Abstract
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 community compositions across
three distinct microbial habitats: water, sinking particles, and sediments. They were sampled along
an inshore-offshore gradient under the influence of the Caloosahatchee River Estuary in Southwest
Florida. The region has experienced rapid coastal development, altering natural hydrology, and was
further impacted by the landfall of Hurricane Ian on September 28, 2022. Environmental parameters
exhibited significant spatiotemporal variation, shaping microbial beta diversity. Notably, sediment
communities experienced the most hurricane-induced disruption but reverted back to predisturbance conditions within six months. All microbial habitats displayed compositional shifts
along the inshore-offshore gradient, driven primarily by riverine and other terrestrial influences.
Across all habitats, Alphaproteobacteria, Bacteroidia, and Gammaproteobacteria were dominant
microbial classes with seasonal and habitat-specific variations. Biogeochemical cycling taxa
exhibited strong habitat specificity: Desulfobulbia were prevalent in sinking particles,
Desulfobacteria dominated sediments, and Nitrosomonaceae and Nitrosopumilaceae were the
principal nitrifiers in water and sediments, respectively. Taxonomic overlap between sediment and
particle-associated communities suggests resuspension as a key process contributing to particle
composition. During the wet season, increased chlorophyll levels in offshore water coincided with
greater microbial community homogeneity across spatial zones, suggesting an influx of decaying
algal particles. Algae-associated taxa such as Saprospiraceae and Pirellulaceae increased during
this period, highlighting their role in organic matter degradation. Several inshore microbial indicators
were detected across all microbial habitats, with specific indicators enriched at the most estuarineinfluenced site, suggesting that the Caloosahatchee River Estuary serves as a reservoir of microbial
diversity. Tracking the relative abundances of microbial amplicon sequence variants over space and
time provides a potential framework for assessing estuarine influence and ecosystem shifts in this
rapidly changing coastal region. Our findings underscore the importance of long-term microbial
monitoring for understanding biogeochemical cycling and ecosystem resilience in dynamic
estuarine-coastal interfaces.
