DNA in seawater captures tropical biodiversity

Jun 4, 2020

Accurate, rapid, and comprehensive biodiversity assessments are very important to understand how ecosystems are changing, and what areas of the ocean should be protected. The problem is that most species are very small, difficult to identify and they are very good at hiding. As a result, it has been impossible to quantify biodiversity beyond the most conspicuous species like fish and corals.

However, most species shed DNA in their surrounding environment in the form of feces, mucus, eggs… We call it environmental DNA (eDNA).

eDNA can be collected and sequenced as a way to understand what species are nearby, but very few studies have tested whether it actually work in very diverse tropical ecosystems. We used a single PCR survey of eDNA in seawater using a broad metazoan primer to characterize differences in community composition between five adjacent habitats at 19 sites across the tropical Caribbean bay of Bocas del Toro in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07%

of the taxa detected by the broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.


Nguyen BN, Shen EW, Seemann J, Correa MSC, O’Donnell JL, Altieri AH, Knowlton N, Crandall KA, Egan SP, McMillan O & Leray M. 2020. Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape Scientific Reports. 10:6729.