Microbial regulatory mechanisms underlying methane emission in rivers with different land covers

Inland rivers play a crucial role in regulating the methane (CH₄) budget via microbial carbon cycling. CH₄ emissions vary significantly among rivers with different land covers, yet the regulatory mechanisms of CH₄-cycling microorganisms across different land covers remain less understood. This study intergrates in-situ CH₄ measurements with amplicon and metagenomic sequencing to investigate CH₄-cycling microbial community composition and metabolic functions in regulating CH₄ emissions across rivers with different land covers. Our results show that agricultural and urban rivers significantly increase riverine CH₄ emission fluxes by 14 and 34 times than forest rivers, respectively. Urban and agricultural river sediments exhibited higher methanogenic abundance, but lower methanotrophic abundance than forest river sediments. Acetoclastic methanogens dominate the methanogenic communities of agricultural rivers, enhanced by high NO₃^- and DOC concentrations. Furthermore, methanogenic metagenome-assembled genomes (MAGs) recovered from agricultural rivers, which affiliated to Methanosarcina, carried the complete set of genes encoding for the enzymes in acetoclastic methanogenesis. In contrast, hydrogenotrophic methanogens drive CH₄ production in urban rivers, favored by low DOC: NH₄⁺ ratios that enable methanogenesis independent of organic carbon. Lower CH₄ emissions in agricultural rivers compared to urban rivers might be partly due to the greater sulfate-dependent anaerobic methane-oxidation. In forest rivers, type I methanotrophs outcompetes methanogens, aided by suitable sediment pH and larger sediment particle sizes, fostering oxic conditions that suppress CH₄ emissions. This study reveals versatile microbial mechanisms underlying riverine CH₄ emissions across land covers, enhancing understanding of microbial-mediated riverine CH₄ cycling.