Methanogens dominate methanotrophs and act as a methane source in aquaculture pond sediments

Aquaculture pond sediments act as hotspots for methane (CH₄) emissions; however, knowledge gaps on the regulation of microorganisms hinder our further understanding of methane dynamics in aquaculture pond sediment. Using field sampling and molecular analysis, we examined CH₄ fluxes, the methanogenic community composition, and their interaction with methanotrophs to comprehensively understand the methane cycling in sediments of aquaculture ponds in northern China. Compared with a fishing pond without feed inputs, the abundances of methanogens mcrA and methanotrophs pmoA genes increased significantly in aquaculture ponds sediments. The dominant methanogens were Methanothrix, Methanoregula, and Methanolinea, and the α-diversity indices of methanogens demonstrated higher levels in 0-5 cm surface sediment. The methanotrophs were dominated by Methylocystis, Methylocaldum, and Methylobacter, and the α-diversity indices of methanotrophs showed no significant difference. The total organic carbon (TOC) contents and oxidation reduction potential (ORP) were the key factors driving methanogenic and methanotrophic communities on methane cycle in aquaculture sediment. The inter-domain ecological network (IDEN) analysis revealed that total number of network nodes, links, connectances, and links per species in the aquaculture sediments presented relatively higher levels, whereas the IDEN modules were fewer. The methanogens dominated in the networks and the interaction of methanogens and methanotrophs was more competitive and complex in aquaculture sediments. These findings highlight the marked methane production in aquaculture sediment, primarily due to the abundance, diversity, and competitive advantage of methanogens over methanotrophic communities.