Driving Soil Microbiome for C-fractions under Tropical Agroforest systems

Agroforestry systems (AFSs) are key components of sustainable land use, integrating trees with crops or pastures to enhance biodiversity, improve soil health, and increase carbon sequestration. This study compared soil organic matter fractions and microbial communities across two AFSs producing cupuaçu/açaí and African mahogany (2-and 30-year-old systems), pasture, and native forest in Tomé-Açu, Brazil. Soil samples were collected from 0-30cm depth and analysed for chemical properties, carbon fractions, δ¹³C, and microbial composition using 16S rRNA and ITS sequencing. Forest soils exhibited the highest total carbon concentrations in all depths, with the highest concentration at 10-20cm (23.2±5.66gC/soil kg). Mineral-associated organic matter (MAOM) declined more sharply with depth than particulate organic matter (POM). Surface POM was higher in the 30-year-old-AFS (10.13±2.7gC/soil kg) than in pasture (3.95±1.38gC/soil kg), reflecting enhanced litter inputs and organic matter turnover in mature agroforestry systems. In contrast, MAOM at 10–20cm was greater in pasture (1.03±0.15gC/soil kg) than in the young AFS (0.73±0.08gC/soil kg), indicating stronger carbon stabilization at depth under pasture management compared to a new production site. However, isotopic analysis revealed that this stabilized carbon derived from original C3 plants. The persistence of POM at depth suggests sustained microbial activity and vertical redistribution of organic inputs. Differences in carbon stocks were closely linked to shifts in microbial community composition: forest soils were associated with Basidiomycota, Mucoromycota, and Proteobacteria, whereas agroforestry systems were linked to Ascomycota, Acidobacteriota, and Actinobacteriota. Overall, long-term agroforestry improves soil carbon stocks and shape microbial communities relative to pasture systems.