Effects of feed input and planting of submerged aquatic vegetation on methanotrophic communities in the surface sediments of aquaculture ponds

Methanotrophs represent the only biological sink for the greenhouse gas methane, and only few studies have focused on methanotrophic communities in aquaculture ponds. Illumina high-throughput sequencing and real-time quantitative PCR were employed to profile the methanotrophic bacterial community and investigate the pmoA gene abundance in surface sediments from crab, oriental river prawn, perch, and Wuchang fish aquaculture ponds. Results revealed that Gammaproteobacteria (mainly the environmental_samples_norank genera) and Alphaproteobacteria (mainly the Methylocystis genera) were the most and second most abundant methanotrophic bacterial classes, respectively. While the species cultivated in these ponds were significantly different, the planting of submerged vegetation and the feed input were the main factors found to shape the methanotrophic bacterial community. Submerged vegetation potentially influenced methanotrophs in two ways: by increasing the alpha diversity of the methanotrophic community or by increasing methanotrophic abundance through inducing anaerobic root zone conditions, thereby increasing methane oxidation potential. The amount of feed input also influenced the methanotrophic communities in the fishponds (especially Wuchang fishponds), possibly through deposition of nitrogen, phosphorous, and organic matter (especially organic matter). These results provide preliminary biological data for the regulation of methanotrophs in aquaculture ponds in the future.