Helping people to care for our ocean

Metabarcoding as a tool for coastal research

Dr Dave Pearton and Dr Sohana Singh

It is no secret that our knowledge of biodiversity is woefully inadequate, and with accelerating global and local threats, we are losing species at an increasing rate, some before they have been discovered or described. The recent Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) report shows that an average of around 25% of species in assessed animal and plant groups are threatened, a figure which is likely to be larger in less well studied groups, particularly the smaller, cryptic species that inhabit the sea floor or swim in the plankton.

Given that biodiversity underpins our natural capital and that healthy, biodiverse ecosystems are essential for healthy, well-nourished people, it is critical to protect it. The challenge is not just to discover and describe all the species out there, but also to track how they are being affected by anthropogenic pressures such as development and climate change.

Rapid advances in DNA sequencing technology and bioinformatics have provided us with the tools to do this. Every species on earth is defined by its genetic code, and by sequencing a distinct segment of its DNA we can create a unique barcode for each species. Metabarcoding is a way of taking a whole mix of organisms from an ecosystem, extracting the DNA from the whole ensemble, and identifying the DNA of each organism simultaneously.

At ORI, metabarcoding is being used to address critical questions for marine conservation along the KZN coast. For example, by determining the macrobenthos composition of seabed sediment samples, we can reveal the patterns in multi-species connectivity and community biodiversity between Marine Protected Areas (MPAs). This is key to determining their usefulness as replacement sources for macrobenthos in areas which have been impacted by land and sea activities.

Like the seabed, the pelagic ecosystem is a hotspot for “unseen biodiversity” such as the drifting larval phases of commercially important crustaceans and fishes that form part of marine zooplankton. By using the power of metabarcoding to sequence entire samples of these tiny, numerous, difficult to identify animals, we can get a snapshot of their biodiversity and determine the connectivity of these floating communities between our MPAs.

Between the sediment and pelagic ecosystems, lie the amazing reefs created by coral species. Most of us are familiar with the myriad of brightly coloured fish living within these ecosystems, but between the cracks and crevices of the reefs lies hidden still more biodiversity. Metabarcoding and eDNA analysis provides us with a new way of exploring this cryptic diversity, as well as the movement and fate of larvae produced from corals and other reef organisms.