Stony Coral Tissue Loss Disease Results in Persistent Microbial-Level Disturbances on Coral Reef Ecosystems.

Stony coral tissue loss disease (SCTLD) has reduced coral diversity and homogenised benthic communities. Beyond coral loss, SCTLD may disrupt microbiome composition and function, affecting reef recovery. We examined microbiome changes of apparently healthy corals, water, and sediment at three patch reefs in the Lower Florida Keys during three SCTLD stages: before (vulnerable), during (epidemic), and after (endemic) the outbreak. SCTLD significantly altered microbial diversity and functional potential within apparently healthy corals and the surrounding reef environment. In corals, microbial alpha and beta diversity were highest at the vulnerable stage before declining by the endemic stage, indicating lingering impacts of SCTLD on microbial diversity. Network neighbour and betweenness analyses revealed a loss in connectivity in microbial communities in coral and sediments during the endemic stage. Microbial functional prediction indicated an increase in multidrug resistance and sulphur cycling genes in corals in the epidemic stage. Predicted nitrogen fixation genes were enriched in epidemic coral and seawater, and endemic coral and sediments. SCTLD-associated taxa increased in apparently healthy corals, water and sediments during the epidemic stage, with some taxa persisting in the reef environment during the endemic stage. Thus, SCTLD likely has lasting taxonomic and functional microbial disruptions in coral reef ecosystems.