Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates
Autor(a) principal: | |
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Data de Publicação: | 2021 |
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/1822/70221 |
Resumo: | Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs. |
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Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebratesaquatic ecosystemsbiomonitoringbioassessmentbenthic macroinvertebratesDNA metabarcodingCiências Naturais::Ciências BiológicasScience & TechnologyBenthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.This work was supported by the "Contrato-Programa" UIDB/04050/2020 and the project NIS-DNA (PTDC/BIA-BMA/29754/2017) funded by national funds through the FCT I.P (Foundation for Science and Technology). Financial support granted by the FCT to S.D. (CEECIND/00667/2017) and B.R.L. (PD/BD/127994/2016) is also acknowledged. A.F.F. was supported by the project FRESHING founded by the FCT and COMPETE (PTDC/AAGMAA/2261/2014-POCI-01-0145-FEDER356016824). M.J.F. was supported by FCT through MARE strategic project UIDB/04292/2020 and Norma Transitoria-DL57/2016.Multidisciplinary Digital Publishing InstituteUniversidade do MinhoDuarte, Sofia Alexandra FerreiraLeite, BárbaraFeio, Maria JoãoCosta, Filipe O.Filipe, Ana Filipa20212021-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/70221engDuarte, S.; Leite, B.R.; Feio, M.J.; Costa, F.O.; Filipe, A.F. Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. Water 2021, 13, 331. https://doi.org/10.3390/w130303312073-444110.3390/w13030331https://www.mdpi.com/2073-4441/13/3/331info: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:RCAAP2023-07-21T12:11:11Zoai:repositorium.sdum.uminho.pt:1822/70221Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:02:54.025237Repositório 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 |
Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates |
title |
Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates |
spellingShingle |
Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates Duarte, Sofia Alexandra Ferreira aquatic ecosystems biomonitoring bioassessment benthic macroinvertebrates DNA metabarcoding Ciências Naturais::Ciências Biológicas Science & Technology |
title_short |
Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates |
title_full |
Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates |
title_fullStr |
Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates |
title_full_unstemmed |
Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates |
title_sort |
Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates |
author |
Duarte, Sofia Alexandra Ferreira |
author_facet |
Duarte, Sofia Alexandra Ferreira Leite, Bárbara Feio, Maria João Costa, Filipe O. Filipe, Ana Filipa |
author_role |
author |
author2 |
Leite, Bárbara Feio, Maria João Costa, Filipe O. Filipe, Ana Filipa |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Duarte, Sofia Alexandra Ferreira Leite, Bárbara Feio, Maria João Costa, Filipe O. Filipe, Ana Filipa |
dc.subject.por.fl_str_mv |
aquatic ecosystems biomonitoring bioassessment benthic macroinvertebrates DNA metabarcoding Ciências Naturais::Ciências Biológicas Science & Technology |
topic |
aquatic ecosystems biomonitoring bioassessment benthic macroinvertebrates DNA metabarcoding Ciências Naturais::Ciências Biológicas Science & Technology |
description |
Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021 2021-01-01T00:00:00Z |
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/1822/70221 |
url |
http://hdl.handle.net/1822/70221 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Duarte, S.; Leite, B.R.; Feio, M.J.; Costa, F.O.; Filipe, A.F. Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. Water 2021, 13, 331. https://doi.org/10.3390/w13030331 2073-4441 10.3390/w13030331 https://www.mdpi.com/2073-4441/13/3/331 |
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 |
Multidisciplinary Digital Publishing Institute |
publisher.none.fl_str_mv |
Multidisciplinary Digital Publishing Institute |
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 |
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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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