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Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes
The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641347/ https://www.ncbi.nlm.nih.gov/pubmed/33147221 http://dx.doi.org/10.1371/journal.pone.0236540 |
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author | McClenaghan, Beverly Fahner, Nicole Cote, David Chawarski, Julek McCarthy, Avery Rajabi, Hoda Singer, Greg Hajibabaei, Mehrdad |
author_facet | McClenaghan, Beverly Fahner, Nicole Cote, David Chawarski, Julek McCarthy, Avery Rajabi, Hoda Singer, Greg Hajibabaei, Mehrdad |
author_sort | McClenaghan, Beverly |
collection | PubMed |
description | The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here, we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea water samples. We found that deep sea water samples (> 1400 m depth) had significantly lower DNA concentrations than surface or mid-depth samples necessitating a refined protocol with a larger sampling volume. We recovered significantly more DNA in large volume water samples (1.5 L) filtered at sea compared to small volume samples (250 mL) held for lab filtration. Furthermore, the number of unique sequences (exact sequence variants; ESVs) recovered per sample was higher in large volume samples. Since the number of ESVs recovered from large volume samples was less variable and consistently high, we recommend the larger volumes when sampling water from the deep ocean. We also identified three primer sets which detected the most fish taxa but recommend using multiple markers due the variability in detection probabilities and taxonomic resolution among fishes for each primer set. Overall, fish diversity results obtained from metabarcoding were comparable to conventional survey methods. While eDNA sampling and processing need be optimized for this unique environment, the results of this study demonstrate that eDNA metabarcoding can facilitate biodiversity surveys in the deep ocean, require less dedicated survey effort per unit identification, and are capable of simultaneously providing valuable information on other taxonomic groups. |
format | Online Article Text |
id | pubmed-7641347 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-76413472020-11-10 Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes McClenaghan, Beverly Fahner, Nicole Cote, David Chawarski, Julek McCarthy, Avery Rajabi, Hoda Singer, Greg Hajibabaei, Mehrdad PLoS One Research Article The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here, we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea water samples. We found that deep sea water samples (> 1400 m depth) had significantly lower DNA concentrations than surface or mid-depth samples necessitating a refined protocol with a larger sampling volume. We recovered significantly more DNA in large volume water samples (1.5 L) filtered at sea compared to small volume samples (250 mL) held for lab filtration. Furthermore, the number of unique sequences (exact sequence variants; ESVs) recovered per sample was higher in large volume samples. Since the number of ESVs recovered from large volume samples was less variable and consistently high, we recommend the larger volumes when sampling water from the deep ocean. We also identified three primer sets which detected the most fish taxa but recommend using multiple markers due the variability in detection probabilities and taxonomic resolution among fishes for each primer set. Overall, fish diversity results obtained from metabarcoding were comparable to conventional survey methods. While eDNA sampling and processing need be optimized for this unique environment, the results of this study demonstrate that eDNA metabarcoding can facilitate biodiversity surveys in the deep ocean, require less dedicated survey effort per unit identification, and are capable of simultaneously providing valuable information on other taxonomic groups. Public Library of Science 2020-11-04 /pmc/articles/PMC7641347/ /pubmed/33147221 http://dx.doi.org/10.1371/journal.pone.0236540 Text en © 2020 McClenaghan et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article McClenaghan, Beverly Fahner, Nicole Cote, David Chawarski, Julek McCarthy, Avery Rajabi, Hoda Singer, Greg Hajibabaei, Mehrdad Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes |
title | Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes |
title_full | Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes |
title_fullStr | Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes |
title_full_unstemmed | Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes |
title_short | Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes |
title_sort | harnessing the power of edna metabarcoding for the detection of deep-sea fishes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641347/ https://www.ncbi.nlm.nih.gov/pubmed/33147221 http://dx.doi.org/10.1371/journal.pone.0236540 |
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