A NEW METHOD FOR DETERMINING ZOOPLANKTON DIVERSITY AND ABUNDANCE FROM SOUTHERN OCEAN CONTINUOUS PLANKTON RECORDER (CPR) COLLECTIONS USING NANOPORE SEQUENCING

Continuous Plankton Recorders (CPRs) have been deployed from underway vessels to enable wide-ranging and economical zooplankton collection across global oceans for nearly a century. However, samples are often incompletely analyzed due to physical damage to specimens and the time and cost of morphological analysis. Polymerase chain reaction (PCR) amplicon sequencing can improve the speed and accuracy of analysis. PCR primers reliably targeting areas of high DNA sequence variability across taxa are essential to reduce the need for group-specific primer sets. To address patchy sequence coverage for Southern-Ocean species, we generated reference sequences using sanger and nanopore sequencing from specimens identified by a taxonomic expert. DNA extraction and amplification protocols were optimized across 9 phyla covering 120+ taxa, testing multiple primer sets targeting the COI gene and 18S ribosomal RNA operon. Ultimately, a novel primer set was developed specifically suited to taxa playing key roles in Southern Ocean ecosystems, covering a range of phyla. By multiplexing amplicons for individual specimens, this method can achieve high throughput and accuracy while providing abundance data. Nanopore sequencing allows for longer amplicons to be used for species discrimination, facilitates in-house sequencing, and is unaffected by co-amplification of target specimens and their associated organisms. This project considers how to address reference sequence database gaps and how to optimize genetics workflows for whole-community zooplankton research.

Presentation Preference: Oral

Primary Presenter: Georgia Pollard, University of Waikato (gp58@students.waikato.ac.nz)

Authors:

Georgia Pollard, University of Waikato  (gp58@students.waikato.ac.nz)

Matt Pinkerton, National Institute of Water and Atmospheric Research  (Matt.Pinkerton@niwa.co.nz)

Mary Sewell, University of Auckland  (m.sewell@auckland.ac.nz)

Moira Décima, University of California, San Diego  (mdecima@ucsd.edu)

Karen Robinson, National Institute of Water and Atmospheric Research  (karen.robinson@niwa.co.nz)

Svenja Halfter, National Institute of Water and Atmospheric Research  (Svenja.Halfter@niwa.co.nz)

Ian McDonald, University of Waikato  (ian.mcdonald@waikato.ac.nz)

Charles Lee, University of Waikato  (charles.lee@waikato.ac.nz)

Craig Cary, University of Waikato  (caryc@waikato.ac.nz)