Utilizing environmental DNA with visual surveys of marine biodiversity in a hyper-diverse and data-poor tropical context

Background/Question/Methods

Monitoring marine communities remains a scientific cornerstone of biodiversity conservation and management. Over the past decade, advancements in environmental DNA (eDNA) research development have shown its applicability to marine ecosystems. So far, however, most of this work has been performed in or by countries in the Global North. Thus, the assumed benefits of eDNA are largely derived from relatively well-resourced contexts that maintain a lot of infrastructural and research support. Here, we tested marine eDNA surveys against existing visual biodiversity surveying methods on coral reefs in Indonesia, a hyper-diverse and data-poor tropical context, to examine its potential utility in helping achieve the country’s conservation objectives. In three regions of Indonesia, visual surveys of fishes and corals were conducted alongside sediment and seawater sampling for eDNA, which were then amplified using a general animal primer. The same ecological analyses were used on the resulting datasets to investigate the patterns and drivers of biodiversity among regions. Given the additional costs of sequencing on existing biodiversity censusing efforts, we posited that marine eDNA had the burden of proof to capture more species that were ecologically meaningful for spatial management island conservation efforts.

Results/Conclusions

We found that while eDNA surveys revealed a diverse array of organisms overall ( >11,000 operational taxonomic units), visual surveys uncovered more fish ( >500 species) and coral (21 families) biodiversity. The visual surveys of fishes also provided more distinct spatial partitioning of communities among regions (R2 = 23.5%, p = 0.001) whose variation could be explained by a greater number of social and environmental variables. These results are in part due to a lower realized sampling effort and detection of species using eDNA in comparison to visual methods, as well as a predictable consequence of underinvestment in database curation and biodiversity research in tropical marine ecosystems. To help emerging economies like Indonesia meet their biodiversity conservation goals, standard eDNA protocols should be used as complements rather than take priority over visual methods; capacity building and database curation are also essential to advancing the applicability of eDNA as a conservation methodology. Our case study highlights the importance of equitable access to genetic infrastructure in global efforts to survey the ocean, which is especially relevant during the United Nations Decade of Ocean Science for Sustainable Development (2021-2030).