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Sample records for subsurface environments diversity

  1. 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

  2. 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)

  3. Karst pools in subsurface environments: collectors of microbial diversity or temporary residence between habitat types.

    PubMed

    Shabarova, Tanja; Pernthaler, Jakob

    2010-04-01

    We studied bacterial diversity and community composition in three shallow pools of a Swiss karst cave system with contrasting hydrological and hydrochemical properties. The microbial assemblages in the pools were remarkably different, and only one operational taxonomic unit of 16S rRNA genes (OTU, 97% similarity) was shared between the three of them (total OTU number in all pools: 150). Unexpectedly high microbial phylotype richness was found even in the two pools without groundwater contact and with low concentrations of organic carbon and total cell numbers (< 10(4) ml(-1)). One of these seepage water fed systems harboured 15 distinct OTUs from several deeply branching lineages of the candidate phylum OP3, whereas representatives of this group were not detected in the other two pools. A tentative phylogeographic analysis of available OP3-related sequences in the context of our data set revealed that there was generally little agreement between the habitats of origin of closely related sequence types. Two bacterial clades affiliated with the obligate methylamine utilizer Methylotenera mobilis were only found in the pool that was exposed to repeated flooding events. These bacteria formed relatively stable populations of up to 6% of total cell counts over periods of several months irrespective of inundation by groundwater. This suggests that karst water may provide a means of transport for these bacteria from terrestrial to freshwater habitats.

  4. 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

  5. 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.

  6. 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 Ashley; Moberly, James G; Shakya, Migun; Vishnivetskaya, T.; Elias, Dwayne A

    2014-01-01

    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.

  7. 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

  8. 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

  9. Microbiology of subsurface environments: Proceedings second investigators' meeting

    SciTech Connect

    Not Available

    1986-01-01

    The agenda of this meeting was to provide for: (1) general reports by the principal investigators on the initial scientific findings from the Savannah River Site cores; (2) a feedback session during which the principal investigators and others in attendance can provide a critique on how the program can be improved; (3) presentations by scientists on research that may be related to the program. The preliminary scientific results indicate that a diverse, metabolically active microbial community is present in unconsolidated materials to depths of 400 meters below the surface of the Savannah River study site. A thorough characterization of samples revealed that deep subsurface environments are inhabited by microorganisms that range from denitrifying, sulfate-reducing, and methanogenic bacteria to aerobic heterotrophs, autotrophs, fungi, and protozoa. These results have implications in the use of indigenous microorganisms for biological decontamination of deep aquifers or as a biobarrier to contaminant movement, development of strategies to cope with health problems arising from contamination of aquifers by pathogenic microorganisms, reduction of biocorrosion of waste containers planned for storage in deep subsurface environments, and as a source of new organisms or metabolic capabilities for biotechnological applications.

  10. Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments.

    PubMed

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

    2014-01-01

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

  11. 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...

  12. Integrated research on subsurface environments in Asian urban areas.

    PubMed

    Taniguchi, Makoto; Burnett, William C; Ness, Gayl D

    2008-10-15

    The RIHN project "Human impacts on urban subsurface environments" aims to suggest improved development plans of urban centers for human well-being. This will be done by examining reconstructed past changes in urban environments, and by developing integrated nature-social models. Subsurface environmental indicators are developed from the points of view of: (1) human activities; (2) climate change; and (3) character of urban development and social policies. Water, heat, and material environments and transport vectors are being evaluated by a number of different approaches. Some of these include investigating changes in groundwater resources using satellite observations, reconstructing effects of climate change and urbanization using subsurface thermal regimes, and evaluating past contamination patterns from preserved subsurface records. In this overview paper, we describe the current status of urbanization in Asia, subsurface water conditions, material and contaminant transport to surface waters by groundwater, and subsurface thermal anomalies due to the heat island effect. The rapid pace of urbanization in Asia requires that we develop a better understanding of how to deal with environmental impacts, both above and below ground.

  13. Active Serpentinization and the Potential for a Diverse Subsurface Biosphere

    NASA Astrophysics Data System (ADS)

    Canovas, P. A.; Shock, E.

    2013-12-01

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

  14. 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...

  15. Examining Deep Subsurface Sulfate Reducing Bacterial Diversity to Test Spatial and Temporal Biogeography

    NASA Astrophysics Data System (ADS)

    Mills, H. J.; Reese, B. K.

    2013-12-01

    In this study, we take advantage of the isolation and scale of the deep marine subsurface to examine microbial biogeography. Unlike other environments, deep marine subsurface provides a unique opportunity to study biogeography across four dimensions. These samples are not only isolated by linear space on a global scale, but they are also temporally isolated by, in some cases, tens of millions of years. Through the support of multiple Integrated Ocean Drilling Program expeditions, we characterized the metabolically active fraction of the subsurface microbial community by targeting and sequencing 16S rRNA gene transcripts (RNA-based analysis). By characterizing the metabolically active fraction, we described lineages that were currently under selective environmental pressure and not relic lineages that may have become dormant or dead at some point in the past. This study was narrowed from the total diversity obtained to provide a detailed examination of the distribution and diversity of sulfate reducing bacteria (SRB); a functional group highly important to and ubiquitous in marine systems. The biogeochemical importance of this functional group, compounded with defined clades makes it a valuable and feasible target for a global biogeography study. SRB lineages from the deep subsurface were compared to contemporary lineages collected from multiple shallow sediment sites that had been extracted and sequenced using the same techniques. The SRB sequences acquired from our databases were clustered using 97% sequence similarity and analyzed using a suite of diversity and statistical tools. The geochemical conditions of the sediments sampled were considered when analyzing the resulting dendrograms and datasets. As hypothesized, lineages from the deep subsurface phylogenetically grouped together. However, similarities were detected to lineages from the shallow modern sediments, suggesting novel lineages may have evolved at a slow rate due to predicted lengthened life cycles

  16. 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.

  17. 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

  18. 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.

  19. Subsurface flow and vegetation patterns in tidal environments

    NASA Astrophysics Data System (ADS)

    Ursino, Nadia; Silvestri, Sonia; Marani, Marco

    2004-05-01

    Tidal environments are characterized by a complex interplay of hydrological, geomorphic, and biological processes, and their understanding and modeling thus require the explicit description of both their biotic and abiotic components. In particular, the presence and spatial distribution of salt marsh vegetation (a key factor in the stabilization of the surface soil) have been suggested to be related to topographic factors and to soil moisture patterns, but a general, process-based comprehension of this relationship has not yet been achieved. The present paper describes a finite element model of saturated-unsaturated subsurface flow in a schematic salt marsh, driven by tidal fluctuations and evapotranspiration. The conditions leading to the establishment of preferentially aerated subsurface zones are studied, and inferences regarding the development and spatial distribution of salt marsh vegetation are drawn, with important implications for the overall ecogeomorphological dynamics of tidal environments. Our results show that subsurface water flow in the marsh induces complex water table dynamics, even when the tidal forcing has a simple sinusoidal form. The definition of a space-dependent aeration time is then proposed to characterize root aeration. The model shows that salt marsh subsurface flow depends on the distance from the nearest creek or channel and that the subsurface water movement near tidal creeks is both vertical and horizontal, while farther from creeks, it is primarily vertical. Moreover, the study shows that if the soil saturated conductivity is relatively low (10-6 m s-1, values quite common in salt marsh areas), a persistently unsaturated zone is present below the soil surface even after the tide has flooded the marsh; this provides evidence of the presence of an aerated layer allowing a prolonged presence of oxygen for aerobic root respiration. The results further show that plant transpiration increases the extent and persistence of the aerated

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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…

  6. Determining the Hydraulic Conductivity of the Subsurface in Wetland Environments

    NASA Astrophysics Data System (ADS)

    Berry, L. E.; Mutiti, S.; Hazzard, S.

    2011-12-01

    Slug tests are a popular method for determining hydraulic conductivity (K) of subsurface material and have the potential to be very accurate because of minimal disturbance to the subsurface. A variety of methods and piezometer construction are widely used for slug tests. Most wetland environments are composed of low K material such as silt or clay, which can make determination of hydrogeologic properties challenging. This study is part of a broader ongoing project to understand the functions of wetlands in Milledgeville, Georgia, a city in the Oconee River Basin (ORB), which straddles the Piedmont and the Coastal Plain. The ORB sits on saprolite and gneiss bedrock, and consequently, its wetlands exhibit a high concentration of clay materials. One site, the Oconee River Greenway, lies along the riverbanks of the Oconee. The second site, Andalusia Farm, is a historical site formerly belonging to writer, Flannery O'Connor. The objective of this study was to determine the best method and/or piezometer type for determining K values for low permeability wetland material. We also investigated the potential of using heat and pressure monitoring to determine horizontal and vertical extent of slug tests. The Greenway wetland has significant seasonal interflow through a relatively more permeable sandy layer. Borehole logs and electrical resistivity profiling were used to study the subsurface stratigraphy. Slug test results from different types of piezometers (borehole, drive point, partially screened and fully screened) were compared. Pressure transducers and HOBO thermisters were used to collect water depth, pressure and temperature data. These results were also compared to results from sediment analyses, in-situ permeameters and heat monitoring. Drive point and borehole piezometers with equal diameters produced comparable K estimates at each site. However, fully screened piezometers of either installation type produced higher K values than partially screened piezometers

  7. 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?

  8. 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.

  9. 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

  10. 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

  11. 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. PMID:26436251

  12. 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.

  13. 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.

  14. Environmental parameters controlling microbial activities in terrestrial subsurface environments

    SciTech Connect

    Kieft, T.L.

    1990-01-01

    This project was begun in July 1988 as part of Phase I of the Deep Microbiology Subprogram. At this time, the Subprogram was preparing for sampling near the Savannah River Site (SRS) from what was being termed the Investigator's Hole.'' This was the fourth hole drilled for sampling in the coastal plain sediments at a site near the SRS. Since there was a possibility of sampling from the saline Triassic basin in the deeper regions in this fourth hole, there was particular interest in quantifying halotolerant microorganisms from these samples and in determining the responses of subsurface microbes to a range of soft concentrations. Further interest in the soft tolerances of microbes from these coastal sediments arose from the fact that all of these sediments were deposited under marine conditions. It was also anticipated that samples would be available from the shallow unsaturated (vadose) zone at this site, so there was interest in quantifying microbial responses to matric water potential as well as solute water potential. The initial objectives of this research project were to: characterize microbial communities in a saline aquifer; determine the potential for microbial metabolism of selected organic compounds in a saline aquifers; characterize microbial communities in unsaturated subsurface materials (vadose zones); and determine the potential for microbial metabolism of selected organic compounds in unsaturated subsurface materials (vadose zones). Samples were collected from the borehole during a period extending from August to October 1988. A total of nine samples were express shipped to New Mexico Tech for analyses. These were all saturated zone samples from six different geological formations. Water contents and water potentials were measured at the time of sample arrival.

  15. 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.

  16. 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.

  17. Erratum to "Integrated research on subsurface environments in Asian urban areas".

    PubMed

    Taniguchi, Makoto; Burnett, William C; Ness, Gayl D

    2009-04-15

    The RIHN project "Human impacts on urban subsurface environments" aims to suggest improved development plans of urban centers for human well-being. This will be done by examining reconstructed past changes in urban environments, and by developing integrated nature-social models. Subsurface environmental indicators are developed from the points of view of: (1) human activities; (2) climate change; and (3) character of urban development and social policies. Water, heat, and material environments and transport vectors are being evaluated by a number of different approaches. Some of these include investigating changes in groundwater resources using satellite observations, reconstructing effects of climate change and urbanization using subsurface thermal regimes, and evaluating past contamination patterns from preserved subsurface records. In this overview paper, we describe the current status of urbanization in Asia, subsurface water conditions, material and contaminant transport to surface waters by groundwater, and subsurface thermal anomalies due to the heat island effect. The rapid pace of urbanization in Asia requires that we develop a better understanding of how to deal with environmental impacts, both above and below ground.

  18. [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

  19. 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.

  20. Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input.

    PubMed

    Cho, J C; Kim, S J

    2000-03-01

    Despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. In this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16S rDNA sequences. The similarity coefficients of restriction fragment length polymorphism (RFLP) patterns of the cloned 16S ribosomal DNAs showed that the bacterial communities in livestock wastewater samples were more closely related to those in contaminated aquifer samples. In addition, calculations of community diversity clearly showed that bacterial communities in the livestock wastewater and the contaminated aquifer were much more diverse than those in the uncontaminated aquifer. Thus, the increase in bacterial-community diversity in the contaminated aquifer was assumed to be due to the infiltration of livestock wastewater, containing high concentrations of diverse microbial flora, into the aquifer. Phylogenetic analysis of the sequences from a subset of the RFLP patterns showed that the Cytophaga-Flexibacter-Bacteroides and low-G+C gram-positive groups originating from livestock wastewater were responsible for the change in the bacterial community in groundwater. This was evidenced by the occurrence of rumen-related sequences not only in the livestock wastewater samples but also in the contaminated-groundwater samples. Rumen-related sequences, therefore, can be used as indicator sequences for fecal contamination of groundwater, particularly from livestock.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

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

    PubMed

    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 × 10(4) 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

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

    PubMed

    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 × 10(4) 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

  10. 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

  11. 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

  12. 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.

  13. Diversity: creating an environment of inclusiveness.

    PubMed

    Swanson, Jane W

    2004-01-01

    Diversity is a concept that most organizations espouse but find challenging to put into practice. It is especially critical for healthcare organizations to be responsive in addressing issues of diversity related to not only employees but also clients. This article identifies the following 3 areas that must be addressed if an organization is to succeed in creating an environment where diversity and inclusiveness are honored: (1) organizations and their leaders need to be aware of their reactions "those who are different" in their organization. This awareness is critical in identifying the underlying obstacles that prevent a truly inclusive workplace; (2) organizations and their leaders need to be able to expand their perspectives allowing them to not only understand but appreciate others. These expanded perspectives can provide a potentially powerful tool for both problem solving and conflict resolution; (3) if organizations and their leaders are actively engaged in exploring options and are open to alternatives, they will find that they not only succeed in creating an environment of inclusiveness but also are in a better position to meet the needs of employees, patients, and a multicultural society. PMID:15446609

  14. 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

  15. 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

  16. 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. PMID:27047476

  17. Multiple metaphor environments: designing for diversity.

    PubMed

    Akoumianakis, D; Stephanidis, C

    2003-01-15

    This paper advances a proposition for the engineering of interactive computer-based environments capable of exhibiting alternative interactive embodiments to cope with diversity in users, interaction platforms and usage contexts. Such systems are referred to as Multiple Metaphor Environments (MME). The theoretical underpinnings of an MME rely on a conception of HCI design as mapping functions in a machine-oriented language (target domain) to symbols in a user-oriented language (source domain), and vice versa. Such a conception, which is rooted in developments in communication theory and the philosophy of language, constitutes the baseline for formulating a proposal for the design of MME. The proposal comprises a set of engineering principles, process-oriented guidelines and design techniques intended to facilitate a detailed account of how interactive systems could be designed to cope with diversity. To aid the articulation of the various properties of MME, we refer to concrete case studies that provide exemplars of novel insights and promising design practices towards the specification of MME.

  18. [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.

  19. 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.

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

    PubMed

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

    2008-06-01

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

  1. 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.

  2. 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

  3. Novel Archaea and Bacteria in a hydrologically isolated deep subsurface environment

    NASA Astrophysics Data System (ADS)

    Chandler, Darrell P.; Brockman, Fred J.; Fredrickson, James K.

    1997-07-01

    Total community DNA and RNA were extracted from a deep (188 m), saturated, mesophilic (17 degree(s)C), low biomass (10(superscript 4) cells g(superscript -1)) subsurface paleosol. 16S rDNA was amplified by PCR using universal eubacterial or archaeal primers and cloned. Cloned 16S rDNA fragments were sequenced and subjected to phylogenetic analysis. A novel clade of Crenarchaea were discovered which are most closely related to a single clone recovered from an Fe-S hot spring (80 degree(s)C). Novel Bacterial sequences were also found which branch deeply in the universal phylogenetic tree in association with Chloroflexus, Deinococcus, and Thermus. Total RNA analysis suggested that the novel Crenarchaea were active in this environment. Geological and hydrologic properties of the sediment indicate that microbial and nutrient transport between individual strata are restricted, and are consistent with chemolithoautotrophic metabolisms of cultured Crenarchaea involving the H(subscript 2)/SO(subscript 4) electron donor/acceptor couple. The physical properties of the surrounding lithologies suggest that these novel microorganisms are descendants of the microbial communities originally deposited with the sediment ca. 6 - 8 Mya. Identification of these novel, active microorganisms in an oligotrophic, hydrologically isolated subsurface system provides an opportunity and species-specific nucleic acid sequences and probes necessary to study long-term microbial survival in terrestrial subsurface environments.

  4. 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).

  5. 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.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2016-10-01

    Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes. PMID:27022994

  8. 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

  9. 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.

  10. 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

  11. A biogeochemical framework for bioremediation of plutonium(V) in the subsurface environment.

    PubMed

    Deo, Randhir P; Rittmann, Bruce E

    2012-07-01

    Accidental release of plutonium (Pu) from storage facilities in the subsurface environment is a concern for the safety of human beings and the environment. Given the complexity of the subsurface environment and multivalent state of Pu, we developed a quantitative biogeochemical framework for bioremediation of Pu(V)O(2) (+) in the subsurface environment. We implemented the framework in the biogeochemical model CCBATCH by expanding its chemical equilibrium for aqueous complexation of Pu and its biological sub-models for including Pu's toxicity and reduction reactions. The quantified framework reveals that most of the Pu(V) is speciated as free Pu(V)O(2) (+) ((aq)), which is a problem if the concentration of free Pu(V)O(2) (+) is ≥28 μM (the half-maximum toxicity value for bacteria able to reduce Pu(V) to Pu(III)PO(4(am))) or ≥250 μM (the full-toxicity value that takes the bioreduction rate to zero). The framework includes bioreduction of Fe(3+) to Fe(2+), which abiotically reduces Pu(V)O(2) (+) to Pu(IV) and then to Pu(III). Biotic (enzymatic) reduction of Pu(V)O(2) (+) directly to Pu(III) by Shewanella alga (S. alga) is also included in the framework. Modeling results also reveal that for formation of Pu(III)PO(4(am)), the desired immobile product, the concentration of coexisting model strong ligand-nitrilotriacetic acid (NTA)-should be less than or equal to the concentration of total Pu(III).

  12. 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

  13. 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

  14. 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). PMID:23398962

  15. 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).

  16. 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.

  17. Laboratory and field evidence for long-term starvation survival of microorganisms in subsurface terrestrial environments

    NASA Astrophysics Data System (ADS)

    Kieft, Thomas L.; Murphy, Ellyn M.; Amy, P. S.; Haldeman, D. L.; Ringelberg, David B.; White, David C.

    1997-07-01

    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 PLFAs. To test survivability of microorganisms over a geologic time scale, we characterized microbial communities in a sequence of unsaturated sediments ranging in age from modern to > 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 makeup of surviving communities, as indicated by PLFA profiles. Sites with different porewater recharge rates and patterns of Pleistocene flooding had different communities. These and other studies provide evidence that microorganisms can survive nutrient limitation for geologic time periods.

  18. 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.

  19. 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

  20. Microbial Diversity in Coastal Subsurface Sediments: a Cultivation Approach Using Various Electron Acceptors and Substrate Gradients

    PubMed Central

    Köpke, Beate; Wilms, Reinhard; Engelen, Bert; Cypionka, Heribert; Sass, Henrik

    2005-01-01

    Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, “Bacteroidetes,” “Fusobacteria,” Actinobacteria, and “Firmicutes.” Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors. PMID:16332756

  1. 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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from

  4. 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. PMID:17540467

  5. 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.

  6. 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

  7. 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. PMID:20602990

  8. 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.

  9. 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. PMID:21902491

  10. 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.

  11. Relationship between the adhesive properties of bacteria and their transport and colonization in the subsurface environment. Final technical report

    SciTech Connect

    Fletcher, M.

    1997-03-13

    The adhesion of bacteria to sediment particle or rock surfaces considerably effects their transport in subsurface environments. This research focuses on the macromolecular properties of bacteria that determine their adhesiveness and on the significance of adhesion in transport of subsurface bacteria. Specific objectives include (1) to obtain adhesion mutants of subsurface Pseudomonas species altered in surface adhesives; (2) to determine alterations in adhesives in selected mutants; (3) to evaluate the effect of adhesiveness on transport and long-term distribution and colonization of bacteria in porous media. Primary methods will be tranposon mutagenesis to generate adhesion mutants, biochemical analyses of cell surface polymers, and the use of laboratory columns containing subsurface materials to study the distribution and transport of bacteria along flow paths over time.

  12. Effects of soil layering and interfacial tension on DNAPL migration in subsurface environments

    SciTech Connect

    Singletary, M.A.; Pennell, K.D.; Ramsburg, A.

    1999-07-01

    A series of tetrachloroethene (PCE) infiltration experiments was conducted in 2-dimensional aquifer cells to investigate the effects of soil layering and interfacial tension on dense non-aqueous phase liquid (DNAPL) infiltration and entrapment in saturated environments. The aquifer cells were packed with a background medium, 20--30 mesh Ottawa sand, and a single low-permeability layer, consisting of either F-70 Ottawa sand or Wurtsmith aquifer material, located near the center of the cell. PCE was introduced approximately 5 cm below the water table at a constant flow rate of 0.05 ml/min. The results of these experiments demonstrate the dramatic effects that interfacial tension reduction can have on DNAPL flow and entrapment in layered subsurface systems. These findings also have implications during field implementation of surfactant enhanced aquifer remediation (SEAR), in which low interfacial tension surfactant formulations may lead to DNAPL migration into fine layers or previously uncontaminated regions of an aquifer.

  13. 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

  14. 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.

  15. 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

  16. 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…

  17. CL-20 Reactivity in the Subsurface Environment and Potential for Migration

    SciTech Connect

    Szecsody, Jim E.; Girvin, Donald C.; Qasim, Mohammad M.

    2004-07-07

    Hexanitrohexaazaisowurtzitane (CL-20) is being considered by DoD as a replacement for existing propellant and explosives. This SERDP-funded study is focused on quantification of geochemical and microbial reactions of CL-20 in sediments and transport in the subsurface environment. CL-20 is unstable in aqueous alkaline conditions (pH > 9.0), but is stable with some sediments for a year or more. Low sorption and slow degradation rates observed with oxic sediments indicate a high potential for deep migration of CL-20 (similar to RDX). Sorption of CL-20 is relatively small (Kd = 0.02 to 4.2 cm3 g-1, which results in only slight to moderate retardation relative to water (i.e., Rf 1.1 to 12). In oxic systems, CL-20 abiotically degrades at slow rates (i.e., 10s to 100s of hours) in a wide variety of sediments, but at fast rates (i.e., minutes) in the presence of 2:1 smectite clays and ferrous iron oxides. CL-20 was degraded rapidly in sediments under iron reducing conditions, demonstrating that reduced iron technologies for groundwater remediation of RDX and TNT may work for CL-20. The degradation process in reduced sediments was investigated further using specific ferrous iron phases. CL-20 was rapidly degraded with adsorbed Fe(II) on amorphous iron oxides or clays, but not adsorbed Fe(II) on silica or feldspar. Because iron oxides delocalize electrons from adsorbed Fe(II), this may increase the rate of CL-20 degradation. CL-20 degradation was also at moderate rates in the presence of minerals containing only structural Fe(II). CL-20 oxic degradation produced 2 to 4 moles of nitrate with little carbon mass, whereas anaerobic degradation produced mainly low-molecular weight compounds that are aromatic. This degradation pathway in a reducing environment may follow C-C bond breaking, as predicted from molecular modeling. Identification of further degradation products and CL-20 mineralization rates is needed to fully assess the impact of these CL-20 transformation rates on

  18. Cyanobacterial diversity and halotolerance in a variable hypersaline environment.

    PubMed

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

    2008-04-01

    The Great Salt Plains (GSP) in north-central Oklahoma, USA is an expansive salt flat (approximately 65 km(2)) that is part of the federally protected Salt Plains National Wildlife Refuge. The GSP serves as an ideal environment to study the microbial diversity of a terrestrial, hypersaline system that experiences wide fluctuations in freshwater influx and diel temperature. Our study assessed cyanobacterial diversity at the GSP by focusing on the taxonomic and physiological diversity of GSP isolates, and the 16S rRNA phylogenetic diversity of isolates and environmental clones from three sites (north, central, and south). Taxonomic diversity of isolates was limited to a few genera (mostly Phormidium and Geitlerinema), but physiological diversity based on halotolerance ranges was strikingly more diverse, even between strains of the same phylotype. The phylogenetic tree revealed diversity that spanned a number of cyanobacterial lineages, although diversity at each site was dominated by only a few phylotypes. Unlike other hypersaline systems, a number of environmental clones from the GSP were members of the heterocystous lineage. Although a number of cyanobacterial isolates were close matches with prevalent environmental clones, it is not certain if these clones reflect the same halotolerance ranges of their matching isolates. This caveat is based on the notable disparities we found between strains of the same phylotype and their inherent halotolerance. Our findings support the hypothesis that variable or poikilotrophic environments promote diversification, and in particular, select for variation in ecotype more than phylotype. PMID:17653786

  19. Diversity of the parachlamydiae in the environment.

    PubMed

    Corsaro, Daniele; Venditti, Danielle

    2006-01-01

    Chlamydiae are obligate intracellular bacteria, parasites of a variety of eukaryotes ranging from amoebae to humans. Among them, the family Parachlamydiaceae comprises endosymbionts of amoebae, mainly Acanthamoeba, currently investigated as emerging pathogens of humans and other vertebrates. 16S rDNA-based PCR culture-independent studies in environmental samples have demonstrated the presence of Chlamydiales in various types of nonmedical habitats. Here we reviewed the biology of the Parachlamydiaceae, and more particularly those studies reporting molecular evidences for their presence in the environment, with a re-analysis of the 16S rDNA phylotypes.

  20. 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.

  1. 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.

  2. Comparison of models of simazine transport and fate in the subsurface environment in a citrus farm.

    PubMed

    Chang, Ni-Bin; Srilakshmi, K R; Parvathinathan, G

    2008-01-01

    Contamination of groundwater by agrochemicals is now widely recognized as an extremely important environmental problem. Modern agricultural practices involve the combined use of irrigation with the application of large amounts of agrochemicals to maximize crop yield. Due to flood irrigation and natural runoff, agricultural activities might generate soil, surface water and groundwater contamination problems and leaching of pesticides. Modeling of the transport and fate of pesticides, such as simazine, may help understand the long-term potential risk to the subsurface environment. This paper illustrates a comparative study via the use of three different pesticide transport simulation models and the applicability of those models in determining the groundwater vulnerability to pesticides contamination in a citrus orchard located at the Lower Rio Grande Valley (LRGV). The three models used in the study are the pesticide root zone model-3 (PRZM-3), the pesticide analytical model (PESTAN) and integrated pesticide transport modeling (IPTM). The concentration values obtained from all three models are in agreement, and they show a decreasing trend from the surface through the vadose zone. The problem is how to use this information and, specifically, how to combine the testimony of a number of experts into a single useful judgment. With the aid of the fuzzy multiattribute decision making method, PRZM-3 is deemed as the most promising one for such precision farming applications.

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

    PubMed

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

    2006-01-01

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

  4. Functional Diversity and Electron Donor Dependence of Microbial Populations Capable of U(VI) Reduction in Radionuclide-Contaminated Subsurface Sediments▿

    PubMed Central

    Akob, Denise M.; Mills, Heath J.; Gihring, Thomas M.; Kerkhof, Lee; Stucki, Joseph W.; Anastácio, Alexandre S.; Chin, Kuk-Jeong; Küsel, Kirsten; Palumbo, Anthony V.; Watson, David B.; Kostka, Joel E.

    2008-01-01

    In order to elucidate the potential mechanisms of U(VI) reduction for the optimization of bioremediation strategies, the structure-function relationships of microbial communities were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate. A polyphasic approach was used to assess the functional diversity of microbial populations likely to catalyze electron flow under conditions proposed for in situ uranium bioremediation. The addition of ethanol and glucose as supplemental electron donors stimulated microbial nitrate and Fe(III) reduction as the predominant terminal electron-accepting processes (TEAPs). U(VI), Fe(III), and sulfate reduction overlapped in the glucose treatment, whereas U(VI) reduction was concurrent with sulfate reduction but preceded Fe(III) reduction in the ethanol treatments. Phyllosilicate clays were shown to be the major source of Fe(III) for microbial respiration by using variable-temperature Mössbauer spectroscopy. Nitrate- and Fe(III)-reducing bacteria (FeRB) were abundant throughout the shifts in TEAPs observed in biostimulated microcosms and were affiliated with the genera Geobacter, Tolumonas, Clostridium, Arthrobacter, Dechloromonas, and Pseudomonas. Up to two orders of magnitude higher counts of FeRB and enhanced U(VI) removal were observed in ethanol-amended treatments compared to the results in glucose-amended treatments. Quantification of citrate synthase (gltA) levels demonstrated a stimulation of Geobacteraceae activity during metal reduction in carbon-amended microcosms, with the highest expression observed in the glucose treatment. Phylogenetic analysis indicated that the active FeRB share high sequence identity with Geobacteraceae members cultivated from contaminated subsurface environments. Our results show that the functional diversity of populations capable of U(VI) reduction is dependent upon the choice of electron donor. PMID:18378664

  5. A multivariate analysis of beta diversity across organisms and environments.

    PubMed

    Soininen, Janne; Lennon, Jack J; Hillebrand, Helmut

    2007-11-01

    We examined variability in hierarchical beta diversity across ecosystems, geographical gradients, and organism groups using multivariate spatial mixed modeling analysis of two independent data sets. The larger data set comprised reported ratios of regional species richness (RSR) to local species richness (LSR) and the second data set consisted of RSR:LSR ratios derived from nested species-area relationships. There was a negative, albeit relatively weak, relationship between beta diversity and latitude. We found only relatively subtle differences in beta diversity among the realms, yet beta diversity was lower in marine systems than in terrestrial or freshwater realms. Beta diversity varied significantly among organisms' major characteristics such as body mass, trophic position, and dispersal type in the larger data set. Organisms that disperse via seeds had highest beta diversity, and passively dispersed organisms showed the lowest beta diversity. Furthermore, autotrophs had lower beta diversity than organisms higher up the food web; omnivores and carnivores had consistently higher beta diversity. This is evidence that beta diversity is simultaneously controlled by extrinsic factors related to geography and environment, and by intrinsic factors related to organism characteristics.

  6. 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

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

    PubMed

    Wang, Y; Papenguth, H W

    2001-02-01

    Microbial reactions play an important role in regulating pore water chemistry as well as secondary mineral distribution in many subsurface systems and, therefore, may directly impact radionuclide migration in those systems. This paper presents a general modeling approach to couple microbial metabolism, redox chemistry, and radionuclide transport in a subsurface environment. To account for the likely achievement of quasi-steady state biomass accumulations in subsurface environments, a modification to the traditional microbial growth kinetic equation is proposed. The conditions for using biogeochemical models with or without an explicit representation of biomass growth are clarified. Based on the general approach proposed in this paper, the couplings of uranium reactions with biogeochemical processes are incorporated into computer code BIORXNTRN Version 2.0. The code is then used to simulate a subsurface contaminant migration scenario, in which a water flow containing both uranium and a complexing organic ligand is recharged into an oxic carbonate aquifer. The model simulation shows that Mn and Fe oxyhydroxides may vary significantly along a flow path. The simulation also shows that uranium(VI) can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

  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. 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

  10. ORGANIC ACID DERIVATIZATION TECHNIQUES APPLIED TO PETROLEUM HYDROCARBON TRANSFORMATIONS IN SUBSURFACE ENVIRONMENTS

    EPA Science Inventory

    Evidence for the natural microbial remediation of subsurface fuel contamination situations should include identification and analysis of transformation or degradation products. In this way. u mass balance between fuel constituents and end products may be approached to monitor cle...

  11. 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

  12. Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems.

    PubMed

    Babatunde, A O; Miranda-CasoLuengo, Raul; Imtiaz, Mehreen; Zhao, Y Q; Meijer, Wim G

    2016-08-01

    This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems (CWs). Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100gBOD5/(m(2)·day), similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus (P), the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10gP/(m(2)·day) based on the performance results obtained within the first 16months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance. PMID:27521934

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

    PubMed

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

    2008-01-01

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

  14. 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

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

    PubMed Central

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

    2008-01-01

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

  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. Microbial diversity of hypersaline environments: a metagenomic approach.

    PubMed

    Ventosa, Antonio; de la Haba, Rafael R; Sánchez-Porro, Cristina; Papke, R Thane

    2015-06-01

    Recent studies based on metagenomics and other molecular techniques have permitted a detailed knowledge of the microbial diversity and metabolic activities of microorganisms in hypersaline environments. The current accepted model of community structure in hypersaline environments is that the square archaeon Haloquadratum waslbyi, the bacteroidete Salinibacter ruber and nanohaloarchaea are predominant members at higher salt concentrations, while more diverse archaeal and bacterial taxa are observed in habitats with intermediate salinities. Additionally, metagenomic studies may provide insight into the isolation and characterization of the principal microbes in these habitats, such as the recently described gammaproteobacterium Spiribacter salinus. PMID:26056770

  18. Maintenance of permeable habitable subsurface environments by earthquakes and tidal stresses

    NASA Astrophysics Data System (ADS)

    Sleep, Norman H.

    2012-10-01

    Life inhabits the subsurface of the Earth down to depths where temperature precludes it. Similar conditions are likely to exist within the traditional habitable zone for objects between 0.1 Earth mass (Mars) and 10 Earth masses (superearth). Long-term cooling and internal radioactivity maintain surface heat flow on the Earth. These heat sources are comparable and likely to be comparable in general within old rocky planets. Surface heat flow scales with mass divided by surface area and hence with surface gravity. The average absolute habitable subsurface thickness scales inversely with heat flow and gravity. Surface gravity varies by only 0.4 g for Mars to 3.15 g for a superearth. This range is less than the regional variation of heat flow on the Earth. Still ocean-boiling asteroid impacts (if they occur) are more likely to sterilize the thin habitable subsurface of large objects than thick habitable subsurface of small ones. Tectonics self-organizes to maintain subsurface permeability and habitability within both stable and active regions on the Earth. Small earthquakes within stable regions allow sudden mixing of water masses. Large earthquakes at plate boundaries allow surface water to descend to great habitable depths. Seismic shaking near major faults cracks shallow rock forming permeable regolith. Strong tidal strains form a similar porous regolith on small bodies such as Enceladus with weak stellar heating. This regolith may be water-saturated within rocky bodies and thus habitable.

  19. Measurement of microbial growth in the low nutrient conditions of a simulated subsurface environment

    NASA Astrophysics Data System (ADS)

    Hand, V. L.; Boult, S.; Vaughan, D. J.; Beadle, I. R.; Humphreys, P.; Wogelius, R. A.

    2003-04-01

    The growth of bacteria in natural porous media may alter porosity and permeability, and therefore hydraulic conductivity. Changes are due both to pore clogging caused by the production of bacterial extracellular polysaccharides (EPS) and the formation of secondary mineral precipitates. Pore clogging has implications not only for fluid flow, but also for contaminant transport. Most biofilm research has been conducted under nutrient rich conditions, quite different from the actual subsurface environment. There is therefore a general need for studies under environmentally relevant conditions. The main objectives were to determine growth under environmental conditions and to produce reproducible homogeneously coated columns of porous media for further experiments on metal transport. Six short columns (length 25mm; diameter 20mm) instrumented with pressure, pH and dissolved oxygen sensors were used. Growth and reproducibility of the biofilm are related to the flow rate, the concentration of the nutrients and the grain size of the porous medium substrate. Two types of porous media were used; a single mineral quartz media with a constant grain size and a natural mixed mineral assemblage of non-uniform grain size. Nutrient used was a landfill derived carbon source present in synthetic trench leachate (STL) diluted with synthetic groundwater (SGW) by a factor of 100. The STL was pumped through each column at a constant, environmentally relevant flow rate of 0.109 ml/min. Experiments were performed under both aerobic and anaerobic conditions contained in a temperature-controlled room at 10^oC. Measurement of the pressure increase within the column apparatus was made, as an increase in pressure is relative to the resistance of the media to flow and indicates biofilm formation and pore clogging within the column. Monitoring of dissolved oxygen shows the metabolic conditions of the bacteria and also the biological oxygen demand. Column effluent was analysed for changes in

  20. [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.

  1. 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. PMID:26279235

  2. 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.

  3. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.

    PubMed

    Edgcomb, Virginia P; Kysela, David T; Teske, Andreas; de Vera Gomez, Alvin; Sogin, Mitchell L

    2002-05-28

    Molecular microbial ecology studies have revealed remarkable prokaryotic diversity in extreme hydrothermal marine environments. There are no comparable reports of culture-independent surveys of eukaryotic life in warm, anoxic marine sediments. By using sequence comparisons of PCR-amplified small subunit ribosomal RNAs, we characterized eukaryotic diversity in hydrothermal vent environments of Guaymas Basin in the Gulf of California. Many sequences from these anoxic sediments and the overlaying seawater represent previously uncharacterized protists, including early branching eukaryotic lineages or extended diversity within described taxa. At least two mechanisms, with overlapping consequences, account for the eukaryotic community structure of this environment. The adaptation to anoxic environments is evidenced by specific affinity of environmental sequences to aerotolerant anaerobic species in molecular trees. This pattern is superimposed against a background of widely distributed aerophilic and aerotolerant protists, some of which may migrate into and survive in the sediment whereas others (e.g., phototrophs) are simply deposited by sedimentary processes. In contrast, bacterial populations in these sediments are primarily characteristic of anoxic, reduced, hydrocarbon-rich sedimentary habitats.

  4. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment

    PubMed Central

    Edgcomb, Virginia P.; Kysela, David T.; Teske, Andreas; de Vera Gomez, Alvin; Sogin, Mitchell L.

    2002-01-01

    Molecular microbial ecology studies have revealed remarkable prokaryotic diversity in extreme hydrothermal marine environments. There are no comparable reports of culture-independent surveys of eukaryotic life in warm, anoxic marine sediments. By using sequence comparisons of PCR-amplified small subunit ribosomal RNAs, we characterized eukaryotic diversity in hydrothermal vent environments of Guaymas Basin in the Gulf of California. Many sequences from these anoxic sediments and the overlaying seawater represent previously uncharacterized protists, including early branching eukaryotic lineages or extended diversity within described taxa. At least two mechanisms, with overlapping consequences, account for the eukaryotic community structure of this environment. The adaptation to anoxic environments is evidenced by specific affinity of environmental sequences to aerotolerant anaerobic species in molecular trees. This pattern is superimposed against a background of widely distributed aerophilic and aerotolerant protists, some of which may migrate into and survive in the sediment whereas others (e.g., phototrophs) are simply deposited by sedimentary processes. In contrast, bacterial populations in these sediments are primarily characteristic of anoxic, reduced, hydrocarbon-rich sedimentary habitats. PMID:12032339

  5. 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.

  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. Environmental parameters controlling microbial activities in terrestrial subsurface environments. Technical completion report

    SciTech Connect

    Kieft, T.L.

    1990-12-31

    This project was begun in July 1988 as part of Phase I of the Deep Microbiology Subprogram. At this time, the Subprogram was preparing for sampling near the Savannah River Site (SRS) from what was being termed the ``Investigator`s Hole.`` This was the fourth hole drilled for sampling in the coastal plain sediments at a site near the SRS. Since there was a possibility of sampling from the saline Triassic basin in the deeper regions in this fourth hole, there was particular interest in quantifying halotolerant microorganisms from these samples and in determining the responses of subsurface microbes to a range of soft concentrations. Further interest in the soft tolerances of microbes from these coastal sediments arose from the fact that all of these sediments were deposited under marine conditions. It was also anticipated that samples would be available from the shallow unsaturated (vadose) zone at this site, so there was interest in quantifying microbial responses to matric water potential as well as solute water potential. The initial objectives of this research project were to: characterize microbial communities in a saline aquifer; determine the potential for microbial metabolism of selected organic compounds in a saline aquifers; characterize microbial communities in unsaturated subsurface materials (vadose zones); and determine the potential for microbial metabolism of selected organic compounds in unsaturated subsurface materials (vadose zones). Samples were collected from the borehole during a period extending from August to October 1988. A total of nine samples were express shipped to New Mexico Tech for analyses. These were all saturated zone samples from six different geological formations. Water contents and water potentials were measured at the time of sample arrival.

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

    PubMed

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

    2015-01-01

    In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca(2+)-OH(-)-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO2) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep's source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes. PMID:25745416

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

    PubMed

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

    2015-01-01

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

  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. 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.

  12. Diversity of Listeria Species in Urban and Natural Environments

    PubMed Central

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

    2012-01-01

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

  13. 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.

  14. Assessment of herbicide transport and distribution in subsurface environments of an orange field.

    PubMed

    Wu, Lei; Ma, Xiao-Yi; Liu, Xia

    2014-08-01

    The demand for assessing both the variability of risk areas and the intensity of pollutant load rates on pesticide transferring to waters in China has been increasingly vigorous in recent decades. Therefore, to explore the transport of linuron with rainfall and irrigation in canopy-soil systems, an integrated pesticide transport modeling system has been selected and verified for simulating the three-phase linuron environmental fate in an orange field of the Three Gorges Reservoir (TGR) area. Results demonstrate that spatio-temporal distributions of linuron in surface soil primarily depend on its properties, rainfall, irrigation, and its applications; the peak levels of linuron in subsurface and deep soil are closely related to the cumulative and delayed effects. The findings may be used for policy supporting of soil-water-crop-pesticide management in an agricultural field of the TGR area. PMID:25306788

  15. Preferential transport of Cryptosporidium parvum oocysts in variably saturated subsurface environments.

    PubMed

    Darnault, Christophe J G; Garnier, Patricia; Kim, Young-Jin; Oveson, Kristina L; Steenhuis, Tammo S; Parlange, J Yves; Jenkins, Michael; Ghiorse, William C; Baveye, Philippe

    2003-01-01

    When oocysts of the protozoan Cryptosporidium parvum contaminate drinking water supplies, they can cause outbreaks of Cryptosporidiosis, a common waterborne disease. Of the different pathways by which oocysts can wind up in drinking water, one has received little attention to date; that is, because soils are often considered to be perfect filters, the transport of oocysts through the subsoil to groundwater is generally ignored. To evaluate the significance of this pathway, a series of laboratory experiments investigated subsurface transport of oocysts. Experiment 1 was carried out in a vertical 18-cm-long column filled either with glass beads or silica sand, under conditions known to foster fingered flow. Experiment 2 involved undisturbed, macroporous soil columns subjected to macropore flow. Experiment 3 aimed to study the lateral flow on an undisturbed soil block. The columns and soil samples were subjected to artificial rainfall and were allowed to reach steady state. At that point, feces of contaminated calves were applied at the surface along with a known amount of potassium chloride to serve as a tracer, and rainfall was continued at the same rate. The breakthrough of oocysts and chloride, monitored in the effluent, demonstrate the importance of preferential flow on the transport of oocysts. Compared with chloride, peak oocyst concentrations were not appreciably delayed and, in some cases, occurred even before the chloride peak. Recovery rates for oocysts were low, ranging from 0.1 to 10.4% of the oocysts originally applied on the columns. However, the numbers of oocysts present in the effluents were still orders of magnitude higher than 10 oocysts, the infectious dose considered by the U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, to be sufficient to cause Cryptosporidiosis in healthy adults. These results suggest that the transport of oocysts in the subsurface via preferential flow may create a significant risk of

  16. The Next Generation of Space Cells for Diverse Environments

    NASA Technical Reports Server (NTRS)

    Landis, Geoffrey A.; Bailey, Sheila; Raffaelle, Ryne; Lyons, Valerie J. (Technical Monitor)

    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.

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

    PubMed

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

    2015-01-01

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

  18. 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

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

    PubMed

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

    2015-01-01

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

  20. 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.

  1. 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

  2. The Martian surface radiation environment - Influence of higher atmospheric pressure and surface or sub-surface water

    NASA Astrophysics Data System (ADS)

    Ehresmann, B.; Böhm, E.; Kohler, J.; Martin, C.; Wimmer-Schweingruber, R. F.; Reitz, G.; Hassler, D. M.; Zeitlin, C. J.

    2011-12-01

    The Noachian epoch (~4.5 - 3.5 billion years ago) is a promising era for a possible emergence of life on Mars. The presence of runoff channels in areas formed during the Noachian suggests that liquid water existed at least sporadically during that time, with liquid water being regarded as a prerequisite for life. To have sustained liquid water, the atmospheric pressure on Noachian Mars must have been significantly higher than in the present. When considering the possibility of life on Noachian Mars, one conceivable restriction is given by the ionizing radiation environment. Using PLANETOCOSMICS- and GEANT4-simulation codes, we calculate the radiation environment on the Martian surface and the resulting radiation exposure for different atmospheric conditions. Here, we present absorbed dose rates resulting from galactic-cosmic-proton and alpha-particle-induced radiation environments, as well as changes of these rates caused by an increase of atmospheric pressure. Furthermore, we analyze which influence the presence of liquid surface water or sub-surface water-ice would have on the radiation environment under these different atmospheric conditions.

  3. 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.

  4. 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. PMID:26414525

  5. Remediation and recovery of uranium from contaminated subsurface environments with electrodes.

    PubMed

    Gregory, Kelvin B; Lovley, Derek R

    2005-11-15

    Previous studies have demonstrated that Geobacter species can effectively remove uranium from contaminated groundwater by reducing soluble U(VI) to the relatively insoluble U(IV) with organic compounds serving as the electron donor. Studies were conducted to determine whether electrodes might serve as an alternative electron donor for U(VI) reduction by a pure culture of Geobacter sulfurreducens and microorganisms in uranium-contaminated sediments. Electrodes poised at -500 mV (vs a Ag/AgCl reference) rapidly removed U(VI) from solution in the absence of cells. However, when the poise at the electrode was removed, all of the U(VI) returned to solution, demonstrating that the electrode did not reduce U(VI). If G. sulfurreducens was present on the electrode, U(VI) did not return to solution until the electrode was exposed to dissolved oxygen. This suggeststhat G. sulfurreducens on the electrode reduced U(VI) to U(IV) which was stably precipitated until reoxidized in the presence of oxygen. When an electrode was placed in uranium-contaminated subsurface sediments, U(VI) was removed and recovered from groundwater using poised electrodes. Electrodes emplaced in flow-through columns of uranium-contaminated sediments readily removed U(VI) from the groundwater, and 87% of the uranium that had been removed was recovered from the electrode surface after the electrode was pulled from the sediments. These results suggest that microorganisms can use electrons derived from electrodes to reduce U(VI) and that it may be possible to remove and recover uranium from contaminated groundwater with poised electrodes.

  6. 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).

  7. Nurses on the move: diversity and the work environment.

    PubMed

    Kingma, Mireille

    2008-04-01

    Over 191 million people make up the international migrant population of today. Their numbers have doubled since 1970, with women now accounting for almost half. The migrant population has been transformed and is changing the very nature of society in both source and destination countries. Greater differences in culture, language, work relationships, and coping mechanisms - in short, greater diversity in society and the workplace - offer many opportunities for excellence in transcultural nursing but also provides fertile ground for discrimination, victimisation, harassment and isolation. This article explores and describes current nurse migration flows, the impact migration has on nurses and the value of positive practice environment for the full integration of international nurses. PMID:18844573

  8. 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

  9. Acidobacteria Phylum Sequences in Uranium-Contaminated Subsurface Sediments Greatly Expand the Known Diversity within the Phylum▿ †

    PubMed Central

    Barns, Susan M.; Cain, Elizabeth C.; Sommerville, Leslie; Kuske, Cheryl R.

    2007-01-01

    The abundance and composition of bacteria of the phylum Acidobacteria were surveyed in subsurface sediments from uranium-contaminated sites using amplification of 16S rRNA genes followed by clone/sequence analysis. Analysis of sequences from this study and public databases produced a revised and greatly expanded phylogeny of the Acidobacteria phylum consisting of 26 subgroups. PMID:17337544

  10. 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

  11. 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

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

    PubMed Central

    Jiang, Xuexia; Dang, Hongyue; Jiao, Nianzhi

    2015-01-01

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

  13. 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

  14. An improved criterion for new particle formation in diverse environments

    SciTech Connect

    Kuang, C.; Riipinen, I.; Sihto, S.-L.; Kulmala, M.; McCormick, A.; McMurry, P.

    2010-03-15

    A dimensionless theory for new particle formation (NPF) was developed, using an aerosol population balance model incorporating recent developments in nucleation rates and measured particle growth rates. Based on this theoretical analysis, it was shown that a dimensionless parameter Lg, characterizing the ratio of the particle scavenging loss rate to the particle growth rate, exclusively determined whether or not NPF would occur on a particular day. This parameter determines the probability that a nucleated particle will grow to a detectable size before being lost by coagulation with the pre-existing aerosol. Cluster-cluster coagulation was shown to contribute negligibly to this survival probability under conditions pertinent to the atmosphere. Data acquired during intensive measurement campaigns in Tecamac (MILAGRO), Atlanta (ANARChE), Boulder, and Hyytiala (QUEST II, QUEST IV, and EUCAARI) were used to test the validity of Lg as an NPF criterion. Measurements included aerosol size distributions down to 3 nm and gas-phase sulfuric acid concentrations. The model was applied to 77 NPF events and 19 non-events (characterized by growth of pre-existing aerosol without NPF) measured in diverse environments with broad ranges in sulfuric acid concentrations, ultrafine number concentrations, aerosol surface areas, and particle growth rates (nearly two orders of magnitude). Across this diverse data set, a nominal value of Lg = 0.7 was found to determine the boundary for the occurrence of NPF, with NPF occurring when Lg < 0.7 and being suppressed when Lg > 0.7. Moreover, nearly 45% of measured Lg values associated with NPF fell in the relatively narrow range of 0.1 < Lg < 0.3.

  15. 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

  16. Pyrosequencing-Based Assessment of the Bacteria Diversity in Surface and Subsurface Peat Layers of a Northern Wetland, with Focus on Poorly Studied Phyla and Candidate Divisions

    PubMed Central

    Liesack, Werner; Dedysh, Svetlana N.

    2013-01-01

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

  17. Effective Listening: Barriers to Listening in a Diverse Business Environment.

    ERIC Educational Resources Information Center

    Simon, Augusta M.

    1991-01-01

    Maintains that listening skills are a critical starting point for the management of diversity in business organizations. Discusses listening barriers which prevent the nurturing of diversity in business. (PRA)

  18. 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.

  19. 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+.

  20. 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.

  1. Development and application of primers for the class Dehalococcoidia (phylum Chloroflexi) enables deep insights into diversity and stratification of subgroups in the marine subsurface.

    PubMed

    Wasmund, Kenneth; Algora, Camelia; Müller, Josefine; Krüger, Martin; Lloyd, Karen G; Reinhardt, Richard; Adrian, Lorenz

    2015-10-01

    Bacteria of the class Dehalococcoidia (DEH) (phylum Chloroflexi) are widely distributed in the marine subsurface and are especially prevalent in deep marine sediments. Nevertheless, little is known about the specific distributions of DEH subgroups at different sites and depths. This study therefore specifically examined the distributions of DEH through depths of various marine sediment cores by quantitative PCR and pyrosequencing using newly designed DEH 16S rRNA gene targeting primers. Quantification of DEH showed populations may establish in shallow sediments (i.e. upper centimetres), although as low relative proportions of total Bacteria, yet often became more prevalent in deeper sediments. Pyrosequencing revealed pronounced diversity co-exists within single biogeochemical zones, and that clear and sometimes abrupt shifts in relative proportions of DEH subgroups occur with depth. These shifts indicate varying metabolic properties exist among DEH subgroups. The distributional changes in DEH subgroups with depth may be related to a combination of biogeochemical factors including the availability of electron acceptors such as sulfate, the composition of organic matter and depositional regimes. Collectively, the results suggest DEH exhibit wider metabolic and genomic diversity than previously recognized, and this contributes to their widespread occurrence in the marine subsurface.

  2. Novel sensing materials for harsh environment subsurface pH sensing applications

    NASA Astrophysics Data System (ADS)

    Wang, Congjun; Su, Xin; Brown, Thomas D.; Ohodnicki, Paul R.

    2015-05-01

    Robust pH sensors that can operate under harsh environmental conditions are valuable for a variety of applications, such as oil and gas production, geological CO2 sequestration, etc. However, despite the significant advance in pH measurement technology, reliable pH sensing at elevated pressures (up to 30,000 psi) and high temperatures (up to 350 °C) remains challenging. We describe an optical pH sensor based on optical fiber technology. A sensing layer that is comprised of metal nanoparticles incorporated in a silica matrix coated on an optical fiber exhibits strong and reversible optical response to pH variation at 80 °C and in solutions with different salt concentrations. The same robust response is also observed at elevated pressures up to 2,000 psi. The optical fiber pH sensor is made of materials with high stability at temperatures at least up to ~ 600 °C. Therefore, this approach provides a new potential means to enable optical pH sensing for extreme environment applications.

  3. 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.

  4. A seismic modelling environment as a research and teaching tool for 3-D subsurface modelling

    NASA Astrophysics Data System (ADS)

    Burford, Dennis J.; Ger, Larry; Blake, Edwin H.; de Wit, Maarten J.; Doucouré, C. Moctar; Hart, Roger J.

    Early geological modelling and visualisation techniques were limited to manual cross-sections or isometric perspectives. Computer modelling has automated this task to a certain degree, but traditional approaches do not allow iterative validation during the modelling process. When the structure is complex and data sparse, as is often the case in geology, interactive 3-D modelling techniques should be employed that can interrogate new and existing data, guided by the geological experience of the modeller. Using the Vredefort dome in South Africa as a case study, we describe a Seismic Modelling Environment (SME) to demonstrate the potential of this type of computer-based modelling and geological visualisation. SME offers a novel approach to interactive 3-D modelling of complex geological structures using an extension of sweep representations and user-controlled forward modelling with seismic analysis for validation. Incorporation of validation techniques allows early confirmation or rejection of models. Tested by a group of third-year geology students, SME's iterative construction and exploration of a 3-D model clearly provided users with a superior understanding through visualisation. SME has, therefore, potential both as an educational as well as a research tool.

  5. Performance of subsurface flow constructed wetland mesocosms in enhancing nutrient removal from municipal wastewater in warm tropical environments.

    PubMed

    Bateganya, Najib Lukooya; Kazibwe, Alex; Langergraber, Guenter; Okot-Okumu, James; Hein, Thomas

    2016-01-01

    Nutrient-rich effluents from municipal wastewater treatment plants (WWTPs) have significantly contributed to eutrophication of surface waters in East Africa. We used vertical (VF, 0.2 m(2)) and horizontal (HF, 0.45 m(2)) subsurface flow (SSF) constructed wetland (CW) configurations to design single-stage mesocosms planted with Cyperus papyrus, and operating under batch hydraulic loading regime (at a mean organic loading rate of 20 g COD m(-2) d(-1) for HF and 77 g COD m(-2) d(-1) for VF beds). The aim of the investigation was to assess the performance of SSF CWs as hotspots of nutrient transformation and removal processes between the WWTP and the receiving natural urban wetland environment in Kampala, Uganda. C. papyrus coupled with batch loading enhanced aerobic conditions and high efficiency regarding the elimination of suspended solids, organic matter, and nutrients with significant performance (P < .05) in VF mesocosms. The mean N and P elimination rates (g m(-2) d(-1)) were 9.16 N and 5.41 P in planted VF, and 1.97 N and 1.02 P in planted HF mesocosms, respectively. The lowest mean nutrient elimination rate (g m(-2) d(-1)) was 1.10 N and 0.62 P found in unplanted HF controls. Nutrient accumulation in plants and sediment retention were found to be essential processes. It can be concluded that whereas the SSF CWs may not function as independent treatment systems, they could be easily adopted as flexible and technologically less intensive options at a local scale, to increase the resilience of receiving environments by buffering peak loads from WWTPs. PMID:26387557

  6. 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…

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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...

  13. 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...

  14. 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 been seeking to…

  15. 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.

  16. Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment.

    PubMed

    Venkatramanan, Raghavee; Prakash, Om; Woyke, Tanja; Chain, Patrick; Goodwin, Lynne A; Watson, David; Brooks, Scott; Kostka, Joel E; Green, Stefan J

    2013-01-01

    Genome sequences for three strains of denitrifying bacteria (Alphaproteobacteria-Afipia sp. strain 1NLS2 and Hyphomicrobium denitrificans strain 1NES1; Firmicutes-Bacillus sp. strain 1NLA3E) isolated from the nitrate- and uranium-contaminated subsurface of the Oak Ridge Integrated Field Research Challenge (ORIFRC) site, Oak Ridge Reservation, TN, are reported. PMID:23833140

  17. Marine subsurface eukaryotes: the fungal majority.

    PubMed

    Edgcomb, Virginia P; Beaudoin, David; Gast, Rebecca; Biddle, Jennifer F; Teske, Andreas

    2011-01-01

    Studies on the microbial communities of deep subsurface sediments have indicated the presence of Bacteria and Archaea throughout the sediment column. Microbial eukaryotes could also be present in deep-sea subsurface sediments; either bacterivorous protists or eukaryotes capable of assimilating buried organic carbon. DNA- and RNA-based clone library analyses are used here to examine the microbial eukaryotic diversity and identify the potentially active members in deep-sea sediment cores of the Peru Margin and the Peru Trench. We compared surface communities with those much deeper in the same cores, and compared cores from different sites. Fungal sequences were most often recovered from both DNA- and RNA-based clone libraries, with variable overall abundances of different sequence types and different dominant clone types in the RNA-based and the DNA-based libraries. Surficial sediment communities were different from each other and from the deep subsurface samples. Some fungal sequences represented potentially novel organisms as well as ones with a cosmopolitan distribution in terrestrial, fresh and salt water environments. Our results indicate that fungi are the most consistently detected eukaryotes in the marine sedimentary subsurface; further, some species may be specifically adapted to the deep subsurface and may play important roles in the utilization and recycling of nutrients.

  18. 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.

  19. 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

  20. 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…

  1. 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.

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

    NASA Technical Reports Server (NTRS)

    Werner, Markus; Bischl, Hermann; Lutz, Erich

    1995-01-01

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

  3. 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

  4. 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…

  5. 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.

  6. 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

  7. 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

  8. Techniques for Assessing the Performance of In Situ Bioreduction and Immobilization of Metals and Radionuclides in Contaminated Subsurface Environments

    NASA Astrophysics Data System (ADS)

    Watson, D. B.; Jardine, P. M.

    2005-05-01

    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 presentation 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

  9. 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

  10. 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.

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

    PubMed

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

    2006-03-01

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

  12. Re-Defining the Subsurface Biosphere: Characterization of Fungal Populations from Energy Limited Deep Marine Subsurface Sediments

    NASA Astrophysics Data System (ADS)

    Reese, B. K.; Ariza, M.; St. Peter, C.; Hoffman, C.; Edwards, K. J.; Mills, H. J.

    2012-12-01

    The detection and characterization of metabolically active fungal populations within the deep marine subsurface will alter current ecosystem models that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations not currently being considered in subsurface energy budgets. Sediments from the South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program (IODP) Expedition 329. Anaerobic and aerobic sediment slurry cultures using fresh sediment began directly following the completion of the Expedition (December 2010). From these cultures, multiple fungal lineages have been isolated on several media types that vary in carbon concentrations. Physical growth parameters of these subsurface fungal isolates were determined and compared to previously characterized lineages. Additionally, the overall diversity of metabolically active and dormant fungal populations was determined using high throughput sequencing of nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. This project provides a robust step in determining the importance and impact of fungal populations within the marine subsurface biosphere.

  13. 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

  14. Actinide immobilization in the subsurface environment by in-situ treatment with a hydrolytically unstable organophosphorus complexant: Uranyl uptake by calcium phytate

    SciTech Connect

    Nash, K.L.; Jensen, M.P.; Schmidt, M.A.

    1997-12-31

    In addition to naturally occurring uranium and thorium, actinide ions exist in the subsurface environment as a result of accidental releases and intentional disposal practices associated with nuclear weapons production. These species present a significant challenge to cost-effective remediation of contaminated environments. An attractive approach to decreasing the probability of actinide migration in the subsurface is to transform the ions into a less mobile form by remote treatment. We have under development a process which relies on a polyfunctional organophosphorus complexant to sequester the mobile metal ions by complexation/cation exchange in the near term, and to subsequently decompose, transforming the actinides into insoluble phosphate mineral forms in the long term. Studies to date include identification of a suitable organophosphorus reagent, profiling of its decomposition kinetics, verification of the formation of phosphate mineral phases upon decomposition of the reagent, and extensive comparison of the actinide uptake ability of the calcium salt of the reagent as compared with hydroxyapatite. In this report, we briefly describe the process with focus on the cation exchange behavior of the calcium salt of the organophosphorus sequestrant.

  15. Lab-scale simulation of the fate and transport of nano zero-valent iron in subsurface environments: aggregation, sedimentation, and contaminant desorption.

    PubMed

    Yin, Ke; Lo, Irene M C; Dong, Haoran; Rao, Pinhua; Mak, Mark S H

    2012-08-15

    Heavy metal removal using nano zero-valent iron (NZVI) has drawn growing attention due to the ease of application and high removal efficiency. However, uncertainties regarding its fate and transport in subsurface environments have raised concerns that require further exploration. In this study, aggregation, sedimentation, and Cr/As desorption of three types of NZVIs were investigated under various conditions. It was found that the aggregation behavior of the NZVIs differed from one another in regard to reaction time and ionic strength, associated with the respective critical size for sedimentation. Sedimentation of NZVIs was positively related to the concentrations and average particle sizes. The sedimentation kinetics of NZVI followed two concomitant processes, i.e., (1) direct sedimentation of larger particles, and (2) initial aggregation and then sedimentation of smaller particles. When loaded with Cr/As, NZVIs tended to deposit faster, possibly due to the precipitation of Cr/As onto the nanoparticle surfaces resulting in larger particle sizes. Moreover, desorption of Cr/As from Cr/As loaded NZVIs was detected in the presence of typical groundwater ions, as well as natural organic matter, and poses a potential risk to the subsurface environment. The desorption of Cr was linearly related to the release of iron ions, while As desorption was mitigated when the immobilization of Cr increased.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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. PMID:26917241

  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. 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.

  3. 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.

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

    PubMed

    Santini, Talitha C; Warren, Lesley A; Kendra, Kathryn E

    2015-08-01

    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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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.

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

    SciTech Connect

    Hwang, C.; Copeland, A.; Lucas, Susan; Lapidus, Alla; Barry, Kerrie W.; Glavina del Rio, T.; Dalin, Eileen; Tice, Hope; Pitluck, S.; Sims, David R.; Brettin, T.; Bruce, David; Detter, J. C.; Han, Cliff F.; Schmutz, Jeremy; Larimer, F.; Land, M.; Hauser, L.; Kyrpides, Nikos C.; Lykidis, Athanasios; Richardson, P. M.; Beliaev, Alex S.; Sanford, Robert A.; Loeffler, Frank E.; Fields, Matthew W.

    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.

  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. 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.

  15. 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. PMID:25903184

  16. 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…

  17. 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.

  18. 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…

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

    PubMed

    Yang, Desirée C; Blair, Kris M; Salama, Nina R

    2016-03-01

    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

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

    PubMed

    Yang, Desirée C; Blair, Kris M; Salama, Nina R

    2016-03-01

    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.

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

    PubMed Central

    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. PMID:26379656

  2. Protist genetic diversity in the acidic hydrothermal environments of Lassen Volcanic National Park, USA.

    PubMed

    Brown, Patricia B; Wolfe, Gordon V

    2006-01-01

    We examined eukaryote genetic diversity in the hydrothermal environments of Lassen Volcanic National Park (LVNP), Northern California. We sampled hydrothermal areas of the Bumpass Hell, Sulfur Works, Devil's Kitchen, and Boiling Springs Lake sites, all of which included diverse acidic pools, mud pots, and streams with visible algal mats and biofilms. Temperatures varied from 15 to 85 degrees C and pH from 1.7 to 5.8. DNA extraction methods compared by denaturing gradient gel electrophoresis fingerprinting exhibited similar patterns, and showed limited diversity of eukaryotic small subunit (SSU) rRNA genes compared with prokaryotes. We successfully amplified eukaryotic SSU rRNA genes from most environments up to 68 degrees C. Cloned rDNA sequences reveal acidophilic protists dominate eukaryotes in LVNP hydrothermal environments. Most sites showed phototrophic assemblages dominated by chlorophytes and stramenopiles (diatoms and chrysophytes). Heterotrophic taxa, though less abundant, included diverse alveolates (ciliates), amoebae, and flagellates. Fungi were also found at most sites, and metazoans (hexapods, nematodes, platyhelminths) were sometimes detected in less acidic environments, especially in algal mats. While many cloned rDNA sequences showed 95%-99% identity to known acidophilic isolates or environmental clones from other acidic sites (Rio Tinto), sequence diversity generally declined both with decreasing pH and increasing temperature, and both were controlling physical variables on the abundance and distribution of organisms at our sites. However, a pool at 68 degrees C with pH 1.7 yielded the greatest number of distinct sequences. While some were likely contaminants from nearby cooler sites, we suggest that Lassen's acidic hydrothermal features may harbor novel protists.

  3. 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.

  4. 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

  5. Emulsion-based encapsulation and delivery of nanoparticles for the controlled release of alkalinity within the subsurface environment

    NASA Astrophysics Data System (ADS)

    Ramsburg, C. A.; Muller, K.; Gill, J.

    2012-12-01

    Many current approaches to managing groundwater contamination rely on further advances in amendment delivery in order to initiate and sustain contaminant degradation or immobilization. In fact, limited or ineffective delivery is often cited when treatment objectives are not attained. Emulsions, specifically oil-in-water emulsions, have demonstrated potential to aid delivery of remediation amendments. Emulsions also afford opportunities to control the release of active ingredients encapsulated within the droplets. Our research is currently focused on the controlled release of nanoparticle-based buffering agents using oil-in-water emulsions. This interest is motivated by the fact that chemical and biological processes employed for the remediation and stewardship of contaminated sites often necessitate control of pH during treatment and, in some cases, long thereafter. Alkalinity-release nanoparticles (e.g., CaCO3, MgO) were suspended within soybean oil and subsequently encapsulated by through the creation of oil-in-water emulsions. These oil-in-water emulsions are designed to have physical properties which are favorable for subsurface delivery (nominal properties: 1 g/mL density; 10 cP viscosity; and 1.5 μm droplet diameter). Buffer capacity titrations suggest that MgO particles are moderately more accessible within the oil phase and nearly twice as effective (on a per mass basis) at releasing alkalinity (as compared to the CaCO3 particles). Results from experiments designed to assess the release kinetics suggest that a linear driving force model is capable of describing the release process and mass transfer coefficients are constant through the reactive life of the emulsion. The release kinetics in emulsions containing MgO particles were found to be three orders of magnitude faster than those quantified for emulsions containing CaCO3. The slower release kinetics of the emulsions containing CaCO3 particles may prove beneficial when considering pH control at sites

  6. 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

  7. 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.

  8. Increased genetic diversity of Viola tricolor L. (Violaceae) in metal-polluted environments.

    PubMed

    Słomka, A; Sutkowska, A; Szczepaniak, M; Malec, P; Mitka, J; Kuta, E

    2011-04-01

    Changes in DNA sequences affecting cryptic intraspecific variability are very important mechanisms of plant microevolutionary processes, initiating species diversification. In polluted environments, intra- and interpopulation changes at the molecular level proceed rapidly and lead to the formation of new ecotypes in a relatively short time. We used ISSR PCR fingerprinting data to analyze the genetic diversity and genetic structure of seven populations of Viola tricolor: four growing on soil contaminated with heavy metals (Zn, Pb, Cd; waste heaps) and three from control soil. The populations from the polluted sites showed higher genetic polymorphism (%(poly)=84%) and gene diversity (H(T)=0.1709) than the control populations (%(poly)=75% and H(T)=0.1448). The number of private markers we detected within metallicolous (MET) populations was more than double that found within non-metallicolous (NON) populations (15 vs. 7). The STRUCTURE and UPGMA analyses showed clear genetic differences between the NON and MET populations. Based on broad analyses of the genetic parameters, we conclude that the effect of these polluted environments on the genetic diversity of the MET populations, separating them from the NON populations, is evidence of microevolutionary processes at species level, leading to species divergence and the emergence of local ecotypes better adapted to their different environments.

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

    PubMed Central

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

    2014-01-01

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

  10. 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. PMID:26858697

  11. 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

  12. 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

  13. Subsurface Ventilation System Description Document

    SciTech Connect

    2000-10-12

    The Subsurface Ventilation System supports the construction and operation of the subsurface repository by providing air for personnel and equipment and temperature control for the underground areas. Although the system is located underground, some equipment and features may be housed or located above ground. The system ventilates the underground by providing ambient air from the surface throughout the subsurface development and emplacement areas. The system provides fresh air for a safe work environment and supports potential retrieval operations by ventilating and cooling emplacement drifts. The system maintains compliance within the limits established for approved air quality standards. The system maintains separate ventilation between the development and waste emplacement areas. The system shall remove a portion of the heat generated by the waste packages during preclosure to support thermal goals. The system provides temperature control by reducing drift temperature to support potential retrieval operations. The ventilation system has the capability to ventilate selected drifts during emplacement and retrieval operations. The Subsurface Facility System is the main interface with the Subsurface Ventilation System. The location of the ducting, seals, filters, fans, emplacement doors, regulators, and electronic controls are within the envelope created by the Ground Control System in the Subsurface Facility System. The Subsurface Ventilation System also interfaces with the Subsurface Electrical System for power, the Monitored Geologic Repository Operations Monitoring and Control System to ensure proper and safe operation, the Safeguards and Security System for access to the emplacement drifts, the Subsurface Fire Protection System for fire safety, the Emplacement Drift System for repository performance, and the Backfill Emplacement and Subsurface Excavation Systems to support ventilation needs.

  14. Subsurface Ventilation System Description Document

    SciTech Connect

    Eric Loros

    2001-07-25

    The Subsurface Ventilation System supports the construction and operation of the subsurface repository by providing air for personnel and equipment and temperature control for the underground areas. Although the system is located underground, some equipment and features may be housed or located above ground. The system ventilates the underground by providing ambient air from the surface throughout the subsurface development and emplacement areas. The system provides fresh air for a safe work environment and supports potential retrieval operations by ventilating and cooling emplacement drifts. The system maintains compliance within the limits established for approved air quality standards. The system maintains separate ventilation between the development and waste emplacement areas. The system shall remove a portion of the heat generated by the waste packages during preclosure to support thermal goals. The system provides temperature control by reducing drift temperature to support potential retrieval operations. The ventilation system has the capability to ventilate selected drifts during emplacement and retrieval operations. The Subsurface Facility System is the main interface with the Subsurface Ventilation System. The location of the ducting, seals, filters, fans, emplacement doors, regulators, and electronic controls are within the envelope created by the Ground Control System in the Subsurface Facility System. The Subsurface Ventilation System also interfaces with the Subsurface Electrical System for power, the Monitored Geologic Repository Operations Monitoring and Control System to ensure proper and safe operation, the Safeguards and Security System for access to the emplacement drifts, the Subsurface Fire Protection System for fire safety, the Emplacement Drift System for repository performance, and the Backfill Emplacement and Subsurface Excavation Systems to support ventilation needs.

  15. [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

  16. [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

  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. Cognitive diversity and team performance in a complex multiple task environment.

    PubMed

    Sauer, Jürgen; Felsing, Tobias; Franke, Holger; Rüttinger, Bruno

    2006-08-15

    This article examines the multiple effects of cognitive diversity in teams operating complex human-machine-systems. The study employed a PC-based multiple-task environment, called the Cabin Air Management System, which models a process control task in the operational context of a spacecraft's life support system. Two types of cognitive diversity were examined: system understanding and team specialization. System understanding referred to the depth of understanding team members were given during training (low-level procedure-oriented vs. high level knowledge-oriented training). Team specialization referred to the degree to which knowledge about system fault scenarios was distributed between team members (specialized vs. non-specialized). A total of 72 participants took part in the study. After having received 4.5 h of training on an individual basis, participants completed a 1-h experimental session, in which they worked in two-person teams on a series of fault scenarios of varying difficulty. Measures were taken of primary and secondary task performance, system intervention and information sampling strategies, system knowledge, subjective operator state, communication patterns and conflict. The results provided evidence for the benefits of cognitive diversity with regard to system understanding. This manifested itself in better primary task performance and more efficient manual system control. No advantages were found for cognitive diversity with regard to specialization. There was no effect of cognitive diversity on intra-team conflict, with conflict levels generally being very low. The article concludes with a discussion of the implications of the findings for the engineering of cognitive diversity in teams operating complex human-machine-systems. PMID:16803725

  19. The Schumann Resonance: A Tool For Exploring The Atmospheric Environment And The Subsurface Of The Planets And Their Satellites

    NASA Astrophysics Data System (ADS)

    Simoes, F.; Hamelin, M.; Berthelier, J.

    2008-12-01

    The propagation of Extremely Low Frequency (ELF) electromagnetic waves in the Earth surface-ionosphere cavity has been studied for more than fifty years to investigate a wide variety of atmospheric and ionospheric phenomena, namely ionospheric dynamics, thunderstorm, and lightning activity. The surface and the ionosphere acting as reflectors of ELF waves define a cavity where ELF can propagate. When the cavity is excited with broadband electromagnetic sources, resonances can develop if the equatorial circumference is approximately equal to an integral number of wavelengths of the propagating waves; this phenomenon is known as Schumann resonance. A similar investigation can be performed for any other planet and satellite, provided this body is wrapped into an ionosphere and a low frequency electromagnetic source exists. There are, however, important differences between the Earth and other bodies, regarding the surface conductivity, the atmospheric electron density, the ionospheric cavity geometry, and the sources of electromagnetic energy. In this work we present a comparative planetology study of ELF wave propagation and atmospheric electricity of several environments, namely Venus, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. We revisit the available models for ELF propagation in several planetary cavities, recapitulate the similarities and differences among the planets, and compare simulations with in situ measurements whenever available. We review the propagation process of ELF electromagnetic waves in planetary cavities, with a particular emphasis on the application of the Schumann resonance observation to investigating the lower ionosphere of Venus and Mars, determining the water content of the gaseous envelope of Uranus and Neptune, and assessing the buried ocean of Titan predicted by theoretical models. The comparison of ELF wave propagation among rocky planets, gaseous giants, and icy satellites can be also used to improve the models of the Earth

  20. 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.

  1. 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.

  2. Wide Distribution and Diversity of Members of the Bacterial Kingdom Acidobacterium in the Environment

    PubMed Central

    Barns, Susan M.; Takala, Shannon L.; Kuske, Cheryl R.

    1999-01-01

    To assess the distribution and diversity of members of the recently identified bacterial kingdom Acidobacterium, members of this kingdom present in 43 environmental samples were surveyed by PCR amplification. A primer designed to amplify rRNA gene sequences (ribosomal DNAs [rDNAs]) from most known members of the kingdom was used to interrogate bulk DNA extracted from the samples. Positive PCR results were obtained with all temperate soil and sediment samples tested, as well as some hot spring samples, indicating that members of this kingdom are very widespread in terrestrial environments. PCR primers specific for four phylogenetic subgroups within the kingdom were used in similar surveys. All four subgroups were detected in most neutral soils and some sediments, while only two of the groups were seen in most low-pH environments. The combined use of these primers allowed identification of a novel lineage within the kingdom in a hot spring environment. Phylogenetic analysis of rDNA sequences from our survey and the literature outlines at least six major subgroups within the kingdom. Taken together, these data suggest that members of the Acidobacterium kingdom are as genetically and metabolically diverse, environmentally widespread and perhaps as ecologically important as the well-known Proteobacteria and gram-positive bacterial kingdoms. PMID:10103274

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

    PubMed

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

    2016-08-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-08-01

    The yeast Candida zemplinina (Starmerella bacillaris) is frequently isolated from grape and wine environments. Its enological use in mixed fermentation with Saccharomyces cerevisiae has been extensively investigated these last few years, and several interesting features including low ethanol production, fructophily, glycerol and other metabolites production, have been described. In addition, molecular tools allowing the characterization of yeast populations have been developed, both at the inter- and intraspecific levels. However, most of these fingerprinting methods are not compatible with population genetics or ecological studies. In this work, we developed 10 microsatellite markers for the C. zemplinina species that were used for the genotyping of 163 strains from nature or various enological regions (28 vineyards/wineries from seven countries). We show that the genetic diversity of C. zemplinina is shaped by geographical localization. Populations isolated from winemaking environments are quite diverse at the genetic level: neither clonal-like behaviour nor specific genetic signature were associated with the different vineyards/wineries. Altogether, these results suggest that C. zemplinina is not under selective pressure in winemaking environments. PMID:26071435

  6. Rao and Wald tests for adaptive detection in partially homogeneous environment with a diversely polarized antenna.

    PubMed

    Zhang, Chaozhu; Zhang, Jing; Liu, Chengyuan

    2013-01-01

    This study considers Rao test and Wald test for adaptive detection based on a diversely polarized antenna (DPA) in partially homogeneous environment. The theoretical expressions for the probability of false alarm and detection are derived, and constant false alarm rate (CFAR) behaviour is remarked on. Furthermore, the monotonicities of detection probability of the two detectors are proved, and a polarization optimization detection algorithm to enhance the detection performance is proposed. The numerical simulations are conducted to attest to the validity of the above theoretical analysis and illustrate the improvement in the detection performance of the proposed optimization algorithm.

  7. Rao and Wald Tests for Adaptive Detection in Partially Homogeneous Environment with a Diversely Polarized Antenna

    PubMed Central

    Zhang, Chaozhu; Zhang, Jing; Liu, Chengyuan

    2013-01-01

    This study considers Rao test and Wald test for adaptive detection based on a diversely polarized antenna (DPA) in partially homogeneous environment. The theoretical expressions for the probability of false alarm and detection are derived, and constant false alarm rate (CFAR) behaviour is remarked on. Furthermore, the monotonicities of detection probability of the two detectors are proved, and a polarization optimization detection algorithm to enhance the detection performance is proposed. The numerical simulations are conducted to attest to the validity of the above theoretical analysis and illustrate the improvement in the detection performance of the proposed optimization algorithm. PMID:24174914

  8. 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.

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

    PubMed

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

    2012-03-01

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

  10. 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

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

    PubMed

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

    2012-03-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution. PMID:22050634

  12. 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.

  13. Low-frequency radar sounding investigations of the North Amargosa Desert, Nevada: A potential analog of conductive subsurface environments on Mars

    NASA Astrophysics Data System (ADS)

    Heggy, Essam; Clifford, Stephen M.; Grimm, Robert E.; Dinwiddie, Cynthia L.; Stamatakos, John A.; Gonzalez, Sarah H.

    2006-05-01

    Theoretical estimates of low-frequency radar sounding performance and its potential for mapping moist subsurface interfaces in conductive environments on Mars are controversial, with predictions of ultimate penetration depth ranging from a few meters to kilometers. To address this issue, we conducted a broadband electromagnetic field survey in which we combined ground penetrating radar (GPR) operating at multiple low frequencies with the transient electromagnetic method (TEM) to investigate the dependence of radar penetration depth on ground resistivity. Surveys were performed in the frequency range 16-100 MHz at two locations on the northwest margin of the Amargosa Desert, Nevada, where numerous Mars-analog investigations have been performed. The surveys were conducted on a 20-m-high homogenous sand dune and on the flanks of a 20-m-high scoria cone and above a buried lava flow. A wet alluvial interface was located at the bottom of each structure. GPR detected the wet alluvium contact at the base of the sand dune, but failed to penetrate to the same depth at the scoria cone under similar residual moisture content. Depths of investigation for both the scoria cone and the buried lava flow were limited to approximately 10 m owing to the presence of conductive inclusions in the first few meters, which are below the radar resolution but dramatically decreased the dynamic of the radar-backscattered echoes and hence the penetration depth. Absorption models constrained by the TEM data are in good agreement with these observations. Depths of investigation varied weakly with frequency owing to substantial, frequency-independent absorption.

  14. Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

    PubMed Central

    Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng

    2014-01-01

    Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions

  15. Dissimilatory Iron Reduction by Microorganisms Under Hot Deep Subsurface Conditions

    NASA Astrophysics Data System (ADS)

    Ruper, S.; Sharma, A.; Scott, J. H.

    2010-04-01

    In subsurface environments the availability of terminal electron acceptors will be the major biogeochemical constraint, before temperature or pressure begin plays a role. Data is presented to show the impact of deep hot subsurface conditions on dissimilatory iron reduction.

  16. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment.

    PubMed

    DeSantis, Todd Z; Brodie, Eoin L; Moberg, Jordan P; Zubieta, Ingrid X; Piceno, Yvette M; Andersen, Gary L

    2007-04-01

    Molecular approaches aimed at detection of a broad-range of prokaryotes in the environment routinely rely on classifying heterogeneous 16S rRNA genes amplified by polymerase chain reaction (PCR) using primers with broad specificity. The general method of sampling and categorizing DNA has been to clone then sequence the PCR products. However, the number of clones required to adequately catalog the majority of taxa in a sample is unwieldy. Alternatively, hybridizing target sequences to a universal 16S rRNA gene microarray may provide a more rapid and comprehensive view of prokaryotic community composition. This study investigated the breadth and accuracy of a microarray in detecting diverse 16S rRNA gene sequence types compared to clone-and-sequencing using three environmental samples: urban aerosol, subsurface soil, and subsurface water. PCR products generated from universal 16S rRNA gene-targeted primers were classified by using either the clone-and-sequence method or by hybridization to a novel high-density microarray of 297,851 probes complementary to 842 prokaryotic subfamilies. The three clone libraries comprised 1391 high-quality sequences. Approximately 8% of the clones could not be placed into a known subfamily and were considered novel. The microarray results confirmed the majority of clone-detected subfamilies and additionally demonstrated greater amplicon diversity extending into phyla not observed by the cloning method. Sequences matching operational taxonomic units within the phyla Nitrospira, Planctomycetes, and TM7, which were uniquely detected by the array, were verified with specific primers and subsequent amplicon sequencing. Subfamily richness detected by the array corresponded well with nonparametric richness predictions extrapolated from clone libraries except in the water community where clone-based richness predictions were greatly exceeded. It was concluded that although the microarray is unreliable in identifying novel prokaryotic taxa, it

  17. 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

  18. 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

  19. [The first results of a study of the phylogenetic diversity of microorganisms in southern Baikal sediments from the area of subsurface depositions of methane hydrates].

    PubMed

    Shubenkova, O V; Zemskaia, T I; Chernitsyna, S M; Khlystov, O M; Triboĭ, T I

    2005-01-01

    Phylogenetic analysis of the bacterial communities in Lake Baikal bottom sediments in the region of subsurface methane hydrate depositions has been carried out using data on 16S rRNA sequences. The composition of these microbial communities is shown to be different in different horizons. Methanotrophic bacteria are found in the surface layer (0-5 cm), and uncultured bacteria constitute a great portion of this population. In deeper sediment layers (92-96 cm), achange in the microbial community occurs; specifically, a decreased homology with the known sequences is observed. The new sequences form separate clusters on a phylogenetic tree, indicating the possibly endemic nature of the bacteria revealed. Organisms related to the genus Pseudomonas constitute the main portion of the population. An archaea-related sequence was found in a horizon containing gas hydrate crystals (100-128 cm). Uncultured bacteria remain predominant. PMID:16119851

  20. 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

  1. A Picture of the Healthful Food Environment in Two Diverse Urban Cities

    PubMed Central

    Lee, Rebecca E.; Heinrich, Katie M.; Medina, Ashley V.; Regan, Gail R.; Reese-Smith, Jacqueline Y.; Jokura, Yuka; Maddock, Jay E.

    2010-01-01

    Background: Local food environments influence fresh produce purchase and consumption, and previous research has found disparities in local food environments by income and ethnicity. Other existing studies have begun to quantify the distribution of food sources, but there has been limited attention to important features or types of healthful food that are available or their quality or cost. Two studies assessed the type, quantity, quality and cost of healthful food from two diverse urban cities, Kansas City, Kansas and Missouri and Honolulu, Hawaii, and evaluated differences by neighborhood income and ethnic composition. Method: A total of 343 food stores in urban neighborhoods were assessed using the one-page Understanding Neighborhood Determinants of Obesity (UNDO) Food Stores Assessment (FSA) measuring healthful foods. US Census data were used to define median household income and ethnic minority concentration. Results: In Study 1, most low socioeconomic status (SES), high ethnic minority neighborhoods had primarily convenience, liquor or small grocery stores. Quality of produce was typically lower, and prices of some foods were more than in comparison neighborhoods. In Study 2, low SES neighborhoods had more convenience and grocery stores. Farmers’ markets and supermarkets had the best produce availability and quality, and farmers’ markets and pharmacies had the lowest prices. Conclusions: Messages emphasizing eating more fruits and vegetables are not realistic in urban, low SES, high ethnic concentration neighborhoods. Farmers’ markets and supermarkets provided the best opportunities for fresh produce. Increasing access to farmers’ markets and supermarkets or reducing prices could improve the local food environment. PMID:20706621

  2. 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. PMID:26777032

  3. 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.

  4. 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.

  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. 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.

  7. Diversity of culturable psychrophilic and psychrotrophic anaerobic bacteria isolated from beef abattoirs and their environments.

    PubMed

    Moschonas, G; Bolton, D J; McDowell, D A; Sheridan, J J

    2011-07-01

    This study identified 431 psychrophilic or psychrotrophic isolates from commercial Irish beef abattoir environments and "blown packs" of vacuum-packed beef, using PCR and 16S rRNA sequencing, and estimated their intraspecies genetic diversity using restriction fragment length polymorphism (RFLP) analysis and spacer region PCR (SR-PCR). Twenty-five species were identified in the 431 isolates, with the most frequently recovered species being Clostridium gasigenes (n=315), Clostridium estertheticum (n=17), and a potentially novel species designated strain TC1 (n=52). These species were previously found to be associated with a particular type of spoilage known as blown-pack spoilage (BPS), which occurs in chilled-stored (i.e., -1.5°C to 4°C) vacuum-packaged meat within 2 to 4 weeks and involves the production of large volumes of gas. Overall, the study demonstrates the considerable and not previously reported diversity of the anaerobic microflora in abattoirs and the presence of a wide range of organisms capable of causing BPS at chilled temperatures. PMID:21498765

  8. 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.

  9. 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.

  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. PMID

  11. 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

  12. 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.

  13. Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility

    PubMed Central

    Osorio, Héctor; Martínez, Verónica; Nieto, Pamela A; Holmes, David S; Quatrini, Raquel

    2008-01-01

    Background Iron is an essential nutrient but can be toxic at high intracellular concentrations and organisms have evolved tightly regulated mechanisms for iron uptake and homeostasis. Information on iron management mechanisms is available for organisms living at circumneutral pH. However, very little is known about how acidophilic bacteria, especially those used for industrial copper bioleaching, cope with environmental iron loads that can be 1018 times the concentration found in pH neutral environments. This study was motivated by the need to fill this lacuna in knowledge. An understanding of how microorganisms thrive in acidic ecosystems with high iron loads requires a comprehensive investigation of the strategies to acquire iron and to coordinate this acquisition with utilization, storage and oxidation of iron through metal responsive regulation. In silico prediction of iron management genes and Fur regulation was carried out for three Acidithiobacilli: Acidithiobacillus ferrooxidans (iron and sulfur oxidizer) A. thiooxidans and A. caldus (sulfur oxidizers) that can live between pH 1 and pH 5 and for three strict iron oxidizers of the Leptospirillum genus that live at pH 1 or below. Results Acidithiobacilli have predicted FeoB-like Fe(II) and Nramp-like Fe(II)-Mn(II) transporters. They also have 14 different TonB dependent ferri-siderophore transporters of diverse siderophore affinity, although they do not produce classical siderophores. Instead they have predicted novel mechanisms for dicitrate synthesis and possibly also for phosphate-chelation mediated iron uptake. It is hypothesized that the unexpectedly large number and diversity of Fe(III)-uptake systems confers versatility to this group of acidophiles, especially in higher pH environments (pH 4–5) where soluble iron may not be abundant. In contrast, Leptospirilla have only a FtrI-Fet3P-like permease and three TonB dependent ferri-dicitrate siderophore systems. This paucity of iron uptake systems could

  14. 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

  15. Single cell genomics of subsurface microorganisms

    NASA Astrophysics Data System (ADS)

    Stepanauskas, R.; Onstott, T. C.; Lau, C.; Kieft, T. L.; Woyke, T.; Rinke, C.; Sczyrba, A.; van Heerden, E.

    2012-12-01

    Recent studies have revealed unexpected abundance and diversity of microorganisms in terrestrial and marine subsurface, providing new perspectives over their biogeochemical significance, evolution, and the limits of life. The now commonly used research tools, such as metagenomics and PCR-based gene surveys enabled cultivation-unbiased analysis of genes encoded by natural microbial communities. However, these methods seldom provide direct evidence for how the discovered genes are organized inside genomes and from which organisms do they come from. Here we evaluated the feasibility of an alternative, single cell genomics approach, in the analysis of subsurface microbial community composition, metabolic potential and microevolution at the Sanford Underground Research Facility (SURF), South Dakota, and the Witwaterstrand Basin, South Africa. We successfully recovered genomic DNA from individual microbial cells from multiple locations, including ultra-deep (down to 3,500 m) and low-biomass (down to 10^3 cells mL^-1) fracture water. The obtained single amplified genomes (SAGs) from SURF contained multiple representatives of the candidate divisions OP3, OP11, OD1 and uncharacterized archaea. By sequencing eight of these SAGs, we obtained the first genome content information for these phylum-level lineages that do not contain a single cultured representative. The Witwaterstrand samples were collected from deep fractures, biogeochemical dating of which suggests isolation from tens of thousands to tens of millions of years. Thus, these fractures may be viewed as "underground Galapagos", a natural, long-term experiment of microbial evolution within well-defined temporal and spatial boundaries. We are analyzing multiple SAGs from these environments, which will provide detailed information about adaptations to life in deep subsurface, mutation rates, selective pressures and gene flux within and across microbial populations.

  16. Diversity of recent tsunami impact, sedimentary record, and hazards from local to distal environments.

    NASA Astrophysics Data System (ADS)

    Richmond, B. M.; Gelfenbaum, G. R.; Jaffe, B. E.; Szczucinski, W.

    2014-12-01

    One of the goals of paleotsunami research is to define the frequency and magnitude of past tsunamis in order to better understand the hazards posed to coastal communities and ecosystems. Field observations and mapping in the aftermath of several recent tsunamis has greatly improved our understanding of the diversity of tsunami impacts in different environments, the variability observed in the sedimentary record of tsunamis, and the change in these characteristics along the tsunami path from the near- to far-field. Recent tsunamis originating in the Indian Ocean (2004), South Pacific (2009), Chile (2010), and Japan (2011) have affected both local and distant coastlines across a wide range of coastal environments and morphologies. Coral reefs, beaches, dunes, coastal plains with wetlands and/or beach ridge complexes, and rocky embayed coasts have been examined for depositional patterns and evidence of erosion, landscape and vegetation change, and, at a number of sites, impacts to the built environment. We summarize deposit variability, including thickness, stratification, and composition, in an effort to document the wide range of observed deposit features. We observed evidence where vegetation can modify the tsunami flow characteristics. Our field efforts did not focus on impacts to coastal structures, but observations during the course of our work can be applied to improve hazard assessment and recognition of vulnerable areas. Tsunami magnitude, deposits, and hazards are most pronounced near the source and tend to decline with distance, although local factors can modify this trend significantly. For example, general trends in the decrease of tsunami height, inundation, and run-up with distance from the source often exhibit local anomalies where interactions between the tsunami characteristics and local physiography, such as slope and orientation of the coast, create complex interactions that may greatly modify general trends. Efforts to relate the sedimentary

  17. 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.

  18. 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

  19. 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. PMID:16872409

  20. 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.

  1. MODELING CONTAMINANT TRANSPORT THROUGH SUBSURFACE SYSTEMS

    EPA Science Inventory

    Modeling of contaminant transport through soil to groundwater to a receptor requires that consideration be given to the many processes which control the transport and fate of chemical constituents in the subsurface environment. These processes include volatilization, degradation,...

  2. Systematic review on embracing cultural diversity for developing and sustaining a healthy work environment in healthcare.

    PubMed

    Pearson, Alan; Srivastava, Rani; Craig, Dianna; Tucker, Donna; Grinspun, Doris; Bajnok, Irmajean; Griffin, Pat; Long, Leslye; Porritt, Kylie; Han, Thuzar; Gi, Aye A

    2007-03-01

    Objectives  The objective of this review was to evaluate evidence on the structures and processes that support development of effective culturally competent practices and a healthy work environment. Culturally competent practices are a congruent set of workforce behaviours, management practices and institutional policies within a practice setting resulting in an organisational environment that is inclusive of cultural and other forms of diversity. Inclusion criteria  This review included quantitative and qualitative evidence, with a particular emphasis on identifying systematic reviews and randomised controlled trials. For quantitative evidence, other controlled, and descriptive designs were also included. For qualitative evidence, all methodologies were considered. Participants were staff, patients, and systems or policies that were involved or affected by concepts of cultural competence in the nursing workforce in a healthcare environment. Types of interventions included any strategy that had a cultural competence component, which influenced the work environment, and/or patient and nursing staff in the environment. The types of outcomes of interest to this review included nursing staff outcomes, patient outcomes, organisational outcomes and systems level outcomes. Search strategy  The search sought both published and unpublished literature written in the English language. A comprehensive three-step search strategy was used, first to identify appropriate key words, second to combine all optimal key words into a comprehensive search strategy for each database and finally to review the reference lists of all included reviews and research reports. The databases searched were CINAHL, Medline, Current Contents, the Database of Abstracts of Reviews of Effectiveness, The Cochrane Library, PsycINFO, Embase, Sociological Abstracts, Econ lit, ABI/Inform, ERIC and PubMed. The search for unpublished literature used Dissertation Abstracts International. Methodological

  3. Species abundance and diversity of Burkholderia cepacia complex in the environment.

    PubMed

    Ramette, Alban; LiPuma, John J; Tiedje, James M

    2005-03-01

    Despite considerable interest in studying Burkholderia cepacia complex in the environment, we still do not have efficient methods to detect, isolate, and screen large numbers of B. cepacia isolates. To better describe the ecology and diversity of B. cepacia complex, a colony hybridization assay was developed to detect specifically all species of the complex based on polymorphism of the variable V3 region of the 16S rRNA sequence. The sensitivity of the assay was dramatically enhanced by using a probe consisting of three repeats of a B. cepacia complex-specific probe, each separated by a phosphoramidite spacer. In addition, a duplex PCR targeting B. cepacia complex-specific recA and 16S rRNA sequences was developed to enable a fast and reliable diagnostic assay for members of the complex. When applied to maize rhizosphere samples, colony hybridization results were in good agreement with those of most-probable-number duplex PCR, both indicating a >100-fold fluctuation of abundance between individual plants. Using restriction analysis of recA for a total of 285 confirmed isolates of the B. cepacia complex, up to seven B. cepacia complex species were identified; however, their diversity and abundance were not evenly distributed among individual plants, and several allelic variants were commonly found from the same rhizosphere sample. These results indicate that not only complex communities of B. cepacia complex species and closely related strains of the same species may coexist at high population levels but also species composition and abundance may dramatically vary between individual plants. PMID:15746318

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

    PubMed

    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

  5. 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. PMID:23135739

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

    PubMed

    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.

  7. Learning Temporal Patterns of Risk in a Predator-Diverse Environment

    PubMed Central

    Bosiger, Yoland J.; Lonnstedt, Oona M.; McCormick, Mark I.; Ferrari, Maud C. O.

    2012-01-01

    Predation plays a major role in shaping prey behaviour. Temporal patterns of predation risk have been shown to drive daily activity and foraging patterns in prey. Yet the ability to respond to temporal patterns of predation risk in environments inhabited by highly diverse predator communities, such as rainforests and coral reefs, has received surprisingly little attention. In this study, we investigated whether juvenile marine fish, Pomacentrus moluccensis (lemon damselfish), have the ability to learn to adjust the intensity of their antipredator response to match the daily temporal patterns of predation risk they experience. Groups of lemon damselfish were exposed to one of two predictable temporal risk patterns for six days. “Morning risk” treatment prey were exposed to the odour of Cephalopholis cyanostigma (rockcod) paired with conspecific chemical alarm cues (simulating a rockcod present and feeding) during the morning, and rockcod odour only in the evening (simulating a rockcod present but not feeding). “Evening risk” treatment prey had the two stimuli presented to them in the opposite order. When tested individually for their response to rockcod odour alone, lemon damselfish from the morning risk treatment responded with a greater antipredator response intensity in the morning than in the evening. In contrast, those lemon damselfish previously exposed to the evening risk treatment subsequently responded with a greater antipredator response when tested in the evening. The results of this experiment demonstrate that P. moluccensis have the ability to learn temporal patterns of predation risk and can adjust their foraging patterns to match the threat posed by predators at a given time of day. Our results provide the first experimental demonstration of a mechanism by which prey in a complex, multi-predator environment can learn and respond to daily patterns of predation risk. PMID:22493699

  8. 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.

  9. 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. PMID:25041632

  10. 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. PMID:24430481

  11. 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

  12. 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.

  13. Global mammal beta diversity shows parallel assemblage structure in similar but isolated environments.

    PubMed

    Penone, Caterina; Weinstein, Ben G; Graham, Catherine H; Brooks, Thomas M; Rondinini, Carlo; Hedges, S Blair; Davidson, Ana D; Costa, Gabriel C

    2016-08-31

    The taxonomic, phylogenetic and trait dimensions of beta diversity each provide us unique insights into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait beta diversity. Conversely, we expect lower phylogenetic diversity, but higher trait biodiversity among assemblages that are connected but are in differing environmental conditions. We calculated all pairwise comparisons of approximately 110 × 110 km grid cells across the globe for more than 5000 mammal species (approx. 70 million comparisons). We considered realms as units representing geographical distance and historical isolation and biomes as units with similar environmental conditions. While beta diversity dimensions were generally correlated, we highlight geographical regions of decoupling among beta diversity dimensions. Our analysis shows that assemblages from tropical forests in different realms had low trait dissimilarity while phylogenetic beta diversity was significantly higher than expected, suggesting potential convergent evolution. Low trait beta diversity was surprisingly not found between isolated deserts, despite harsh environmental conditions. Overall, our results provide evidence for parallel assemblage structure of mammal assemblages driven by environmental conditions at a global scale. PMID:27559061

  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. PMID:27446038

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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. PMID:16391020

  2. 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

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

    PubMed

    Li, Chongping; Lai, Qiliang; 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.

  4. 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

  5. SUBSURFACE REPOSITORY INTEGRATED CONTROL SYSTEM DESIGN

    SciTech Connect

    C.J. Fernado

    1998-09-17

    The purpose of this document is to develop preliminary high-level functional and physical control system architectures for the proposed subsurface repository at Yucca Mountain. This document outlines overall control system concepts that encompass and integrate the many diverse systems being considered for use within the subsurface repository. This document presents integrated design concepts for monitoring and controlling the diverse set of subsurface operations. The subsurface repository design will be composed of a series of diverse systems that will be integrated to accomplish a set of overall functions and objectives. The subsurface repository contains several Instrumentation and Control (I&C) related systems including: waste emplacement systems, ventilation systems, communication systems, radiation monitoring systems, rail transportation systems, ground control monitoring systems, utility monitoring systems (electrical, lighting, water, compressed air, etc.), fire detection and protection systems, retrieval systems, and performance confirmation systems. Each of these systems involve some level of I&C and will typically be integrated over a data communication network. The subsurface I&C systems will also integrate with multiple surface-based site-wide systems such as emergency response, health physics, security and safeguards, communications, utilities and others. The scope and primary objectives of this analysis are to: (1) Identify preliminary system level functions and interface needs (Presented in the functional diagrams in Section 7.2). (2) Examine the overall system complexity and determine how and on what levels these control systems will be controlled and integrated (Presented in Section 7.2). (3) Develop a preliminary subsurface facility-wide design for an overall control system architecture, and depict this design by a series of control system functional block diagrams (Presented in Section 7.2). (4) Develop a series of physical architectures that

  6. 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.

  7. 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. PMID:25727367

  8. 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.'

  9. 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.

  10. 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. PMID:11554487

  11. 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.

  12. The termite group I phylum is highly diverse and widespread in the environment.

    PubMed

    Herlemann, Daniel P R; Geissinger, Oliver; Brune, Andreas

    2007-10-01

    The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of "Endomicrobia," which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to "Endomicrobia." Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

  13. The little bacteria that can – diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments

    PubMed Central

    Taş, Neslihan; Van Eekert, Miriam H. A.; De Vos, Willem M.; Smidt, Hauke

    2010-01-01

    Summary The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely ‘Dehalococcoides’ spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase‐encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments. PMID:21255338

  14. Component-Based Framework for Subsurface Simulations

    SciTech Connect

    Palmer, Bruce J.; Fang, Yilin; Hammond, Glenn E.; Gurumoorthi, Vidhya

    2007-08-01

    Simulations in the subsurface environment represent a broad range of phenomena covering an equally broad range of scales. Developing modelling capabilities that can integrate models representing different phenomena acting at different scales present formidable challenges both from the algorithmic and computer science perspective. This paper will describe the development of an integrated framework that will be used to combine different models into a single simulation. Initial work has focused on creating two frameworks, one for performing smooth particle hydrodynamics (SPH) simulations of fluid systems, the other for performing grid-based continuum simulations of reactive subsurface flow. The SPH framework is based on a parallel code developed for doing pore scale simulations, the continuum grid-based framework is based on the STOMP (Subsurface Transport Over Multiple Phases) code developed at PNNL. Future work will focus on combining the frameworks together to perform multiscale, multiphysics simulations of reactive subsurface flow.

  15. 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…

  16. Cotton flowers: Pollen and petal humidity sensitivities determine reproductive competitiveness in diverse environments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study investigated the abiotic stress tolerance of mature cotton [Gossypium hirsutum (L.)] pollen and identified genetic variability among the six cotton lines studied. Genetic diversity in pollen viability was observed following a 6.5 h exposure to 25% relative humidity (RH). NM67, DP565, and...

  17. Broad diversity of conjugative plasmids in integron-carrying bacteria from wastewater environments.

    PubMed

    Moura, Alexandra; Oliveira, Cláudia; Henriques, Isabel; Smalla, Kornelia; Correia, António

    2012-05-01

    In this study we assessed the occurrence, diversity and conjugative potential of plasmids in integron-carrying Aeromonas and Enterobacteriaceae from wastewaters. Sixty-six strains were included as donors in mating assays using rifampicin-resistant Escherichia coli and Pseudomonas putida recipient strains. The diversity of plasmids from donors and transconjugants (resistant to tetracycline or streptomycin) was evaluated by restriction analysis and replicon typing targeting 19 incompatibility groups. Restriction patterns revealed a diverse plasmid pool present in these strains. Plasmids were assigned to FrepB (Aeromonas salmonicida, Aeromonas veronii, Aeromonas sp., E. coli, Enterobacter sp.), FIC (A. salmonicida, Aeromonas sp.), FIA (Shigella sp.), I1 (A. veronii, Aeromonas sp., E. coli), HI1 (E. coli) and U (Aeromonas media) replicons. Nevertheless, 50% of the plasmids could not be assigned to any replicon type. Among integron-positive transconjugants, FrepB, I1 and HI1 replicons were detected. Results showed that wastewaters enclose a rich plasmid pool associated with integron-carrying bacteria, capable of conjugating to different bacterial hosts. Moreover, replicons detected in this study in Aeromonas strains expand our current knowledge of plasmid diversity in this genus. PMID:22409355

  18. Broad diversity of conjugative plasmids in integron-carrying bacteria from wastewater environments.

    PubMed

    Moura, Alexandra; Oliveira, Cláudia; Henriques, Isabel; Smalla, Kornelia; Correia, António

    2012-05-01

    In this study we assessed the occurrence, diversity and conjugative potential of plasmids in integron-carrying Aeromonas and Enterobacteriaceae from wastewaters. Sixty-six strains were included as donors in mating assays using rifampicin-resistant Escherichia coli and Pseudomonas putida recipient strains. The diversity of plasmids from donors and transconjugants (resistant to tetracycline or streptomycin) was evaluated by restriction analysis and replicon typing targeting 19 incompatibility groups. Restriction patterns revealed a diverse plasmid pool present in these strains. Plasmids were assigned to FrepB (Aeromonas salmonicida, Aeromonas veronii, Aeromonas sp., E. coli, Enterobacter sp.), FIC (A. salmonicida, Aeromonas sp.), FIA (Shigella sp.), I1 (A. veronii, Aeromonas sp., E. coli), HI1 (E. coli) and U (Aeromonas media) replicons. Nevertheless, 50% of the plasmids could not be assigned to any replicon type. Among integron-positive transconjugants, FrepB, I1 and HI1 replicons were detected. Results showed that wastewaters enclose a rich plasmid pool associated with integron-carrying bacteria, capable of conjugating to different bacterial hosts. Moreover, replicons detected in this study in Aeromonas strains expand our current knowledge of plasmid diversity in this genus.

  19. Correlation analysis of genetic diversity and population structure of Houttuynia cordata Thunb with regard to environment.

    PubMed

    Zhong, J; Wu, F-C; Qiu, P; Dai, L-J

    2016-01-01

    To study the levels of genetic diversity, and population structure, of Houttuynia cordata Thunb, the genetic background and relationships of populations were analyzed in terms of environmental factors. The genetic diversity and population structure of H. cordata were investigated using sequence-related amplified polymorphisms and correlation with environmental factors was analyzed using the SPSS software. Two thousand one hundred sixty-three sites were amplified from 41 pairs of primers, 1825 of which were polymorphic, and the percentage of polymorphic loci was 84.37%; the percentage of polymorphic sites was 72.14 and 67.77% at the species and population level, respectively. The observed number of alleles was 1.52 and 1.30 at species and population level, respectively. The effective number of alleles was 1.38 and 1.24 at species and population level, respectively. The Nei's diversity was 0.26 and 0.15 at species and population level, respectively. The Shannon's information index was 0.87 and 0.63 at species and population level, respectively. The genetic differentiation coefficient of populations was 0.51, and 12 populations were divided into three classes based on D = 0.20; the genetic diversities of different populations are correlated at different significance levels (P < 0.05) with environmental factors. Genetic differentiation existed among populations and the populations exhibited heteroplasmy. PMID:27525953

  20. The Relationship between Student Body Racial Composition and the Normative Environment toward Diversity at Community Colleges

    ERIC Educational Resources Information Center

    Jones, Willis A.

    2013-01-01

    While there has been increased scholarship in recent years on diversity in higher education, most of this research has failed to include 2-year institutions in its analyses. This study examined whether the racial composition of the community college student body is correlated with an institution's normative climate toward three diversity…

  1. Correlation analysis of genetic diversity and population structure of Houttuynia cordata Thunb with regard to environment.

    PubMed

    Zhong, J; Wu, F-C; Qiu, P; Dai, L-J

    2016-01-01

    To study the levels of genetic diversity, and population structure, of Houttuynia cordata Thunb, the genetic background and relationships of populations were analyzed in terms of environmental factors. The genetic diversity and population structure of H. cordata were investigated using sequence-related amplified polymorphisms and correlation with environmental factors was analyzed using the SPSS software. Two thousand one hundred sixty-three sites were amplified from 41 pairs of primers, 1825 of which were polymorphic, and the percentage of polymorphic loci was 84.37%; the percentage of polymorphic sites was 72.14 and 67.77% at the species and population level, respectively. The observed number of alleles was 1.52 and 1.30 at species and population level, respectively. The effective number of alleles was 1.38 and 1.24 at species and population level, respectively. The Nei's diversity was 0.26 and 0.15 at species and population level, respectively. The Shannon's information index was 0.87 and 0.63 at species and population level, respectively. The genetic differentiation coefficient of populations was 0.51, and 12 populations were divided into three classes based on D = 0.20; the genetic diversities of different populations are correlated at different significance levels (P < 0.05) with environmental factors. Genetic differentiation existed among populations and the populations exhibited heteroplasmy.

  2. Habitats as complex odour environments: how does plant diversity affect herbivore and parasitoid orientation?

    PubMed

    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

  3. 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

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

    PubMed Central

    2013-01-01

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

  5. Plant growth promotion potential is equally represented in diverse grapevine root-associated bacterial communities from different biopedoclimatic environments.

    PubMed

    Marasco, Ramona; Rolli, Eleonora; Fusi, Marco; Cherif, Ameur; Abou-Hadid, Ayman; El-Bahairy, Usama; Borin, Sara; 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

  6. 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

  7. 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…

  8. 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…

  9. 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…

  10. 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.

  11. 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…

  12. Global Gradients in Vertebrate Diversity Predicted by Historical Area-Productivity Dynamics and Contemporary Environment

    PubMed Central

    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. PMID:22479151

  13. 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.

  14. 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.

  15. 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.

  16. 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...

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Lateral subsurface flow pathways in a semiarid Ponderosa pine hillslope

    NASA Astrophysics Data System (ADS)

    Newman, Brent D.; Campbell, Andrew R.; Wilcox, Bradford P.

    1998-12-01

    The mechanisms controlling lateral subsurface flow in semiarid environments have received relatively little attention despite the fact that lateral subsurface flow can be an important runoff process in these environments. The objective of the current study is to better understand lateral subsurface flow process in semiarid environments. Natural chloride, dissolved organic carbon, and stable isotope (δD and δ18O) tracers were used to investigate the lateral subsurface flow process and the chemical changes that occur as a result of lateral subsurface flow. Observed differences in chemistry between soil matrix water and lateral subsurface flow were large (for example, chloride concentrations in matrix soil water samples were >200 mg/L, compared with only 2 mg/L in lateral subsurface flow samples obtained at the same time). This difference in chemistry is indicative of a two-domain flow system in which macropores conduct lateral subsurface flow that is not in chemical or hydrological equilibrium with the soil matrix. The size of precipitation events appeared to have a strong influence on the variations in old/new water percentages, and examples of both old and new water dominated events were observed. There were also large variations in the chemistry of lateral subsurface flow with time. For example, chloride and dissolved organic carbon concentrations were 10 and 70 times greater, respectively, under saturated conditions than under unsaturated conditions.

  3. 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.

  4. 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.

  5. 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.

  6. 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. PMID:19285208

  7. Gastrointestinal nematode species diversity in Soay sheep kept in a natural environment without active parasite control.

    PubMed

    Sinclair, Rona; Melville, Lynsey; Sargison, Fiona; Kenyon, Fiona; Nussey, Dan; Watt, Kathryn; Sargison, Neil

    2016-08-30

    Molecular methods based on ITS2 sequence analysis were used to identify strongylid parasites and describe their diversity in a management intervention and anthelmintic drug treatment-free sheep flock. Fourteen different nematode parasite species were identified in the flock and the results showed a greater level of nematode species diversity than is normally reported in managed farmed flocks, with the presence of parasites such as Bunostomum trigonocephalum, Ostertagia leptospicularis, Spiculopteragia houdemeri and Trichostrongylus retortaeformis that are considered to be absent or rare in sheep kept in comparable localities. The implied prevalences of Haemonchus contortus in lambs, and of Trichostrongylus axei in lambs, ewes and rams, were higher than those in farmed sheep kept in similar regions, while those of Teladorsagia circumcincta and Trichostrongylus vitrinus were lower. Comparison of the patterns of nematode parasite infection between the summer and autumn sampling periods showed differences from the scenarios that are commonplace in comparable managed flocks; with T. vitrinus burdens of the lambs being higher in the summer than in the winter, and Oesophagostomum venulosum being the predominant nematode species in the adult sheep during the summer, while more-or-less absent from these groups during the winter. Rams played an important role in the epidemiology of certain parasitic nematode species. The relatively non-pathogenic O. venulosum was the only parasitic nematode species to predominate in any group during the study. This preliminary characterisation of the nematode parasite burdens of sheep extensively grazed on diverse unimproved pastures will aid in the understanding of the parasitological consequences of intensive grazing management and of the manner in which modern agriculture upsets the equilibrium between parasites and their hosts. These factors must be accounted for when defining the concept of sustainable parasite control and informing

  8. Gastrointestinal nematode species diversity in Soay sheep kept in a natural environment without active parasite control.

    PubMed

    Sinclair, Rona; Melville, Lynsey; Sargison, Fiona; Kenyon, Fiona; Nussey, Dan; Watt, Kathryn; Sargison, Neil

    2016-08-30

    Molecular methods based on ITS2 sequence analysis were used to identify strongylid parasites and describe their diversity in a management intervention and anthelmintic drug treatment-free sheep flock. Fourteen different nematode parasite species were identified in the flock and the results showed a greater level of nematode species diversity than is normally reported in managed farmed flocks, with the presence of parasites such as Bunostomum trigonocephalum, Ostertagia leptospicularis, Spiculopteragia houdemeri and Trichostrongylus retortaeformis that are considered to be absent or rare in sheep kept in comparable localities. The implied prevalences of Haemonchus contortus in lambs, and of Trichostrongylus axei in lambs, ewes and rams, were higher than those in farmed sheep kept in similar regions, while those of Teladorsagia circumcincta and Trichostrongylus vitrinus were lower. Comparison of the patterns of nematode parasite infection between the summer and autumn sampling periods showed differences from the scenarios that are commonplace in comparable managed flocks; with T. vitrinus burdens of the lambs being higher in the summer than in the winter, and Oesophagostomum venulosum being the predominant nematode species in the adult sheep during the summer, while more-or-less absent from these groups during the winter. Rams played an important role in the epidemiology of certain parasitic nematode species. The relatively non-pathogenic O. venulosum was the only parasitic nematode species to predominate in any group during the study. This preliminary characterisation of the nematode parasite burdens of sheep extensively grazed on diverse unimproved pastures will aid in the understanding of the parasitological consequences of intensive grazing management and of the manner in which modern agriculture upsets the equilibrium between parasites and their hosts. These factors must be accounted for when defining the concept of sustainable parasite control and informing

  9. Application of a Human Fecal Marker Assay to Diverse Coastal Environments in California and Hawaii

    NASA Astrophysics Data System (ADS)

    Layton, B.; Boehm, A.

    2007-05-01

    Bacterial pollution at beaches is a growing problem of increasing national concern. Currently, the EPA uses Enterococcus as one measure of water quality for recreational contact. Recent work has suggested that rather than indicating anthropogenic pollution, enterococci may be indigenous to the environment. A human-specific gene marker for Enterococcus faecium (known as esp) was recently proposed as a molecular test for bacterial contamination of human origin. The present study applied the esp gene assay to a variety of coastal environments in California and Hawaii, including groundwater, sand, freshwater creeks, estuaries, and the surf zone. Results indicate that enterococci of human origin are present in many of these environments, suggesting that at least a portion of the bacterial pollution at these sites is a result of anthropogenic inputs rather than autochthonous microbial populations.

  10. Influence of ethnicity on recreation and natural environment use patterns: Managing recreation sites for ethnic and racial diversity

    NASA Astrophysics Data System (ADS)

    Baas, John M.; Ewert, Alan; Chavez, Deborah J.

    1993-07-01

    Management of natural environment sites is becoming increasingly complex because of the influx of urbanized society into wildland areas. This worldwide phenomenon impacts a wide range of countries. In southern California ethnicity is often a major factor influencing recreation site use and behavior at sites in the wildland-urban interface. This study investigated the role of ethnicity and race on the use patterns, perception of environment, and recreation behaviors at an outdoor recreation site visited by an ethnically diverse population. Two research questions were asked: (1) What ethnic groups engage in outdoor recreation at this site, and (2) what differences can be assigned to these various groups? Data were collected from 250 recreationists during 1991. Three major ethnic groups were identified, and statistically significant differences were found in the importance of site attributes, activity participation, and in preferred and actual communication channels. Management implications and strategies based on group differences are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    One of the objectives of IODP Expedition 330, Louisville Seamount Trail, was to sample and learn about the subsurface biosphere in the Louisville Seamount Chain (LSC). Seamounts are volcanic constructs that are ubiquitous along the seafloor - models suggest there are >100,000 seamounts of >1 km in height globally (Wessel et al., 2010). Therefore, knowledge about microbiology in the LSC subsurface can broadly be interpreted as representative of much the seafloor. In addition, despite the fact that the vast majority of the sea floor is comprised of crust >10 Ma, the majority of work to date has focused on young sites with active hydrology. Our presentation summarizes work focusing on subsurface microbiology from two different LSC seamounts: holes U1374A (65-71 Ma) and U1376A (64 Ma). We here present data for microbial biomass in the LSC subsurface using a method we developed to quantify microbial biomass in subseafloor ocean crust. We also present results from pyrotag analysis of 15 samples from holes U1374A and holes U1376A, representing several different lithologies from 40-491 meters below seafloor (mbsf) in hole U1374A and from 29-174 mbsf in hole U1376A. Finally, we present preliminary analysis of metagenomic sequencing from three of the samples from Hole U1376A. Biomass was low in the subsurface of both seamounts, ranging from below detection to ~104 cells cm-3. Bacteria comprised >99% of the prokaryotic community in LSC subsurface samples, therefore, bacterial diversity was assessed through 454 pyrosequencing of the V4V6 region of the 16S rRNA gene. Rarefaction analysis indicates that bacterial communities from the LSC subsurface are low diversity, on the order of a few hundred operational taxonomic units per sample. The phyla Actinobacteria, Bacteroidetes, Firmicutes and the classes α-, β- and γ-Proteobacteria are most abundant in the LSC subsurface. Within these, the orders Actinomycetales, Sphingobacteriales, Bacillales and Burkholderiales are the most

  12. AFM studies in diverse ionic environments of nucleosomes reconstituted on the 601 positioning sequence.

    PubMed

    Nazarov, Igor; Chekliarova, Iana; Rychkov, Georgy; Ilatovskiy, Andrey V; Crane-Robinson, Colyn; Tomilin, Alexey

    2016-02-01

    Atomic force microscopy (AFM) was used to study mononucleosomes reconstituted from a DNA duplex of 353 bp containing the strong 601 octamer positioning sequence, together with recombinant human core histone octamers. Three parameters were measured: 1) the length of DNA wrapped around the core histones; 2) the number of superhelical turns, calculated from the total angle through which the DNA is bent, and 3) the volume of the DNA-histone core. This approach allowed us to define in detail the structural diversity of nucleosomes caused by disassembly of the octasome to form subnucleosomal structures containing hexasomes, tetrasomes and disomes. At low ionic strength (TE buffer) and in the presence of physiological concentrations of monovalent cations, the majority of the particles were subnucleosomal, but physiological concentrations of bivalent cations resulted in about half of the nucleosomes being canonical octasomes in which the exiting DNA duplexes cross orthogonally. The dominance of this last species explains why bivalent but not monovalent cations can induce the initial step towards compaction and convergence of neighboring nucleosomes in nucleosomal arrays to form the chromatin fiber in the absence of linker histone. The observed nucleosome structural diversity may reflect the functional plasticity of nucleosomes under physiological conditions.

  13. AFM studies in diverse ionic environments of nucleosomes reconstituted on the 601 positioning sequence.

    PubMed

    Nazarov, Igor; Chekliarova, Iana; Rychkov, Georgy; Ilatovskiy, Andrey V; Crane-Robinson, Colyn; Tomilin, Alexey

    2016-02-01

    Atomic force microscopy (AFM) was used to study mononucleosomes reconstituted from a DNA duplex of 353 bp containing the strong 601 octamer positioning sequence, together with recombinant human core histone octamers. Three parameters were measured: 1) the length of DNA wrapped around the core histones; 2) the number of superhelical turns, calculated from the total angle through which the DNA is bent, and 3) the volume of the DNA-histone core. This approach allowed us to define in detail the structural diversity of nucleosomes caused by disassembly of the octasome to form subnucleosomal structures containing hexasomes, tetrasomes and disomes. At low ionic strength (TE buffer) and in the presence of physiological concentrations of monovalent cations, the majority of the particles were subnucleosomal, but physiological concentrations of bivalent cations resulted in about half of the nucleosomes being canonical octasomes in which the exiting DNA duplexes cross orthogonally. The dominance of this last species explains why bivalent but not monovalent cations can induce the initial step towards compaction and convergence of neighboring nucleosomes in nucleosomal arrays to form the chromatin fiber in the absence of linker histone. The observed nucleosome structural diversity may reflect the functional plasticity of nucleosomes under physiological conditions. PMID:26586109

  14. Phenotypic diversity amongst strains of Pleurotus sajor-caju: implications for cultivation in arid environments.

    PubMed

    Kashangura, Chenjerayi; Hallsworth, John E; Mswaka, Allen Y

    2006-03-01

    In arid regions, biodiversity and biomass are limited by water availability, and this problem has been compounded by desertification associated with global climate change. The saprotrophic macrofungi that are indigenous to hot subtropical and tropical regions, such as Pleurotus spp., can play key roles in water sequestration, nutrient cycling, human nutrition, and bioremediation of waste materials. We studied 15 strains of Pleurotus sajor-caju, a widespread and phenotypically-diverse species, to establish variability in growth response and primordium development over a range of stress parameters: osmotic potential (-0.5 to -5 MPa), temperature (5-40 degrees C) and pH (2-12). The initiation of primordia precedes basidiome production and therefore represents a key stage in bioremediation strategies and fungi-driven nutrient cycles. Primordia were produced at low pH (4-6), at suboptimal growth temperatures (< or =25 degrees C), and under moderate water stress (-0.5 to -3.5 MPa). Although the growth windows for different strains were similar, their maximum growth rates and the optimum conditions for growth varied. We discuss the phenotypic diversity of Pleurotus strains and discuss their potential for cultivation, bioremediation and ecological regeneration.

  15. EIAGRID: In-field optimization of seismic data acquisition by real-time subsurface imaging using a remote GRID computing environment.

    NASA Astrophysics Data System (ADS)

    Heilmann, B. Z.; Vallenilla Ferrara, A. M.

    2009-04-01

    The constant growth of contaminated sites, the unsustainable use of natural resources, and, last but not least, the hydrological risk related to extreme meteorological events and increased climate variability are major environmental issues of today. Finding solutions for these complex problems requires an integrated cross-disciplinary approach, providing a unified basis for environmental science and engineering. In computer science, grid computing is emerging worldwide as a formidable tool allowing distributed computation and data management with administratively-distant resources. Utilizing these modern High Performance Computing (HPC) technologies, the GRIDA3 project bundles several applications from different fields of geoscience aiming to support decision making for reasonable and responsible land use and resource management. In this abstract we present a geophysical application called EIAGRID that uses grid computing facilities to perform real-time subsurface imaging by on-the-fly processing of seismic field data and fast optimization of the processing workflow. Even though, seismic reflection profiling has a broad application range spanning from shallow targets in a few meters depth to targets in a depth of several kilometers, it is primarily used by the hydrocarbon industry and hardly for environmental purposes. The complexity of data acquisition and processing poses severe problems for environmental and geotechnical engineering: Professional seismic processing software is expensive to buy and demands large experience from the user. In-field processing equipment needed for real-time data Quality Control (QC) and immediate optimization of the acquisition parameters is often not available for this kind of studies. As a result, the data quality will be suboptimal. In the worst case, a crucial parameter such as receiver spacing, maximum offset, or recording time turns out later to be inappropriate and the complete acquisition campaign has to be repeated. The

  16. 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

  17. 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...

  18. 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…

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. Diversity of primary CL textures in quartz from porphyry environments: implication for origin of quartz eyes

    NASA Astrophysics Data System (ADS)

    Vasyukova, O. V.; Kamenetsky, V. S.; Goemann, K.; Davidson, P.

    2013-10-01

    Porphyry-style mineralization is related to the intrusion and crystallization of small stocks, which can be of different compositions (from intermediate to felsic) and can intrude into different host rocks (from magmatic to sedimentary). We used cathodoluminescence and electron probe microanalysis to study the internal textures of more than 300 quartz eyes from six porphyry deposits, Panguna (Papua New Guinea), Far Southeast porphyry (Philippines), Batu Hijau (Indonesia), Antapaccay (Peru), Rio Blanco (Chile) and Climax (USA). Significant diversity of the internal textures in quartz eyes was revealed, sometimes even within a single sample. Quartz grains with Ti-rich cores surrounded by Ti-poor mantles were found next to the grains showing the opposite Ti distribution or only slight Ti fluctuations.We propose that diversity of the internal patterns in quartz eyes can actually reflect in situ crystallization history, and that prolonged crystallization after magma emplacement under conditions of continuous cooling can account for the observed features of internal textures. Formation of quartz eyes begins at high temperatures with crystallization of high titanium Quartz 1, which as the melt becomes more and more evolved and cooler, is overgrown by low Ti Quartz 2. Subsequent fluid exsolution brings about dramatic change in the melt composition: OH - , alkalis and other Cl-complexed elements partition into the fluid phase, whereas Ti stays in the melt, contributing to a rapid increase in Ti activity. Separation of the fluid and its further cooling causes disequilibrium in the system, and the Quartz 2 becomes partially resorbed. Exsolution of the fluid gradually builds up the pressure until it exceeds the yield strength of the host rocks and they then fracture. This pressure release most likely triggers crystallization of Quartz 3, which is higher in Ti than Quartz 2 because Ti activity in the melt is higher and pressure of crystallization is lower. As a result of the

  5. 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

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

    PubMed

    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

    2015-09-01

    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

  7. 75 FR 1276 - Requirements for Subsurface Safety Valve Equipment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-11

    ... verification information for subsurface safety valves intended for use in high pressure high temperature... requirements for subsurface safety valves operating in high pressure, high temperature (HPHT) environments in... Edition of API Spec 14A because it updated the design validation and functional testing...

  8. 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.

  9. 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

    2016-01-01

    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. PMID:26952213

  10. Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments.

    PubMed

    Eyice, Özge; Schäfer, Hendrik

    2016-01-01

    One-carbon compounds such as methanol, dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are significant intermediates in biogeochemical cycles. They are suggested to affect atmospheric chemistry and global climate. Methylotrophic microorganisms are considered as a significant sink for these compounds; therefore, we analyzed the diversity of terrestrial bacteria that utilize methanol, DMS and DMSO as carbon and energy source using culture-dependent and culture-independent methods. The effect of habitat type on the methylotrophic community structure was also investigated in rhizosphere and bulk soil. While thirteen strains affiliated to the genera Hyphomicrobium, Methylobacterium, Pseudomonas, Hydrogenophaga, Rhodococcus, Flavobacterium and Variovorax were isolated, denaturing gradient gel electrophoresis revealed the dominance of Thiobacillus, Rhodococcus, Flavobacterium and Bacteroidetes species. Furthermore, methylotrophic communities that degrade methanol or DMS are not shaped by terrestrial habitat type. Rhizosphere and soil samples showed dominance of Methylophilus spp. and Methylovorus spp. for methanol enrichments; Cytophaga spp., Pseudomonas tremae and Thiobacillus thioparus for DMS enrichments. PMID:26475353

  11. 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.

  12. 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

  13. 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

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

    PubMed

    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., Fe(2+) from near 0 to 6.2 mg/L and Σ S(2-) 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

  15. 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

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

    PubMed

    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., Fe(2+) from near 0 to 6.2 mg/L and Σ S(2-) 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

  17. 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.

  18. 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.

  19. 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

  20. Functional diversity in European estuaries: Relating the composition of fish assemblages to the abiotic environment

    NASA Astrophysics Data System (ADS)

    Nicolas, D.; Lobry, J.; Le Pape, O.; Boët, P.

    2010-07-01

    Based on a large standardised data set, the present study proposed a meta-analysis to describe general patterns in the functional diversity of estuarine fish assemblage in terms of both number of species and density along the European Atlantic coast. Fish species collected from 31 European estuaries from Portugal to Scotland were allocated to functional groups according to their ecological utilization of estuaries. A clustering analysis was performed to compare the overall functional structure of estuaries based on fish composition. Generalised linear models were computed to identify relationships between large-scale abiotic and intra-estuarine descriptors and functional attributes of estuarine fish assemblages. The total number of species, and more especially of marine species, was higher in larger estuaries with a wide entrance and, locally, in polyhaline waters. The total density was mainly related to the proportion of intertidal mudflats and, locally, was greater in mesohaline waters. In terms of relative density, northern systems were dominated by marine and catadromous species, while estuarine species were prevalent in the southern ones.

  1. 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

  2. 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

  3. Genome Diversity of Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients and the Hospital Environment

    PubMed Central

    Finnan, Shirley; Morrissey, John P.; O'Gara, Fergal; Boyd, E. Fidelma

    2004-01-01

    Pseudomonas aeruginosa is a gram-negative rod that is ubiquitous in nature. P. aeruginosa is also the quintessential opportunistic pathogen, causing a wide variety of infections in compromised hosts. In cystic fibrosis patients, P. aeruginosa is the leading cause of death. In this study, the evolutionary genetic relationships among 17 P. aeruginosa isolates were examined by comparative sequence analysis of the housekeeping gene encoding malate dehydrogenase and the chaperone groEL. The P. aeruginosa isolates examined included the sequenced strain PAO1, 11 strains recovered from cystic fibrosis patients in Ireland, 4 environmental isolates recovered from a hospital environment, and 1 isolate recovered from a plant rhizosphere. Phylogenetically, clinical and environmental isolates clustered together with one another on the mdh gene tree. At the groEL locus, among the 17 isolates examined, only two polymorphic sites were observed, highlighting the close genetic relationship between isolates from these different environments. Phenotypic analysis of 12 traits among our isolates, however, found that only clinical isolates produced phenazines and elastase. Furthermore, molecular analysis of the distribution of 15 regions associated with virulence showed that two of the environmental isolates examined lacked the majority of regions. Among the clinical isolates examined, the 15 virulence regions were variably present. The distribution of two prophages (Bacto1, Pf1) was also determined, with most isolates encoding both these regions. Of the four genomic islands (the flagellum island and PAGI-1, -2, and -3) examined, only two isolates contained the flagellum island, and PAGI-1, -2, and -3 were absent from all isolates tested. Our data demonstrate the significant role horizontal gene transfer and recombination, together with gene loss, play in the evolution of this important human pathogen. PMID:15583313

  4. 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.

  5. 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

  6. Subsurface connection methods for subsurface heaters

    SciTech Connect

    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.

  7. 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

  8. SUBSURFACE EMPLACEMENT TRANSPORTATION SYSTEM

    SciTech Connect

    T. Wilson; R. Novotny

    1999-11-22

    The objective of this analysis is to identify issues and criteria that apply to the design of the Subsurface Emplacement Transportation System (SET). The SET consists of the track used by the waste package handling equipment, the conductors and related equipment used to supply electrical power to that equipment, and the instrumentation and controls used to monitor and operate those track and power supply systems. Major considerations of this analysis include: (1) Operational life of the SET; (2) Geometric constraints on the track layout; (3) Operating loads on the track; (4) Environmentally induced loads on the track; (5) Power supply (electrification) requirements; and (6) Instrumentation and control requirements. This analysis will provide the basis for development of the system description document (SDD) for the SET. This analysis also defines the interfaces that need to be considered in the design of the SET. These interfaces include, but are not limited to, the following: (1) Waste handling building; (2) Monitored Geologic Repository (MGR) surface site layout; (3) Waste Emplacement System (WES); (4) Waste Retrieval System (WRS); (5) Ground Control System (GCS); (6) Ex-Container System (XCS); (7) Subsurface Electrical Distribution System (SED); (8) MGR Operations Monitoring and Control System (OMC); (9) Subsurface Facility System (SFS); (10) Subsurface Fire Protection System (SFR); (11) Performance Confirmation Emplacement Drift Monitoring System (PCM); and (12) Backfill Emplacement System (BES).

  9. 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.

  10. 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.

  11. 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.

  12. Recovery of humic-reducing bacteria from a diversity of environments.

    PubMed

    Coates, J D; Ellis, D J; Blunt-Harris, E L; Gaw, C V; Roden, E E; Lovley, D R

    1998-04-01

    To evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. These included lake sediments, pristine and contaminated wetland sediments, and marine sediments. In each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (AQDS), as the electron acceptor were members of the family Geobacteraceae. This was true whether the AQDS-reducing bacteria were enriched prior to isolation on solid media or were recovered from the highest positive dilutions of sediments in liquid media. All of the isolates tested not only conserved energy to support growth from acetate oxidation coupled to AQDS reduction but also could oxidize acetate with highly purified soil humic acids as the sole electron acceptor. All of the isolates tested were also able to grow with Fe(III) serving as the sole electron acceptor. This is consistent with previous studies that have suggested that the capacity for Fe(III) reduction is a common feature of all members of the Geobacteraceae. These studies demonstrate that the potential for microbial humic substance reduction can be found in a wide variety of sediment types and suggest that Geobacteraceae species might be important humic-reducing organisms in sediments.

  13. Marine bacterioplankton diversity and community composition in an antarctic coastal environment.

    PubMed

    Lo Giudice, Angelina; Caruso, Consolazione; Mangano, Santina; Bruni, Vivia; De Domenico, Maria; Michaud, Luigi

    2012-01-01

    The bacterial community inhabiting the water column at Terra Nova Bay (Ross Sea, Antarctica) was examined by the fluorescent in situ hybridization (FISH) technique and the genotypic and phenotypic characterization of 606 bacterial isolates. Overall, the FISH analysis revealed a bacterioplankton composition that was typical of Antarctic marine environments with the Cytophaga/Flavobacter (CF) group of Bacteroidetes that was equally dominant with the Actinobacteria and Gammaproteobacteria. As sampling was performed during the decay of sea-ice, it is plausible to assume the origin of Bacteroidetes from the sea-ice compartment where they probably thrive in high concentration of DOM which is efficiently remineralized to inorganic nutrients. This finding was supported by the isolation of Gelidibacter, Polaribacter, and Psychroflexus members (generally well represented in Antarctic sea-ice) which showed the ability to hydrolyze macromolecules, probably through the production of extracellular enzymes. A consistently pronounced abundance of the Gammaproteobacteria (67.8%) was also detected within the cultivable fraction. Altogether, the genera Psychromonas and Pseudoalteromonas accounted for 65.4% of total isolates and were ubiquitous, thus suggesting that they may play a key role within the analyzed bacterioplankton community. In particular, Pseudoalteromonas isolates possessed nitrate reductase and were able to hydrolyze substrates for protease, esterase, and β-galactosidase, thus indicating their involvement in the carbon and nitrogen cycling. Finally, the obtained results highlight the ability of the Actinobacteria to survive and proliferate in the Terra Nova Bay seawater as they generally showed a wide range of salt tolerance and appeared to be particularly competitive with strictly marine bacteria by better utilizing supplied carbon sources. PMID:21748267

  14. 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.

  15. 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.

  16. Surface and subsurface nitrate flow pathways on a watershed scale.

    PubMed

    Daughtry, C S; Gish, T J; Dulaney, W P; Walthall, C L; Kung, K J; McCarty, G W; Angier, J T; Buss, P

    2001-11-30

    Determining the interaction and impact of surface runoff and subsurface flow processes on the environment has been hindered by our inability to characterize subsurface soil structures on a watershed scale. Ground penetrating radar (GPR) data were collected and evaluated in determining subsurface hydrology at four small watersheds in Beltsville, MD. The watersheds have similar textures, organic matter contents, and yield distributions. Although the surface slope was greater on one of the watersheds, slope alone could not explain why it also had a nitrate runoff flux that was 18 times greater than the other three watersheds. Only with knowledge of the subsurface hydrology could the surface runoff differences be explained. The subsurface hydrology was developed by combining GPR and surface topography in a geographic information system. Discrete subsurface flow pathways were identified and confirmed with color infrared imagery, real-time soil moisture monitoring, and yield monitoring. The discrete subsurface flow patterns were also useful in understanding observed nitrate levels entering the riparian wetland and first order stream. This study demonstrated the impact that subsurface stratigraphy can have on water and nitrate (NO3-N) fluxes exiting agricultural lands, even when soil properties, yield distributions, and climate are similar. Reliable protocols for measuring subsurface fluxes of water and chemicals need to be developed.

  17. Investigating hypoxia in aquatic environments: diverse approaches to addressing a complex phenomenon

    NASA Astrophysics Data System (ADS)

    Friedrich, J.; Janssen, F.; Aleynik, D.; Bange, H. W.; Boltacheva, N.; Çagatay, M. N.; Dale, A. W.; Etiope, G.; Erdem, Z.; Geraga, M.; Gilli, A.; Gomoiu, M. T.; Hall, P. O. J.; Hansson, D.; He, Y.; Holtappels, M.; Kirf, M. K.; Kononets, M.; Konovalov, S.; Lichtschlag, A.; Livingstone, D. M.; Marinaro, G.; Mazlumyan, S.; Naeher, S.; North, R. P.; Papatheodorou, G.; Pfannkuche, O.; Prien, R.; Rehder, G.; Schubert, C. J.; Soltwedel, T.; Sommer, S.; Stahl, H.; Stanev, E. V.; Teaca, A.; Tengberg, A.; Waldmann, C.; Wehrli, B.; Wenzhöfer, F.

    2014-02-01

    In this paper we provide an overview of new knowledge on oxygen depletion (hypoxia) and related phenomena in aquatic systems resulting from the EU-FP7 project HYPOX ("In situ monitoring of oxygen depletion in hypoxic ecosystems of coastal and open seas, and landlocked water bodies", http://www.hypox.net). In view of the anticipated oxygen loss in aquatic systems due to eutrophication and climate change, HYPOX was set up to improve capacities to monitor hypoxia as well as to understand its causes and consequences. Temporal dynamics and spatial patterns of hypoxia were analyzed in field studies in various aquatic environments, including the Baltic Sea, the Black Sea, Scottish and Scandinavian fjords, Ionian Sea lagoons and embayments, and Swiss lakes. Examples of episodic and rapid (hours) occurrences of hypoxia, as well as seasonal changes in bottom-water oxygenation in stratified systems, are discussed. Geologically driven hypoxia caused by gas seepage is demonstrated. Using novel technologies, temporal and spatial patterns of water-column oxygenation, from basin-scale seasonal patterns to meter-scale sub-micromolar oxygen distributions, were resolved. Existing multidecadal monitoring data were used to demonstrate the imprint of climate change and eutrophication on long-term oxygen distributions. Organic and inorganic proxies were used to extend investigations on past oxygen conditions to centennial and even longer timescales that cannot be resolved by monitoring. The effects of hypoxia on faunal communities and biogeochemical processes were also addressed in the project. An investigation of benthic fauna is presented as an example of hypoxia-devastated benthic communities that slowly recover upon a reduction in eutrophication in a system where naturally occurring hypoxia overlaps with anthropogenic hypoxia. Biogeochemical investigations reveal that oxygen intrusions have a strong effect on the microbially mediated

  18. 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

  19. 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

  20. 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.

  1. 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. PMID:15006809

  2. 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

  3. 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.

  4. 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.

  5. Comparative genomics of IncP-1ε plasmids from water environments reveals diverse and unique accessory genetic elements.

    PubMed

    Oliveira, Cláudia S; Moura, Alexandra; Henriques, Isabel; Brown, Celeste J; Rogers, Linda M; Top, Eva M; Correia, António

    2013-11-01

    The goal of this study was to determine and compare the complete genome sequences of three new broad-host-range conjugative plasmids. Plasmids pMLUA1, pMLUA3 and pMLUA4 were previously recovered from estuarine water by exogenous plasmid isolation and ranged in size from ∼55 to 59 kb. Comparative genomics showed that their backbone region was identical to the prototype pKJK5 and other IncP1-ε plasmids captured from soils. The accessory region was inserted between the tra region and parA, and presented the typical IncP-1ε ISPa17 and Tn402-like transposon modules. Nevertheless, new class 1 integrons were identified (In794, carrying aadA5 and In795, carrying qacF5-aadA5), as well as a composite transposon IS26-msr(E)-mph(E)-IS26 carrying genes that confer resistance to macrolides. A new insertion sequence, termed ISUnCu17, was also identified on pMLUA3. The architecture of the accessory regions implies the occurrence of multiple insertions and deletions. These data support the notion that IncP-1 plasmids from the ε subgroup are proficient in the capture of diverse genetic elements, including antibiotic resistance genes, and thus may contribute to the co-selection of several resistance determinants. This study constitutes the first report of completely sequenced IncP-1ε plasmids from water environments, and enhances our understanding of the geographic distribution and genetic diversity of these replicons.

  6. Anaerobic microbial transformations in subsurface environments

    SciTech Connect

    Bollag, J.M.; Berry, D.F.; Chanmugathas, P.

    1985-04-01

    The first draft of a literature review article entitled, ''Metabolism of Homocyclic (Benzenoid) and Heterocyclic Aromatic Compounds by Microorganisms Under Anaerobic Conditions'' is completed. The article covers biodegradation of both heterocyclic and homocyclic aromatic compounds under a variety of conditions including nitrate reducing, fermentation, sulfate reducing, and methanogensis. Laboratory experiments have been designed to study the anaerobic biotransformation processes involving organic substance derived from energy residual wastes. The test compounds selected for the initial anaerobic biodegradation experiments include aniline, indole, and pyridine. A Hungate apparatus is presently in operation.

  7. 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.

  8. Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination.

    PubMed

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

    2010-05-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available 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 complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences 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 and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface. PMID:20305024

  9. Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination.

    PubMed

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

    2010-05-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available 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 complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences 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 and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

  10. Denitrifying Bacteria Isolated from Terrestrial Subsurface Sediments Exposed to Mixed-Waste Contamination▿ †

    PubMed Central

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

    2010-01-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available 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 complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences 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 and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface. PMID:20305024

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

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

    SciTech Connect

    Shih, Patrick

    2012-03-22

    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.

  19. 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.

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

    PubMed

    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 NH(4) (+). The reported fluid chemistry included N(2), NH(4) (+) (5-112 μM), NO(2) (-) (27-48 μM), and NO(3) (-) (17-72 μM). In this study, the correlation between low NH(4) (+) concentrations in dominantly meteoric fluids and higher NH(4) (+) in rock-reacted fluids is used to hypothesize that NH(4) (+) is sourced from NH(4) (+)-bearing biotite. However, biotite samples from the host rocks and ore-body minerals were analyzed by Fourier transform infrared (FTIR) microscopy and none-contained NH(4) (+). However, the nitrogenase-encoding gene nifH was successfully amplified from DNA of the fluid sample with high NH(4) (+), suggesting that subsurface microbes have the capability to fix N(2). If so, unregulated nitrogen fixation may account for the relatively high NH(4) (+) concentrations in the fluids. Additionally, the amoA and nxrB genes for archaeal ammonium monooxygenase and nitrite oxidoreductase, respectively, were amplified from the high NH(4) (+) 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 NH(4) (+) 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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. PMID:23701175

  7. Subsurface geomicrobiology of the Iberian Pyritic Belt, a terrestrial analogue of Mars

    NASA Astrophysics Data System (ADS)

    Amils, Ricardo

    Terrestrial subsurface geomicrobiology is a matter of growing interest on many levels. From a fundamental point of view, it seeks to determine whether life can be sustained in the absence of radiation. From an astrobiological point of view, it is an interesting model for early life on Earth, as well as a representation of life as it could occur in other planetary bodies, e.g., Mars. Ŕ Tinto is an unusual extreme acidic environment due to its size, constant acidic pH, high ıo concentration of heavy metals and high level of microbial diversity. Ŕ Tinto rises in the core of ıo the Iberian Pyritic Belt (IPB), one of the biggest sulfidic ore deposits in the world. Today it is clear that the extreme characteristics of Ŕ Tinto are not due to acid mine drainage resulting ıo from mining activity. To explore the hypothesis that a continuous underground reactor of chemolithotrophic microorganisms thriving in the rich sulfidic minerals of the IPB is responsible for the extreme conditions found in the river, a drilling project has been developed to detect evidence of subsurface microbial activity and potential resources to support these microbial communities in situ from retrieved cores (MARTE project). Preliminary results clearly show that there is an active subsurface geomicrobiology in the Iberian Pyritic Belt associated to places were ground waters intersects the sulfidic ore body.

  8. 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.

  9. 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.

  10. Microbiological Transformations of Radionuclides in the Subsurface

    SciTech Connect

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

    2010-01-04

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

  11. New technologies for subsurface barrier wall construction

    SciTech Connect

    Mutch, R.D. Jr.; Ash, R.E. IV; Caputi, J.R.

    1996-12-31

    New technologies for subsurface barrier wall construction are entering the marketplace at an unprecedented pace. Much of this innovation centers around construction of geomembrane barrier walls but also includes advancements in self-hardening slurries and in permeation grouts, involving such diverse materials as colloidal silica gel and montan wax emulsions. These advancements come at a time when subsurface barrier walls are cautiously emerging out of the technological closet. During much of the 1980s, barrier walls of any type were regarded in some quarters as crude and antiquated. It was correspondingly predicted that remediation would be dominated by emerging treatment technologies such as bioremediation, air sparging, and surfactant flushing. Notwithstanding the considerable successes of these emerging technologies, particularly bioremediation, the fact remains that a significant percentage of Superfund, RCRA-corrective action and other waste disposal sites present hydrogeologic, chemical, and waste matrix complexities that far exceed the capabilities of current treatment-based remedial technologies. Consequently, containment-based technologies such as subsurface barrier walls and caps are being recognized once again as irreplaceable components of practical remediation programs at many complex sites.

  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. 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

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

    PubMed

    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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Metalliferous Biosignatures for Deep Subsurface Microbial Activity.

    PubMed

    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.

  1. Metalliferous Biosignatures for Deep Subsurface Microbial Activity.

    PubMed

    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. PMID:26376912

  2. 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.

  3. 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

  4. Aspergillus flavus diversity on crops and in the environment can be exploited to reduce aflatoxin exposure and improve health

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Humans and animals are exposed to aflatoxins, toxic carcinogenic fungal metabolites, through consumption of contaminated food and feed. Aspergillus flavus, the primary causal agent of crop aflatoxin contamination, is composed of phenotypically and genotypically diverse vegetative compatibility group...

  5. 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.

  6. 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

  7. Diversity and Equity in the Lab: Preparing Scientists and Engineers for Inclusive Teaching in Courses and Research Environments

    NASA Astrophysics Data System (ADS)

    Hunter, L.; Seagroves, S.; Metevier, A. J.; Kluger-Bell, B.; Raschke, L.; Jonsson, P.; Porter, J.; Brown, C.; Roybal, G.; Shaw, J.

    2010-12-01

    Despite high attrition rates in college-level science, technology, engineering, and math (STEM) courses, with even higher rates for women and underrepresented minorities, not enough attention has been given to higher education STEM classroom practices that may limit the retention of students from diverse backgrounds. The Professional Development Program (PDP) has developed a range of professional development activities aimed at helping participants learn about diversity and equity issues, integrate inclusive teaching strategies into their own instructional units, and reflect on their own teaching practices. In the PDP, all participants develop and teach a STEM laboratory activity that enables their students to practice scientific inquiry processes as they gain an understanding of scientific concepts. In addition, they are asked to consider diversity and equity issues in their activity design and teaching. The PDP supports participants in this challenging endeavor by engaging them in activities that are aligned with a PDP-defined Diversity & Equity Focus Area that includes five emphases: 1) Multiple ways to learn, communicate and succeed; 2) Learners' goals, interests, motivation, and values; 3) Beliefs and perceptions about ability to achieve; 4) Inclusive collaboration and equitable participation; 5) Social identification within STEM culture. We describe the PDP Diversity & Equity focus, the five emphases, and the supporting activities that have been designed and implemented within the PDP, as well as future directions for our diversity and equity efforts.

  8. 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

  9. Diversity And Abundance Of Deep-Water Coral Mounds In The Straits Of Florida: A Result of Adaptability To Local Environments?

    NASA Astrophysics Data System (ADS)

    Correa, T. B.; Grasmueck, M.; Eberli, G.; Viggiano, D. A.; Rosenberg, A.; Reed, J. K.

    2007-12-01

    is lessened. Corals in these raised locations also benefit from increased exposure to nutrient-rich tidal currents, supporting a denser live coral coverage. Sub-bottom profiles of the MT site show undulating coral ridges developed on top of a relatively flat sub-surface, indicating that antecedent topography is not the only factor determining mound distribution. The integrated AUV data suggest that variable environmental factors, such as sedimentation and current patterns, contribute to the high diversity between coral mound sites of the Straits of Florida. Environmental conditions change over distances of only a few kilometers creating localized and diverse deep-water coral habitats. The deepwater fauna adapts to the local oceanographic and geological conditions. This results in an unexpectedly high abundance of deep-water coral communities with diverse expressions.

  10. Environment.

    ERIC Educational Resources Information Center

    White, Gilbert F.

    1980-01-01

    Presented are perspectives on the emergence of environmental problems. Six major trends in scientific thinking are identified including: holistic approaches to examining environments, life support systems, resource management, risk assessment, streamlined methods for monitoring environmental change, and emphasis on the global framework. (Author/SA)

  11. 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.

  12. 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.

  13. Subsurface Facility System Description Document

    SciTech Connect

    Eric Loros

    2001-07-31

    The Subsurface Facility System encompasses the location, arrangement, size, and spacing of the underground openings. This subsurface system includes accesses, alcoves, and drifts. This system provides access to the underground, provides for the emplacement of waste packages, provides openings to allow safe and secure work conditions, and interfaces with the natural barrier. This system includes what is now the Exploratory Studies Facility. The Subsurface Facility System physical location and general arrangement help support the long-term waste isolation objectives of the repository. The Subsurface Facility System locates the repository openings away from main traces of major faults, away from exposure to erosion, above the probable maximum flood elevation, and above the water table. The general arrangement, size, and spacing of the emplacement drifts support disposal of the entire inventory of waste packages based on the emplacement strategy. The Subsurface Facility System provides access ramps to safely facilitate development and emplacement operations. The Subsurface Facility System supports the development and emplacement operations by providing subsurface space for such systems as ventilation, utilities, safety, monitoring, and transportation.

  14. 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

  15. Effect of the Environment on Genotypic Diversity of Actinomyces naeslundii and Streptococcus oralis in the Oral Biofilm

    PubMed Central

    Paddick, James S.; Brailsford, Susan R.; Kidd, Edwina A. M.; Gilbert, Steven C.; Clark, Douglas T.; Alam, Sharmin; Killick, Zoe J.; Beighton, David

    2003-01-01

    The genotypic diversity of Actinomyces naeslundii genospecies 2 (424 isolates) and Streptococcus oralis (446 isolates) strains isolated from two sound approximal sites in all subjects who were either caries active (seven subjects) or caries free (seven subjects) was investigated by using the repetitive extragenic palindromic PCR. The plaque from the caries-active subjects harbored significantly greater proportions of mutans streptococci and lactobacilli and a smaller proportion of A. naeslundii organisms than the plaque sampled from the caries-free subjects. These data confirmed that the sites of the two groups of subjects were subjected to different environmental stresses, probably determined by the prevailing or fluctuating acidic pH values. We tested the hypothesis that the microfloras of the sites subjected to greater stresses (the plaque samples from the caries-active subjects) would exhibit reduced genotypic diversity since the sites would be less favorable. We found that the diversity of A. naeslundii strains did not change (χ2 = 0.68; P = 0.41) although the proportional representa