Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: McClenaghan, Beverly, Fahner, Nicole, Cote, David, Chawarski, Julek, McCarthy, Avery, Rajabi, Hoda, Singer, Greg, Hajibabaei, Mehrdad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
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
_version_ 1783605897497411584
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
work_keys_str_mv AT mcclenaghanbeverly harnessingthepowerofednametabarcodingforthedetectionofdeepseafishes
AT fahnernicole harnessingthepowerofednametabarcodingforthedetectionofdeepseafishes
AT cotedavid harnessingthepowerofednametabarcodingforthedetectionofdeepseafishes
AT chawarskijulek harnessingthepowerofednametabarcodingforthedetectionofdeepseafishes
AT mccarthyavery harnessingthepowerofednametabarcodingforthedetectionofdeepseafishes
AT rajabihoda harnessingthepowerofednametabarcodingforthedetectionofdeepseafishes
AT singergreg harnessingthepowerofednametabarcodingforthedetectionofdeepseafishes
AT hajibabaeimehrdad harnessingthepowerofednametabarcodingforthedetectionofdeepseafishes