eDNA Metabarcoding

02/02/2022

Environmental DNA (eDNA) metabarcoding is a novel, non-invasive method for monitoring and assessing biodiversity. It involves extracting DNA from samples taken from the environment via water, sediment, or air, amplifying it using general or universal primers in a polymerase chain reaction, and sequencing it using high-throughput sequencing to generate thousands to millions of reads. I am involved in the Mzansi-eDNA project, a nationwide community science initiative that aims to integrate education and biodiversity inventory, assessment, and monitoring by collecting and analyzing environmental DNA collected by volunteers from a variety of habitats and ecosystems across South Africa. In addition, Mzansi-eDNA teaches the public about biodiversity conservation and human-induced environmental change by giving community scientists both online and in-person training.

Within marine spatial planning frameworks, marine protected areas (MPAs) are important tools to promote ocean health, and to build social, ecological and economic resilience (i.e., Blue Economy). Reel Science Coalition (RSC, non-profit organisation) has been engaged in planning and implementing a shore-based research program within the Helderberg Marine Protected Area (HMPA) of South Africa for assessing and monitoring surf-zone fish community composition and species abundance with seine net and tag-and-release surveys. The structure of fish assemblages accounted for by different sampling methods (e.g., net types, visual surveys) can differ significantly, even among similar ones, in terms of species composition, functional groups (ecological and trophic guilds), and fish size distribution. Consequently, a cross-validation of fish sampling methodologies is necessary to ensure standardization and comparability of monitoring methods.

Under Mzansi-eDNA, I am the principle investigator of the EDNAM project that aims to apply marine eDNA metabarcoding, at a temporal and spatial scale, as an alternative for the monitoring and assessment of fish communities in the HMPA, to get a near-holistic view of fish community structure and site occupancy rates in the HMPA, and to understand the strengths and limitations of each sampling approach. It is envisaged that eDNA metabarcoding will enable genetic-informed management actions necessary for marine ecosystem management, and to protect and sustain the Blue Economy.