Next generation sequencing reveals the hidden diversity of zooplankton assemblages
Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detectio...
Gespeichert in:
| Veröffentlicht in: | PloS one 2013-11, Vol.8 (11), p.e81327-e81327 |
|---|---|
| Hauptverfasser: | , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e81327 |
|---|---|
| container_issue | 11 |
| container_start_page | e81327 |
| container_title | PloS one |
| container_volume | 8 |
| creator | Lindeque, Penelope K Parry, Helen E Harmer, Rachel A Somerfield, Paul J Atkinson, Angus |
| description | Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel.
Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, |
| doi_str_mv | 10.1371/journal.pone.0081327 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1449332593</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A478392551</galeid><doaj_id>oai_doaj_org_article_d7c50a3f9ef34f62a8e4385fb6b27bf3</doaj_id><sourcerecordid>A478392551</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-d9787a67ce09248ff0d66bd0956d415c171fca375cb11791ad18f424c1e7037c3</originalsourceid><addsrcrecordid>eNqNkluL1DAcxYso7jr6DUQLgujDjLk0TfsiLIuXgcWF9fIa0uSfNmOnmU3awfXTmzrdZSr7IIW2JL9zkpycJHmO0QpTjt9t3OA72a52roMVQgWmhD9ITnFJyTIniD48-j9JnoSwQYjRIs8fJyckI1nGKT9Nrr7Arz6toQMve-u6NMD1AJ2yXZ162INsQ9o3kDZWa-hSbffgg-1vUmfS387tWtn97KNMhgDbqpU1hKfJIxNl8Gz6LpLvHz98O_-8vLj8tD4_u1iqvCT9Upe84DLnClBJssIYpPO80qhkuc4wU5hjoyTlTFUY8xJLjQsT960wcES5oovk5cF317ogpjiCwFlWUkpYfC2S9YHQTm7Eztut9DfCSSv-DjhfC-l7q1oQmiuGJDUlGJqZnMgCMlowU-UV4ZUZvd5Pqw3VFrSCrveynZnOZzrbiNrtBS0IYgWKBm8mA-9ixKEXWxsUtDFBcMO4b1YyxnM2oq_-Qe8_3UTVMh7AdsbFddVoKs4yXtCSMIYjtbqHio-GrVWxO8bG8Zng7UwQmT52pJZDCGL99er_2csfc_b1EdvEZvVNcO0wti7MwewAKu9C8GDuQsZIjNW_TUOM1RdT9aPsxfEF3Yluu07_AGgS_s8</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1449332593</pqid></control><display><type>article</type><title>Next generation sequencing reveals the hidden diversity of zooplankton assemblages</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS)</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Lindeque, Penelope K ; Parry, Helen E ; Harmer, Rachel A ; Somerfield, Paul J ; Atkinson, Angus</creator><contributor>Ianora, Adrianna</contributor><creatorcontrib>Lindeque, Penelope K ; Parry, Helen E ; Harmer, Rachel A ; Somerfield, Paul J ; Atkinson, Angus ; Ianora, Adrianna</creatorcontrib><description>Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel.
Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups.
Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0081327</identifier><identifier>PMID: 24244737</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Biodiversity ; Biogeochemical cycles ; Biotechnology ; Communities ; Community structure ; Copepoda ; Crustaceans ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Ecological function ; Environmental changes ; Fish ; Food sources ; Gene sequencing ; High-Throughput Nucleotide Sequencing - methods ; Identification ; Laboratories ; Larvae ; Library collections ; Life support systems ; Long term changes ; Marine conservation ; Marine ecosystems ; Microbiota ; Microscopy ; Morphology ; Multiprocessing ; Museums ; Nucleotide sequence ; Observatories ; Oceans ; Parasites ; Phylogenetics ; Plankton ; Quality control ; Rare species ; Ribonucleic acid ; Ribosomal RNA ; RNA ; rRNA 18S ; Species diversity ; Species richness ; Studies ; Taxonomy ; Zooplankton ; Zooplankton - classification ; Zooplankton - genetics</subject><ispartof>PloS one, 2013-11, Vol.8 (11), p.e81327-e81327</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Lindeque et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Lindeque et al 2013 Lindeque et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-d9787a67ce09248ff0d66bd0956d415c171fca375cb11791ad18f424c1e7037c3</citedby><cites>FETCH-LOGICAL-c692t-d9787a67ce09248ff0d66bd0956d415c171fca375cb11791ad18f424c1e7037c3</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/PMC3820580/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820580/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24244737$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Ianora, Adrianna</contributor><creatorcontrib>Lindeque, Penelope K</creatorcontrib><creatorcontrib>Parry, Helen E</creatorcontrib><creatorcontrib>Harmer, Rachel A</creatorcontrib><creatorcontrib>Somerfield, Paul J</creatorcontrib><creatorcontrib>Atkinson, Angus</creatorcontrib><title>Next generation sequencing reveals the hidden diversity of zooplankton assemblages</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel.
Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups.
Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.</description><subject>Analysis</subject><subject>Animals</subject><subject>Biodiversity</subject><subject>Biogeochemical cycles</subject><subject>Biotechnology</subject><subject>Communities</subject><subject>Community structure</subject><subject>Copepoda</subject><subject>Crustaceans</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Ecological function</subject><subject>Environmental changes</subject><subject>Fish</subject><subject>Food sources</subject><subject>Gene sequencing</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Identification</subject><subject>Laboratories</subject><subject>Larvae</subject><subject>Library collections</subject><subject>Life support systems</subject><subject>Long term changes</subject><subject>Marine conservation</subject><subject>Marine ecosystems</subject><subject>Microbiota</subject><subject>Microscopy</subject><subject>Morphology</subject><subject>Multiprocessing</subject><subject>Museums</subject><subject>Nucleotide sequence</subject><subject>Observatories</subject><subject>Oceans</subject><subject>Parasites</subject><subject>Phylogenetics</subject><subject>Plankton</subject><subject>Quality control</subject><subject>Rare species</subject><subject>Ribonucleic acid</subject><subject>Ribosomal RNA</subject><subject>RNA</subject><subject>rRNA 18S</subject><subject>Species diversity</subject><subject>Species richness</subject><subject>Studies</subject><subject>Taxonomy</subject><subject>Zooplankton</subject><subject>Zooplankton - classification</subject><subject>Zooplankton - genetics</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</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><sourceid>DOA</sourceid><recordid>eNqNkluL1DAcxYso7jr6DUQLgujDjLk0TfsiLIuXgcWF9fIa0uSfNmOnmU3awfXTmzrdZSr7IIW2JL9zkpycJHmO0QpTjt9t3OA72a52roMVQgWmhD9ITnFJyTIniD48-j9JnoSwQYjRIs8fJyckI1nGKT9Nrr7Arz6toQMve-u6NMD1AJ2yXZ162INsQ9o3kDZWa-hSbffgg-1vUmfS387tWtn97KNMhgDbqpU1hKfJIxNl8Gz6LpLvHz98O_-8vLj8tD4_u1iqvCT9Upe84DLnClBJssIYpPO80qhkuc4wU5hjoyTlTFUY8xJLjQsT960wcES5oovk5cF317ogpjiCwFlWUkpYfC2S9YHQTm7Eztut9DfCSSv-DjhfC-l7q1oQmiuGJDUlGJqZnMgCMlowU-UV4ZUZvd5Pqw3VFrSCrveynZnOZzrbiNrtBS0IYgWKBm8mA-9ixKEXWxsUtDFBcMO4b1YyxnM2oq_-Qe8_3UTVMh7AdsbFddVoKs4yXtCSMIYjtbqHio-GrVWxO8bG8Zng7UwQmT52pJZDCGL99er_2csfc_b1EdvEZvVNcO0wti7MwewAKu9C8GDuQsZIjNW_TUOM1RdT9aPsxfEF3Yluu07_AGgS_s8</recordid><startdate>20131107</startdate><enddate>20131107</enddate><creator>Lindeque, Penelope K</creator><creator>Parry, Helen E</creator><creator>Harmer, Rachel A</creator><creator>Somerfield, Paul J</creator><creator>Atkinson, Angus</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><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>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20131107</creationdate><title>Next generation sequencing reveals the hidden diversity of zooplankton assemblages</title><author>Lindeque, Penelope K ; Parry, Helen E ; Harmer, Rachel A ; Somerfield, Paul J ; Atkinson, Angus</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-d9787a67ce09248ff0d66bd0956d415c171fca375cb11791ad18f424c1e7037c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Biodiversity</topic><topic>Biogeochemical cycles</topic><topic>Biotechnology</topic><topic>Communities</topic><topic>Community structure</topic><topic>Copepoda</topic><topic>Crustaceans</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Ecological function</topic><topic>Environmental changes</topic><topic>Fish</topic><topic>Food sources</topic><topic>Gene sequencing</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Identification</topic><topic>Laboratories</topic><topic>Larvae</topic><topic>Library collections</topic><topic>Life support systems</topic><topic>Long term changes</topic><topic>Marine conservation</topic><topic>Marine ecosystems</topic><topic>Microbiota</topic><topic>Microscopy</topic><topic>Morphology</topic><topic>Multiprocessing</topic><topic>Museums</topic><topic>Nucleotide sequence</topic><topic>Observatories</topic><topic>Oceans</topic><topic>Parasites</topic><topic>Phylogenetics</topic><topic>Plankton</topic><topic>Quality control</topic><topic>Rare species</topic><topic>Ribonucleic acid</topic><topic>Ribosomal RNA</topic><topic>RNA</topic><topic>rRNA 18S</topic><topic>Species diversity</topic><topic>Species richness</topic><topic>Studies</topic><topic>Taxonomy</topic><topic>Zooplankton</topic><topic>Zooplankton - classification</topic><topic>Zooplankton - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lindeque, Penelope K</creatorcontrib><creatorcontrib>Parry, Helen E</creatorcontrib><creatorcontrib>Harmer, Rachel A</creatorcontrib><creatorcontrib>Somerfield, Paul J</creatorcontrib><creatorcontrib>Atkinson, Angus</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lindeque, Penelope K</au><au>Parry, Helen E</au><au>Harmer, Rachel A</au><au>Somerfield, Paul J</au><au>Atkinson, Angus</au><au>Ianora, Adrianna</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Next generation sequencing reveals the hidden diversity of zooplankton assemblages</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-11-07</date><risdate>2013</risdate><volume>8</volume><issue>11</issue><spage>e81327</spage><epage>e81327</epage><pages>e81327-e81327</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel.
Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups.
Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24244737</pmid><doi>10.1371/journal.pone.0081327</doi><tpages>e81327</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2013-11, Vol.8 (11), p.e81327-e81327 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1449332593 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Animals Biodiversity Biogeochemical cycles Biotechnology Communities Community structure Copepoda Crustaceans Deoxyribonucleic acid DNA DNA sequencing Ecological function Environmental changes Fish Food sources Gene sequencing High-Throughput Nucleotide Sequencing - methods Identification Laboratories Larvae Library collections Life support systems Long term changes Marine conservation Marine ecosystems Microbiota Microscopy Morphology Multiprocessing Museums Nucleotide sequence Observatories Oceans Parasites Phylogenetics Plankton Quality control Rare species Ribonucleic acid Ribosomal RNA RNA rRNA 18S Species diversity Species richness Studies Taxonomy Zooplankton Zooplankton - classification Zooplankton - genetics |
| title | Next generation sequencing reveals the hidden diversity of zooplankton assemblages |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-04T23%3A29%3A55IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Next%20generation%20sequencing%20reveals%20the%20hidden%20diversity%20of%20zooplankton%20assemblages&rft.jtitle=PloS%20one&rft.au=Lindeque,%20Penelope%20K&rft.date=2013-11-07&rft.volume=8&rft.issue=11&rft.spage=e81327&rft.epage=e81327&rft.pages=e81327-e81327&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0081327&rft_dat=%3Cgale_plos_%3EA478392551%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1449332593&rft_id=info:pmid/24244737&rft_galeid=A478392551&rft_doaj_id=oai_doaj_org_article_d7c50a3f9ef34f62a8e4385fb6b27bf3&rfr_iscdi=true |