Publicação
Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed
| Resumo: | Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling and analytical efforts are needed to improve biodiversity estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade‐offs to design effective eDNA metabarcoding monitoring studies. We conducted a water eDNA survey of vertebrates in a Mediterranean watershed to identify key methodological factors influencing species richness and composition estimates. We examined the impacts of using high‐ versus low‐capacity filtration capsules, varying levels of biological and technical replication, and the pooling of PCR replicates before indexing. The primary sources of variation identified were capsule filtration capacity and site replication across the watershed. While biological replication within sites and PCR replication also improved biodiversity estimates, their effects were comparatively smaller. Pooling PCR replicates before indexing performed more poorly than analysing them independently. Methodological impacts were stronger on terrestrial than on aquatic species. Based on these results, we recommend that priority should be given to high‐capacity filtration and sampling across multiple sites. Site‐level replication deserves lower priority, especially when filtering large water volumes. PCR replication is crucial for detecting rare species but should be balanced with increased site sampling and eventually site‐level replication. Avoiding the pooling of PCR replicates is important to enhance sensitivity for rare species. Overall, we stress the importance of balancing methodological choices with resource constraints and monitoring goals, and we emphasise the need for research assessing methodological trade‐offs in different study systems. |
|---|---|
| Autores principais: | Veríssimo, Joana |
| Outros Autores: | Lopes‐Lima, Manuel; Amaral, Fábio; Chaves, Cátia; Fernandes, Vasco; Kemanja, Mutaleni; Teixeira, Amilcar; Martins, Filipa M. S.; Beja, Pedro |
| Assunto: | Biodiversity monitoring Environmental DNA Freshwater ecosystems High-throughput sequencing Metabarcoding Replication |
| Ano: | 2025 |
| País: | Portugal |
| Tipo de documento: | artigo |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Instituto Politécnico de Bragança |
| Idioma: | inglês |
| Origem: | Biblioteca Digital do IPB |
| _version_ | 1867172829342990336 |
|---|---|
| author | Veríssimo, Joana |
| author2 | Lopes‐Lima, Manuel Amaral, Fábio Chaves, Cátia Fernandes, Vasco Kemanja, Mutaleni Teixeira, Amilcar Martins, Filipa M. S. Beja, Pedro |
| author2_role | author author author author author author author author |
| author_facet | Veríssimo, Joana Lopes‐Lima, Manuel Amaral, Fábio Chaves, Cátia Fernandes, Vasco Kemanja, Mutaleni Teixeira, Amilcar Martins, Filipa M. S. Beja, Pedro |
| author_role | author |
| contributor_name_str_mv | Biblioteca Digital do IPB |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Veríssimo, Joana\"},{\"Person.name\":\"Lopes‐Lima, Manuel\"},{\"Person.name\":\"Amaral, Fábio\"},{\"Person.name\":\"Chaves, Cátia\"},{\"Person.name\":\"Fernandes, Vasco\"},{\"Person.name\":\"Kemanja, Mutaleni\"},{\"Person.name\":\"Teixeira, Amilcar\",\"Person.identifier.orcid\":\"0000-0001-5336-1174\"},{\"Person.name\":\"Martins, Filipa M. S.\"},{\"Person.name\":\"Beja, Pedro\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Biblioteca Digital do IPB |
| datacite.creators.creator.creatorName.fl_str_mv | Veríssimo, Joana Lopes‐Lima, Manuel Amaral, Fábio Chaves, Cátia Fernandes, Vasco Kemanja, Mutaleni Teixeira, Amilcar Martins, Filipa M. S. Beja, Pedro |
| datacite.date.Accepted.fl_str_mv | 2025-01-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2025-07-21T13:36:53Z |
| datacite.date.embargoed.fl_str_mv | 2025-07-21T13:36:53Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.subjects.subject.fl_str_mv | Biodiversity monitoring Environmental DNA Freshwater ecosystems High-throughput sequencing Metabarcoding Replication |
| datacite.titles.title.fl_str_mv | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed |
| dc.contributor.none.fl_str_mv | Biblioteca Digital do IPB |
| dc.creator.none.fl_str_mv | Veríssimo, Joana Lopes‐Lima, Manuel Amaral, Fábio Chaves, Cátia Fernandes, Vasco Kemanja, Mutaleni Teixeira, Amilcar Martins, Filipa M. S. Beja, Pedro |
| dc.date.Accepted.fl_str_mv | 2025-01-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2025-07-21T13:36:53Z |
| dc.date.embargoed.fl_str_mv | 2025-07-21T13:36:53Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10198/34680 |
| dc.language.none.fl_str_mv | eng |
| dc.publisher.none.fl_str_mv | Wiley |
| dc.rights.cclincense.fl_str_mv | http://creativecommons.org/licenses/by/4.0/ |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| dc.subject.none.fl_str_mv | Biodiversity monitoring Environmental DNA Freshwater ecosystems High-throughput sequencing Metabarcoding Replication |
| dc.title.fl_str_mv | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_6501 |
| description | Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling and analytical efforts are needed to improve biodiversity estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade‐offs to design effective eDNA metabarcoding monitoring studies. We conducted a water eDNA survey of vertebrates in a Mediterranean watershed to identify key methodological factors influencing species richness and composition estimates. We examined the impacts of using high‐ versus low‐capacity filtration capsules, varying levels of biological and technical replication, and the pooling of PCR replicates before indexing. The primary sources of variation identified were capsule filtration capacity and site replication across the watershed. While biological replication within sites and PCR replication also improved biodiversity estimates, their effects were comparatively smaller. Pooling PCR replicates before indexing performed more poorly than analysing them independently. Methodological impacts were stronger on terrestrial than on aquatic species. Based on these results, we recommend that priority should be given to high‐capacity filtration and sampling across multiple sites. Site‐level replication deserves lower priority, especially when filtering large water volumes. PCR replication is crucial for detecting rare species but should be balanced with increased site sampling and eventually site‐level replication. Avoiding the pooling of PCR replicates is important to enhance sensitivity for rare species. Overall, we stress the importance of balancing methodological choices with resource constraints and monitoring goals, and we emphasise the need for research assessing methodological trade‐offs in different study systems. |
| dirty | 0 |
| eu_rights_str_mv | openAccess |
| format | article |
| fulltext.url.fl_str_mv | https://bibliotecadigital.ipb.pt/bitstreams/1444827f-f2b9-4bd2-9d03-00e5b7f00008/download |
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| identifier.url.fl_str_mv | http://hdl.handle.net/10198/34680 |
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| institution | Instituto Politécnico de Bragança |
| instname_str | Instituto Politécnico de Bragança |
| language | eng |
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| network_name_str | Biblioteca Digital do IPB |
| oai_identifier_str | oai:bibliotecadigital.ipb.pt:10198/34680 |
| organization_str_mv | urn:organizationAcronym:ipb |
| person_str_mv | Veríssimo, Joana Lopes‐Lima, Manuel Amaral, Fábio Chaves, Cátia Fernandes, Vasco Kemanja, Mutaleni Teixeira, Amilcar Teixeira, Amilcar https://www.ciencia-id.pt/9510-3CF3-0393 9510-3CF3-0393 http://orcid.org/0000-0001-5336-1174 0000-0001-5336-1174 Martins, Filipa M. S. Beja, Pedro |
| publishDate | 2025 |
| publisher.none.fl_str_mv | Wiley |
| reponame_str | Biblioteca Digital do IPB |
| repository_id_str | urn:repositoryAcronym:ipb |
| service_str_mv | urn:repositoryAcronym:ipb |
| spelling | engWileyengEnvironmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling and analytical efforts are needed to improve biodiversity estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade‐offs to design effective eDNA metabarcoding monitoring studies. We conducted a water eDNA survey of vertebrates in a Mediterranean watershed to identify key methodological factors influencing species richness and composition estimates. We examined the impacts of using high‐ versus low‐capacity filtration capsules, varying levels of biological and technical replication, and the pooling of PCR replicates before indexing. The primary sources of variation identified were capsule filtration capacity and site replication across the watershed. While biological replication within sites and PCR replication also improved biodiversity estimates, their effects were comparatively smaller. Pooling PCR replicates before indexing performed more poorly than analysing them independently. Methodological impacts were stronger on terrestrial than on aquatic species. Based on these results, we recommend that priority should be given to high‐capacity filtration and sampling across multiple sites. Site‐level replication deserves lower priority, especially when filtering large water volumes. PCR replication is crucial for detecting rare species but should be balanced with increased site sampling and eventually site‐level replication. Avoiding the pooling of PCR replicates is important to enhance sensitivity for rare species. Overall, we stress the importance of balancing methodological choices with resource constraints and monitoring goals, and we emphasise the need for research assessing methodological trade‐offs in different study systems.application/pdfengNavigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean WatershedVeríssimo, JoanaLopes‐Lima, ManuelAmaral, FábioChaves, CátiaFernandes, VascoKemanja, MutaleniPersonalTeixeira, AmilcarDSpacehttp://dspace.org/items/4f0753fd-4b4f-46f6-8e2f-20c7f835a32aDSpacehttp://dspace.org/items/4f0753fd-4b4f-46f6-8e2f-20c7f835a32aTeixeiraAmilcarCiência IDhttps://www.ciencia-id.pt9510-3CF3-0393ORCIDhttp://orcid.org0000-0001-5336-1174Scopus Author IDhttps://www.scopus.com7202385393Martins, Filipa M. S.Beja, PedroHostingInstitutionOrganizationalBiblioteca Digital do IPBe-mailmailto:dspace@ipb.ptdspace@ipb.ptISSNIsPartOf1755-098XDOIIsPartOf10.1111/1755-0998.140822025-07-21T13:36:53Z20252025-01-01T00:00:00ZHandlehttp://hdl.handle.net/10198/34680http://purl.org/coar/access_right/c_abf2open accessBiodiversity monitoringEnvironmental DNAFreshwater ecosystemsHigh-throughput sequencingMetabarcodingReplication770041 bytesliteraturehttp://purl.org/coar/resource_type/c_6501journal article2025http://creativecommons.org/licenses/by/4.0/http://purl.org/coar/access_right/c_abf2application/pdffulltexthttps://bibliotecadigital.ipb.pt/bitstreams/1444827f-f2b9-4bd2-9d03-00e5b7f00008/downloadMolecular Ecology Resources256114 |
| spellingShingle | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed Veríssimo, Joana Biodiversity monitoring Environmental DNA Freshwater ecosystems High-throughput sequencing Metabarcoding Replication |
| status | SINGLETON |
| subject.fl_str_mv | Biodiversity monitoring Environmental DNA Freshwater ecosystems High-throughput sequencing Metabarcoding Replication |
| title | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed |
| title_full | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed |
| title_fullStr | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed |
| title_full_unstemmed | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed |
| title_short | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed |
| title_sort | Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed |
| topic | Biodiversity monitoring Environmental DNA Freshwater ecosystems High-throughput sequencing Metabarcoding Replication |
| topic_facet | Biodiversity monitoring Environmental DNA Freshwater ecosystems High-throughput sequencing Metabarcoding Replication |
| url | http://hdl.handle.net/10198/34680 |
| visible | 1 |