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

Abstract

Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community normore » neutral processes influenced succession following perturbation.« less

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1512151
DOE Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 17; Journal Issue: 3; Journal ID: ISSN 1462-2912
Country of Publication:
United States
Language:
English

Citation Formats

Handley, Kim M, Wrighton, Kelly C, Miller, Christopher S, Wilkins, Michael J, Kantor, Rose S, Thomas, Brian C, Williams, Kenneth H, Gilbert, Jack A, Long, Philip E, and Banfield, Jillian F. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.. United States: N. p., 2015. Web. doi:10.1111/1462-2920.12467.
Handley, Kim M, Wrighton, Kelly C, Miller, Christopher S, Wilkins, Michael J, Kantor, Rose S, Thomas, Brian C, Williams, Kenneth H, Gilbert, Jack A, Long, Philip E, & Banfield, Jillian F. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.. United States. doi:10.1111/1462-2920.12467.
Handley, Kim M, Wrighton, Kelly C, Miller, Christopher S, Wilkins, Michael J, Kantor, Rose S, Thomas, Brian C, Williams, Kenneth H, Gilbert, Jack A, Long, Philip E, and Banfield, Jillian F. Sun . "Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.". United States. doi:10.1111/1462-2920.12467.
@article{osti_1512151,
title = {Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.},
author = {Handley, Kim M and Wrighton, Kelly C and Miller, Christopher S and Wilkins, Michael J and Kantor, Rose S and Thomas, Brian C and Williams, Kenneth H and Gilbert, Jack A and Long, Philip E and Banfield, Jillian F},
abstractNote = {Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.},
doi = {10.1111/1462-2920.12467},
journal = {Environmental Microbiology},
issn = {1462-2912},
number = 3,
volume = 17,
place = {United States},
year = {2015},
month = {3}
}

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M.</span> </li> <li> Bioinformatics, Vol. 26, Issue 13</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1093/bioinformatics/btq243" class="text-muted" target="_blank" rel="noopener noreferrer">10.1093/bioinformatics/btq243<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1038/163688a0" target="_blank" rel="noopener noreferrer" class="name">Measurement of Diversity<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="1949-04-01">April 1949</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Simpson, E. H.</span> </li> <li> Nature, Vol. 163, Issue 4148</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1038/163688a0" class="text-muted" target="_blank" rel="noopener noreferrer">10.1038/163688a0<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1128/AEM.71.12.8228-8235.2005" target="_blank" rel="noopener noreferrer" class="name">UniFrac: a New Phylogenetic Method for Comparing Microbial Communities<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2005-12-01">December 2005</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Lozupone, C.; Knight, R.</span> </li> <li> Applied and Environmental Microbiology, Vol. 71, Issue 12</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1128/AEM.71.12.8228-8235.2005" class="text-muted" target="_blank" rel="noopener noreferrer">10.1128/AEM.71.12.8228-8235.2005<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1128/AEM.02881-07" target="_blank" rel="noopener noreferrer" class="name">Functional Diversity and Electron Donor Dependence of Microbial Populations Capable of U(VI) Reduction in Radionuclide-Contaminated Subsurface Sediments<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2008-03-31">March 2008</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Akob, D. M.; Mills, H. J.; Gihring, T. M.</span> </li> <li> Applied and Environmental Microbiology, Vol. 74, Issue 10</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1128/AEM.02881-07" class="text-muted" target="_blank" rel="noopener noreferrer">10.1128/AEM.02881-07<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> </div> <div class="pagination-container small"> <a class="pure-button prev page" href="#" rel="prev"><span class="fa fa-angle-left"></span></a><ul class="pagination d-inline-block" style="padding-left:.2em;"></ul><a class="pure-button next page" href="#" rel="next"><span class="fa fa-angle-right"></span></a> </div> </div> </div> <div class="col-sm-3 order-sm-3"> <ul class="nav nav-stacked"> <li class="active"><a href="" class="reference-type-filter tab-nav" data-tab="biblio-references" data-filter="type" data-pattern="*"><span class="fa fa-angle-right"></span> All References</a></li> <li class="small" style="margin-left:.75em; text-transform:capitalize;"><a href="" class="reference-type-filter tab-nav" data-tab="biblio-references" data-filter="type" data-pattern="journal"><span class="fa fa-angle-right"></span> journal<small class="text-muted"> (71)</small></a></li> </ul> <div style="margin-top:2em;"> <form class="pure-form small text-muted reference-search"> <label for="reference-search-text" class="sr-only">Search</label> <input class="search form-control pure-input-1" id="reference-search-text" placeholder="Search" style="margin-bottom:10px;" /> <fieldset> <div style="margin-left:1em; font-weight:normal; line-height: 1.6em;"><input type="radio" class="sort" name="references-sort" data-sort="name" style="position:relative;top:2px;" id="reference-search-sort-name"><label for="reference-search-sort-name" style="margin-left: .3em;">Sort by title</label></div> <div style="margin-left:1em; font-weight:normal; line-height: 1.6em;"><input type="radio" class="sort" name="references-sort" data-sort="date" data-order="desc" style="position:relative;top:2px;" id="reference-search-sort-date"><label for="reference-search-sort-date" style="margin-left: .3em;">Sort by date</label></div> </fieldset> <div class="text-left" style="margin-left:1em;"> <a href="" class="filter-clear clearfix" title="Clear filter / sort" style="font-weight:normal; float:none;">[ × clear filter / sort ]</a> </div> </form> </div> </div> </div> </section> <section id="biblio-related" class="tab-content tab-content-sec " data-tab="biblio"> <div class="row"> <div class="col-sm-9 order-sm-9"> <section id="biblio-similar" class="tab-content tab-content-sec active" data-tab="related"> <div class="padding"> <p class="lead text-muted" style="font-size: 18px; margin-top:0px;">Similar records in OSTI.GOV collections:</p> <aside> <ul class="item-list" itemscope itemtype="http://schema.org/ItemList" style="padding-left:0; list-style-type: none;"> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="0" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1391703-disturbed-subsurface-microbial-communities-follow-equivalent-trajectories-despite-different-structural-starting-points-microbial-community-succession-disturbance" itemprop="url">Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points: Microbial community succession and disturbance</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Handley, Kim M.</span> ; <span class="author">Wrighton, Kelly C.</span> ; <span class="author">Miller, Christopher S.</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - Environmental Microbiology</span> </span> </div> <div class="abstract">Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.1111/1462-2920.12467" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1391703" data-product-type="Journal Article" data-product-subtype="AC" >10.1111/1462-2920.12467</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="1" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1184285-disturbed-subsurface-microbial-communities-follow-equivalent-trajectories-despite-different-structural-starting-points" itemprop="url">Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Handley, Kim M.</span> ; <span class="author">Wrighton, Kelly C.</span> ; <span class="author">Miller, Christopher S.</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - Environmental Microbiology, 17(3):622-636</span> </span> </div> <div class="abstract">We explored the impact of the starting community composition and structure on ecosystem response to perturbations using organic carbon amendment experiments. Subsurface sediment was partitioned into flow-through columns, and the microbial communities were initially stimulated in situ by addition of acetate as a carbon and electron donor source. This drove community richness and evenness down, and pushed the system into a new biogeochemical state characterized by iron reduction. Reconstructed near-full-length 16S rRNA gene sequence analysis indicated a concomitant enrichment of Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After 10 to 12 days, acetate was exchange for lactate in a subset of columns.<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> Following the clear onset of sulfate reduction (35 days after acetate-amendment), acetate was substituted for lactate in additional columns. Acetatestimulated communities differed markedly during each biogeochemical regime and at each lactate-switch. Regardless, however, of when communities were switched to lactate, they followed comparable trajectories with respect to composition and structure, with convergence evident one week after each switch, and marked after one month of lactate amendment. During sulfate reduction all treatments were enriched in Firmicutes and a number of species likely involved in sulfate reduction (notably Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum). Lactate treatments were distinguished by substantially lower relative abundances of Desulfotomaculum and Bacteroidetes, and enrichments of Psychrosinus and Clostridiales species. Results imply that the structure of the starting community was not significant in controlling organism selection in community succession.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.1111/1462-2920.12467" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1184285" data-product-type="Journal Article" data-product-subtype="AC" >10.1111/1462-2920.12467</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="2" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1399243-impact-organic-carbon-electron-donors-microbial-community-development-under-iron-sulfate-reducing-conditions" itemprop="url">Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Kwon, Man Jae</span> ; <span class="author">O’Loughlin, Edward J.</span> ; <span class="author">Boyanov, Maxim I.</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - PLoS ONE</span> </span> </div> <div class="abstract">Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <span class="fa fa-book text-muted" aria-hidden="true"></span> Cited by 9<div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.1371/journal.pone.0146689" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1399243" data-product-type="Journal Article" data-product-subtype="AM" >10.1371/journal.pone.0146689</a></span></li> <li class="pure-menu-item"><span class="item-info-ftlink"><a class="misc fulltext-link " href="/servlets/purl/1399243" title="Link to document media" target="_blank" rel="noopener" data-ostiid="1399243" data-product-type="Journal Article" data-product-subtype="AM" >Full Text Available</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="3" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1088112-biostimulation-induces-syntrophic-interactions-impact-cycling-sediment-microbial-community" itemprop="url">Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Handley, KM</span> ; <span class="author">Verberkmoes, Nathan C</span> ; <span class="author">Steefel, Carl I</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - The ISME Journal</span> </span> </div> <div class="abstract">Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used community proteogenomics to test the hypothesis that excess input of acetate activates syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer. Genomic sequences from the community recovered during microbial sulfate reduction were used to econstruct, de novo, near-complete genomes for Desulfobacter (Deltaproteobacteria) and relatives of Sulfurovum and Sulfurimonas (Epsilonproteobacteria), and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen-fixation (Nif) and acetate oxidation to CO2 during amendment. Results suggest less abundant Desulfuromonadales and Bacteroidetes also actively contributed to CO2 production via the TCA cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. Modeling shows that this reaction was thermodynamically possible, and kinetically favorable relative to acetate-dependent denitrification. We conclude that high-levels of carbon amendment aimed to stimulate anaerobic heterotrophy led to carbon fixation in co-dependent chemoautotrophs. These results have implications for understanding complex ecosystem behavior, and show that high levels of organic carbon supplementation can expand the range of microbial functionalities accessible for ecosystem manipulation.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.1038/ismej.2012.148" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1088112" data-product-type="Journal Article" data-product-subtype="AC" >10.1038/ismej.2012.148</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="4" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1047981-high-density-phylochip-profiling-stimulated-aquifer-microbial-communities-reveals-complex-response-acetate-amendment" itemprop="url">High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Handley, Kim M.</span> ; <span class="author">Wrighton, Kelly E.</span> ; <span class="author">Piceno, Y. M.</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - FEMS Microbiology Ecology</span> </span> </div> <div class="abstract">There is increasing interest in harnessing the functional diversity of indigenous microbial communities to transform and remediate a wide range of environmental contaminants. Understanding the response of communities to stimulation, including flanking taxa, presents important opportunities for optimizing remediation approaches. We used high-density PhyloChip microarray analysis to comprehensively determine community membership and abundance patterns amongst a suite of samples from U(VI) bioremediation experiments. Samples were unstimulated or collected during Fe(III) and sulfate reduction from an acetate-augmented aquifer in Rifle, Colorado, and from laboratory experiments using field-collected materials. Results showed the greatest diversity in abundant SRB lineages was present in naturally-reduced<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> sediment. Desulfuromonadales and Desulfobacterales were consistently identified as the dominant Fe(III)- and sulfate-reducing bacteria (IRB and SRB) throughout acetate amendment experiments. Stimulated communities also exhibited a high degree of functional redundancy amongst enriched flanking members. Not surprisingly, competition for both sulfate and iron was evident amongst abundant taxa, but the distribution and abundance of these ancillary SRB (Peptococcaceae, Desulfovibrionales and Syntrophobacterales), and lineages containing IRB (excluding Desulfobacteraceae) was heterogeneous amongst sample types. Interesting, amongst the most abundant taxa, particularly during sulfate reduction, were Epsilonproteobacteria that perform microaerobic or nitrate-dependant sulfur oxidation, and a number of bacteria other than Geobacteraceae that may enzymatically reduce U(VI). Finally, in depth community probing with PhyloChip determined the efficacy of experimental approaches, notably revealing striking similarity amongst stimulated sediment (from drill cores and in-situ columns) and groundwater communities, and demonstrating that sediment-packed in-situ (down-well) columns served as an ideal method for subsurface biostimulation.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.1111/j.1574-6941.2012.01363.x" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1047981" data-product-type="Journal Article" data-product-subtype="AC" >10.1111/j.1574-6941.2012.01363.x</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> </ul> </aside> </div> </section> </div> <div class="col-sm-3 order-sm-3"> <ul class="nav nav-stacked"> <li class="active"><a class="tab-nav disabled" data-tab="related" style="color: #636c72 !important; opacity: 1;"><span class="fa fa-angle-right"></span> Similar Records</a></li> </ul> </div> </div> </section> </div></div> </div> </div> </section> <footer class="" style="background-color:#f9f9f9; /* padding-top: 0.5rem; */"> <div class="footer-minor"> <div class="container"> <hr class="footer-separator" /> <div class="text-center" style="margin-top:1.25rem;"> <div class="pure-menu pure-menu-horizontal"> <ul class="pure-menu-list" id="footer-org-menu"> <li class="pure-menu-item d-block d-inline-small"> <a href="https://energy.gov" target="_blank" rel="noopener noreferrer"> <img src="data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==" class="sprite sprite-footer-us-doe-min" alt="U.S. Department of Energy" /> </a> </li> <li class="pure-menu-item d-block d-inline-small"> <a href="https://www.energy.gov/science/office-science" target="_blank" rel="noopener noreferrer"> <img src="data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==" class="sprite sprite-footer-office-of-science-min" alt="Office of Science" /> </a> </li> <li class="pure-menu-item d-block d-inline-small"> <a href="/"> <img src="data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==" class="sprite sprite-footer-osti-min" alt="Office of Scientific and Technical Information" /> </a> </li> </ul> </div> </div> <div class="text-center small" style="margin-top:0.5em;margin-bottom:2.0rem;"> <div class="pure-menu pure-menu-horizontal"> <ul class="pure-menu-list"> <li class="pure-menu-item"><a href="/disclaim" class="pure-menu-link"><span class="fa fa-institution"></span> Website Policies <span class="d-none d-sm-inline" style="color:#737373;">/ Important Links</span></a></li> <li class="pure-menu-item"><a href="/contact" class="pure-menu-link"><span class="fa fa-comments-o"></span> Contact Us</a></li> <li class="d-block d-md-none mb-1"></li> <li class="pure-menu-item"><a href="https://www.facebook.com/ostigov" target="_blank" rel="noopener noreferrer" class="pure-menu-link social"><span class="fa fa-facebook" style=""></span></a></li> <li class="pure-menu-item"><a href="https://twitter.com/OSTIgov" target="_blank" rel="noopener noreferrer" class="pure-menu-link social"><span class="fa fa-twitter" style=""></span></a></li> <li class="pure-menu-item"><a href="https://www.youtube.com/user/ostigov" target="_blank" rel="noopener noreferrer" class="pure-menu-link social"><span class="fa fa-youtube-play" style=""></span></a></li> </ul> </div> </div> </div> </div> </footer> <link href="/css/ostigov.fonts.191107.1502.css" rel="stylesheet"> <script src="/js/ostigov.191107.1502.js"></script><noscript></noscript> <script defer src="/js/ostigov.biblio.191107.1502.js"></script><noscript></noscript> <script defer src="/js/lity.js"></script><noscript></noscript> <script async type="text/javascript" src="/js/Universal-Federated-Analytics-Min.js?agency=DOE" id="_fed_an_ua_tag"></script><noscript></noscript> </body> <!-- OSTI.GOV v.191107.1502 --> </html>