Seasonal and Spatial Microbial Community Dynamics Along the Shallow Southwest Florida Continental Shelf

Microbial communities play a crucial role in coastal ecosystem function, yet their seasonal and spatial dynamics in response to environmental change remain underexplored in tropical and subtropical regions. This yearlong study investigated microbial composition in water, sinking particles, and sediments along an inshore–offshore gradient influenced by the Caloosahatchee River Estuary in southwest Florida. The region has been altered by rapid coastal development and was struck by Hurricane Ian in September 2022. Environmental parameters exhibited significant spatiotemporal variation, shaping microbial beta diversity in all habitats. Sediment communities showed the greatest hurricane-induced disruption but returned to pre-disturbance conditions within six months. Dominant microbial classes included Alphaproteobacteria, Bacteroidia, and Gammaproteobacteria. Biogeochemical cycling taxa displayed strong habitat specificity, such as Desulfobulbia which dominated sinking particles, Desulfobacteria which was abundant in sediments, and Nitrosomonadaceae and Nitrosopumilaceae which were key nitrifiers in water and sediments, respectively. Particle–sediment taxonomic overlap suggests resuspension processes. Several inshore microbial indicators were consistently present across microbial habitats, especially at estuarine sites, suggesting the estuary as a microbial diversity reservoir for the coastal zone. These results highlight the value of long-term microbial monitoring to understand ecosystem change and resilience in dynamic coastal environments.