Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples
DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programs, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characteri...
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fttriple:oai:gotriple.eu:50|dedup_wf_001::9ee7f59a6513210e2d713cf8ece6b849 2023-05-15T18:25:54+02:00 Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples Deagle, Bruce E. Clarke, Laurence J. Kitchener, John A. Polanowski, Andrea M. Davidson, Andrew T. 2017-11-21 https://doi.org/10.5061/dryad.c75sj undefined unknown Dryad https://dx.doi.org/10.5061/dryad.c75sj http://dx.doi.org/10.5061/dryad.c75sj lic_creative-commons 10.5061/dryad.c75sj oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:99350 oai:easy.dans.knaw.nl:easy-dataset:99350 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 DNA Barcoding biomonitoring quantitative metabarcoding eDNA high-throughput sequencing Life sciences medicine and health care envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2017 fttriple https://doi.org/10.5061/dryad.c75sj 2023-01-22T16:53:24Z DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programs, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterised biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n= 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker. DNA 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 large plankton such as krill masked the presence of smaller species. We investigated adding a fixed amount of exogenous DNA to samples as an internal control to allow determination of relative plankton biomass. Overall, the metabarcoding 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 DNA metabarcoding from the current snapshot studies to the requirements of a long-term monitoring program. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring. 1_CPR_DNA_sequencesDNA sequences (merged sequence text files in FASTA format) for each sample as well as various files (mostly .csv format) with information on the identity of samples, taxonomy assigned to OTUs, etc. needed for initial data processing. These files are called in the r code (1) ... Dataset Southern Ocean Unknown Southern Ocean |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
DNA Barcoding biomonitoring quantitative metabarcoding eDNA high-throughput sequencing Life sciences medicine and health care envir geo |
spellingShingle |
DNA Barcoding biomonitoring quantitative metabarcoding eDNA high-throughput sequencing Life sciences medicine and health care envir geo Deagle, Bruce E. Clarke, Laurence J. Kitchener, John A. Polanowski, Andrea M. Davidson, Andrew T. Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
topic_facet |
DNA Barcoding biomonitoring quantitative metabarcoding eDNA high-throughput sequencing Life sciences medicine and health care envir geo |
description |
DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programs, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterised biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n= 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker. DNA 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 large plankton such as krill masked the presence of smaller species. We investigated adding a fixed amount of exogenous DNA to samples as an internal control to allow determination of relative plankton biomass. Overall, the metabarcoding 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 DNA metabarcoding from the current snapshot studies to the requirements of a long-term monitoring program. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring. 1_CPR_DNA_sequencesDNA sequences (merged sequence text files in FASTA format) for each sample as well as various files (mostly .csv format) with information on the identity of samples, taxonomy assigned to OTUs, etc. needed for initial data processing. These files are called in the r code (1) ... |
format |
Dataset |
author |
Deagle, Bruce E. Clarke, Laurence J. Kitchener, John A. Polanowski, Andrea M. Davidson, Andrew T. |
author_facet |
Deagle, Bruce E. Clarke, Laurence J. Kitchener, John A. Polanowski, Andrea M. Davidson, Andrew T. |
author_sort |
Deagle, Bruce E. |
title |
Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_short |
Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_full |
Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_fullStr |
Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_full_unstemmed |
Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples |
title_sort |
data from: genetic monitoring of open ocean biodiversity: an evaluation of dna metabarcoding for processing continuous plankton recorder samples |
publisher |
Dryad |
publishDate |
2017 |
url |
https://doi.org/10.5061/dryad.c75sj |
geographic |
Southern Ocean |
geographic_facet |
Southern Ocean |
genre |
Southern Ocean |
genre_facet |
Southern Ocean |
op_source |
10.5061/dryad.c75sj oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:99350 oai:easy.dans.knaw.nl:easy-dataset:99350 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
https://dx.doi.org/10.5061/dryad.c75sj http://dx.doi.org/10.5061/dryad.c75sj |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.c75sj |
_version_ |
1766207616489357312 |