Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs

Coral reefsare dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfallsof municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coraltissue samples (mucus and polyps) were characterized to determine relationships between microbial communities in these matrices and those in reefwater and coraltissues. Significant differences in microbial communities were noted among all sample types but varied between sampling area. Contamination from outfallswas found to be the greatest potential source of LBSP influencing native microbial community structure among all reefsamples, although pollution from inlets was also noted. Notably, reefwater and coraltissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. Results of this study provide new insights into how microbial communities from LBSP can impact coral reefsin Southeast Florida and suggest that wastewater outfallsmay have a greater influence on the microbial diversity and structure of these reefcommunities than do contaminants carried in runoff although the influence of runoff and coastal inlet discharge on coral reefsare still substantial. IMPORTANCE Coral reefsare known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reefcommunities and coastal receiving waters. Runoff delivered through inlet discharges impacted coralmicrobial communities, but impacts from oceanic outfallscarrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coralmicrobiomes may be influenced by the microbiological quality of treated wastewater.