DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/50360 |
Resumo: | Morphology-based profling of benthic communities has been extensively applied to aquatic ecosystems’ health assessment. However, it remains a low-throughput, and sometimes ambiguous, procedure. Despite DNA metabarcoding has been applied to marine benthos, a comprehensive approach providing species-level identifcations for estuarine macrobenthos is still lacking. Here we report a combination of experimental and feld studies to assess the aptitude of COI metabarcoding to provide robust species-level identifcations for high-throughput monitoring of estuarine macrobenthos. To investigate the ability of metabarcoding to detect all species present in bulk DNA extracts, we contrived three phylogenetically diverse communities, and applied four diferent primer pairs to generate PCR products within the COI barcode region. Between 78–83% of the species in the contrived communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct estuarine sites. Our results indicate that species richness would be considerably underestimated if only morphological methods were used: globally 27 species identifed through morphology versus 61 detected by metabarcoding. Although further refnement is required to improve efciency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifcations in estuarine macrobenthos monitoring. |
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DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communitiesScience & TechnologyMorphology-based profling of benthic communities has been extensively applied to aquatic ecosystems’ health assessment. However, it remains a low-throughput, and sometimes ambiguous, procedure. Despite DNA metabarcoding has been applied to marine benthos, a comprehensive approach providing species-level identifcations for estuarine macrobenthos is still lacking. Here we report a combination of experimental and feld studies to assess the aptitude of COI metabarcoding to provide robust species-level identifcations for high-throughput monitoring of estuarine macrobenthos. To investigate the ability of metabarcoding to detect all species present in bulk DNA extracts, we contrived three phylogenetically diverse communities, and applied four diferent primer pairs to generate PCR products within the COI barcode region. Between 78–83% of the species in the contrived communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct estuarine sites. Our results indicate that species richness would be considerably underestimated if only morphological methods were used: globally 27 species identifed through morphology versus 61 detected by metabarcoding. Although further refnement is required to improve efciency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifcations in estuarine macrobenthos monitoring.This study has been funded by the project “Te NextSea: Next generation monitoring of coastal ecosystems in a scenario of global change” (operação NORTE-01-0145-FEDER-000032), supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). JL was supported by a PhD fellowship (SFRH/BD/69750/2010) from FCT. Tis study had the fnancial support of Fundação para a Ciência e Tecnologia (FCT), through the strategic project UID/MAR/04292/2013 granted to MARE. Te authors would like to thank Stephanie Boilard (Biodiversity Institute of Ontario) for her support in the lab work.info:eu-repo/semantics/publishedVersionNature Publishing GroupUniversidade do MinhoLobo, JorgeShokralla, ShadiCosta, Maria HelenaHajibabaei, MehrdadCosta, Filipe O.20172017-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/50360engLobo J, Shokralla S, Costa MH, Hajibabaei M, Costa FO (2017). DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities Scientific Reports 7: 15618. doi:10.1038/s41598-017-15823-62045-232210.1038/s41598-017-15823-629142319info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:47:12Zoai:repositorium.sdum.uminho.pt:1822/50360Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:45:17.895344Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities |
title |
DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities |
spellingShingle |
DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities Lobo, Jorge Science & Technology |
title_short |
DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities |
title_full |
DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities |
title_fullStr |
DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities |
title_full_unstemmed |
DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities |
title_sort |
DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities |
author |
Lobo, Jorge |
author_facet |
Lobo, Jorge Shokralla, Shadi Costa, Maria Helena Hajibabaei, Mehrdad Costa, Filipe O. |
author_role |
author |
author2 |
Shokralla, Shadi Costa, Maria Helena Hajibabaei, Mehrdad Costa, Filipe O. |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Lobo, Jorge Shokralla, Shadi Costa, Maria Helena Hajibabaei, Mehrdad Costa, Filipe O. |
dc.subject.por.fl_str_mv |
Science & Technology |
topic |
Science & Technology |
description |
Morphology-based profling of benthic communities has been extensively applied to aquatic ecosystems’ health assessment. However, it remains a low-throughput, and sometimes ambiguous, procedure. Despite DNA metabarcoding has been applied to marine benthos, a comprehensive approach providing species-level identifcations for estuarine macrobenthos is still lacking. Here we report a combination of experimental and feld studies to assess the aptitude of COI metabarcoding to provide robust species-level identifcations for high-throughput monitoring of estuarine macrobenthos. To investigate the ability of metabarcoding to detect all species present in bulk DNA extracts, we contrived three phylogenetically diverse communities, and applied four diferent primer pairs to generate PCR products within the COI barcode region. Between 78–83% of the species in the contrived communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct estuarine sites. Our results indicate that species richness would be considerably underestimated if only morphological methods were used: globally 27 species identifed through morphology versus 61 detected by metabarcoding. Although further refnement is required to improve efciency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifcations in estuarine macrobenthos monitoring. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017 2017-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/50360 |
url |
http://hdl.handle.net/1822/50360 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Lobo J, Shokralla S, Costa MH, Hajibabaei M, Costa FO (2017). DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities Scientific Reports 7: 15618. doi:10.1038/s41598-017-15823-6 2045-2322 10.1038/s41598-017-15823-6 29142319 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Nature Publishing Group |
publisher.none.fl_str_mv |
Nature Publishing Group |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799133017487179776 |