Longitudinal microbiomes of coral and near-coral seawater are influenced by disease phase

Stony coral tissue loss disease (SCTLD) has caused dramatic coral declines across the Caribbean since 2014. SCTLD affects the coral microbiome, but there is limited understanding of how SCTLD impacts coral microbiomes through time. In a longitudinal design, coral tissue and near-coral seawater were repeatedly sampled from the same Colpophyllia natans colonies in St. John, United States (US) Virgin Islands, over 4 years. We identified the associated bacteria and archaea using 16S ribosomal RNA gene sequencing. Coral microbiomes exhibited high beta diversity regardless of disease state, both within and between colonies, suggesting dysbiosis prior to SCTLD exposure. By contrast, the microbial composition of near-coral seawater overlying non-diseased colonies was generally consistent. SCTLD disrupted the near-coral seawater microbiome but only during the epidemic phase when pathogen load is likely higher on the reef. This study suggests that non-invasive seawater microbiomes may be a useful tool for monitoring and understanding coral reef health threats.