Vertical distribution and environmental controls of methane cycling processes and associated microbial communities in Lake Chaohu sediments

Methane cycling in eutrophic freshwater lake sediments plays a crucial role in global greenhouse gas emissions. However, the vertical distribution patterns of methane cycling-related microbial processes and their controlling factors remain poorly understood in these ecosystems. Here, we quantified the activity potentials of methane cycling processes in sediments through culture experiments with different treatments, integrating molecular microbiology (metagenomics and qPCR) and sediment characteristics. Results revealed that activity potentials of methane cycling-related processes decreased with sediment depth, while the abundances of genes including mcrA, pmoA, NC10 pmoA, and ANME-2d mcrA showed significantly different patterns in their vertical distribution. A shift from acetotrophic to hydrogenotrophic methanogenesis was observed with increasing depth, occurring at 15–20 cm depth. Moreover, nitrate served as the predominant environmental driver of methane cycling in Lake Chaohu sediments. Significant differences were observed in both community composition and dominant genera of methane cycling-related microorganisms between the 0–20 cm and 20–45 cm sediment layers, with the upper layer dominated by aerobic methane oxidation and the lower layer characterized by nitrate-dependent anaerobic methane oxidation and methanogenesis. This study provides the first comprehensive investigation of methane cycling activity potentials and describes the distribution and environmental controls of methane cycling-related microbes across different sediment depths in a eutrophic freshwater lake. These findings advance our understanding of methane cycling processes in eutrophic lake sediments, providing crucial data and a theoretical foundation for understanding the natural sources and sinks of greenhouse gases, as well as potential strategies for mitigating methane emissions from eutrophic lakes.