WorldWideScience

Sample records for subsurface community composition

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

    Science.gov (United States)

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

    2015-01-01

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

  2. Microbial communities in the deep subsurface

    Science.gov (United States)

    Krumholz, Lee R.

    The diversity of microbial populations and microbial communities within the earth's subsurface is summarized in this review. Scientists are currently exploring the subsurface and addressing questions of microbial diversity, the interactions among microorganisms, and mechanisms for maintenance of subsurface microbial communities. Heterotrophic anaerobic microbial communities exist in relatively permeable sandstone or sandy sediments, located adjacent to organic-rich deposits. These microorganisms appear to be maintained by the consumption of organic compounds derived from adjacent deposits. Sources of organic material serving as electron donors include lignite-rich Eocene sediments beneath the Texas coastal plain, organic-rich Cretaceous shales from the southwestern US, as well as Cretaceous clays containing organic materials and fermentative bacteria from the Atlantic Coastal Plain. Additionally, highly diverse microbial communities occur in regions where a source of organic matter is not apparent but where igneous rock is present. Examples include the basalt-rich subsurface of the Columbia River valley and the granitic subsurface regions of Sweden and Canada. These subsurface microbial communities appear to be maintained by the action of lithotrophic bacteria growing on H2 that is chemically generated within the subsurface. Other deep-dwelling microbial communities exist within the deep sediments of oceans. These systems often rely on anaerobic metabolism and sulfate reduction. Microbial colonization extends to the depths below which high temperatures limit the ability of microbes to survive. Energy sources for the organisms living in the oceanic subsurface may originate as oceanic sedimentary deposits. In this review, each of these microbial communities is discussed in detail with specific reference to their energy sources, their observed growth patterns, and their diverse composition. This information is critical to develop further understanding of subsurface

  3. Complete Subsurface Elemental Composition Measurements With PING

    Science.gov (United States)

    Parsons, A. M.

    2012-01-01

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

  4. Acclimation of subsurface microbial communities to mercury

    DEFF Research Database (Denmark)

    de Lipthay, Julia R; Rasmussen, Lasse D; Øregaard, Gunnar

    2008-01-01

    of mercury tolerance and functional versatility of bacterial communities in contaminated soils initially were higher for surface soil, compared with the deeper soils. However, following new mercury exposure, no differences between bacterial communities were observed, which indicates a high adaptive potential......We studied the acclimation to mercury of bacterial communities of different depths from contaminated and noncontaminated floodplain soils. The level of mercury tolerance of the bacterial communities from the contaminated site was higher than those of the reference site. Furthermore, the level...... of the subsurface communities, possibly due to differences in the availability of mercury. IncP-1 trfA genes were detected in extracted community DNA from all soil depths of the contaminated site, and this finding was correlated to the isolation of four different mercury-resistance plasmids, all belonging...

  5. Cultivation Of Deep Subsurface Microbial Communities

    Science.gov (United States)

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

    2018-01-01

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

  6. NABIR Assessment Element, Expanded Rapid, Comprehensive, Lipid Biomarker Analysis for Subsurface, Community Composition and Nutritional/Physiological Status as Monitors of Remediation and Detoxification Effectiveness

    International Nuclear Information System (INIS)

    David C. White

    2005-01-01

    NABIR funding at the University of Tennessee Center for Biomarker Analysis (CBA) has led to several key contributions to the investigation of bioremediation of metals and radionuclides. This lab has played an integral part in assessing microbial communities at the field scale at the ORNL FRC (Istok et al., 2004) and two UMTRA sites (Anderson et al., 2003, Chang et al., 2001). Our work over the period of the grant has resulted in 42-peer reviewed publications, 62 presentations (14 of which were international), and one patent pending. Currently CBA has 2 papers in press. The main objectives relating to the field portion of this program were to provide comprehensive biomarker analysis for NABIR collaborators to enhance the understanding of microbial geo-bioprocesses involved in the effective immobilization of metals (We have worked with and published or currently are publishing with 10 groups of NAIBR investigators). The laboratory portion of our research centered on methods development and has led to three major innovations that could result in a systematic way of evaluating sites for potential bioremediation. The first of these is the development of an in situ sampling device (Peacock et al., 2004, Anderson et al., 2003, Istok et al., 2004) for the collection and concentration of microbial biomass. The second is the development of expanded lipid analysis based on the significantly greater sensitivity and selectivity of the LC/MS/MS that allows the analysis of respiratory quinones, diglycerides, sterols, intact phospholipids, poly-hydroxyalkonates, and potentially archaeol, and caldarchaeols from archea. These new analyses are accomplished more rapidly and with increased sensitivities and resolution than in the past (Lytle et al., 2000a, 2000b, 2001a, Geyer et al., 2004). The third advance is the coupling of lipid analysis with 13C enrichment experiments (Lytle et al., 2001b, Geyer et al. 2005). With this technique it is now possible to follow the active portion of

  7. Influence of groundwater composition on subsurface iron and arsenic removal

    KAUST Repository

    Moed, David H.; Van Halem, Doris; Verberk, J. Q J C; Amy, Gary L.; Van Dijk, Johannis C.

    2012-01-01

    Subsurface arsenic and iron removal (SAR/SIR) is a novel technology to remove arsenic, iron and other groundwater components by using the subsoil. This research project investigated the influence of the groundwater composition on subsurface treatment. In anoxic sand column experiments, with synthetic groundwater and virgin sand, it was found that several dissolved substances in groundwater compete for adsorption sites with arsenic and iron. The presence of 0.01 mmol L -1phosphate, 0.2 mmol L -1 silicate, and 1 mmol L -1 nitrate greatly reduced the efficiency of SAR, illustrating the vulnerability of this technology in diverse geochemical settings. SIR was not as sensitive to other inorganic groundwater compounds, though iron retardation was limited by 1.2 mmol L -1 calcium and 0.06 mmol L -1 manganese. © IWA Publishing 2012.

  8. Influence of groundwater composition on subsurface iron and arsenic removal

    KAUST Repository

    Moed, David H.

    2012-06-01

    Subsurface arsenic and iron removal (SAR/SIR) is a novel technology to remove arsenic, iron and other groundwater components by using the subsoil. This research project investigated the influence of the groundwater composition on subsurface treatment. In anoxic sand column experiments, with synthetic groundwater and virgin sand, it was found that several dissolved substances in groundwater compete for adsorption sites with arsenic and iron. The presence of 0.01 mmol L -1phosphate, 0.2 mmol L -1 silicate, and 1 mmol L -1 nitrate greatly reduced the efficiency of SAR, illustrating the vulnerability of this technology in diverse geochemical settings. SIR was not as sensitive to other inorganic groundwater compounds, though iron retardation was limited by 1.2 mmol L -1 calcium and 0.06 mmol L -1 manganese. © IWA Publishing 2012.

  9. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site

    Energy Technology Data Exchange (ETDEWEB)

    Green, Stefan [Florida State University; Prakash, Om [Florida State University; Jasrotia, Puja [Florida State University; Overholt, Will [Florida State University; Cardenas, Erick [Michigan State University, East Lansing; Hubbard, Daniela [Florida State University; Tiedje, James M. [Michigan State University, East Lansing; Watson, David B [ORNL; Schadt, Christopher Warren [ORNL; Brooks, Scott C [ORNL; Kostka, Joel [Florida State University

    2011-01-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of ribosomal RNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure, and denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as concentration of nitrogen species, oxygen and sampling season did not appear to strongly influence the distribution of Rhodanobacter. Results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  10. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.

    Science.gov (United States)

    Green, Stefan J; Prakash, Om; Jasrotia, Puja; Overholt, Will A; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M; Watson, David B; Schadt, Christopher W; Brooks, Scott C; Kostka, Joel E

    2012-02-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  11. Ibuprofen removal in horizontal subsurface flow constructed wetlands: treatment performance and fungal community dynamics.

    Science.gov (United States)

    Zhang, Dongqing; Luo, Jinxue; Lee, Zarraz May Ping; Gersberg, Richard M; Liu, Yu; Tan, Soon Keat; Ng, Wun Jern

    2016-01-01

    The treatment performance of ibuprofen (IBP)-enriched wastewater by horizontal subsurface flow constructed wetlands planted with cattail (Typha angustifolia) and unplanted control mesocosms was investigated. Removal efficiencies of IBP were significantly (p fungal community in these wetland systems. The overall diversity of the fungal community was reduced under the IBP exposure. Taxonomic analysis revealed that 62.2% of the fungal sequences were affiliated with Basidiomycota, followed by Ascomycota (37.4%) at the phylum level. Uncultured fungus (48.2%), Chaetomium sp. (14.2%), Aspergillus sp. (12.4%), Trichoderma sp. (5.7%), Cladosporium sp. (5.4%), and Emericellopsis sp. (5.2%) were identified as dominant genera. At the genus level, a distinct profile of the fungal community in the IBP-enriched mesocosms was observed as compared to the control beds, and as well specific fungal genera were enhanced in the planted beds, regardless of IBP enrichment. However, despite these differences, the composition of the fungal community (as measured by Bray-Curtis similarity) was mostly unaffected by the significant IBP enrichment. On the other hand, a consistent similarity pattern of fungal community structure in the planted mesocosms suggests that the presence of higher macrophytes in the wetland systems may well help shape the fungal community structure.

  12. Deep Subsurface Microbial Communities Shaped by the Chicxulub Impactor

    Science.gov (United States)

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

    2017-12-01

    . These data show that the deep biosphere can preserve the imprint of catastrophe long after these events. In this case, the distribution of deep subsurface microbial communities reflects the lithological sequence established during the substantial impact-induced geological rearrangements that occurred in the first hours of the Cenozoic.

  13. Subsurface microbial communities and degradative capacities during trichloroethylene bioremediation

    International Nuclear Information System (INIS)

    Pfiffner, S.M.; Ringelberg, D.B.; Hedrick, D.B.; Phelps, T.J.; Palumbo, A.V.

    1995-01-01

    Subsurface amendments of air, methane, and nutrients were investigated for the in situ stimulation of trichloroethylene- degrading microorganisms at the US DOE Savannah River Integrated Demonstration. Amendments were injected into a lower horizontal well coupled with vacuum extraction from the vadose zone horizontal well. The amendments were sequenced to give increasingly more aggressive treatments. Microbial populations and degradative capacities were monitored in groundwaters samples bimonthly

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

    Science.gov (United States)

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

    2013-07-01

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

  15. An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments. Final report

    International Nuclear Information System (INIS)

    Pfiffner, Susan

    2010-01-01

    The objective of this research was to examine the importance of microbial community structure in influencing uranium reduction rates in subsurface sediments. If the redox state alone is the key to metal reduction, then any organisms that can utilize the oxygen and nitrate in the subsurface can change the geochemical conditions so metal reduction becomes an energetically favored reaction. Thus, community structure would not be critical in determining rates or extent of metal reduction unless community structure influenced the rate of change in redox. Alternatively, some microbes may directly catalyze metal reduction (e.g., specifically reduce U). In this case the composition of the community may be more important and specific types of electron donors may promote the production of communities that are more adept at U reduction. Our results helped determine if the type of electron donor or the preexisting community is important in the bioremediation of metal-contaminated environments subjected to biostimulation. In a series of experiments at the DOE FRC site in Oak Ridge we have consistently shown that all substrates promoted nitrate reduction, while glucose, ethanol, and acetate always promoted U reduction. Methanol only occasionally promoted extensive U reduction which is possibly due to community heterogeneity. There appeared to be limitations imposed on the community related to some substrates (e.g. methanol and pyruvate). Membrane lipid analyses (phospholipids and respiratory quinones) indicated different communities depending on electron donor used. Terminal restriction fragment length polymorphism and clone libraries indicated distinct differences among communities even in treatments that promoted U reduction. Thus, there was enough metabolic diversity to accommodate many different electron donors resulting in the U bioimmobilization.

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

    Science.gov (United States)

    Ellerbrock, Ruth H.; Kaiser, Michael

    2010-05-01

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

  17. Immunological techniques as tools to characterize the subsurface microbial community at a trichloroethylene contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Fliermans, C.B.; Dougherty, J.M.; Franck, M.M.; McKinzey, P.C.; Hazen, T.C.

    1992-01-01

    Effective in situ bioremediation strategies require an understanding of the effects pollutants and remediation techniques have on subsurface microbial communities. Therefore, detailed characterization of a site's microbial communities is important. Subsurface sediment borings and water samples were collected from a trichloroethylene (TCE) contaminated site, before and after horizontal well in situ air stripping and bioventing, as well as during methane injection for stimulation of methane-utilizing microorganisms. Subsamples were processed for heterotrophic plate counts, acridine orange direct counts (AODC), community diversity, direct fluorescent antibodies (DFA) enumeration for several nitrogen-transforming bacteria, and Biolog [reg sign] evaluation of enzyme activity in collected water samples. Plate counts were higher in near-surface depths than in the vadose zone sediment samples. During the in situ air stripping and bioventing, counts increased at or near the saturated zone, remained elevated throughout the aquifer, but did not change significantly after the air stripping. Sporadic increases in plate counts at different depths as well as increased diversity appeared to be linked to differing lithologies. AODCs were orders of magnitude higher than plate counts and remained relatively constant with depth except for slight increases near the surface depths and the capillary fringe. Nitrogen-transforming bacteria, as measured by serospecific DFA, were greatly affected both by the in situ air stripping and the methane injection. Biolog[reg sign] activity appeared to increase with subsurface stimulation both by air and methane. The complexity of subsurface systems makes the use of selective monitoring tools imperative.

  18. Immunological techniques as tools to characterize the subsurface microbial community at a trichloroethylene contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Fliermans, C.B.; Dougherty, J.M.; Franck, M.M.; McKinzey, P.C.; Hazen, T.C.

    1992-12-31

    Effective in situ bioremediation strategies require an understanding of the effects pollutants and remediation techniques have on subsurface microbial communities. Therefore, detailed characterization of a site`s microbial communities is important. Subsurface sediment borings and water samples were collected from a trichloroethylene (TCE) contaminated site, before and after horizontal well in situ air stripping and bioventing, as well as during methane injection for stimulation of methane-utilizing microorganisms. Subsamples were processed for heterotrophic plate counts, acridine orange direct counts (AODC), community diversity, direct fluorescent antibodies (DFA) enumeration for several nitrogen-transforming bacteria, and Biolog {reg_sign} evaluation of enzyme activity in collected water samples. Plate counts were higher in near-surface depths than in the vadose zone sediment samples. During the in situ air stripping and bioventing, counts increased at or near the saturated zone, remained elevated throughout the aquifer, but did not change significantly after the air stripping. Sporadic increases in plate counts at different depths as well as increased diversity appeared to be linked to differing lithologies. AODCs were orders of magnitude higher than plate counts and remained relatively constant with depth except for slight increases near the surface depths and the capillary fringe. Nitrogen-transforming bacteria, as measured by serospecific DFA, were greatly affected both by the in situ air stripping and the methane injection. Biolog{reg_sign} activity appeared to increase with subsurface stimulation both by air and methane. The complexity of subsurface systems makes the use of selective monitoring tools imperative.

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

    Science.gov (United States)

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

    2015-01-01

    Despite many studies of subsurface imaging of carbon nanotube (CNT)-polymer composites via scanning electron microscopy (SEM), significant controversy exists concerning the imaging depth and contrast mechanisms. We studied CNT-polyimide composites and, by threedimensional reconstructions of captured stereo-pair images, determined that the maximum SEM imaging depth was typically hundreds of nanometers. The contrast mechanisms were investigated over a broad range of beam accelerating voltages from 0.3 to 30 kV, and ascribed to modulation by embedded CNTs of the effective secondary electron (SE) emission yield at the polymer surface. This modulation of the SE yield is due to non-uniform surface potential distribution resulting from current flows due to leakage and electron beam induced current. The importance of an external electric field on SEM subsurface imaging was also demonstrated. The insights gained from this study can be generally applied to SEM nondestructive subsurface imaging of conducting nanostructures embedded in dielectric matrices such as graphene-polymer composites, silicon-based single electron transistors, high resolution SEM overlay metrology or e-beam lithography, and have significant implications in nanotechnology.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kostka, Joel E. [Florida State Univ., Tallahassee, FL (United States); Prakash, Om [Florida State Univ., Tallahassee, FL (United States); Green, Stefan J. [Florida State Univ., Tallahassee, FL (United States); Akob, Denise [Florida State Univ., Tallahassee, FL (United States); Jasrotia, Puja [Florida State Univ., Tallahassee, FL (United States); Kerkhof, Lee [Rutgers Univ., New Brunswick, NJ (United States); Chin, Kuk-Jeong [Georgia State Univ., Atlanta, GA (United States); Sheth, Mili [Georgia State Univ., Atlanta, GA (United States); Keller, Martin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Venkateswaran, Amudhan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Elkins, James G. [Univ. of Illinois, Urbana-Champaign, IL (United States); Stucki, Joseph W. [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2012-05-01

    Our objectives were to: 1) isolate and characterize novel anaerobic prokaryotes from subsurface environments exposed to high levels of mixed contaminants (U(VI), nitrate, sulfate), 2) elucidate the diversity and distribution of metabolically active metal- and nitrate-reducing prokaryotes in subsurface sediments, and 3) determine the biotic and abiotic mechanisms linking electron transport processes (nitrate, Fe(III), and sulfate reduction) to radionuclide reduction and immobilization. Mechanisms of electron transport and U(VI) transformation were examined under near in situ conditions in sediment microcosms and in field investigations. Field sampling was conducted at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee. The ORFRC subsurface is exposed to mixed contamination predominated by uranium and nitrate. In short, we effectively addressed all 3 stated objectives of the project. In particular, we isolated and characterized a large number of novel anaerobes with a high bioremediation potential that can be used as model organisms, and we are now able to quantify the function of subsurface sedimentary microbial communities in situ using state-of-the-art gene expression methods (molecular proxies).

  1. Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia

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    Axel eSchippers

    2012-01-01

    Full Text Available Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 meters below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises R/V Meteor 72/5 and 76/1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, CARD-FISH and quantitative real-time PCR (Q-PCR. Total cell counts decreased with depths from 109 – 1010 cells /mL at the sediment surface to 107 – 109 cells /mL below one meter depth. Based on CARD-FISH and Q-PCR analysis overall similar proportions of Bacteria and Archaea were determined. The down core quantitative distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes as well as functional genes involved in different biogeochemical processes was successfully revealed by Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were as highly abundant as Archaea and Bacteria, respectively. Less abundant but detectable in most of the samples in high gene copy numbers were Eukarya and the Fe(III- and Mn(IV-reducing bacterial group Geobacteriaceae (off Namibia as well as the functional genes cbbL encoding for the large subunit of Rubisco, the functional genes dsrA and aprA of sulfate-reducers and the gene mcrA of methanogens. Overall the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-06-15

    (comprising 50% to 100% of rRNA detected). (2) We demonstrated for the first time that the function of microbial communities can be quantified in subsurface sediments using messenger RNA assays (molecular proxies) under in situ conditions. (3) Active Geobacteraceae were identified and phylogenetically characterized from the cDNA of messenger RNA extracted from ORFRC subsurface sediment cores. Multiple clone sequences were retrieved from G. uraniireducens, G. daltonii, and G. metallireducens. (4) Results show that Geobacter strain FRC-32 is capable of growth on benzoate, toluene and benzene as the electron donor, thereby providing evidence that this strain is physiologically distinct from other described members of the subsurface Geobacter clade. (5) Fe(III)-reducing bacteria transform structural Fe in clay minerals from their layer edges rather than from their basal surfaces.

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

    Science.gov (United States)

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

    2004-01-01

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

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

    Science.gov (United States)

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

    2008-02-01

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

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

    Science.gov (United States)

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

    2008-02-01

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

  7. Active microbial community structure of deep subsurface sediments within Baltic Sea Basin

    Science.gov (United States)

    Reese, B. K.; Zinke, L.; Carvalho, G.; Lloyd, K. G.; Marshall, I.; Shumaker, A.; Amend, J.

    2014-12-01

    The Baltic Sea Basin (BSB) is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of climatic fluctuations over past tens of thousands of years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates make this an ideal setting to understand the microbial structure of a deep biosphere community in a relatively high carbon, and thus high-energy environment, compared to other deep subsurface sites. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The active microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further refine our understanding of the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

  8. Composition and dynamic of benthic macroinvertebrates community ...

    African Journals Online (AJOL)

    the purpose to analyze the taxonomic composition, the structure of benthic macroinvertebrates community and the composite ... differences relative to the spatial and temporal variation in the taxonomic composition. ... changes in the structure of macroinvertebrates community ... 2007) with an annual growth rate of 2.4% rely.

  9. Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments.

    Directory of Open Access Journals (Sweden)

    Robert J Martinez

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

  10. Marine Subsurface Microbial Communities Across a Hydrothermal Gradient in Okinawa Trough Sediments

    Science.gov (United States)

    Brandt, L. D.; Hser Wah Saw, J.; Ettema, T.; House, C. H.

    2015-12-01

    IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 meters below sea floor (mbsf). Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 mbsf. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data shows a shift over 15 mbsf from a heterogeneous community of cosmopolitan marine subsurface taxa toward an archaeal-dominated community in the deepest horizons of the predicted biosphere. Notably, the phylum Chloroflexi represents a substantial taxon through most horizons, where it appears to be replaced below 10 mbsf by punctuations of thermophilic and methanotrophic Archaea and Miscellaneous Crenarchaeotic Group abundances. DNA from the aforementioned transition horizons was further analyzed using metagenomic sequencing. Preliminary taxonomic analysis of the metagenomic data agrees well with amplicon data in capturing the shift in relative abundance of Archaea increasing with depth. Additionally, reverse gyrase, a gene found exclusively in hyperthermophilic microorganisms, was recovered only in the metagenome of the deepest horizon. A BLAST search of this protein sequence against the GenBank non-redudnant protein database produced top hits with reverse gyrase from Thermococcus and Pyrococcus, which are

  11. Bacterial diversity and community structure of a sub-surface aquifer exposed to realistic low herbicide concentrations

    DEFF Research Database (Denmark)

    Lipthay, Julia R. de; Johnsen, Kaare; Albrechtsen, H.-J.

    2004-01-01

    contaminants. We examined the effect of in situ exposure to realistic low concentrations of herbicides on the microbial diversity and community structure of sub-surface sediments from a shallow aquifer near Vejen (Denmark). Three different community analyses were performed: colony morphology typing, sole...... community analyses. In contrast, no significant effect was found on the bacterial diversity, except for the culturable fraction where a significantly increased richness and Shannon index was found in the herbicide acclimated sediments. The results of this study show that in situ exposure of sub-surface...... aquifers to realistic low concentrations of herbicides may alter the overall structure of a natural bacterial community, although significant effects on the genetic diversity and carbon substrate usage cannot be detected. The observed impact was probably due to indirect effects. In future investigations...

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

    Science.gov (United States)

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

    2017-12-01

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

  13. Bacterial community composition in reclaimed and unreclaimed ...

    African Journals Online (AJOL)

    AJL-021

    2013-07-24

    Jul 24, 2013 ... characteristics, chemical speciation of heavy metals Cu, Cd and Zn were revealed to ... Phylogenetic analysis indicated that bacteria in these two samples fell into 12 ... plant community and the abundance and composition of.

  14. Resistance of Terrestrial Microbial Communities to Impack of Physical Conditinos of Subsurface Layers of Martian Regolith

    Science.gov (United States)

    Cheptsov, V. S.; Vorobyova, E. A.

    2017-05-01

    Currently, astrobiology is focused on Mars as one of the most perspective objects in the Solar System to search for microbial life. It was assumed that the putative biosphere of Mars could be cryopreserved and had been stored for billions of years in anabiotic state like microbial communities of Arctic and Antarctic permafrost deposits have been preserved till now for millions of years. In this case microbial cells should be not able to repair the damages or these processes have to be significantly depressed, and the main factor causing cell's death should be ionizing radiation. In a series of experiments we simulated the effects of combination of physical factors known as characteristics of the Martian regolith (and close to the space environment) on the natural microbial communities inhabiting xerophytic harsh habitats with extreme temperature conditions: polar permafrost and desert soils. The aim of the study was to examine the cumulative effect of factors (gamma radiation, low temperature, low pressure) to assess the possibility of metabolic reactions, and to find limits of the viability of natural microbial communities after exposure to the given conditions. It was found that microbial biomarkers could be reliably detected in soil samples after radiation dose accumulation up to 1 MGy (not further investigated) in combination with exposure to low temperature and low pressure. Resistance to extremely high doses of radiation in simulated conditions proves that if there was an Earth-like biosphere on the early Mars microorganisms could survive in the surface or subsurface layers of the Martian regolith for more than tens of millions of years after climate change. The study gives also some new grounds for the approval of transfer of viable microorganisms in space.

  15. An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments

    International Nuclear Information System (INIS)

    Kostka, Joel E.

    2008-01-01

    This project represented a joint effort between Oak Ridge National Laboratory (ORNL), the University of Tennessee (UT), and Florida State University (FSU). ORNL served as the lead in-stitution with Dr. A.V. Palumbo responsible for project coordination, integration, and deliver-ables. In situ uranium bioremediation is focused on biostimulating indigenous microorganisms through a combination of pH neutralization and the addition of large amounts of electron donor. Successful biostimulation of U(VI) reduction has been demonstrated in the field and in the laboratory. However, little data is available on the dynamics of microbial populations capable of U(VI) reduction, and the differences in the microbial community dynamics between proposed electron donors have not been explored. In order to elucidate the potential mechanisms of U(VI) reduction for optimization of bioremediation strategies, structure-function relationships of microbial populations were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate from the Oak Ridge Field Research Center (ORFRC), Oak Ridge, Tennessee.

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

    Science.gov (United States)

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

    2016-01-01

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

  17. Predicting community composition from pairwise interactions

    Science.gov (United States)

    Friedman, Jonathan; Higgins, Logan; Gore, Jeff

    The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

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

    Science.gov (United States)

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

    2013-07-01

    We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations

  19. The community ecology of pathogens: coinfection, coexistence and community composition.

    Science.gov (United States)

    Seabloom, Eric W; Borer, Elizabeth T; Gross, Kevin; Kendig, Amy E; Lacroix, Christelle; Mitchell, Charles E; Mordecai, Erin A; Power, Alison G

    2015-04-01

    Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology. © 2015 John Wiley & Sons Ltd/CNRS.

  20. Preliminary biological sampling of GT3 and BT1 cores and the microbial community dynamics of existing subsurface wells

    Science.gov (United States)

    Kraus, E. A.; Stamps, B. W.; Rempfert, K. R.; Ellison, E. T.; Nothaft, D. B.; Boyd, E. S.; Templeton, A. S.; Spear, J. R.

    2017-12-01

    Subsurface microbial life is poorly understood but potentially very important to the search for life on other planets as well as increasing our understanding of Earth's geobiological processes. Fluids and rocks of actively serpentinizing subsurface environments are a recent target of biological study due to their apparent ubiquity across the solar system. Areas of serpentinization can contain high concentrations of molecular hydrogen, H2, that can serve as the dominant fuel source for subsurface microbiota. Working with the Oman Drilling Project, DNA and RNA were extracted from fluids of seven alkaline wells and two rock cores from drill sites GT3 and BT1 within the Samail ophiolite. DNA and cDNA (produced via reverse transcription from the recovered RNA) were sequenced using universal primers to identify microbial life across all three domains. Alkaline subsurface fluids support a microbial community that changes with pH and host-rock type. In peridotite with pH values of >11, wells NSHQ 14 and WAB 71 have high relative abundances of Meiothermus, Methanobacterium, the family Nitrospiraceae, and multiple types of the class Dehalococcoidia. While also hosted in peridotite but at pH 8.5, wells WAB 104 and 105 have a distinct, more diverse microbial community. This increased variance in community make-up is seen in wells that sit near/at the contact of gabbro and peridotite formations as well. Core results indicate both sampled rock types host a very low biomass environment subject to multiple sources of contamination during the drilling process. Suggestions for contaminant reduction, such as having core handlers wear nitrile gloves and flame-sterilizing the outer surfaces of core rounds for biological sampling, would have minimal impact to overall ODP coreflow and maximize the ability to better understand in situ microbiota in this low-biomass serpentinizing subsurface environment. While DNA extraction was successful with gram amounts of crushed rock, much can be

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

    Science.gov (United States)

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

    2017-12-01

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

  2. Microbial community composition affects soil fungistasis.

    Science.gov (United States)

    de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J A; Kowalchuk, George A; van Veen, Johannes A

    2003-02-01

    Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

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

    OpenAIRE

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

    2016-01-01

    The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of five years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a tempera...

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

    Energy Technology Data Exchange (ETDEWEB)

    Moser, Duane P.; Bruckner, Jim; Fisher, Jen; Czerwinski, Ken; Russell, Charles E.; Zavarin, Mavrik

    2010-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-13

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

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

    International Nuclear Information System (INIS)

    Moser, Duane P.; Bruckner, Jim; Fisher, Jen; Czerwinski, Ken; Russell, Charles E.; Zavarin, Mavrik

    2010-01-01

    This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse and divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H 2 and SO 4 2- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

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

    2011-12-01

    With the goal of developing a deterministic understanding of the microbiological and geochemical processes controlling subsurface environments, groundwater bacterial communities were collected from the Rifle Integrated Field Research Challenge (IFRC) site. Biomass from three temporal acetate-stimulated groundwater samples were collected during a period of dominant Fe(III)-reduction, in a region of the aquifer that had previously received acetate amendment the year prior. Phylogenetic analysis revealed a diverse Bacterial community, notably devoid of Archaea with 249 taxa from 9 Bacterial phyla including the dominance of uncultured candidate divisions, BD1-5, OD1, and OP11. We have reconstructed 86 partial to near-complete genomes and have performed a detailed characterization of the underlying metabolic potential of the ecosystem. We assessed the natural variation and redundancy in multi-heme c-type cytochromes, sulfite reductases, and central carbon metabolic pathways. Deep genomic sampling indicated the community contained various metabolic pathways: sulfur oxidation coupled to microaerophilic conditions, nitrate reduction with both acetate and inorganic compounds as donors, carbon and nitrogen fixation, antibiotic warfare, and heavy-metal detoxification. Proteomic investigations using predicted proteins from metagenomics corroborated that acetate oxidation is coupled to reduction of oxygen, sulfur, nitrogen, and iron across the samples. Of particular interest was the detection of acetate oxidizing and sulfate reducing proteins from a Desulfotalea-like bacterium in all three time points, suggesting that aqueous sulfide produced by active sulfate-reducing bacteria could contribute to abiotic iron reduction during the dominant iron reduction phase. Additionally, proteogenomic analysis verified that a large portion of the community, including members of the uncultivated BD1-5, are obligate fermenters, characterized by the presence of hydrogen-evolving hydrogenases

  9. Feeding guild composition of a macrobenthic subtidal community along a depth gradient

    Directory of Open Access Journals (Sweden)

    Marina Dolbeth

    2009-06-01

    Full Text Available The feeding guild composition of a macrobenthic community from southern Portugal was studied along a depth gradient (1.3 to 32 m. This gradient comprised shallow areas with severe physical stress and deeper areas with no significant hydrodynamic impact at the seafloor. The main goal was to determine the influence of the spatial and temporal differences of the hydrodynamic impact at the seafloor on the feeding guild composition of the macrobenthic community. The feeding guild composition changed gradually with depth, which reflects the differences in the hydrodynamics impact at the seafloor. Herbivores and sand-lickers dominated at the shallowest depths with fine sands, which correlated with higher levels of primary production. Scavengers were also distributed in the shallow areas, which was associated with the lower predation impact. Suspension feeders, in accordance with their physiological requirements, were distributed in coarser sands subjected to a physical impact. Carnivores, surface deposit feeders and sub-surface deposit feeders were distributed mainly below 8 m depth, where there was no significant impact from the wave climate. Carnivores were associated with coarser sands and were mainly small polychaetes and nemerteans. Sub-surface and surface deposit feeders were more abundant in the deepest areas of the depth gradient with fine sands and mud deposits with higher organic content. However, surface deposit feeders also occurred at shallower depths. Some seasonal differences related to disturbance impacts were found in the numerical dominance of the feeding guilds.

  10. Exogenous Nitrogen Addition Reduced the Temperature Sensitivity of Microbial Respiration without Altering the Microbial Community Composition

    Directory of Open Access Journals (Sweden)

    Hui Wei

    2017-12-01

    Full Text Available Atmospheric nitrogen (N deposition is changing in both load quantity and chemical composition. The load effects have been studied extensively, whereas the composition effects remain poorly understood. We conducted a microcosm experiment to study how N chemistry affected the soil microbial community composition characterized by phospholipid fatty acids (PLFAs and activity indicated by microbial CO2 release. Surface and subsurface soils collected from an old-growth subtropical forest were supplemented with three N-containing materials (ammonium, nitrate, and urea at the current regional deposition load (50 kg ha-1 yr-1 and incubated at three temperatures (10, 20, and 30°C to detect the interactive effects of N deposition and temperature. The results showed that the additions of N, regardless of form, did not alter the microbial PLFAs at any of the three temperatures. However, the addition of urea significantly stimulated soil CO2 release in the early incubation stage. Compared with the control, N addition consistently reduced the temperature dependency of microbial respiration, implying that N deposition could potentially weaken the positive feedback of the warming-stimulated soil CO2 release to the atmosphere. The consistent N effects for the surface and subsurface soils suggest that the effects of N on soil microbial communities may be independent of soil chemical contents and stoichiometry.

  11. Hydrothermal Fluid Permeability, Temperature, and Nutrient Fluxes: Three Controls on the Structure and the Dynamics of Subsurface Extremophilic Microbe Communities

    Science.gov (United States)

    Ryan, M. P.; Yang, J.

    2002-05-01

    We continue to develop a set of models whose aim is to provide broad constraints on the range of possible community structures for subsurface thermally-tolerant microbes. We combine studies of the three-dimensional internal structure of the dike and sill complexes of active volcanoes, studies of the scale- and direction-dependent 3-D in-situ permeability of intrusive and extrusive rocks from in-situ and laboratory data, numerical modelling of hydrothermal convection in volcanic interiors, data on the optimal metabolic and life-limiting thermal requirements of extremophilic microbes, with the set of nutrients and nutrient pathways required for the survival of given species of thermophiles and hyperthermophiles. With this mix of data bases and analysis tools, we can begin to divine a set of broad theoretical guidelines for constraining the structure and dynamics of extremophilic communities in the subsurface environments of volcanoes. We are searching for the first-order controls on transport. The effects of mineral attachment, detachment, and microbial reproduction may be incorporated in refinements of this basic model. Critical thermal intervals and/or isotherms that correlate with (1) optimal metabolic and (2) life-limiting temperatures for thermophilic microbes are, e.g., in degrees Celcius: Thermus thermophilius [70, 85]; Thermomicrobium roseum [70-75, 85]; Thermus aquaticus [70, 79]; and Sulfolobus acidocaldarius [70-75, 90]. Numerical models of the convective migration of thermophilic (50-80 C), and hyperthermophilic (80-113 C) microbes and their macromolecular amino acid building blocks (113- ~200 C) have been developed that explicitly incorporate the roles of fractures and fluid properties. Fluid transport properties are evaluated through the optimal metabolic and life-limiting temperate ranges and beyond. These models quantify our intuition with respect to controls on community structure and dynamics. Important relationships appear to be: (1) Great

  12. Patterns of vegetation and grasshopper community composition.

    Science.gov (United States)

    Kemp, W P; Harvey, S J; O'Neill, K M

    1990-06-01

    A study was conducted to evaluate differences in rangeland grasshopper communities over environmental gradients in Gallatin Valley, Montana, USA. The concept of habitat type (Daubenmire 1966) was used as a basis for discriminating between groupings of patches based on vegetation. A total of 39 patches were selected that represented five recognized grassland habitat types (Mueggler and Stewart 1980), as well as two disturbed types (replanting within a known habitat type). Repeated sampling in 1988 of both the insect and plant communities yielded a total of 40 grasshopper (19 664 individuals) and 97 plant species. Detrended Correspondence Analysis (DCA) indicated that patch classifications based on presence and percent cover of plants were appropriate and showed good between-group (habitat type) separation for patches along gradients of precipitation/elevation and plant community complexity. Results from undisturbed habitats showed that plant and grasshopper species composition changed over observed environmental gradients and suggested that habitat type influenced not only species presence, but also relative abundance. Discussion is presented that relates results with patch-use and core and satellite species paradigms.

  13. Mineralogical composition changes of postagrogenic soils under different plant communities.

    Science.gov (United States)

    Churilin, Nikita; Chizhikova, Natalia; Varlamov, Evgheni; Churilina, Alexandra

    2017-04-01

    Plant communities play the leading role in transformation of soil. The need of studying former arable lands increases due to large number of abandoned lands in Russia. It is necessary to study mineralogical composition of soils involved into natural processes to understand the trends of their development after agricultural activities in the past. The aim of the study is to identify changes in mineralogical composition of soils under the influence of different plant communities. Soils were sampled in the south of Arkhangelsk region, Ustyansky district, near Akichkin Pochinok village. Soils are formed on clay moraine of Moscow glaciation. Soil profiles were dug on interfluve. We selected 4 plant communities on different stages of succession: upland meadow with domination of sod grasses (Phleum pratense, Agrostis tenuis), 16-year-old birch forest where dominants are herbaceous plants such as Poa sp., Chamerion angustiflium, Agrostis tenuis, 16-year-old spruce forest with no herbaceous vegetation and 70-year-old bilberry spruce forest with domination of Vaccinium myrtillus and Vaccinium vitis-idaea. To separate soil fractions mineral content. We noticed a clear differentiation of studied soils both in the content of fraction and composition of minerals. Mineralogical composition and major mineral phases correlation of profiles under 70 years and 16 years of spruce forests are different. Mineralogical content in upper part of profile under the young spruce is more differentiated than in old spruce forest: the amount of quartz and kaolinite increases in upper horizon, although in this case the overall pattern of profile formation of clay material during podzolization remains unchanged. There is more substantial desilting under the birch forest, compared with profile under the spruce of same age within top 50 cm. Under the meadow vegetation we've discovered differentiation in mineral composition. Upper horizons contain smectite phase and differ from the underlying

  14. Differential Muon Tomography to Continuously Monitor Changes in the Composition of Subsurface Fluids

    Science.gov (United States)

    Coleman, Max; Kudryavtsev, Vitaly A.; Spooner, Neil J.; Fung, Cora; Gluyas, John

    2013-01-01

    Muon tomography has been used to seek hidden chambers in Egyptian pyramids and image subsurface features in volcanoes. It seemed likely that it could be used to image injected, supercritical carbon dioxide as it is emplaced in porous geological structures being used for carbon sequestration, and also to check on subsequent leakage. It should work equally well in any other application where there are two fluids of different densities, such as water and oil, or carbon dioxide and heavy oil in oil reservoirs. Continuous monitoring of movement of oil and/or flood fluid during enhanced oil recovery activities for managing injection is important for economic reasons. Checking on leakage for geological carbon storage is essential both for safety and for economic purposes. Current technology (for example, repeat 3D seismic surveys) is expensive and episodic. Muons are generated by high- energy cosmic rays resulting from supernova explosions, and interact with gas molecules in the atmosphere. This innovation has produced a theoretical model of muon attenuation in the thickness of rock above and within a typical sandstone reservoir at a depth of between 1.00 and 1.25 km. Because this first simulation was focused on carbon sequestration, the innovators chose depths sufficient for the pressure there to ensure that the carbon dioxide would be supercritical. This innovation demonstrates for the first time the feasibility of using the natural cosmic-ray muon flux to generate continuous tomographic images of carbon dioxide in a storage site. The muon flux is attenuated to an extent dependent on, amongst other things, the density of the materials through which it passes. The density of supercritical carbon dioxide is only three quarters that of the brine in the reservoir that it displaces. The first realistic simulations indicate that changes as small as 0.4% in the storage site bulk density could be detected (equivalent to 7% of the porosity, in this specific case). The initial

  15. An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments

    International Nuclear Information System (INIS)

    Pfiffner, Susan M.; Brandt, Craig C.; Kostka, Joel E.; Palumbo, Anthony V.

    2005-01-01

    Our current research represents a joint effort between Oak Ridge National Laboratory (ORNL), Florida State University (FSU), and the University of Tennessee. ORNL will serve as the lead institution with Dr. A.V. Palumbo responsible for project coordination, integration, and deliverables. This project was initiated in November, 2004, in the Integrative Studies Element of the NABIR program. The overall goal of our project is to provide an improved understanding of the relationships between microbial community structure, geochemistry, and metal reduction rates. The research seeks to address the following questions: Is the metabolic diversity of the in situ microbial community sufficiently large and redundant that bioimmobilization of uranium will occur regardless of the type of electron donor added to the system? Are their donor specific effects that lead to enrichment of specific community members that then impose limits on the functional capabilities of the system? Will addition of humics change rates of uranium reduction without changing community structure? Can resource-ratio theory be used to understand changes in uranium reduction rates and community structure with respect to changing C:P ratios?

  16. CHEMICAL COMPOSITION CHANGE OF SUBSURFACE SNOW IN EAST ANTARCTICA WITH DISTANCE FROM THE COAST

    Directory of Open Access Journals (Sweden)

    L. P. Golobokova

    2012-01-01

    Full Text Available The paper presents data on chemical composition of snow in theAntarcticasampled along the first tractor traverse during the 53th Russian Antarctic Expedition from Station Progress (the sea coast to Station Vostok (1,276 kmfrom Progress. Specific features of horizontal and depth distribution of chemical components in snow revealed differences in conditions of formation of snow cover along the traverse in both spatial and time scales. Chemical composition of snow depends on the sources of admixture inputs onto the surface of the ice sheet (marine, continental and volcanic. The influence of sea factor decreases with the distance from the coast. Calculated factor of element enrichment indicated that some ions in snow cover were of continental origin in the middle of the traverse. Elevated concentrations of sulphate ions were recorded in snow-firn cores at 130–150 cmfrom the surface. They were attributed to signals of the Pinatubo volcano eruption (1991. Accumulation rate of snow was calculated for the traverse sites based on the depth of the Pinatubo layer.

  17. Imaging latex–carbon nanotube composites by subsurface electrostatic force microscopy

    International Nuclear Information System (INIS)

    Patel, Sajan; Petty, Clayton W.; Krafcik, Karen Lee

    2016-01-01

    Electrostatic modes of atomic force microscopy have shown to be non-destructive and relatively simple methods for imaging conductors embedded in insulating polymers. Here we use electrostatic force microscopy to image the dispersion of carbon nanotubes in a latex-based conductive composite, which brings forth features not observed in previously studied systems employing linear polymer films. A fixed-potential model of the probe-nanotube electrostatics is presented which in principle gives access to the conductive nanoparticle's depth and radius, and the polymer film dielectric constant. Comparing this model to the data results in nanotube depths that appear to be slightly above the film–air interface. Furthermore, this result suggests that water-mediated charge build-up at the film–air interface may be the source of electrostatic phase contrast in ambient conditions.

  18. Microbial community analysis of shallow subsurface samples with PCR-DGGE

    Energy Technology Data Exchange (ETDEWEB)

    Itaevaara, M.; Suihko, M. -L.; Kapanen, A.; Piskonen, R.; Juvonen, R. [VTT Biotechnology, Espoo (Finland)

    2005-11-15

    This work is part of the site investigations for the disposal of spent nuclear fuel in Olkiluoto bedrock. The purpose of the research was to study the suitability of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) method for monitoring of hydrogeomicrobiology of Olkiluoto repository site. PCR-DGGE method has been applied for monitoring microbial processes in several applications. The benefit of the method is that microorganisms are not cultivated but the presence of microbial communities can be monitored by direct DNA extractions from the environmental samples. Partial 16SrDNA gene sequence is specifically amplified by PCR (polymerase chain reaction) which detect bacteria as a group. The gene sequences are separated in DGGE, and the nucleotide bands are then cut out, extracted, sequenced and identified by the genelibraries by e.g. Blast program. PCR-DGGE method can be used to detect microorganisms which are present abundantly in the microbial communities because small quantities of genes cannot be separated reliably. However, generally the microorganisms involved in several environmental processes are naturally enriched and present as major population. This makes it possible to utilize PCRDGGE as a monitoring method. In this study, we studied the structure of microbial communities in ten ground water samples originating from Olkiluoto. Two universal bacterial primer sets were compared which amplified two different regions of the 16SrDNA gene. The longer sequence amplified resulted in fewer bands in DGGE, in addition there were problems with purification of the sequences after DGGE. The shorter sequence gave more bands in DGGE and more clear results without any amplification problems. Comparison of the sequences from the gene-libraries resulted in the detection of the same species by both primer sets, in addition some different species were detected. Several species were anaerobic bacteria, such as acetogenic and sulphate reducing

  19. Microbial community analysis of shallow subsurface samples with PCR-DGGE

    International Nuclear Information System (INIS)

    Itaevaara, M.; Suihko, M.-L.; Kapanen, A.; Piskonen, R.; Juvonen, R.

    2005-11-01

    This work is part of the site investigations for the disposal of spent nuclear fuel in Olkiluoto bedrock. The purpose of the research was to study the suitability of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) method for monitoring of hydrogeomicrobiology of Olkiluoto repository site. PCR-DGGE method has been applied for monitoring microbial processes in several applications. The benefit of the method is that microorganisms are not cultivated but the presence of microbial communities can be monitored by direct DNA extractions from the environmental samples. Partial 16SrDNA gene sequence is specifically amplified by PCR (polymerase chain reaction) which detect bacteria as a group. The gene sequences are separated in DGGE, and the nucleotide bands are then cut out, extracted, sequenced and identified by the genelibraries by e.g. Blast program. PCR-DGGE method can be used to detect microorganisms which are present abundantly in the microbial communities because small quantities of genes cannot be separated reliably. However, generally the microorganisms involved in several environmental processes are naturally enriched and present as major population. This makes it possible to utilize PCRDGGE as a monitoring method. In this study, we studied the structure of microbial communities in ten ground water samples originating from Olkiluoto. Two universal bacterial primer sets were compared which amplified two different regions of the 16SrDNA gene. The longer sequence amplified resulted in fewer bands in DGGE, in addition there were problems with purification of the sequences after DGGE. The shorter sequence gave more bands in DGGE and more clear results without any amplification problems. Comparison of the sequences from the gene-libraries resulted in the detection of the same species by both primer sets, in addition some different species were detected. Several species were anaerobic bacteria, such as acetogenic and sulphate reducing

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

    Science.gov (United States)

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

    2001-12-01

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

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

    Science.gov (United States)

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

    2010-09-01

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

  2. Subsurface Halophilic Microbial Communities in the Hyperarid Core of the Atacama Desert: An Analog for Possible Subsurface Life in Regolith on Mars

    Science.gov (United States)

    Oren, A.; Warren-Rhodes, K.; Rainey, F. T.; Ewing, S.; McKay, C. P.

    2003-12-01

    The Atacama Desert in its driest portion provides an interesting analog for possible past or present life in the Martian regolith. In the hyperarid core of the Atacama, surface soils are virtually abiotic, with no plants and "near sterile" concentrations of heterotrophic bacteria (i.e., exceedingly low densities of approximately 100 colony forming units per gram soil). The dearth of microbial life at the surface is likely maintained through extremely low water availability, low organic content and the highly oxidizing nature of the soil. In marked contrast to the surface, however, extremely halophilic microorganisms exist in salt layers 1.2-1.5m below the surface. Mineralogical analyses indicate the layers are predominantly halite (70% NaCl) but also contain sodium nitrate (5% NaNO3). Culturing and polar lipid analyses suggest the halophiles are archaeal Halobacterium-like motile rods. Microclimate monitoring at 1m indicates a soil relative humidity of 20% which is stable year-round even during decadal rain events such as that experienced in July 2002. This suggests the layers are isolated from even significant moisture influxes at the surface. Although further research is necessary, important parallels exist between this Earthly desert analog and the possible existence and detection of subsurface life on Mars despite harsh abiotic conditions at the surface.

  3. Molecular analysis of deep subsurface bacteria

    International Nuclear Information System (INIS)

    Jimenez Baez, L.E.

    1989-09-01

    Deep sediments samples from site C10a, in Appleton, and sites, P24, P28, and P29, at the Savannah River Site (SRS), near Aiken, South Carolina were studied to determine their microbial community composition, DNA homology and mol %G+C. Different geological formations with great variability in hydrogeological parameters were found across the depth profile. Phenotypic identification of deep subsurface bacteria underestimated the bacterial diversity at the three SRS sites, since bacteria with the same phenotype have different DNA composition and less than 70% DNA homology. Total DNA hybridization and mol %G+C analysis of deep sediment bacterial isolates suggested that each formation is comprised of different microbial communities. Depositional environment was more important than site and geological formation on the DNA relatedness between deep subsurface bacteria, since more 70% of bacteria with 20% or more of DNA homology came from the same depositional environments. Based on phenotypic and genotypic tests Pseudomonas spp. and Acinetobacter spp.-like bacteria were identified in 85 million years old sediments. This suggests that these microbial communities might have been adapted during a long period of time to the environmental conditions of the deep subsurface

  4. Determination of strontium isotopic composition in natural waters: examples of application in subsurface waters of the coastal zone of Bragantina region, Para, BR

    International Nuclear Information System (INIS)

    Bordalo, Adriana Oliveira; Moura, Candido Augusto Veloso; Scheller, Thomas

    2007-01-01

    Analytical procedures used for determining the concentrations and isotope composition of strontium in subsurface waters, by mass spectrometry, are described. Sampling was performed in coastal plateaus, salt marsh and mangrove environments in the coastal region of Para. Coastal plateau waters have δ 87 Sr between 1.51 and 6.26 per mille and Sr concentration bellow 58 ppb. Salt marsh waters show δ 87 Sr between 0.55 and 0.90 per mille and Sr concentration between 93 and 114 ppm, while mangrove waters have δ 87 Sr per mille around zero and Sr concentration above 15 ppm. Differences in the 87 Sr/ 86 Sr ratio in these subsurface waters are detected, as well as seasonal variations in the coastal plateau waters. (author)

  5. Spatial patterns and links between microbial community composition and function in cyanobacterial mats

    KAUST Repository

    Alnajjar, Mohammad Ahmad; Ramette, Alban; Kü hl, Michael; Hamza, Waleed; Klatt, Judith M.; Polerecky, Lubos

    2014-01-01

    We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. © 2014 Al-Najjar, Ramette, Kühl, Hamza, Klatt and Polerecky.

  6. Spatial patterns and links between microbial community composition and function in cyanobacterial mats

    KAUST Repository

    Alnajjar, Mohammad Ahmad

    2014-08-06

    We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats\\' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. © 2014 Al-Najjar, Ramette, Kühl, Hamza, Klatt and Polerecky.

  7. Effects of hydrogen peroxide bleaching strips on tooth surface color, surface microhardness, surface and subsurface ultrastructure, and microchemical (Raman spectroscopic) composition.

    Science.gov (United States)

    Duschner, Heinz; Götz, Hermann; White, Donald J; Kozak, Kathleen M; Zoladz, James R

    2006-01-01

    This study examined the effects of hydrogen peroxide tooth bleaching strips on the surface hardness and morphology of enamel and the ultrastructure and chemical composition of enamel and dentin in vitro. Sound human molars were ground and polished to prepare a uniform substrate for bleaching treatments. A cycling treatment methodology was employed which alternated ex vivo human salivary exposures with bleaching treatments under conditions of controlled temperature and durations of treatment. Bleaching treatments included commercial Crest Whitestrips bleaching strips, which utilize hydrogen peroxide in a gel as the in situ bleaching source at 6.0 and 6.5% concentrations of H2O2. Control treatments included an untreated group. Crest Whitestrips bleaching included treatment exposures simulating 2x the recommended clinical exposures (28 hours bleaching). Surface color measurements were taken prior to and following bleaching to ensure tooth bleaching activity. The effects of bleach on physical properties of enamel were assessed with microhardness measures. Ultrastructural effects were classified by surface and subsurface confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) techniques. In addition, the effects of bleaching on tooth microchemical composition was studied in different tooth regions by coincident assessment of Raman spectroscopic signature. Color assessments confirmed significant ex vivo tooth bleaching by Whitestrips. Surface microhardness and SEM measures revealed no deleterious effects on the enamel surfaces. CLSM micromorphological assessments supported the safety of hydrogen peroxide bleaching strips both on surface and subsurface enamel, DEJ, and dentin ultrastructure. Raman spectroscopy analysis demonstrated no obvious effects of bleaching treatments on the microchemical composition of enamel and dentin. These results confirm that tooth bleaching with hydrogen peroxide whitening strips does not produce changes in surface/subsurface

  8. Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition.

    Science.gov (United States)

    Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

    2017-11-01

    The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.

  9. Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

    Directory of Open Access Journals (Sweden)

    Jacob D. Hosen

    2017-08-01

    Full Text Available Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition

  10. Bacterial community composition in reclaimed and unreclaimed ...

    African Journals Online (AJOL)

    An investigation was conducted to compare the microbial community structures between contaminated and reclaimed mine tailings of Dexing copper mine, Jiangxi province, China. Sample T1 was obtained from tailings site, where reclamation of phytostabilization has been conducted for 20 years successfully whereas, the ...

  11. A Finite Difference, Semi-implicit, Equation-of-State Efficient Algorithm for the Compositional Flow Modeling in the Subsurface: Numerical Examples

    KAUST Repository

    Saavedra, Sebastian

    2012-07-01

    The mathematical model that has been recognized to have the more accurate approximation to the physical laws govern subsurface hydrocarbon flow in reservoirs is the Compositional Model. The features of this model are adequate to describe not only the performance of a multiphase system but also to represent the transport of chemical species in a porous medium. Its importance relies not only on its current relevance to simulate petroleum extraction processes, such as, Primary, Secondary, and Enhanced Oil Recovery Process (EOR) processes but also, in the recent years, carbon dioxide (CO2) sequestration. The purpose of this study is to investigate the subsurface compositional flow under isothermal conditions for several oil well cases. While simultaneously addressing computational implementation finesses to contribute to the efficiency of the algorithm. This study provides the theoretical framework and computational implementation subtleties of an IMplicit Pressure Explicit Composition (IMPEC)-Volume-balance (VB), two-phase, equation-of-state, approach to model isothermal compositional flow based on the finite difference scheme. The developed model neglects capillary effects and diffusion. From the phase equilibrium premise, the model accounts for volumetric performances of the phases, compressibility of the phases, and composition-dependent viscosities. The Equation of State (EoS) employed to approximate the hydrocarbons behaviour is the Peng Robinson Equation of State (PR-EOS). Various numerical examples were simulated. The numerical results captured the complex physics involved, i.e., compositional, gravitational, phase-splitting, viscosity and relative permeability effects. Regarding the numerical scheme, a phase-volumetric-flux estimation eases the calculation of phase velocities by naturally fitting to phase-upstream-upwinding. And contributes to a faster computation and an efficient programming development.

  12. Effects of Surface and Subsurface Bed Material Composition on Gravel Transport and Flow Competence Relations—Possibilities for Prediction

    Science.gov (United States)

    Bunte, K.; Abt, S. R.; Swingle, K. W.; Cenderelli, D. A.; Gaeuman, D. A.

    2014-12-01

    Bedload transport and flow competence relations are difficult to predict in coarse-bedded steep streams where widely differing sediment supply, bed stability, and complex flow hydraulics greatly affect amounts and sizes of transported gravel particles. This study explains how properties of bed material surface and subsurface size distributions are directly related to gravel transport and may be used for prediction of gravel transport and flow competence relations. Gravel transport, flow competence, and bed material size were measured in step-pool and plane-bed streams. Power functions were fitted to gravel transport QB=aQb and flow competence Dmax=cQd relations; Q is water discharge. Frequency distributions of surface FDsurf and subsurface FDsub bed material were likewise described by power functions FDsurf=hD j and FDsub=kDm fitted over six 0.5-phi size classes within 4 to 22.4 mm. Those gravel sizes are typically mobile even in moderate floods. Study results show that steeper subsurface bed material size distributions lead to steeper gravel transport and flow competence relations, whereas larger amounts of sediment contained in those 6 size bedmaterial classes (larger h and k) flatten the relations. Similarly, steeper surface size distributions decrease the coefficients of the gravel transport and flow competence relations, whereas larger amounts of sediment within the six bed material classes increase the intercepts of gravel transport and flow competence relations. Those relations are likely causative in streams where bedload stems almost entirely from the channel bed as opposed to direct (unworked) contributions from hillslopes and tributaries. The exponent of the subsurface bed material distribution m predicted the gravel transport exponent b with r2 near 0.7 and flow competence exponent d with r2 near 0.5. The intercept of bed surface distributions h increased the intercept a of gravel transport and c of the flow competence relations with r2 near 0.6.

  13. Soil biodiversity and soil community composition determine ecosystem multifunctionality

    Science.gov (United States)

    Wagg, Cameron; Bender, S. Franz; Widmer, Franco; van der Heijden, Marcel G. A.

    2014-01-01

    Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth’s biodiversity is literally hidden below ground. Whether reductions of biodiversity in soil communities below ground have consequences for the overall performance of an ecosystem remains unresolved. It is important to investigate this in view of recent observations that soil biodiversity is declining and that soil communities are changing upon land use intensification. We established soil communities differing in composition and diversity and tested their impact on eight ecosystem functions in model grassland communities. We show that soil biodiversity loss and simplification of soil community composition impair multiple ecosystem functions, including plant diversity, decomposition, nutrient retention, and nutrient cycling. The average response of all measured ecosystem functions (ecosystem multifunctionality) exhibited a strong positive linear relationship to indicators of soil biodiversity, suggesting that soil community composition is a key factor in regulating ecosystem functioning. Our results indicate that changes in soil communities and the loss of soil biodiversity threaten ecosystem multifunctionality and sustainability. PMID:24639507

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

    Science.gov (United States)

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

    2015-06-30

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

  15. Subsurface probing

    International Nuclear Information System (INIS)

    Lytle, R.J.

    1978-01-01

    Imaging techniques that can be used to translate seismic and electromagnetic wave signals into visual representation are briefly discussed. The application of these techniques is illustrated on the example of determining the subsurface structure of a proposed power plant. Imaging makes the wave signals intelligible to the non-geologists. R and D work needed in this area are tabulated

  16. Effects of viruses and predators on prokaryotic community composition.

    Science.gov (United States)

    Jardillier, Ludwig; Bettarel, Yvan; Richardot, Mathilde; Bardot, Corinne; Amblard, Christian; Sime-Ngando, Télesphore; Debroas, Didier

    2005-11-01

    Dialysis bags were used to examine the impact of predation and viral lysis on prokaryotic community composition (PCC) over a 5-day experiment in the oligomesotrophic Lake Pavin (France). The impact of the different predator communities (protists and metazoans) of prokaryotes was estimated by water fractionation (protists, which also affected PCC, whereas viruses seemed to be essentially responsible for profound changes in PCC via direct and indirect actions.

  17. THE EFFECT OF VARIOUS PARAMETERS ON DRY SLIDING WEAR BEHAVIOR AND SUBSURFACE OF AGED HYBRID METAL MATRIX COMPOSITES USING TAGUCHI TECHNIQUE

    Directory of Open Access Journals (Sweden)

    B.M. Viswanatha

    2017-06-01

    Full Text Available The effects of applied load, sliding speed and sliding distance on the dry sliding wear behavior of aged Al-SiCp-Gr composites were investigated. The specimen were fabricated by stir-casting technique. The pin-on-disc wear testing machine was used to investigate the wear rate by design of experiments based on L27 using Taguchi technique. Sliding distance was the most important variable that influenced the wear rate followed by sliding speed and applied load. The worn out surfaces were analyzed by SEM and EDS to study the subsurface mechanism of wear. The addition of reinforcements showed improved tribological behavior of the composite than base alloy.

  18. Invasion of nitrite oxidizer dominated communities: interactions between propagule pressure and community composition

    DEFF Research Database (Denmark)

    Kinnunen, Marta; Dechesne, Arnaud; Albrechtsen, Hans-Jørgen

    consider a broader community ecology framework. For example, the effect of propagule pressure, often studied in macro-ecology, has rarely been examined for microbial communities. Also, the interactions between processes governing community assembly and propagule pressure on invasion success have never been...... by nitrite oxidizer strain (Candidatus Nitrotoga sp. HW29) at 3 different propagule pressures. The reactors were then operated another 2 weeks before analyzing community composition by targeted qPCRs and 16S rRNA gene amplicon analysis. We successfully assembled resident communities with different ratios...

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  1. Metagenomic evidence for H2 oxidation and H2 production by serpentinite-hosted subsurface microbial communities

    Directory of Open Access Journals (Sweden)

    William J Brazelton

    2012-01-01

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

  2. Invasion in microbial communities: Role of community composition and assembly processes

    DEFF Research Database (Denmark)

    Kinnunen, Marta

    of microbial community assembly. Biotic factors include interactions between different microbial groups as well as the community response to alien species – invaders. Microbial invasions can have significant effects on the composition and functioning of resident communities. There is, however, lack......Microbes contribute to all biogeochemical cycles on earth and are responsible for key biological processes that support the survival of plants and animals. There is increased interest in controlling and managing microbial communities in different ecosystems in order to make targeted microbiological...... processes more effective. In order to manage microbial communities, it is essential to understand the factors that shape and influence microbial community composition. In addition to abiotic factors, such as environmental conditions and resource availability, biotic factors also shape the dynamics...

  3. Stormwater runoff drives viral community composition changes in inland freshwaters

    Science.gov (United States)

    Williamson, Kurt E.; Harris, Jamie V.; Green, Jasmin C.; Rahman, Faraz; Chambers, Randolph M.

    2014-01-01

    Storm events impact freshwater microbial communities by transporting terrestrial viruses and other microbes to freshwater systems, and by potentially resuspending microbes from bottom sediments. The magnitude of these impacts on freshwater ecosystems is unknown and largely unexplored. Field studies carried out at two discrete sites in coastal Virginia (USA) were used to characterize the viral load carried by runoff and to test the hypothesis that terrestrial viruses introduced through stormwater runoff change the composition of freshwater microbial communities. Field data gathered from an agricultural watershed indicated that primary runoff can contain viral densities approximating those of receiving waters. Furthermore, viruses attached to suspended colloids made up a large fraction of the total load, particularly in early stages of the storm. At a second field site (stormwater retention pond), RAPD-PCR profiling showed that the viral community of the pond changed dramatically over the course of two intense storms while relatively little change was observed over similar time scales in the absence of disturbance. Comparisons of planktonic and particle-associated viral communities revealed two completely distinct communities, suggesting that particle-associated viruses represent a potentially large and overlooked portion of aquatic viral abundance and diversity. Our findings show that stormwater runoff can quickly change the composition of freshwater microbial communities. Based on these findings, increased storms in the coastal mid-Atlantic region predicted by most climate change models will likely have important impacts on the structure and function of local freshwater microbial communities. PMID:24672520

  4. Variability in Parasites' Community Structure and Composition in Cat ...

    African Journals Online (AJOL)

    This study investigated the composition and structure of the parasite communities in Cat fish with respect to levels of water pollution in Lake Victoria. A total of 1071 Clarias gariepinus with mean TL range of 19 to 27 cm were analyzed from three localities in Mwanza Gulf (Kirumba, 298 fish infected with 15 parasite species), ...

  5. Spatial variation of bacterial community composition near the Luzon ...

    African Journals Online (AJOL)

    Spatial variation of bacterial community composition near the Luzon strait assessed by polymerase chain reaction-denaturing gradient gel electrophoresis ... chain reaction (PCR)-amplified bacterial 16S ribosomal deoxyribonucleic acid (DNA) gene fragments and interpreted the results; its relationship with physical and ...

  6. Composition and abundance of the zooplankton community in the ...

    African Journals Online (AJOL)

    The taxonomic composition of the zooplankton community of the Bitter Lakes, Egypt, was examined in 2003–2004 in relation to the spatial and temporal distribution of environmental factors. Copepoda were dominant, forming 49% of the zooplankton, followed by Protista at 37%. During the autumn, zooplankton in Small ...

  7. The Serpentinite Subsurface Microbiome

    Science.gov (United States)

    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.

  8. Phytoplankton pigment patterns and community composition in the northern South China Sea during winter

    Science.gov (United States)

    Zhai, Hongchang; Ning, Xiuren; Tang, Xuexi; Hao, Qiang; Le, Fengfeng; Qiao, Jing

    2011-03-01

    Phytoplankton pigment patterns and community composition were investigated in the northern South China Sea using high-performance liquid chromatography and the CHEMTAX software from February 11 to 23, 2009. We recognized four different vertical distribution patterns of pigments: chlorophyll a (Chi a)-like type, divinyl chlorophyll a (DV Chi a) type, even distribution type, and surface type. The average value of ratios of accessory photo-protective pigments (APP) to accessory photo-synthetic pigments was 0.89±0.63 in the upper 50 m and 0.16±0.06 below 50 m depth. With increasing depth, APP decreased and photo-synthetically active radiation was attenuated. There was an obvious succession in the phytoplankton community from inshore to the open sea. Diatoms were dominant in the inshore region, while pelagophytes, Prochlorococcus, cyanobacteria and prymnesiophytes were dominant in the open sea. The vertical distribution of phytoplankton also differed greatly from inshore to the open sea. In the coastal and shelf region, diatoms were important components in the whole water column. Cyanobacteria also had a high abundance at the Subsurface Chlorophyll a Maxima (SCM) in the shelf region. In the slope and open sea, Prochlorococcus and cyanobacteria were important groups above the SCM, while pelagophytes dominated below the SCM.

  9. Summary of Inorganic Compositional Data for Groundwater, Soil-Water, and Surface-Water Samples at the Headgate Draw Subsurface Drip Irrigation Site

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-01-01

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

  10. Subsurface iron and arsenic removal: Low-cost technology for community-based water supply in Bangladesh

    KAUST Repository

    Van Halem, Doris; Heijman, Bas G J; Johnston, Richard Bart; Huq, Imamul M.; Ghosh, Sanchari K.; Verberk, Jasper Q J C; Amy, Gary L.; Van Dijk, Johannis C.

    2010-01-01

    The principle of subsurface or in situ iron and arsenic removal is that aerated water is periodically injected into an anoxic aquifer through a tube well, displacing groundwater containing Fe(II). An oxidation zone is created around the tube well where Fe(II) is oxidised. The freshly formed iron hydroxide surfaces provide new sorption sites for soluble Fe(II) andarsenic. The system's efficiency is determined based on the ratio between abstracted volume with reduced iron/arsenic concentrations (V) and the injected volume (Vi). In the field studypresented in this paper, the small-scale application of this technology was investigated in rural Bangladesh. It was found that at small injection volumes (>1m3) iron removal was successful and became more effective with every successive cycle. For arsenic, however, the system did not prove to be very effective yet. Arsenic retardation was only limited and breakthrough of 10mg/L (WHO guideline) was observed before V/Vi = 1, which corresponds to arrival of groundwater at the well. Possible explanations for insufficient arsenic adsorption are the short contact times within the oxidation zone, and the presence of competing anions, like phosphate. © IWA Publishing 2010.

  11. Subsurface iron and arsenic removal: Low-cost technology for community-based water supply in Bangladesh

    KAUST Repository

    Van Halem, Doris

    2010-12-01

    The principle of subsurface or in situ iron and arsenic removal is that aerated water is periodically injected into an anoxic aquifer through a tube well, displacing groundwater containing Fe(II). An oxidation zone is created around the tube well where Fe(II) is oxidised. The freshly formed iron hydroxide surfaces provide new sorption sites for soluble Fe(II) andarsenic. The system\\'s efficiency is determined based on the ratio between abstracted volume with reduced iron/arsenic concentrations (V) and the injected volume (Vi). In the field studypresented in this paper, the small-scale application of this technology was investigated in rural Bangladesh. It was found that at small injection volumes (>1m3) iron removal was successful and became more effective with every successive cycle. For arsenic, however, the system did not prove to be very effective yet. Arsenic retardation was only limited and breakthrough of 10mg/L (WHO guideline) was observed before V/Vi = 1, which corresponds to arrival of groundwater at the well. Possible explanations for insufficient arsenic adsorption are the short contact times within the oxidation zone, and the presence of competing anions, like phosphate. © IWA Publishing 2010.

  12. Macrofouling community structure in Kanayama Bay, Kii Peninsula (Japan)

    Digital Repository Service at National Institute of Oceanography (India)

    Raveendran, T.V.; Harada, E.

    An investigation on the macrofouling community in Kanayama Bay, Kill Peninsula, Japan was undertaken from June 1994 to May 1995 by exposing fiber reinforced plastic (FRP) panels at subsurface and bottom (2.2 m) depths. The composition and abundance...

  13. Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

    Science.gov (United States)

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

    2013-01-01

    Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

  14. A glimpse into the future composition of marine phytoplankton communities

    Directory of Open Access Journals (Sweden)

    Esteban eAcevedo-Trejos

    2014-07-01

    Full Text Available It is expected that climate change will have significant impacts on ecosystems. Most model projections agree that the ocean will experience stronger stratification and less nutrient supply from deep waters. These changes will likely affect marine phytoplankton communities and will thus impact on the higher trophic levels of the oceanic food web. The potential consequences of future climate change on marine microbial communities can be investigated and predicted only with the help of mathematical models. Here we present the application of a model that describes aggregate properties of marine phytoplankton communities and captures the effects of a changing environment on their composition and adaptive capacity. Specifically, the model describes the phytoplankton community in terms of total biomass, mean cell size, and functional diversity. The model is applied to two contrasting regions of the Atlantic Ocean (tropical and temperate and is tested under two emission scenarios: SRES A2 or ``business as usual'' and SRES B1 or ``local utopia''. We find that all three macroecological properties will decline during the next century in both regions, although this effect will be more pronounced in the temperate region. Being consistent with previous model predictions, our results show that a simple trait-based modelling framework represents a valuable tool for investigating how phytoplankton communities may reorganize under a changing climate.

  15. UASB followed by Sub-Surface Horizontal Flow Phytodepuration for the Treatment of the Sewage Generated by a Small Rural Community

    Directory of Open Access Journals (Sweden)

    Massimo Raboni

    2014-10-01

    Full Text Available The paper presents the results of an experimental process designed for the treatment of the sewage generated by a rural community located in the north-east of Brazil. The process consists of a preliminary mechanical treatment adopting coarse screens and grit traps, followed by a biological treatment in a UASB reactor and a sub-surface horizontal flow phytodepuration step. The use of a UASB reactor equipped with a top cover, as well as of the phytodepuration process employing a porous medium, showed to present important health advantages. In particular, there were no significant odor emissions and there was no evidence of the proliferation of insects and other disease vectors. The plant achieved the following mean abatement efficiencies: 92.9% for BOD5, 79.2% for COD and 94% for Suspended Solids. With regard to fecal indicators average efficiencies of 98.8% for fecal coliforms and 97.9% for fecal enterococci were achieved. The UASB reactor showed an important role in achieving this result. The research was also aimed at evaluating the optimal operating conditions for the UASB reactor in terms of hydraulic load and organic volumetric loading. The achieved results hence indicated that the process may be highly effective for small rural communities in tropical and sub-tropical areas.

  16. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

    Directory of Open Access Journals (Sweden)

    Yang Zamin K

    2010-05-01

    Full Text Available Abstract Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

  17. Enterotypes in the landscape of gut microbial community composition

    DEFF Research Database (Denmark)

    Costea, Paul I.; Hildebrand, Falk; Manimozhiyan, Arumugam

    2017-01-01

    Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met...... with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical...... contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept....

  18. Wild Bee Community Composition and Foraging Behaviour in Commercial Strawberries

    DEFF Research Database (Denmark)

    Ahrenfeldt, Erica Juel

    possibly due to the low biodiversity offered by many commercially driven, single species, Danish forests. At field scale (I) bee species richness was higher in field margins compared to field centres but there was no difference between centre and margin in body-size or activity-density. Sampling time had...... an effect on wild bee community composition with higher activity-density and species richness in late May and late June than in early and mid-June (II). Results thus indicate that functional diversity of visiting wild bee assemblages in strawberry differs depending on the spatial and time scale...

  19. Skewed matrilineal genetic composition in a small wild chimpanzee community.

    Science.gov (United States)

    Shimada, Makoto K; Hayakawa, Sachiko; Fujita, Shiho; Sugiyama, Yukimaru; Saitou, Naruya

    2009-01-01

    Maternal kinship is important in primate societies because it affects individual behaviour as well as the sustainability of populations. All members of the Bossou chimpanzee community are descended from 8 individuals (herein referred to as original adults) who were already adults or subadults when field observations were initiated in 1976 and whose genetic relationships were unknown. Sequencing of the control region on the maternally inherited mtDNA revealed that 4 (1 male and 3 females) of the 8 original adults shared an identical haplotype. We investigated the effects of the skewed distribution of mtDNA haplotypes on the following two outcomes. First, we demonstrated that the probability of mtDNA haplotype extinction would be increased under such a skewed composition in a small community. Second, the ratio of potential mating candidates to competitors is likely to decrease if chimpanzees become aware of maternal kinship and avoid incest. We estimated that the magnitude of the decrease in the ratio is 10 times greater in males than in females. Here we demonstrate a scenario in which this matrilineal skewness in a small community accelerates extinction of mtDNA haplotype, which will make it more difficult to find a suitable mate within the community. 2008 S. Karger AG, Basel.

  20. Cultivating the Deep Subsurface Microbiome

    Science.gov (United States)

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

    2017-12-01

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

  1. How microbial community composition regulates coral disease development.

    Directory of Open Access Journals (Sweden)

    Justin Mao-Jones

    2010-03-01

    Full Text Available Reef coral cover is in rapid decline worldwide, in part due to bleaching (expulsion of photosynthetic symbionts and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral: the resident microbial community-which is critical to the healthy functioning of the coral holobiont-is replaced by pathogenic microbes, often species of Vibrio. In this paper we develop computational models for microbial community dynamics in the mucus layer in order to understand how the surface microbial community responds to changes in environmental conditions, and under what circumstances it becomes vulnerable to overgrowth by pathogens. Some of our model's assumptions and parameter values are based on Vibrio spp. as a model system for other established and emerging coral pathogens. We find that the pattern of interactions in the surface microbial community facilitates the existence of alternate stable states, one dominated by antibiotic-producing beneficial microbes and the other pathogen-dominated. A shift to pathogen dominance under transient stressful conditions, such as a brief warming spell, may persist long after environmental conditions have returned to normal. This prediction is consistent with experimental findings that antibiotic properties of Acropora palmata mucus did not return to normal long after temperatures had fallen. Long-term loss of antibiotic activity eliminates a critical component in coral defense against disease, giving pathogens an extended opportunity to infect and spread within the host, elevating the risk of coral bleaching, disease, and mortality.

  2. How microbial community composition regulates coral disease development.

    Science.gov (United States)

    Mao-Jones, Justin; Ritchie, Kim B; Jones, Laura E; Ellner, Stephen P

    2010-03-30

    Reef coral cover is in rapid decline worldwide, in part due to bleaching (expulsion of photosynthetic symbionts) and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral: the resident microbial community-which is critical to the healthy functioning of the coral holobiont-is replaced by pathogenic microbes, often species of Vibrio. In this paper we develop computational models for microbial community dynamics in the mucus layer in order to understand how the surface microbial community responds to changes in environmental conditions, and under what circumstances it becomes vulnerable to overgrowth by pathogens. Some of our model's assumptions and parameter values are based on Vibrio spp. as a model system for other established and emerging coral pathogens. We find that the pattern of interactions in the surface microbial community facilitates the existence of alternate stable states, one dominated by antibiotic-producing beneficial microbes and the other pathogen-dominated. A shift to pathogen dominance under transient stressful conditions, such as a brief warming spell, may persist long after environmental conditions have returned to normal. This prediction is consistent with experimental findings that antibiotic properties of Acropora palmata mucus did not return to normal long after temperatures had fallen. Long-term loss of antibiotic activity eliminates a critical component in coral defense against disease, giving pathogens an extended opportunity to infect and spread within the host, elevating the risk of coral bleaching, disease, and mortality.

  3. Microbial activity in the terrestrial subsurface

    International Nuclear Information System (INIS)

    Kaiser, J.P.; Bollag, J.M.

    1990-01-01

    Little is known about the layers under the earth's crust. Only in recent years have techniques for sampling the deeper subsurface been developed to permit investigation of the subsurface environment. Prevailing conditions in the subsurface habitat such as nutrient availability, soil composition, redox potential, permeability and a variety of other factors can influence the microflora that flourish in a given environment. Microbial diversity varies between geological formations, but in general sandy soils support growth better than soils rich in clay. Bacteria predominate in subsurface sediments, while eukaryotes constitute only 1-2% of the microorganisms. Recent investigations revealed that most uncontaminated subsurface soils support the growth of aerobic heteroorganotrophic bacteria, but obviously anaerobic microorganisms also exist in the deeper subsurface habitat. The microorganisms residing below the surface of the earth are capable of degrading both natural and xenobiotic contaminants and can thereby adapt to growth under polluted conditions. (author) 4 tabs, 77 refs

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

    Science.gov (United States)

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

    2007-01-01

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

  5. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    International Nuclear Information System (INIS)

    Widenfalk, Anneli; Bertilsson, Stefan; Sundh, Ingvar; Goedkoop, Willem

    2008-01-01

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points

  6. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    Energy Technology Data Exchange (ETDEWEB)

    Widenfalk, Anneli [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)], E-mail: anneli.widenfalk@kemi.se; Bertilsson, Stefan [Limnology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvaegen 20, SE-752 36 Uppsala (Sweden); Sundh, Ingvar [Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, SE-750 07 Uppsala (Sweden); Goedkoop, Willem [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)

    2008-04-15

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points.

  7. Effects of biochar blends on microbial community composition in two coastal plain soils

    Science.gov (United States)

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

  8. Subsurface microbial habitats on Mars

    Science.gov (United States)

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

    1991-01-01

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

  9. Keep your Sox on: Community genomics-directed isolation and microscopic characterization of the dominant subsurface sulfur-oxidizing bacterium in a sediment aquifer

    Science.gov (United States)

    Mullin, S. W.; Wrighton, K. C.; Luef, B.; Wilkins, M. J.; Handley, K. M.; Williams, K. H.; Banfield, J. F.

    2012-12-01

    Community genomics and proteomics (proteogenomics) can be used to predict the metabolic potential of complex microbial communities and provide insight into microbial activity and nutrient cycling in situ. Inferences regarding the physiology of specific organisms then can guide isolation efforts, which, if successful, can yield strains that can be metabolically and structurally characterized to further test metagenomic predictions. Here we used proteogenomic data from an acetate-stimulated, sulfidic sediment column deployed in a groundwater well in Rifle, CO to direct laboratory amendment experiments to isolate a bacterial strain potentially involved in sulfur oxidation for physiological and microscopic characterization (Handley et al, submitted 2012). Field strains of Sulfurovum (genome r9c2) were predicted to be capable of CO2 fixation via the reverse TCA cycle and sulfur oxidation (Sox and SQR) coupled to either nitrate reduction (Nap, Nir, Nos) in anaerobic environments or oxygen reduction in microaerobic (cbb3 and bd oxidases) environments; however, key genes for sulfur oxidation (soxXAB) were not identified. Sulfidic groundwater and sediment from the Rifle site were used to inoculate cultures that contained various sulfur species, with and without nitrate and oxygen. We isolated a bacterium, Sulfurovum sp. OBA, whose 16S rRNA gene shares 99.8 % identity to the gene of the dominant genomically characterized strain (genome r9c2) in the Rifle sediment column. The 16S rRNA gene of the isolate most closely matches (95 % sequence identity) the gene of Sulfurovum sp. NBC37-1, a genome-sequenced deep-sea sulfur oxidizer. Strain OBA grew via polysulfide, colloidal sulfur, and tetrathionate oxidation coupled to nitrate reduction under autotrophic and mixotrophic conditions. Strain OBA also grew heterotrophically, oxidizing glucose, fructose, mannose, and maltose with nitrate as an electron acceptor. Over the range of oxygen concentrations tested, strain OBA was not

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

    Directory of Open Access Journals (Sweden)

    Xiao-Xiao Li

    2017-06-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

  12. Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities.

    Science.gov (United States)

    Strickland, Michael S; McCulley, Rebecca L; Nelson, Jim A; Bradford, Mark A

    2015-01-01

    Inputs of low molecular weight carbon (LMW-C) to soil - primarily via root exudates- are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands) were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ∼3% of the variation observed in function. In comparison, land cover and site explained ∼46 and ∼41% of the variation, respectively. This suggests that exudate composition has little influence on function compared to site/land cover specific factors. Supporting the finding that exudate effects were minor, we found that an absence of LMW-C elicited the greatest difference in function compared to those treatments receiving any LMW-C. Additionally, exudate treatments did not alter microbial community composition and observable differences were instead due to land cover. These results confirm the strong effects of land cover/site legacies on soil microbial communities. In contrast, short-term changes in exudate composition, at meaningful concentrations, may have little impact on microbial function and composition.

  13. Does stability in local community composition depend on temporal variation in rates of dispersal and connectivity?

    Science.gov (United States)

    Valanko, Sebastian; Norkko, Joanna; Norkko, Alf

    2015-04-01

    In ecology understanding variation in connectivity is central for how biodiversity is maintained. Field studies on dispersal and temporal dynamics in community regulating processes are, however, rare. We test the short-term temporal stability in community composition in a soft-sediment benthic community by determining among-sampling interval similarity in community composition. We relate stability to in situ measures of connectivity (wind, wave, current energy) and rates of dispersal (quantified in different trap types). Waves were an important predictor of when local community taxa are most likely to disperse in different trap-types, suggesting that wave energy is important for connectivity in a region. Community composition at the site was variable and changed stochastically over time. We found changes in community composition (occurrence, abundance, dominance) to be greater at times when connectivity and rates of dispersal were low. In response to periods of lower connectedness dominant taxa in the local community only exhibited change in their relative abundance. In contrast, locally less abundant taxa varied in both their presence, as well as in relative abundance. Constancy in connectivity and rates of dispersal promotes community stability and persistence, suggesting that local community composition will be impacted by changes in the spatial extent over which immigration and emigration operates in the region. Few empirical studies have actually measured dispersal directly in a multi-species context to demonstrate the role it plays in maintaining local community structure. Even though our study does not evaluate coexistence over demographic time scales, it importantly demonstrates that dispersal is not only important in initial recruitment or following a disturbance, but also key in maintaining local community composition.

  14. Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

    Science.gov (United States)

    Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

    2016-10-01

    Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (PPCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (Pmicrobial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water based on CCA analysis, while NO3 was the only factor in sediment. Published by Elsevier B.V.

  15. Fish community composition, seasonality and abundance in Fortaleza Lagoon, cidreira

    Directory of Open Access Journals (Sweden)

    Lúcia Cabral Schifino

    2004-09-01

    Full Text Available The Fortaleza Lagoon belongs to the Southern Tramandaí subsystem, formed by lagoons disposed linearly on the north-south direction (30º 08’S, 50º 13’W. The objective of this study was to describe some aspects related to the composition of the fish community of Fortaleza Lagoon. Samples were collected monthly from November 1998 to October 1999. The specimens were captured at four previously determined points in the lagoon, and classified in five orders, 12 families and 22 species. Cyphocharax voga, Hyphessobrycon luetkenii, Oligosarcus jenynsii, Oligosarcus robustus and Loricariichthys anus were more abundant species. Amongst the sampled species only two could not be characterised as freshwater species: Centropomus sp (marine and Lycengraulius grossidens (estuarine. The ichthyofauna of the lagoon was predominantly composed by constant species.A Planície Costeira do Rio Grande do Sul é formada por uma série de corpos d’água, dispostos em seqüência ao longo da costa. A lagoa da Fortaleza pertence ao subsistema lagunar Tramandaí-Sul que é composto por lagoas, dispostas linearmente no sentido norte-sul. O do presente estudo teve como objetivo descrever alguns aspectos relacionados à composição da comunidade de peixes da Lagoa da Fortaleza. As amostragens foram realizadas, mensalmente, no período de novembro de 1998 a outubro de 1999. Os exemplares foram capturados em 4 pontos da lagoa previamente determinados e classificados em 5 ordens, 11 famílias e 22 espécies. As espécies Cyphocharax voga, Hyphessobrycon luetkenii, Oligosarcus jenynsii, Oligosarcus robustus e Loricariichthys anus mostraram-se as mais abundantes. Entre as espécies coletadas apenas duas não caracterizam espécies de água doce: Centropomus sp (marinha and Lycengraulius grossidens (estuarina. A ictiofauna da lagoa caracterizou-se por uma predominância de espécies constantes.

  16. Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

    Science.gov (United States)

    Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

    2017-01-01

    The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

  17. Neighboring trees affect ectomycorrhizal fungal community composition in a woodland-forest ecotone.

    Science.gov (United States)

    Hubert, Nathaniel A; Gehring, Catherine A

    2008-09-01

    Ectomycorrhizal fungi (EMF) are frequently species rich and functionally diverse; yet, our knowledge of the environmental factors that influence local EMF diversity and species composition remains poor. In particular, little is known about the influence of neighboring plants on EMF community structure. We tested the hypothesis that the EMF of plants with heterospecific neighbors would differ in species richness and community composition from the EMF of plants with conspecific neighbors. We conducted our study at the ecotone between pinyon (Pinus edulis)-juniper (Juniperus monosperma) woodland and ponderosa pine (Pinus ponderosa) forest in northern Arizona, USA where the dominant trees formed associations with either EMF (P. edulis and P. ponderosa) or arbuscular mycorrhizal fungi (AMF; J. monosperma). We also compared the EMF communities of pinyon and ponderosa pines where their rhizospheres overlapped. The EMF community composition, but not species richness of pinyon pines was significantly influenced by neighboring AM juniper, but not by neighboring EM ponderosa pine. Ponderosa pine EMF communities were different in species composition when growing in association with pinyon pine than when growing in association with a conspecific. The EMF communities of pinyon and ponderosa pines were similar where their rhizospheres overlapped consisting of primarily the same species in similar relative abundance. Our findings suggest that neighboring tree species identity shaped EMF community structure, but that these effects were specific to host-neighbor combinations. The overlap in community composition between pinyon pine and ponderosa pine suggests that these tree species may serve as reservoirs of EMF inoculum for one another.

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

    Directory of Open Access Journals (Sweden)

    Ziye eHu

    2014-07-01

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

  19. Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities

    Directory of Open Access Journals (Sweden)

    Michael S Strickland

    2015-08-01

    Full Text Available Inputs of low molecular weight carbon (LMW-C to soil −primarily via root exudates− are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ~3% of the variation observed in function. In comparison, land cover and site explained ~46 and ~41% of the variation, respectively. This suggests that exudate composition has little influence on function

  20. Large grazers modify effects of aboveground-belowground interactions on small-scale plant community composition

    NARCIS (Netherlands)

    Veen, G. F. (Ciska); Geuverink, Elzemiek; Olff, Han; Schmid, Bernhard

    Aboveground and belowground organisms influence plant community composition by local interactions, and their scale of impact may vary from millimeters belowground to kilometers aboveground. However, it still poorly understood how large grazers that select their forage on large spatial scales

  1. Large grazers modify effects of aboveground–belowground interactions on small-scale plant community composition

    NARCIS (Netherlands)

    Veen, G.F.; Geuverink, E.; Olff, H.

    2012-01-01

    Aboveground and belowground organisms influence plant community composition by local interactions, and their scale of impact may vary from millimeters belowground to kilometers aboveground. However, it still poorly understood how large grazers that select their forage on large spatial scales

  2. Rapid adjustment of bird community compositions to local climatic variations and its functional consequences.

    Science.gov (United States)

    Gaüzère, Pierre; Jiguet, Frédéric; Devictor, Vincent

    2015-09-01

    The local spatial congruence between climate changes and community changes has rarely been studied over large areas. We proposed one of the first comprehensive frameworks tracking local changes in community composition related to climate changes. First, we investigated whether and how 12 years of changes in the local composition of bird communities were related to local climate variations. Then, we tested the consequences of this climate-induced adjustment of communities on Grinnellian (habitat-related) and Eltonian (function-related) homogenization. A standardized protocol monitoring spatial and temporal trends of birds over France from 2001 to 2012 was used. For each plot and each year, we used the spring temperature and the spring precipitations and calculated three indices reflecting the thermal niche, the habitat specialization, and the functional originality of the species within a community. We then used a moving-window approach to estimate the spatial distribution of the temporal trends in each of these indices and their congruency with local climatic variations. Temperature fluctuations and community dynamics were found to be highly variable in space, but their variations were finely congruent. More interestingly, the community adjustment to temperature variations was nonmonotonous. Instead, unexplained fluctuations in community composition were observed up to a certain threshold of climate change intensity, above which a change in community composition was observed. This shift corresponded to a significant decrease in the relative abundance of habitat specialists and functionally original species within communities, regardless of the direction of temperature change. The investigation of variations in climate and community responses appears to be a central step toward a better understanding of climate change effects on biodiversity. Our results suggest a fine-scale and short-term adjustment of community composition to temperature changes. Moreover

  3. Effect of soil properties and hydrology on Archaeal community composition in three temperate grasslands on peat

    DEFF Research Database (Denmark)

    Görres, Carolyn-Monika; Conrad, Ralf; Petersen, Søren O

    2013-01-01

    Grasslands established on drained peat soils are regarded as negligible methane (CH4) sources; however, they can still exhibit considerable soil CH4 dynamics. We investigated archaeal community composition in two different fen peat soils and one bog peat soil under permanent grassland in Denmark........ Overall, there seemed to be a significant coupling between peat type and archaeal community composition, with local hydrology modifying the strength of this coupling....

  4. Linking the composition of bacterial and archaeal communities to characteristics of soil and flora composition in the Atlantic rainforest

    NARCIS (Netherlands)

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of

  5. Epiphytic Macrolichen Community Composition Database—epiphytic lichen synusiae in forested areas of the US

    Science.gov (United States)

    Sarah. Jovan

    2012-01-01

    The Forest Inventory and Analysis (FIA) Program's Lichen Communities Indicator is used for tracking epiphytic macrolichen diversity and is applied for monitoring air quality and climate change effects on forest health in the United States. Started in 1994, the Epiphytic Macrolichen Community Composition Database (GIVD ID NA-US-012) now has over 8,000 surveys of...

  6. Determinants of terrestrial arthropod community composition at Cape Hallett, Antarctica

    CSIR Research Space (South Africa)

    Sinclair, BJ

    2006-09-01

    Full Text Available . wadei. Arthropods were absent from areas occupied by the large Adelie penguin colony. There was some distinction among arthropod communities of different habitats, with water and a lichen species (indicative of scree slope habitats) ranking...

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

    Science.gov (United States)

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

    2016-12-01

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

  8. Does mechanical disturbance affect the performance and species composition of submerged macrophyte communities?

    Science.gov (United States)

    Zhang, Qian; Xu, Ying-Shou; Huang, Lin; Xue, Wei; Sun, Gong-Qi; Zhang, Ming-Xiang; Yu, Fei-Hai

    2014-05-01

    Submerged macrophyte communities are frequently subjected to disturbance of various frequency and strength. However, there is still little experimental evidence on how mechanical disturbance affects the performance and species composition of such plant communities. In a greenhouse experiment, we constructed wetland communities consisting of five co-occurring clonal submerged macrophyte species (Hydrilla verticillata, Elodea canadensis, Ceratophyllum demersum, Chara fragilis, and Myriophyllum spicatum) and subjected these communities to three mechanical disturbance regimes (no, moderate and strong disturbance). Strong mechanical disturbance greatly decreased overall biomass, number of shoot nodes and total shoot length, and increased species diversity (evenness) of the total community. It also substantially decreased the growth of the most abundant species (H. verticillata), but did not affect growth of the other four species. Our data reveal that strong disturbance can have different effects on different submerged macrophyte species and thus alters the performance and species composition of submerged macrophyte communities.

  9. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

    Science.gov (United States)

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

  10. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

    Science.gov (United States)

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

  11. Microbial community composition of transiently wetted Antarctic Dry Valley soils.

    Science.gov (United States)

    Niederberger, Thomas D; Sohm, Jill A; Gunderson, Troy E; Parker, Alexander E; Tirindelli, Joëlle; Capone, Douglas G; Carpenter, Edward J; Cary, Stephen C

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm(3) for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.

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

    Directory of Open Access Journals (Sweden)

    Courtney R. A. Toth

    2018-01-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

  14. Gender and Race, Online Communities, and Composition Classrooms

    Science.gov (United States)

    Morris, Jill

    2011-01-01

    As the culmination of a two-year long Internet ethnographic study of three separate sites, I use examples of women and minorities fighting against discrimination online to explore the power structures inherent to networks and how these might affect classroom practice. I will show how our ordinary assumptions in rhetoric and composition as well as…

  15. Coral Reef Community Composition in the Context of Disturbance History on the Great Barrier Reef, Australia

    Science.gov (United States)

    Graham, Nicholas A. J.; Chong-Seng, Karen M.; Huchery, Cindy; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.

    2014-01-01

    Much research on coral reefs has documented differential declines in coral and associated organisms. In order to contextualise this general degradation, research on community composition is necessary in the context of varied disturbance histories and the biological processes and physical features thought to retard or promote recovery. We conducted a spatial assessment of coral reef communities across five reefs of the central Great Barrier Reef, Australia, with known disturbance histories, and assessed patterns of coral cover and community composition related to a range of other variables thought to be important for reef dynamics. Two of the reefs had not been extensively disturbed for at least 15 years prior to the surveys. Three of the reefs had been severely impacted by crown-of-thorns starfish outbreaks and coral bleaching approximately a decade before the surveys, from which only one of them was showing signs of recovery based on independent surveys. We incorporated wave exposure (sheltered and exposed) and reef zone (slope, crest and flat) into our design, providing a comprehensive assessment of the spatial patterns in community composition on these reefs. Categorising corals into life history groupings, we document major coral community differences in the unrecovered reefs, compared to the composition and covers found on the undisturbed reefs. The recovered reef, despite having similar coral cover, had a different community composition from the undisturbed reefs, which may indicate slow successional processes, or a different natural community dominance pattern due to hydrology and other oceanographic factors. The variables that best correlated with patterns in the coral community among sites included the density of juvenile corals, herbivore fish biomass, fish species richness and the cover of macroalgae. Given increasing impacts to the Great Barrier Reef, efforts to mitigate local stressors will be imperative to encouraging coral communities to persist into

  16. Microbial community composition is unaffected by anode potential

    KAUST Repository

    Zhu, Xiuping

    2014-01-21

    There is great controversy on how different set anode potentials affect the performance of a bioelectrochemical system (BES). It is often reported that more positive potentials improve acclimation and performance of exoelectrogenic biofilms, and alter microbial community structure, while in other studies relatively more negative potentials were needed to achieve higher current densities. To address this issue, the biomass, electroactivity, and community structure of anodic biofilms were examined over a wide range of set anode potentials (-0.25, -0.09, 0.21, 0.51, and 0.81 V vs a standard hydrogen electrode, SHE) in single-chamber microbial electrolysis cells. Maximum currents produced using a wastewater inoculum increased with anode potentials in the range of -0.25 to 0.21 V, but decreased at 0.51 and 0.81 V. The maximum currents were positively correlated with increasing biofilm biomass. Pyrosequencing indicated biofilm communities were all similar and dominated by bacteria most similar to Geobacter sulfurreducens. Differences in anode performance with various set potentials suggest that the exoelectrogenic communities self-regulate their exocellular electron transfer pathways to adapt to different anode potentials. © 2013 American Chemical Society.

  17. Microbial community composition is unaffected by anode potential

    KAUST Repository

    Zhu, Xiuping; Yates, Matthew D.; Hatzell, Marta C.; Rao, Hari Ananda; Saikaly, Pascal; Logan, Bruce E.

    2014-01-01

    There is great controversy on how different set anode potentials affect the performance of a bioelectrochemical system (BES). It is often reported that more positive potentials improve acclimation and performance of exoelectrogenic biofilms, and alter microbial community structure, while in other studies relatively more negative potentials were needed to achieve higher current densities. To address this issue, the biomass, electroactivity, and community structure of anodic biofilms were examined over a wide range of set anode potentials (-0.25, -0.09, 0.21, 0.51, and 0.81 V vs a standard hydrogen electrode, SHE) in single-chamber microbial electrolysis cells. Maximum currents produced using a wastewater inoculum increased with anode potentials in the range of -0.25 to 0.21 V, but decreased at 0.51 and 0.81 V. The maximum currents were positively correlated with increasing biofilm biomass. Pyrosequencing indicated biofilm communities were all similar and dominated by bacteria most similar to Geobacter sulfurreducens. Differences in anode performance with various set potentials suggest that the exoelectrogenic communities self-regulate their exocellular electron transfer pathways to adapt to different anode potentials. © 2013 American Chemical Society.

  18. Spatial variation of bacterial community composition near the Luzon ...

    African Journals Online (AJOL)

    use

    2011-11-23

    Nov 23, 2011 ... However, little information of spatial variation of bacterial community ... GF/F glass fiber (0.45 µm, 47 mm diameter, Whatman Japan. Limited., Tokyo ... the research vessel using a CTD system (Sea-Bird Electronics, Inc.,. USA).

  19. Zooplankton composition and community structure in Lake Tiga ...

    African Journals Online (AJOL)

    Zooplankton in Lake Tiga was identified and its community structure assessed between March 2009 and March 2011. A total of 54 species of zooplankton was recorded, comprising two species of Protozoa, 26 species of Rotifera, eight species of Copepoda, 11 species of Cladocera, four species of Ostracoda and three ...

  20. Nitrification at different salinities: Biofilm community composition and physiological plasticity.

    Science.gov (United States)

    Gonzalez-Silva, Blanca M; Jonassen, Kjell Rune; Bakke, Ingrid; Østgaard, Kjetill; Vadstein, Olav

    2016-05-15

    This paper describes an experimental study of microbial communities of three moving bed biofilm reactors (MBBR) inoculated with nitrifying cultures originated from environments with different salinity; freshwater, brackish (20‰) and seawater. All reactors were run until they operated at a conversion efficiency of >96%. The microbial communities were profiled using 454-pyrosequencing of 16S rRNA gene amplicons. Statistical analysis was used to investigate the differences in microbial community structure and distribution of the nitrifying populations with different salinity environments. Nonmetric multidimensional scaling analysis (NMDS) and the PERMANOVA test based on Bray-Curtis similarities revealed significantly different community structure in the three reactors. The brackish reactor showed lower diversity index than fresh and seawater reactors. Venn diagram showed that 60 and 78% of the total operational taxonomic units (OTUs) in the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) guild, respectively, were unique OTUs for a given reactor. Similarity Percentages (SIMPER) analysis showed that two-thirds of the total difference in community structure between the reactors was explained by 10 OTUs, indicating that only a small number of OTUs play a numerically dominant role in the nitrification process. Acute toxicity of salt stress on ammonium and nitrite oxidizing activities showed distinctly different patterns, reaching 97% inhibition of the freshwater reactor for ammonium oxidation rate. In the brackish culture, inhibition was only observed at maximal level of salinity, 32‰. In the fully adapted seawater culture, higher activities were observed at 32‰ than at any of the lower salinities. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Receding Water Line and Interspecific Competition Determines Plant Community Composition and Diversity in Wetlands in Beijing

    Science.gov (United States)

    Wang, Zhengjun; Gong, Huili; Zhang, Jing

    2015-01-01

    Climate and human-induced wetland degradation has accelerated in recent years, not only resulting in reduced ecosystem services but also greatly affecting the composition and diversity of wetland plant communities. To date, the knowledge of the differences in community parameters and their successional trends in degraded wetlands remains scarce. Here based on remote sensing images, geographic information system technology, and statistical methods, we produced a successional gradient map of the Yeyahu Wetland Nature Reserve in Beijing, which has experienced a steady decline in water level in recent decades. In addition, we analyzed community composition and diversity along with each identified gradient. The results showed that community diversity decreases while dominance increases with the progress of succession, with the highest diversity occurring during the early stage of succession. Moreover, the community demonstrates greater similarity among subareas during later successional stages, and the similarity coefficients calculated from the important value (IV) of each species are more accurate. Correlation analysis showed that the impact of soil factors on diversity was not significant at a subarea scale, although these nutrients showed an increasing trend with the community succession. Furthermore, the IVs of the dominant species had a particularly significant impact on diversity, showing a significantly negative correlation with diversity indices and a significantly positive correlation with dominance indices. Further analysis showed that the retreat of water level resulted from sustained drought and local human activities was a major extrinsic driving force resulting in observed differences in the community successional stages, which resulted in differences in community composition and diversity. On the other hand, interspecific competition was the main intrinsic mechanism, which significantly influenced the IVs of the dominant species and community diversity

  2. Electrical Subsurface Grounding Analysis

    International Nuclear Information System (INIS)

    J.M. Calle

    2000-01-01

    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

  3. Experimental soil warming shifts the fungal community composition at the alpine treeline.

    Science.gov (United States)

    Solly, Emily F; Lindahl, Björn D; Dawes, Melissa A; Peter, Martina; Souza, Rômulo C; Rixen, Christian; Hagedorn, Frank

    2017-07-01

    Increased CO 2 emissions and global warming may alter the composition of fungal communities through the removal of temperature limitation in the plant-soil system, faster nitrogen (N) cycling and changes in the carbon (C) allocation of host plants to the rhizosphere. At a Swiss treeline featuring Larix decidua and Pinus uncinata, the effects of multiple years of CO 2 enrichment and experimental soil warming on the fungal community composition in the organic horizons were analysed using 454-pyrosequencing of ITS2 amplicons. Sporocarp production and colonization of ectomycorrhizal root tips were investigated in parallel. Fungal community composition was significantly altered by soil warming, whereas CO 2 enrichment had little effect. Tree species influenced fungal community composition and the magnitude of the warming responses. The abundance of ectomycorrhizal fungal taxa was positively correlated with N availability, and ectomycorrhizal taxa specialized for conditions of high N availability proliferated with warming, corresponding to considerable increases in inorganic N in warmed soils. Traits related to N utilization are important in determining the responses of ectomycorrhizal fungi to warming in N-poor cold ecosystems. Shifts in the overall fungal community composition in response to higher temperatures may alter fungal-driven processes with potential feedbacks on ecosystem N cycling and C storage at the alpine treeline. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  4. Deep subsurface microbial processes

    Science.gov (United States)

    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

  5. Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

    Science.gov (United States)

    Flues, Sebastian; Bass, David; Bonkowski, Michael

    2017-08-01

    Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Effects of triclosan on bacterial community composition and ...

    Science.gov (United States)

    Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, Vibrio, a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm) can induce a significant Vibrio growth response (68–1,700 fold increases) in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary), Doctors Arm Canal (Big Pine Key, FL), and Clam Bank Landing (North Inlet Estuary, Georgetown, SC). Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of Vibrionaceae (17-fold), Pseudoalteromonadaceae (65-fold), Alteromonadaceae (108-fold), Colwelliaceae (430-fold), and Oceanospirillaceae (1,494-fold). While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to u

  7. Site Recommendation Subsurface Layout

    International Nuclear Information System (INIS)

    C.L. Linden

    2000-01-01

    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 andO 2000e) and the ''Emplacement Drift System Description Document'' (CRWMS M andO 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

  8. Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

    Science.gov (United States)

    Starke, Verena; Kirshtein, Julie; Fogel, Marilyn L.; Steele, Andrew

    2013-01-01

    Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

  9. Impact of nutrient composition on a degradative biofilm community

    DEFF Research Database (Denmark)

    Møller, Søren; Korber, Darren R.; Wolfaardt, Gideon M.

    1997-01-01

    (Trypticase soy broth), the biofilms underwent an architectural change which included the loss of mound structures and the formation of a more homogeneous biofilm. Neutrally charged fluorescent dextrans, which upon hydration become cationic, were observed to bind to mounds, as well as to the basal cell layer......, in 14-day biofilms. In contrast, polyanionic dextrans bound only to the basal cell layer, indicating that this material incorporated sites with both positive and negative charge. The results from this study indicate that nutrient composition has a significant impact on both the architecture...

  10. Subsurface Contamination Control

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Science.gov (United States)

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

    2007-01-01

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

  12. Community composition of target vs. non-target fungi in fungicide treated wheat

    DEFF Research Database (Denmark)

    Knorr, Kamilla; Jørgensen, Lise Nistrup; Justesen, Annemarie Fejer

    2012-01-01

    disease in wheat and within the last decade, new aggressive strains of yellow rust has caused severe epidemics that lead to substantial yield losses. This study explored the community composition of target versus non-target fungi in yellow rust infected wheat as affected by treatment timing and dose......Fungicide treatments are common control strategies used to manage fungal pathogens in agricultural fields, however, effects of treatments on the composition of total fungal communities, including non-target fungi, in the phyllosphere is not well known. Yellow rust (Puccinia striiformis) is a common...

  13. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere.

    Science.gov (United States)

    Knief, Claudia; Ramette, Alban; Frances, Lisa; Alonso-Blanco, Carlos; Vorholt, Julia A

    2010-06-01

    The plant phyllosphere constitutes a habitat for numerous microorganisms; among them are members of the genus Methylobacterium. Owing to the ubiquitous occurrence of methylobacteria on plant leaves, they represent a suitable target for studying plant colonization patterns. The influence of the factor site, host plant species, time and the presence of other phyllosphere bacteria on Methylobacterium community composition and population size were evaluated in this study. Leaf samples were collected from Arabidopsis thaliana or Medicago truncatula plants and from the surrounding plant species at several sites. The abundance of cultivable Methylobacterium clearly correlated with the abundance of other phyllosphere bacteria, suggesting that methylobacteria constitute a considerable and rather stable fraction of the phyllosphere microbiota under varying environmental conditions. Automated ribosomal intergenic spacer analysis (ARISA) was applied to characterize the Methylobacterium community composition and showed the presence of similar communities on A. thaliana plants at most sites in 2 consecutive years of sampling. A substantial part of the observed variation in the community composition was explained by site and plant species, especially in the case of the plants collected at the Arabidopsis sites (50%). The dominating ARISA peaks that were detected on A. thaliana plants were found on other plant species grown at the same site, whereas some different peaks were detected on A. thaliana plants from other sites. This indicates that site-specific factors had a stronger impact on the Methylobacterium community composition than did plant-specific factors and that the Methylobacterium-plant association is not highly host plant species specific.

  14. Submerged macrophytes modify bacterial community composition in sediments in a large, shallow, freshwater lake.

    Science.gov (United States)

    Zhao, Da-Yong; Liu, Peng; Fang, Chao; Sun, Yi-Meng; Zeng, Jin; Wang, Jian-Qun; Ma, Ting; Xiao, Yi-Hong; Wu, Qinglong L

    2013-04-01

    Submerged aquatic macrophytes are an important part of the lacustrine ecosystem. In this study, the bacterial community compositions in the rhizosphere sediments from three kinds of submerged macrophytes (Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans) were investigated to determine whether submerged macrophytes could drive the variation of bacterial community in the eutrophic Taihu Lake, China. Molecular techniques, including terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene and clone libraries, were employed to analyze the bacterial community compositions. Remarkable differences of the T-RFLP patterns were observed among the different samples, and the results of LIBSHUFF analysis also confirmed that the bacterial community compositions in the rhizosphere sediments of three kinds of submerged macrophytes were statistically different from that of the unvegetated sediment. Acidobacteria, Deltaproteobacteria, and Betaproteobacteria were the dominant bacterial groups in the rhizosphere sediments of Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans, respectively, accounting for 15.38%, 29.03%, and 18.00% of the total bacterial abundances. Our study demonstrated that submerged macrophytes could influence the bacterial community compositions in their rhizosphere sediments, suggesting that macrophytes have an effect on the cycling and transportation of nutrients in the freshwater lake ecosystem.

  15. Predictability of bee community composition after floral removals differs by floral trait group.

    Science.gov (United States)

    Urban-Mead, Katherine R

    2017-11-01

    Plant-bee visitor communities are complex networks. While studies show that deleting nodes alters network topology, predicting these changes in the field remains difficult. Here, a simple trait-based approach is tested for predicting bee community composition following disturbance. I selected six fields with mixed cover of flower species with shallow (open) and deep (tube) nectar access, and removed all flowers or flower heads of species of each trait in different plots paired with controls, then observed bee foraging and composition. I compared the bee community in each manipulated plot with bees on the same flower species in control plots. The bee morphospecies composition in manipulations with only tube flowers remaining was the same as that in the control plots, while the bee morphospecies on only open flowers were dissimilar from those in control plots. However, the proportion of short- and long-tongued bees on focal flowers did not differ between control and manipulated plots for either manipulation. So, bees within some functional groups are more strongly linked to their floral trait partners than others. And, it may be more fruitful to describe expected bee community compositions in terms of relative proportions of relevant ecological traits than species, particularly in species-diverse communities. © 2017 The Author(s).

  16. Diversity and Community Composition of Vertebrates in Desert River Habitats

    Science.gov (United States)

    Free, C. L.; Baxter, G. S.; Dickman, C. R.; Lisle, A.; Leung, L. K.-P.

    2015-01-01

    Animal species are seldom distributed evenly at either local or larger spatial scales, and instead tend to aggregate in sites that meet their resource requirements and maximise fitness. This tendency is likely to be especially marked in arid regions where species could be expected to concentrate at resource-rich oases. In this study, we first test the hypothesis that productive riparian sites in arid Australia support higher vertebrate diversity than other desert habitats, and then elucidate the habitats selected by different species. We addressed the first aim by examining the diversity and composition of vertebrate assemblages inhabiting the Field River and adjacent sand dunes in the Simpson Desert, western Queensland, over a period of two and a half years. The second aim was addressed by examining species composition in riparian and sand dune habitats in dry and wet years. Vertebrate species richness was estimated to be highest (54 species) in the riverine habitats and lowest on the surrounding dune habitats (45 species). The riverine habitats had different species pools compared to the dune habitats. Several species, including the agamid Gowidon longirostris and tree frog Litoria rubella, inhabited the riverine habitats exclusively, while others such as the skinks Ctenotus ariadnae and C. dux were captured only in the dune habitats. The results suggest that, on a local scale, diversity is higher along riparian corridors and that riparian woodland is important for tree-dependent species. Further, the distribution of some species, such as Mus musculus, may be governed by environmental variables (e.g. soil moisture) associated with riparian corridors that are not available in the surrounding desert environment. We conclude that inland river systems may be often of high conservation value, and that management should be initiated where possible to alleviate threats to their continued functioning. PMID:26637127

  17. Predicting ecosystem vulnerability to biodiversity loss from community composition.

    Science.gov (United States)

    Heilpern, Sebastian A; Weeks, Brian C; Naeem, Shahid

    2018-05-01

    Ecosystems vary widely in their responses to biodiversity change, with some losing function dramatically while others are highly resilient. However, generalizations about how species- and community-level properties determine these divergent ecosystem responses have been elusive because potential sources of variation (e.g., trophic structure, compensation, functional trait diversity) are rarely evaluated in conjunction. Ecosystem vulnerability, or the likely change in ecosystem function following biodiversity change, is influenced by two types of species traits: response traits that determine species' individual sensitivities to environmental change, and effect traits that determine a species' contribution to ecosystem function. Here we extend the response-effect trait framework to quantify ecosystem vulnerability and show how trophic structure, within-trait variance, and among-trait covariance affect ecosystem vulnerability by linking extinction order and functional compensation. Using in silico trait-based simulations we found that ecosystem vulnerability increased when response and effect traits positively covaried, but this increase was attenuated by decreasing trait variance. Contrary to expectations, in these communities, both functional diversity and trophic structure increased ecosystem vulnerability. In contrast, ecosystem functions were resilient when response and effect traits covaried negatively, and variance had a positive effect on resiliency. Our results suggest that although biodiversity loss is often associated with decreases in ecosystem functions, such effects are conditional on trophic structure, and the variation within and covariation among response and effect traits. Taken together, these three factors can predict when ecosystems are poised to lose or gain function with ongoing biodiversity change. © 2018 by the Ecological Society of America.

  18. Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities.

    Science.gov (United States)

    Moora, Mari; Davison, John; Öpik, Maarja; Metsis, Madis; Saks, Ülle; Jairus, Teele; Vasar, Martti; Zobel, Martin

    2014-12-01

    Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  19. Bacterial community composition of a wastewater treatment system reliant on N{sub 2} fixation

    Energy Technology Data Exchange (ETDEWEB)

    Reid, N.M.; Bowers, T.H.; Lloyd-Jones, G. [Scion, Rotorua (New Zealand)

    2008-05-15

    The temporal stability and change of the dominant phylogenetic groups of the domain bacteria were studied in a model plant-based industrial wastewater treatment system showing high levels of organic carbon removal supported by high levels of N{sub 2} fixation. Community profiles were obtained through terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA amplicons followed by sequencing. Bacterial community profiles showed that ten common terminal restriction fragments made up approximately 50% of the measured bacterial community. As much as 42% of the measured bacterial community could be monitored by using quantitative PCR and primers that targeted three dominant operational taxonomic units. Despite changes in wastewater composition and dissolved oxygen levels, the bacterial community composition appeared stable and was dominated by {alpha}-Proteobacteria and {beta}-Proteobacteria, with a lesser amount of the highly diverse bacterial phylum Bacteroidetes. A short period of considerable change in the bacterial community composition did not appear to affect treatment performance indicating functional redundancy in this treatment system. (orig.)

  20. Impact of enzymatic digestion on bacterial community composition in CF airway samples.

    Science.gov (United States)

    Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

    2017-01-01

    Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced identification of Staphylococcus aureus is a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

  1. Body composition as a frailty marker for the elderly community

    Directory of Open Access Journals (Sweden)

    Falsarella GR

    2015-10-01

    Full Text Available Gláucia Regina Falsarella,1 Lívia Pimenta Renó Gasparotto,1 Caroline Coutinho Barcelos,2 Ibsen Bellini Coimbra,1,2 Maria Clara Moretto,1 Mauro Alexandre Pascoa,3 Talita C B Rezende Ferreira,1 Arlete Maria Valente Coimbra1,41Gerontology Program, Faculty of Medical Sciences, 2Department of Medical Clinics, Faculty of Medical Sciences, 3Department Biodynamics of Movement, Faculty of Physical Education, 4Family Health Program, Gerontology Program, Faculty of Medical Sciences, State University of Campinas (Unicamp, Campinas, São Paulo, BrazilBackground: Body composition (BC in the elderly has been associated with diseases and mortality; however, there is a shortage of data on frailty in the elderly.Objective: To investigate the association between BC and frailty, and identify BC profiles in nonfrail, prefrail, and frail elderly people.Methods: A cross-sectional study comprising 235 elderly (142 females and 93 males aged ≥65 years, from the city of Amparo, State of São Paulo, Brazil, was undertaken. Sociodemographic and cognitive features, comorbidities, medication, frailty, body mass index (BMI, muscle mass, fat mass, bone mass, and fat percent (% data were evaluated. Aiming to examine the relationship between BC and frailty, the Mann–Whitney and Kruskal–Wallis nonparametric tests were applied. The statistical significance level was P<0.05.Results: The nonfrail elderly showed greater muscle mass and greater bone mass compared with the prefrail and frail ones. The frail elderly had greater fat % than the nonfrail elderly. There was a positive association between grip strength and muscle mass with bone mass (P<0.001, and a negative association between grip strength and fat % (P<0.001. Gait speed was positively associated with fat mass (P=0.038 and fat % (P=0.002. The physical activity level was negatively associated with fat % (P=0.022. The weight loss criterion was positively related to muscle mass (P<0.001, bone mass (P=0.009, fat mass

  2. Bacterial community composition and extracellular enzyme activity in temperate streambed sediment during drying and rewetting.

    Directory of Open Access Journals (Sweden)

    Elisabeth Pohlon

    Full Text Available Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany. Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes

  3. Brazilian kefir: structure, microbial communities and chemical composition

    Science.gov (United States)

    Magalhães, Karina Teixeira; de Melo Pereira, Gilberto Vinícius; Campos, Cássia Roberta; Dragone, Giuliano; Schwan, Rosane Freitas

    2011-01-01

    Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5%) were the major isolated group identified, followed by yeasts (30.6%) and acetic acid bacteria (8.9%). Lactobacillus paracasei (89 isolates), Lactobacillus parabuchneri (41 isolates), Lactobacillus casei (32 isolates), Lactobacillus kefiri (31 isolates), Lactococcus lactis (24 isolates), Acetobacter lovaniensis (32 isolates), Kluyveromyces lactis (31 isolates), Kazachstania aerobia (23 isolates), Saccharomyces cerevisiae (41 isolates) and Lachancea meyersii (15 isolates) were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long) cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml. PMID:24031681

  4. Brazilian kefir: structure, microbial communities and chemical composition

    Directory of Open Access Journals (Sweden)

    Karina Teixeira Magalhães

    2011-06-01

    Full Text Available Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5% were the major isolated group identified, followed by yeasts (30.6% and acetic acid bacteria (8.9%. Lactobacillus paracasei (89 isolates, Lactobacillus parabuchneri (41 isolates, Lactobacillus casei (32 isolates, Lactobacillus kefiri (31 isolates, Lactococcus lactis (24 isolates, Acetobacter lovaniensis (32 isolates, Kluyveromyces lactis (31 isolates, Kazachstania aerobia (23 isolates, Saccharomyces cerevisiae (41 isolates and Lachancea meyersii (15 isolates were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml.

  5. Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection.

    Directory of Open Access Journals (Sweden)

    Apollo Stacy

    2016-12-01

    Full Text Available Iron is an essential nutrient for bacterial pathogenesis, but in the host, iron is tightly sequestered, limiting its availability for bacterial growth. Although this is an important arm of host immunity, most studies examine how bacteria respond to iron restriction in laboratory rather than host settings, where the microbiome can potentially alter pathogen strategies for acquiring iron. One of the most important transcriptional regulators controlling bacterial iron homeostasis is Fur. Here we used a combination of RNA-seq and chromatin immunoprecipitation (ChIP-seq to characterize the iron-restricted and Fur regulons of the biofilm-forming opportunistic pathogen Aggregatibacter actinomycetemcomitans. We discovered that iron restriction and Fur regulate 4% and 3.5% of the genome, respectively. While most genes in these regulons were related to iron uptake and metabolism, we found that Fur also directly regulates the biofilm-dispersing enzyme Dispersin B, allowing A. actinomycetemcomitans to escape from iron-scarce environments. We then leveraged these datasets to assess the availability of iron to A. actinomycetemcomitans in its primary infection sites, abscesses and the oral cavity. We found that A. actinomycetemcomitans is not restricted for iron in a murine abscess mono-infection, but becomes restricted for iron upon co-infection with the oral commensal Streptococcus gordonii. Furthermore, in the transition from health to disease in human gum infection, A. actinomycetemcomitans also becomes restricted for iron. These results suggest that host iron availability is heterogeneous and dependent on the infecting bacterial community.

  6. RNA preservation agents and nucleic acid extraction method bias perceived bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Ann McCarthy

    Full Text Available Bias is a pervasive problem when characterizing microbial communities. An important source is the difference in lysis efficiencies of different populations, which vary depending on the extraction protocol used. To avoid such biases impacting comparisons between gene and transcript abundances in the environment, the use of one protocol that simultaneously extracts both types of nucleic acids from microbial community samples has gained popularity. However, knowledge regarding tradeoffs to combined nucleic acid extraction protocols is limited, particularly regarding yield and biases in the observed community composition. Here, we evaluated a commercially available protocol for simultaneous extraction of DNA and RNA, which we adapted for freshwater microbial community samples that were collected on filters. DNA and RNA yields were comparable to other commonly used, but independent DNA and RNA extraction protocols. RNA protection agents benefited RNA quality, but decreased DNA yields significantly. Choice of extraction protocol influenced the perceived bacterial community composition, with strong method-dependent biases observed for specific phyla such as the Verrucomicrobia. The combined DNA/RNA extraction protocol detected significantly higher levels of Verrucomicrobia than the other protocols, and those higher numbers were confirmed by microscopic analysis. Use of RNA protection agents as well as independent sequencing runs caused a significant shift in community composition as well, albeit smaller than the shift caused by using different extraction protocols. Despite methodological biases, sample origin was the strongest determinant of community composition. However, when the abundance of specific phylogenetic groups is of interest, researchers need to be aware of the biases their methods introduce. This is particularly relevant if different methods are used for DNA and RNA extraction, in addition to using RNA protection agents only for RNA

  7. Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone.

    Science.gov (United States)

    Richa, Kumari; Balestra, Cecilia; Piredda, Roberta; Benes, Vladimir; Borra, Marco; Passarelli, Augusto; Margiotta, Francesca; Saggiomo, Maria; Biffali, Elio; Sanges, Remo; Scanlan, David J; Casotti, Raffaella

    2017-09-01

    Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria , Gammaproteobacteria , and Bacteroidetes Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for coastal zones is of critical importance, considering that these areas are highly productive and anthropogenically impacted. Their richness and evenness, as well as their potential activity, are very important to assess ecosystem health and functioning. Here, we investigated bacterial distribution, community composition, and potential metabolic activity in the GON, which is an ideal test site due to its heterogeneous environment characterized by a complex hydrodynamics and terrestrial inputs of varied quantities and quality. Our study demonstrates that bacterioplankton communities in this region are highly diverse and strongly regulated by a combination of different environmental

  8. Carbon dioxide and submersed macrophytes in lakes: linking functional ecology to community composition.

    Science.gov (United States)

    Titus, John E; Pagano, Angela M

    2017-12-01

    Evaluating plant community response to atmospheric CO 2 rise is critical to predicting ecosystem level change. Freshwater lakes offer a model system for examining CO 2 effects as submersed macrophyte species differ greatly in their growth responses to CO 2 enrichment, and free CO 2 concentrations among these habitats show a wide range of natural, spatial variation. We determined free CO 2 concentrations in the water column and sediment porewater in littoral zones with pH macrophyte communities coupled with greenhouse-derived growth responses to CO 2 enrichment of constituent species to test two hypotheses: (1) CCRI, which is higher for communities dominated by species with greater growth responses to CO 2 enrichment, is positively correlated to free [CO 2 ] in the water column, and (2) in natural communities, the percent of sediment CO 2 -using species, which are relatively unresponsive to CO 2 enrichment, is negatively correlated to free [CO 2 ]. A significant positive correlation (P = 0.003) between our physiologically based CCRI and the concentration of free CO 2 in the water column supported our primary hypothesis that sites with higher levels of free CO 2 are dominated by species with greater growth responses to CO 2 enrichment. Our CCRI is also highly significantly correlated (P macrophyte community composition. Further, we demonstrate the utility of a physiologically-based index of community composition, our CCRI, as an ecologically valid measure of community response to CO 2 . © 2017 by the Ecological Society of America.

  9. Herbivory of an invasive slug is affected by earthworms and the composition of plant communities.

    Science.gov (United States)

    Zaller, Johann G; Parth, Myriam; Szunyogh, Ilona; Semmelrock, Ines; Sochurek, Susanne; Pinheiro, Marcia; Frank, Thomas; Drapela, Thomas

    2013-05-13

    Biodiversity loss and species invasions are among the most important human-induced global changes. Moreover, these two processes are interlinked as ecosystem invasibility is considered to increase with decreasing biodiversity. In temperate grasslands, earthworms serve as important ecosystem engineers making up the majority of soil faunal biomass. Herbivore behaviour has been shown to be affected by earthworms, however it is unclear whether these effects differ with the composition of plant communities. To test this we conducted a mesocosm experiment where we added earthworms (Annelida: Lumbricidae) to planted grassland communities with different plant species composition (3 vs. 12 plant spp.). Plant communities had equal plant densities and ratios of the functional groups grasses, non-leguminous forbs and legumes. Later, Arion vulgaris slugs (formerly known as A. lusitanicus; Gastropoda: Arionidae) were added and allowed to freely choose among the available plant species. This slug species is listed among the 100 worst alien species in Europe. We hypothesized that (i) the food choice of slugs would be altered by earthworms' specific effects on the growth and nutrient content of plant species, (ii) slug herbivory will be less affected by earthworms in plant communities containing more plant species than in those with fewer plant species because of a more readily utilization of plant resources making the impacts of earthworms less pronounced. Slug herbivory was significantly affected by both earthworms and plant species composition. Slugs damaged 60% less leaves when earthworms were present, regardless of the species composition of the plant communities. Percent leaf area consumed by slugs was 40% lower in communities containing 12 plant species; in communities containing only three species earthworms increased slug leaf area consumption. Grasses were generally avoided by slugs. Leaf length and number of tillers was increased in mesocosms containing more plant

  10. Final Technical Report: Role of Methanotrophs in Metal Mobilization, Metal Immobilization and Mineral Weathering: Effects on the In Situ Microbial Community and the Sustainability of Subsurface Water Systems

    Energy Technology Data Exchange (ETDEWEB)

    Semrau, Jeremy D. [Univ. of Michigan, Ann Arbor, MI (United States); DiSpirito, Alan A. [Iowa State Univ., Ames, IA (United States)

    2016-11-06

    Activities from this DOE sponsored project can be divided into four broad areas: (1) investigations into the potential of methanobactin, a biogenic metal-binding agent produced by methanotrophs, in mitigating mercury toxicity; (2) elucidation of the genetic basis for methanobactin synthesis from methanotrophs; (3) examination of differential gene expression of M. trichosporium OB3b when grown in the presence of varying amounts of copper and/or cerium, and (4) collection and characterization of soil cores from Savannah River Test Site to determine the ubiquity of methanobactin producing methanotrophs. From these efforts, we have conclusively shown that methanobactin can strongly bind mercury as Hg[II], and in so doing significantly reduce the toxicity of this metal to microbes. Further, we have deduced the genetic basis of methanobactin production in methanotrophs, enabling us to construct mutants such that we can now ascribe function to different genes as well as propose a pathway for methanobactin biosynthesis. We have also clear evidence that copper and cerium (as an example of a rare earth element) dramatically affect gene expression in methanotrophs, and thus have an important impact on the activity and application of these microbes to a variety of environmental and industrial issues. Finally, we successfully isolated one methanotroph from the deep subsurface of the Savannah River Test Site and characterized the ability of different forms of methanobactin to mobilize copper and mercury from these soils.

  11. Long-term effects of plant diversity and composition on soil nematode communities in grassland.

    NARCIS (Netherlands)

    Viketoft, M.; Bengtsson, J.; Sohlenius, B.; Berg, M.P.; Petchey, O.; Palmborg, C.; Huss-Daniel, K.

    2009-01-01

    An important component of plant-soil feedbacks is how plant species identity and diversity influence soil organism communities. We examine the effects of grassland plant species growing alone and together up to a richness of 12 species on nematode diversity and feeding group composition, eight years

  12. Fire effects on the composition of a bird community in an amazonian Savanna (Brazil

    Directory of Open Access Journals (Sweden)

    R. Cintra

    Full Text Available The effects of fire on the composition of a bird community were investigated in an Amazonian savanna near Alter-do-Chão, Pará (Brazil. Mist-net captures and visual counts were used to assess species richness and bird abundance pre- and post-fire in an approximately 20 ha area. Visual counts along transects were used to survey birds in an approximately 2000 ha area in a nearby area. Results using the same method of ordination analysis (multidimensional scaling showed significant effects of fire in the 20 ha and 2000 ha areas and strongly suggest direct effects on bird community composition. However, the effects were different at different spatial scales and/or in different years, indicating that the effects of fire vary spatially and/or temporally. Bird community composition pre-fire was significantly different from that found post-fire. Using multiple regression analysis it was found that the numbers of burned and unburned trees were not significantly related to either bird species richness or bird abundance. Two months after the fire, neither bird species richness nor bird abundance was significantly related to the number of flowering trees (Lafoensia pacari or fruiting trees (Byrsonima crassifolia. Since fire is an annual event in Alter-do-Chão and is becoming frequent in the entire Amazon, bird community composition in affected areas could be constantly changing in time and space.

  13. Effects of Biochar Blends on Microbial Community Composition in Two Coastal Plain Soils

    Directory of Open Access Journals (Sweden)

    Thomas F. Ducey

    2015-11-01

    Full Text Available The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure. These impacts are modulated not only by the biochar composition, but also on the soil’s physicochemical characteristics. This indicates that soil characteristics must be considered prior to biochar amendment. A significant portion of the soils of the southeastern coastal plain are severely degraded and, therefore, candidates for biochar amendment to strengthen soil fertility. In this study we focused on two common soil series in the southeastern coastal plain, utilizing feedstocks endemic to the area. We chose feedstocks in four ratios (100% pine chip; 80:20 mixture of pine chip to poultry litter; 50:50 mixture of pine chip to poultry litter; 100% poultry litter prior to pyrolysis and soil amendment as a biochar product. Soil was analyzed for bioavailable nutrients via Mehlich-1 extractions, as well as microbial community composition using phospholipid fatty acid analysis (PLFA. Our results demonstrated significant shifts in microbial community composition in response to biochar amendment, the effects of which were greatest with 100% poultry litter biochar. Strong relationships between PLFAs and several Mehlich-1 extractable nutrients (Al, Cu, Fe, and P were observed.

  14. COMMUNITY SCALE STREAM TAXA SENSITIVITIES TO DIFFERENT COMPOSITIONS OF EXCESS TOTAL DISSOLVED SOLIDS

    Science.gov (United States)

    Model stream chronic dosing studies (42 d) were conducted with three total dissolved solids (TDS) recipes. The recipes differed in composition of major ions. Community scale emergence was compared with single-species responses conducted simultaneously using the whole effluent tox...

  15. From traits to life-history strategies: Deconstructing fish community composition across European seas

    DEFF Research Database (Denmark)

    Pécuchet, Lauréne; Lindegren, Martin; Hidalgo, Manuel

    2017-01-01

    The life history of a species is determined by trade-offs between growth, survival and reproduction to maximize fitness in a given environment. Following a theoretical model, we investigate whether the composition of marine fish communities can be understood in terms of a set of lifehistory...

  16. Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

    Science.gov (United States)

    Mitchell A. Pavao-Zuckerman; David C. Coleman

    2007-01-01

    We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

  17.   Diversity and composition of palm communities (Arecaceae) in Quintana Roo Mexico

    DEFF Research Database (Denmark)

    Alvarado, Arturo A.; Calvo, Luz M.; Duno, Rodrigo

      We compared composition and diversity of palm (Arecaceae) communities in three forest types along a gradient from dry deciduous, over intermediate to wet evergreen forest in Quintana Roo, Mexico. In forty-nine 5×500-m transects, we counted 52,612 individuals representing 14 species in 11 genera...

  18. Contribution of trace metals in structuring in situ macroinvertebrate community composition along a salinity gradient

    NARCIS (Netherlands)

    Peeters, E.T.H.M.; Gardeniers, J.J.P.; Koelmans, A.A.

    2000-01-01

    Macroinvertebrates were studied along a salinity gradient in the North Sea Canal, The Netherlands, to quantify the effect of trace metals (cadmium, copper, lead, zinc) on community composition. In addition, two methods for assessing metal bioavailability (normalizing metal concentrations on organic

  19. Plankton community composition and vertical migration during polar night in Kongsfjorden

    DEFF Research Database (Denmark)

    Grenvald, Julie Cornelius; Callesen, Trine Abraham; Daase, Malin

    2016-01-01

    characterize the plankton community composition during the polar night using water samplers and zooplankton net samples (50, 64, 200, 1500 lm), supplemented by acoustics (ADCPs, 300 kHz), to address a previously unresolved question–which species of zooplankton perform diel vertical migration during the polar...

  20. Subsurface barrier verification technologies, informal report

    International Nuclear Information System (INIS)

    Heiser, J.H.

    1994-06-01

    One of the more promising remediation options available to the DOE waste management community is subsurface barriers. Some of the uses of subsurface barriers include surrounding and/or containing buried waste, as secondary confinement of underground storage tanks, to direct or contain subsurface contaminant plumes and to restrict remediation methods, such as vacuum extraction, to a limited area. To be most effective the barriers should be continuous and depending on use, have few or no breaches. A breach may be formed through numerous pathways including: discontinuous grout application, from joints between panels and from cracking due to grout curing or wet-dry cycling. The ability to verify barrier integrity is valuable to the DOE, EPA, and commercial sector and will be required to gain full public acceptance of subsurface barriers as either primary or secondary confinement at waste sites. It is recognized that no suitable method exists for the verification of an emplaced barrier's integrity. The large size and deep placement of subsurface barriers makes detection of leaks challenging. This becomes magnified if the permissible leakage from the site is low. Detection of small cracks (fractions of an inch) at depths of 100 feet or more has not been possible using existing surface geophysical techniques. Compounding the problem of locating flaws in a barrier is the fact that no placement technology can guarantee the completeness or integrity of the emplaced barrier. This report summarizes several commonly used or promising technologies that have been or may be applied to in-situ barrier continuity verification

  1. Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

    Science.gov (United States)

    Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

    2011-10-01

    Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  2. Progressive biogeochemical transformation of placer gold particles drives compositional changes in associated biofilm communities.

    Science.gov (United States)

    Rea, Maria Angelica; Standish, Christopher D; Shuster, Jeremiah; Bissett, Andrew; Reith, Frank

    2018-05-03

    Biofilms on placer gold (Au)-particle surfaces drive Au solubilization and re-concentration thereby progressively transforming the particles. Gold solubilization induces Au-toxicity; however, Au-detoxifying community members ameliorates Au-toxicity by precipitating soluble Au to metallic Au. We hypothesize that Au-dissolution and re-concentration (precipitation) places selective pressures on associated microbial communities, leading to compositional changes and subsequent Au-particle transformation. We analyzed Au-particles from eight United Kingdom sites using next generation sequencing, electron microscopy and micro-analyses. Gold particles contained biofilms composed of prokaryotic cells and extracellular polymeric substances intermixed with (bio)minerals. Across all sites communities were dominated by Proteobacteria (689, 97% Operational Taxonomic Units, 59.3% of total reads), with β-Proteobacteria being the most abundant. A wide range of Au-morphotypes including nanoparticles, micro-crystals, sheet-like Au and secondary rims, indicated that dissolution and re-precipitation occurred, and from this transformation indices were calculated. Multivariate statistical analyses showed a significant relationship between the extent of Au-particle transformation and biofilm community composition, with putative metal-resistant Au-cycling taxa linked to progressive Au transformation. These included the genera Pseudomonas, Leptothrix and Acinetobacter. Additionally, putative exoelectrogenic genera Rhodoferax and Geobacter were highly abundant. In conclusion, biogeochemical Au-cycling and Au-particle transformation occurred at all sites and exerted a strong influence on biofilm community composition.

  3. Storm-scale dynamics of bacterial community composition in throughfall and stemflow

    Science.gov (United States)

    Van Stan, J. T., II; Teachey, M. E.; Pound, P.; Ottesen, E. A.

    2017-12-01

    Transport of bacteria between ecosystem spheres can significantly affect microbially-mediated biogeochemical processes. During rainfall, there is a large, temporally-concentrated exchange of bacteria between the forest phyllosphere and the pedosphere by rain dripping from canopy surfaces, as throughfall (TF), and draining to the stem, as stemflow (SF). Many phyllosphere bacteria possibly transported by TF and SF have been linked to important litter and soil processes (like cyanobacteria and actinobacteria). Despite this, no work has applied high throughput DNA sequencing to assess the community composition of bacteria transported by TF and SF. We characterized bacterial community composition for TF and SF from an epiphyte-laden (Tillandsia usneoides L., Spanish moss) southern live oak (Quercus virginiana) forest in southeastern Georgia (USA) to address two hypotheses: that bacterial community composition will differ between (1) TF and SF, and (2) TF sampled beneath bare and epiphyte-laden canopy. Variability in family-level bacterial abundance, Bray-Curtis dissimilarity, and Shannon diversity index was greater between storms than between net rainfall fluxes. In fact, TF and SF bacterial communities were relatively similar for individual storms and may be driven by pre-storm atmospheric deposition rather than the communities affixed to leaves, bark, and epiphyte surfaces.

  4. High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

    DEFF Research Database (Denmark)

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob

    2014-01-01

    In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High......-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized...... that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide...

  5. Associations between retail food store exterior advertisements and community demographic and socioeconomic composition.

    Science.gov (United States)

    Isgor, Zeynep; Powell, Lisa; Rimkus, Leah; Chaloupka, Frank

    2016-05-01

    This paper examines the association between the prevalence of various types of outdoor food and beverage advertising found on the building exteriors and properties of retail food outlets and community racial/ethnic and socioeconomic composition in a nationwide sample of food outlets in the U.S. Our major finding from multivariable analysis is that food stores in low-income communities have higher prevalence of all food and beverage ads, including those for unhealthy products such as regular soda, controlling for community racial/ethnic composition and other covariates. This adds to growing research pointing to socioeconomic disparities in food and beverage marketing exposure. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Bacterial community composition and potential driving factors in different reef habitats of the Spermonde Archipelago, Indonesia

    DEFF Research Database (Denmark)

    Kegler, Hauke F.; Lukman, Muhammad; Teichberg, Mirta

    2017-01-01

    Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along...... a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross shelf environmental and water quality gradient. The main research questions were: (1) How do water....../Shigella (Gammaproteobacteria) and Raistonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes...

  7. Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake.

    Science.gov (United States)

    Qin, H; Han, C; Jin, Z; Wu, L; Deng, H; Zhu, G; Zhong, W

    2018-07-01

    The aim of this study was to explore the vertical distribution traits of anaerobic ammonium-oxidizing (anammox) bacterial relative abundance and community composition along the oxic/anoxic sediment profiles in a shallow lake. The Illumina Miseq-based sequencing and quantitative polymerase chain reactions were utilized to analyse relative abundance of anammox hydrazine synthase (hzsB) gene in comparison with bacterial 16S rRNA genes, anammox bacterial relative abundance (the number of anammox sequences divided by total number of sequences), community composition and diversity in sediments. The relative abundance of hzsB gene at the low-nitrogen (LN) site in the lake sediments showed that the vertical distribution of anammox bacteria increased to a peak, then decreased with increasing depth. Moreover, the relative abundance of hzsB gene at the high-nitrogen site was significantly lower than that at the LN site. Additionally, the community composition results showed that Candidatus Brocadia sp. was the dominant genus. In addition, the anammox bacterial diversity was also site specific. Redundancy analysis showed that the total N and the NH 4 + -N content might be the most important factors affecting anammox bacterial community composition in the studied sites. The results revealed the specific vertical variance of anammox bacterial distribution and community composition in oxic/anoxic sediments of a eutrophic shallow lake. This is the first study to demonstrate that anammox bacteria displayed the particular distribution in freshwater sediments, which implied a strong response to the anthropogenic eutrophication. © 2018 The Society for Applied Microbiology.

  8. Structure and composition of oligohaline marsh plant communities exposed to salinity pulses

    Science.gov (United States)

    Howard, R.J.; Mendelssohn, I.A.

    2000-01-01

    The response of two oligohaline marsh macrophyte communities to pulses of increased salinity was studied over a single growing season in a greenhouse experiment. The plant communities were allowed a recovery period in freshwater following the pulse events. The experimental treatments included: (1) salinity influx rate (rate of salinity increase from 0 to 12 gl-1); (2) duration of exposure to elevated salinity; and (3) water depth. The communities both included Sagittaria lancifolia L.; the codominant species were Eleocharis palustris (L.) Roemer and J.A. Schultes in community 1 and Schoenoplectus americanus (Pers.) Volk. ex Schinz and R. Keller in community 2. Effects of the treatments on sediment chemical characteristics (salinity, pH, redox potential, and sulfide and ammonium concentrations) and plant community attributes (aboveground and belowground biomass, stem density, leaf tissue nutrients, and species richness) were examined. The treatment effects often interacted to influence sediment and plant communities characteristics following recovery in fresh water. Salinity influx rate per se, however, had little effect on the abiotic or biotic response variables; significant influx effects were found when the 0 gl-1 (zero influx) treatment was compared to the 12 gl-1 treatments, regardless of the rate salinity was raised. A salinity level of 12 gl-1 had negative effects on plant community structure and composition; these effects were usually associated with 3 months of salinity exposure. Water depth often interacted with exposure duration, but increased water depth did independently decrease the values of some community response measures. Community 1 was affected more than community 2 in the most extreme salinity treatment (3 months exposure/15-cm water depth). Although species richness in both communities was reduced, structural changes were more dramatic in community 1. Biomass and stem density were reduced in community 1 overall and in both dominant species

  9. Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.

    Directory of Open Access Journals (Sweden)

    Julia A F Langer

    Full Text Available The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta. Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.

  10. Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.

    Science.gov (United States)

    Langer, Julia A F; Sharma, Rahul; Schmidt, Susanne I; Bahrdt, Sebastian; Horn, Henriette G; Algueró-Muñiz, María; Nam, Bora; Achterberg, Eric P; Riebesell, Ulf; Boersma, Maarten; Thines, Marco; Schwenk, Klaus

    2017-01-01

    The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.

  11. SUBSURFACE EMPLACEMENT TRANSPORTATION SYSTEM

    International Nuclear Information System (INIS)

    Wilson, T.; Novotny, R.

    1999-01-01

    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)

  12. The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

    Science.gov (United States)

    Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

    2016-01-01

    Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

  13. Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia)

    Science.gov (United States)

    Schneider, Dominik; Engelhaupt, Martin; Allen, Kara; Kurniawan, Syahrul; Krashevska, Valentyna; Heinemann, Melanie; Nacke, Heiko; Wijayanti, Marini; Meryandini, Anja; Corre, Marife D.; Scheu, Stefan; Daniel, Rolf

    2015-01-01

    Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio

  14. Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents.

    Science.gov (United States)

    Ochoa-Hueso, Raúl; Collins, Scott L; Delgado-Baquerizo, Manuel; Hamonts, Kelly; Pockman, William T; Sinsabaugh, Robert L; Smith, Melinda D; Knapp, Alan K; Power, Sally A

    2018-03-05

    The effects of short-term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness, and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought-induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant-microbial interactions and a

  15. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

    Directory of Open Access Journals (Sweden)

    Erin A Gontang

    Full Text Available Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

  16. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

    Science.gov (United States)

    Gontang, Erin A; Aylward, Frank O; Carlos, Camila; Glavina Del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A; Tringe, Susannah G; Currie, Cameron R; Kolter, Roberto

    2017-01-01

    Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

  17. Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.

    Directory of Open Access Journals (Sweden)

    Ryan J Newton

    Full Text Available Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls. Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise

  18. Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia

    Directory of Open Access Journals (Sweden)

    Dominik eSchneider

    2015-12-01

    Full Text Available Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use system comprised rubber agroforests (jungle rubber, rubber plantation and oil plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 20,494 bacterial and 1,762 archaeal Operational Taxonomic Units at species level (97% genetic identity. Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to

  19. LIBS Sensor for Sub-surface CO2 Leak Detection in Carbon Sequestration

    Directory of Open Access Journals (Sweden)

    Jinesh JAIN

    2017-07-01

    Full Text Available Monitoring carbon sequestration poses numerous challenges to the sensor community. For example, the subsurface environment is notoriously harsh, with large potential mechanical, thermal, and chemical stresses, making long-term stability and survival a challenge to any potential in situ monitoring method. Laser induced breakdown spectroscopy (LIBS has been demonstrated as a promising technology for chemical monitoring of harsh environments and hard to reach places. LIBS has a real- time monitoring capability and can be used for the elemental and isotopic analysis of solid, liquid, and gas samples. The flexibility of the probe design and the use of fiber- optics has made LIBS particularly suited for remote measurements. The paper focuses on developing a LIBS instrument for downhole high-pressure, high-temperature brine experiments, where CO2 leakage could result in changes in the trace mineral composition of an aquifer. The progress in fabricating a compact, robust, and simple LIBS sensor for widespread subsurface leak detection is presented.

  20. Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

    Science.gov (United States)

    Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

    2009-09-01

    Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

  1. Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems

    Directory of Open Access Journals (Sweden)

    Kezia eGoldmann

    2015-11-01

    Full Text Available Fungal communities have been shown to be highly sensitive towards shifts in plant diversity and species composition in forest ecosystems. However, little is known about the impact of forest management on fungal diversity and community composition of geographically separated sites. This study examined the effects of four different forest management types on soil fungal communities. These forest management types include age class forests of young managed beech (Fagus sylvatica L., with beech stands age of approximately 30 years, age class beech stands with an age of approximately 70 years, unmanaged beech stands, and coniferous stands dominated by either pine (Pinus sylvestris L. or spruce (Picea abies Karst. which are located in three study sites across Germany. Soil were sampled from 48 study plots and we employed fungal ITS rDNA pyrotag sequencing to assess the soil fungal diversity and community structure.We found that forest management type significantly affects the Shannon diversity of soil fungi and a significant interaction effect of study site and forest management on the fungal OTU richness. Consequently distinct fungal communities were detected in the three study sites and within the four forest management types, which were mainly related to the main tree species. Further analysis of the contribution of soil properties revealed that C/N ratio being the most important factor in all the three study sites whereas soil pH was significantly related to the fungal community in two study sites. Functional assignment of the fungal communities indicated that 38% of the observed communities were Ectomycorrhizal fungi (ECM and their distribution is significantly influenced by the forest management. Soil pH and C/N ratio were found to be the main drivers of the ECM fungal community composition. Additional fungal community similarity analysis revealed the presence of study site and management type specific ECM genera.This study extends our knowledge

  2. Forest Management Type Influences Diversity and Community Composition of Soil Fungi across Temperate Forest Ecosystems.

    Science.gov (United States)

    Goldmann, Kezia; Schöning, Ingo; Buscot, François; Wubet, Tesfaye

    2015-01-01

    Fungal communities have been shown to be highly sensitive toward shifts in plant diversity and species composition in forest ecosystems. However, little is known about the impact of forest management on fungal diversity and community composition of geographically separated sites. This study examined the effects of four different forest management types on soil fungal communities. These forest management types include age class forests of young managed beech (Fagus sylvatica L.), with beech stands age of approximately 30 years, age class beech stands with an age of approximately 70 years, unmanaged beech stands, and coniferous stands dominated by either pine (Pinus sylvestris L.) or spruce (Picea abies Karst.) which are located in three study sites across Germany. Soil were sampled from 48 study plots and we employed fungal ITS rDNA pyrotag sequencing to assess the soil fungal diversity and community structure. We found that forest management type significantly affects the Shannon diversity of soil fungi and a significant interaction effect of study site and forest management on the fungal operational taxonomic units richness. Consequently distinct fungal communities were detected in the three study sites and within the four forest management types, which were mainly related to the main tree species. Further analysis of the contribution of soil properties revealed that C/N ratio being the most important factor in all the three study sites whereas soil pH was significantly related to the fungal community in two study sites. Functional assignment of the fungal communities indicated that 38% of the observed communities were Ectomycorrhizal fungi (ECM) and their distribution is significantly influenced by the forest management. Soil pH and C/N ratio were found to be the main drivers of the ECM fungal community composition. Additional fungal community similarity analysis revealed the presence of study site and management type specific ECM genera. This study extends our

  3. Species richness and floristic composition of Choco Region plant communities Species richness and floristic composition of Choco Region plant communities

    Directory of Open Access Journals (Sweden)

    Gentry Alwyn H.

    1986-12-01

    Full Text Available The Chocó phytogeographical region of coastal Colombia and adjacent Ecuador is well known as a region of unusually high endemism in plants (GENTRY, 1982a, 1986b, birds (TERBORGH & WINTER, 1982, and butterflies (BROWN, 1975, 1982. The region is also reputed to be unusually diverse biologically (GENTRY, 1978, 1982a but much of the data base for this assumption is rather anecdotal and for birds and heliconiinae butterflies (probably the best known groups of organisms it is clear that faunistic community diversity of the coastal Chocó is substantially less than in much of upper Amazonia (J. TERBORGH, pers. comm., K. BROWN, pers. comm.. El Choco la región fitogeográfica de la costa de Colombia y adyacente al Ecuador es conocido como una región de inusualmente alto endemismo en plantas (Gentry, 1982a, 1986b, pájaros (Terborgh y Winter, 1982, y las mariposas (Brown, 1975, 1982. La región también es conocida por ser inusualmente diversa biológicamente (Gentry, 1978, 1982a, pero gran parte de la base de datos para estesuposición es bastante anecdótico y para las aves y mariposas Heliconiinae (prooably los grupos más conocidos de organismos, está claro que la diversidad faunística comunidad del Chaco costera es sustancialmente menor que en gran parte de la Amazonia superior (J. Terborgh, com. pers., K . BROWN, com. pers..El único dato de nivel comunitario disponible para las plantas de la costa Colombia es la forma incompleta analizado 1000 m2 muestra de todas las plantas de más de2.5 cm dbh procedente de Tutunendó, incluido en Gentry (1982b de los patrones de diversidad neotropicales. Choco muestra de Gentry tenía el más alto número de especies de una serie de sitios de muestra y similares que llegaron a la conclusión de que nivel de riqueza de especies vegetales comunidad aumenta directamente con la precipitación. Muchos 1.000 m2 adicionales están disponibles, tanto desde el Chocoregión y de las especies ricas en bosques de Alto

  4. The effects of coastal development on sponge abundance, diversity, and community composition on Jamaican coral reefs.

    Science.gov (United States)

    Stubler, Amber D; Duckworth, Alan R; Peterson, Bradley J

    2015-07-15

    Over the past decade, development along the northern coast of Jamaica has accelerated, resulting in elevated levels of sedimentation on adjacent reefs. To understand the effects of this development on sponge community dynamics, we conducted surveys at three locations with varying degrees of adjacent coastal development to quantify species richness, abundance and diversity at two depths (8-10 m and 15-18 m). Sediment accumulation rate, total suspended solids and other water quality parameters were also quantified. The sponge community at the location with the least coastal development and anthropogenic influence was often significantly different from the other two locations, and exhibited higher sponge abundance, richness, and diversity. Sponge community composition and size distribution were statistically different among locations. This study provides correlative evidence that coastal development affects aspects of sponge community ecology, although the precise mechanisms are still unclear. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Rapid decay of tree-community composition in Amazonian forest fragments

    Science.gov (United States)

    Laurance, William F.; Nascimento, Henrique E. M.; Laurance, Susan G.; Andrade, Ana; Ribeiro, José E. L. S.; Giraldo, Juan Pablo; Lovejoy, Thomas E.; Condit, Richard; Chave, Jerome; Harms, Kyle E.; D'Angelo, Sammya

    2006-01-01

    Forest fragmentation is considered a greater threat to vertebrates than to tree communities because individual trees are typically long-lived and require only small areas for survival. Here we show that forest fragmentation provokes surprisingly rapid and profound alterations in Amazonian tree-community composition. Results were derived from a 22-year study of exceptionally diverse tree communities in 40 1-ha plots in fragmented and intact forests, which were sampled repeatedly before and after fragment isolation. Within these plots, trajectories of change in abundance were assessed for 267 genera and 1,162 tree species. Abrupt shifts in floristic composition were driven by sharply accelerated tree mortality and recruitment within ≈100 m of fragment margins, causing rapid species turnover and population declines or local extinctions of many large-seeded, slow-growing, and old-growth taxa; a striking increase in a smaller set of disturbance-adapted and abiotically dispersed species; and significant shifts in tree size distributions. Even among old-growth trees, species composition in fragments is being restructured substantially, with subcanopy species that rely on animal seed-dispersers and have obligate outbreeding being the most strongly disadvantaged. These diverse changes in tree communities are likely to have wide-ranging impacts on forest architecture, canopy-gap dynamics, plant–animal interactions, and forest carbon storage. PMID:17148598

  6. Metals other than uranium affected microbial community composition in a historical uranium-mining site.

    Science.gov (United States)

    Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

    2015-12-01

    To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

  7. Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

    Science.gov (United States)

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Microbial community composition and dynamics of moving bed biofilm reactor systems treating municipal sewage.

    Science.gov (United States)

    Biswas, Kristi; Turner, Susan J

    2012-02-01

    Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescence in situ hybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated by Clostridia and sulfate-reducing members of the Deltaproteobacteria (SRBs). FISH analyses indicated morphological differences in the Deltaproteobacteria detected at the two plants and also revealed distinctive clustering between SRBs and members of the Methanosarcinales, which were the only Archaea detected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of the Gammaproteobacteria and Betaproteobacteria. This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.

  9. Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

    Science.gov (United States)

    Múrria, Cesc; Bonada, Núria; Vellend, Mark; Zamora-Muñoz, Carmen; Alba-Tercedor, Javier; Sainz-Cantero, Carmen Elisa; Garrido, Josefina; Acosta, Raul; El Alami, Majida; Barquín, Jose; Derka, Tomáš; Álvarez-Cabria, Mario; Sáinz-Bariain, Marta; Filipe, Ana F; Vogler, Alfried P

    2017-11-01

    Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels. © 2017 John Wiley & Sons Ltd.

  10. Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

    Directory of Open Access Journals (Sweden)

    Chris L Dupont

    Full Text Available Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

  11. RNA-Based Assessment of Diversity and Composition of Active Archaeal Communities in the German Bight

    Directory of Open Access Journals (Sweden)

    Bernd Wemheuer

    2012-01-01

    Full Text Available Archaea play an important role in various biogeochemical cycles. They are known extremophiles inhabiting environments such as thermal springs or hydrothermal vents. Recent studies have revealed a significant abundance of Archaea in moderate environments, for example, temperate sea water. Nevertheless, the composition and ecosystem function of these marine archaeal communities is largely unknown. To assess diversity and composition of active archaeal communities in the German Bight, seven marine water samples were taken and studied by RNA-based analysis of ribosomal 16S rRNA. For this purpose, total RNA was extracted from the samples and converted to cDNA. Archaeal community structures were investigated by pyrosequencing-based analysis of 16S rRNA amplicons generated from cDNA. To our knowledge, this is the first study combining next-generation sequencing and metatranscriptomics to study archaeal communities in marine habitats. The pyrosequencing-derived dataset comprised 62,045 archaeal 16S rRNA sequences. We identified Halobacteria as the predominant archaeal group across all samples with increased abundance in algal blooms. Thermoplasmatales (Euryarchaeota and the Marine Group I (Thaumarchaeota were identified in minor abundances. It is indicated that archaeal community patterns were influenced by environmental conditions.

  12. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  13. Improving the biodegradative capacity of subsurface bacteria

    International Nuclear Information System (INIS)

    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

  14. Subsurface quality assurance practices

    International Nuclear Information System (INIS)

    1987-08-01

    This report addresses only the concept of applying Nuclear Quality Assurance (NQA) practices to repository shaft and subsurface design and construction; how NQA will be applied; and the level of detail required in the documentation for construction of a shaft and subsurface repository in contrast to the level of detail required in the documentation for construction of a traditional mine. This study determined that NQA practices are viable, attainable, as well as required. The study identified the appropriate NQA criteria and the repository's major structures, systems, items, and activities to which the criteria are applicable. A QA plan, for design and construction, and a list of documentation, for construction, are presented. 7 refs., 1 fig., 18 tabs

  15. Drivers of cyanobacterial diversity and community composition in mangrove soils in south-east Brazil.

    Science.gov (United States)

    Rigonato, Janaina; Kent, Angela D; Alvarenga, Danillo O; Andreote, Fernando D; Beirigo, Raphael M; Vidal-Torrado, Pablo; Fiore, Marli F

    2013-04-01

    Cyanobacteria act as primary producers of carbon and nitrogen in nutrient-poor ecosystems such as mangroves. This important group of microorganisms plays a critical role in sustaining the productivity of mangrove ecosystems, but the structure and function of cyanobacteria assemblages can be perturbed by anthropogenic influences. The aim of this work was to assess the community structure and ecological drivers that influence the cyanobacterial community harboured in two Brazilian mangrove soils, and examine the long-term effects of oil contamination on these keystone species. Community fingerprinting results showed that, although cyanobacterial communities are distinct between the two mangroves, the structure and diversity of the assemblages exhibit similar responses to environmental gradients. In each ecosystem, cyanobacteria occupying near-shore areas were similar in composition, indicating importance of marine influences for structuring the community. Analysis of 16S rRNA sequences revealed the presence of diverse cyanobacterial communities in mangrove sediments, with clear differences among mangrove habitats along a transect from shore to forest. While near-shore sites in both mangroves were mainly occupied by Prochlorococcus and Synechococcus genera, sequences retrieved from other mangrove niches were mainly affiliated with uncultured cyanobacterial 16S rRNA. The most intriguing finding was the large number of potentially novel cyanobacteria 16S rRNA sequences obtained from a previously oil-contaminated site. The abundance of cyanobacterial 16S rRNA sequences observed in sites with a history of oil contamination was significantly lower than in the unimpacted areas. This study emphasized the role of environmental drivers in determining the structure of cyanobacterial communities in mangrove soils, and suggests that anthropogenic impacts may also act as ecological filters that select cyanobacterial taxa. These results are an important contribution to our

  16. Impact of enzymatic digestion on bacterial community composition in CF airway samples

    Directory of Open Access Journals (Sweden)

    Kayla M. Williamson

    2017-05-01

    Full Text Available Background Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF. We sought to evaluate the effect of enzymatic digestion (EnzD prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP samples from patients with CF. Methods DNA from 81 samples (39 sputum and 42 OP collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA of individual genera for paired samples with and without EnzD. Results Shannon Diversity Index (alpha-diversity decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn, whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella (p < 0.01, Streptococcus (p < 0.01, and Rothia (p < 0.01. Staphylococcus (p < 0.01 was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella (p < 0.01, Granulicatella (p < 0.01, Prevotella (p < 0.01, and Gemella (p = 0.02. In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. Discussion We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP

  17. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

    Science.gov (United States)

    Herfort, Lydie; Crump, Byron C; Fortunato, Caroline S; McCue, Lee Ann; Campbell, Victoria; Simon, Holly M; Baptista, António M; Zuber, Peter

    2017-12-01

    Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ( 3 H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1-24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2-3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the

  18. Subsurface contaminants focus area

    International Nuclear Information System (INIS)

    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

  19. Subsurface contaminants focus area

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  20. Reconstructing riverine mesohabitat unit composition using fish community data and an autecology matrix.

    Science.gov (United States)

    Suen, J P; Su, W C

    2010-09-01

    This research proposes a simplified method for estimating the mesohabitat composition that would favour members of a given set of aquatic species. The simulated composition of four types of mesohabitat units (deep pool, shallow pool, deep riffle and shallow riffle) could guide the design of in-stream structures in creating pool-riffle systems with ecological reference. Fish community data and an autecology matrix are used to support the development of a stream mesohabitat simulation based on regression models for reaches in mid to upper-order streams. The fish community-mesohabitat model results constitute a reference condition that can be used to guide stream restoration and ecological engineering decisions aimed at maintaining the natural ecological integrity and diversity of rivers. © 2010 The Authors. Journal compilation © 2010 The Fisheries Society of the British Isles.

  1. PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances

    OpenAIRE

    Tang, Zheng-Zheng; Chen, Guanhua; Alekseyenko, Alexander V.

    2016-01-01

    Motivation: Recent advances in sequencing technology have made it possible to obtain high-throughput data on the composition of microbial communities and to study the effects of dysbiosis on the human host. Analysis of pairwise intersample distances quantifies the association between the microbiome diversity and covariates of interest (e.g. environmental factors, clinical outcomes, treatment groups). In the design of these analyses, multiple choices for distance metrics are available. Most di...

  2. Effect of ammonium and acetate on methanogenic pathway and methanogenic community composition

    DEFF Research Database (Denmark)

    Fotidis, Ioannis; Karakashev, Dimitar Borisov; Kotsopoulos, T. A.

    2013-01-01

    exposure to different ammonia concentrations. The methanogenic pathway was determined by following the production of (14) CH(4) and (14) CO(2) from acetate labeled in the methyl group (C-2). Microbial communities' composition was determined by fluorescence in situ hybridization. Upon acclimatization......Methanogenesis from acetate (aceticlastic methanogenesis or syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis) is the most important step for the biogas process. The major environmental factors influencing methanogenesis are volatile fatty acids, ammonia, p...

  3. Effects of food on bacterial community composition associated with the copepod Acartia tonsa Dana

    OpenAIRE

    Tang, Kam; Dziallas, Claudia; Hutalle-Schmelzer, Kristine; Grossart, Hans-Peter

    2009-01-01

    The estuarine copepod Acartia tonsa naturally carried diverse strains of bacteria on its body. The bacterial community composition (BCC) remained very conservative even when the copepod was fed different axenic algal species, indicating that the food per se did not much affect BCC associated with the copepod. In xenic algal treatments, however, copepod-associated BCC differed with each alga fed, even though the same bacterial source was used to inoculate the algae. In addition, starved copepo...

  4. The effect of increased loads of dissolved organic matter on estuarine microbial community composition and function

    DEFF Research Database (Denmark)

    Traving, Sachia J.; Rowe, Owen; Jakobsen, Nina M.

    2017-01-01

    Increased river loads are projected as one of the major consequences of climate change in the northern hemisphere, leading to elevated inputs of riverine dissolved organic matter (DOM) and inorganic nutrients to coastal ecosystems. The objective of this study was to investigate the effects of ele...... supply to the Baltic Sea will be efficiently mineralized by microbes. This will have consequences for bacterioplankton and phytoplankton community composition and function, and significantly affect nutrient biogeochemistry....

  5. A dinosaur community composition dataset for the Late Cretaceous Nemegt Basin of Mongolia

    Directory of Open Access Journals (Sweden)

    G.F. Funston

    2018-02-01

    Full Text Available Dinosaur community composition data for eleven fossil localities in the Late Cretaceous Nemegt Basin of Mongolia are compiled from field observations and records in the literature. Counts were generated from skeletons and represent numbers of individuals preserved in each locality. These data were used in the analyses of Funston et al. [1] “Oviraptorosaur anatomy, diversity, and ecology in the Nemegt Basin” in the Nemegt Ecosystems Special Issue of Palaeogeography, Palaeoclimatology, Palaeoecology, where the results are discussed.

  6. Community composition and diversity of ground beetles (Coleoptera: Carabidae) in Yaoluoping National Nature Reserve

    Science.gov (United States)

    Li, Wen-Bo; Liu, Nai-Yi; Wu, Yun-He; Zhang, Yu-Cai; Xu, Qin; Chu, Jun; Wang, Shu-Yan

    2017-01-01

    Abstract This study used pitfall trapping to examine community composition and diversity of ground beetles in five different habitats (coniferous, deciduous, mixed coniferous, farmland, and settlements) within Anhui Yaoluoping National Nature Reserve from May to September 2014. In total, 1,352 ground beetles were collected, belonging to 16 genera and 44 species. Of these, four dominant species Dolichus halensis, Harpalus pastor, Carabus casaleianus, and Pheropsophus jessoensis were identified, respectively, comprising 370, 177, 131, and 123 individuals. The deciduous forest showed greater diversity (3.78 according to Shannon–Weiner index), equitability (0.80 according to Pielou’s index), and dominance (9.52 according to Simpson’s index) when compared with farmland, but species richness in the deciduous forest (27) was lower than that in farmland (35). One-way analysis of variance showed that ground beetle species composition and abundance among different habitats varied significantly. Cluster analysis and principal coordinate analysis showed that farmland shared low community similarity with other habitat types, and coniferous and mixed coniferous forests shared similar community types. Our results indicate that species composition, abundance, and diversity of ground beetles are affected by different habitat types, with deciduous forest types being critical in maintaining the diversity of rare species. We recommend reducing cultivated farmland area and increasing the area of carefully planned deciduous forest in order to better protect ground beetle diversity in the region.

  7. Rapid plant evolution in the presence of an introduced species alters community composition.

    Science.gov (United States)

    Smith, David Solance; Lau, Matthew K; Jacobs, Ryan; Monroy, Jenna A; Shuster, Stephen M; Whitham, Thomas G

    2015-10-01

    Because introduced species may strongly interact with native species and thus affect their fitness, it is important to examine how these interactions can cascade to have ecological and evolutionary consequences for whole communities. Here, we examine the interactions among introduced Rocky Mountain elk, Cervus canadensis nelsoni, a common native plant, Solidago velutina, and the diverse plant-associated community of arthropods. While introduced species are recognized as one of the biggest threats to native ecosystems, relatively few studies have investigated an evolutionary mechanism by which introduced species alter native communities. Here, we use a common garden design that addresses and supports two hypotheses. First, native S. velutina has rapidly evolved in the presence of introduced elk. We found that plants originating from sites with introduced elk flowered nearly 3 weeks before plants originating from sites without elk. Second, evolution of S. velutina results in a change to the plant-associated arthropod community. We found that plants originating from sites with introduced elk supported an arthropod community that had ~35 % fewer total individuals and a different species composition. Our results show that the impacts of introduced species can have both ecological and evolutionary consequences for strongly interacting species that subsequently cascade to affect a much larger community. Such evolutionary consequences are likely to be long-term and difficult to remediate.

  8. Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment.

    Science.gov (United States)

    Angell, John H; Peng, Xuefeng; Ji, Qixing; Craick, Ian; Jayakumar, Amal; Kearns, Patrick J; Ward, Bess B; Bowen, Jennifer L

    2018-01-01

    Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes ( amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

  9. The Role of Abiotic Environmental Conditions and Herbivory in Shaping Bacterial Community Composition in Floral Nectar

    Science.gov (United States)

    Samuni-Blank, Michal; Izhaki, Ido; Laviad, Sivan; Bar-Massada, Avi; Gerchman, Yoram; Halpern, Malka

    2014-01-01

    Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that “everything is everywhere, but the environment selects”. Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs. PMID:24922317

  10. Seed bank and big sagebrush plant community composition in a range margin for big sagebrush

    Science.gov (United States)

    Martyn, Trace E.; Bradford, John B.; Schlaepfer, Daniel R.; Burke, Ingrid C.; Laurenroth, William K.

    2016-01-01

    The potential influence of seed bank composition on range shifts of species due to climate change is unclear. Seed banks can provide a means of both species persistence in an area and local range expansion in the case of increasing habitat suitability, as may occur under future climate change. However, a mismatch between the seed bank and the established plant community may represent an obstacle to persistence and expansion. In big sagebrush (Artemisia tridentata) plant communities in Montana, USA, we compared the seed bank to the established plant community. There was less than a 20% similarity in the relative abundance of species between the established plant community and the seed bank. This difference was primarily driven by an overrepresentation of native annual forbs and an underrepresentation of big sagebrush in the seed bank compared to the established plant community. Even though we expect an increase in habitat suitability for big sagebrush under future climate conditions at our sites, the current mismatch between the plant community and the seed bank could impede big sagebrush range expansion into increasingly suitable habitat in the future.

  11. Biogeochemical interactions control a temporal succession in the elemental composition of marine communities

    KAUST Repository

    Martiny, Adam C.; Talarmin, Agathe Anne Gaelle; Mouginot, Cé line; Lee, Jeanette A.; Huang, Jeremy S.; Gellene, Alyssa G.; Caron, David A.

    2015-01-01

    Recent studies have revealed clear regional differences in the particulate organic matter composition and stoichiometry of plankton communities. In contrast, less is known about potential mechanisms and patterns of temporal changes in the elemental composition of marine systems. Here, we monitored weekly changes in environmental conditions, phytoplankton abundances, and particulate organic carbon, nitrogen, and phosphorus concentrations over a 3-yr period. We found that variation in the particulate organic matter (POM) concentrations and ratios were related to seasonal oscillations of environmental conditions and phytoplankton abundances. Periods with low temperature, high nutrient concentrations and a dominance of large phytoplankton corresponded to low C : N : P and vice-versa for warmer periods during the summer and fall. In addition to seasonal changes, we observed a multiyear increase in POM C : P and N : P that might be associated with the Pacific Decadal Oscillation. Finally, there was substantial short-term variability in all factors but similar linkages between environmental variability and elemental composition as observed on seasonal and interannual time-scales. Using a feed-forward neural network, we could explain a large part of the variation in POM concentrations and ratios based on changes in environmental conditions and phytoplankton abundances. The apparent links across all time-scales between changes in physics, chemistry, phytoplankton, and POM concentrations and ratios suggest we have identified key controls of the elemental composition of marine communities in this region.

  12. Biogeochemical interactions control a temporal succession in the elemental composition of marine communities

    KAUST Repository

    Martiny, Adam C.

    2015-11-23

    Recent studies have revealed clear regional differences in the particulate organic matter composition and stoichiometry of plankton communities. In contrast, less is known about potential mechanisms and patterns of temporal changes in the elemental composition of marine systems. Here, we monitored weekly changes in environmental conditions, phytoplankton abundances, and particulate organic carbon, nitrogen, and phosphorus concentrations over a 3-yr period. We found that variation in the particulate organic matter (POM) concentrations and ratios were related to seasonal oscillations of environmental conditions and phytoplankton abundances. Periods with low temperature, high nutrient concentrations and a dominance of large phytoplankton corresponded to low C : N : P and vice-versa for warmer periods during the summer and fall. In addition to seasonal changes, we observed a multiyear increase in POM C : P and N : P that might be associated with the Pacific Decadal Oscillation. Finally, there was substantial short-term variability in all factors but similar linkages between environmental variability and elemental composition as observed on seasonal and interannual time-scales. Using a feed-forward neural network, we could explain a large part of the variation in POM concentrations and ratios based on changes in environmental conditions and phytoplankton abundances. The apparent links across all time-scales between changes in physics, chemistry, phytoplankton, and POM concentrations and ratios suggest we have identified key controls of the elemental composition of marine communities in this region.

  13. The Effects of Disturbance History on Ground-Layer Plant Community Composition in British Columbia

    Directory of Open Access Journals (Sweden)

    Michael Ton

    2016-05-01

    Full Text Available Plant communities are sensitive to perturbations and may display alternative recovery pathways depending on disturbance history. In sub-boreal lodgepole pine forests of central interior British Columbia, Canada, fire and logging are two widespread landscape disturbances that overlap in many regions. We asked whether cumulative, short-interval disturbance from logging and fire resulted in different ground-layer plant communities than resulted from fire alone. Using field-collected data, we compared the taxonomic composition and functional traits of 3-year old plant communities that were either harvested 6-to-13 years prior, or not harvested prior to being burned in a large stand-replacing fire. The taxonomic composition diverged between the two treatments, driven primarily by differences in a few key indicator species such as Petasites frigidus and Vaccinium membranaceum. Analysis of individual species’ morphological traits indicated that only a few species vary in size in relation to disturbance history. Our data suggest that a history of forest harvest leaves a subtle footprint on post-fire ground-layer plant communities at early stages of succession.

  14. Abundance, diversity and community composition of free-living protozoa on vegetable sprouts.

    Science.gov (United States)

    Chavatte, N; Lambrecht, E; Van Damme, I; Sabbe, K; Houf, K

    2016-05-01

    Interactions with free-living protozoa (FLP) have been implicated in the persistence of pathogenic bacteria on food products. In order to assess the potential involvement of FLP in this contamination, detailed knowledge on their occurrence, abundance and diversity on food products is required. In the present study, enrichment and cultivation methods were used to inventory and quantify FLP on eight types of commercial vegetable sprouts (alfalfa, beetroot, cress, green pea, leek, mung bean, red cabbage and rosabi). In parallel, total aerobic bacteria and Escherichia coli counts were performed. The vegetable sprouts harbored diverse communities of FLP, with Tetrahymena (ciliate), Bodo saltans and cercomonads (flagellates), and Acanthamoeba and Vannella (amoebae) as the dominant taxa. Protozoan community composition and abundance significantly differed between the sprout types. Beetroot harbored the most abundant and diverse FLP communities, with many unique species such as Korotnevella sp., Vannella sp., Chilodonella sp., Podophrya sp. and Sphaerophrya sp. In contrast, mung bean sprouts were species-poor and had low FLP numbers. Sampling month and company had no significant influence, suggesting that seasonal and local factors are of minor importance. Likewise, no significant relationship between protozoan community composition and bacterial load was observed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Assessment of Zooplankton Community Composition along a Depth Profile in the Central Red Sea

    KAUST Repository

    Pearman, John K.

    2015-07-17

    The composition of zooplankton in the water column has received limited attention in the main body of the Red Sea and this study investigates the change in the community both spatially and temporally across 11 stations in the central Red Sea. Using molecular methods to target the v9 region of the 18S rRNA gene a total of approximately 11.5 million reads were sequenced resulting in 2528 operational taxonomic units (OTUs) at 97% similarity. The phylum Arthropoda dominated in terms of reads accounting for on average 86.2% and 65.3% for neuston nets and vertical multinets respectively. A reduction in the number of OTUs was noticed with depth for both total metazoa and Maxillopoda whilst there was also a significant change in the composition of the Maxillopoda community. The genus Corycaeus had a higher proportion of reads in the epipelagic zone with Pleuromamma becoming increasingly dominant with depth. No significant difference was observed in the community between night and day sampling however there was a significant difference in the zooplankton community between two sampling periods separated by 10 days.

  16. Productivity and species composition of algal mat communities exposed to a fluctuating thermal regime

    International Nuclear Information System (INIS)

    Tison, D.L.; Wilde, E.W.; Pope, D.H.; Fliermans, C.B.

    1981-01-01

    Algal mat communities growing in thermal effluents of production nuclear reactors at the Savannah River Plant, near Aiken, SC, are exposed to large temperature fluctuations resulting from reactor operations. Rates of primary production and species composition were monitored at 4 sites along a thermal gradient in a trough microcosm to determine how these large temperature fluctuations affected productivity and algal community structure. Blue-green algae (cyanobacteria) were the only phototrophic primary producers growing in water above 45 0 C. These thermophiles were able to survive and apparently adapt to ambient temperatures when the reactor was shut down. The algal mat communities exposed to 14 C-labeled dissolved organic compounds and a decrease in primary production were observed during periods of thermal fluctuation. The results show that the dominant phototrophs in this artificially heated aquatic habitat have been selected for their abiity to survive large temperature fluctuations and are similar to those of natural hot springs

  17. Organic fertilization alters the community composition of root associated fungi in Pisum sativum

    DEFF Research Database (Denmark)

    Yu, L.; Nicolaisen, M.; Ravnskov, S.

    2013-01-01

    Organic fertilization is well known to affect individual functional groups of root associated fungi such as arbuscular mycorrhizal (AM) fungi and root pathogens, but limited information is available on the effect of organic fertilization at the fungal community composition level. The main objective...... of the present study was to examine the response of communities of root associated fungi in Pisum sativum to Protamylasse, an organic fertilizer used in pea production. Plants were grown in pots with field soil amended with four different levels of Protamylasse. 454 pyrosequencing was employed to examine......, the organic fertilizer Protamylasse clearly affects communities of root associated fungi, which seems to be linked to the life strategy of the different functional groups of root associated fungi. --------------------------------------------------------------------------------...

  18. Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

    DEFF Research Database (Denmark)

    Bang-Andreasen, Toke; Nielsen, Jeppe T.; Voriskova, Jana

    2017-01-01

    Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid......-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse...... and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha(-1). We used culture-based enumerations of general bacteria, Pseudomonas...

  19. Spatial distribution of microbial biomass, activity, community structure, and the biodegradation of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) in the subsurface.

    Science.gov (United States)

    Federle, T W; Ventullo, R M; White, D C

    1990-12-01

    The vertical distribution of microbial biomass, activity, community structure and the mineralization of xenobiotic chemicals was examined in two soil profiles in northern Wisconsin. One profile was impacted by infiltrating wastewater from a laundromat, while the other served as a control. An unconfined aquifer was present 14 meters below the surface at both sites. Biomass and community structure were determined by acridine orange direct counts and measuring concentrations of phospholipid-derived fatty acids (PLFA). Microbial activity was estimated by measuring fluorescein diacetate (FDA) hydrolysis, thymidine incorporation into DNA, and mixed amino acid (MAA) mineralization. Mineralization kinetics of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) were determined at each depth. Except for MAA mineralization rates, measures of microbial biomass and activity exhibited similar patterns with depth. PLFA concentration and rates of FDA hydrolysis and thymidine incorporation decreased 10-100 fold below 3 m and then exhibited little variation with depth. Fungal fatty acid markers were found at all depths and represented from 1 to 15% of the total PLFAs. The relative proportion of tuberculostearic acid (TBS), an actinomycete marker, declined with depth and was not detected in the saturated zone. The profile impacted by wastewater exhibited higher levels of PLFA but a lower proportion of TBS than the control profile. This profile also exhibited faster rates of FDA hydrolysis and amino acid mineralization at most depths. LAS was mineralized in the upper 2 m of the vadose zone and in the saturated zone of both profiles. Little or no LAS biodegradation occurred at depths between 2 and 14 m. LAE was mineralized at all depths in both profiles, and the mineralization rate exhibited a similar pattern with depth as biomass and activity measurements. In general, biomass and biodegradative activities were much lower in groundwater than in soil samples obtained

  20. Method of solution mining subsurface orebodies to reduce restoration activities

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, G.J.

    1984-01-24

    A method of solution mining is claimed wherein a lixiviant containing both leaching and oxidizing agents is injected into the subsurface orebody. The composition of the lixiviant is changed by reducing the level of oxidizing agent to zero so that soluble species continue to be removed from the subsurface environment. This reduces the uranium level of the ground water aquifer after termination of the lixiviant injection.

  1. The effect of positive interactions on temporal turnover of community composition along an environmental gradient.

    Directory of Open Access Journals (Sweden)

    Youshi Wang

    Full Text Available It has been demonstrated that the interplay between negative and positive interactions simultaneously shapes community structure and composition. However, few studies have attempted to examine the effect of facilitation on compositional changes in communities through time. Additionally, due to the difficulties in collecting the long-term data, it would be useful to indicate the rate of temporal turnover using a readily obtainable metric. Using an individual-based model incorporating plant strategies, we examined the role of facilitation on the temporal turnover of communities located at different positions along an environmental gradient for three model scenarios: CM without facilitation; CFM-U, a unimodal relationship between facilitation and environmental severity; and CFM-L, a positively linear relationship between facilitation and environmental severity. Our results demonstrated that facilitation could increase, decrease or have no remarkable effect on temporal turnover. The specific outcome depended on the location of the focal community across the environmental gradient and the model employed. Compared with CM, the inclusion of positive interactions (i.e. CFM-U and CFM-L, at intermediate environmental stress levels (such as S = 0.7 and 0.8 resulted in lower Bray-Curtis similarity values; at other severity levels, facilitation slowed down (such as S = 0.3 and 0.4 at low to medium stress levels, and S = 0.9 at high stress levels or had only a subtle effect (such as at S = 0.1 on temporal turnover. We also found that the coefficient of variation (CV in species abundances and the rate of temporal variability showed a significant quadratic relationship. Our theoretical analysis contributes to the understanding of factors driving temporal turnover in biotic communities, and presents a potential metric (i.e. CV in species abundances assessing the consequences of ongoing environmental change on community structure.

  2. The effect of positive interactions on temporal turnover of community composition along an environmental gradient.

    Science.gov (United States)

    Wang, Youshi; Yang, Zhiyong; Zhou, Shurong; Soininen, Janne; Ai, Dexiecuo; Li, Yali; Chu, Chengjin

    2013-01-01

    It has been demonstrated that the interplay between negative and positive interactions simultaneously shapes community structure and composition. However, few studies have attempted to examine the effect of facilitation on compositional changes in communities through time. Additionally, due to the difficulties in collecting the long-term data, it would be useful to indicate the rate of temporal turnover using a readily obtainable metric. Using an individual-based model incorporating plant strategies, we examined the role of facilitation on the temporal turnover of communities located at different positions along an environmental gradient for three model scenarios: CM without facilitation; CFM-U, a unimodal relationship between facilitation and environmental severity; and CFM-L, a positively linear relationship between facilitation and environmental severity. Our results demonstrated that facilitation could increase, decrease or have no remarkable effect on temporal turnover. The specific outcome depended on the location of the focal community across the environmental gradient and the model employed. Compared with CM, the inclusion of positive interactions (i.e. CFM-U and CFM-L), at intermediate environmental stress levels (such as S = 0.7 and 0.8) resulted in lower Bray-Curtis similarity values; at other severity levels, facilitation slowed down (such as S = 0.3 and 0.4 at low to medium stress levels, and S = 0.9 at high stress levels) or had only a subtle effect (such as at S = 0.1) on temporal turnover. We also found that the coefficient of variation (CV) in species abundances and the rate of temporal variability showed a significant quadratic relationship. Our theoretical analysis contributes to the understanding of factors driving temporal turnover in biotic communities, and presents a potential metric (i.e. CV in species abundances) assessing the consequences of ongoing environmental change on community structure.

  3. Effects of simulated acid rain on soil fauna community composition and their ecological niches.

    Science.gov (United States)

    Wei, Hui; Liu, Wen; Zhang, Jiaen; Qin, Zhong

    2017-01-01

    Acid rain is one of the severest environmental issues globally. Relative to other global changes (e.g., warming, elevated atmospheric [CO 2 ], and nitrogen deposition), however, acid rain has received less attention than its due. Soil fauna play important roles in multiple ecological processes, but how soil fauna community responds to acid rain remains less studied. This microcosm experiment was conducted using latosol with simulated acid rain (SAR) manipulations to observe potential changes in soil fauna community under acid rain stress. Four pH levels, i.e., pH 2.5, 3.5, 4.5, and 5.5, and a neutral control of pH 7.0 were set according to the current pH condition and acidification trend of precipitation in southern China. As expected, we observed that the SAR treatments induced changes in soil fauna community composition and their ecological niches in the tested soil; the treatment effects tended to increase as acidity increased. This could be attributable to the environmental stresses (such as acidity, porosity and oxygen supply) induced by the SAR treatments. In addition to direct acidity effect, we propose that potential changes in permeability and movability of water and oxygen in soils induced by acid rain could also give rise to the observed shifts in soil fauna community composition. These are most likely indirect pathways of acid rain to affect belowground community. Moreover, we found that nematodes, the dominating soil fauna group in this study, moved downwards to mitigate the stress of acid rain. This is probably detrimental to soil fauna in the long term, due to the relatively severer soil conditions in the deep than surface soil layer. Our results suggest that acid rain could change soil fauna community and the vertical distribution of soil fauna groups, consequently changing the underground ecosystem functions such as organic matter decomposition and greenhouse gas emissions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Compositional divergence and convergence in local communities and spatially structured landscapes.

    Directory of Open Access Journals (Sweden)

    Tancredi Caruso

    Full Text Available Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence than, less dissimilar (convergence than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect. The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community

  5. Impact of Anthracene Exposure on Bacterial Community Composition and Function in an Egyptian Marine Environment

    International Nuclear Information System (INIS)

    Zakaria, A.E.M.; Lappin-Scott, H.

    2013-01-01

    The application of bioremediation technology for pollution treatment requires more knowledge about how do microbial communities respond to pollutant exposure. The main goals of this study are to investigate the behavior of natural bacterial microflora of Suez Gulf (SGM) in response to exposure to different concentrations of Polycyclic Aromatic Hydrocarbons (PAHs) for different periods. In this study, anthracene, as a model of (PAHs) was added in different concentrations, (30,150 and 500 ppm) to fertilized Suez Gulf water in shaking microcosms to examine the possible shifts in bacterial community composition and function. Changes in bacterial community composition was followed up after different periods of exposure (0, 6, 12, and 18) days to the above mentioned concentrations of anthracene by profiling the amplified product of 16S rDNA via denaturing gradient gel electrophoresis (DGGE) of SGM in treated microcosm separately. DGGE profiles revealed remarkable changes in diversity due to exposure concentration and duration to anthracene. A diverse relationship between anthracene concentration and bacterial diversity was detected. On the other hand, changes in community function were determined by testing the biodegradation capabilities of the consortia after different exposures separately in microcosms containing 50 ppm of anthracene for 14 days. The remaining anthracene was extracted and monitored by high performance liquid chromatography (HPLC) and DGGE profiles of amplified 16S rDNA extracted from parallel biodegradation microcosms were examined to indicate the effects of pre-exposure to different concentrations for different periods to PAHs on the bacterial community compositions. The results confirm that the long term effects of pre exposure to high concentrations of PAH on the bacterial community composition, suggesting that that some organisms can be used as a bio marker indicating the exposures of the marine environment to high concentrations of PAHs. HPLC

  6. Biofouling of reverse-osmosis membranes during tertiary wastewater desalination: microbial community composition.

    Science.gov (United States)

    Al Ashhab, Ashraf; Herzberg, Moshe; Gillor, Osnat

    2014-03-01

    Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community. Copyright © 2013

  7. Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice.

    Science.gov (United States)

    Hatam, Ido; Lange, Benjamin; Beckers, Justin; Haas, Christian; Lanoil, Brian

    2016-10-01

    Arctic sea ice can be classified into two types: seasonal ice (first-year ice, FYI) and multi-year ice (MYI). Despite striking differences in the physical and chemical characteristics of FYI and MYI, and the key role sea ice bacteria play in biogeochemical cycles of the Arctic Ocean, there are a limited number of studies comparing the bacterial communities from these two ice types. Here, we compare the membership and composition of bacterial communities from FYI and MYI sampled north of Ellesmere Island, Canada. Our results show that communities from both ice types were dominated by similar class-level phylogenetic groups. However, at the operational taxonomic unit (OTU) level, communities from MYI and FYI differed in both membership and composition. Communities from MYI sites had consistent structure, with similar membership (presence/absence) and composition (OTU abundance) independent of location and year of sample. By contrast, communities from FYI were more variable. Although FYI bacterial communities from different locations and different years shared similar membership, they varied significantly in composition. Should these findings apply to sea ice across the Arctic, we predict increased compositional variability in sea ice bacterial communities resulting from the ongoing transition from predominantly MYI to FYI, which may impact nutrient dynamics in the Arctic Ocean.

  8. The Brazilian freshwater wetscape: Changes in tree community diversity and composition on climatic and geographic gradients.

    Directory of Open Access Journals (Sweden)

    Florian Wittmann

    Full Text Available Wetlands harbor an important compliment of regional plant diversity, but in many regions data on wetland diversity and composition is still lacking, thus hindering our understanding of the processes that control it. While patterns of broad-scale terrestrial diversity and composition typically correlate with contemporary climate it is not clear to what extent patterns in wetlands are complimentary, or conflicting. To elucidate this, we consolidate data from wetland forest inventories in Brazil and examine patterns of diversity and composition along temperature and rainfall gradients spanning five biomes. We collated 196 floristic inventories covering an area >220 ha and including >260,000 woody individuals. We detected a total of 2,453 tree species, with the Amazon alone accounting for nearly half. Compositional patterns indicated differences in freshwater wetland floras among Brazilian biomes, although biomes with drier, more seasonal climates tended to have a larger proportion of more widely distributed species. Maximal alpha diversity increased with annual temperature, rainfall, and decreasing seasonality, patterns broadly consistent with upland vegetation communities. However, alpha diversity-climate relationships were only revealed at higher diversity values associated with the uppermost quantiles, and in most sites diversity varied irrespective of climate. Likewise, mean biome-level differences in alpha-diversity were unexpectedly modest, even in comparisons of savanna-area wetlands to those of nearby forested regions. We describe attenuated wetland climate-diversity relationships as a shifting balance of local and regional effects on species recruitment. Locally, excessive waterlogging strongly filters species able to colonize from regional pools. On the other hand, increased water availability can accommodate a rich community of drought-sensitive immigrant species that are able to track buffered wetland microclimates. We argue that

  9. The effect of native and introduced biofuel crops on the composition of soil biota communities

    Science.gov (United States)

    Frouz, Jan; Hedenec, Petr

    2016-04-01

    Biofuel crops are an accepted alternative to fossil fuels, but little is known about the ecological impact of their production. The aim of this contribution is to study the effect of native (Salix viminalis and Phalaris arundinacea) and introduced (Helianthus tuberosus, Reynoutria sachalinensis and Silphium perfoliatum) biofuel crop plantations on the soil biota in comparison with cultural meadow vegetation used as control. The study was performed as part of a split plot field experiment of the Crop Research Institute in the city of Chomutov (Czech Republic). The composition of the soil meso- and macrofauna community, composition of the cultivable fraction of the soil fungal community, cellulose decomposition (using litter bags), microbial biomass, basal soil respiration and PLFA composition (incl. F/B ratio) were studied in each site. The C:N ratio and content of polyphenols differed among plant species, but these results could not be considered significant between introduced and native plant species. Abundance of the soil meso- and macrofauna was higher in field sites planted with S. viminalis and P. arundinacea than those planted with S. perfoliatum, H. tuberosus and R. sachalinensis. RDA and Monte Carlo Permutation Test showed that the composition of the faunal community differed significantly between various native and introduced plants. Significantly different basal soil respiration was found in sites planted with various energy crops; however, this difference was not significant between native and introduced species. Microbial biomass carbon and cellulose decomposition did not exhibit any statistical differences among the biofuel crops. The largest statistically significant difference we found was in the content of actinobacterial and bacterial (bacteria, G+ bacteria and G- bacteria) PLFA in sites overgrown by P. arundinacea compared to introduced as well as native biofuel crops. In conclusion, certain parameters significantly differ between various native

  10. Preliminary evaluation of an in vivo fluorometer to quantify algal periphyton biomass and community composition

    Science.gov (United States)

    Harris, Theodore D.; Graham, Jennifer L.

    2015-01-01

    The bbe-Moldaenke BenthoTorch (BT) is an in vivo fluorometer designed to quantify algal biomass and community composition in benthic environments. The BT quantifies total algal biomass via chlorophyll a (Chl-a) concentration and may differentiate among cyanobacteria, green algae, and diatoms based on pigment fluorescence. To evaluate how BT measurements of periphytic algal biomass (as Chl-a) compared with an ethanol extraction laboratory analysis, we collected BT- and laboratory-measured Chl-a data from 6 stream sites in the Indian Creek basin, Johnson County, Kansas, during August and September 2012. BT-measured Chl-a concentrations were positively related to laboratory-measured concentrations (R2 = 0.47); sites with abundant filamentous algae had weaker relations (R2 = 0.27). Additionally, on a single sample date, we used the BT to determine periphyton biomass and community composition upstream and downstream from 2 wastewater treatment facilities (WWTF) that discharge into Indian Creek. We found that algal biomass increased immediately downstream from the WWTF discharge then slowly decreased as distance from the WWTF increased. Changes in periphyton community structure also occurred; however, there were discrepancies between BT- and laboratory-measured community composition data. Most notably, cyanobacteria were present at all sites based on BT measurements but were present at only one site based on laboratory-analyzed samples. Overall, we found that the BT compared reasonably well with laboratory methods for relative patterns in Chl-a but not as well with absolute Chl-aconcentrations. Future studies need to test the BT over a wider range of Chl-aconcentrations, in colored waters, and across various periphyton assemblages.

  11. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

    Science.gov (United States)

    Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

    2015-01-01

    Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices.

    Science.gov (United States)

    Pellissier, Loïc; Oppliger, Anne; Hirzel, Alexandre H; Savova-Bianchi, Dessislava; Mbayo, Guilain; Mascher, Fabio; Kellenberger, Stefan; Niculita-Hirzel, Hélène

    2016-01-29

    Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km(2) along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO3 concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices

    Science.gov (United States)

    Pellissier, Loïc; Oppliger, Anne; Hirzel, Alexandre H.; Savova-Bianchi, Dessislava; Mbayo, Guilain; Mascher, Fabio; Kellenberger, Stefan

    2016-01-01

    Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km2 along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO3 concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities. PMID:26826229

  14. Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development.

    Science.gov (United States)

    Martínez-García, Laura B; Richardson, Sarah J; Tylianakis, Jason M; Peltzer, Duane A; Dickie, Ian A

    2015-03-01

    Little is known about the response of arbuscular mycorrhizal fungal communities to ecosystem development. We use a long-term soil chronosequence that includes ecosystem progression and retrogression to quantify the importance of host plant identity as a factor driving fungal community composition during ecosystem development. We identified arbuscular mycorrhizal fungi and plant species from 50 individual roots from each of 10 sites spanning 5-120 000 yr of ecosystem age using terminal restriction fragment length polymorphism (T-RFLP), Sanger sequencing and pyrosequencing. Arbuscular mycorrhizal fungal communities were highly structured by ecosystem age. There was strong niche differentiation, with different groups of operational taxonomic units (OTUs) being characteristic of early succession, ecosystem progression and ecosystem retrogression. Fungal alpha diversity decreased with ecosystem age, whereas beta diversity was high at early stages and lower in subsequent stages. A total of 39% of the variance in fungal communities was explained by host plant and site age, 29% of which was attributed to host and the interaction between host and site (24% and 5%, respectively). The strong response of arbuscular mycorrhizal fungi to ecosystem development appears to be largely driven by plant host identity, supporting the concept that plant and fungal communities are tightly coupled rather than independently responding to habitat. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  15. Composition and structure of bird communities in vegetational gradients of Bodoquena Mountains, western Brazil

    Directory of Open Access Journals (Sweden)

    MAURICIO N. GODOI

    2016-03-01

    Full Text Available ABSTRACT The informations of bird species distribution in different habitats and the structure of their communities are crucial for bird conservation. We tested the differences in composition, richness and abundance of birds in different phytophysiognomies at Bodoquena Mountains, western Brazil, and we demonstrated the variations in richness and abundance of birds between different trophic groups. Sampling was conducted between July 2011 and June 2012 in 200 point counts arranged in the study area. A total of 3350 contacts were obtained belonging to 156 bird species. Woodland savannas, seasonal forests and arboreal savannas had higher bird abundance and richness, while riparian forests, clean pastures and dirty pastures had smaller values of these parameters. The bird community was organized according to local vegetational gradient, with communities of forests, open areas and savannas, although many species occurred in more than one vegetation type. The insectivorous, omnivorous, frugivorous and gramnivorous birds composed most of the community. These data showed how important environmental heterogeneity is to bird communities. Furthermore, the presence of extensive patches of natural habitats, the small distance between these patches and the permeability of pastures, with high arboreal and shrubby cover, are indicated as important factors to maintain the bird diversity.

  16. Intensification of agriculture, landscape composition and wild bee communities: A large scale study in four European countries

    NARCIS (Netherlands)

    Feon, Le V.; Schermann-Legionnet, A.; Delettre, Y.; Aviron, S.; Billeter, R.; Bugter, R.J.F.; Hendrickx, F.; Burel, F.

    2010-01-01

    The impacts of agricultural practices and landscape composition on bee communities were investigated in 14 sites located in four Western European countries (Belgium, France, the Netherlands and Switzerland). Standardized interviews with farmers assessed agricultural practices in terms of

  17. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

    NARCIS (Netherlands)

    Henderson, G.; Cox, F.; Ganesh, S.; Jonker, A.; Young, W.; Janssen, P.H.; Bannink, A.; Dieho, K.; Dijkstra, J.

    2015-01-01

    Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was

  18. Assessing historical fish community composition using surveys, historical collection data, and species distribution models.

    Science.gov (United States)

    Labay, Ben; Cohen, Adam E; Sissel, Blake; Hendrickson, Dean A; Martin, F Douglas; Sarkar, Sahotra

    2011-01-01

    Accurate establishment of baseline conditions is critical to successful management and habitat restoration. We demonstrate the ability to robustly estimate historical fish community composition and assess the current status of the urbanized Barton Creek watershed in central Texas, U.S.A. Fish species were surveyed in 2008 and the resulting data compared to three sources of fish occurrence information: (i) historical records from a museum specimen database and literature searches; (ii) a nearly identical survey conducted 15 years earlier; and (iii) a modeled historical community constructed with species distribution models (SDMs). This holistic approach, and especially the application of SDMs, allowed us to discover that the fish community in Barton Creek was more diverse than the historical data and survey methods alone indicated. Sixteen native species with high modeled probability of occurrence within the watershed were not found in the 2008 survey, seven of these were not found in either survey or in any of the historical collection records. Our approach allowed us to more rigorously establish the true baseline for the pre-development fish fauna and then to more accurately assess trends and develop hypotheses regarding factors driving current fish community composition to better inform management decisions and future restoration efforts. Smaller, urbanized freshwater systems, like Barton Creek, typically have a relatively poor historical biodiversity inventory coupled with long histories of alteration, and thus there is a propensity for land managers and researchers to apply inaccurate baseline standards. Our methods provide a way around that limitation by using SDMs derived from larger and richer biodiversity databases of a broader geographic scope. Broadly applied, we propose that this technique has potential to overcome limitations of popular bioassessment metrics (e.g., IBI) to become a versatile and robust management tool for determining status of

  19. Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition.

    Science.gov (United States)

    Kohrs, F; Heyer, R; Bissinger, T; Kottler, R; Schallert, K; Püttker, S; Behne, A; Rapp, E; Benndorf, D; Reichl, U

    2017-08-01

    Complex microbial communities are the functional core of anaerobic digestion processes taking place in biogas plants (BGP). So far, however, a comprehensive characterization of the microbiomes involved in methane formation is technically challenging. As an alternative, enriched communities from laboratory-scale experiments can be investigated that have a reduced number of organisms and are easier to characterize by state of the art mass spectrometric-based (MS) metaproteomic workflows. Six parallel laboratory digesters were inoculated with sludge from a full-scale BGP to study the development of enriched microbial communities under defined conditions. During the first three month of cultivation, all reactors (R1-R6) were functionally comparable regarding biogas productions (375-625 NL L reactor volume -1 d -1 ), methane yields (50-60%), pH values (7.1-7.3), and volatile fatty acids (VFA, 1 gNH 3 L -1 ) showed an increase to pH 7.5-8.0, accumulation of acetate (>10 mM), and decreasing biogas production (<125 NL L reactor volume -1 d -1 ). Tandem MS (MS/MS)-based proteotyping allowed the identification of taxonomic abundances and biological processes. Although all reactors showed similar performances, proteotyping and terminal restriction fragment length polymorphisms (T-RFLP) fingerprinting revealed significant differences in the composition of individual microbial communities, indicating multiple steady-states. Furthermore, cellulolytic enzymes and cellulosomal proteins of Clostridium thermocellum were identified to be specific markers for the thermophilic reactors (R3, R4). Metaproteins found in R3 indicated hydrogenothrophic methanogenesis, whereas metaproteins of acetoclastic methanogenesis were identified in R4. This suggests not only an individual evolution of microbial communities even for the case that BGPs are started at the same initial conditions under well controlled environmental conditions, but also a high compositional variance of microbiomes under

  20. Floral diversity increases beneficial arthropod richness and decreases variability in arthropod community composition.

    Science.gov (United States)

    Bennett, Ashley B; Gratton, Claudio

    2013-01-01

    Declines in species diversity resulting from anthropogenic alterations of the environment heighten the need to develop management strategies that conserve species and ecosystem services. This study examined how native plant species and their diversity influence the abundance and richness of beneficial arthropods, a functionally important group that provides ecosystem services such as pollination and natural pest suppression. Beneficial arthropods were sampled in replicated study plots containing native perennials planted in one-, two-, and seven-species mixtures. We found plant diversity had a positive impact on arthropod richness but not on arthropod abundance. An analysis of arthropod community composition revealed that each flower species attracted a different assemblage of beneficial arthropods. In addition, the full seven-species mixture also attracted a distinct arthropod community compared to single-species monocultures. Using a multivariate approach, we determined whether arthropod assemblages in two- and seven-species plots were additive and could be predicted based on assemblages from their component single-species plots. On average, assemblages in diverse plots were nonadditive when compared to assemblages predicted using single-species plots. Arthropod assemblages in two-species plots most closely resembled those of only one of the flower species in the mixture. However, the arthropod assemblages in seven-species plots, although statistically deviating from the expectation of an additive model, more closely resembled predicted communities compared to the assemblages found in two-species plots, suggesting that variability in arthropod community composition decreased as planting diversity increased. Our study demonstrates that careful selection of plants in managed landscapes can augment beneficial arthropod richness and support a more predictable arthropod community, suggesting that planning and design efforts could shape arthropod assemblages in natural

  1. Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities.

    Science.gov (United States)

    Lindh, Markus V; Figueroa, Daniela; Sjöstedt, Johanna; Baltar, Federico; Lundin, Daniel; Andersson, Agneta; Legrand, Catherine; Pinhassi, Jarone

    2015-01-01

    Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates.

  2. Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities

    Directory of Open Access Journals (Sweden)

    Markus V Lindh

    2015-04-01

    Full Text Available Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, intensifying loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2 and Bothnian Sea (salinity 3.6 water. Baltic Proper bacteria generally reached higher abundance than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating a higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating replacement. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating adjustment. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, the original triggering, or priming effect, resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment, and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial

  3. Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient

    Science.gov (United States)

    Chapman, Eric; Cadillo-Quiroz, Hinsby; Childers, Daniel L.; Turetsky, Merritt R.; Waldrop, Mark P.

    2017-01-01

    Climate change is modifying global biogeochemical cycles. Microbial communities play an integral role in soil biogeochemical cycles; knowledge about microbial composition helps provide a mechanistic understanding of these ecosystem-level phenomena. Next generation sequencing approaches were used to investigate changes in microbial functional groups during ecosystem development, in response to climate change, in northern boreal wetlands. A gradient of wetlands that developed following permafrost degradation was used to characterize changes in the soil microbial communities that mediate C cycling: a bog representing an “undisturbed” system with intact permafrost, and a younger bog and an older bog that formed following the disturbance of permafrost thaw. Reference 16S rRNA databases and several diversity indices were used to assess structural differences among these communities, to assess relationships between soil microbial community composition and various environmental variables including redox potential and pH. Rates of potential CO2 and CH4 gas production were quantified to correlate sequence data with gas flux. The abundance of organic C degraders was highest in the youngest bog, suggesting higher rates of microbial processes, including potential CH4 production. In addition, alpha diversity was also highest in the youngest bog, which seemed to be related to a more neutral pH and a lower redox potential. These results could potentially be driven by increased niche differentiation in anaerobic soils. These results suggest that ecosystem structure, which was largely driven by changes in edaphic and plant community characteristics between the “undisturbed” permafrost bog and the two bogs formed following permafrost thaw, strongly influenced microbial function.

  4. Soil biochar amendment shapes the composition of N_2O-reducing microbial communities

    International Nuclear Information System (INIS)

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H.; Kappler, Andreas; Behrens, Sebastian

    2016-01-01

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N_2O) emissions. N_2O is a potent greenhouse gas. The main sources of N_2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N_2O emission mitigation and the abundance and activity of N_2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N_2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N_2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N_2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N_2O-reducing microbial taxa. • Taxonomic shifts among N_2O-reducing microbes might explain lower N_2O emissions.

  5. Soil biochar amendment shapes the composition of N{sub 2}O-reducing microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Harter, Johannes; Weigold, Pascal [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); El-Hadidi, Mohamed; Huson, Daniel H. [Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen (Germany); Kappler, Andreas [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Behrens, Sebastian, E-mail: sbehrens@umn.edu [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Drive S.E., Minneapolis, MN 55455-0116 (United States); BioTechnology Institute, 140 Gortner Labs, 1479 Gortner Avenue, St. Paul, MN 55108-6106 (United States)

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N{sub 2}O) emissions. N{sub 2}O is a potent greenhouse gas. The main sources of N{sub 2}O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N{sub 2}O emission mitigation and the abundance and activity of N{sub 2}O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N{sub 2}O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N{sub 2}O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N{sub 2}O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N{sub 2}O-reducing microbial taxa. • Taxonomic shifts among N{sub 2}O-reducing microbes

  6. The Importance of Biotic vs. Abiotic Drivers of Local Plant Community Composition Along Regional Bioclimatic Gradients.

    Directory of Open Access Journals (Sweden)

    Kari Klanderud

    Full Text Available We assessed if the relative importance of biotic and abiotic factors for plant community composition differs along environmental gradients and between functional groups, and asked which implications this may have in a warmer and wetter future. The study location is a unique grid of sites spanning regional-scale temperature and precipitation gradients in boreal and alpine grasslands in southern Norway. Within each site we sampled vegetation and associated biotic and abiotic factors, and combined broad- and fine-scale ordination analyses to assess the relative explanatory power of these factors for species composition. Although the community responses to biotic and abiotic factors did not consistently change as predicted along the bioclimatic gradients, abiotic variables tended to explain a larger proportion of the variation in species composition towards colder sites, whereas biotic variables explained more towards warmer sites, supporting the stress gradient hypothesis. Significant interactions with precipitation suggest that biotic variables explained more towards wetter climates in the sub alpine and boreal sites, but more towards drier climates in the colder alpine. Thus, we predict that biotic interactions may become more important in alpine and boreal grasslands in a warmer future, although more winter precipitation may counteract this trend in oceanic alpine climates. Our results show that both local and regional scales analyses are needed to disentangle the local vegetation-environment relationships and their regional-scale drivers, and biotic interactions and precipitation must be included when predicting future species assemblages.

  7. Changes in ground beetle diversity and community composition in age structured forests (Coleoptera, Carabidae

    Directory of Open Access Journals (Sweden)

    Kathryn Riley

    2011-11-01

    Full Text Available We examined diversity, community composition, and wing-state of Carabidae as a function of forest age in Piedmont North Carolina. Carabidae were collected monthly from 396 pitfall traps (12×33 sites from March 2009 through February 2010, representing 5 forest age classes approximately 0, 10, 50, 85, and 150 years old. A total of 2,568 individuals, representing 30 genera and 63 species, were collected. Carabid species diversity, as estimated by six diversity indices, was significantly different between the oldest and youngest forest age classes for four of the six indices. Most carabid species were habitat generalists, occurring in all or most of the forest age classes. Carabid species composition varied across forest age classes. Seventeen carabid species were identified as potential candidates for ecological indicators of forest age. Non-metric multidimensional scaling (NMDS showed separation among forest age classes in terms of carabid beetle community composition. The proportion of individuals capable of flight decreased significantly with forest age.

  8. Subsurface Biogeochemistry of Actinides

    Energy Technology Data Exchange (ETDEWEB)

    Kersting, Annie B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Univ. Relations and Science Education; Zavarin, Mavrik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Glenn T. Seaborg Inst.

    2016-06-29

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

  9. [Composition diversity of lactic acid bacteria (LAB) community Al2 used for alfalfa silage].

    Science.gov (United States)

    Wang, Xiao-Fen; Gao, Li-Juan; Yang, Hong-Yan; Wang, Wei-Dong; Cui, Zong-Jun

    2006-10-01

    Alfalfa is the most important forage grass that is difficult to ensile for good quality. Using silage inoculants are the important way for preservation of alfalfa silage. Through continuous restricted subcultivation, a lactic acid bacteria (LAB) community Al2 was selected from well-fermented alfalfa silage. Plate isolation and Denaturing Gradient Gel Electrophoresis (DGGE), construction of 16S rDNA clone library were used to identify the composition diversity of Al2 community, with 7 strains detected, and they were all belonged to Lactobacillus. The composition ratios of the 7 strains were 55.21%, 19.79%, 14.58%, 3.13%, 3.13%, 3.13%, 1.03% according to 16S rDNA clone library. Al2-1i, Al2-2i, Al2-3i, corresponding to L. plantarum (99.9%), L. kimchii (99.4%), L. farciminis (100%) were detected by plate isolation. Among 3 isolates, Al2-1i had the highest ability of dropping pH and producing lactic acid, and the amount of lactic acid was reach to 18g/L at 24h cultivated in MRS media. The ability of dropping pH and producing lactic acid of Al2-3i was the lowest. From DGGE profiles, the dominant strains in Al2 community were L. plantarum and L. kimchii. L. plantarum was detected during the whole process, and L. kimchii was detected in the later phase.

  10. Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat.

    Science.gov (United States)

    dC Rubin, Sergio S; Marín, Irma; Gómez, Manuel J; Morales, Eduardo A; Zekker, Ivar; San Martín-Uriz, Patxi; Rodríguez, Nuria; Amils, Ricardo

    2017-09-01

    Salar de Uyuni (SdU), with a geological history that reflects 50 000 years of climate change, is the largest hypersaline salt flat on Earth and is estimated to be the biggest lithium reservoir in the world. Its salinity reaches saturation levels for NaCl, a kosmotropic salt, and high concentrations of MgCL 2 and LiCl, both salts considered important chaotrophic stressors. In addition, extreme temperatures, anoxic conditions, high UV irradiance, high albedo and extremely low concentrations of phosphorous, make SdU a unique natural extreme environment in which to contrast hypotheses about limiting factors of life diversification. Geophysical studies of brines from different sampling stations show that water activity is rather constant along SdU. Geochemical measurements show significant differences in magnesium concentration, ranging from 0.2 to 2M. This work analyses the prokaryotic diversity and community structure at four SdU sampling stations, selected according to their location and ionic composition. Prokaryotic communities were composed of both Archaea (with members of the classes Halobacteria, Thermoplasmata and Nanohaloarchaea, from the Euryarchaeota and Nanohaloarcheota phyla respectively) and Bacteria (mainly belonging to Bacteroidetes and Proteobacteria phyla). The important differences in composition of microbial communities inversely correlate with Mg 2+ concentration, suggesting that prokaryotic diversity at SdU is chaotropic dependent. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce.

    Science.gov (United States)

    Rastogi, Gurdeep; Sbodio, Adrian; Tech, Jan J; Suslow, Trevor V; Coaker, Gitta L; Leveau, Johan H J

    2012-10-01

    The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009-2010 crop cycle. Total bacterial populations averaged between 10(5) and 10(6) per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial 'core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment.

  12. Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

    Science.gov (United States)

    Rastogi, Gurdeep; Sbodio, Adrian; Tech, Jan J; Suslow, Trevor V; Coaker, Gitta L; Leveau, Johan H J

    2012-01-01

    The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009–2010 crop cycle. Total bacterial populations averaged between 105 and 106 per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial ‘core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment. PMID:22534606

  13. ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

    Science.gov (United States)

    Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

    2015-01-01

    Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

  14. Temporal Variations in the Abundance and Composition of Biofilm Communities Colonizing Drinking Water Distribution Pipes

    Science.gov (United States)

    Kelly, John J.; Minalt, Nicole; Culotti, Alessandro; Pryor, Marsha; Packman, Aaron

    2014-01-01

    Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities within the pipes were analyzed by heterotrophic plate counts and tag pyrosequencing of 16S rRNA genes, respectively. Bacterial numbers varied significantly based on sampling date and were positively correlated with water temperature and the concentration of nitrate. However, there was no significant relationship between the concentration of disinfectant in the drinking water (monochloramine) and the abundance of bacteria within the biofilms. Pyrosequencing analysis identified a total of 677 operational taxonomic units (OTUs) (3% distance) within the biofilms but indicated that community diversity was low and varied between sampling dates. Biofilms were dominated by a few taxa, specifically Methylomonas, Acinetobacter, Mycobacterium, and Xanthomonadaceae, and the dominant taxa within the biofilms varied dramatically between sampling times. The drinking water characteristics most strongly correlated with bacterial community composition were concentrations of nitrate, ammonium, total chlorine and monochloramine, as well as alkalinity and hardness. Biofilms from the sampling date with the highest nitrate concentration were the most abundant and diverse and were dominated by Acinetobacter. PMID:24858562

  15. Can differences in soil community composition after peat meadow restoration lead to different decomposition and mineralization rates?

    NARCIS (Netherlands)

    Dijk, van J.; Didden, W.A.M.; Kuenen, F.; Bodegom, van P.M.; Verhoef, H.A.; Aerts, R.

    2009-01-01

    Reducing decomposition and mineralization of organic matter by increasing groundwater levels is a common approach to reduce plant nutrient availability in many peat meadow restoration projects. The soil community is the main driver of these processes, but how community composition is affected by

  16. Response of herbaceous plant community diversity and composition to overstorey harvest within riparian management zones in Northern Hardwoods

    Science.gov (United States)

    Eric K. Zenner; Michelle A. Martin; Brian J. Palik; Jerilynn E. Peck; Charles R. Blinn

    2013-01-01

    Partial timber harvest within riparian management zones (RMZs) may permit active management of riparian forests while protecting stream ecosystems, but impacts on herbaceous communities are poorly understood. We compared herbaceous plant community abundance, diversity and composition in RMZs along small streams in northern Minnesota, USA, among four treatments before...

  17. Free-living protozoa in drinking water supplies: community composition and role as hosts for Legionella pneumophila

    NARCIS (Netherlands)

    Valster, R.M.

    2011-01-01

    Free-living protozoa in drinking water supplies: community composition and role as hosts for Legionella pneumophila


    Free-living protozoa, which feed on bacteria, play an important role in the communities of microorganisms and invertebrates in drinking water supplies and in (warm)

  18. Community composition of picoeukaryotes in the South China Sea during winter

    Science.gov (United States)

    Lin, Yun-Chi; Chiang, Kuo-Ping; Kang, Lee-Kuo

    2017-07-01

    Picoeukaryotes, the smallest protists, are highly diverse and abundant in the ocean. However, little information is available about their community composition in the tropical northwestern Pacific Ocean. This study collected surface and deep chlorophyll maximum (DCM) waters from the South China Sea (SCS) to study the picoeukaryotic composition by constructing clone libraries of the 18S rRNA gene. The libraries were dominated by the heterotrophic organisms, alveolates and Rhizaria, which accounted for 46% and 16% of total clones, respectively. MALV-I was the most abundant group in alveolates, and Rhizaria appears to be a key organism in the SCS, particularly within DCM layers. These results indicate that parasitism is significant in the oligotrophic and tropical SCS. Apart from core-dinoflagellates, chlorophytes, haptophytes, cryptophytes and pelagophytes were other important contributors to primary production in pico-sized fraction based on quantitative and qualitative data.

  19. Management of microbial community composition, architecture and performance in autotrophic nitrogen removing bioreactors through aeration regimes

    DEFF Research Database (Denmark)

    Mutlu, A. Gizem

    to describe aggregation and architectural evolution in nitritation/anammox reactors, incorporating the possible influences of intermediates formed with intermittent aeration. Community analysis revealed an abundant fraction of heterotrophic types despite the absence of organic carbon in the feed. The aerobic...... and anaerobic ammonia oxidizing guilds were dominated by fast-growing Nitrosomonas spp. and Ca. Brocadia spp., while the nitrite oxidizing guild was dominated by high affinity Nitrospira spp. Emission of nitrous oxide (N2O) was evaluated from both reactors under dynamic aeration regimes. Contrary to the widely...... impacts could be isolated, increasing process understanding. It was demonstrated that aeration strategy can be used as a powerful tool to manipulate the microbial community composition, its architecture and reactor performance. We suggest operation via intermittent aeration with short aerated periods...

  20. Impact of fishing on size composition and diversity of demersal fish communities

    DEFF Research Database (Denmark)

    Bianchi, G.; Gislason, Henrik; Graham, K.

    2000-01-01

    . but particularly in high-latitude regions, we observe a decreasing trend in the slope, reflecting changes in size composition toward a relative decline in larger fish. The results from tropical regions are less conclusive, partly owing to the difficulty in obtaining consistent data series, but probably also......By analysing data sets from different world regions we add evidence to documented changes in demersal fish community structure that may be related to fishing. Changes are analysed by community properties that might be expected to capture relevant overall changes - size spectra slopes and intercepts...... because the generally higher growth rates of the constituent species make the slope less sensitive to changes in fishing. No evidence was found of any decline in species richness, while changes in diversity (richness and evenness) were caused either by changes in patterns of dominance or by changes...

  1. Arbuscular mycorrhizal fungal community composition associated with Juniperus brevifolia in native Azorean forest

    Science.gov (United States)

    Melo, Catarina Drumonde; Luna, Sara; Krüger, Claudia; Walker, Christopher; Mendonça, Duarte; Fonseca, Henrique M. A. C.; Jaizme-Vega, Maria; da Câmara Machado, Artur

    2017-02-01

    The communities of glomeromycotan fungi (arbuscular mycorrhizal fungi, AMF) under native Juniperus brevifolia forest from two Azorean islands, Terceira and São Miguel, were compared, mainly by spore morphology, and when possible, by molecular analysis. Thirty-nine morphotypes were detected from 12 genera. Glomeromycotan fungal richness was similar in Terceira and São Miguel, but significantly different among the four fragments of native forest. Spore diversity and community composition differed significantly between the two islands. The less degraded island, Terceira, showed 10 exclusive morphotypes including more rare types, whereas the more disturbed forest on São Miguel showed 13 morphs, mostly of common types. Forests from Terceira were dominated by Acaulosporaceae and Glomeraceae. Whereas members of Acaulosporaceae, Glomeraceae and Ambisporaceae were most frequent and abundant in those from São Miguel. Spore abundance was greatest on Terceira, and correlated with soil chemical properties (pH), average monthly temperature and relative humidity.

  2. Nitrogen Deposition Reduces Decomposition Rates Through Shifts in Microbial Community Composition and Function

    Science.gov (United States)

    Waldrop, M.; Zak, D.; Sinsabaugh, R.

    2002-12-01

    Atmospheric nitrogen (N) deposition may alter soil biological activity in northern hardwood forests by repressing phenol oxidase enzyme activity and altering microbial community composition, thereby slowing decomposition and increasing the export of phenolic compounds. We tested this hypothesis by adding 13C-labelled cellobiose, vanillin, and catechol to control and N fertilized soils (30 and 80 kg ha-1) collected from three forests; two dominated by Acer Saccharum and one dominated by Quercus Alba and Quercus Velutina. While N deposition increased total microbial respiration, it decreased soil oxidative enzyme activities, resulting in slower degradation rates of all compounds, and larger DOC pools. This effect was larger in the oak forest, where fungi dominate C-cycling processes. DNA and 13C-phospolipid analyses showed that N addition altered the fungal community and reduced the activity of fungal and bacterial populations in soil, potentially explaining reduced soil enzyme activities and incomplete decomposition.

  3. Household waste compositional analysis variation from insular communities in the framework of waste prevention strategy plans

    International Nuclear Information System (INIS)

    Zorpas, Antonis A.; Lasaridi, Katia; Voukkali, Irene; Loizia, Pantelitsa; Chroni, Christina

    2015-01-01

    Highlights: • Waste framework directive has set clear waste prevention procedures. • Household Compositional analysis. • Waste management plans. • Zero waste approach. • Waste generation. - Abstract: Waste management planning requires reliable data regarding waste generation, affecting factors on waste generation and forecasts of waste quantities based on facts. In order to decrease the environmental impacts of waste management the choice of prevention plan as well as the treatment method must be based on the features of the waste that are produced in a specific area. Factors such as culture, economic development, climate, and energy sources have an impact on waste composition; composition influences the need of collecting waste more or less frequently of waste collection and disposition. The research question was to discover the main barriers concerning the compositional analysis in Insular Communities under warm climate conditions and the findings from this study enabled the main contents of a waste management plan to be established. These included advice to residents on waste minimisation, liaison with stakeholders and the expansion of kerbside recycling schemes

  4. Household waste compositional analysis variation from insular communities in the framework of waste prevention strategy plans

    Energy Technology Data Exchange (ETDEWEB)

    Zorpas, Antonis A., E-mail: antonis.zorpas@ouc.ac.cy [Cyprus Open University, Faculty of Pure and Applied Science, Environmental Conservation and Management, P.O. Box 12794, 2252 Latsia, Nicosia (Cyprus); Lasaridi, Katia, E-mail: klasaridi@hua.gr [Harokopio University, Department of Geography, 70 El. Venizelou, 176 71 Athens, Kallithea (Greece); Voukkali, Irene [Institute of Environmental Technology and Sustainable Development, ENVITECH LTD, Department of Research and Development, P.O. Box 34073, 5309 (Cyprus); Loizia, Pantelitsa, E-mail: irenevoukkali@envitech.org [Institute of Environmental Technology and Sustainable Development, ENVITECH LTD, Department of Research and Development, P.O. Box 34073, 5309 (Cyprus); Chroni, Christina [Harokopio University, Department of Geography, 70 El. Venizelou, 176 71 Athens, Kallithea (Greece)

    2015-04-15

    Highlights: • Waste framework directive has set clear waste prevention procedures. • Household Compositional analysis. • Waste management plans. • Zero waste approach. • Waste generation. - Abstract: Waste management planning requires reliable data regarding waste generation, affecting factors on waste generation and forecasts of waste quantities based on facts. In order to decrease the environmental impacts of waste management the choice of prevention plan as well as the treatment method must be based on the features of the waste that are produced in a specific area. Factors such as culture, economic development, climate, and energy sources have an impact on waste composition; composition influences the need of collecting waste more or less frequently of waste collection and disposition. The research question was to discover the main barriers concerning the compositional analysis in Insular Communities under warm climate conditions and the findings from this study enabled the main contents of a waste management plan to be established. These included advice to residents on waste minimisation, liaison with stakeholders and the expansion of kerbside recycling schemes.

  5. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism

    DEFF Research Database (Denmark)

    Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone

    2017-01-01

    . In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic...... efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane....

  6. Trait-specific responses of wild bee communities to landscape composition, configuration and local factors.

    Directory of Open Access Journals (Sweden)

    Sebastian Hopfenmüller

    Full Text Available Land-use intensification and loss of semi-natural habitats have induced a severe decline of bee diversity in agricultural landscapes. Semi-natural habitats like calcareous grasslands are among the most important bee habitats in central Europe, but they are threatened by decreasing habitat area and quality, and by homogenization of the surrounding landscape affecting both landscape composition and configuration. In this study we tested the importance of habitat area, quality and connectivity as well as landscape composition and configuration on wild bees in calcareous grasslands. We made detailed trait-specific analyses as bees with different traits might differ in their response to the tested factors. Species richness and abundance of wild bees were surveyed on 23 calcareous grassland patches in Southern Germany with independent gradients in local and landscape factors. Total wild bee richness was positively affected by complex landscape configuration, large habitat area and high habitat quality (i.e. steep slopes. Cuckoo bee richness was positively affected by complex landscape configuration and large habitat area whereas habitat specialists were only affected by the local factors habitat area and habitat quality. Small social generalists were positively influenced by habitat area whereas large social generalists (bumblebees were positively affected by landscape composition (high percentage of semi-natural habitats. Our results emphasize a strong dependence of habitat specialists on local habitat characteristics, whereas cuckoo bees and bumblebees are more likely affected by the surrounding landscape. We conclude that a combination of large high-quality patches and heterogeneous landscapes maintains high bee species richness and communities with diverse trait composition. Such diverse communities might stabilize pollination services provided to crops and wild plants on local and landscape scales.

  7. Trait-specific responses of wild bee communities to landscape composition, configuration and local factors.

    Science.gov (United States)

    Hopfenmüller, Sebastian; Steffan-Dewenter, Ingolf; Holzschuh, Andrea

    2014-01-01

    Land-use intensification and loss of semi-natural habitats have induced a severe decline of bee diversity in agricultural landscapes. Semi-natural habitats like calcareous grasslands are among the most important bee habitats in central Europe, but they are threatened by decreasing habitat area and quality, and by homogenization of the surrounding landscape affecting both landscape composition and configuration. In this study we tested the importance of habitat area, quality and connectivity as well as landscape composition and configuration on wild bees in calcareous grasslands. We made detailed trait-specific analyses as bees with different traits might differ in their response to the tested factors. Species richness and abundance of wild bees were surveyed on 23 calcareous grassland patches in Southern Germany with independent gradients in local and landscape factors. Total wild bee richness was positively affected by complex landscape configuration, large habitat area and high habitat quality (i.e. steep slopes). Cuckoo bee richness was positively affected by complex landscape configuration and large habitat area whereas habitat specialists were only affected by the local factors habitat area and habitat quality. Small social generalists were positively influenced by habitat area whereas large social generalists (bumblebees) were positively affected by landscape composition (high percentage of semi-natural habitats). Our results emphasize a strong dependence of habitat specialists on local habitat characteristics, whereas cuckoo bees and bumblebees are more likely affected by the surrounding landscape. We conclude that a combination of large high-quality patches and heterogeneous landscapes maintains high bee species richness and communities with diverse trait composition. Such diverse communities might stabilize pollination services provided to crops and wild plants on local and landscape scales.

  8. Shift in the microbial community composition of surface water and sediment along an urban river.

    Science.gov (United States)

    Wang, Lan; Zhang, Jing; Li, Huilin; Yang, Hong; Peng, Chao; Peng, Zhengsong; Lu, Lu

    2018-06-15

    Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve

    Directory of Open Access Journals (Sweden)

    Min Liu

    2017-12-01

    Full Text Available Invasion by exotic plant species can alter ecosystem function and reduce native plant diversity, but relatively little is known about their effects on belowground microbial communities. Here we investigated the effects of exotic cordgrass (Spartina alterniflora invasion on the distribution of soil bacterial communities in a mangrove nature reserve of the Jiulong River Estuary, southeast China using high-throughput sequencing of 16S rRNA gene and multivariate statistical analysis. Our results showed that S. alterniflora invasion altered soil properties, and significantly increased soil bacterial taxa richness, primarily by stimulating an increase in conditionally rare or rare taxa, and changes in community composition and function. Abundant, conditionally rare and rare subcommunities exhibited similar response patterns to environment changes, with both conditionally rare and rare taxa showing a stronger response than abundant ones. Habitat generalists were detected among abundant, conditionally rare and rare taxa, whereas habitat specialists were only identified among conditionally rare taxa and rare taxa. In addition, we found that vegetation was the key factor driving these patterns. However, our comparative analysis indicated that both environmental selection, and neutral process, significantly contributed to soil bacterial community assembly. These results could improve the understanding of the microbial processes and mechanisms of cordgrass invasion, and offer empirical data of use in the restoration and management of the mangrove wetlands.

  10. Agricultural Land Use Determines the Trait Composition of Ground Beetle Communities.

    Science.gov (United States)

    Hanson, Helena I; Palmu, Erkki; Birkhofer, Klaus; Smith, Henrik G; Hedlund, Katarina

    2016-01-01

    In order to improve biological control of agricultural pests, it is fundamental to understand which factors influence the composition of natural enemies in agricultural landscapes. In this study, we aimed to understand how agricultural land use affects a number of different traits in ground beetle communities to better predict potential consequences of land-use change for ecosystem functioning. We studied ground beetles in fields with different agricultural land use ranging from frequently managed sugar beet fields, winter wheat fields to less intensively managed grasslands. The ground beetles were collected in emergence tents that catch individuals overwintering locally in different life stages and with pitfall traps that catch individuals that could have a local origin or may have dispersed into the field. Community weighted mean values for ground beetle traits such as body size, flight ability and feeding preference were estimated for each land-use type and sampling method. In fields with high land-use intensity the average body length of emerging ground beetle communities was lower than in the grasslands while the average body length of actively moving communities did not differ between the land-use types. The proportion of ground beetles with good flight ability or a carnivorous diet was higher in the crop fields as compared to the grasslands. Our study highlights that increasing management intensity reduces the average body size of emerging ground beetles and the proportion of mixed feeders. Our results also suggest that the dispersal ability of ground beetles enables them to compensate for local management intensities.

  11. Impact of copper on the diazotroph abundance and community composition during swine manure composting.

    Science.gov (United States)

    Yin, Yanan; Gu, Jie; Wang, Xiaojuan; Zhang, Kaiyu; Hu, Ting; Ma, Jiyue; Wang, Qianzhi

    2018-05-01

    Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg -1 ) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women

    Science.gov (United States)

    Brotman, Rebecca M.; Bradford, L. Latey; Conrad, Melissa; Gajer, Pawel; Ault, Kevin; Peralta, Ligia; Forney, Larry J.; Carlton, Jane M.; Abdo, Zaid; Ravel, Jacques

    2012-01-01

    Objectives Some vaginal bacterial communities are thought to prevent infection by sexually transmitted organisms. Prior work demonstrated that the vaginal microbiota of reproductive-age women cluster into five types of bacterial communities; 4 dominated by Lactobacillus species (L. iners, L. crispatus, L. gasseri, L. jensenii), and one (termed community state type (CST) IV) lacking significant numbers of lactobacilli and characterized by higher proportions of Atopobium, Prevotella, Parvimonas, Sneathia, Gardnerella, Mobiluncus, and other taxa. We sought to evaluate the relationship between vaginal bacterial composition and Trichomonas vaginalis. Methods Self-collected vaginal swabs were obtained cross-sectionally from 394 women equally representing four ethnic/racial groups. T. vaginalis screening was performed using PCR targeting the 18S rRNA and β-tubulin genes. Vaginal bacterial composition was characterized by pyrosequencing of barcoded 16S rRNA genes. A panel of eleven microsatellite markers was used to genotype T. vaginalis. The association between vaginal microbiota and T. vaginalis was evaluated by exact logistic regression. Results T. vaginalis was detected in 2.8% of participants (11/394). Of the eleven T. vaginalis-positive cases, eight (72%) were categorized as CST-IV, two (18%) as communities dominated by L. iners and one (9%) as L. crispatus-dominated (p-value:0.05). CST-IV microbiota were associated with an 8-fold increased odds of detecting T. vaginalis compared to women in the L. crispatus-dominated state (OR:8.26, 95% CI:1.07–372.65). Seven of the 11 T. vaginalis isolates were assigned to two genotypes. Conclusion T. vaginalis was associated with vaginal microbiota consisting of low proportions of lactobacilli and high proportions of Mycoplasma, Parvimonas, Sneathia, and other anaerobes. PMID:23007708

  13. Discontinuity in the responses of ecosystem processes and multifunctionality to altered soil community composition.

    Science.gov (United States)

    Bradford, Mark A; Wood, Stephen A; Bardgett, Richard D; Black, Helaina I J; Bonkowski, Michael; Eggers, Till; Grayston, Susan J; Kandeler, Ellen; Manning, Peter; Setälä, Heikki; Jones, T Hefin

    2014-10-07

    Ecosystem management policies increasingly emphasize provision of multiple, as opposed to single, ecosystem services. Management for such "multifunctionality" has stimulated research into the role that biodiversity plays in providing desired rates of multiple ecosystem processes. Positive effects of biodiversity on indices of multifunctionality are consistently found, primarily because species that are redundant for one ecosystem process under a given set of environmental conditions play a distinct role under different conditions or in the provision of another ecosystem process. Here we show that the positive effects of diversity (specifically community composition) on multifunctionality indices can also arise from a statistical fallacy analogous to Simpson's paradox (where aggregating data obscures causal relationships). We manipulated soil faunal community composition in combination with nitrogen fertilization of model grassland ecosystems and repeatedly measured five ecosystem processes related to plant productivity, carbon storage, and nutrient turnover. We calculated three common multifunctionality indices based on these processes and found that the functional complexity of the soil communities had a consistent positive effect on the indices. However, only two of the five ecosystem processes also responded positively to increasing complexity, whereas the other three responded neutrally or negatively. Furthermore, none of the individual processes responded to both the complexity and the nitrogen manipulations in a manner consistent with the indices. Our data show that multifunctionality indices can obscure relationships that exist between communities and key ecosystem processes, leading us to question their use in advancing theoretical understanding--and in management decisions--about how biodiversity is related to the provision of multiple ecosystem services.

  14. Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

    Directory of Open Access Journals (Sweden)

    Nicolas Chemidlin Prévost-Bouré

    Full Text Available Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2: i to examine their spatial structuring; ii to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescommunities' composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at

  15. Legacy effects of no-analogue disturbances alter plant community diversity and composition in semi-arid sagebrush steppe

    Science.gov (United States)

    Ripplinger, Julie; Franklin, Janet; Edwards, Thomas C.

    2015-01-01

    Questions(i) What role does the type of managed disturbance play in structuring sagebrush steppe plant communities? (ii) How does the composition of post-disturbance plant communities change with time since disturbance? (iii) Does plant community diversity change over time following managed disturbance?LocationField study within the sagebrush steppe ecosystem. Rich County, Utah, USA.MethodsWe developed a chronosequence spanning up to 50 yrs post-treatment to study sagebrush steppe vegetation dynamics. Direct ordination was used to examine plant community composition by managed disturbance type and time since disturbance, and factorial analysis of covariance was used to examine diversity dynamics following disturbance. Indicator species values were calculated in order to identify characteristic species for each disturbance type.ResultsPlant communities experienced a shift toward distinct community composition for each of the three managed disturbance types, and gave no indication of returning to untreated community composition or diversity. Small post-disturbance increases in the number of non-native grass species were observed in the treatments relative to reference, with native forb species making the largest contribution to altered composition. On fire- and chemically-treated sites the proportional native forb species richness increased over time since disturbance, while the proportional contribution of non-native forbs to total species richness decreased. For all three treatment types, native grasses contributed less on average to total richness than on reference sites, while non-native grasses made up a higher proportion of total richness.ConclusionsCommon shrubland management techniques have legacy effects on the composition and diversity of sagebrush steppe plant communities, and no-analogue disturbances, such as chemical or mechanical treatments, have more pronounced legacy effects than treatments similar to natural disturbance regimes (fire). This study

  16. Introduction: energy and the subsurface

    Science.gov (United States)

    Viswanathan, Hari S.

    2016-01-01

    This theme issue covers topics at the forefront of scientific research on energy and the subsurface, ranging from carbon dioxide (CO2) sequestration to the recovery of unconventional shale oil and gas resources through hydraulic fracturing. As such, the goal of this theme issue is to have an impact on the scientific community, broadly, by providing a self-contained collection of articles contributing to and reviewing the state-of-the-art of the field. This collection of articles could be used, for example, to set the next generation of research directions, while also being useful as a self-study guide for those interested in entering the field. Review articles are included on the topics of hydraulic fracturing as a multiscale problem, numerical modelling of hydraulic fracture propagation, the role of computational sciences in the upstream oil and gas industry and chemohydrodynamic patterns in porous media. Complementing the reviews is a set of original research papers covering growth models for branched hydraulic crack systems, fluid-driven crack propagation in elastic matrices, elastic and inelastic deformation of fluid-saturated rock, reaction front propagation in fracture matrices, the effects of rock mineralogy and pore structure on stress-dependent permeability of shales, topographic viscous fingering and plume dynamics in porous media convection. This article is part of the themed issue ‘Energy and the subsurface’. PMID:27597784

  17. Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

    Science.gov (United States)

    He, Shaomei; Malfatti, Stephanie A; McFarland, Jack W; Anderson, Frank E; Pati, Amrita; Huntemann, Marcel; Tremblay, Julien; Glavina del Rio, Tijana; Waldrop, Mark P; Windham-Myers, Lisamarie; Tringe, Susannah G

    2015-05-19

    Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities

  18. New steady-state microbial community compositions and process performances in biogas reactors induced by temperature disturbances

    DEFF Research Database (Denmark)

    Luo, Gang; De Francisci, Davide; Kougias, Panagiotis

    2015-01-01

    that stochastic factors had a minor role in shaping the profile of the microbial community composition and activity in biogas reactors. On the contrary, temperature disturbance was found to play an important role in the microbial community composition as well as process performance for biogas reactors. Although...... three different temperature disturbances were applied to each biogas reactor, the increased methane yields (around 10% higher) and decreased volatile fatty acids (VFAs) concentrations at steady state were found in all three reactors after the temperature disturbances. After the temperature disturbance...... in shaping the profile of the microbial community composition and activity in biogas reactors. New steady-state microbial community profiles and reactor performances were observed in all the biogas reactors after the temperature disturbance....

  19. Subsurface Ventilation System Description Document

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Subsurface Ventilation System Description Document

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  1. Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain.

    Science.gov (United States)

    Kumar, Arvind; Rai, Lal Chand

    2017-07-01

    Soil quality is an important factor and maintained by inhabited microorganisms. Soil physicochemical characteristics determine indigenous microbial population and rice provides food security to major population of the world. Therefore, this study aimed to assess the impact of physicochemical variables on bacterial community composition and diversity in conventional paddy fields which could reflect a real picture of the bacterial communities operating in the paddy agro-ecosystem. To fulfill the objective; soil physicochemical characterization, bacterial community composition and diversity analysis was carried out using culture-independent PCR-DGGE method from twenty soils distributed across eight districts. Bacterial communities were grouped into three clusters based on UPGMA cluster analysis of DGGE banding pattern. The linkage of measured physicochemical variables with bacterial community composition was analyzed by canonical correspondence analysis (CCA). CCA ordination biplot results were similar to UPGMA cluster analysis. High levels of species-environment correlations (0.989 and 0.959) were observed and the largest proportion of species data variability was explained by total organic carbon (TOC), available nitrogen, total nitrogen and pH. Thus, results suggest that TOC and nitrogen are key regulators of bacterial community composition in the conventional paddy fields. Further, high diversity indices and evenness values demonstrated heterogeneity and co-abundance of the bacterial communities.

  2. Biofilm scrubbing for restoration—algae community composition and succession in artificial streams

    Directory of Open Access Journals (Sweden)

    Magdalena Mayr

    2016-09-01

    Full Text Available Photoautotrophic biofilms play a pivotal role in self-purification of rivers. We took advantage of the biofilm’s cleaning capacity by applying artificial stream mesocosms, called algae turf scrubberTM (ATS, to reduce the nutrient load of a highly eutrophicated backwater in Vienna (Austria. Since purification strongly depends on benthic algae on the ATS, we focused on the algae community composition and succession. Estimation of coverage, photographic documentation for micromapping, species identification and pigment analyses were carried out. Already one week after exposition, 20–30 different taxa were recorded, suggesting a rapid colonization of the substrate. In total around 200 taxa were identified, mainly belonging to Chlorophyta, Bacillariophyceae and Cyanoprokaryota. Nonmetric multidimensional scaling implied that season and succession strongly influenced species composition on the ATS and a minimum turnover of 0.28 indicates a development towards a more stable community at the end of experiments. We measured maximum biomass production of ~250 g m−2 in June and August and during a period of 5 months nearly 19 kg ha−1 phosphorus could be removed. ATS systems proved to retain nutrients and produce algae biomass in an environmentally friendly and cost effective way and thus support restoration of highly eutrophicated water bodies.

  3. The Effects of Different Forest Loggings on Forest Birds Community Composition in Shastkolateh Forest, Gorgan

    Directory of Open Access Journals (Sweden)

    F. Parsaei

    2014-06-01

    Full Text Available The species composition of a bird community is dependent upon many factors. Within any geographic area, vegetation structure may be the most important factor. The changes of bird community composition based on foraging behavior in relation to 3 different harvesting systems, including strip cutting, group selection logging, and single tree selection logging, was evaluated in a virgin area in this study. Birds and environmental variables were detected within 103 circle sampling plots with 25m radius. Based on the results, 4 groups of birds were observed in treatments based on the foraging behavior. Group 1 was ground foragers, group 2 consisted of foliage gleaning, group 3 included flycatchers, and group 4 represented bark foraging. The first group had the highest abundance in the strip treatment. The second group in group selection treatment, and the third and fourth groups had the highest abundance in the virgin area and then, in single tree selection treatment. The first group showed the highest correlation with shrub and herb or grass layer, stone cover and the number of trees 10-20m in height. The second, third and fourth groups showed the highest correlation with the number of trees>20m in height, basal areas, dead trees number, and the number of fagus trees. The results showed the single cutting treatment had a relatively minor effect on mature forest bird species and were more appropriate and sustainable methods to reduce the negative effects of forest harvesting on the birds.

  4. Alterations in soil microbial community composition and biomass following agricultural land use change.

    Science.gov (United States)

    Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

    2016-11-04

    The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

  5. Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments.

    Science.gov (United States)

    Zhao, Dayong; He, Xiaowei; Huang, Rui; Yan, Wenming; Yu, Zhongbo

    2017-07-01

    Ammonia oxidation is a crucial process in global nitrogen cycling, which is catalyzed by the ammonia oxidizers. Emergent plants play important roles in the freshwater ecosystem. Therefore, it is meaningful to investigate the effects of emergent macrophytes on the abundance and community composition of ammonia oxidizers. In the present study, two commonly found emergent macrophytes (Zizania caduciflora and Phragmitas communis) were obtained from freshwater lakes and the abundance and community composition of the ammonia-oxidizing prokaryotes in the rhizosphere sediments of these emergent macrophytes were investigated. The abundance of the bacterial amoA gene was higher in the rhizosphere sediments of the emergent macrophytes than those of bulk sediments. Significant positive correlation was found between the potential nitrification rates (PNRs) and the abundance of bacterial amoA gene, suggesting that ammonia-oxidizing bacteria (AOB) might play an important role in the nitrification process of the rhizosphere sediments of emergent macrophytes. The Nitrosotalea cluster is the dominant ammonia-oxidizing archaea (AOA) group in all the sediment samples. Analysis of AOB group showed that the N. europaeal cluster dominated the rhizosphere sediments of Z. caduciflora and the bulk sediments, whereas the Nitrosospira cluster was the dominant AOB group in the rhizosphere sediments of P. communis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Macrophyte Species Drive the Variation of Bacterioplankton Community Composition in a Shallow Freshwater Lake

    Science.gov (United States)

    Zeng, Jin; Bian, Yuanqi; Xing, Peng

    2012-01-01

    Macrophytes play an important role in structuring aquatic ecosystems. In this study, we explored whether macrophyte species are involved in determining the bacterioplankton community composition (BCC) in shallow freshwater lakes. The BCC in field areas dominated by different macrophyte species in Taihu Lake, a large, shallow freshwater lake, was investigated over a 1-year period. Subsequently, microcosm experiments were conducted to determine if single species of different types of macrophytes in an isolated environment would alter the BCC. Denaturing gradient gel electrophoresis (DGGE), followed by cloning and sequence analysis of selected samples, was employed to analyze the BCC. The DGGE results of the field investigations indicated that the BCC changed significantly from season to season and that the presence of different macrophyte species resulted in lower BCC similarities in the summer and fall. LIBSHUFF analysis of selected clone libraries from the summer demonstrated different BCCs in the water column surrounding different macrophytes. Relative to the field observations, the microcosm studies indicated that the BCC differed more pronouncedly when associated with different species of macrophytes, which was also supported by LIBSHUFF analysis of the selected clone libraries. Overall, this study suggested that macrophyte species might be an important factor in determining the composition of bacterial communities in this shallow freshwater lake and that the species-specific influence of macrophytes on BCC is variable with the season and distance. PMID:22038598

  7. Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

    Science.gov (United States)

    Bacci, Giovanni; Ceccherini, Maria Teresa; Bani, Alessia; Bazzicalupo, Marco; Castaldini, Maurizio; Galardini, Marco; Giovannetti, Luciana; Mocali, Stefano; Pastorelli, Roberta; Pantani, Ottorino Luca; Arfaioli, Paola; Pietramellara, Giacomo; Viti, Carlo; Nannipieri, Paolo; Mengoni, Alessio

    2015-03-01

    We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

  8. Effect evaluation of uranium mining effluents on the density and composition of the phytoplankton community

    International Nuclear Information System (INIS)

    Roque, Claudio V.; Azevedo, Heliana de; Bruschi, Armando L.; Ferrari, Carla R.; Ronqui, Leilane B.; Campos, Michelle B.; Nascimento, Marcos Roberto L.; Rodgher, Suzelei

    2011-01-01

    Located in the region of the Pocos de Caldas Plateau, the Osamu Utsumi mine is the first uranium extraction and production mine to have its deposits explored in Brazil and it is situated on the premises of the Brazilian Nuclear Industries Ore Treatment Unit (UTM/INB). Within the UTM/INB installations, water samplings were carried out every three months (from October 2008 to July 2009) in three points (P1, P2 and P3): P1 (pit mine), P2 (Tailings Management Facility/TMF) and P3 (environment). The objective of the current study was to evaluate density and composition of the phytoplankton community, as well as chemical characteristics of water samples from UTM/INB effluents, which present different pH levels (ranging from acidic to alkaline). In the current study, values of pH, total nitrogen, total phosphorus, silicate, sulfate (SO 4 -2 ), fluoride, uranium, thorium and chlorophyll a were determined, as well as composition and density of the phytoplankton community. After comparing the three sampling points, it was verified that Cyanophyceae presented greater tolerance to chemical conditions of the water such as elevated concentrations of sulfate, fluoride, uranium and thorium, as well as pH variations, since this class was detected in all studied environments. (author)

  9. Fish Community Composition and Habitat Use in the Eg-Uur River System, Mongolia

    Directory of Open Access Journals (Sweden)

    Norman Mercado-Silva

    2008-06-01

    Full Text Available Mongolian rivers and their fi sh communities have suffered severe impacts from anthropogenic activities. However, the remoteness of some systems has allowed for the conservation of unique fi sh faunas, including robust populations of Hucho taimen . Conservation of H. taimen requires understanding the composition and ecology of other fi shes in the community. Using multiple sampling techniques, direct observation, and existing literature, we assessed the composition, relative abundance, and ecological attributes of fi shes in the Eg-Uur watershed (Selenge basin. We collected 6 of 12 species known in the watershed. Phoxinus cf. phoxinus and Lota lota were the most and least abundant species, respectively. We failed to detect H. taimen , indicating low abundance or unknown habitat requirements for juveniles. We compared the effectiveness of different sampling techniques (with electro fi shing producing the highest species richness, constructed length-weight relationships for four species , and identi fi ed ecological attributes (i.e., trophic guild, preferred habitat for resident fi shes.

  10. Diet compositions and trophic guild structure of the eastern Chukchi Sea demersal fish community

    Science.gov (United States)

    Whitehouse, George A.; Buckley, Troy W.; Danielson, Seth L.

    2017-01-01

    Fishes are an important link in Arctic marine food webs, connecting production of lower trophic levels to apex predators. We analyzed 1773 stomach samples from 39 fish species collected during a bottom trawl survey of the eastern Chukchi Sea in the summer of 2012. We used hierarchical cluster analysis of diet dissimilarities on 21 of the most well sampled species to identify four distinct trophic guilds: gammarid amphipod consumers, benthic invertebrate generalists, fish and shrimp consumers, and zooplankton consumers. The trophic guilds reflect dominant prey types in predator diets. We used constrained analysis of principal coordinates (CAP) to determine if variation within the composite guild diets could be explained by a suite of non-diet variables. All CAP models explained a significant proportion of the variance in the diet matrices, ranging from 7% to 25% of the total variation. Explanatory variables tested included latitude, longitude, predator length, depth, and water mass. These results indicate a trophic guild structure is present amongst the demersal fish community during summer in the eastern Chukchi Sea. Regular monitoring of the food habits of the demersal fish community will be required to improve our understanding of the spatial, temporal, and interannual variation in diet composition, and to improve our ability to identify and predict the impacts of climate change and commercial development on the structure and functioning of the Chukchi Sea ecosystem.

  11. Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

    Science.gov (United States)

    Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P A; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

    2014-01-01

    Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescommunities' composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to 120 km radius) and/or medium (40 to 65 km radius) spatial scales, suggesting dispersal limitations at these scales.

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

    International Nuclear Information System (INIS)

    Baldwin, Brett R.; Peacock, Aaron D.; Gan, M.; Resch, Charles T.; Arntzen, Evan V.; Smithgall, A.N.; Pfiffner, S.; Freifeld, Barry M.; White, D.C.; Long, Philip E.

    2009-01-01

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

  13. Importance of earthworm-seed interactions for the composition and structure of plant communities: A review

    Science.gov (United States)

    Forey, Estelle; Barot, Sébastien; Decaëns, Thibaud; Langlois, Estelle; Laossi, Kam-Rigne; Margerie, Pierre; Scheu, Stefan; Eisenhauer, Nico

    2011-11-01

    Soil seed bank composition and dynamics are crucial elements for the understanding of plant population and community ecology. Earthworms are increasingly recognized as important dispersers and predators of seeds. Through direct and indirect effects they influence either positively or negatively the establishment and survival of seeds and seedlings. Seedling establishment is affected by a variety of earthworm-mediated mechanisms, such as selective seed ingestion and digestion, acceleration or deceleration of germination, and seed transport. Earthworm casts deposited on the soil surface and the entrance of earthworm burrows often contain viable seeds and constitute important regeneration niches for plant seedlings and therefore likely favour specific seed traits. However, the role of earthworms as seed dispersers, mediators of seed bank dynamics and seed predators has not been considered in concert. The overall effect of earthworms on plant communities remains little understood. Most knowledge is based on laboratory studies on temperate species and future work has to explore the biological significance of earthworm-seed interactions under more natural conditions. In this review we summarize the current knowledge on earthworm-seed interactions and discuss factors determining these interactions. We highlight that this interaction may be an underappreciated, yet major driving force for the dynamics of soil seed banks and plant communities which most likely have experienced co-evolutionary processes. Despite the experimental bias, we hypothesize that the knowledge gathered in the present review is of crucial relevance for restoration and conservation ecology. For instance, as earthworms emerge as successful and ubiquitous invaders in various ecosystems, the summarized information might serve as a basis for realistic estimations and modelling of consequences on native plant communities. We depict promising directions of future research and point to the need to consider

  14. Non-Random Variability in Functional Composition of Coral Reef Fish Communities along an Environmental Gradient.

    Science.gov (United States)

    Plass-Johnson, Jeremiah G; Taylor, Marc H; Husain, Aidah A A; Teichberg, Mirta C; Ferse, Sebastian C A

    2016-01-01

    degradation of coral reefs is associated with increased variability in fish community functional composition resulting from selective impacts on specific traits, thereby affecting the functional response of these communities to increasing perturbations.

  15. Effect of investigator disturbance in experimental forensic entomology: succession and community composition.

    Science.gov (United States)

    De Jong, G D; Hoback, W W

    2006-06-01

    Carrion insect succession studies have historically used repeated sampling of single or a few carcasses to produce data, either weighing the carcasses, removing a qualitative subsample of the fauna present, or both, on every visit over the course of decomposition and succession. This study, conducted in a set of related experimental hypotheses with two trials in a single season, investigated the effect that repeated sampling has on insect succession, determined by the number of taxa collected on each visit and by community composition. Each trial lasted at least 21 days, with daily visits on the first 14 days. Rat carcasses used in this study were all placed in the field on the same day, but then either sampled qualitatively on every visit (similar to most succession studies) or ignored until a given day of succession, when they were sampled qualitatively (a subsample) and then destructively sampled in their entirety. Carcasses sampled on every visit were in two groups: those from which only a sample of the fauna was taken and those from which a sample of fauna was taken and the carcass was weighed for biomass determination. Of the carcasses visited only once, the number of taxa in subsamples was compared to the actual number of taxa present when the carcass was destructively sampled to determine if the subsamples adequately represented the total carcass fauna. Data from the qualitative subsamples of those carcasses visited only once were also compared to data collected from carcasses that were sampled on every visit to investigate the effect of the repeated sampling. A total of 39 taxa were collected from carcasses during the study and the component taxa are discussed individually in relation to their role in succession. Number of taxa differed on only one visit between the qualitative subsamples and the actual number of taxa present, primarily because the organisms missed by the qualitative sampling were cryptic (hidden deep within body cavities) or rare (only

  16. Determination of strontium isotopic composition in natural waters: examples of application in subsurface waters of the coastal zone of Bragantina region, Para, BR; Determinacao da composicao isotopica de estroncio em aguas naturais: exemplos de sua aplicacao em aguas subsuperficiais da zona costeira na regiao Bragantina-PA

    Energy Technology Data Exchange (ETDEWEB)

    Bordalo, Adriana Oliveira; Moura, Candido Augusto Veloso; Scheller, Thomas [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Centro de Geociencias]. E-mail: adriana@ufpa.br

    2007-07-15

    Analytical procedures used for determining the concentrations and isotope composition of strontium in subsurface waters, by mass spectrometry, are described. Sampling was performed in coastal plateaus, salt marsh and mangrove environments in the coastal region of Para. Coastal plateau waters have {delta}{sup 87}Sr between 1.51 and 6.26 per mille and Sr concentration bellow 58 ppb. Salt marsh waters show {delta}{sup 87}Sr between 0.55 and 0.90 per mille and Sr concentration between 93 and 114 ppm, while mangrove waters have {delta}{sup 87}Sr per mille around zero and Sr concentration above 15 ppm. Differences in the {sup 87}Sr/{sup 86}Sr ratio in these subsurface waters are detected, as well as seasonal variations in the coastal plateau waters. (author)

  17. The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale.

    Science.gov (United States)

    Hazard, Christina; Gosling, Paul; van der Gast, Christopher J; Mitchell, Derek T; Doohan, Fiona M; Bending, Gary D

    2013-03-01

    Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis ('everything is everywhere, but, the environment selects') was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.

  18. Structure and Composition of Leachfield Bacterial Communities: Role of Soil Texture, Depth and Septic Tank Effluent Inputs

    Directory of Open Access Journals (Sweden)

    Janet A. Atoyan

    2012-09-01

    Full Text Available Although groundwater quality depends on microbial processes in the soil treatment area (STA of onsite wastewater treatment systems (OWTS, our understanding of the development of these microbial communities is limited. We examined the bacterial communities of sand, sandy loam, and clay STAs at different depths in response to septic tank effluent (STE addition using mesocosms. Terminal restriction fragment length polymorphism (TRFLP analysis was used to compare the bacterial community structure and composition of STE, native soil prior to STE addition (UNX and soil exposed to STE (EXP. Principal component analysis separated communities with depth in sand but not in sandy loam or clay. Indices of richness, diversity, and evenness followed the order: sandy loam > sand > clay. Analysis of TRF peaks indicated that STE contributed least to the composition of STA bacterial communities (5%–16%, followed by UNX soil (18%–48%, with the highest proportion of the community made up of TRFs not detected previously in either UNX or STE (50%–82% for all three soils. Soil type and depth can have a marked effect on the structure and composition of STA bacterial communities, and on the relative contribution of native soil and STE to these communities.

  19. Effect of ocean acidification on the fatty acid composition of a natural plankton community

    Directory of Open Access Journals (Sweden)

    E. Leu

    2013-02-01

    Full Text Available The effect of ocean acidification on the fatty acid composition of a natural plankton community in the Arctic was studied in a large-scale mesocosm experiment, carried out in Kongsfjorden (Svalbard, Norway at 79° N. Nine mesocosms of ~50 m3 each were exposed to 8 different pCO2 levels (from natural background conditions to ~1420 μatm, yielding pH values (on the total scale from ~8.3 to 7.5. Inorganic nutrients were added on day 13. The phytoplankton development during this 30-day experiment passed three distinct phases: (1 prior to the addition of inorganic nutrients, (2 first bloom after nutrient addition, and (3 second bloom after nutrient addition. The fatty acid composition of the natural plankton community was analysed and showed, in general, high percentages of polyunsaturated fatty acids (PUFAs: 44–60% of total fatty acids. Positive correlations with pCO2 were found for most PUFAs during phases 2 and/or 3, with the exception of 20:5n3 (eicosapentaenoic acid, EPA, an important diatom marker. These correlations are probably linked to changes in taxonomic composition in response to pCO2. While diatoms (together with prasinophytes and haptophytes increased during phase 3 mainly in the low and intermediate pCO2 treatments, dinoflagellates were favoured by high CO2 concentrations during the same time period. This is reflected in the development of group-specific fatty acid trophic markers. No indications were found for a generally detrimental effect of ocean acidification on the planktonic food quality in terms of essential fatty acids.

  20. Effect of ocean acidification on the fatty acid composition of a natural plankton community

    Science.gov (United States)

    Leu, E.; Daase, M.; Schulz, K. G.; Stuhr, A.; Riebesell, U.

    2013-02-01

    The effect of ocean acidification on the fatty acid composition of a natural plankton community in the Arctic was studied in a large-scale mesocosm experiment, carried out in Kongsfjorden (Svalbard, Norway) at 79° N. Nine mesocosms of ~50 m3 each were exposed to 8 different pCO2 levels (from natural background conditions to ~1420 μatm), yielding pH values (on the total scale) from ~8.3 to 7.5. Inorganic nutrients were added on day 13. The phytoplankton development during this 30-day experiment passed three distinct phases: (1) prior to the addition of inorganic nutrients, (2) first bloom after nutrient addition, and (3) second bloom after nutrient addition. The fatty acid composition of the natural plankton community was analysed and showed, in general, high percentages of polyunsaturated fatty acids (PUFAs): 44-60% of total fatty acids. Positive correlations with pCO2 were found for most PUFAs during phases 2 and/or 3, with the exception of 20:5n3 (eicosapentaenoic acid, EPA), an important diatom marker. These correlations are probably linked to changes in taxonomic composition in response to pCO2. While diatoms (together with prasinophytes and haptophytes) increased during phase 3 mainly in the low and intermediate pCO2 treatments, dinoflagellates were favoured by high CO2 concentrations during the same time period. This is reflected in the development of group-specific fatty acid trophic markers. No indications were found for a generally detrimental effect of ocean acidification on the planktonic food quality in terms of essential fatty acids.

  1. How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions?

    Science.gov (United States)

    Munoz, François; Ramesh, B R; Couteron, Pierre

    2014-08-01

    Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k) is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I

  2. Composition and function of the microbial community related with the nitrogen cycling on the potato rhizosphere

    International Nuclear Information System (INIS)

    Florez Zapata, Nathalia; Garcia, Juan Carlos; Del Portillo, Patricia; Restrepo, Silvia; Uribe Velez, Daniel

    2013-01-01

    In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbial communities related with the N cycle of S. tuberosum group phureja rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy. Few significant differences between the community compositions at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population's selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil's physicalchemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.

  3. COMPOSITION AND FUNCTION OF THE MICROBIAL COMMUNITY RELATED WITH THE NITROGEN CYCLING ON THE POTATO RHIZOSPHERE

    Directory of Open Access Journals (Sweden)

    Nathalia Maria Vanesa Florez Zapata

    2013-09-01

    Full Text Available In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants’ nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbal[trm1]  communities related with the N cycle of S. tuberosum group phureja  rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy.  Few significant differences between the community composition at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population’s selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas, appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil’s physical-chemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.

  4. Species composition and community structure of subtropical forest stands in western himalayan foothills of kashmir

    International Nuclear Information System (INIS)

    Shaheen, H.; Malik, N. M.; Dar, M. E. U. I.

    2015-01-01

    Lesser Himalayan subtropical forests have unique species composition due to diverse climatic and topographic factors which create numerous microhabitats. Phytosociological characteristics, structural attributes and biological spectrum of plant communities in the forests of Himalayan foothills in Kashmir were analyzed. A total of 65 species belonging to 26 plant families were recorded constituting 6 plant communities. Average value of diversity recorded for the communities was 2.44; species richness 4.01; whereas evenness was found to be 0.48. The species data indicated random distribution of species with a hump shaped diversity pattern directly correlated with increasing altitude. Themeda anathera was the dominant species with an importance value percentage of 14.7 percentage followed by Pinus roxburghii (9.6 percentage), Mallotus philippenensis (5.2 percentage), Malvastrum coromandelianum (5.1 percentage), Acacia modesta (5 percentage), Olea ferruginea (3.8 percentage) and Oxalis corniculata (3.2 percentage). Vegetation was dominated by Therophytes (30 percentage) and megaphanerophytes (23.3) with dominant leaf spectrum as leptophylls (31.6 percentage). Thirty seven percent plants had medicinal values followed by 31 percentage having fodder values where as 12 percentage used as fuel. Principal component analyses and cluster analyses revealed the association of dominant species with specific sites due to prevailing environmental conditions. The distribution of species in ordination diagrams indicated a continuous change in species composition along the altitudinal gradient. Key stone tree species were subject to immense tree felling resulting in deteriorating changes in forest structure. Visual indicators showed over grazing at all the studied sites evident from the dominance of unpalatable species. Local forest stands demand immediate attention of policy makers as well as forest management so that local diversity and floristic richness could be conserved and

  5. Fish-mediated changes in bacterioplankton community composition: an in situ mesocosm experiment

    Science.gov (United States)

    Luo, Congqiang; Yi, Chunlong; Ni, Leyi; Guo, Longgen

    2017-06-01

    We characterized variations in bacterioplankton community composition (BCC) in mesocosms subject to three different treatments. Two groups contained fish (group one: Cyprinus carpio; group two: Hypophthalmichthys molitrix); and group three, the untreated mesocosm, was the control. Samples were taken seven times over a 49-day period, and BCC was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (qPCR). Results revealed that introduction of C. carpio and H. molitrix had a remarkable impact on the composition of bacterioplankton communities, and the BCC was significantly different between each treatment. Sequencing of DGGE bands revealed that the bacterioplankton community in the different treatment groups was consistent at a taxonomic level, but differed in its abundance. H. molitrix promoted the richness of Alphaproteobacteria and Actinobacteria, while more bands affiliated to Cyanobacteria were detected inC. carpio mesocosms. The redundancy analysis (RDA) result demonstrated that the BCC was closely related to the bottom-up (total phosphorus, chlorophyll a, phytoplankton biomass) and top-down forces (biomass of copepods and cladocera) in C. carpio and control mesocosms, respectively. We found no evidence for top-down regulation of BCC by zooplankton in H. molitrix mesocosms, while grazing by protozoa (heterotrophic nanoflagellates, ciliates) became the major way to regulate BCC. Total bacterioplankton abundances were significantly higher in C. carpio mesocosms because of high nutrient concentration and suspended solids. Our study provided insights into the relationship between fish and bacterioplankton at species level, leading to a deep understanding of the function of the microbial loop and the aquatic ecosystem.

  6. Fish-mediated changes in bacterioplankton community composition: an in situ mesocosm experiment

    Science.gov (United States)

    Luo, Congqiang; Yi, Chunlong; Ni, Leyi; Guo, Longgen

    2018-03-01

    We characterized variations in bacterioplankton community composition (BCC) in mesocosms subject to three different treatments. Two groups contained fish (group one: Cyprinus carpio; group two: Hypophthalmichthys molitrix); and group three, the untreated mesocosm, was the control. Samples were taken seven times over a 49-d period, and BCC was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (qPCR). Results revealed that introduction of C. carpio and H. molitrix had a remarkable impact on the composition of bacterioplankton communities, and the BCC was significantly different between each treatment. Sequencing of DGGE bands revealed that the bacterioplankton community in the different treatment groups was consistent at a taxonomic level, but differed in its abundance. H. molitrix promoted the richness of Alphaproteobacteria and Actinobacteria, while more bands affiliated to Cyanobacteria were detected in C. carpio mesocosms. The redundancy analysis (RDA) result demonstrated that the BCC was closely related to the bottom-up (total phosphorus, chlorophyll a, phytoplankton biomass) and top-down forces (biomass of copepods and cladocera) in C. carpio and control mesocosms, respectively. We found no evidence for top-down regulation of BCC by zooplankton in H. molitrix mesocosms, while grazing by protozoa (heterotrophic nanoflagellates, ciliates) became the major way to regulate BCC. Total bacterioplankton abundances were significantly higher in C. carpio mesocosms because of high nutrient concentration and suspended solids. Our study provided insights into the relationship between fish and bacterioplankton at species level, leading to a deep understanding of the function of the microbial loop and the aquatic ecosystem.

  7. Composition and temporal patterns of larval fish communities in Chesapeake and Delaware Bays

    Directory of Open Access Journals (Sweden)

    Filipe Ribeiro

    2015-11-01

    Full Text Available Comparing larval fish assemblages in different estuaries provides insights about the coastal distribution of larval populations, larval transport, and adult spawning locations (Ribeiro et al. 2015. We simultaneously compared the larval fish assemblages entering two Middle Atlantic Bight (MAB estuaries (Delaware Bay and Chesapeake Bay, USA through weekly sampling from 2007 to 2009. In total, 43 taxa (32 families and 36 taxa (24 families were collected in Delaware and Chesapeake Bays, respectively. Mean taxonomic diversity, mean richness, and evenness were generally lower in Delaware Bay. Communities of both bays were dominated by Anchoa spp., Gobiosoma spp., Micropogonias undulatus, and Brevoortia tyrannus; Paralichthys spp. was more abundant in Delaware Bay and Microgobius thalassinus was more abundant in Chesapeake Bay. Inter-annual variation in the larval fish communities was low at both sites, with a relatively consistent composition across years, but strong seasonal (intra-annual variation in species composition occurred in both bays. Two groups were identified in Chesapeake Bay: a ‘winter’ group dominated by shelf-spawned species (e.g. M. undulatus and a ‘summer’ group comprising obligate estuarine species and coastal species (e.g. Gobiosoma spp. and Cynoscion regalis, respectively. In Delaware Bay, 4 groups were identified: a ‘summer’ group of mainly obligate estuarine fishes (e.g. Menidia sp. being replaced by a ‘fall’ group (e.g. Ctenogobius boleosoma and Gobionellus oceanicus; ‘winter’ and ‘spring’ groups were dominated by shelf-spawned (e.g. M. undulatus and Paralichthys spp. and obligate estuarine species (e.g. Leiostomus xanthurus and Pseudopleuronectes americanus, respectively. This study demonstrates that inexpensive and simultaneous sampling in different estuaries provides important insights into the variability in community structure of fish assemblages at large spatial scales.

  8. Hydrogen utilization potential in subsurface sediments

    Directory of Open Access Journals (Sweden)

    Rishi Ram Adhikari

    2016-01-01

    Full Text Available 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.

  9. Development of a molecular approach to describe the composition of Trichoderma communities.

    Science.gov (United States)

    Meincke, Remo; Weinert, Nicole; Radl, Viviane; Schloter, Michael; Smalla, Kornelia; Berg, Gabriele

    2010-01-01

    Trichoderma and its teleomorphic stage Hypocrea play a key role for ecosystem functioning in terrestrial habitats. However, little is known about the ecology of the fungus. In this study we developed a novel Trichoderma-specific primer pair for diversity analysis. Based on a broad range master alignment, specific Trichoderma primers (ITSTrF/ITSTrR) were designed that comprise an approximate 650bp fragment of the internal transcribed spacer region from all taxonomic clades of the genus Trichoderma. This amplicon is suitable for identification with TrichoKey and TrichoBLAST. Moreover, this primer system was successfully applied to study the Trichoderma communities in the rhizosphere of different potato genotypes grown at two field sites in Germany. Cloning and sequencing confirmed the specificity of the primer and revealed a site-dependent Trichoderma composition. Based on the new primer system a semi-nested approach was used to generate amplicons suitable for denaturing gradient gel electrophoresis (DGGE) analysis and applied to analyse Trichoderma communities in the rhizosphere of potatoes. High field heterogeneity of Trichoderma communities was revealed by both DGGE. Furthermore, qPCR showed significantly different Trichoderma copy numbers between the sites. Copyright 2009 Elsevier B.V. All rights reserved.

  10. Water level changes affect carbon turnover and microbial community composition in lake sediments.

    Science.gov (United States)

    Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; Kayler, Zachary E; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

    2016-05-01

    Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. (13)C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. © FEMS 2016.

  11. Effects of rodent community diversity and composition on prevalence of an endemic bacterial pathogen - Bartonella

    Science.gov (United States)

    Bai, Y.; Kosoy, M.Y.; Calisher, C.H.; Cully, J.F.; Collinge, S.K.

    2009-01-01

    By studying Bartonella prevalence in rodent communities from 23 geographic sites in the western United States and one site in northern Mexico, the present study focused on the effects of rodent community diversity (measured by richness and Shannon index) and composition on prevalence of Bartonella infections. The analysis showed negative correlations of Bartonella prevalence with rodent richness and Shannon index. Further, Bartonella prevalence varied among rodent genera/species. Three models were applied to explain the observations. (1) Within-species/genus transmission: Bartonella strains usually are host-specific and adding non-host species would decrease Bartonella prevalence in its principal host through reduction of host contact (encounter reduction); (2) Frequency-dependence: Adding hosts would decrease the proportion of all infected individuals in the community, resulting in a reduction in the number of contacts between susceptible and infected individuals that usually leads to transmission (transmission reduction); and (3) Dominant species effect: Dominant species, if not susceptible to Bartonellae, can constrain the abundance of susceptible hosts (susceptible host regulation). These mechanisms work in concert; and the level of Bartonella prevalence is an outcome of regulation of all of these mechanisms on the entire system.

  12. Solar PAR and UVR modify the community composition and photosynthetic activity of sea ice algae.

    Science.gov (United States)

    Enberg, Sara; Piiparinen, Jonna; Majaneva, Markus; Vähätalo, Anssi V; Autio, Riitta; Rintala, Janne-Markus

    2015-10-01

    The effects of increased photosynthetically active radiation (PAR) and ultraviolet radiation (UVR) on species diversity, biomass and photosynthetic activity were studied in fast ice algal communities. The experimental set-up consisted of nine 1.44 m(2) squares with three treatments: untreated with natural snow cover (UNT), snow-free (PAR + UVR) and snow-free ice covered with a UV screen (PAR). The total algal biomass, dominated by diatoms and dinoflagellates, increased in all treatments during the experiment. However, the smaller biomass growth in the top 10-cm layer of the PAR + UVR treatment compared with the PAR treatment indicated the negative effect of UVR. Scrippsiella complex (mainly Scrippsiella hangoei, Biecheleria baltica and Gymnodinium corollarium) showed UV sensitivity in the top 5-cm layer, whereas Heterocapsa arctica ssp. frigida and green algae showed sensitivity to both PAR and UVR. The photosynthetic activity was highest in the top 5-cm layer of the PAR treatment, where the biomass of the pennate diatom Nitzschia frigida increased, indicating the UV sensitivity of this species. This study shows that UVR is one of the controlling factors of algal communities in Baltic Sea ice, and that increased availability of PAR together with UVR exclusion can cause changes in algal biomass, photosynthetic activity and community composition. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Subsurface Facility System Description Document

    International Nuclear Information System (INIS)

    Eric Loros

    2001-01-01

    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. Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

    Directory of Open Access Journals (Sweden)

    Maaike evan Agtmaal

    2015-07-01

    Full Text Available There is increasing evidence that microbial volatiles (VOCs play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD, a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are

  15. Subsurface remote sensing

    International Nuclear Information System (INIS)

    Schweitzer, Jeffrey S.; Groves, Joel L.

    2002-01-01

    Subsurface remote sensing measurements are widely used for oil and gas exploration, for oil and gas production monitoring, and for basic studies in the earth sciences. Radiation sensors, often including small accelerator sources, are used to obtain bulk properties of the surrounding strata as well as to provide detailed elemental analyses of the rocks and fluids in rock pores. Typically, instrument packages are lowered into a borehole at the end of a long cable, that may be as long as 10 km, and two-way data and instruction telemetry allows a single radiation instrument to operate in different modes and to send the data to a surface computer. Because these boreholes are often in remote locations throughout the world, the data are frequently transmitted by satellite to various locations around the world for almost real-time analysis and incorporation with other data. The complete system approach that permits rapid and reliable data acquisition, remote analysis and transmission to those making decisions is described

  16. Intra- and interspecific differences in diet quality and composition in a large herbivore community.

    Directory of Open Access Journals (Sweden)

    Claire Redjadj

    Full Text Available Species diversity in large herbivore communities is often explained by niche segregation allowed by differences in body mass and digestive morphophysiological features. Based on large number of gut samples in fall and winter, we analysed the temporal dynamics of diet composition, quality and interspecific overlap of 4 coexisting mountain herbivores. We tested whether the relative consumption of grass and browse differed among species of different rumen types (moose-type and intermediate-type, whether diet was of lower quality for the largest species, whether we could identify plant species which determined diet quality, and whether these plants, which could be "key-food-resources" were similar for all herbivores. Our analyses revealed that (1 body mass and rumen types were overall poor predictors of diet composition and quality, although the roe deer, a species with a moose-type rumen was confirmed as an "obligatory non grazer", while red deer, the largest species, had the most lignified diet; (2 diet overlap among herbivores was well predicted by rumen type (high among species of intermediate types only, when measured over broad plant groups, (3 the relationship between diet composition and quality differed among herbivore species, and the actual plant species used during winter which determined the diet quality, was herbivore species-specific. Even if diets overlapped to a great extent, the species-specific relationships between diet composition and quality suggest that herbivores may select different plant species within similar plant group types, or different plant parts and that this, along with other behavioural mechanisms of ecological niche segregation, may contribute to the coexistence of large herbivores of relatively similar body mass, as observed in mountain ecosystems.

  17. Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

    KAUST Repository

    Li, D.

    2012-07-13

    This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

  18. Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

    KAUST Repository

    Li, D.; Sharp, J. O.; Saikaly, Pascal; Ali, Shahjahan; Alidina, M.; Alarawi, M. S.; Keller, S.; Hoppe-Jones, C.; Drewes, J. E.

    2012-01-01

    This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

  19. Acceleration and novelty: community restoration speeds recovery and transforms species composition in Andean cloud forest.

    Science.gov (United States)

    Wilson, Sarah Jane; Rhemtulla, Jeanine M

    2016-01-01

    Community-based tropical forest restoration projects, often promoted as a win-win solution for local communities and the environment, have increased dramatically in number in the past decade. Many such projects are underway in Andean cloud forests, which, given their extremely high biodiversity and history of extensive clearing, are understudied. This study investigates the efficacy of community-based tree-planting projects to accelerate cloud forest recovery, as compared to unassisted natural regeneration. This study takes place in northwest Andean Ecuador, where the majority of the original, highly diverse cloud forests have been cleared, in five communities that initiated tree-planting projects to restore forests in 2003. In 2011, we identified tree species along transects in planted forests (n = 5), naturally regenerating forests (n = 5), and primary forests (n = 5). We also surveyed 120 households about their restoration methods, tree preferences, and forest uses. We found that tree diversity was higher in planted than in unplanted secondary forest, but both were less diverse than primary forests. Ordination analysis showed that all three forests had distinct species compositions, although planted forests shared more species with primary forests than did unplanted forests. Planted forests also contained more animal-dispersed species in both the planted canopy and in the unplanted, regenerating understory than unplanted forests, and contained the highest proportion of species with use value for local people. While restoring forest increased biodiversity and accelerated forest recovery, restored forests may also represent novel ecosystems that are distinct from the region's previous ecosystems and, given their usefulness to people, are likely to be more common in the future.

  20. Agricultural Land Use Determines the Trait Composition of Ground Beetle Communities.

    Directory of Open Access Journals (Sweden)

    Helena I Hanson

    Full Text Available In order to improve biological control of agricultural pests, it is fundamental to understand which factors influence the composition of natural enemies in agricultural landscapes. In this study, we aimed to understand how agricultural land use affects a number of different traits in ground beetle communities to better predict potential consequences of land-use change for ecosystem functioning. We studied ground beetles in fields with different agricultural land use ranging from frequently managed sugar beet fields, winter wheat fields to less intensively managed grasslands. The ground beetles were collected in emergence tents that catch individuals overwintering locally in different life stages and with pitfall traps that catch individuals that could have a local origin or may have dispersed into the field. Community weighted mean values for ground beetle traits such as body size, flight ability and feeding preference were estimated for each land-use type and sampling method. In fields with high land-use intensity the average body length of emerging ground beetle communities was lower than in the grasslands while the average body length of actively moving communities did not differ between the land-use types. The proportion of ground beetles with good flight ability or a carnivorous diet was higher in the crop fields as compared to the grasslands. Our study highlights that increasing management intensity reduces the average body size of emerging ground beetles and the proportion of mixed feeders. Our results also suggest that the dispersal ability of ground beetles enables them to compensate for local management intensities.

  1. Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems.

    Science.gov (United States)

    Li, Dong; Sharp, Jonathan O; Saikaly, Pascal E; Ali, Shahjahan; Alidina, Mazahirali; Alarawi, Mohammed S; Keller, Stephanie; Hoppe-Jones, Christiane; Drewes, Jörg E

    2012-10-01

    This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

  2. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

    Science.gov (United States)

    Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

    2016-12-01

    Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

  3. Hot spring microbial community composition, morphology, and carbon fixation: implications for interpreting the ancient rock record

    Science.gov (United States)

    Schuler, Caleb G.; Havig, Jeff R.; Hamilton, Trinity L.

    2017-11-01

    Microbial communities in hydrothermal systems exist in a range of macroscopic morphologies including stromatolites, mats, and filaments. The architects of these structures are typically autotrophic, serving as primary producers. Structures attributed to microbial life have been documented in the rock record dating back to the Archean including recent reports of microbially-related structures in terrestrial hot springs that date back as far as 3.5 Ga. Microbial structures exhibit a range of complexity from filaments to more complex mats and stromatolites and the complexity impacts preservation potential. As a result, interpretation of these structures in the rock record relies on isotopic signatures in combination with overall morphology and paleoenvironmental setting. However, the relationships between morphology, microbial community composition, and primary productivity remain poorly constrained. To begin to address this gap, we examined community composition and carbon fixation in filaments, mats, and stromatolites from the Greater Obsidian Pool Area (GOPA) of the Mud Volcano Area, Yellowstone National Park, WY. We targeted morphologies dominated by bacterial phototrophs located in close proximity within the same pool which are exposed to similar geochemistry as well as bacterial mat, algal filament and chemotrophic filaments from nearby springs. Our results indicate i) natural abundance δ13C values of biomass from these features (-11.0 to -24.3 ‰) are similar to those found in the rock record; ii) carbon uptake rates of photoautotrophic communities is greater than chemoautotrophic; iii) oxygenic photosynthesis, anoxygenic photosynthesis, and chemoautotrophy often contribute to carbon fixation within the same morphology; and iv) increasing phototrophic biofilm complexity corresponds to a significant decrease in rates of carbon fixation—filaments had the highest uptake rates whereas carbon fixation by stromatolites was significantly lower. Our data highlight

  4. Hot Spring Microbial Community Composition, Morphology, and Carbon Fixation: Implications for Interpreting the Ancient Rock Record

    Directory of Open Access Journals (Sweden)

    Caleb G. Schuler

    2017-11-01

    Full Text Available Microbial communities in hydrothermal systems exist in a range of macroscopic morphologies including stromatolites, mats, and filaments. The architects of these structures are typically autotrophic, serving as primary producers. Structures attributed to microbial life have been documented in the rock record dating back to the Archean including recent reports of microbially-related structures in terrestrial hot springs that date back as far as 3.5 Ga. Microbial structures exhibit a range of complexity from filaments to more complex mats and stromatolites and the complexity impacts preservation potential. As a result, interpretation of these structures in the rock record relies on isotopic signatures in combination with overall morphology and paleoenvironmental setting. However, the relationships between morphology, microbial community composition, and primary productivity remain poorly constrained. To begin to address this gap, we examined community composition and carbon fixation in filaments, mats, and stromatolites from the Greater Obsidian Pool Area (GOPA of the Mud Volcano Area, Yellowstone National Park, WY. We targeted morphologies dominated by bacterial phototrophs located in close proximity within the same pool which are exposed to similar geochemistry as well as bacterial mat, algal filament and chemotrophic filaments from nearby springs. Our results indicate (i natural abundance δ13C values of biomass from these features (−11.0 to −24.3‰ are similar to those found in the rock record; (ii carbon uptake rates of photoautotrophic communities is greater than chemoautotrophic; (iii oxygenic photosynthesis, anoxygenic photosynthesis, and chemoautotrophy often contribute to carbon fixation within the same morphology; and (iv increasing phototrophic biofilm complexity corresponds to a significant decrease in rates of carbon fixation—filaments had the highest uptake rates whereas carbon fixation by stromatolites was significantly lower

  5. Biofouling community composition across a range of environmental conditions and geographical locations suitable for floating marine renewable energy generation.

    Science.gov (United States)

    Macleod, Adrian K; Stanley, Michele S; Day, John G; Cook, Elizabeth J

    2016-01-01

    Knowledge of biofouling typical of marine structures is essential for engineers to define appropriate loading criteria in addition to informing other stakeholders about the ecological implications of creating novel artificial environments. There is a lack of information regarding biofouling community composition (including weight and density characteristics) on floating structures associated with future marine renewable energy generation technologies. A network of navigation buoys were identified across a range of geographical areas, environmental conditions (tidal flow speed, temperature and salinity), and deployment durations suitable for future developments. Despite the perceived importance of environmental and temporal factors, geographical location explained the greatest proportion of the observed variation in community composition, emphasising the importance of considering geography when assessing the impact of biofouling on device functioning and associated ecology. The principal taxa associated with variation in biofouling community composition were mussels (Mytilus edulis), which were also important when determining loading criteria.

  6. Modeling plant composition as community continua in a forest landscape with LiDAR and hyperspectral remote sensing.

    Science.gov (United States)

    Hakkenberg, C R; Peet, R K; Urban, D L; Song, C

    2018-01-01

    In light of the need to operationalize the mapping of forest composition at landscape scales, this study uses multi-scale nested vegetation sampling in conjunction with LiDAR-hyperspectral remotely sensed data from the G-LiHT airborne sensor to map vascular plant compositional turnover in a compositionally and structurally complex North Carolina Piedmont forest. Reflecting a shift in emphasis from remotely sensing individual crowns to detecting aggregate optical-structural properties of forest stands, predictive maps reflect the composition of entire vascular plant communities, inclusive of those species smaller than the resolution of the remotely sensed imagery, intertwined with proximate taxa, or otherwise obscured from optical sensors by dense upper canopies. Stand-scale vascular plant composition is modeled as community continua: where discrete community-unit classes at different compositional resolutions provide interpretable context for continuous gradient maps that depict n-dimensional compositional complexity as a single, consistent RGB color combination. In total, derived remotely sensed predictors explain 71%, 54%, and 48% of the variation in the first three components of vascular plant composition, respectively. Among all remotely sensed environmental gradients, topography derived from LiDAR ground returns, forest structure estimated from LiDAR all returns, and morphological-biochemical traits determined from hyperspectral imagery each significantly correspond to the three primary axes of floristic composition in the study site. Results confirm the complementarity of LiDAR and hyperspectral sensors for modeling the environmental gradients constraining landscape turnover in vascular plant composition and hold promise for predictive mapping applications spanning local land management to global ecosystem modeling. © 2017 by the Ecological Society of America.

  7. A trait-based approach to understanding marine communities composition, assembly and diversity

    DEFF Research Database (Denmark)

    Pécuchet, Lauréne

    are characterised by their taxonomic diversity, such as their species richness or the evenness in their abundances. However, there is growing evidence that it is not the taxonomic identity of the species per se that control its presence and abundance in a given environment but its characteristics. Species traits......, we studied the diversity and the processes influencing the composition of demersal fish communities in the Baltic Sea. While species richness was sharply decreasing from the saline Kattegat to the brackish Gdansk Bay, trait richness tended to decrease at a lower rate. We found that the species co...... acting on the species. The strategies’ prevalence exhibited strong geographical patterns which could be explained by spatial variability in annual sea surface temperature, temperature seasonality, depth and fishing intensity. Due to their tight coupling to the environment, notably temperature and fishing...

  8. Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.

    Science.gov (United States)

    Arroyo, Paula; Sáenz de Miera, Luis E; Ansola, Gemma

    2015-02-15

    Bacteria are key players in wetland ecosystems, however many essential aspects regarding the ecology of wetland bacterial communities remain unknown. The present study characterizes soil bacterial communities from natural and constructed wetlands through the pyrosequencing of 16S rDNA genes in order to evaluate the influence of wetland variables on bacterial community composition and structure. The results show that the composition of soil bacterial communities was significantly associated with the wetland type (natural or constructed wetland), the type of environment (lagoon, Typha or Salix) and three continuous parameters (SOM, COD and TKN). However, no clear associations were observed with soil pH. Bacterial diversity values were significantly lower in the constructed wetland with the highest inlet nutrient concentrations. The abundances of particular metabolic groups were also related to wetland characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Seismic characterisation of subsurface structural features of parts of ...

    African Journals Online (AJOL)

    A total of thirty-four migrated 2D seismic reflection lines and two composite well logs have been interpreted with a view to unravel the subsurface geological ... The interpretation procedure includes horizon identification, fault mapping, timing of horizons at selected shot points, posting of times, time-depth conversion and ...

  10. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Phoebe Dreux Chappell

    2013-09-01

    Full Text Available Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a three-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a three-month-old Haida eddy remained largely (>80% similar over a two-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

  11. Long-term agricultural fertilization alters arbuscular mycorrhizal fungal community composition and barley (Hordeum vulgare) mycorrhizal carbon and phosphorus exchange.

    Science.gov (United States)

    Williams, Alwyn; Manoharan, Lokeshwaran; Rosenstock, Nicholas P; Olsson, Pål Axel; Hedlund, Katarina

    2017-01-01

    Agricultural fertilization significantly affects arbuscular mycorrhizal fungal (AMF) community composition. However, the functional implications of community shifts are unknown, limiting understanding of the role of AMF in agriculture. We assessed AMF community composition at four sites managed under the same nitrogen (N) and phosphorus (P) fertilizer regimes for 55 yr. We also established a glasshouse experiment with the same soils to investigate AMF-barley (Hordeum vulgare) nutrient exchange, using carbon ( 13 C) and 33 P isotopic labelling. N fertilization affected AMF community composition, reducing diversity; P had no effect. In the glasshouse, AMF contribution to plant P declined with P fertilization, but was unaffected by N. Barley C allocation to AMF also declined with P fertilization. As N fertilization increased, C allocation to AMF per unit of P exchanged increased. This occurred with and without P fertilization, and was concomitant with reduced barley biomass. AMF community composition showed no relationship with glasshouse experiment results. The results indicate that plants can reduce C allocation to AMF in response to P fertilization. Under N fertilization, plants allocate an increasing amount of C to AMF and receive relatively less P. This suggests an alteration in the terms of P-C exchange under N fertilization regardless of soil P status. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  12. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    Science.gov (United States)

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Bacterial community composition in the water column of a lake formed by a former uranium open pit mine.

    Science.gov (United States)

    Edberg, Frida; Andersson, Anders F; Holmström, Sara J M

    2012-11-01

    Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

  14. Free-living protozoa in drinking water supplies: community composition and role as hosts for Legionella pneumophila

    OpenAIRE

    Valster, R.M.

    2011-01-01

    Free-living protozoa in drinking water supplies: community composition and role as hosts for Legionella pneumophila Free-living protozoa, which feed on bacteria, play an important role in the communities of microorganisms and invertebrates in drinking water supplies and in (warm) tap water installations. Several bacteria, including opportunistic human pathogens such as Legionella pneumophila, are able to survive and replicate within protozoan hosts, and certain free-living protozoa are opp...

  15. The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale

    OpenAIRE

    Hazard, Christina; Gosling, Paul; van der Gast, Christopher J; Mitchell, Derek T; Doohan, Fiona M; Bending, Gary D

    2012-01-01

    Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis (‘everything is everywhere, but, the environment selects') was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Loliu...

  16. Prokaryotic community composition in alkaline-fermented skate (Raja pulchra).

    Science.gov (United States)

    Jang, Gwang Il; Kim, Gahee; Hwang, Chung Yeon; Cho, Byung Cheol

    2017-02-01

    Prokaryotes were extracted from skates and fermented skates purchased from fish markets and a local manufacturer in South Korea. The prokaryotic community composition of skates and fermented skates was investigated using 16S rRNA pyrosequencing. The ranges for pH and salinity of the grinded tissue extract from fermented skates were 8.4-8.9 and 1.6-6.6%, respectively. Urea and ammonia concentrations were markedly low and high, respectively, in fermented skates compared to skates. Species richness was increased in fermented skates compared to skates. Dominant and predominant bacterial groups present in the fermented skates belonged to the phylum Firmicutes, whereas those in skates belonged to Gammaproteobacteria. The major taxa found in Firmicutes were Atopostipes (Carnobacteriaceae, Lactobacillales) and/or Tissierella (Tissierellaceae, Tissierellales). A combination of RT-PCR and pyrosequencing for active bacterial composition showed that the dominant taxa i.e., Atopostipes and Tissierella, were active in fermented skate. Those dominant taxa are possibly marine lactic acid bacteria. Marine bacteria of the taxa Lactobacillales and/or Clostridia seem to be important in alkaline fermentation of skates. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    Science.gov (United States)

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils. PMID:26739424

  18. Differences in composition of shallow-water marine benthic communities associated with two ophiolitic rock substrata

    Science.gov (United States)

    Bavestrello, Giorgio; Bo, Marzia; Betti, Federico; Canessa, Martina; Gaggero, Laura; Rindi, Fabio; Cattaneo-Vietti, Riccardo

    2018-01-01

    On marine rocky shores, several physical, chemical and biological processes operate to maintain the benthic assemblages' heterogeneity, but among the abiotic factors, the composition and texture of the rocky substrata have been only sporadically considered. However, biomineralogical studies have demonstrated an unsuspected ability of the benthic organisms to interact at different levels with rocky substrata. Therefore, the mineralogy of the substratum can affect the structure of benthic communities. To evaluate this hypothesis, the macrobenthic assemblages developed on two different ophiolitic rocks (serpentinites and metagabbros) in contact at a restricted stretch of the western Ligurian Riviera (western Mediterranean Sea), with identical environmental and climatic conditions, were analysed. Samplings were carried out at four bathymetric levels (+1m, 0m, -1m, and -3m respect to the mean sea level) and the analysis of the data evidenced differences in terms of species distribution and percent coverage. Algal communities growing on metagabbros were poorer in species richness and showed a much simpler structure when compared to the assemblages occurring on the serpentinites. The most widely distributed animal organism, the barnacle Chthamalus stellatus, was dominant on serpentinites, and virtually absent on metagabbros. Our results suggest a complex pattern of interactions between lithology and benthic organisms operating through processes of inhibition/facilitation related to the mineral properties of the substratum.

  19. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

    Directory of Open Access Journals (Sweden)

    Luisa W. Hugerth

    2017-09-01

    Full Text Available Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

  20. Annual glyphosate treatments alter growth of unaffected bentgrass (Agrostis weeds and plant community composition.

    Directory of Open Access Journals (Sweden)

    Collin W Ahrens

    Full Text Available Herbicide resistance is becoming more common in weed ecotypes and crop species including turfgrasses, but current gaps in knowledge limit predictive ecological risk assessments and risk management plans. This project examined the effect of annual glyphosate applications on the vegetative growth and reproductive potential of two weedy bentgrasses, creeping bentgrass (CB and redtop (RT, where the glyphosate resistance (GR trait was mimicked by covering the bentgrass plants during glyphosate application. Five field plots were studied in habitats commonly inhabited by weedy bentgrasses including an agricultural hayfield, natural meadow, and wasteland. Results showed that annual glyphosate treatment improved bentgrass survivorship, vegetative growth, and reproductive potential compared with bentgrass in unsprayed subplots. In the second year of growth, RT plants had an 86-fold increase in flower number in glyphosate-treated subplots versus controls, while CB plants had a 20-fold increase. At the end of the three year study, plant community composition had changed in glyphosate-treated subplots in hayfield and meadow plots compared to controls. Soils in subplots receiving glyphosate had higher nitrate concentrations than controls. This is the first study to mimic the GR trait in bentgrass plants with the goal of quantifying bentgrass response to glyphosate selection pressure and understanding the impacts on surrounding plant communities.

  1. Community Composition and Abundance of Anammox Bacteria in Cattail Rhizosphere Sediments at Three Phenological Stages.

    Science.gov (United States)

    Zhou, Xiaohong; Zhang, Jinping; Wen, Chunzi

    2017-11-01

    The distribution of anammox bacteria in rhizosphere sediments of cattail (Typha orientalis) at different phenological stages was investigated. Results showed that the number of 16S rRNA gene copies of the anammox bacteria was considerably higher in the rhizosphere sediment than in the nonrhizosphere sediment and control sediment. The abundances of the anammox bacteria exhibited striking temporal variations in the three different cattail phenological stages. In addition, the Chao1 and Shannon H indexes of the anammox bacteria in cattail rhizosphere sediments had evident spatial and temporal variations at different phenological stages. Four anammox genera (Brocadia, Kuenenia, Jettenia, and a new cluster) were detected and had proportions of 34.18, 45.57, 0.63, and 19.62%, respectively. The CCA analysis results indicated that Cu, TN, Pb, and Zn were pivotal factors that affect anammox bacteria composition. The PCoA analysis results indicated that the community structure at the rhizosphere and nonrhizosphere sediments collected on July was relatively specific and was different from sediments collected on other months, suggesting that cattail can influence the community structures of the anammox bacteria at the maturity stage.

  2. Floristic composition and community structure of epiphytic angiosperms in a terra firme forest in central Amazonia

    Directory of Open Access Journals (Sweden)

    Mariana Victória Irume

    2013-06-01

    Full Text Available This survey aimed to describe the floristic composition and structure of the epiphytic community occurring in a terra firme forest in the city of Coari, Brazil, in the Amazon region. Data collection was performed with a 1.5 ha plot method, with which upland, slope and lowland habitats were sampled. All angiosperm epiphytes and their host plants (diameter at breast height > 10 cm were sampled. We recorded 3.528 individuals in 13 families, 48 genera and 164 species. Araceae was the most prevalent family with regard to the importance value and stood out in all related parameters, followed by Bromeliaceae, Cyclanthaceae and Orchidaceae. The species with the highest epiphytic importance values were Guzmania lingulata (L. Mez. and Philodendron linnaei Kunth. The predominant life form was hemiepiphytic. Estimated floristic diversity was 3.2 (H'. The studied epiphytic community was distributed among 727 host plants belonging to 40 families, 123 genera and 324 species. One individual of Guarea convergens T.D. Penn. was the host with the highest richness and abundance of epiphytes. Stems/trunks of host plants were the most colonized segments, and the most favorable habitat for epiphytism was the lowlands, where 84.1% of species and 48.2% of epiphytic specimens were observed.

  3. Endemicity, biogeograhy, composition, and community structure on a northeast pacific seamount.

    Directory of Open Access Journals (Sweden)

    Craig R McClain

    Full Text Available The deep ocean greater than 1 km covers the majority of the earth's surface. Interspersed on the abyssal plains and continental slope are an estimated 14000 seamounts, topographic features extending 1000 m off the seafloor. A variety of hypotheses are posited that suggest the ecological, evolutionary, and oceanographic processes on seamounts differ from those governing the surrounding deep sea. The most prominent and oldest of these hypotheses, the seamount endemicity hypothesis (SMEH, states that seamounts possess a set of isolating mechanisms that produce highly endemic faunas. Here, we constructed a faunal inventory for Davidson Seamount, the first bathymetric feature to be characterized as a 'seamount', residing 120 km off the central California coast in approximately 3600 m of water (Fig 1. We find little support for the SMEH among megafauna of a Northeast Pacific seamount; instead, finding an assemblage of species that also occurs on adjacent continental margins. A large percentage of these species are also cosmopolitan with ranges extending over much of the Pacific Ocean Basin. Despite the similarity in composition between the seamount and non-seamount communities, we provide preliminary evidence that seamount communities may be structured differently and potentially serve as source of larvae for suboptimal, non-seamount habitats.

  4. Richness, composition and trophic groups of an avian community in the Pernambuco Endemism Centre, Alagoas, Brazil

    Directory of Open Access Journals (Sweden)

    GUILHERME S. TOLEDO-LIMA

    2014-09-01

    Full Text Available In northeastern Brazil, the reduction of the natural forest cover to a series of small, isolated fragments has had negative consequences for the local avian fauna, in particular, a loss of the more specialized species, while the populations of some generalists have tended to increase. The present study focuses on the composition and trophic groups of a bird community on a farm in the northeastern Brazilian state of Alagoas. Monthly surveys were conducted between November 2008 and October 2009, based on mist-netting and systematic observations. Overall, 112 species were recorded, of which 76 were associated with the two forest fragments surveyed, while all the others were observed exclusively in the surrounding matrix of pasture and orchards. The bird community presented a predominance of insectivorous species, followed by omnivores. However, specialized trunk-creeping and understory insectivores accounted for only around 15% of the species in this feeding category. The reduced diversity of other guilds and species with more specialized diets, and the complete absence of sensitive species such as large parrots and raptors, reflects the severe fragmentation and degradation of the local forests, which has greatly reduced the availability of dietary resources and breeding sites.

  5. Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.

    Science.gov (United States)

    Liu, Jingjing; Wu, Weixiang; Chen, Chongjun; Sun, Faqian; Chen, Yingxu

    2011-09-01

    In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.

  6. Environmental controls on phytoplankton community composition in the Thames plume, U.K.

    Science.gov (United States)

    Weston, Keith; Greenwood, Naomi; Fernand, Liam; Pearce, David J.; Sivyer, David B.

    2008-11-01

    The aim of this study was to investigate controls on the phytoplankton community composition and biogeochemistry of the estuarine plume zone of the River Thames, U.K. using an instrumented moored buoy for in situ measurements and preserved sample collection, and laboratory-based measurements from samples collected at the same site. Instrumentation on the moored buoy enabled high frequency measurements of a suite of environmental variables including in situ chlorophyll, water-column integrated irradiance, macronutrients throughout an annual cycle for 2001 e.g. nitrate and silicate, and phytoplankton biomass and species composition. The Thames plume region acts as a conduit for fluvial nutrients into the wider southern North Sea with typical winter concentrations of 45 μM nitrate, 17 μM silicate and 2 μM phosphate measured. The spring bloom resulted from water-column integrated irradiance increasing above 60 W h m - 2 d - 1 and was initially dominated by a diatom bloom mainly composed of Nitzschia sp. and Odontella sinesis. The spring bloom then switched after ˜ 30 days to become dominated by the flagellate Phaeocystis reaching a maximum chlorophyll concentration of 37.8 μg L - 1 . During the spring bloom there were high numbers of the heterotrophic dinoflagellates Gyrodinium spirale and Katodinium glaucum that potentially grazed the phytoplankton bloom. This diatom-flagellate switch was predicted to be due to a combination of further increasing water-column integrated irradiance > 100 W h m - 2 d - 1 and/or silicate reaching potentially limiting concentrations (nutrient and phytoplankton processing and transport to the southern North Sea. The use of a combination of moorings and ship-based sampling was essential in understanding the factors influencing nutrient transport, phytoplankton biomass and species composition in this shelf sea plume region.

  7. Bacterioplankton diversity and community composition in the Southern Lagoon of Venice.

    Science.gov (United States)

    Simonato, Francesca; Gómez-Pereira, Paola R; Fuchs, Bernhard M; Amann, Rudolf

    2010-04-01

    The Lagoon of Venice is a large water basin that exchanges water with the Northern Adriatic Sea through three large inlets. In this study, the 16S rRNA approach was used to investigate the bacterial diversity and community composition within the southern basin of the Lagoon of Venice and at one inlet in October 2007 and June 2008. Comparative sequence analysis of 645 mostly partial 16S rRNA gene sequences indicated high diversity and dominance of Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes at the lagoon as well as at the inlet station, therefore pointing to significant mixing. Many of these sequences were close to the 16S rRNA of marine, often coastal, bacterioplankton, such as the Roseobacter clade, the family Vibrionaceae, and class Flavobacteria. Sequences of Actinobacteria were indicators of a freshwater input. The composition of the bacterioplankton was quantified by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) with a set of rRNA-targeted oligonucleotide probes. CARD-FISH counts corroborated the dominance of members of the phyla Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes. When assessed by a probe set for the quantification of selected clades within Alphaproteobacteria and Gammaproteobacteria, bacterioplankton composition differed between October 2007 and June 2008, and also between the inlet and the lagoon. In particular, members of the readily culturable copiotrophic gammaproteobacterial genera Vibrio, Alteromonas and Pseudoalteromonas were enriched in the southern basin of the Lagoon of Venice. Interestingly, the alphaproteobacterial SAR11 clade and related clusters were also present in high abundances at the inlet and within the lagoon, which was indicative of inflow of water from the open sea.

  8. Impacts of Fertilization Regimes on Arbuscular Mycorrhizal Fungal (AMF) Community Composition Were Correlated with Organic Matter Composition in Maize Rhizosphere Soil.

    Science.gov (United States)

    Zhu, Chen; Ling, Ning; Guo, Junjie; Wang, Min; Guo, Shiwei; Shen, Qirong

    2016-01-01

    The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well-established yet. A field experiment located in northeast China in typical black soil (Chernozem) was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC-MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2%) of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus . The co-occurrence patterns in treatments with and without organic manure amendment were analyzed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three operational taxonomic units (OTUs) belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on

  9. Impacts of fertilization regimes on arbuscular mycorrhizal fungal (AMF community composition were correlated with organic matter composition in maize rhizosphere soil

    Directory of Open Access Journals (Sweden)

    Chen Zhu

    2016-11-01

    Full Text Available The understanding of the response of arbuscular mycorrhizal fungi (AMF community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well established yet. A field experiment located in northeast China in typical black soil (Chernozem was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC-MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2% of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analysed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three OTUs belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on AMF community

  10. Subsurface Geotechnical Parameters Report

    International Nuclear Information System (INIS)

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

    2003-01-01

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

  11. Subsurface Geotechnical Parameters Report

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-12-17

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

  12. Monitoring of the microbial community composition of the saline aquifers during CO2 storage by fluorescence in situ hybridisation

    OpenAIRE

    Daria Morozova; M. Wandrey; Mashal Alawi; Martin Zimmer; Andrea Vieth-Hillebrand [Vieth; M. Zettlitzer; Hilke Würdemann

    2010-01-01

    This study reveals the first analyses of the composition and activity of the microbial community of a saline CO2 storage aquifer. Microbial monitoring during CO2 injection has been reported. By using fluorescence in situ hybridisation (FISH), we have shown that the microbial community was strongly influenced by the CO2 injection. Before CO2 arrival, up to 6 × 106 cells ml−1 were detected by DAPI staining at a depth of 647 m below the surface. The microbial community was dominated by the dom...

  13. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.

    Science.gov (United States)

    Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone; Dopson, Mark

    2017-08-09

    A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface. Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation. These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses

  14. Effect of salinity on nitrogenase activity and composition of the active diazotrophic community in intertidal microbial mats

    NARCIS (Netherlands)

    Severin, I.; Confurius-Guns, V.; Stal, L.J.

    2012-01-01

    Microbial mats are often found in intertidal areas experiencing a large range of salinities. This study investigated the effect of changing salinities on nitrogenase activity and on the composition of the active diazotrophic community ( transcript libraries) of three types of microbial mats situated

  15. Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir

    Czech Academy of Sciences Publication Activity Database

    Šimek, Karel; Pernthaler, J.; Weinbauer, M. G.; Horňák, K.; Dolan, J. R.; Nedoma, Jiří; Mašin, M.; Amann, R.

    2001-01-01

    Roč. 67, č. 6 (2001), s. 2723-2733 ISSN 0099-2240 R&D Projects: GA ČR GA206/99/0028; GA AV ČR IPP1011802 Grant - others:CNRS(FR) PICS1111 Keywords : bacterial community composition * protozoan grazing * viral lysis Subject RIV: EE - Microbiology, Virology Impact factor: 3.688, year: 2001

  16. Effects of phosphorus addition on soil microbial biomass and community composition in three forest types in tropical China

    DEFF Research Database (Denmark)

    Liu, Lei; Gundersen, Per; Zhang, Tao

    2012-01-01

    Elevated nitrogen (N) deposition in humid tropical regions may aggravate phosphorus (P) deficiency in forest on old weathered soil found in these regions. From January 2007 to August 2009, we studied the responses of soil microbial biomass and community composition to P addition (in two monthly...

  17. Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands

    Czech Academy of Sciences Publication Activity Database

    Oja, J.; Vahtra, J.; Bahram, M.; Kohout, Petr; Kull, T.; Rannap, R.; Köljalg, U.; Tedersoo, L.

    2017-01-01

    Roč. 27, č. 4 (2017), s. 355-367 ISSN 0940-6360 Institutional support: RVO:67985939 Keywords : mycorrhiza * orchids * fungal community composition * calcareous grassland * spatial distribution * grazing intensity Subject RIV: EF - Botanics OBOR OECD: Ecology Impact factor: 3.047, year: 2016

  18. Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China

    NARCIS (Netherlands)

    Wu, Q.L.; Zwart, G.; Schauer, M.; Kamst-van Agterveld, M.P.; Hahn, M.W.

    2006-01-01

    The influence of altitude and salinity on bacterioplankton community composition (BCC) in 16 high-mountain lakes located at altitudes of 2,817 to 5,134 m on the Eastern Qinghai-Xizang (Tibetan) Plateau, China, spanning a salinity gradient from 0.02% (freshwater) to 22.3% (hypersaline), was

  19. Community composition, structure, and interrelationships in the marine intertidal Endocladia muricata – Balanus glandula association in Monterey Bay, California

    NARCIS (Netherlands)

    Glynn, Peter W.

    1965-01-01

    Studies of the community composition, structure and species interrelationships of the Endocladia-Balanus association were carried out on the rocky shores at the Hopkins Marine Station, Pacific Grove, California, over the period 1959—1961. The organisms making up this biotic association form a

  20. Geological differentiation explains diversity and composition of fish communities in upland streams in the southern Amazon of Colombia

    NARCIS (Netherlands)

    Arbeláez, F.; Duivenvoorden, J.F.; Maldonado-Ocampo, J.A.

    2008-01-01

    Fish biomass, species richness and composition were compared between upland streams draining two contrasting geological units (Pebas and Tsa) in Colombian Amazonia. Because Pebas sediments reportedly show higher levels of base concentrations than Tsa sediments, we expected that the fish communities

  1. Trends in NDVI and tundra community composition in the Arctic of NE Alaska between 1984 and 2009

    Science.gov (United States)

    Robert R. Pattison; Janet C. Jorgenson; Martha K. Raynolds; Jeffery M. Welker

    2015-01-01

    As Arctic ecosystems experience increases in surface air temperatures, plot-level analyses of tundra vegetation composition suggest that there are important changes occurring in tundra communities that are typified by increases in shrubs and declines in non-vascular species. At the same time analyses of NDVI indicate that the Arctic tundra is greening. Few studies have...

  2. Geobacteraceae community composition is related to hydrochemistry and biodegradetion in an iron-reducing aquifer polluted by a neigbour landfill

    NARCIS (Netherlands)

    Lin, B; van Breukelen, B.M.; van Verseveld, H.W.; Westerhoff, H.V.; Roling, W.F.M.

    2005-01-01

    Relationships between community composition of the iron-reducing Geobacteraceae, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent Geobacteraceae 16S rRNA gene-targeting techniques.

  3. Geobacteraceae community composition is related to hydrochemistry and biodegradation in an iron-reducing aquifer polluted by a neighboring landfill.

    NARCIS (Netherlands)

    Lin, B.; Braster, M.; van Breukelen, B.M.; van Verseveld, H.W.; Westerhoff, H.V.; Roling, W.F.M.

    2005-01-01

    Relationships between community composition of the iron-reducing Geobacteraceae, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent Geobacteraceae 16S rRNA gene-targeting techniques.

  4. Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity

    NARCIS (Netherlands)

    Zhang, Shuting; Liu, Xiaojiao; Jiang, Qipeng; Shen, Guihua; Ding, Wei

    2017-01-01

    Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high

  5. Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea

    NARCIS (Netherlands)

    Yokokawa, Taichi; De Corte, Daniele; Sintes, Eva; Herndl, Gerhard J.

    2010-01-01

    To determine the variation of bacterial activity and community composition between and within specific water masses, samples were collected throughout the water column at 5 stations in the eastern Mediterranean Sea corresponding to the regions of the northern Aegean, mid-Aegean, western Cretan,

  6. Responses of plant community composition and biomass production to warming and nitrogen deposition in a temperate meadow ecosystem.

    Science.gov (United States)

    Zhang, Tao; Guo, Rui; Gao, Song; Guo, Jixun; Sun, Wei

    2015-01-01

    Climate change has profound influences on plant community composition and ecosystem functions. However, its effects on plant community composition and biomass production are not well understood. A four-year field experiment was conducted to examine the effects of warming, nitrogen (N) addition, and their interactions on plant community composition and biomass production in a temperate meadow ecosystem in northeast China. Experimental warming had no significant effect on plant species richness, evenness, and diversity, while N addition highly reduced the species richness and diversity. Warming tended to reduce the importance value of graminoid species but increased the value of forbs, while N addition had the opposite effect. Warming tended to increase the belowground biomass, but had an opposite tendency to decrease the aboveground biomass. The influences of warming on aboveground production were dependent upon precipitation. Experimental warming had little effect on aboveground biomass in the years with higher precipitation, but significantly suppressed aboveground biomass in dry years. Our results suggest that warming had indirect effects on plant production via its effect on the water availability. Nitrogen addition significantly increased above- and below-ground production, suggesting that N is one of the most important limiting factors determining plant productivity in the studied meadow steppe. Significant interactive effects of warming plus N addition on belowground biomass were also detected. Our observations revealed that environmental changes (warming and N deposition) play significant roles in regulating plant community composition and biomass production in temperate meadow steppe ecosystem in northeast China.

  7. Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

    KAUST Repository

    Tian, R.-M.; Wang, Y.; Bougouffa, Salim; Gao, Z.-M.; Cai, L.; Zhang, W.-P.; Bajic, Vladimir B.; Qian, P.-Y.

    2014-01-01

    and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S

  8. Trophic structure of cold-water coral communities revealed from the analysis of tissue isotopes and fatty acid composition

    NARCIS (Netherlands)

    Van Oevelen, D.; Duineveld, G.; Lavaleye, M.S.S.; Kutti, T.; Soetaert, K.

    2018-01-01

    The trophic structure of cold-water coral reef communities at two contrasting locations, the 800-m deep Belgica Mounds (Irish margin) and the 300-m deep Træna reefs (Norwegian Shelf), was investigated using stable isotope (δ13C and δ15N) and fatty-acid composition analysis. A broad range of

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

    Science.gov (United States)

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

    2007-12-01

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

  10. Composites

    International Nuclear Information System (INIS)

    Kasen, M.B.

    1983-01-01

    This chapter discusses the roles of composite laminates and aggregates in cryogenic technology. Filamentary-reinforced composites are emphasized because they are the most widely used composite materials. Topics considered include composite systems and terminology, design and fabrication, composite failure, high-pressure reinforced plastic laminates, low-pressure reinforced plastics, reinforced metals, selectively reinforced structures, the effect of cryogenic temperatures, woven-fabric and random-mat composites, uniaxial fiber-reinforced composites, composite joints in cryogenic structures, joining techniques at room temperature, radiation effects, testing laminates at cryogenic temperatures, static and cyclic tensile testing, static and cyclic compression testing, interlaminar shear testing, secondary property tests, and concrete aggregates. It is suggested that cryogenic composite technology would benefit from the development of a fracture mechanics model for predicting the fitness-for-purpose of polymer-matrix composite structures

  11. SUBSURFACE CONSTRUCTION AND DEVELOPMENT ANALYSIS

    International Nuclear Information System (INIS)

    N.E. Kramer

    1998-01-01

    The purpose of this analysis is to identify appropriate construction methods and develop a feasible approach for construction and development of the repository subsurface facilities. The objective of this analysis is to support development of the subsurface repository layout for License Application (LA) design. The scope of the analysis for construction and development of the subsurface Repository facilities covers: (1) Excavation methods, including application of knowledge gained from construction of the Exploratory Studies Facility (ESF). (2) Muck removal from excavation headings to the surface. This task will examine ways of preventing interference with other subsurface construction activities. (3) The logistics and equipment for the construction and development rail haulage systems. (4) Impact of ground support installation on excavation and other construction activities. (5) Examination of how drift mapping will be accomplished. (6) Men and materials handling. (7) Installation and removal of construction utilities and ventilation systems. (8) Equipping and finishing of the emplacement drift mains and access ramps to fulfill waste emplacement operational needs. (9) Emplacement drift and access mains and ramps commissioning prior to handover for emplacement operations. (10) Examination of ways to structure the contracts for construction of the repository. (11) Discussion of different construction schemes and how to minimize the schedule risks implicit in those schemes. (12) Surface facilities needed for subsurface construction activities

  12. Program overview: Subsurface science program

    International Nuclear Information System (INIS)

    1994-03-01

    The OHER Subsurface Science Program is DOE's core basic research program concerned with subsoils and groundwater. These practices have resulted in contamination by mixtures of organic chemicals, inorganic chemicals, and radionuclides. A primary long-term goal is to provide a foundation of knowledge that will lead to the reduction of environmental risks and to cost-effective cleanup strategies. Since the Program was initiated in 1985, a substantial amount of research in hydrogeology, subsurface microbiology, and the geochemistry of organically complexed radionuclides has been completed, leading to a better understanding of contaminant transport in groundwater and to new insights into microbial distribution and function in the subsurface environments. The Subsurface Science Program focuses on achieving long-term scientific advances that will assist DOE in the following key areas: providing the scientific basis for innovative in situ remediation technologies that are based on a concept of decontamination through benign manipulation of natural systems; understanding the complex mechanisms and process interactions that occur in the subsurface; determining the influence of chemical and geochemical-microbial processes on co-contaminant mobility to reduce environmental risks; improving predictions of contaminant transport that draw on fundamental knowledge of contaminant behavior in the presence of physical and chemical heterogeneities to improve cleanup effectiveness and to predict environmental risks

  13. Interactive effects of warming and increased precipitation on community structure and composition in an annual forb dominated desert steppe.

    Directory of Open Access Journals (Sweden)

    Yanhui Hou

    Full Text Available To better understand how warming, increased precipitation and their interactions influence community structure and composition, a field experiment simulating hydrothermal interactions was conducted at an annual forb dominated desert steppe in northern China over 2 years. Increased precipitation increased species richness while warming significantly decreased species richness, and their effects were additive rather than interactive. Although interannual variations in weather conditions may have a major affect on plant community composition on short term experiments, warming and precipitation treatments affected individual species and functional group composition. Warming caused C4 grasses such as Cleistogenes squarrosa to increase while increased precipitation caused the proportions of non-perennial C3 plants like Artemisia capillaris to decrease and perennial C4 plants to increase.

  14. Dramatic changes in ectomycorrhizal community composition, root tip abundance and mycelial production along a stand-scale nitrogen deposition gradient

    DEFF Research Database (Denmark)

    Kjøller, Rasmus; Nilsson, Lars Ola; Hansen, Karin

    2012-01-01

    • Nitrogen (N) availability is known to influence ectomycorrhizal fungal components, such as fungal community composition, biomass of root tips and production of mycelia, but effects have never been demonstrated within the same forest. • We measured concurrently the abundance of ectomycorrhizal...... root tips and the production of external mycelia, and explored the changes in the ectomycorrhizal community composition, across a stand-scale N deposition gradient (from 27 to 43 kg N ha¿¹ yr¿¹) at the edge of a spruce forest. The N status was affected along the gradient as shown by a range of N...... availability indices. • Ectomycorrhizal root tip abundance and mycelial production decreased five and 10-fold, respectively, with increasing N deposition. In addition, the ectomycorrhizal fungal community changed and the species richness decreased. The changes were correlated with the measured indices of N...

  15. Microbial Community Composition of Polyhydroxyalkanoate-Accumulating Organisms in Full-Scale Wastewater Treatment Plants Operated in Fully Aerobic Mode

    Science.gov (United States)

    Oshiki, Mamoru; Onuki, Motoharu; Satoh, Hiroyasu; Mino, Takashi

    2013-01-01

    The removal of biodegradable organic matter is one of the most important objectives in biological wastewater treatments. Polyhydroxyalkanoate (PHA)-accumulating organisms (PHAAOs) significantly contribute to the removal of biodegradable organic matter; however, their microbial community composition is mostly unknown. In the present study, the microbial community composition of PHAAOs was investigated at 8 full-scale wastewater treatment plants (WWTPs), operated in fully aerobic mode, by fluorescence in situ hybridization (FISH) analysis and post-FISH Nile blue A (NBA) staining techniques. Our results demonstrated that 1) PHAAOs were in the range of 11–18% in the total number of cells, and 2) the microbial community composition of PHAAOs was similar at the bacterial domain/phylum/class/order level among the 8 full-scale WWTPs, and dominant PHAAOs were members of the class Alphaproteobacteria and Betaproteobacteria. The microbial community composition of α- and β-proteobacterial PHAAOs was examined by 16S rRNA gene clone library analysis and further by applying a set of newly designed oligonucleotide probes targeting 16S rRNA gene sequences of α- or β-proteobacterial PHAAOs. The results demonstrated that the microbial community composition of PHAAOs differed in the class Alphaproteobacteria and Betaproteobacteria, which possibly resulted in a different PHA accumulation capacity among the WWTPs (8.5–38.2 mg-C g-VSS−1 h−1). The present study extended the knowledge of the microbial diversity of PHAAOs in full-scale WWTPs operated in fully aerobic mode. PMID:23257912

  16. Community Composition and Ultrastructure of a Nitrate-Dependent Anaerobic Methane-Oxidizing Enrichment Culture.

    Science.gov (United States)

    Gambelli, Lavinia; Guerrero-Cruz, Simon; Mesman, Rob J; Cremers, Geert; Jetten, Mike S M; Op den Camp, Huub J M; Kartal, Boran; Lueke, Claudia; van Niftrik, Laura

    2018-02-01

    Methane is a very potent greenhouse gas and can be oxidized aerobically or anaerobically through microbe-mediated processes, thus decreasing methane emissions in the atmosphere. Using a complementary array of methods, including phylogenetic analysis, physiological experiments, and light and electron microscopy techniques (including electron tomography), we investigated the community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic oxidation of methane (AOM) was coupled to nitrate reduction. A membrane bioreactor was seeded with AOM biomass and continuously fed with excess methane. After 150 days, the bioreactor reached a daily consumption of 10 mmol nitrate · liter -1 · day -1 The biomass consisted of aggregates that were dominated by nitrate-dependent anaerobic methane-oxidizing " Candidatus Methanoperedens"-like archaea (40%) and nitrite-dependent anaerobic methane-oxidizing " Candidatus Methylomirabilis"-like bacteria (50%). The " Ca Methanoperedens" spp. were identified by fluorescence in situ hybridization and immunogold localization of the methyl-coenzyme M reductase (Mcr) enzyme, which was located in the cytoplasm. The " Ca Methanoperedens" sp. aggregates consisted of slightly irregular coccoid cells (∼1.5-μm diameter) which produced extruding tubular structures and putative cell-to-cell contacts among each other. " Ca Methylomirabilis" sp. bacteria exhibited the polygonal cell shape typical of this genus. In AOM archaea and bacteria, cytochrome c proteins were localized in the cytoplasm and periplasm, respectively, by cytochrome staining. Our results indicate that AOM bacteria and archaea might work closely together in the process of anaerobic methane oxidation, as the bacteria depend on the archaea for nitrite. Future studies will be aimed at elucidating the function of the cell-to-cell interactions in nitrate-dependent AOM. IMPORTANCE Microorganisms performing nitrate- and nitrite-dependent anaerobic

  17. PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances.

    Science.gov (United States)

    Tang, Zheng-Zheng; Chen, Guanhua; Alekseyenko, Alexander V

    2016-09-01

    Recent advances in sequencing technology have made it possible to obtain high-throughput data on the composition of microbial communities and to study the effects of dysbiosis on the human host. Analysis of pairwise intersample distances quantifies the association between the microbiome diversity and covariates of interest (e.g. environmental factors, clinical outcomes, treatment groups). In the design of these analyses, multiple choices for distance metrics are available. Most distance-based methods, however, use a single distance and are underpowered if the distance is poorly chosen. In addition, distance-based tests cannot flexibly handle confounding variables, which can result in excessive false-positive findings. We derive presence-weighted UniFrac to complement the existing UniFrac distances for more powerful detection of the variation in species richness. We develop PERMANOVA-S, a new distance-based method that tests the association of microbiome composition with any covariates of interest. PERMANOVA-S improves the commonly-used Permutation Multivariate Analysis of Variance (PERMANOVA) test by allowing flexible confounder adjustments and ensembling multiple distances. We conducted extensive simulation studies to evaluate the performance of different distances under various patterns of association. Our simulation studies demonstrate that the power of the test relies on how well the selected distance captures the nature of the association. The PERMANOVA-S unified test combines multiple distances and achieves good power regardless of the patterns of the underlying association. We demonstrate the usefulness of our approach by reanalyzing several real microbiome datasets. miProfile software is freely available at https://medschool.vanderbilt.edu/tang-lab/software/miProfile z.tang@vanderbilt.edu or g.chen@vanderbilt.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  18. Mosquito community composition in dynamic landscapes from the Atlantic Forest biome (Diptera, Culicidae

    Directory of Open Access Journals (Sweden)

    Mário Luís Pessôa Guedes

    2014-03-01

    Full Text Available Mosquito community composition in dynamic landscapes from the Atlantic Forest biome (Diptera, Culicidae. Considering that some species of Culicidae are vectors of pathogens, both the knowledge of the diversity of the mosquito fauna and how some environment factors influence in it, are important subjects. In order to address the composition of Culicidae species in a forest reserve in southern Atlantic Forest, we compared biotic and abiotic environmental determinants and how they were associated with the occurrence of species between sunset and sunrise. The level of conservation of the area was also considered. The investigation was carried out at Reserva Natural do Morro da Mina, in Antonina, state of Paraná, Brazil. We performed sixteen mosquito collections employing Shannon traps at three-hour intervals, from July 2008 to June 2009. The characterization of the area was determined using ecological indices of diversity, evenness, dominance and similarity. We compared the frequency of specimens with abiotic variables, i.e., temperature, relative humidity and pluviosity. Seven thousand four hundred ten mosquito females were captured. They belong to 48 species of 12 genera. The most abundant genera were Anopheles, Culex, Coquillettidia, Aedes and Runchomyia. Among the species, the most abundant was Anopheles cruzii, the primary vector of Plasmodium spp. in the Atlantic Forest. Results of the analyses showed that the abiotic variables we tested did not influence the occurrence of species, although certain values suggested that there was an optimum range for the occurrence of culicid species. It was possible to detect the presence of species of Culicidae with different epidemiologic profiles and habitat preference.

  19. Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard

    Directory of Open Access Journals (Sweden)

    P. Kotas

    2018-03-01

    Full Text Available The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS, and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs. We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects, mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.

  20. Microbial plankton communities in the coastal southeastern Black Sea: biomass, composition and trophic interactions

    Directory of Open Access Journals (Sweden)

    Ulgen Aytan

    2018-04-01

    Full Text Available Summary: We investigated biomass and composition of the pico-, nano- and microplankton communities in a coastal station of the southeastern Black Sea during 2011. We also examined trophic interactions within these communities from size-fractionated dilution experiments in February, June and December. Autotrophic and heterotrophic biomasses showed similar seasonal trends, with a peak in June, but heterotrophs dominated throughout the year. Autotrophic biomass was mainly comprised by nanoflagellates and diatoms in the first half of the year, and by dinoflagellates and Synechococcus spp. in the second half. Heterotrophic biomass was mostly dominated by heterotrophic bacteria, followed by nanoflagellates and microzooplankton. Dilution experiments suggest that nano- and microzooplankton were significant consumers of autotrophs and heterotrophic bacteria. More than 100% of bacterial production was consumed by grazers in all experiments, while 46%, 21% and 30% of daily primary production were consumed in February, June and December, respectively. In February, autotrophs were the main carbon source, but in December, it was heterotrophic bacteria. An intermediate situation was observed in June, with similar carbon flows from autotrophs and heterotrophic bacteria. Size-fraction dilution experiments suggested that heterotrophic nanoflagellates are an important link between the high heterotrophic bacterial biomass and microzooplankton. In summary, these results indicate that nano- and microzooplankton were responsible for comprising a significant fraction of total microbial plankton biomass, standing stocks, growth and grazing processes. This suggests that in 2011, the microbial food web was an important compartment of the planktonic food web in the coastal southeastern Black Sea. Keywords: Phytoplankton, Microzooplankton, Carbon biomass, Microbial food web, Grazing, Black Sea

  1. Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors

    Science.gov (United States)

    Williams, Thomas R.

    2014-01-01

    ABSTRACT The aerial surfaces of plants, or phyllosphere, are microbial habitats important to plant and human health. In order to accurately investigate microbial interactions in the phyllosphere under laboratory conditions, the composition of the phyllosphere microbiota should be representative of the diversity of microorganisms residing on plants in nature. We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce. The bacterial diversity on laboratory-grown plants was also significantly lower and contained relatively higher proportions of Betaproteobacteria as opposed to the Gammaproteobacteria-enriched communities on field lettuce. Incubation of field-grown Romaine lettuce plants in environmental growth chambers for 2 weeks resulted in bacterial cell densities and taxa similar to those on plants in the field but with less diverse bacterial populations overall. In comparison, the inoculation of laboratory-grown Romaine lettuce plants with either freshly collected or cryopreserved microorganisms recovered from field lettuce resulted in the development of a field-like microbiota on the lettuce within 2 days of application. The survival of an inoculated strain of Escherichia coli O157:H7 was unchanged by microbial community transfer; however, the inoculation of E. coli O157:H7 onto those plants resulted in significant shifts in the abundance of certain taxa. This finding was strictly dependent on the presence of a field-associated as opposed to a laboratory-associated microbiota on the plants. Phyllosphere microbiota transplantation in the laboratory will be useful for elucidating microbial interactions on plants that are important to agriculture and microbial food safety. PMID:25118240

  2. Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)

    Science.gov (United States)

    Kotas, Petr; Šantrůčková, Hana; Elster, Josef; Kaštovská, Eva

    2018-03-01

    The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS), and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level) were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs). We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects), mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.

  3. Effects of topoclimatic complexity on the composition of woody plant communities.

    Science.gov (United States)

    Oldfather, Meagan F; Britton, Matthew N; Papper, Prahlad D; Koontz, Michael J; Halbur, Michelle M; Dodge, Celeste; Flint, Alan L; Flint, Lorriane E; Ackerly, David D

    2016-01-01

    Topography can create substantial environmental variation at fine spatial scales. Shaped by slope, aspect, hill-position and elevation, topoclimate heterogeneity may increase ecological diversity, and act as a spatial buffer for vegetation responding to climate change. Strong links have been observed between climate heterogeneity and species diversity at broader scales, but the importance of topoclimate for woody vegetation across small spatial extents merits closer examination. We established woody vegetation monitoring plots in mixed evergreen-deciduous woodlands that spanned topoclimate gradients of a topographically heterogeneous landscape in northern California. We investigated the association between the structure of adult and regenerating size classes of woody vegetation and multidimensional topoclimate at a fine scale. We found a significant effect of topoclimate on both single-species distributions and community composition. Effects of topoclimate were evident in the regenerating size class for all dominant species (four Quercus spp., Umbellularia californica and Pseudotsuga menziesii) but only in two dominant species (Quercus agrifolia and Quercus garryana) for the adult size class. Adult abundance was correlated with water balance parameters (e.g. climatic water deficit) and recruit abundance was correlated with an interaction between the topoclimate parameters and conspecific adult abundance (likely reflecting local seed dispersal). However, in all cases, the topoclimate signal was weak. The magnitude of environmental variation across our study site may be small relative to the tolerance of long-lived woody species. Dispersal limitations, management practices and patchy disturbance regimes also may interact with topoclimate, weakening its influence on woody vegetation distributions. Our study supports the biological relevance of multidimensional topoclimate for mixed woodland communities, but highlights that this relationship might be mediated by

  4. Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils.

    Science.gov (United States)

    Liu, Kaihui; Ding, Xiaowei; Tang, Xiaofei; Wang, Jianjun; Li, Wenjun; Yan, Qingyun; Liu, Zhenghua

    2018-01-01

    Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline-alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity ( P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi ( P analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.

  5. Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline–Alkaline Soils

    Science.gov (United States)

    Liu, Kaihui; Ding, Xiaowei; Tang, Xiaofei; Wang, Jianjun; Li, Wenjun; Yan, Qingyun; Liu, Zhenghua

    2018-01-01

    Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi. PMID:29535703

  6. Subsurface Fire Hazards Technical Report

    International Nuclear Information System (INIS)

    Logan, R.C.

    1999-01-01

    The results from this report are preliminary and cannot be used as input into documents supporting procurement, fabrication, or construction. This technical report identifies fire hazards and proposes their mitigation for the subsurface repository fire protection system. The proposed mitigation establishes the minimum level of fire protection to meet NRC regulations, DOE fire protection orders, that ensure fire containment, adequate life safety provisions, and minimize property loss. Equipment requiring automatic fire suppression systems is identified. The subsurface fire hazards that are identified can be adequately mitigated

  7. Integrated Surface/subsurface flow modeling in PFLOTRAN

    Energy Technology Data Exchange (ETDEWEB)

    Painter, Scott L [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-10-01

    Understanding soil water, groundwater, and shallow surface water dynamics as an integrated hydrological system is critical for understanding the Earth’s critical zone, the thin outer layer at our planet’s surface where vegetation, soil, rock, and gases interact to regulate the environment. Computational tools that take this view of soil moisture and shallow surface flows as a single integrated system are typically referred to as integrated surface/subsurface hydrology models. We extend the open-source, highly parallel, subsurface flow and reactive transport simulator PFLOTRAN to accommodate surface flows. In contrast to most previous implementations, we do not represent a distinct surface system. Instead, the vertical gradient in hydraulic head at the land surface is neglected, which allows the surface flow system to be eliminated and incorporated directly into the subsurface system. This tight coupling approach leads to a robust capability and also greatly simplifies implementation in existing subsurface simulators such as PFLOTRAN. Successful comparisons to independent numerical solutions build confidence in the approximation and implementation. Example simulations of the Walker Branch and East Fork Poplar Creek watersheds near Oak Ridge, Tennessee demonstrate the robustness of the approach in geometrically complex applications. The lack of a robust integrated surface/subsurface hydrology capability had been a barrier to PFLOTRAN’s use in critical zone studies. This work addresses that capability gap, thus enabling PFLOTRAN as a community platform for building integrated models of the critical zone.

  8. Bacterial community composition in Brazilian Anthrosols and adjacent soils characterized using culturing and molecular identification.

    Science.gov (United States)

    O'Neill, B; Grossman, J; Tsai, M T; Gomes, J E; Lehmann, J; Peterson, J; Neves, E; Thies, J E

    2009-07-01

    Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared from soil extracts to isolate bacteria unique to the two soil types and then sequenced their 16S rRNA genes to determine their phylogenetic placement. Higher numbers of culturable bacteria, by over two orders of magnitude at the deepest sampling depths, were counted in the Anthrosols. Sequences of bacteria isolated on soil extract media yielded five possible new bacterial families. Also, a higher number of families in the bacteria were represented by isolates from the deeper soil depths in the Anthrosols. Higher bacterial populations and a greater diversity of isolates were found in all of the Anthrosols, to a depth of up to 1 m, compared to adjacent soils located within 50-500 m of their associated Anthrosols. Compared to standard culture media, soil extract media revealed diverse soil microbial populations adapted to the unique biochemistry and physiological ecology of these Anthrosols.

  9. Evaluation of the microbial community, acidity and proximate composition of akamu, a fermented maize food.

    Science.gov (United States)

    Obinna-Echem, Patience C; Kuri, Victor; Beal, Jane

    2014-01-30

    Akamu is a lactic acid-fermented cereal-based food that constitutes a major infant complementary food in most West African countries. The identities of LAB populations from DGGE analysis and conventionally isolated LAB and yeasts from traditionally fermented akamu were confirmed by PCR sequencing analysis. The relationships between pH, acidity and lactic acid levels and proximate composition of the akamu samples were investigated. The LAB communities in the akamu samples comprised mainly Lactobacillus species, including Lb. fermentum, Lb. plantarum, Lb. delbrueckii ssp. bulgaricus and Lb. helveticus, as well as Lactococcus lactis ssp. cremoris. Identified yeasts were Candida tropicalis, Candida albicans, Clavispora lusitaniae and Saccharomyces paradoxus. Low pH (3.22-3.95) was accompanied by high lactic acid concentrations (43.10-84.29 mmol kg⁻¹). Protein (31.88-74.32 g kg⁻¹) and lipid (17.74-36.83 g kg⁻¹ contents were negatively correlated with carbohydrate content (897.48-926.20 g kg⁻¹, of which ≤1 g kg⁻¹ was sugars). Ash was either not detected or present only in trace amounts (≤4 g kg⁻¹). Energy levels ranged from 17.29 to 18.37 kJ g⁻¹. The akamu samples were predominantly starchy foods and had pH < 4.0 owing to the activities of fermentative LAB. © 2013 Society of Chemical Industry.

  10. Spatiotemporal variation of bacterial community composition and possible controlling factors in tropical shallow lagoons.

    Science.gov (United States)

    Laque, Thaís; Farjalla, Vinicius F; Rosado, Alexandre S; Esteves, Francisco A

    2010-05-01

    Bacterial community composition (BCC) has been extensively related to specific environmental conditions. Tropical coastal lagoons present great temporal and spatial variation in their limnological conditions, which, in turn, should influence the BCC. Here, we sought for the limnological factors that influence, in space and time, the BCC in tropical coastal lagoons (Rio de Janeiro State, Brazil). The Visgueiro lagoon was sampled monthly for 1 year and eight lagoons were sampled once for temporal and spatial analysis, respectively. BCC was evaluated by bacteria-specific PCR-DGGE methods. Great variations were observed in limnological conditions and BCC on both temporal and spatial scales. Changes in the BCC of Visgueiro lagoon throughout the year were best related to salinity and concentrations of NO (3) (-) , dissolved phosphorus and chlorophyll-a, while changes in BCC between lagoons were best related to salinity and dissolved phosphorus concentration. Salinity has a direct impact on the integrity of the bacterial cell, and it was previously observed that phosphorus is the main limiting nutrient to bacterial growth in these lagoons. Therefore, we conclude that great variations in limnological conditions of coastal lagoons throughout time and space resulted in different BCCs and salinity and nutrient concentration, particularly dissolved phosphorus, are the main limnological factors influencing BCC in these tropical coastal lagoons.

  11. Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields.

    Science.gov (United States)

    Bai, Li; Cui, Jiaqi; Jie, Weiguang; Cai, Baiyan

    2015-11-01

    We used rhizosphere soil sampled from one field during zero year and two years of continuous cropping of high-protein soybean to analyze the taxonomic community compositions of fungi during periods of high-incidence of root rot. Our objectives were to identify the dominant pathogens in order to provide a theoretical basis for the study of pathogenesis as well as control tactics for soybean root rot induced by continuous cropping. A total of 17,801 modified internal transcribed spacer (ITS) sequences were obtained from three different soybean rhizosphere soil samples after zero year and 1 or 2 years of continuous cropping using 454 high-throughput sequencing. The dominant eumycote fungal were identified to be Ascomycota and Basidiomycota in the three soil samples. Continuous cropping of soybean affected the diversity of fungi in rhizosphere soils and increased the abundance of Thelebolus and Mortierellales significantly. Thanatephorus, Fusarium, and Alternaria were identified to be the dominant pathogenic fungal genera in rhizosphere soil from continuously cropped soybean fields. Copyright © 2015 Elsevier GmbH. All rights reserved.

  12. British Container Breeding Mosquitoes: The Impact of Urbanisation and Climate Change on Community Composition and Phenology

    Science.gov (United States)

    Townroe, Susannah; Callaghan, Amanda

    2014-01-01

    The proliferation of artificial container habitats in urban areas has benefitted urban adaptable mosquito species globally. In areas where mosquitoes transmit viruses and parasites, it can promote vector population productivity and fuel mosquito-borne disease outbreaks. In Britain, storage of water in garden water butts is increasing, potentially expanding mosquito larval habitats and influencing population dynamics and mosquito-human contact. Here we show that the community composition, abundance and phenology of mosquitoes breeding in experimental water butt containers were influenced by urbanisation. Mosquitoes in urban containers were less species-rich but present in significantly higher densities (100.4±21.3) per container than those in rural containers (77.7±15.1). Urban containers were dominated by Culex pipiens (a potential vector of West Nile Virus [WNV]) and appear to be increasingly exploited by Anopheles plumbeus (a human-biting potential WNV and malaria vector). Culex phenology was influenced by urban land use type, with peaks in larval abundances occurring earlier in urban than rural containers. Among other factors, this was associated with an urban heat island effect which raised urban air and water temperatures by 0.9°C and 1.2°C respectively. Further increases in domestic water storage, particularly in urban areas, in combination with climate changes will likely alter mosquito population dynamics in the UK. PMID:24759617

  13. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.

    Directory of Open Access Journals (Sweden)

    Alexander J Probst

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

  14. Composition

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2011-01-01

    Strategies are open compositions to be realised by improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". Caution: streaming the sound files will in some cases only provide a few minutes' sample. Please DOWNLOAD them to hear them in full...

  15. Composition

    DEFF Research Database (Denmark)

    2014-01-01

    Memory Pieces are open compositions to be realised solo by an improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". Caution: streaming the sound files will in some cases only provide a few minutes' sample. Please DOWNLOAD them to hear them...

  16. Rainfall and Coconut Accession Explain the Composition and Abundance of the Community of Potential Auchenorrhyncha Phytoplasma Vectors in Brazil.

    Science.gov (United States)

    Silva, Flaviana G; Passos, Eliana M; Diniz, Leandro E C; Farias, Adriano P; Teodoro, Adenir V; Fernandes, Marcelo F; Dollet, Michel

    2018-04-05

    Coconut plantations are attacked by the lethal yellowing (LY), which is spreading rapidly with extremely destructive effects in several countries. The disease is caused by phytoplasmas that occur in the plant phloem and are transmitted by Haplaxius crudus (Van Duzee) (Auchenorrhyncha: Cixiidae). Owing to their phloem-sap feeding habit, other planthopper species possibly act as vectors. Here, we aimed at assessing the seasonal variation in the Auchenorrhyncha community in six dwarf coconut accessions. Also, we assessed the relative contribution of biotic (coconut accession) and abiotic (rainfall, temperature) in explaining Auchenorrhyncha composition and abundance. The Auchenorrhyncha community was monthly evaluated for 1 yr using yellow sticky traps. Among the most abundant species, Oecleus sp., Balclutha sp., Deltocephalinae sp.2, Deltocephalinae sp.3, Cenchreini sp., Omolicna nigripennis Caldwell (Derbidae), and Cedusa sp. are potential phytoplasma vectors. The composition of the Auchenorrhyncha community differed between dwarf coconut accessions and periods, namely, in March and April (transition from dry to rainy season) and August (transition from rainy to dry season). In these months, Oecleus sp. was predominantly found in the accessions Cameroon Red Dwarf, Malayan Red Dwarf, and Brazilian Red Dwarf Gramame, while Cenchreini sp. and Bolbonota sp. were dominant in the accessions Brazilian Yellow Dwarf Gramame, Malayan Yellow Dwarf, and Brazilian Green Dwarf Jequi. We conclude that dwarf coconut host several Auchenorrhyncha species potential phytoplasma vectors. Furthermore, coconut accessions could be exploited in breeding programs aiming at prevention of LY. However, rainfall followed by accessions mostly explained the composition and abundance of the Auchenorrhyncha community.

  17. Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant.

    Directory of Open Access Journals (Sweden)

    Elisabet Marti

    Full Text Available Antibiotic resistance represents a global health problem, requiring better understanding of the ecology of antibiotic resistance genes (ARGs, their selection and their spread in the environment. Antibiotics are constantly released to the environment through wastewater treatment plant (WWTP effluents. We investigated, therefore, the effect of these discharges on the prevalence of ARGs and bacterial community composition in biofilm and sediment samples of a receiving river. We used culture-independent approaches such as quantitative PCR to determine the prevalence of eleven ARGs and 16S rRNA gene-based pyrosequencing to examine the composition of bacterial communities. Concentration of antibiotics in WWTP influent and effluent were also determined. ARGs such as qnrS, bla TEM, bla CTX-M, bla SHV, erm(B, sul(I, sul(II, tet(O and tet(W were detected in all biofilm and sediment samples analyzed. Moreover, we observed a significant increase in the relative abundance of ARGs in biofilm samples collected downstream of the WWTP discharge. We also found significant differences with respect to community structure and composition between upstream and downstream samples. Therefore, our results indicate that WWTP discharges may contribute to the spread of ARGs into the environment and may also impact on the bacterial communities of the receiving river.

  18. Instrumented Moles for Planetary Subsurface Regolith Studies

    Science.gov (United States)

    Richter, L. O.; Coste, P. A.; Grzesik, A.; Knollenberg, J.; Magnani, P.; Nadalini, R.; Re, E.; Romstedt, J.; Sohl, F.; Spohn, T.

    2006-12-01

    Soil-like materials, or regolith, on solar system objects provide a record of physical and/or chemical weathering processes on the object in question and as such possess significant scientific relevance for study by landed planetary missions. In the case of Mars, a complex interplay has been at work between impact gardening, aeolian as well as possibly fluvial processes. This resulted in regolith that is texturally as well as compositionally layered as hinted at by results from the Mars Exploration Rover (MER) missions which are capable of accessing shallow subsurface soils by wheel trenching. Significant subsurface soil access on Mars, i.e. to depths of a meter or more, remains to be accomplished on future missions. This has been one of the objectives of the unsuccessful Beagle 2 landed element of the ESA Mars Express mission having been equipped with the Planetary Underground Tool (PLUTO) subsurface soil sampling Mole system capable of self-penetration into regolith due to an internal electro-mechanical hammering mechanism. This lightweight device of less than 900 g mass was designed to repeatedly obtain and deliver to the lander regolith samples from depths down to 2 m which would have been analysed for organic matter and, specifically, organic carbon from potential extinct microbial activity. With funding from the ESA technology programme, an evolved Mole system - the Instrumented Mole System (IMS) - has now been developed to a readiness level of TRL 6. The IMS is to serve as a carrier for in situ instruments for measurements in planetary subsurface soils. This could complement or even eliminate the need to recover samples to the surface. The Engineering Model hardware having been developed within this effort is designed for accommodating a geophysical instrument package (Heat Flow and Physical Properties Package, HP3) that would be capable of measuring regolith physical properties and planetary heat flow. The chosen design encompasses a two-body Mole

  19. Ability of surface and subsurface death assemblages to track km-scale spatial and decade-scale temporal variability in living communities: Tests using the urban southern California continental shelf

    Science.gov (United States)

    Kidwell, Susan M.; Tomasovych, Adam

    2016-04-01

    Actualistic analysis of death assemblages has always focused on quantifying, and achieving a mechanistic understanding of, the reliability of deep-time records, and is now additionally motivated to assess natural conditions before human impacts. The southern California continental shelf permits us to evaluate the ability of time-averaged death assemblages to detect known variability in urban nutrients, which increased from the early 20th Century up until the 1972 Clean Water Act. Biomonitoring since then documents strong declines in populations of pollution- and hypoxia-tolerant species, especially the chemosymbiontic lucinid bivalve Parvilucina tenuisculpta. This shelf is taphonomically challenging -- median shell ages are 50-100 y, only 1% of shells survive, the mixed-zone is ~25 cm thick, and siliciclastic accumulation is slow, in contrast to sediment-trapping estuaries and lagoons. Nonetheless, both surficial death and buried core assemblages capture first-order urban trends, albeit with significant damping of the large, spatially localized mid-20th Century pulse in Parvilucina abundance. Paleoecologists will thus detect but under-estimate the original magnitude of even strong past excursions in community composition, an important bounding condition for both recent- and deep-time analysis.

  20. Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific

    Directory of Open Access Journals (Sweden)

    Xin Sun

    2017-06-01

    Full Text Available The ozone-depleting and greenhouse gas, nitrous oxide (N2O, is mainly consumed by the microbially mediated anaerobic process, denitrification. N2O consumption is the last step in canonical denitrification, and is also the least O2 tolerant step. Community composition of total and active N2O consuming bacteria was analyzed based on total (DNA and transcriptionally active (RNA nitrous oxide reductase (nosZ genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N2O concentration but not O2. Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number was similar to or even larger than in anoxic waters, implying the potential for N2O consumption even in the oxygenated surface water.

  1. Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific

    Science.gov (United States)

    Sun, Xin; Jayakumar, Amal; Ward, Bess B.

    2017-01-01

    The ozone-depleting and greenhouse gas, nitrous oxide (N2O), is mainly consumed by the microbially mediated anaerobic process, denitrification. N2O consumption is the last step in canonical denitrification, and is also the least O2 tolerant step. Community composition of total and active N2O consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase (nosZ) genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N2O concentration but not O2. Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number) was similar to or even larger than in anoxic waters, implying the potential for N2O consumption even in the oxygenated surface water. PMID:28702012

  2. Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna.

    Directory of Open Access Journals (Sweden)

    Annika Busse

    Full Text Available The mechanisms which structure communities have been the focus of a large body of research. Here, we address the question if habitat characteristics describing habitat quality may drive changes in community composition and beta diversity of bromeliad-inhabiting microfauna. In our system, changes in canopy cover along an environmental gradient may affect resource availability, disturbance in form of daily water temperature fluctuations and predation, and thus may lead to changes in community structure of bromeliad microfauna through differences in habitat quality along this gradient. Indeed, we observed distinct changes in microfauna community composition along the environmental gradient explained by changes in the extent of daily water temperature fluctuations. We found beta diversity to be higher under low habitat quality (low canopy cover than under high habitat quality (high canopy cover, which could potentially be explained by a higher relative importance of stochastic processes under low habitat quality. We also partitioned beta diversity into turnover and nestedness components and we found a nested pattern of beta diversity along the environmental gradient, with communities from the lower-quality habitat being nested subsets of communities from the higher-quality habitat. However, this pattern resulted from an increase in microfauna alpha diversity with an increase in habitat quality. By providing insights into microfauna-environment relationships our results contribute to the mechanistic understanding of community dynamics in small freshwater bodies. Here, we highlight the importance of habitat characteristics representing habitat quality in structuring communities, and suggest that this information may help to improve conservation practices of small freshwater ecosystems.

  3. Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna

    Science.gov (United States)

    Antiqueira, Pablo A. P.; Neutzling, Alexandre S.; Wolf, Anna M.; Romero, Gustavo Q.; Petermann, Jana S.

    2018-01-01

    The mechanisms which structure communities have been the focus of a large body of research. Here, we address the question if habitat characteristics describing habitat quality may drive changes in community composition and beta diversity of bromeliad-inhabiting microfauna. In our system, changes in canopy cover along an environmental gradient may affect resource availability, disturbance in form of daily water temperature fluctuations and predation, and thus may lead to changes in community structure of bromeliad microfauna through differences in habitat quality along this gradient. Indeed, we observed distinct changes in microfauna community composition along the environmental gradient explained by changes in the extent of daily water temperature fluctuations. We found beta diversity to be higher under low habitat quality (low canopy cover) than under high habitat quality (high canopy cover), which could potentially be explained by a higher relative importance of stochastic processes under low habitat quality. We also partitioned beta diversity into turnover and nestedness components and we found a nested pattern of beta diversity along the environmental gradient, with communities from the lower-quality habitat being nested subsets of communities from the higher-quality habitat. However, this pattern resulted from an increase in microfauna alpha diversity with an increase in habitat quality. By providing insights into microfauna-environment relationships our results contribute to the mechanistic understanding of community dynamics in small freshwater bodies. Here, we highlight the importance of habitat characteristics representing habitat quality in structuring communities, and suggest that this information may help to improve conservation practices of small freshwater ecosystems. PMID:29401522

  4. Feasibility of a subsurface storage

    International Nuclear Information System (INIS)

    1998-11-01

    This report analyses the notion of subsurface storage under the scientifical, technical and legal aspects. This reflection belongs to the studies about long duration storage carried out in the framework of the axis 3 of the December 30, 1991 law. The report comprises 3 parts. The first part is a synthesis of the complete subsurface storage study: definitions, aim of the report, very long duration storage paradigm, description files of concepts, thematic synthesis (legal aspects, safety, monitoring, sites, seismicity, heat transfers, corrosion, concretes, R and works, handling, tailings and dismantlement, economy..), multi-criteria/multi-concept cross-analysis. The second part deals with the technical aspects of the subsurface storage: safety approach (long duration impact, radiation protection, mastery of effluents), monitoring strategy, macroscopic inventory of B-type waste packages, inventory of spent fuels, glasses, hulls and nozzles, geological contexts in the French territory (sites selection and characterization), on-site activities, hydrogeological and geochemical aspects, geo-technical works and infrastructures organization, subsurface seismic effects, cooling modes (ventilation, heat transfer with the geologic environment), heat transfer research programs (convection, poly-phase cooling in porous media), handling constraints, concretes (use, behaviour, durability), corrosion of metallic materials, technical-economical analysis, international context (experience feedback from Sweden (CLAB) and the USA (Yucca Mountain), other European and French facilities). The last part of the report is a graphical appendix with 3-D views and schemes of the different concepts. (J.S.)

  5. Safety analysis in subsurface repositories

    International Nuclear Information System (INIS)

    1985-06-01

    The development of mathematical models to represent the repository-geosphere-biosphere system, and the development of a structure for data acquisition, processing, and use to analyse the safety of subsurface repositories, are presented. To study the behavior of radionuclides in geosphere a laboratory to determine the hydrodynamic dispersion coefficient was constructed. (M.C.K.) [pt

  6. SUBSURFACE VISUAL ALARM SYSTEM ANALYSIS

    International Nuclear Information System (INIS)

    D.W. Markman

    2001-01-01

    The ''Subsurface Fire Hazard Analysis'' (CRWMS M andO 1998, page 61), and the document, ''Title III Evaluation Report for the Surface and Subsurface Communication System'', (CRWMS M andO 1999a, pages 21 and 23), both indicate the installed communication system is adequate to support Exploratory Studies Facility (ESF) activities with the exception of the mine phone system for emergency notification purposes. They recommend the installation of a visual alarm system to supplement the page/party phone system The purpose of this analysis is to identify data communication highway design approaches, and provide justification for the selected or recommended alternatives for the data communication of the subsurface visual alarm system. This analysis is being prepared to document a basis for the design selection of the data communication method. This analysis will briefly describe existing data or voice communication or monitoring systems within the ESF, and look at how these may be revised or adapted to support the needed data highway of the subsurface visual alarm. system. The existing PLC communication system installed in subsurface is providing data communication for alcove No.5 ventilation fans, south portal ventilation fans, bulkhead doors and generator monitoring system. It is given that the data communication of the subsurface visual alarm system will be a digital based system. It is also given that it is most feasible to take advantage of existing systems and equipment and not consider an entirely new data communication system design and installation. The scope and primary objectives of this analysis are to: (1) Briefly review and describe existing available data communication highways or systems within the ESF. (2) Examine technical characteristics of an existing system to disqualify a design alternative is paramount in minimizing the number of and depth of a system review. (3) Apply general engineering design practices or criteria such as relative cost, and degree

  7. Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland.

    Directory of Open Access Journals (Sweden)

    Erica N Spotswood

    Full Text Available Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species, temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

  8. Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland.

    Science.gov (United States)

    Spotswood, Erica N; Bartolome, James W; Allen-Diaz, Barbara

    2015-01-01

    Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

  9. Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

    KAUST Repository

    Tian, R.-M.

    2014-11-04

    Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. IMPORTANCE This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper

  10. Martian sub-surface ionising radiation: biosignatures and geology

    Directory of Open Access Journals (Sweden)

    J. M. Ward

    2007-07-01

    Full Text Available The surface of Mars, unshielded by thick atmosphere or global magnetic field, is exposed to high levels of cosmic radiation. This ionising radiation field is deleterious to the survival of dormant cells or spores and the persistence of molecular biomarkers in the subsurface, and so its characterisation is of prime astrobiological interest. Here, we present modelling results of the absorbed radiation dose as a function of depth through the Martian subsurface, suitable for calculation of biomarker persistence. A second major implementation of this dose accumulation rate data is in application of the optically stimulated luminescence technique for dating Martian sediments.

    We present calculations of the dose-depth profile in the Martian subsurface for various scenarios: variations of surface composition (dry regolith, ice, layered permafrost, solar minimum and maximum conditions, locations of different elevation (Olympus Mons, Hellas basin, datum altitude, and increasing atmospheric thickness over geological history. We also model the changing composition of the subsurface radiation field with depth compared between Martian locations with different shielding material, determine the relative dose contributions from primaries of different energies, and discuss particle deflection by the crustal magnetic fields.

  11. Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors.

    Science.gov (United States)

    Pervin, Hasina M; Dennis, Paul G; Lim, Hui J; Tyson, Gene W; Batstone, Damien J; Bond, Philip L

    2013-12-01

    Temperature-phased anaerobic digestion (TPAD) is an emerging technology that facilitates improved performance and pathogen destruction in anaerobic sewage sludge digestion by optimising conditions for 1) hydrolytic and acidogenic organisms in a first-stage/pre-treatment reactor and then 2) methogenic populations in a second stage reactor. Pre-treatment reactors are typically operated at 55-65 °C and as such select for thermophilic bacterial communities. However, details of key microbial populations in hydrolytic communities and links to functionality are very limited. In this study, experimental thermophilic pre-treatment (TP) and control mesophilic pre-treatment (MP) reactors were operated as first-stages of TPAD systems treating activated sludge for 340 days. The TP system was operated sequentially at 50, 60 and 65 °C, while the MP rector was held at 35 °C for the entire period. The composition of microbial communities associated with the MP and TP pre-treatment reactors was characterised weekly using terminal-restriction fragment length polymorphism (T-RFLP) supported by clone library sequencing of 16S rRNA gene amplicons. The outcomes of this approach were confirmed using 454 pyrosequencing of gene amplicons and fluorescence in-situ hybridisation (FISH). TP associated bacterial communities were dominated by populations affiliated to the Firmicutes, Thermotogae, Proteobacteria and Chloroflexi. In particular there was a progression from Thermotogae to Lutispora and Coprothermobacter and diversity decreased as temperature and hydrolysis performance increased. While change in the composition of TP associated bacterial communities was attributable to temperature, that of MP associated bacterial communities was related to the composition of the incoming feed. This study determined processes driving the dynamics of key microbial populations that are correlated with an enhanced hydrolytic functionality of the TPAD system. Copyright © 2013 Elsevier Ltd. All rights

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

    Directory of Open Access Journals (Sweden)

    Lisa eGieg

    2013-06-01

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

  13. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

    Science.gov (United States)

    Oberbeckmann, Sonja; Osborn, A Mark; Duhaime, Melissa B

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET

  14. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris

    Science.gov (United States)

    Osborn, A. Mark

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5–6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae—all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the

  15. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

    Directory of Open Access Journals (Sweden)

    Sonja Oberbeckmann

    Full Text Available Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate (PET drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates and diatoms (e.g. Coscinodiscophytina, Bacillariophytina. The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact

  16. Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community.

    Science.gov (United States)

    Hughes, Rebecca-Ayme; Zhang, Yunlong; Zhang, Ran; Williams, Philip G; Lindsey, Jonathan S; Miller, Eric S

    2017-10-01

    The cyanobacterial culture HT-58-2 was originally described as a strain of Tolypothrix nodosa with the ability to produce tolyporphins, which comprise a family of distinct tetrapyrrole macrocycles with reported efflux pump inhibition properties. Upon reviving the culture from what was thought to be a nonextant collection, studies of culture conditions, strain characterization, phylogeny, and genomics have been undertaken. Here, HT-58-2 was shown by 16S rRNA analysis to closely align with Brasilonema strains and not with Tolypothrix isolates. Light, fluorescence, and scanning electron microscopy revealed cyanobacterium filaments that are decorated with attached bacteria and associated with free bacteria. Metagenomic surveys of HT-58-2 cultures revealed a diversity of bacteria dominated by Erythrobacteraceae , 97% of which are Porphyrobacter species. A dimethyl sulfoxide washing procedure was found to yield enriched cyanobacterial DNA (presumably by removing community bacteria) and sequence data sufficient for genome assembly. The finished, closed HT-58-2Cyano genome consists of 7.85 Mbp (42.6% G+C) and contains 6,581 genes. All genes for biosynthesis of tetrapyrroles (e.g., heme, chlorophyll a , and phycocyanobilin) and almost all for cobalamin were identified dispersed throughout the chromosome. Among the 6,177 protein-encoding genes, coding sequences (CDSs) for all but two of the eight enzymes for conversion of glutamic acid to protoporphyrinogen IX also were found within one major gene cluster. The cluster also includes 10 putative genes (and one hypothetical gene) encoding proteins with domains for a glycosyltransferase, two cytochrome P450 enzymes, and a flavin adenine dinucleotide (FAD)-binding protein. The composition of the gene cluster suggests a possible role in tolyporphin biosynthesis. IMPORTANCE A worldwide search more than 25 years ago for cyanobacterial natural products with anticancer activity identified a culture (HT-58-2) from Micronesia that

  17. Assessment of Zooplankton Community Composition along a Depth Profile in the Central Red Sea

    KAUST Repository

    Pearman, John K.; Irigoien, Xabier

    2015-01-01

    community. The genus Corycaeus had a higher proportion of reads in the epipelagic zone with Pleuromamma becoming increasingly dominant with depth. No significant difference was observed in the community between night and day sampling however there was a

  18. Biodiversity and community composition of sediment macrofauna associated with deep-sea Lophelia pertusa habitats in the Gulf of Mexico

    Science.gov (United States)

    Demopoulos, Amanda W.J.; Bourque, Jill R.; Frometa, Janessy

    2014-01-01

    Scleractinian corals create three-dimensional reefs that provide sheltered refuges, facilitate sediment accumulation, and enhance colonization of encrusting fauna. While heterogeneous coral habitats can harbor high levels of biodiversity, their effect on the community composition within nearby sediments remains unclear, particularly in the deep sea. Sediment macrofauna from deep-sea coral habitats (Lophelia pertusa) and non-coral, background sediments