Multiscale Patterns of Bacterial and Protist Diversity Across Red Sea Coral Reefs.

Coral reef microbial communities play pivotal roles in ecosystem functioning but remain understudied, particularly across spatial gradients and domains. Here, we use environmental DNA (eDNA) metabarcoding of 16S and 18S rRNA genes to profile bacterial and protistan communities in surface sediments from six coral reefs along the central Red Sea. At each reef, we sampled both exposed (seaward) and sheltered (shoreward) sites, enabling a multiscale analysis of diversity and community composition. We found significant differences in alpha and beta diversity between reefs and between exposure sites within reefs for both microbial groups. Redundancy analysis (RDA) and PERMANOVA revealed reef identity and exposure category as key structuring factors. Indicator species analysis and Random Forest classification identified microbial taxa predictive of exposure gradients, with several exact sequence variants (ESVs) serving as robust bioindicators in both methods. Bacterial and protistan communities exhibited overlapping but distinct patterns, highlighting their complementary ecological roles. Our results underscore the importance of fine-scale habitat heterogeneity in shaping reef microbial assemblages and support the integration of multi-domain eDNA data into coral reef monitoring frameworks.