Soil microbiome community composition shaped by soil depth in a wetland with diel variations in methane emissions

Wetlands play a disproportionally important role in the global methane cycle due to their unique hydrological and biogeochemical characteristics. Understanding the complex interplay among microbial communities, habitat and geochemical processes is key for assessing their response to environmental changes and their contribution to greenhouse gas dynamics. This study investigated the spatiotemporal and depth relationships among methane fluxes, soil geochemistry, and microbiome communities in a subtropical wetland using 16S rRNA sequencing, methane flux measurements, and soil profiling. We find that soil chemical properties and methane are linked to the variations in soil microbial communities. However, soil depth is the primary factor structuring microbial communities, with surface soils supporting high abundance of iron-methane cycling microbes and evidence of direct interspecies electron transfer (DIET) pathways. Interconnected processes involving methanogens, syntrophs, sulphur reducing bacteria, and fermentative bacteria were prominent in surface soils, likely facilitating organic matter decomposition and methane production. Variations in diurnal methane dynamics and water chemistry were linked to shifts in the relative abundance of microbial taxa, such as Methylomirabilaceae, Syntrophobacter, and Syntrophorhabdus . Water lilies ( Nymphaea sp.) are possibly influencing microbial activity and methane emissions in wetlands by supplying organic matter and oxygen to the soil. Overall, our results show that soils depth drove microbial community, with abiotic (e.g. temperature) and biotic factors (e.g. vegetation) influencing spatiotemporal variation in wetland methane fluxes. Understanding the complex drivers of methanogenesis in wetlands is essential for refining global methane budgets and accurately modelling future climate scenarios in the face of accelerating environmental change. • Surface and subsurface depths drove the prokaryotic community structure • Diel gas flux did not match community composition shifts • Vegetation likely influences depth differences in lily wetland • Putative functions of prokaryotes suggest diverse metabolic activity in soils