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Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes

Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and res...

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Autores principales: Klymus, Katy E., Marshall, Nathaniel T., Stepien, Carol A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436814/
https://www.ncbi.nlm.nih.gov/pubmed/28542313
http://dx.doi.org/10.1371/journal.pone.0177643
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author Klymus, Katy E.
Marshall, Nathaniel T.
Stepien, Carol A.
author_facet Klymus, Katy E.
Marshall, Nathaniel T.
Stepien, Carol A.
author_sort Klymus, Katy E.
collection PubMed
description Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring. We employed careful primer design and in vitro testing with mock communities to assess ability of the markers to amplify and sequence targeted species DNA, while retaining rank abundance information. In our mock communities, read abundances reflected the initial input abundance, with regressions having significant slopes (p<0.05) and high coefficients of determination (R(2)) for all comparisons. Tests on field environmental samples revealed similar ability of our markers to measure relative abundance. Due to the limited reference sequence data available for these invertebrate species, care must be taken when analyzing results and identifying sequence reads to species level. These markers extend eDNA metabarcoding research for molluscs and appear relevant to other invertebrate taxa, such as rotifers and bryozoans. Furthermore, the sphaeriid mussel assay is group-specific, exclusively amplifying bivalves in the Sphaeridae family and providing species-level identification. Our assays provide useful tools for managers and conservation scientists, facilitating early detection of invasive species as well as improving resolution of mollusc diversity.
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spelling pubmed-54368142017-05-27 Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes Klymus, Katy E. Marshall, Nathaniel T. Stepien, Carol A. PLoS One Research Article Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring. We employed careful primer design and in vitro testing with mock communities to assess ability of the markers to amplify and sequence targeted species DNA, while retaining rank abundance information. In our mock communities, read abundances reflected the initial input abundance, with regressions having significant slopes (p<0.05) and high coefficients of determination (R(2)) for all comparisons. Tests on field environmental samples revealed similar ability of our markers to measure relative abundance. Due to the limited reference sequence data available for these invertebrate species, care must be taken when analyzing results and identifying sequence reads to species level. These markers extend eDNA metabarcoding research for molluscs and appear relevant to other invertebrate taxa, such as rotifers and bryozoans. Furthermore, the sphaeriid mussel assay is group-specific, exclusively amplifying bivalves in the Sphaeridae family and providing species-level identification. Our assays provide useful tools for managers and conservation scientists, facilitating early detection of invasive species as well as improving resolution of mollusc diversity. Public Library of Science 2017-05-18 /pmc/articles/PMC5436814/ /pubmed/28542313 http://dx.doi.org/10.1371/journal.pone.0177643 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
Klymus, Katy E.
Marshall, Nathaniel T.
Stepien, Carol A.
Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
title Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
title_full Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
title_fullStr Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
title_full_unstemmed Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
title_short Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
title_sort environmental dna (edna) metabarcoding assays to detect invasive invertebrate species in the great lakes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436814/
https://www.ncbi.nlm.nih.gov/pubmed/28542313
http://dx.doi.org/10.1371/journal.pone.0177643
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