spectrum β-lactamases (CTX-M-14, -15, -3, -10, and SHV-12), 16S rRNA methylases (armA and rmtB), and plasmid-mediated quinolone resistance determinants [qnrA, B, S, aac(6')-Ib-cr]. Using pulsed-field gel electrophoresis (PFGE), the 35 isolates were grouped into 12 clusters that were further identified as 15 sequence types (STs) by multilocus sequence typing. ST11 K. pneumoniae was the predominant clone attributed to the outbreak. blaKPC-2 was carried in plasmids of various sizes and incompatibility types. The genetic environment analysis, based on genetic structure in the plasmid pKP048, revealed five distinct platforms: the most prevalent structure was the continual occurrence in diverse STs (ST11, ST258, ST340, ST395, ST437, and ST494), harboring plasmid of blaKPC-2 in a genetic environment flanked by ISKpn8 and ISKpn6 like. This study highlights the continued evolution of the genetic environment of the blaKPC-2 gene in our hospital and movement to multiple plasmid backbones that results in acquisition by multiple clones of K. pneumoniae.

  17. SUBSURFACE VISUAL ALARM SYSTEM ANALYSIS

    SciTech Connect

    D.W. Markman

    2001-08-06

    The ''Subsurface Fire Hazard Analysis'' (CRWMS M&O 1998, page 61), and the document, ''Title III Evaluation Report for the Surface and Subsurface Communication System'', (CRWMS M&O 1999a, pages 21 and 23), both indicate the installed communication system is adequate to support Exploratory Studies Facility (ESF) activities with the exception of the mine phone system for emergency notification purposes. They recommend the installation of a visual alarm system to supplement the page/party phone system The purpose of this analysis is to identify data communication highway design approaches, and provide justification for the selected or recommended alternatives for the data communication of the subsurface visual alarm system. This analysis is being prepared to document a basis for the design selection of the data communication method. This analysis will briefly describe existing data or voice communication or monitoring systems within the ESF, and look at how these may be revised or adapted to support the needed data highway of the subsurface visual alarm. system. The existing PLC communication system installed in subsurface is providing data communication for alcove No.5 ventilation fans, south portal ventilation fans, bulkhead doors and generator monitoring system. It is given that the data communication of the subsurface visual alarm system will be a digital based system. It is also given that it is most feasible to take advantage of existing systems and equipment and not consider an entirely new data communication system design and installation. The scope and primary objectives of this analysis are to: (1) Briefly review and describe existing available data communication highways or systems within the ESF. (2) Examine technical characteristics of an existing system to disqualify a design alternative is paramount in minimizing the number of and depth of a system review. (3) Apply general engineering design practices or criteria such as relative cost, and degree of

  18. Investigation of microbial diversity in a desert Mars-like environment: Mars Desert Research Station (MDRS), Utah

    NASA Astrophysics Data System (ADS)

    Direito, Maria Susana; Staats, Martijn; Foing, Bernard H.; Ehrenfreund, Pascale; Roling, Wilfred

    The Utah Mars Desert Research Station (MDRS) harbours geo-morphology and geo-processes analogues to the planet Mars. Soil samples were collected during the EuroGeoMars campaign (from 24 January to 1 March 2009) from different locations and depths [1]. Samples were distributed among scientific collaborator institutes for analysis of microbial diversity, amino acid content and degradation, content of PAH or larger organic molecules, and respective soil properties. Our sample analysis had the objective of characterizing the microbial communities in this Mars analogue: DNA isolation, PCR (Polymerase Chain Reaction) using primers for DNA amplification of Bacteria, Archaea and Eukarya ribosomal RNA (rRNA) gene fragments, DGGE (Denaturing Gradient Gel Electrophoresis) and clone library construction with the final aim of sequencing. Results indicate that life is present in all the three domains of life (Archaea, Bacteria and Eukarya), while the most diversity was found in the domain Bacteria. Microorgan-isms are heterogeneously present and their identities are currently investigated. The obtained information will be later related to the other scientific analysis in order to obtain a better understanding of this Mars analogue site, which in turn will provide important information for the search for life on Mars. [1] Foing, B.H. et al . (2009). Exogeolab lander/rover instruments and EuroGeoMars MDRS campaign. LPI, 40, 2567.

  19. 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.

  20. The Pedagogy of the Marginalized: Understanding How Historically Disadvantaged Students Negotiate Their Epistemic Access in a Diverse University Environment

    ERIC Educational Resources Information Center

    Cross, Michael; Atinde, Vivian

    2015-01-01

    This article explores how successful undergraduate students from marginalized communities or historically disadvantaged backgrounds negotiate their performance within a university environment. It addresses one important question: How did they make their way up the academic ladder in the face of hardship determined by their unique historical…

  1. The VIPER project (Visualization Integration Platform for Exploration Research): a biologically inspired autonomous reconfigurable robotic platform for diverse unstructured environments

    NASA Astrophysics Data System (ADS)

    Schubert, Oliver J.; Tolle, Charles R.

    2004-09-01

    Over the last decade the world has seen numerous autonomous vehicle programs. Wheels and track designs are the basis for many of these vehicles. This is primarily due to four main reasons: a vast preexisting knowledge base for these designs, energy efficiency of power sources, scalability of actuators, and the lack of control systems technologies for handling alternate highly complex distributed systems. Though large efforts seek to improve the mobility of these vehicles, many limitations still exist for these systems within unstructured environments, e.g. limited mobility within industrial and nuclear accident sites where existing plant configurations have been extensively changed. These unstructured operational environments include missions for exploration, reconnaissance, and emergency recovery of objects within reconfigured or collapsed structures, e.g. bombed buildings. More importantly, these environments present a clear and present danger for direct human interactions during the initial phases of recovery operations. Clearly, the current classes of autonomous vehicles are incapable of performing in these environments. Thus the next generation of designs must include highly reconfigurable and flexible autonomous robotic platforms. This new breed of autonomous vehicles will be both highly flexible and environmentally adaptable. Presented in this paper is one of the most successful designs from nature, the snake-eel-worm (SEW). This design implements shape memory alloy (SMA) actuators which allow for scaling of the robotic SEW designs from sub-micron scale to heavy industrial implementations without major conceptual redesigns as required in traditional hydraulic, pneumatic, or motor driven systems. Autonomous vehicles based on the SEW design posses the ability to easily move between air based environments and fluid based environments with limited or no reconfiguration. Under a SEW designed vehicle, one not only achieves vastly improved maneuverability within a

  2. Diversity of Salmonella Strains Isolated from the Aquatic Environment as Determined by Serotyping and Amplification of the Ribosomal DNA Spacer Regions

    PubMed Central

    Baudart, Julia; Lemarchand, Karine; Brisabois, Anne; Lebaron, Philippe

    2000-01-01

    Salmonella species are pathogenic bacteria often detected in sewage, freshwater, marine coastal water, and groundwater. Salmonella spp. can survive for long periods in natural waters, and the persistence of specific and epidemic strains is of great concern in public health. However, the diversity of species found in the natural environment remains unknown. The aim of this study was to investigate the diversity of Salmonella strains isolated from different natural aquatic systems within a Mediterranean coastal watershed (river, wastewater, and marine coastal areas). A total of 574 strains isolated from these natural environments were identified by both conventional serotyping and the ribosomal spacer-heteroduplex polymorphism (RS-HP) method (M. A. Jensen and N. Straus, PCR Methods Appl. 3:186–194, 1993). More than 40 different serotypes were found, and some serotypes probably mobilized from widespread animal-rearing activities were detected only during storm events. These serotypes may be good indicators of specific contamination sources. Furthermore, the RS-HP method based on the PCR amplification of the intergenic spacer region between the 16S and 23S rRNA genes can produce amplicon profiles allowing the discrimination of species at both serotype and intraserotype levels. This method represents a powerful tool that could be used for rapid typing of Salmonella isolates. PMID:10742240

  3. 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

  4. 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 H2, CH4, Ca(2+), Mg(2+), [Formula: see text], [Formula: see text], trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation

  5. 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 H2, CH4, Ca2+, Mg2+, NO3more » $-$, 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

  6. Subsurface Electromagnetic Target Characterization and Identification

    DTIC Science & Technology

    1979-06-01

    B. Subsurface Electromagnetic Video Pulse Radar System 5 C. The Subsurface Targets 11 D. Raw Measured Waveforms 14 E. Processed Waveforms 15 III...259 r i. I .. . . .... .. . . . . .;. . . . .. .. o _ • v . . • • • -• -. . .. -"... .. . II II LIST OF FIGURES Figure Page 1 The subsurface pulse ...7 3 Typical raw waveform received by the pulse radar system ..... ................... .i..... 9 4 Physical characteristics of the subsurface

  7. Local forest environment largely affects below-ground growth, clonal diversity and fine-scale spatial genetic structure in the temperate deciduous forest herb Paris quadrifolia.

    PubMed

    Jacquemyn, Hans; Brys, Rein; Honnay, Olivier; Hermy, Martin; Roldán-Ruiz, Isabel

    2005-12-01

    Paris quadrifolia (herb Paris) is a long-lived, clonal woodland herb that shows strong differences in local population size and shoot density along an environmental gradient of soil and light conditions. This environmentally based structuring may be mediated by differences in clonal growth and seedling recruitment through sexual reproduction. To study the interrelationship between environmental conditions and spatial patterns of clonal growth, the spatial genetic structure of four P. quadrifolia populations growing in strongly contrasting sites was determined. In the first place, plant excavations were performed in order to (i) determine differences in below-ground growth of genets, (ii) investigate connectedness of ramets and (iii) determine total genet size. Although no differences in internode length were found among sites, clones in moist sites were much smaller (genets usually consisted of 1-3 interconnected shoots, most of them flowering) than genets in dry sites, which consisted of up to 15 interconnected shoots, the majority of which were vegetative. Further, amplified fragment length polymorphism (AFLP) markers were used. Clonal diversity was higher in populations located in moist and productive ash-poplar forests compared to those found in drier and less productive mixed forest sites (G/N: 0.27 and 0.14 and Simpson's D: 0.84 and 0.75, respectively). Patterns of spatial population genetic structure under dry conditions revealed several large clones dominating the entire population, whereas in moist sites many small genets were observed. Nevertheless, strong spatial genetic structure of the genet population was observed. Our results clearly demonstrate that patterns of clonal diversity and growth form of P. quadrifolia differ among environments. Limited seedling recruitment and large clone sizes due to higher connectedness of ramets explain the low clonal diversity in dry sites. In moist sites, higher levels of clonal diversity and small clone sizes

  8. Is working in culturally diverse working environment associated with physicians' work-related well-being? A cross-sectional survey study among Finnish physicians.

    PubMed

    Aalto, Anna-Mari; Heponiemi, Tarja; Väänänen, Ari; Bergbom, Barbara; Sinervo, Timo; Elovainio, Marko

    2014-08-01

    International mobility of health care professionals is increasing, though little is known about how working in a culturally diverse team affects the native physicians' psychosocial work environment. We examined Finnish physicians' perceptions of work-related wellbeing according to whether they had foreign-born colleagues (FBCs) in their work unit. We also examined whether work-related resources moderate the potential association between work-related wellbeing and working alongside FBCs. A cross-sectional survey was conducted for a random sample of physicians in Finland in 2010 (3826 respondents, response rate 55%). Analyses were restricted to native Finnish physicians working in public health care. The results were analyzed by ANCOVA. In unadjusted analyses, having FBCs was related to poor team climate (p<0.001) and poor job satisfaction (p=0.001). Those physicians who reported high procedural justice and high job control perceived also higher job satisfaction even if they had many FBCs in the work unit (p=0.007 for interaction between FBCs and procedural justice and p<0.001 for interaction between FBCs and job control). These associations were robust to adjustments for age, sex, health care sector, specialization, on-call duty, employment contract, full-time employment and leadership position. The results indicate that culturally diverse work units face challenges related to team climate and job satisfaction. The results also show that leadership plays an important role in culturally diverse work units. The potential challenges of culturally diverse teams for native physicians may be reduced by fair decision-making and by increasing physicians' job control.

  9. 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

  10. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

    PubMed Central

    Sullivan, Matthew B; Huang, Katherine H; Ignacio-Espinoza, Julio C; Berlin, Aaron M; Kelly, Libusha; Weigele, Peter R; DeFrancesco, Alicia S; Kern, Suzanne E; Thompson, Luke R; Young, Sarah; Yandava, Chandri; Fu, Ross; Krastins, Bryan; Chase, Michael; Sarracino, David; Osburne, Marcia S; Henn, Matthew R; Chisholm, Sallie W

    2010-01-01

    T4-like myoviruses are ubiquitous, and their genes are among the most abundant documented in ocean systems. Here we compare 26 T4-like genomes, including 10 from non-cyanobacterial myoviruses, and 16 from marine cyanobacterial myoviruses (cyanophages) isolated on diverse Prochlorococcus or Synechococcus hosts. A core genome of 38 virion construction and DNA replication genes was observed in all 26 genomes, with 32 and 25 additional genes shared among the non-cyanophage and cyanophage subsets, respectively. These hierarchical cores are highly syntenic across the genomes, and sampled to saturation. The 25 cyanophage core genes include six previously described genes with putative functions (psbA, mazG, phoH, hsp20, hli03, cobS), a hypothetical protein with a potential phytanoyl-CoA dioxygenase domain, two virion structural genes, and 16 hypothetical genes. Beyond previously described cyanophage-encoded photosynthesis and phosphate stress genes, we observed core genes that may play a role in nitrogen metabolism during infection through modulation of 2-oxoglutarate. Patterns among non-core genes that may drive niche diversification revealed that phosphorus-related gene content reflects source waters rather than host strain used for isolation, and that carbon metabolism genes appear associated with putative mobile elements. As well, phages isolated on Synechococcus had higher genome-wide %G+C and often contained different gene subsets (e.g. petE, zwf, gnd, prnA, cpeT) than those isolated on Prochlorococcus. However, no clear diagnostic genes emerged to distinguish these phage groups, suggesting blurred boundaries possibly due to cross-infection. Finally, genome-wide comparisons of both diverse and closely related, co-isolated genomes provide a locus-to-locus variability metric that will prove valuable for interpreting metagenomic data sets. PMID:20662890

  11. 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.

  12. Staphylococcal adaptation to diverse physiologic niches: an overview of transcriptomic and phenotypic changes in different biological environments

    PubMed Central

    Dastgheyb, Sana S; Otto, Michael

    2015-01-01

    Host niches can differ strongly regarding, for example, oxygen tension, pH or nutrient availability. Staphylococcus aureus and other staphylococci are common colonizers of human epithelia as well as important human pathogens. The phenotypes that they show in different host environments, and the corresponding bacterial transcriptomes and proteomes, are currently under intense investigation. In this review, we examine the available literature describing staphylococcal phenotypes, such as expression of virulence factors, gross morphologic characteristics and growth patterns, in various physiological environments. Going forward, these studies will help researchers and clinicians to form an enhanced and more detailed picture of the interactions existing between the host and staphylococci as some of its most frequent colonizers and invaders. PMID:26584249

  13. Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.

    PubMed

    Baker, Brett J; Saw, Jimmy H; Lind, Anders E; Lazar, Cassandre Sara; Hinrichs, Kai-Uwe; Teske, Andreas P; Ettema, Thijs J G

    2016-02-15

    The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.

  14. 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

  15. Armored Enzyme Nanoparticles for Remediation of Subsurface

    SciTech Connect

    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; 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.

  16. Reflectance Spectra Diversity of Silica-Rich Materials: Sensitivity to Environment and Implications for Detections on Mars

    NASA Technical Reports Server (NTRS)

    Rice, M. S.; Cloutis, E. A.; Bell, J. F., III; Bish, D. L.; Horgan, B. H.; Mertzman, S. A.; Craig, M. A.; Renault, R. W.; Gautason, B.; Mountain, B.

    2013-01-01

    Hydrated silica-rich materials have recently been discovered on the surface of Mars by the Mars Exploration Rover (MER) Spirit, the Mars Reconnaissance Orbiter (MRO) Compact Reconnaissance Imaging Spectrometer for Mars (CRISM), and the Mars Express Observatoire pour la Mineralogie, l'Eau, les Glaces, et l'Activite'(OMEGA) in several locations. Having been interpreted as hydrothermal deposits and aqueous alteration products, these materials have important implications for the history of water on the martian surface. Spectral detections of these materials in visible to near infrared (Vis NIR) wavelengths have been based on a H2O absorption feature in the 934-1009 nm region seen with Spirit s Pancam instrument, and on SiOH absorption features in the 2.21-2.26 micron range seen with CRISM. Our work aims to determine how the spectral reflectance properties of silica-rich materials in Vis NIR wavelengths vary as a function of environmental conditions and formation. Here we present laboratory reflectance spectra of a diverse suite of silica-rich materials (chert, opal, quartz, natural sinters and synthetic silica) under a range of grain sizes and temperature, pressure, and humidity conditions. We find that the H2O content and form of H2O/OH present in silica-rich materials can have significant effects on their Vis NIR spectra. Our main findings are that the position of the approx.1.4 microns OH feature and the symmetry of the approx.1.9 microns feature can be used to discern between various forms of silica-rich materials, and that the ratio of the approx.2.2 microns (SiOH) and approx.1.9 microns (H2O) band depths can aid in distinguishing between silica phases (opal-A vs. opal-CT) and formation conditions (low vs. high temperature). In a case study of hydrated silica outcrops in Valles Marineris, we show that careful application of a modified version of these spectral parameters to orbital near-infrared spectra (e.g., from CRISM and OMEGA) can aid in characterizing the

  17. Species associations structured by environment and land-use history promote beta-diversity in a temperate forest.

    PubMed

    Murphy, Stephen J; Audino, Livia D; Whitacre, James; Eck, Jenalle L; Wenzel, John W; Queenborough, Simon A; Comita, Liza S

    2015-03-01

    Patterns of diversity and community composition in forests are controlled by a combination of environmental factors, historical events, and stochastic or neutral mechanisms. Each of these processes has been linked to forest community assembly, but their combined contributions to alpha and beta-diversity in forests has not been well explored. Here we use variance partitioning to analyze approximately 40,000 individual trees of 49 species, collected within 137 ha of sampling area spread across a 900-ha temperate deciduous forest reserve in Pennsylvania to ask (1) To what extent is site-to-site variation in species richness and community composition of a temperate forest explained by measured environmental gradients and by spatial descriptors (used here to estimate dispersal-assembly or unmeasured, spatially structured processes)? (2) How does the incorporation of land-use history information increase the importance attributed to deterministic community assembly? and (3) How do the distributions and abundances of individual species within the community correlate with these factors? Environmental variables (i.e., topography, soils, and distance to stream), spatial descriptors (i.e., spatial eigenvectors derived from Cartesian coordinates), and land-use history variables (i.e., land-use type and intensity, forest age, and distance to road), explained about half of the variation in both species richness and community composition. Spatial descriptors explained the most variation, followed by measured environmental variables and then by land- use history. Individual species revealed variable responses to each of these sets of predictor variables. Several species were associated with stream habitats, and others were strictly delimited across opposing north- and south-facing slopes. Several species were also associated with areas that experienced recent (i.e., <100 years) human land-use impacts. These results indicate that deterministic factors, including environmental and

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

    PubMed

    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

    2013-03-01

    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, t