Microbial Diversity in Uranium Mining-Impacted Soils as Revealed by High-Density 16S Microarray and Clone Library
Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray f...
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| Veröffentlicht in: | Microbial ecology 2010, Vol.59 (1), p.94-108 |
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| creator | Rastogi, Gurdeep Osman, Shariff Vaishampayan, Parag A Andersen, Gary L Stetler, Larry D Sani, Rajesh K |
| description | Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site. |
| doi_str_mv | 10.1007/s00248-009-9598-5 |
| format | Article |
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Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.</description><identifier>ISSN: 0095-3628</identifier><identifier>EISSN: 1432-184X</identifier><identifier>DOI: 10.1007/s00248-009-9598-5</identifier><identifier>PMID: 19888627</identifier><identifier>CODEN: MCBEBU</identifier><language>eng</language><publisher>New York: New York : Springer-Verlag</publisher><subject>Acid soils ; Agricultural soils ; Bacteria - classification ; Bacteria - drug effects ; Bacteria - genetics ; Base Sequence ; Biodiversity ; Biological and medical sciences ; Biomedical and Life Sciences ; Diversity indices ; Ecology ; Environmental Monitoring ; Fundamental and applied biological sciences. Psychology ; Gene Library ; Geoecology/Natural Processes ; Hills ; Industrial Waste ; Libraries ; Life Sciences ; Metals mining ; Microbial activity ; Microbial Ecology ; Microbiology ; Mining ; Molecular Sequence Data ; Nature Conservation ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Proteobacteria ; RNA, Ribosomal, 16S - genetics ; Sedimentary soils ; Sediments ; Soil - analysis ; Soil bacteria ; SOIL MICROBIOLOGY ; Soil Pollutants - analysis ; Soil pollution ; Soil samples ; Uranium ; Uranium - analysis ; Water Quality/Water Pollution ; X-ray fluorescence</subject><ispartof>Microbial ecology, 2010, Vol.59 (1), p.94-108</ispartof><rights>Copyright 2010 Springer Science+Business Media, Inc.</rights><rights>Springer Science+Business Media, LLC 2009</rights><rights>2015 INIST-CNRS</rights><rights>Springer Science+Business Media, LLC 2010</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c505t-18bafdd8cb2b596987cdd8ba294781a64819cb94674a238c90af095cb52ce45e3</citedby><cites>FETCH-LOGICAL-c505t-18bafdd8cb2b596987cdd8ba294781a64819cb94674a238c90af095cb52ce45e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/27770598$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/27770598$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,776,780,799,881,4009,27902,27903,27904,41467,42536,51297,57995,58228</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22496769$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19888627$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1154146$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Rastogi, Gurdeep</creatorcontrib><creatorcontrib>Osman, Shariff</creatorcontrib><creatorcontrib>Vaishampayan, Parag A</creatorcontrib><creatorcontrib>Andersen, Gary L</creatorcontrib><creatorcontrib>Stetler, Larry D</creatorcontrib><creatorcontrib>Sani, Rajesh K</creatorcontrib><creatorcontrib>Subsurface Biogeochemical Research (SBR)</creatorcontrib><title>Microbial Diversity in Uranium Mining-Impacted Soils as Revealed by High-Density 16S Microarray and Clone Library</title><title>Microbial ecology</title><addtitle>Microb Ecol</addtitle><addtitle>Microb Ecol</addtitle><description>Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.</description><subject>Acid soils</subject><subject>Agricultural soils</subject><subject>Bacteria - classification</subject><subject>Bacteria - drug effects</subject><subject>Bacteria - genetics</subject><subject>Base Sequence</subject><subject>Biodiversity</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Diversity indices</subject><subject>Ecology</subject><subject>Environmental Monitoring</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Library</subject><subject>Geoecology/Natural Processes</subject><subject>Hills</subject><subject>Industrial Waste</subject><subject>Libraries</subject><subject>Life Sciences</subject><subject>Metals mining</subject><subject>Microbial activity</subject><subject>Microbial Ecology</subject><subject>Microbiology</subject><subject>Mining</subject><subject>Molecular Sequence Data</subject><subject>Nature Conservation</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Phylogeny</subject><subject>Proteobacteria</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sedimentary soils</subject><subject>Sediments</subject><subject>Soil - analysis</subject><subject>Soil bacteria</subject><subject>SOIL MICROBIOLOGY</subject><subject>Soil Pollutants - analysis</subject><subject>Soil pollution</subject><subject>Soil samples</subject><subject>Uranium</subject><subject>Uranium - analysis</subject><subject>Water Quality/Water Pollution</subject><subject>X-ray fluorescence</subject><issn>0095-3628</issn><issn>1432-184X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9ks9vFCEcxYnR2LX6B3hQiUnjaRQYfh7N1tom25i4buKNAMNs2cwwW5hpsv-9tLPp3jwReJ_vg5cHAO8x-ooREt8yQoTKCiFVKaZkxV6ABaY1qbCkf1-CRRFYVXMiz8CbnHcIYcFJ_RqcYSWl5EQswP1tcGmwwXTwMjz4lMN4gCHCTTIxTD28DTHEbXXT740bfQPXQ-gyNBn-9g_edOXEHuB12N5Vlz4-DWO-hk-mJiVzgCY2cNkN0cNVsMmkw1vwqjVd9u-O6znYXP34s7yuVr9-3iy_ryrHEBtLBGvappHOEssUV1K4srOGKCokNpxKrJxVlAtqSC2dQqYtcZ1lxHnKfH0OPs--Qx6Dzi6M3t25IUbvRo0xo5jyAn2ZoX0a7iefR92H7HzXmeiHKWuFKBW1IuRk90zuhinFkkATjCiWTIgC4Rkq8XNOvtX7FPoSWmOkHyvTc2W6NKMfK9OszHw8Gk-2981p4thRAS6OgMnOdG1pxoX8zBFCFRdcFY7MXC5S3Pp0euH_bv8wD-3yOKSTqRACFaLon2a9NYM221Qu3qwJwnX5S4pSJut_b-i_zQ</recordid><startdate>2010</startdate><enddate>2010</enddate><creator>Rastogi, Gurdeep</creator><creator>Osman, Shariff</creator><creator>Vaishampayan, Parag A</creator><creator>Andersen, Gary L</creator><creator>Stetler, Larry D</creator><creator>Sani, Rajesh K</creator><general>New York : Springer-Verlag</general><general>Springer Science + Business Media, Inc</general><general>Springer-Verlag</general><general>Springer</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7SN</scope><scope>7T7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>F1W</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>H95</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>L.G</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7QO</scope><scope>OTOTI</scope></search><sort><creationdate>2010</creationdate><title>Microbial Diversity in Uranium Mining-Impacted Soils as Revealed by High-Density 16S Microarray and Clone Library</title><author>Rastogi, Gurdeep ; Osman, Shariff ; Vaishampayan, Parag A ; Andersen, Gary L ; Stetler, Larry D ; Sani, Rajesh K</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c505t-18bafdd8cb2b596987cdd8ba294781a64819cb94674a238c90af095cb52ce45e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Acid soils</topic><topic>Agricultural soils</topic><topic>Bacteria - classification</topic><topic>Bacteria - drug effects</topic><topic>Bacteria - genetics</topic><topic>Base Sequence</topic><topic>Biodiversity</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Diversity indices</topic><topic>Ecology</topic><topic>Environmental Monitoring</topic><topic>Fundamental and applied biological sciences. 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Shariff</au><au>Vaishampayan, Parag A</au><au>Andersen, Gary L</au><au>Stetler, Larry D</au><au>Sani, Rajesh K</au><aucorp>Subsurface Biogeochemical Research (SBR)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Microbial Diversity in Uranium Mining-Impacted Soils as Revealed by High-Density 16S Microarray and Clone Library</atitle><jtitle>Microbial ecology</jtitle><stitle>Microb Ecol</stitle><addtitle>Microb Ecol</addtitle><date>2010</date><risdate>2010</risdate><volume>59</volume><issue>1</issue><spage>94</spage><epage>108</epage><pages>94-108</pages><issn>0095-3628</issn><eissn>1432-184X</eissn><coden>MCBEBU</coden><abstract>Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.</abstract><cop>New York</cop><pub>New York : Springer-Verlag</pub><pmid>19888627</pmid><doi>10.1007/s00248-009-9598-5</doi><tpages>15</tpages></addata></record> |
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| ispartof | Microbial ecology, 2010, Vol.59 (1), p.94-108 |
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| source | MEDLINE; Jstor Complete Legacy; Springer Nature - Complete Springer Journals |
| subjects | Acid soils Agricultural soils Bacteria - classification Bacteria - drug effects Bacteria - genetics Base Sequence Biodiversity Biological and medical sciences Biomedical and Life Sciences Diversity indices Ecology Environmental Monitoring Fundamental and applied biological sciences. Psychology Gene Library Geoecology/Natural Processes Hills Industrial Waste Libraries Life Sciences Metals mining Microbial activity Microbial Ecology Microbiology Mining Molecular Sequence Data Nature Conservation Oligonucleotide Array Sequence Analysis Phylogeny Proteobacteria RNA, Ribosomal, 16S - genetics Sedimentary soils Sediments Soil - analysis Soil bacteria SOIL MICROBIOLOGY Soil Pollutants - analysis Soil pollution Soil samples Uranium Uranium - analysis Water Quality/Water Pollution X-ray fluorescence |
| title | Microbial Diversity in Uranium Mining-Impacted Soils as Revealed by High-Density 16S Microarray and Clone Library |
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