The microbial fingerprint: fine-scale environmental, genetic, and temporal factors drive the reef metagenome during coral spawning

Abstract Understanding the stability of microbial community assembly on coral reefs is crucial for determining their response to changing environments. Here, we evaluate how the marine sediment, water column, and mountainous star coral (Orbicella faveolata) metagenomic communities shift over temporal, spatial, and genetic gradients, centered on the annual coral spawning event on St. Croix, USVI. Using low-coverage shotgun sequencing and a reference-free approach, we characterized metagenomic communities and additionally report 15 metagenome-assembled genomes from environmental samples. We show that diel time can be as important as kilometer-scale distance in structuring the coral-associated and marine sediment community structure, albeit with other highly local factors (genotype, within-reef location) driving most variation. Through multivariate machine learning methods, we find several taxa and metabolic pathways enriched over time, where broad metagenomic community shifts may be linked with concurrent temperature increase or the annual coral spawning event. As understanding the coral microbiome in the context of its environment becomes increasingly important, our research underscores the importance of small-scale variation, both spatially and temporally, in structuring coral reef metagenomic communities. Competing Interest Statement The authors have declared no competing interest. Footnotes Manuscript updated to revise inferences about effects of spawning; minor content revisions for language throughout; rework of discussion and introduction