Agroforestry development drives a progressive shift from physicochemical to microbially mediated organic matter cycling in tropical soils

Land-use change in tropical soils alters dissolved organic matter (DOM) chemistry and carbon cycling, however, linkages to microbial functions remain unresolved. We tested whether microbial carbon-degradation potential is associated with DOM composition along an Amazonian agroforestry chronosequence (10, 20, and 30 years), using adjacent pasture and primary forest as references. We integrated shotgun metagenomics with high-resolution mass spectrometry to couple carbohydrate-active enzyme (CAZymes) profiles to DOM composition. Soil chemistry explained 41.6% of the variability in microbial composition, while land-use type accounted for 28.5% of DOM variability. Seasonality did not affect microbial composition but was a significant source of variation in DOM. Relative to pasture, agroforests showed higher potential for sucrose and α-glucan degradation and a greater abundance of aliphatic DOM, indicating enhanced microbial processing. Older agroforests were enriched in genes targeting lignin and microbial-derived substrates such as peptidoglycan, resembling primary forest, whereas younger agroforests had higher abundances of GH36, GH5, and CE3 genes linked to cellulose and hemicellulose degradation, resembling pasture. Soil pH and available P were marginally associated with microbial-derived compound degradation, while pH, P, and Ca showed a stronger association with plant-derived compound processing. These results suggest that as agroforestry develops, carbon cycling may shift from physicochemical to microbial regulation, while DOM remained related to vegetation inputs and seasonality. Soil management of pH and available P during early establishment could support this transition, but the recovery may take decades.