Consistent drivers of coastal biodiversity across the tree of life

Coastal ecosystems are threatened by global change but remain understudied despite their importance for biodiversity and human society. For instance, most coastal studies and monitoring programs focus on a few groups of organisms owing to methodological limitations. However, high-throughput sequencing of environmental DNA (eDNA) now facilitates taxonomically broad studies of coastal biodiversity. Here, we conducted a very comprehensive study of coastal biodiversity patterns using multi-marker eDNA metabarcoding of nearly 1000 water and sediment samples covering the strong salinity gradient from the North Sea to the Baltic Sea. We included the major coastal habitat types and measured a range of environmental variables. Importantly, we found that across the tree of life: (i) salinity was the best predictor of community composition and richness, (ii) hard-bottomed habitats were coastal biodiversity hotspots regarding both species richness and unique sequences, and (iii) water and sediment samples harboured very different biological communities. Furthermore, we found geographically structured intraspecific genetic variation and detected 90 marine species not previously documented in Denmark. Our study suggests similar drivers of coastal biodiversity and community composition across the tree of life and demonstrates the potential of holistic eDNA biomonitoring for future management of coastal ecosystems locally and globally.