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Abstract Leaf litter in coastal wetlands lays the foundation for carbon storage, and the creation of coastal wetland soils. As climate change alters the biogeochemical conditions and macrophyte composition of coastal wetlands, a better understanding of the interactions between microbial communities, changing chemistry, and leaf litter is required to understand the dynamics of coastal litter breakdown in changing wetlands. Coastal wetlands are dynamic systems with shifting biogeochemical conditions, with both tidal and seasonal redox fluctuations, and marine subsidies to inland habitats. Here, we investigated gene expression associated with various microbial redox pathways to understand how changing conditions are affecting the benthic microbial communities responsible for litter breakdown in coastal wetlands. We performed a reciprocal transplant of leaf litter from four distinct plant species along freshwater‐to‐marine gradients in the Florida Coastal Everglades, tracking changes in environmental and litter biogeochemistry, as well as benthic microbial gene expression associated with varying redox conditions, carbon degradation, and phosphorus acquisition. Early litter breakdown varied primarily by species, with highest breakdown in coastal species, regardless of the site they were at during breakdown, while microbial gene expression showed a strong seasonal relationship between sulfate cycling and salinity, and was not correlated with breakdown rates. The effect of salinity is likely a combination of direct effects, and indirect effects from associated marine subsidies. We found a positive correlation between sulfate uptake and salinity during January with higher freshwater inputs to coastal areas. However, we found a peak of dissimilatory sulfate reduction at intermediate salinity during April when freshwater inputs to coastal sites are lower. The combination of these two results suggests that sulfate acquisition is limiting to microbes when freshwater inputs are high, but that when marine influence increases and sulfate becomes more available, dissimilatory sulfate reduction becomes a key microbial process. As marine influence in coastal wetlands increases with climate change, our study suggests that sulfate dynamics will become increasingly important to microbial communities colonizing decomposing leaf litter. 

Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This study provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) together with nutrient concentrations and environmental parameters at 14 sites along two transects covering two distinctly different drainages: the peat-based Shark River Slough (SRS) and marl-based Taylor Slough/Panhandle (TS/Ph). Both bacterial as well as eukaryotic community structures varied significantly along the salinity gradient. Although freshwater communities were relatively similar in both transects, bacterioplankton community composition at the ecotone (where freshwater and marine water mix) differed significantly. The most abundant taxa in the freshwater marshes include heterotrophic Polynucleobacter sp. and potentially phagotrophic cryptomonads of the genus Chilomonas, both of which could be key players in the transfer of detritus-based biomass to higher trophic levels.