Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges do...
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| Veröffentlicht in: | Nature biotechnology 2006-10, Vol.24 (10), p.1263-1269 |
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| creator | Martín, Héctor García Ivanova, Natalia Kunin, Victor Warnecke, Falk Barry, Kerrie W McHardy, Alice C Yeates, Christine He, Shaomei Salamov, Asaf A Szeto, Ernest Dalin, Eileen Putnam, Nik H Shapiro, Harris J Pangilinan, Jasmyn L Rigoutsos, Isidore Kyrpides, Nikos C Blackall, Linda Louise McMahon, Katherine D Hugenholtz, Philip |
| description | Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, “
Candidatus
Accumulibacter phosphatis.” The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of
A. phosphatis
in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the
A. phosphatis
genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems. |
| doi_str_mv | 10.1038/nbt1247 |
| format | Article |
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Candidatus
Accumulibacter phosphatis.” The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of
A. phosphatis
in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the
A. phosphatis
genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems.</description><identifier>ISSN: 1087-0156</identifier><identifier>EISSN: 1546-1696</identifier><identifier>DOI: 10.1038/nbt1247</identifier><identifier>PMID: 16998472</identifier><identifier>CODEN: NABIF9</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>Adaptation, Biological ; Agriculture ; Betaproteobacteria - genetics ; Betaproteobacteria - metabolism ; Bioinformatics ; Biological and medical sciences ; Biomedical and Life Sciences ; Biomedical Engineering/Biotechnology ; Biomedicine ; Biotechnology ; Cultivation ; Economics ; Fundamental and applied biological sciences. Psychology ; Genome, Bacterial ; Genomics ; Life Sciences ; Microbiology ; Organic waste treatment ; Phosphorus ; Phosphorus - isolation & purification ; Phosphorus - metabolism ; Phosphorus removal ; Sewage - microbiology ; Sludge ; Waste Disposal, Fluid ; Water treatment</subject><ispartof>Nature biotechnology, 2006-10, Vol.24 (10), p.1263-1269</ispartof><rights>Springer Nature America, Inc. 2006</rights><rights>2007 INIST-CNRS</rights><rights>COPYRIGHT 2006 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Oct 2006</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c606t-4d71cc4a31c4f5db80c44efc715a042d50693864e9e2e5f758e928d7b36cfb8c3</citedby><cites>FETCH-LOGICAL-c606t-4d71cc4a31c4f5db80c44efc715a042d50693864e9e2e5f758e928d7b36cfb8c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nbt1247$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nbt1247$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18218432$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16998472$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Martín, Héctor García</creatorcontrib><creatorcontrib>Ivanova, Natalia</creatorcontrib><creatorcontrib>Kunin, Victor</creatorcontrib><creatorcontrib>Warnecke, Falk</creatorcontrib><creatorcontrib>Barry, Kerrie W</creatorcontrib><creatorcontrib>McHardy, Alice C</creatorcontrib><creatorcontrib>Yeates, Christine</creatorcontrib><creatorcontrib>He, Shaomei</creatorcontrib><creatorcontrib>Salamov, Asaf A</creatorcontrib><creatorcontrib>Szeto, Ernest</creatorcontrib><creatorcontrib>Dalin, Eileen</creatorcontrib><creatorcontrib>Putnam, Nik H</creatorcontrib><creatorcontrib>Shapiro, Harris J</creatorcontrib><creatorcontrib>Pangilinan, Jasmyn L</creatorcontrib><creatorcontrib>Rigoutsos, Isidore</creatorcontrib><creatorcontrib>Kyrpides, Nikos C</creatorcontrib><creatorcontrib>Blackall, Linda Louise</creatorcontrib><creatorcontrib>McMahon, Katherine D</creatorcontrib><creatorcontrib>Hugenholtz, Philip</creatorcontrib><title>Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities</title><title>Nature biotechnology</title><addtitle>Nat Biotechnol</addtitle><addtitle>Nat Biotechnol</addtitle><description>Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, “
Candidatus
Accumulibacter phosphatis.” The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of
A. phosphatis
in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the
A. phosphatis
genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. 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Psychology</subject><subject>Genome, Bacterial</subject><subject>Genomics</subject><subject>Life Sciences</subject><subject>Microbiology</subject><subject>Organic waste treatment</subject><subject>Phosphorus</subject><subject>Phosphorus - isolation & purification</subject><subject>Phosphorus - metabolism</subject><subject>Phosphorus removal</subject><subject>Sewage - microbiology</subject><subject>Sludge</subject><subject>Waste Disposal, Fluid</subject><subject>Water treatment</subject><issn>1087-0156</issn><issn>1546-1696</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqN0d9r1TAUB_AiiptT_A-kCNPtoTNJ0zR9nGPqYDKZP56EkqYnXUabXHPazf33nnEvXLYnCSEh-SQh55tlrzk74qzUH0I3cyHrJ9kur6QquGrUU5ozXReMV2one4F4zRhTUqnn2Q7tN1rWYjf7_RVmM0CIk7e5CWa8Q495dPl8G3MIVyZY6PPOxzEO3poxX11FpJ4WzBNM8YaWDk4_frs8zHFc-gFyG6dpCX72gC-zZ86MCK82417289Ppj5MvxfnF57OT4_PCKqbmQvY1t1aaklvpqr7TzEoJzta8MkyKvmKqKbWS0ICAytWVhkbovu5KZV2nbbmXvVvfu0rxzwI4t5NHC-NoAsQFW8FqUZZMEXz7CF7HJdGvyQhRUqkYI3S0RoMZofXBxTkZS60HKlIM4DytH_OG81oJrunA4YMDZGb4Ow9mQWzPvl_-v7349dC-X1ubImIC166Sn0y6azlr72NvN7GTfLP519JN0G_dJmcC-xtgkFJ0iXL1uHWa3pPlvTtYO6StMEDaFujxm_8A52e_6Q</recordid><startdate>20061001</startdate><enddate>20061001</enddate><creator>Martín, Héctor García</creator><creator>Ivanova, Natalia</creator><creator>Kunin, Victor</creator><creator>Warnecke, Falk</creator><creator>Barry, Kerrie W</creator><creator>McHardy, Alice C</creator><creator>Yeates, Christine</creator><creator>He, Shaomei</creator><creator>Salamov, Asaf A</creator><creator>Szeto, Ernest</creator><creator>Dalin, Eileen</creator><creator>Putnam, Nik H</creator><creator>Shapiro, Harris J</creator><creator>Pangilinan, Jasmyn L</creator><creator>Rigoutsos, Isidore</creator><creator>Kyrpides, Nikos C</creator><creator>Blackall, Linda Louise</creator><creator>McMahon, Katherine D</creator><creator>Hugenholtz, Philip</creator><general>Nature Publishing Group US</general><general>Nature</general><general>Nature Publishing Group</general><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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7P</scope><scope>M7S</scope><scope>MBDVC</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7QL</scope></search><sort><creationdate>20061001</creationdate><title>Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities</title><author>Martín, Héctor García ; Ivanova, Natalia ; Kunin, Victor ; Warnecke, Falk ; Barry, Kerrie W ; McHardy, Alice C ; Yeates, Christine ; He, Shaomei ; Salamov, Asaf A ; Szeto, Ernest ; Dalin, Eileen ; Putnam, Nik H ; Shapiro, Harris J ; Pangilinan, Jasmyn L ; Rigoutsos, Isidore ; Kyrpides, Nikos C ; Blackall, Linda Louise ; McMahon, Katherine D ; Hugenholtz, Philip</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c606t-4d71cc4a31c4f5db80c44efc715a042d50693864e9e2e5f758e928d7b36cfb8c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Adaptation, Biological</topic><topic>Agriculture</topic><topic>Betaproteobacteria - genetics</topic><topic>Betaproteobacteria - metabolism</topic><topic>Bioinformatics</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedical Engineering/Biotechnology</topic><topic>Biomedicine</topic><topic>Biotechnology</topic><topic>Cultivation</topic><topic>Economics</topic><topic>Fundamental and applied biological sciences. 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Biotechnol</addtitle><date>2006-10-01</date><risdate>2006</risdate><volume>24</volume><issue>10</issue><spage>1263</spage><epage>1269</epage><pages>1263-1269</pages><issn>1087-0156</issn><eissn>1546-1696</eissn><coden>NABIF9</coden><abstract>Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, “
Candidatus
Accumulibacter phosphatis.” The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of
A. phosphatis
in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the
A. phosphatis
genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>16998472</pmid><doi>10.1038/nbt1247</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Nature biotechnology, 2006-10, Vol.24 (10), p.1263-1269 |
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| language | eng |
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| source | MEDLINE; Springer Nature - Complete Springer Journals; Nature Journals Online |
| subjects | Adaptation, Biological Agriculture Betaproteobacteria - genetics Betaproteobacteria - metabolism Bioinformatics Biological and medical sciences Biomedical and Life Sciences Biomedical Engineering/Biotechnology Biomedicine Biotechnology Cultivation Economics Fundamental and applied biological sciences. Psychology Genome, Bacterial Genomics Life Sciences Microbiology Organic waste treatment Phosphorus Phosphorus - isolation & purification Phosphorus - metabolism Phosphorus removal Sewage - microbiology Sludge Waste Disposal, Fluid Water treatment |
| title | Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities |
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