Shifts in vegetation impact estuary microbiomes

Coastal wetlands, including mangrove-cordgrass mosaics, are among Earth’s most effective carbon stores sequestering >1 Pg C/year. Rapid sea level rise, warming, and storm intensification are now reshaping these habitats. Vegetation type influences root exudates, sediment redox profiles, and organic matter quality. However, the impacts of vegetation on microbe–virus networks that mediate carbon burial and nutrient cycling remain unclear. Here, we sampled coastal sediment profiles in patches of cordgrass (dominated by Sporobolus alterniflorus ), black mangrove ( Avicennia germinans ), and seagrass on the Texas Gulf Coast. We obtained 491 bacterial and archaeal metagenome assembled genomes (MAGs) and 1,097 viral MAGs (vMAGs) from 55 surface sediment samples spanning day and night during summer and fall. Phylogenetic and comparative analyses revealed dominant lineages across the distinct vegetation types, organized into metabolic guilds based on similar protein compositions, revealing contrasting and complementary sulfur, iron, and nitrogen cycling pathways that regulate greenhouse gas emissions and encode genes important for carbon metabolism. Inference from virus–host linkages revealed that dominant lineages were infected, and viral communities have genes for organic carbon degradation, potentially shaping the microbial community dynamics in this ecosystem. This spatio-temporal characterization of estuary ecotone microbiomes provides a framework to better understand the diversity and metabolism of these productive coastal ecosystems.