Data

Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples

Australian Antarctic Division
Deagle, B. ; DEAGLE, BRUCE
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.5061/dryad.c75sj&rft.title=Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples&rft.identifier=10.5061/dryad.c75sj&rft.publisher=Australian Antarctic Data Centre&rft.description=Data stored in a Dryad package (doi:10.5061/dryad.c75sj) associated with the publication:Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples Authors: Bruce Deagle , Laurence Clarke , John Kitchener, Andrea Polanowski, Andrew Davidson. Molecular Ecology Resources.The Continuous Plankton Recorder (CPR) has been used to characterise zooplankton biodiversity along transects covering hundreds of thousands of kilometres in the Southern Ocean CPR survey. Plankton collected by the CPR is currently identified using is classical taxonomy (i.e. using a microscope and morphological features). We investigated the potential to use DNA metabarcoding (species identification from DNA mixtures using high-throughput DNA sequencing) as a tool for rapid collection of taxonomic data from CPR samples.In our study, zooplankton were collected on CPR silks along two transects between Tasmania and Macquarie Island. Plankton were identified using standard microscopic methods and by sequencing a mitochondrial COI marker. Data provided in the Dryad Data entry include the DNA sequences (Illumina MiSeq) recovered, the morphological identifications and the R-code used to analyse these data.The results from our study show that a DNA-based approach increased the number of metazoan species identified and provided high resolution taxonomy of groups problematic in conventional surveys (e.g. larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from larger plankton (such as krill) masked the presence of smaller species. Overall, the genetic data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing this powerful DNA metabarcoding approach from the current snapshot studies to the requirements of a long-term monitoring program.Progress Code: completed&rft.creator=Deagle, B. &rft.creator=DEAGLE, BRUCE &rft.date=2017&rft.coverage=westlimit=155.03906; southlimit=-52.48278; eastlimit=155.03906; northlimit=-52.48278&rft.coverage=westlimit=155.03906; southlimit=-52.48278; eastlimit=155.03906; northlimit=-52.48278&rft_rights=These data are available from DRYAD at the provided URL.&rft_rights=Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/legalcode&rft_rights=This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/). Please follow DRAYD guidelines when using these data.&rft_rights=This metadata record is publicly available.&rft_subject=biota&rft_subject=oceans&rft_subject=EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > AQUATIC ECOSYSTEMS > PLANKTON > ZOOPLANKTON&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL)&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ECHINODERMS&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > CNIDARIANS > HYDROZOANS&rft_subject=DNA BARCODING&rft_subject=DNA SEQUENCES&rft_subject=CPR > Continuous Plankton Recorder&rft_subject=R/V AA > R/V Aurora Australis&rft_subject=AMD/AU&rft_subject=AMD&rft_subject=CEOS&rft_subject=GEOGRAPHIC REGION > POLAR&rft_subject=OCEAN > SOUTHERN OCEAN&rft.type=dataset&rft.language=English Access the data
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These data are available from DRYAD at the provided URL.

This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/). Please follow DRAYD guidelines when using these data.

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Data stored in a Dryad package (doi:10.5061/dryad.c75sj) associated with the publication:

Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples Authors: Bruce Deagle , Laurence Clarke , John Kitchener, Andrea Polanowski, Andrew Davidson. Molecular Ecology Resources.

The Continuous Plankton Recorder (CPR) has been used to characterise zooplankton biodiversity along transects covering hundreds of thousands of kilometres in the Southern Ocean CPR survey. Plankton collected by the CPR is currently identified using is classical taxonomy (i.e. using a microscope and morphological features). We investigated the potential to use DNA metabarcoding (species identification from DNA mixtures using high-throughput DNA sequencing) as a tool for rapid collection of taxonomic data from CPR samples.

In our study, zooplankton were collected on CPR silks along two transects between Tasmania and Macquarie Island. Plankton were identified using standard microscopic methods and by sequencing a mitochondrial COI marker. Data provided in the Dryad Data entry include the DNA sequences (Illumina MiSeq) recovered, the morphological identifications and the R-code used to analyse these data.

The results from our study show that a DNA-based approach increased the number of metazoan species identified and provided high resolution taxonomy of groups problematic in conventional surveys (e.g. larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from larger plankton (such as krill) masked the presence of smaller species. Overall, the genetic data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing this powerful DNA metabarcoding approach from the current snapshot studies to the requirements of a long-term monitoring program.

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Progress Code: completed

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Purpose
Comparison between morphological taxonomy and DNA metabarcoding for processing continuous plankton recorder samples

Data time period: 2015-04-06 to 2015-04-20

This dataset is part of a larger collection

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155.03906,-52.48278

155.03906,-52.48278

text: westlimit=155.03906; southlimit=-52.48278; eastlimit=155.03906; northlimit=-52.48278

Subjects
AMD | AMD/AU | CEOS | CPR > Continuous Plankton Recorder | DNA BARCODING | DNA SEQUENCES | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL) | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > CNIDARIANS > HYDROZOANS | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ECHINODERMS | EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > AQUATIC ECOSYSTEMS > PLANKTON > ZOOPLANKTON | GEOGRAPHIC REGION > POLAR | OCEAN > SOUTHERN OCEAN | R/V AA > R/V Aurora Australis | biota | oceans |

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Access the data at DRYAD. (GET DATA)

doi : http://dx.doi.org/doi:10.5061/dryad.c75sj

Public information for AAS project AAS_4313 (PROJECT HOME PAGE)

url : https://projects.aad.gov.au/search_projects_results.cfm?project_no=AAS_4313

Citation reference for this metadata record and dataset. (VIEW RELATED INFORMATION)

url : https://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_4313_Genetic_CPR

Identifiers
ACN 633 798 857