Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder
Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship‐based bulk plankton sampling and morphologi...
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Blackwell Publishing Ltd
2021
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Online Access: | https://doi.org/10.1111/mec.15587 http://www.ncbi.nlm.nih.gov/pubmed/32767849 http://ecite.utas.edu.au/142798 |
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ftunivtasecite:oai:ecite.utas.edu.au:142798 2023-05-15T18:25:43+02:00 Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder Suter, L Polanowski, AM Clarke, LJ Kitchener, LA Deagle, BE 2021 https://doi.org/10.1111/mec.15587 http://www.ncbi.nlm.nih.gov/pubmed/32767849 http://ecite.utas.edu.au/142798 en eng Blackwell Publishing Ltd http://dx.doi.org/10.1111/mec.15587 Suter, L and Polanowski, AM and Clarke, LJ and Kitchener, LA and Deagle, BE, Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder, Molecular Ecology, 30, (13) pp. 3140-3157. ISSN 0962-1083 (2021) [Refereed Article] http://www.ncbi.nlm.nih.gov/pubmed/32767849 http://ecite.utas.edu.au/142798 Biological Sciences Ecology Marine and estuarine ecology (incl. marine ichthyology) Refereed Article PeerReviewed 2021 ftunivtasecite https://doi.org/10.1111/mec.15587 2021-09-27T22:16:46Z Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship‐based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton biodiversity as conventional CPR bulk sampling (~1,500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (a) conventional morphological CPR sampling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired samples, respectively). A metazoan‐targeted cytochrome c oxidase I (COI) marker was used to characterize species‐level diversity. In the 2 L seawater eDNA samples, this marker amplified large amounts of non‐metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR samples. COI metabarcoding of bulk DNA samples mostly avoided nonmetazoan amplifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote‐targeted 18S ribosomal RNA marker detected a higher proportion, but lower diversity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean biodiversity. Article in Journal/Newspaper Southern Ocean Copepods eCite UTAS (University of Tasmania) Southern Ocean Molecular Ecology |
institution |
Open Polar |
collection |
eCite UTAS (University of Tasmania) |
op_collection_id |
ftunivtasecite |
language |
English |
topic |
Biological Sciences Ecology Marine and estuarine ecology (incl. marine ichthyology) |
spellingShingle |
Biological Sciences Ecology Marine and estuarine ecology (incl. marine ichthyology) Suter, L Polanowski, AM Clarke, LJ Kitchener, LA Deagle, BE Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
topic_facet |
Biological Sciences Ecology Marine and estuarine ecology (incl. marine ichthyology) |
description |
Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship‐based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton biodiversity as conventional CPR bulk sampling (~1,500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (a) conventional morphological CPR sampling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired samples, respectively). A metazoan‐targeted cytochrome c oxidase I (COI) marker was used to characterize species‐level diversity. In the 2 L seawater eDNA samples, this marker amplified large amounts of non‐metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR samples. COI metabarcoding of bulk DNA samples mostly avoided nonmetazoan amplifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote‐targeted 18S ribosomal RNA marker detected a higher proportion, but lower diversity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean biodiversity. |
format |
Article in Journal/Newspaper |
author |
Suter, L Polanowski, AM Clarke, LJ Kitchener, LA Deagle, BE |
author_facet |
Suter, L Polanowski, AM Clarke, LJ Kitchener, LA Deagle, BE |
author_sort |
Suter, L |
title |
Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_short |
Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_full |
Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_fullStr |
Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_full_unstemmed |
Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_sort |
capturing open ocean biodiversity: comparing environmental dna metabarcoding to the continuous plankton recorder |
publisher |
Blackwell Publishing Ltd |
publishDate |
2021 |
url |
https://doi.org/10.1111/mec.15587 http://www.ncbi.nlm.nih.gov/pubmed/32767849 http://ecite.utas.edu.au/142798 |
geographic |
Southern Ocean |
geographic_facet |
Southern Ocean |
genre |
Southern Ocean Copepods |
genre_facet |
Southern Ocean Copepods |
op_relation |
http://dx.doi.org/10.1111/mec.15587 Suter, L and Polanowski, AM and Clarke, LJ and Kitchener, LA and Deagle, BE, Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder, Molecular Ecology, 30, (13) pp. 3140-3157. ISSN 0962-1083 (2021) [Refereed Article] http://www.ncbi.nlm.nih.gov/pubmed/32767849 http://ecite.utas.edu.au/142798 |
op_doi |
https://doi.org/10.1111/mec.15587 |
container_title |
Molecular Ecology |
_version_ |
1766207344725721088 |