Comparing Microbial Communities of Diseased and Healthy Isopora palifera Corals and Adjacent Waters at the Cocos (Keeling) Islands.

Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood. Microorganisms are integral to coral health, but the role of bacterial communities in GAs remains unclear. We investigated an outbreak of GAs in Isopora palifera at the Cocos (Keeling) Islands using 16S rRNA amplicon sequencing to compare bacterial communities of GA-affected and asymptomatic corals, surrounding water and potential pollution sources. Significant differences in bacterial beta diversity were observed across sites, with an interaction between location and coral health status. Coral and water samples hosted distinct microbial communities, but there was no evidence linking GA-affected corals to local pollution. Moreover, no consistent bacterial taxa were associated with disease, suggesting that resident microbes may not be primary drivers of GAs. However, our study does not account for transient microbes that may have initiated GAs. Our findings challenge assumptions of single-agent causality and microbial compositional homogeneity in coral diseases. This study advances understanding of microbial dynamics in coral disease ecology and underscores the importance of early-stage investigation and functional metagenomics to identify viral, fungal and microbial functional shifts in disease emergence. Studying outbreaks in minimally impacted systems offers valuable baselines for disentangling natural disease processes.