Uncovering Variable Hidden Communities in the 'Bare Space' of Coral Reefs using Environmental DNA Metabarcoding

Conventional biodiversity monitoring often underestimate the biodiversity present in 'bare space' areas of marine ecosystems, leading to a limited understanding of species richness and crucial ecological changes. In this study, we employed vacuum sampling and multiple marker environmental DNA (eDNA) metabarcoding to assess the biodiversity of Epilithic Algal Matrix (EAM) communities in the 'bare space' of two remote reefs in the South China Sea. Our findings confirm that despite being covered by algal turfs, these 'bare space' areas harbor a high diversity of bacteria, microalgae, and mini-metazoans reveal by multiple marker eDNA metabarcoding targeting prokaryote 16S, eukaryote 18S, and invertebrate COI genes. Our results revealed the significant variations in species composition among different habitats, and algal canopy height may be an important indicator of community structure change. Additionally, our results highlight the potential role of microbes, including Proteobacteria, cyanobacteria and microalgae, in influencing the variability of community structure through interactions with other organisms. Understanding the biodiversity of 'bare space' areas is essential as they contribute significantly to the overall biodiversity and functioning of coral reef ecosystems. Our research provides a straightforward and comprehensive approach, employing high taxonomic resolution, to address species composition variability in these often overlooked areas within highly diverse marine ecosystems.