Rapid urbanization and agriculture have led to loss of wetlands and their ecosystem services in the Sacramento-San Joaquin Delta and the San Francisco Bay. The United States Geological Survey (USGS), through their wetland restoration project on Twitchell Island, has established the potential of wetlands as carbon sinks. However, wetlands are also natural sources of methane (CH4), a greenhouse gas (GHG) 20X more potent than CO2.

Interestingly, in most saline environments, sulfate-reducing bacteria are expected to outcompete methanogens resulting in decreased CH4 emission. But this is not the case with South San Francisco Bay (SSFB) salt ponds, formerly tidal marshes but later used for industrial salt production, which have been found to be major CH4 producers. This study aims to determine the microbial structure and source of substrates for methane production in restored, unrestored, and historical salt ponds in the SSFB area.

To address this, we used metagenomics, biogeochemical approaches, and greenhouse gas measurements to identify differences in microbial communities and interactions in the three habitats. Our analysis revealed pond type-specific microbial communities and spatial heterogeneity. Furthermore, the samples share similar and distinct microbial communities along salinity gradients. Subsequently, these site-specific differences (1) are associated with different photosynthetic and metabolic pathways; (2) are weakly correlated with elevated methane flux as determined by methyl coenzyme M reductase subunit A (mcr A) gene relative abundance; (3) suggest glycine betaine as source of noncompetitive methylated subtrates. Overall, this study provides evidence that distinct microbial interactions lead to the establishment of environment-specific microbial pattern assemblies. This work can potentially contribute in monitoring, and implementing more efficient conservation, restoration, and management project of hypersaline wetland.