Bacterial diversity and community composition from seasurface to subseafloor
We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of...
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| Veröffentlicht in: | The ISME Journal 2016-04, Vol.10 (4), p.979-989 |
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| creator | Walsh, Emily A Kirkpatrick, John B Rutherford, Scott D Smith, David C Sogin, Mitchell D'Hondt, Steven |
| description | We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O
2
minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment. |
| doi_str_mv | 10.1038/ismej.2015.175 |
| format | Article |
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minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.</description><identifier>ISSN: 1751-7362</identifier><identifier>EISSN: 1751-7370</identifier><identifier>DOI: 10.1038/ismej.2015.175</identifier><identifier>PMID: 26430855</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/326/171 ; Bacteria ; Bacteria - genetics ; Biodiversity ; Biomedical and Life Sciences ; Chlorophyll - chemistry ; Cluster Analysis ; Community composition ; Deep sea ; DNA, Bacterial - genetics ; Ecology ; Evolutionary Biology ; Geography ; Geologic Sediments - microbiology ; Life Sciences ; Microbial Ecology ; Microbial Genetics and Genomics ; Microbiology ; Ocean floor ; Oceans and Seas ; Original ; original-article ; Oxygen - chemistry ; RNA, Ribosomal, 16S - genetics ; Sediments ; Sequence Analysis, DNA ; Water column ; Water depth ; Water Microbiology</subject><ispartof>The ISME Journal, 2016-04, Vol.10 (4), p.979-989</ispartof><rights>The Author(s) 2016</rights><rights>Copyright Nature Publishing Group Apr 2016</rights><rights>Copyright © 2016 International Society for Microbial Ecology 2016 International Society for Microbial Ecology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c557t-c65961334650d39f2d46835a172a1ca53cc052ccce2325d123f3a6489f808cfa3</citedby><cites>FETCH-LOGICAL-c557t-c65961334650d39f2d46835a172a1ca53cc052ccce2325d123f3a6489f808cfa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4796937/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4796937/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26430855$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Walsh, Emily A</creatorcontrib><creatorcontrib>Kirkpatrick, John B</creatorcontrib><creatorcontrib>Rutherford, Scott D</creatorcontrib><creatorcontrib>Smith, David C</creatorcontrib><creatorcontrib>Sogin, Mitchell</creatorcontrib><creatorcontrib>D'Hondt, Steven</creatorcontrib><title>Bacterial diversity and community composition from seasurface to subseafloor</title><title>The ISME Journal</title><addtitle>ISME J</addtitle><addtitle>ISME J</addtitle><description>We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O
2
minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.</description><subject>631/326/171</subject><subject>Bacteria</subject><subject>Bacteria - genetics</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Chlorophyll - chemistry</subject><subject>Cluster Analysis</subject><subject>Community composition</subject><subject>Deep sea</subject><subject>DNA, Bacterial - genetics</subject><subject>Ecology</subject><subject>Evolutionary Biology</subject><subject>Geography</subject><subject>Geologic Sediments - microbiology</subject><subject>Life Sciences</subject><subject>Microbial Ecology</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiology</subject><subject>Ocean floor</subject><subject>Oceans and Seas</subject><subject>Original</subject><subject>original-article</subject><subject>Oxygen - chemistry</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sediments</subject><subject>Sequence Analysis, DNA</subject><subject>Water column</subject><subject>Water depth</subject><subject>Water Microbiology</subject><issn>1751-7362</issn><issn>1751-7370</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqNkctPAyEQxonR2Fq9ejSbePGyLY8Fdi8m2vhKmnjRM6EsVJrdpcJuk_730odNNR68wDDzmw-YD4BLBIcIknxkQ63nQwwRHSJOj0A_rijlhMPjfcxwD5yFMIeQcsb4KehhlhGYU9oHk3upWu2trJLSLrUPtl0lsikT5eq6a9anGC1czFvXJMa7Oglahs4bqXTSuiR005gwlXP-HJwYWQV9sdsH4P3x4W38nE5en17Gd5NUUcrbVDFaMERIxigsSWFwmbGcUIk4lkhJSpSCFCulNCaYlggTQyTL8sLkMFdGkgG43eouummtS6Wb1stKLLytpV8JJ634WWnsh5i5pch4wQrCo8DNTsC7z06HVtQ2KF1VstGuCwLxOCiKccb-g5Ic8ixDEb3-hc5d55s4iQ2FCcRFEanhllLeheC12b8bQbH2VGw8FWtPYx-NDVeHv93j3yZGYLQFQiw1M-0P7v1b8gtok64e</recordid><startdate>20160401</startdate><enddate>20160401</enddate><creator>Walsh, Emily A</creator><creator>Kirkpatrick, John B</creator><creator>Rutherford, Scott D</creator><creator>Smith, David C</creator><creator>Sogin, Mitchell</creator><creator>D'Hondt, Steven</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</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>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</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>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</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>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>SOI</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20160401</creationdate><title>Bacterial diversity and community composition from seasurface to subseafloor</title><author>Walsh, Emily A ; Kirkpatrick, John B ; Rutherford, Scott D ; Smith, David C ; Sogin, Mitchell ; D'Hondt, Steven</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c557t-c65961334650d39f2d46835a172a1ca53cc052ccce2325d123f3a6489f808cfa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>631/326/171</topic><topic>Bacteria</topic><topic>Bacteria - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The ISME Journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Walsh, Emily A</au><au>Kirkpatrick, John B</au><au>Rutherford, Scott D</au><au>Smith, David C</au><au>Sogin, Mitchell</au><au>D'Hondt, Steven</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Bacterial diversity and community composition from seasurface to subseafloor</atitle><jtitle>The ISME Journal</jtitle><stitle>ISME J</stitle><addtitle>ISME J</addtitle><date>2016-04-01</date><risdate>2016</risdate><volume>10</volume><issue>4</issue><spage>979</spage><epage>989</epage><pages>979-989</pages><issn>1751-7362</issn><eissn>1751-7370</eissn><abstract>We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O
2
minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>26430855</pmid><doi>10.1038/ismej.2015.175</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 631/326/171 Bacteria Bacteria - genetics Biodiversity Biomedical and Life Sciences Chlorophyll - chemistry Cluster Analysis Community composition Deep sea DNA, Bacterial - genetics Ecology Evolutionary Biology Geography Geologic Sediments - microbiology Life Sciences Microbial Ecology Microbial Genetics and Genomics Microbiology Ocean floor Oceans and Seas Original original-article Oxygen - chemistry RNA, Ribosomal, 16S - genetics Sediments Sequence Analysis, DNA Water column Water depth Water Microbiology |
| title | Bacterial diversity and community composition from seasurface to subseafloor |
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