Functional Microbes Mediate the Impact of Soil Depth and Anthropogenic Activities on Greenhouse Gas Fluxes in the Yellow River Delta, China

Coastal wetlands represent significant sources of greenhouse gases (GHGs) and serve as crucial ecological interfaces between terrestrial and marine environments, substantially contributing to global biogeochemical cycles. However, GHG emission fluxes are strongly influenced by complex anthropogenic activities, yet their underlying microbial mechanisms remain poorly understood. This study investigated seven representative human-impacted sites within the Yellow River Delta. Employing a combined approach of in vitro microcosm cultivation, molecular biology, and multivariate statistical analysis, we investigated the integrated mechanisms controlling nitrous oxide (N2O) and methane (CH4) fluxes, with consideration of soil depth, environmental factors, microbial communities, and functional microbes. The results indicated that significant differences in GHG fluxes among different anthropogenic activities and soil depths (p < 0.05). Surface soil N2O fluxes were positive within sewage irrigation areas (20.98–35.08 mg N2O-N m−2 hr−1) and tourism development areas (12.52–23.87 mg N2O-N m−2 hr−1), while mariculture areas displayed negative fluxes. CH4 fluxes were positive exclusively in natural areas (surface soil: 25.02–55.54 mg CH4-C m−2 hr−1; deep soil: 8.38–356.68 mg CH4-C m−2 hr−1), while other areas predominantly showed negative values (surface soil: −130.98–44.32 mg CH4-C m−2 hr−1; deep soil: −106.16–65.24 mg CH4-C m−2 hr−1). Furthermore, a structural equations model highlighted the pivotal role of key functional microbes in soil carbon–nitrogen cycling (e.g., nirK, nosZII, and SRB) involved in soil carbon–nitrogen cycling in negatively regulating N2O and CH4 fluxes. The study also revealed distinct microbial responses across diverse habitats, underscoring the significant role of Proteobacteria in wetland soil. This research enhances our understanding of GHG dynamics in coastal wetlands and provides scientific evidence and potential regulatory pathways for enhancing soil biological mitigation functions and achieving carbon neutrality and sustainability within wetland ecosystems.