Environmental DNA of Kelp Communities

Environmental DNA (eDNA) metabarcoding is a cutting-edge research technique that can be used to study the biodiversity of entire ecosystems. Every organism sheds DNA into its environment, which can be collected, for example, by filtering just a litre of seawater. This DNA is then sequenced to reveal a comprehensive picture of the organisms present, and specific genetic markers can even be applied to target particular groups.

Prof. Sophie von der Heyden at Stellenbosch University is one of the leading experts in eDNA. In 2022, Sophie invited Jannes to join Emma Rossouw’s BSc. Honours project. The water sampling and diving for this project (including repeated night dives) created a strong bond within the team. Emma’s study was the first to sample a complete community from a single site in the Great African Seaforest, uncovering DNA fragments representing almost 1,000 “species” from just a few litres of water.

This success led to the MSc. project of Kira Courtaillac, in which Kira and Jannes sampled water along the full distribution of the Great African Seaforest. Under Sophie’s leadership, Kira’s analysis revealed distinct fish communities in different kelp forest ecoregions, detected 140 fish species, and provided valuable insights into optimal sampling techniques for eDNA-based fish monitoring with important implications for conservation management.

Sophie’s eDNA research continues with a growing team, even as Jannes became less actively involved. In 2024, Sophie designed a project testing both active and passive sampling techniques, with Jannes and guest researcher Daniel Estevez-Barcia conducting a 24-hour field experiment. This work was further applied by Amy Doorman in her Honours thesis, which revealed clear community patterns between the west and east sides of the Cape Peninsula, demonstrating the power of eDNA for ecosystem-level research. Kira’s main paper remains the first to examine the Great African Seaforest as a whole, establishing a biodiversity baseline in an ocean that is rapidly changing.

We feel very honoured to have contributed to the first eDNA studies in the Great African Seaforest. The work of the von der Heyden Lab provides a broader, pattern-focused approach that complements our diving and documentation of physical organisms. eDNA helps detect rare and elusive species, offering a completely different lens for understanding this large-scale marine ecosystem. It is incredibly exciting to combine in-depth field knowledge and the human experience of being close to the seaforest with the broad-scale patterns revealed through eDNA. We look forward to continuing to learn from the excellent work of the von der Heyden Lab, while also sharing our growing species expertise and local knowledge to strengthen these efforts together.