Forest conversion and root trenching reshape microbial functions regulating root litter decomposition and soil carbon dynamics

Root litter decomposition is a key process shaping soil organic carbon (SOC) dynamics, mediated by interactions among ectomycorrhizal (ECM) fungi, saprotrophic (SAP) fungi, and bacteria. However, the microbial mechanisms regulating SOC dynamics across forest types remain unclear. Here, we used a trenching experiment in paired natural forest and plantation systems to evaluate changes in microbial communities, enzyme activities, carbon-degradation gene abundance, and root litter decomposition. After two years of decomposition, root litter in the plantation retained significantly more carbon, cellulose, and lignin than that in natural forests. Plantation soils exhibited significantly higher abundance of microbial genes associated with SOC degradation, including those related to starch, cellulose, hemicellulose, pectin, chitin, and lignin. Effect size of trenching on chitin degradation gene was greater in the plantation (Cohen's d = 1.044, 95 % CI: 0.039–2.022) than in the natural forest. While trenching had no significant main effect on most enzyme activities, a significant interaction between forest type and trenching was observed for peroxidase ( P < 0.05). In natural forests, structural equation modeling (SEM) revealed that trenching altered the bacterial-to-fungal biomass ratio, which in turn affected phenoloxidase activity and was associated with lignin and cellulose remaining in root litter. Our findings demonstrate that root litter decomposed more slowly in plantations than in natural forests, despite higher SOC-degradation gene abundance. In natural forests, microbial community composition influenced oxidative enzyme activity, which was closely linked to litter decomposition. Overall, enzyme activity, rather than gene abundance, better explained short-term SOC dynamics, highlighting the need to integrate microbial function into carbon models. • Root litter decomposed more slowly in plantations than in natural forests. • Plantation soils had more SOC-degradation genes despite slower decomposition. • Trenching increased chitin-degradation genes more in plantations. • Enzyme activity, not gene abundance, better explained short-term SOC dynamics. • In natural forests, microbial shifts influenced oxidative enzymes and litter decay.