Data

Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems

Australian Ocean Data Network
Clarke, L., Suter, L., Polanowski, A., Deagle, B., Stark, J. and Johnstone, G.J. ; CLARKE, LAURENCE ; SUTER, LEONIE ; POLANOWSKI, ANDREA ; DEAGLE, BRUCE ; STARK, JONNY ; JOHNSTONE, GLENN JAMES
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=http://data.aad.gov.au/metadata/records/AAS_5097_DAP_nearshore_benthic_DNA_metabarcoding&rft.title=Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems&rft.identifier=http://data.aad.gov.au/metadata/records/AAS_5097_DAP_nearshore_benthic_DNA_metabarcoding&rft.publisher=Australian Antarctic Data Centre&rft.description=Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations (including Ellis Fjord, Warriner Channel, Hawker Channel, Abatus Bay, Powell Point, Shirokaya Bay, and Weddell Arm) in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla (including nematodes, cnidaria, echinoderms, chordates, arthropods, annelids, rotifers and molluscs) across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. Please cite: Clarke LJ et al. (2021). Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ, DOI: 10.7717/peerj.12458 This work was completed as part of the Davis Aerodrome Project (DAP).Progress Code: completedStatement: Only a small proportion of DNA sequences were assigned to the target taxa (multicellular animals, or metazoa). Samples that yielded less than 1000 metazoan DNA sequence reads are unlikely to provide sufficient DNA sequence depth to properly characterise metazoan diversity in those samples, and were excluded. Non-invasive, “capture-free” approaches like eDNA also raise the question: how do we know an organism detected with eDNA is really there? The issue is discussed in the final paragraph of the article.&rft.creator=Clarke, L., Suter, L., Polanowski, A., Deagle, B., Stark, J. and Johnstone, G.J. &rft.creator=CLARKE, LAURENCE &rft.creator=SUTER, LEONIE &rft.creator=POLANOWSKI, ANDREA &rft.creator=DEAGLE, BRUCE &rft.creator=STARK, JONNY &rft.creator=JOHNSTONE, GLENN JAMES &rft.date=2021&rft.coverage=westlimit=77.88451; southlimit=-68.63487; eastlimit=78.39757; northlimit=-68.42426&rft.coverage=westlimit=77.88451; southlimit=-68.63487; eastlimit=78.39757; northlimit=-68.42426&rft.coverage=uplimit=39; downlimit=3.6&rft.coverage=uplimit=39; downlimit=3.6&rft_rights=This metadata record is publicly available.&rft_rights=These data are not yet publicly available for download.&rft_rights= 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 instructions listed in the citation reference provided at http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_5097_DAP_nearshore_benthic_DNA_metabarcoding when using these data. http://creativecommons.org/licenses/by/4.0/).&rft_rights=Portable Network Graphic&rft_rights=https://i.creativecommons.org/l/by/3.0/88x31.png&rft_rights=Creative Commons by Attribution logo&rft_rights=Attribution 4.0 International (CC BY 4.0)&rft_rights=Legal code for Creative Commons by Attribution 4.0 International license&rft_rights=Attribution 4.0 International (CC BY 4.0)&rft_rights= https://creativecommons.org/licenses/by/4.0/legalcode&rft_subject=oceans&rft_subject=biota&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > MOLLUSKS&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ROTIFERS&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > SEGMENTED WORMS (ANNELIDS)&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ECHINODERMS&rft_subject=EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > CNIDARIANS&rft_subject=EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC&rft_subject=ENVIRONMENTAL DNA&rft_subject=DNA METABARCODING&rft_subject=CYTOCHROME C OXIDASE SUBUNIT I (COI)&rft_subject=METAZOAN&rft_subject=NEMATODES&rft_subject=CNIDARIA&rft_subject=ECHINODERMS&rft_subject=CHORDATES&rft_subject=ARTHROPODS&rft_subject=ANNELIDS&rft_subject=ROTIFERS&rft_subject=MOLLUSCS&rft_subject=ILLUMINA MISEQ&rft_subject=ADS > Automated DNA Sequencer&rft_subject=LABORATORY&rft_subject=AMD/AU&rft_subject=AMD&rft_subject=CEOS&rft_subject=GEOGRAPHIC REGION > POLAR&rft_subject=CONTINENT > ANTARCTICA > VESTFOLD HILLS&rft.type=dataset&rft.language=English Access the data
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This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/).

Please follow instructions listed in the citation reference provided at http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_5097_DAP_nearshore_benthic_DNA_metabarcoding when using these data.
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These data are not yet publicly available for download.

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Brief description

Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations (including Ellis Fjord, Warriner Channel, Hawker Channel, Abatus Bay, Powell Point, Shirokaya Bay, and Weddell Arm) in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla (including nematodes, cnidaria, echinoderms, chordates, arthropods, annelids, rotifers and molluscs) across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. Please cite: Clarke LJ et al. (2021). Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ, DOI: 10.7717/peerj.12458 This work was completed as part of the Davis Aerodrome Project (DAP).

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Progress Code: completed
Statement: Only a small proportion of DNA sequences were assigned to the target taxa (multicellular animals, or metazoa). Samples that yielded less than 1000 metazoan DNA sequence reads are unlikely to provide sufficient DNA sequence depth to properly characterise metazoan diversity in those samples, and were excluded. Non-invasive, “capture-free” approaches like eDNA also raise the question: how do we know an organism detected with eDNA is really there? The issue is discussed in the final paragraph of the article.

Notes

Purpose
To explore the potential of environmental DNA (eDNA) as a metazoan biodiversity monitoring tool for Antarctic benthic ecosystems. Specifically: (1) Are there differences between sediment and water eDNA samples in terms of (a) number of reads assigned to metazoans, non-metazoans, and unclassified, (b) the number of metazoan species detected, (c) metazoan community composition? (2) Does eDNA-based species richness decrease with sediment depth, similar to trends observed in morphology-based studies? (3) Do environmental parameters (e.g., depth, distance to open ocean) influence community composition in water eDNA?

Data time period: 2019-11-13 to 2019-12-14

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78.39757,-68.42426 78.39757,-68.63487 77.88451,-68.63487 77.88451,-68.42426 78.39757,-68.42426

78.14104,-68.529565

text: westlimit=77.88451; southlimit=-68.63487; eastlimit=78.39757; northlimit=-68.42426

text: uplimit=39; downlimit=3.6

Subjects
ADS > Automated DNA Sequencer | AMD | AMD/AU | ANNELIDS | ARTHROPODS | CEOS | CHORDATES | CNIDARIA | CONTINENT > ANTARCTICA > VESTFOLD HILLS | CYTOCHROME C OXIDASE SUBUNIT I (COI) | DNA METABARCODING | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > CNIDARIANS | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ECHINODERMS | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > MOLLUSKS | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ROTIFERS | EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > SEGMENTED WORMS (ANNELIDS) | EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC | ECHINODERMS | ENVIRONMENTAL DNA | GEOGRAPHIC REGION > POLAR | ILLUMINA MISEQ | LABORATORY | METAZOAN | MOLLUSCS | NEMATODES | ROTIFERS | biota | oceans |

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uri : https://data.aad.gov.au/eds/5424/download

Identifiers
  • global : AAS_5097_DAP_nearshore_benthic_DNA_metabarcoding
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