bioRxiv2026
Although wetlands are increasingly recognized as important contributors to the global methane budget, the microorganisms and processes involved methane cycling are poorly characterized, particularly in coastal brackish and saline systems. Here, we investigated microbial and geochemical factors contributing to methane dynamics in three coastal wetlands with different salinities, dominant vegetation types, and soil chemical characteristics. These included a freshwater flotant marsh, a cypress swamp, and a mesohaline salt marsh. Specifically, we paired methane porewater concentrations, surface fluxes, geochemistry, and 16S rRNA gene sequencing to address how microbial community composition links to porewater concentrations and its potential effects on emissions. We found that porewater methane concentrations across sites were the highest in the swamp, followed by the salt marsh and the flotant marsh, and were explained by methanogen richness and abundance. While methane-cycling microbial communities were significantly structured by salinity, two microbial taxa (Methanosaeta and Methanomicrobiaceae) were present across all sites. Hydrogenotrophs were the most abundant methanogen functional group, with Methanomicrobiaceae and Methanobacterium discriminant among wetlands. In contrast, methanotroph functional types varied among wetlands. Type I dominated the freshwater flotant marsh, while the anaerobic methanotrophic archaea the saltwater marsh. These findings contribute to an enhanced understanding of the microbiological contributions to methane emissions from coastal wetlands. Scientific Significance Statement TopicThis study provides critical insights into the microbial and geochemical controls on methane emissions across coastal wetlands along a salinity gradient. Challenging the prevailing paradigm, methane porewater concentrations did not inversely correlate with salinity, as the swamp site with intermediate salinity exhibited the highest concentrations. Methanogen richness and abundance emerged as strong predictors of methane concentrations, while methanotroph richness had no predictive value. Two core methanogens, Methanosaeta and Methanomicrobiaceae, were consistently present across all wetland types. The findings highlight potential role of the water column as a biological methane filter, especially in saline environments. This study significantly advances the understanding of methane cycling in coastal wetlands by decoupling methane emissions from salinity gradients and emphasizing the role of microbial communities and local environmental factors. These insights are essential for refining biogeochemical models to forecast greenhouse gas emissions under sea-level rise and saltwater intrusion scenarios. Scientific Significance Statement OutletThis work integrates microbial ecology, geochemistry, and ecosystem structure to address interdisciplinary questions relevant to the limnological community. Here, we reveal how microbial community composition, rather than salinity alone, predicts methane emissions, offering a fresh perspective into carbon cycling in estuarine and coastal environments. The findings also provide critical insights for improving greenhouse gas emission models to predict climate change feedback from coastal areas.