eDNA metabarcoding illuminates species diversity and composition of three phyla (chordata, mollusca and echinodermata) across Indonesian coral reefs

Environmental DNA (eDNA) metabarcoding is an evolving tool that can provide broader assessments of marine biodiversity than conventional visual census methods. The outputs of this approach are, therefore, crucial to provide data for conservation priorities and to support fisheries management. We conducted a study using eDNA metabarcoding to understand the distribution of marine biodiversity across Indonesia and to investigate the abundance of three major phyla that comprise a majority of marine biodiversity. In this study, a total of 13,819,634 reads corresponding to 23,252 unique sequences belonging to the phyla Chordata, Mollusca, and Echinodermata were generated from COI amplicons obtained from 92 seawater eDNA samples collected from nine locations and 17 sites. Beta diversity differed significantly across locations (PERMANOVA: p < 0.05) based on Bray–Curtis and Jaccard indices. Taxa of interest were not distributed equally and there were no discernible patterns detected across the sampling area. This might be due to the highly variable percentage of sequenced species between families, preventing robust estimation of species richness. Overall, 45% of reads were identified to species level while 55% were classified as unidentified taxa. Interestingly, the percentage of unidentified taxa was similar between two locations with distinct characteristics representing eastern and western extremities of the sampling region. Despite a relatively poor rate of assignment to species level, our results highlight unprecedented levels of marine biodiversity and strong differences in species composition. This further supports the contention that the eDNA approach is a sensitive method that can provide useful data, in particular to detect changes in species composition. Importantly, this method is clearly advantageous to evaluate marine biodiversity on a large scale and can provide data to support region-wide coral reef management strategies. Knowing species diversity and the degree to which various taxa are distributed is a fundamental for advancing our knowledge of marine ecology and can play an important role in forecasting population dynamics and evolution as well as in refining conservation practices.