Consistent functional genes in methanogens along soil profiles in a temperate marshland

CH₄ production potential declines along soil profile in a temperate marshland. Key methanogenic groups decline more sharply with depth than gene abundance. Methanogenic groups correlate more strongly with soil properties than genes. Methanogen functional group strategy outweigh genetic potential in CH₄ regulation. Wetlands are the primary natural source of atmospheric methane (CH₄), the second most potent greenhouse gas. CH₄ production mainly occurs along the soil profile, while how functional genes associated with CH₄ production change along soil profile remains elusive. Our study integrated depth-stratified (0–100 cm) measurements of CH₄ production potential, soil characteristics, methanogenic gene abundance, and methanogen community composition involved in different methanogenesis pathways in a temperate marshland, northeast China, to explore how microbial and soil environmental factors regulate CH₄ production potential. Our results showed that CH₄ production potential decreased significantly with increasing soil depth, consistent with the decline in total microbial biomass, gene abundance, and community diversity. Moreover, methanogenic functional groups with distinct ecological strategies exhibited more pronounced shifts than functional genes in four pathways, particularly the H₂/CO₂ and methylotrophic facultative group declined significantly with depth. Furthermore, methanogenic functional groups showed stronger correlations with soil properties (e.g., NO₃⁻-N, NH₄⁺-N, TN, SWC, MBC, and MBN) than functional genes. Structural equation modeling revealed that soil physicochemical properties and methanogenic functional group composition (not gene relative abundance) significantly impacted CH₄ production potential, with coefficients of 0.67 and 0.41, respectively. Our findings establish that functional group identity, reflecting ecological strategy, supersedes genetic potential in regulating CH₄ production along soil profiles. This study offers critical insights into vertical variations in microbial control over wetland CH₄ cycling and advocates microbial models that use microbial biomass to represent microbial functions.