Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring

Bibliographic Details
Main Author: Martins, Filipa M.S.
Publication Date: 2019
Other Authors: Galhardo, Mafalda, Filipe, Ana F., Teixeira, Amilcar, Pinheiro, Paulo, Paupério, Joana, Alves, Paulo C., Beja, Pedro
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10400.5/18086
Summary: Resource Article
id RCAP_8376d5afca4075f9e74c76d1fab62127
oai_identifier_str oai:repositorio.ulisboa.pt:10400.5/18086
network_acronym_str RCAP
network_name_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository_id_str https://opendoar.ac.uk/repository/7160
spelling Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoringbenthic macroinvertebratesDNA extractionDNA metabarcodingfreshwater bioassessmentpreservative ethanolWater Framework DirectiveResource ArticleDNA metabarcoding can contribute to improving cost‐effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time‐consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column‐based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic‐based enzymatic protocol (BEAD), and a 313‐bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7–14 than 1–7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoringJohn Wiley and SonsRepositório da Universidade de LisboaMartins, Filipa M.S.Galhardo, MafaldaFilipe, Ana F.Teixeira, AmilcarPinheiro, PauloPaupério, JoanaAlves, Paulo C.Beja, Pedro2019-07-02T11:27:32Z20192019-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.5/18086engMol Ecol Resour. 2019;19:863–87610.1111/1755-0998.13012info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2025-03-17T15:56:45Zoai:repositorio.ulisboa.pt:10400.5/18086Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-29T03:58:33.558833Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
title Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
spellingShingle Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
Martins, Filipa M.S.
benthic macroinvertebrates
DNA extraction
DNA metabarcoding
freshwater bioassessment
preservative ethanol
Water Framework Directive
title_short Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
title_full Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
title_fullStr Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
title_full_unstemmed Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
title_sort Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
author Martins, Filipa M.S.
author_facet Martins, Filipa M.S.
Galhardo, Mafalda
Filipe, Ana F.
Teixeira, Amilcar
Pinheiro, Paulo
Paupério, Joana
Alves, Paulo C.
Beja, Pedro
author_role author
author2 Galhardo, Mafalda
Filipe, Ana F.
Teixeira, Amilcar
Pinheiro, Paulo
Paupério, Joana
Alves, Paulo C.
Beja, Pedro
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Martins, Filipa M.S.
Galhardo, Mafalda
Filipe, Ana F.
Teixeira, Amilcar
Pinheiro, Paulo
Paupério, Joana
Alves, Paulo C.
Beja, Pedro
dc.subject.por.fl_str_mv benthic macroinvertebrates
DNA extraction
DNA metabarcoding
freshwater bioassessment
preservative ethanol
Water Framework Directive
topic benthic macroinvertebrates
DNA extraction
DNA metabarcoding
freshwater bioassessment
preservative ethanol
Water Framework Directive
description Resource Article
publishDate 2019
dc.date.none.fl_str_mv 2019-07-02T11:27:32Z
2019
2019-01-01T00:00:00Z
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/10400.5/18086
url http://hdl.handle.net/10400.5/18086
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Mol Ecol Resour. 2019;19:863–876
10.1111/1755-0998.13012
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 John Wiley and Sons
publisher.none.fl_str_mv John Wiley and Sons
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
_version_ 1833601896570421248

Similar Items