Oyster Reefs Are Reservoirs for Potential Pathogens in a Highly Disturbed Subtropical Estuary

Estuaries worldwide are grappling with deteriorating water quality and benthic conditions that coincide with the rising detection of pathogenic and potentially pathogenic microbes (PPM). Both indigenous PPM and those that enter estuaries through urban and agricultural runoff are funneled through suspension-feeding organisms and deposited onto the benthos, where they can be moved through food webs. This study explored PPM communities in the Indian River Lagoon system, a biodiverse but urbanized estuary in east central Florida (USA). PPM were surveyed in estuary water, at stormwater outfalls, and in biodeposits of a key suspension feeder, the eastern oyster Crassostrea virginica. A total of 52 microbial exact sequence variants, with per-sample relative abundances up to 61.4%, were identified as PPM. The biodeposits contained relatively more abundant and diverse PPM than the water samples. PPM community composition also differed between seasons and between biodeposits and water. The community differences were driven primarily by Vibrio and Pseudoalteromonas spp. This investigation provides evidence that, through biodeposition, oyster reefs in the IRL estuary are a reservoir for PPM, and it documents some taxa of concern that should be conclusively identified and investigated for their pathogenicity and potential to pervade food webs and fisheries.