Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels
To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nit...
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| Veröffentlicht in: | Environmental science & technology 2009-05, Vol.43 (10), p.3529-3534 |
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| creator | Waldron, Patricia J Wu, Liyou Nostrand, Joy D. Van Schadt, Chris W He, Zhili Watson, David B Jardine, Philip M Palumbo, Anthony V Hazen, Terry C Zhou, Jizhong |
| description | To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17−70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination. |
| doi_str_mv | 10.1021/es803423p |
| format | Article |
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Van ; Schadt, Chris W ; He, Zhili ; Watson, David B ; Jardine, Philip M ; Palumbo, Anthony V ; Hazen, Terry C ; Zhou, Jizhong</creator><creatorcontrib>Waldron, Patricia J ; Wu, Liyou ; Nostrand, Joy D. Van ; Schadt, Chris W ; He, Zhili ; Watson, David B ; Jardine, Philip M ; Palumbo, Anthony V ; Hazen, Terry C ; Zhou, Jizhong ; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)</creatorcontrib><description>To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17−70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.</description><identifier>ISSN: 0013-936X</identifier><identifier>EISSN: 1520-5851</identifier><identifier>DOI: 10.1021/es803423p</identifier><identifier>PMID: 19544850</identifier><identifier>CODEN: ESTHAG</identifier><language>eng</language><publisher>Washington, DC: American Chemical Society</publisher><subject>Applied sciences ; Bacteria - genetics ; Biodegradation, Environmental ; BIOREMEDIATION ; CARBON ; Carbon - analysis ; Characterization of Natural and Affected Environments ; Cluster Analysis ; CONTAMINATION ; DNA ; Environmental monitoring ; Exact sciences and technology ; FUNCTIONALS ; GENES ; Genes, Bacterial ; Genetic diversity ; Genetic Variation ; Groundwater ; HEAVY METALS ; Metals - metabolism ; Microbiology ; MICROORGANISMS ; MONITORING ; NITROGEN ; Nitrogen - analysis ; Oligonucleotide Array Sequence Analysis ; Organic Chemicals - analysis ; Oxidation-Reduction ; Pollution ; PROBES ; Soil Microbiology ; SULFATES ; Sulfur - metabolism ; TECHNETIUM ; URANIUM ; Water Pollutants, Chemical - analysis ; Water Supply</subject><ispartof>Environmental science & technology, 2009-05, Vol.43 (10), p.3529-3534</ispartof><rights>Copyright © 2009 American Chemical Society</rights><rights>2009 INIST-CNRS</rights><rights>Copyright American Chemical Society May 15, 2009</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a463t-556ca281acfb15ade1f68bb3d58a7899422af164920d0fe7829a5102637c4b2d3</citedby><cites>FETCH-LOGICAL-a463t-556ca281acfb15ade1f68bb3d58a7899422af164920d0fe7829a5102637c4b2d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/es803423p$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/es803423p$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>230,314,776,780,881,2752,27053,27901,27902,56713,56763</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21500913$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19544850$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/973687$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Waldron, Patricia J</creatorcontrib><creatorcontrib>Wu, Liyou</creatorcontrib><creatorcontrib>Nostrand, Joy D. Van</creatorcontrib><creatorcontrib>Schadt, Chris W</creatorcontrib><creatorcontrib>He, Zhili</creatorcontrib><creatorcontrib>Watson, David B</creatorcontrib><creatorcontrib>Jardine, Philip M</creatorcontrib><creatorcontrib>Palumbo, Anthony V</creatorcontrib><creatorcontrib>Hazen, Terry C</creatorcontrib><creatorcontrib>Zhou, Jizhong</creatorcontrib><creatorcontrib>Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)</creatorcontrib><title>Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels</title><title>Environmental science & technology</title><addtitle>Environ. Sci. Technol</addtitle><description>To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17−70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.</description><subject>Applied sciences</subject><subject>Bacteria - genetics</subject><subject>Biodegradation, Environmental</subject><subject>BIOREMEDIATION</subject><subject>CARBON</subject><subject>Carbon - analysis</subject><subject>Characterization of Natural and Affected Environments</subject><subject>Cluster Analysis</subject><subject>CONTAMINATION</subject><subject>DNA</subject><subject>Environmental monitoring</subject><subject>Exact sciences and technology</subject><subject>FUNCTIONALS</subject><subject>GENES</subject><subject>Genes, Bacterial</subject><subject>Genetic diversity</subject><subject>Genetic Variation</subject><subject>Groundwater</subject><subject>HEAVY METALS</subject><subject>Metals - metabolism</subject><subject>Microbiology</subject><subject>MICROORGANISMS</subject><subject>MONITORING</subject><subject>NITROGEN</subject><subject>Nitrogen - analysis</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Organic Chemicals - analysis</subject><subject>Oxidation-Reduction</subject><subject>Pollution</subject><subject>PROBES</subject><subject>Soil Microbiology</subject><subject>SULFATES</subject><subject>Sulfur - metabolism</subject><subject>TECHNETIUM</subject><subject>URANIUM</subject><subject>Water Pollutants, Chemical - analysis</subject><subject>Water Supply</subject><issn>0013-936X</issn><issn>1520-5851</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpl0U2LFDEQBuAgijuuHvwDEgURD6357E4fx8EdhREPKnhrqtNpNkt3MqbSLoN_3iwz7ICeQhUPVeEtQp5z9o4zwd87NEwqIfcPyIprwSptNH9IVoxxWbWy_nlBniDeMMaEZOYxueCtVspotiJ_rpZgs48BJrp1wdF1SnCoPgC6ga5L94AeaRzpF29T7H1hmzjPS_D5QL_ltNi8JEd9oNsUlzDcQnYJ6a3P1xRKDwbvQr4bsIkhw-wDlHLnfrsJn5JHI0zonp3eS_Lj6uP3zadq93X7ebPeVaBqmSutawvCcLBjzzUMjo-16Xs5aAONaVslBIy8Vq1gAxtdY0QLuuRSy8aqXgzykrw8zo2YfYfWZ2evbQzB2dy1jaxNU8ybo9mn-GtxmLvZo3XTBMHFBbtGK61E2VLkq3_kTVxSSQq7ki5vlNayoLdHVEJDTG7s9snPkA4dZ93dzbr7mxX74jRw6Wc3nOXpSAW8PgFAC9OYIFiP905wzVjL5dmBxfOn_l_4FxzlqjI</recordid><startdate>20090515</startdate><enddate>20090515</enddate><creator>Waldron, Patricia J</creator><creator>Wu, Liyou</creator><creator>Nostrand, Joy D. 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Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17−70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.</abstract><cop>Washington, DC</cop><pub>American Chemical Society</pub><pmid>19544850</pmid><doi>10.1021/es803423p</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Applied sciences Bacteria - genetics Biodegradation, Environmental BIOREMEDIATION CARBON Carbon - analysis Characterization of Natural and Affected Environments Cluster Analysis CONTAMINATION DNA Environmental monitoring Exact sciences and technology FUNCTIONALS GENES Genes, Bacterial Genetic diversity Genetic Variation Groundwater HEAVY METALS Metals - metabolism Microbiology MICROORGANISMS MONITORING NITROGEN Nitrogen - analysis Oligonucleotide Array Sequence Analysis Organic Chemicals - analysis Oxidation-Reduction Pollution PROBES Soil Microbiology SULFATES Sulfur - metabolism TECHNETIUM URANIUM Water Pollutants, Chemical - analysis Water Supply |
| title | Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels |
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