Data from: 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 and important open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship-based bulk plankton sampling...
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ftzenodo:oai:zenodo.org:3968733 2024-09-15T18:37:20+00:00 Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder Suter, Leonie Polanowski, Andrea Clarke, Laurence Kitchener, John Deagle, Bruce 2020-07-31 https://doi.org/10.5061/dryad.w3r2280mq unknown Zenodo https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.w3r2280mq oai:zenodo.org:3968733 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Continuous Plankton Recorder open ocean biomonitoring info:eu-repo/semantics/other 2020 ftzenodo https://doi.org/10.5061/dryad.w3r2280mq 2024-07-27T02:31:11Z Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast and important 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 biodiversity as conventional CPR bulk sampling (~1500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (i) conventional morphological CPR sampling and (ii) 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 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 non-metazoan 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. All raw fastq files were uploaded (gz compressed). They originate from two separate sequencing runs - file names starting with "V4." are from the first run, file names starting with e.g. "003_V4." ... Other/Unknown Material Southern Ocean Copepods Zenodo |
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Continuous Plankton Recorder open ocean biomonitoring |
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Continuous Plankton Recorder open ocean biomonitoring Suter, Leonie Polanowski, Andrea Clarke, Laurence Kitchener, John Deagle, Bruce Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
topic_facet |
Continuous Plankton Recorder open ocean biomonitoring |
description |
Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast and important 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 biodiversity as conventional CPR bulk sampling (~1500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (i) conventional morphological CPR sampling and (ii) 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 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 non-metazoan 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. All raw fastq files were uploaded (gz compressed). They originate from two separate sequencing runs - file names starting with "V4." are from the first run, file names starting with e.g. "003_V4." ... |
format |
Other/Unknown Material |
author |
Suter, Leonie Polanowski, Andrea Clarke, Laurence Kitchener, John Deagle, Bruce |
author_facet |
Suter, Leonie Polanowski, Andrea Clarke, Laurence Kitchener, John Deagle, Bruce |
author_sort |
Suter, Leonie |
title |
Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_short |
Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_full |
Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_fullStr |
Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_full_unstemmed |
Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder |
title_sort |
data from: capturing open ocean biodiversity: comparing environmental dna metabarcoding to the continuous plankton recorder |
publisher |
Zenodo |
publishDate |
2020 |
url |
https://doi.org/10.5061/dryad.w3r2280mq |
genre |
Southern Ocean Copepods |
genre_facet |
Southern Ocean Copepods |
op_relation |
https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.w3r2280mq oai:zenodo.org:3968733 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.w3r2280mq |
_version_ |
1810481702137495552 |