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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ftzenodo:oai:zenodo.org:4940284 2024-09-15T18:37:22+00:00 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 unknown Zenodo https://doi.org/10.1111/1755-0998.12740 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.c75sj oai:zenodo.org:4940284 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode biomonitoring quantitative metabarcoding info:eu-repo/semantics/other 2017 ftzenodo https://doi.org/10.5061/dryad.c75sj10.1111/1755-0998.12740 2024-07-26T17:07:54Z 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_sequences DNA 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) below. ... Other/Unknown Material Southern Ocean Zenodo |
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topic |
biomonitoring quantitative metabarcoding |
spellingShingle |
biomonitoring quantitative metabarcoding 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 |
biomonitoring quantitative metabarcoding |
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_sequences DNA 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) below. ... |
format |
Other/Unknown Material |
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 |
Zenodo |
publishDate |
2017 |
url |
https://doi.org/10.5061/dryad.c75sj |
genre |
Southern Ocean |
genre_facet |
Southern Ocean |
op_relation |
https://doi.org/10.1111/1755-0998.12740 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.c75sj oai:zenodo.org:4940284 |
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.c75sj10.1111/1755-0998.12740 |
_version_ |
1810481737170419712 |