eDNA metabarcoding as a biomonitoring tool for marine protected areas

Monitoring of marine protected areas (MPAs) is critical for marine ecosystem management, yet current protocols rely on SCUBA-based visual surveys that are costly and time consuming, limiting their scope and effectiveness. Environmental DNA (eDNA) metabarcoding is a promising alternative for marine e...

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Autores principales: Gold, Zachary, Sprague, Joshua, Kushner, David J., Zerecero Marin, Erick, Barber, Paul H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904164/
https://www.ncbi.nlm.nih.gov/pubmed/33626067
http://dx.doi.org/10.1371/journal.pone.0238557
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author Gold, Zachary
Sprague, Joshua
Kushner, David J.
Zerecero Marin, Erick
Barber, Paul H.
author_facet Gold, Zachary
Sprague, Joshua
Kushner, David J.
Zerecero Marin, Erick
Barber, Paul H.
author_sort Gold, Zachary
collection PubMed
description Monitoring of marine protected areas (MPAs) is critical for marine ecosystem management, yet current protocols rely on SCUBA-based visual surveys that are costly and time consuming, limiting their scope and effectiveness. Environmental DNA (eDNA) metabarcoding is a promising alternative for marine ecosystem monitoring, but more direct comparisons to visual surveys are needed to understand the strengths and limitations of each approach. This study compares fish communities inside and outside the Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA metabarcoding and underwater visual census surveys. Results from eDNA captured 76% (19/25) of fish species and 95% (19/20) of fish genera observed during pairwise underwater visual census. Species missed by eDNA were due to the inability of MiFish 12S barcodes to differentiate species of rockfishes (Sebastes, n = 4) or low site occupancy rates of crevice-dwelling Lythrypnus gobies. However, eDNA detected an additional 23 fish species not recorded in paired visual surveys, but previously reported from prior visual surveys, highlighting the sensitivity of eDNA. Significant variation in eDNA signatures by location (50 m) and site (~1000 m) demonstrates the sensitivity of eDNA to address key questions such as community composition inside and outside MPAs. Results demonstrate the utility of eDNA metabarcoding for monitoring marine ecosystems, providing an important complementary tool to visual methods.
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spelling pubmed-79041642021-03-02 eDNA metabarcoding as a biomonitoring tool for marine protected areas Gold, Zachary Sprague, Joshua Kushner, David J. Zerecero Marin, Erick Barber, Paul H. PLoS One Research Article Monitoring of marine protected areas (MPAs) is critical for marine ecosystem management, yet current protocols rely on SCUBA-based visual surveys that are costly and time consuming, limiting their scope and effectiveness. Environmental DNA (eDNA) metabarcoding is a promising alternative for marine ecosystem monitoring, but more direct comparisons to visual surveys are needed to understand the strengths and limitations of each approach. This study compares fish communities inside and outside the Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA metabarcoding and underwater visual census surveys. Results from eDNA captured 76% (19/25) of fish species and 95% (19/20) of fish genera observed during pairwise underwater visual census. Species missed by eDNA were due to the inability of MiFish 12S barcodes to differentiate species of rockfishes (Sebastes, n = 4) or low site occupancy rates of crevice-dwelling Lythrypnus gobies. However, eDNA detected an additional 23 fish species not recorded in paired visual surveys, but previously reported from prior visual surveys, highlighting the sensitivity of eDNA. Significant variation in eDNA signatures by location (50 m) and site (~1000 m) demonstrates the sensitivity of eDNA to address key questions such as community composition inside and outside MPAs. Results demonstrate the utility of eDNA metabarcoding for monitoring marine ecosystems, providing an important complementary tool to visual methods. Public Library of Science 2021-02-24 /pmc/articles/PMC7904164/ /pubmed/33626067 http://dx.doi.org/10.1371/journal.pone.0238557 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Gold, Zachary
Sprague, Joshua
Kushner, David J.
Zerecero Marin, Erick
Barber, Paul H.
eDNA metabarcoding as a biomonitoring tool for marine protected areas
title eDNA metabarcoding as a biomonitoring tool for marine protected areas
title_full eDNA metabarcoding as a biomonitoring tool for marine protected areas
title_fullStr eDNA metabarcoding as a biomonitoring tool for marine protected areas
title_full_unstemmed eDNA metabarcoding as a biomonitoring tool for marine protected areas
title_short eDNA metabarcoding as a biomonitoring tool for marine protected areas
title_sort edna metabarcoding as a biomonitoring tool for marine protected areas
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904164/
https://www.ncbi.nlm.nih.gov/pubmed/33626067
http://dx.doi.org/10.1371/journal.pone.0238557
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