Preliminary characterization of coral reef diversity using environmental DNA in a hyper-diverse context

Monitoring coral reef communities remains a scientific cornerstone of marine biodiversity conservation and management. Environmental DNA (eDNA) has recently emerged as a passive detection tool to enumerate organisms in dynamic marine systems. The utility of eDNA to provide meaningful results for coral reef conservation and management in Indonesia, a hyper-diverse and data-limited tropical area, however, remains poorly understood. In this study, we conducted seawater and sediment eDNA surveys in three regions of Indonesia and amplified them using a general metazoan primer. We found that eDNA revealed a diverse array of reef organisms overall (>11,000 amplicon sequence variants, or ASVs), including species of management importance (i.e., sharks and mollusks) that are otherwise missed by conventional surveying methods. Most fish and coral eDNA detections were verified by our concurrent visual surveys of those taxonomic groups, demonstrating the utility of these two methods as complementary approaches for broad-scale reef bioassessment. Almost half of the ASVs, however, were unclassified Eukaryotes. We estimated that with our eDNA protocol, 119-197 water samples and 259-375 sediment samples would be needed to recover the complete suite of operational taxonomic units (a genetic proxy for species) in each region. Despite not reaching the full saturation of potential diversity or taxonomic detection within regions, eDNA sampling revealed community compositions were regionally distinct, even though water and sediment samples differed in community structure and exhibited high heterogeneity. Our precursory examination of a taxonomically-broad eDNA survey in Indonesia highlights the short and long-term utility of the method as a confirmatory and complementary tool for biomonitoring, research, and conservation purposes. Nonetheless, more rigorous sampling, methodological refinements, and database curation are needed for eDNA to reach its full potential in Indonesia.