Metabarcoding of zooplankton to derive indicators of pelagic ecosystem status

Jenny A. Huggett; Johan C. Groeneveld; Sohana P. Singh; Sandi Willows-Munro; Ashrenee Govender; Riaan Cedras; Shaun H.P. Deyzel

doi:10.17159/sajs.2022/12977

Authors

Jenny A. Huggett 1.Oceans and Coastal Research, Department of Forestry, Fisheries and the Environment (DFFE), Cape Town, South Africa; 2.Department of Biological Sciences, University of Cape Town, Cape Town, South Africa https://orcid.org/0000-0001-9315-8672
Johan C. Groeneveld 1.Oceanographic Research Institute, Durban, South Africa; 2.School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa https://orcid.org/0000-0002-9831-9073
Sohana P. Singh Oceanographic Research Institute, Durban, South Africa https://orcid.org/0000-0003-3484-7800
Sandi Willows-Munro School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa https://orcid.org/0000-0002-2860-4610
Ashrenee Govender School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa https://orcid.org/0000-0002-2860-4610
Riaan Cedras Department of Biodiversity and Conservation Biology, University of the Western Cape, Cape Town, South Africa https://orcid.org/0000-0003-0562-4173
Shaun H.P. Deyzel 1.South African Environmental Observation Network (SAEON), Elwandle Coastal Node, Gqeberha, South Africa; 2.Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha, South Africa https://orcid.org/0000-0002-1255-6167

DOI:

https://doi.org/10.17159/sajs.2022/12977

Keywords:

barcoding reference databases, climate change, essential ocean variables, ocean observations, zooplankton biodiversity

Abstract

Zooplankton play a key role in marine food webs and carbon cycling and are useful indicators of climaterelated changes and ocean health in pelagic ecosystems. Zooplankton are traditionally identified to species through microscopy, but new molecular techniques have enabled the identification of individual specimens (DNA barcoding) or multiple species in the same sample (DNA metabarcoding). Metabarcoding has been tested and refined using zooplankton collected in South African waters for the first time. Challenges to the implementation of DNA-based methods to measure zooplankton biodiversity easily and routinely include an incomplete DNA barcode reference library, logistical complexity and uptake of the new technology by environmental management agencies. These challenges call for a national effort to intensify zooplankton barcoding initiatives and to effectively engage stakeholders in developing a roadmap towards application of DNA-based methods in marine environmental management.

Significance:

Metabarcoding has been successfully applied to marine zooplankton for the first time in South Africa, demonstrating its potential as a tool to generate ecosystem indicators during routine ocean observations.
National barcoding efforts must be intensified to provide a comprehensive reference library of zooplankton DNA.
Effective engagement with stakeholders is required to overcome logistical and policy challenges, and to provide a roadmap towards application of DNA-based methods in marine environmental management.