Ecological functions of soil microbes in climate regulation and soil processes

Soil microorganisms are key regulators of climate-relevant soil functions because they control carbon turnover and the production and consumption of the greenhouse gases CO2, CH4, N2O. This review summarise recent advances in the microbial mechanisms responsible for greenhouse gas production, consumption, and regulation in soils, with emphasis on methanogens, methanotrophs, nitrifiers, denitrifiers, and associated functional guilds. We discuss how microbial metabolism drives organic matter decomposition, soil–plant–microbe interactions, mineralisation of nutrients, and how microbial necromass, extracellular polymeric substances, and biofilm mechanisms contribute to soil aggregate stability, soil organic carbon retention, and the regulation of greenhouse gas emissions. We evaluate how land use intensification, monoculture, agrochemical inputs, intensive cultivation, and climate extremes interfere with these processes, while highlighting the roles of microbial diversity and functional redundancy in buffering ecosystem disturbance. Furthermore, we assessed microbial indicators that can support climate-smart soil management by linking community composition, functional gene abundance and expression (such as nifH, amoA, nirK, nirS, and nosZ), enzyme activities, and ecosystem processes. We then convert the most recent evidence to management guidance, showing that reduced tillage, organic amendments, cover cropping, legume rotations, biofertilisers, and mycorrhizal inoculants can improve nutrient use efficiency, reduce fertiliser dependence, mitigate greenhouse gas emissions and enhance soil resilience. Despite substantial progress, major gaps remain in linking microbial trait to field-scale CO2, CH4, and N2O fluxes in the standardisation of microbial indicators, and developing real-time monitoring framework for site-specific intervention. A clearer mechanistic understanding of soil microorganisms is therefore essential for advancing climate-smart and sustainable agriculture.