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Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples

Citation

Deagle, BE and Clarke, LJ and Kitchener, JA and Polanowski, AM and Davidson, AT, Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples, Molecular Ecology Resources, 18, (3) pp. 391-406. ISSN 1755-098X (2018) [Refereed Article]

Copyright Statement

Copyright 2017 Commonwealth of Australia

DOI: doi:10.1111/1755-0998.12740

Abstract

DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programmes, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterized 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 represent 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 programme. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring.

Item Details

Item Type:Refereed Article
Keywords:biomonitoring, DNA barcoding, environmental DNA, high-throughput sequencing
Research Division:Biological Sciences
Research Group:Ecology
Research Field:Marine and Estuarine Ecology (incl. Marine Ichthyology)
Objective Division:Environment
Objective Group:Flora, Fauna and Biodiversity
Objective Field:Marine Flora, Fauna and Biodiversity
Author:Deagle, BE (Dr Bruce Deagle)
Author:Clarke, LJ (Dr Laurence Clarke)
ID Code:123158
Year Published:2018 (online first 2017)
Web of Science® Times Cited:3
Deposited By:CRC-Antarctic Climate & Ecosystems
Deposited On:2017-12-19
Last Modified:2018-05-15
Downloads:1 View Download Statistics

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