Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding
Autor(a) principal: | |
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Data de Publicação: | 2020 |
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/1822/72689 |
Resumo: | Meiofaunal organisms play a key role in estuarine ecosystems, being responsible for significant ecological processes. However, meiofauna constitutes a particularly difficult community to be monitored through conventional morphology-based approaches. New emerging tools, such as DNA metabarcoding, facilitate the access to these communities and provide an opportunity to develop routine monitoring programs. In the present study, the small-scale spatial variation of meiofaunal communities in the Lima estuary (NW Portugal) was investigated using DNA metabarcoding. The first stage of the study aimed to establish the amount of sediment sample to be used for DNA extraction and to test six primer pairs, three of them amplifying fragments from the mitochondrial cytochrome c oxidase gene (COI) and three other the nuclear ribosomal 18S rRNA gene (18S). In a subsequent stage, sediment samples were collected in four stations along an estuarine gradient (salinity ranging between 9 and 28), in which six sampling points about 4–5 m apart were considered: three in the high intertidal and three in the mid intertidal. After the DNA extraction from sediments, COI and 18S amplicon libraries were produced and sequenced in an Illumina MiSeq platform. OTUs (operational taxonomic units) recovered by either COI or 18S displayed generally high turnover in occurrence among sampling points within a station and tidal horizon, among tidal horizons within a station, and among stations of distinct salinity (approx. 60–93%). Both markers recorded little variation among stations in OTU richness and in the taxonomic composition of the most dominant groups. However, the meiofauna detected differed qualitatively between the two markers used; Amoebozoa and Cnidaria were mostly detected with COI while Ciliophora and Platyhelminthes with 18S. In addition, the structure of the meiofauna community diverged significantly among stations and was strongly influenced by salinity and sediment features. Globally, results indicated a highly patchy distribution of meiofauna taxa in the Lima estuary, revealed by the high OTU turnover even between sampling points only a few meters apart. Hence, eDNA-based meiofauna surveys require consideration of the necessary sampling effort on relatively small spatial scales, as well as an appreciation of the tidal level-induced variation of these communities. |
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Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcodingMeiofaunaEstuariesDNA metabarcodingIntertidal variationPatchinessProtocol optimisationCiências Naturais::Ciências BiológicasScience & TechnologyMeiofaunal organisms play a key role in estuarine ecosystems, being responsible for significant ecological processes. However, meiofauna constitutes a particularly difficult community to be monitored through conventional morphology-based approaches. New emerging tools, such as DNA metabarcoding, facilitate the access to these communities and provide an opportunity to develop routine monitoring programs. In the present study, the small-scale spatial variation of meiofaunal communities in the Lima estuary (NW Portugal) was investigated using DNA metabarcoding. The first stage of the study aimed to establish the amount of sediment sample to be used for DNA extraction and to test six primer pairs, three of them amplifying fragments from the mitochondrial cytochrome c oxidase gene (COI) and three other the nuclear ribosomal 18S rRNA gene (18S). In a subsequent stage, sediment samples were collected in four stations along an estuarine gradient (salinity ranging between 9 and 28), in which six sampling points about 4–5 m apart were considered: three in the high intertidal and three in the mid intertidal. After the DNA extraction from sediments, COI and 18S amplicon libraries were produced and sequenced in an Illumina MiSeq platform. OTUs (operational taxonomic units) recovered by either COI or 18S displayed generally high turnover in occurrence among sampling points within a station and tidal horizon, among tidal horizons within a station, and among stations of distinct salinity (approx. 60–93%). Both markers recorded little variation among stations in OTU richness and in the taxonomic composition of the most dominant groups. However, the meiofauna detected differed qualitatively between the two markers used; Amoebozoa and Cnidaria were mostly detected with COI while Ciliophora and Platyhelminthes with 18S. In addition, the structure of the meiofauna community diverged significantly among stations and was strongly influenced by salinity and sediment features. Globally, results indicated a highly patchy distribution of meiofauna taxa in the Lima estuary, revealed by the high OTU turnover even between sampling points only a few meters apart. Hence, eDNA-based meiofauna surveys require consideration of the necessary sampling effort on relatively small spatial scales, as well as an appreciation of the tidal level-induced variation of these communities.This study was funded by the project “The 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). Maria Fais and Sofia Duarte were supported, respectively by a PhD (SFRH/BD/113547/2015) and a post-doc fellowship (SFRH/BPD/109842/2015) from FCT. The authors would like to thank Prof. Jesús Troncoso (University of Vigo) and Prof. Pedro Gomes (University of Minho) for their availability and hospitality for the lab processing, as well as Barbara Leite (University of Minho) and Manuel Mendoza (University of Vigo) for their help during the sampling and data analysis phases, respectively.ElsevierUniversidade do MinhoFais, MariaDuarte, Sofia Alexandra FerreiraVieira, P. E.Sousa, Ronaldo GomesHajibabaei, MehrdadCanchaya, Carlos AlbertoCosta, Filipe O.20202020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/72689engFais, M., Duarte, S., Vieira, P. E., Sousa, R., Hajibabaei, M., Canchaya, C. A., & Costa, F. O. (2020). Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding. Estuarine, Coastal and Shelf Science, 238, 106683. doi: https://doi.org/10.1016/j.ecss.2020.1066830272-771410.1016/j.ecss.2020.106683https://www.sciencedirect.com/science/article/pii/S0272771419306663info: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:RCAAP2023-07-21T12:09:02Zoai:repositorium.sdum.uminho.pt:1822/72689Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:00:22.990163Repositório 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 |
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding |
title |
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding |
spellingShingle |
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding Fais, Maria Meiofauna Estuaries DNA metabarcoding Intertidal variation Patchiness Protocol optimisation Ciências Naturais::Ciências Biológicas Science & Technology |
title_short |
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding |
title_full |
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding |
title_fullStr |
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding |
title_full_unstemmed |
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding |
title_sort |
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding |
author |
Fais, Maria |
author_facet |
Fais, Maria Duarte, Sofia Alexandra Ferreira Vieira, P. E. Sousa, Ronaldo Gomes Hajibabaei, Mehrdad Canchaya, Carlos Alberto Costa, Filipe O. |
author_role |
author |
author2 |
Duarte, Sofia Alexandra Ferreira Vieira, P. E. Sousa, Ronaldo Gomes Hajibabaei, Mehrdad Canchaya, Carlos Alberto Costa, Filipe O. |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Fais, Maria Duarte, Sofia Alexandra Ferreira Vieira, P. E. Sousa, Ronaldo Gomes Hajibabaei, Mehrdad Canchaya, Carlos Alberto Costa, Filipe O. |
dc.subject.por.fl_str_mv |
Meiofauna Estuaries DNA metabarcoding Intertidal variation Patchiness Protocol optimisation Ciências Naturais::Ciências Biológicas Science & Technology |
topic |
Meiofauna Estuaries DNA metabarcoding Intertidal variation Patchiness Protocol optimisation Ciências Naturais::Ciências Biológicas Science & Technology |
description |
Meiofaunal organisms play a key role in estuarine ecosystems, being responsible for significant ecological processes. However, meiofauna constitutes a particularly difficult community to be monitored through conventional morphology-based approaches. New emerging tools, such as DNA metabarcoding, facilitate the access to these communities and provide an opportunity to develop routine monitoring programs. In the present study, the small-scale spatial variation of meiofaunal communities in the Lima estuary (NW Portugal) was investigated using DNA metabarcoding. The first stage of the study aimed to establish the amount of sediment sample to be used for DNA extraction and to test six primer pairs, three of them amplifying fragments from the mitochondrial cytochrome c oxidase gene (COI) and three other the nuclear ribosomal 18S rRNA gene (18S). In a subsequent stage, sediment samples were collected in four stations along an estuarine gradient (salinity ranging between 9 and 28), in which six sampling points about 4–5 m apart were considered: three in the high intertidal and three in the mid intertidal. After the DNA extraction from sediments, COI and 18S amplicon libraries were produced and sequenced in an Illumina MiSeq platform. OTUs (operational taxonomic units) recovered by either COI or 18S displayed generally high turnover in occurrence among sampling points within a station and tidal horizon, among tidal horizons within a station, and among stations of distinct salinity (approx. 60–93%). Both markers recorded little variation among stations in OTU richness and in the taxonomic composition of the most dominant groups. However, the meiofauna detected differed qualitatively between the two markers used; Amoebozoa and Cnidaria were mostly detected with COI while Ciliophora and Platyhelminthes with 18S. In addition, the structure of the meiofauna community diverged significantly among stations and was strongly influenced by salinity and sediment features. Globally, results indicated a highly patchy distribution of meiofauna taxa in the Lima estuary, revealed by the high OTU turnover even between sampling points only a few meters apart. Hence, eDNA-based meiofauna surveys require consideration of the necessary sampling effort on relatively small spatial scales, as well as an appreciation of the tidal level-induced variation of these communities. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020 2020-01-01T00:00:00Z |
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/1822/72689 |
url |
http://hdl.handle.net/1822/72689 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Fais, M., Duarte, S., Vieira, P. E., Sousa, R., Hajibabaei, M., Canchaya, C. A., & Costa, F. O. (2020). Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding. Estuarine, Coastal and Shelf Science, 238, 106683. doi: https://doi.org/10.1016/j.ecss.2020.106683 0272-7714 10.1016/j.ecss.2020.106683 https://www.sciencedirect.com/science/article/pii/S0272771419306663 |
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info:eu-repo/semantics/openAccess |
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openAccess |
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application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier |
publisher.none.fl_str_mv |
Elsevier |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799132398389035008 |