Rubber based agroforestry systems enhance soil organic carbon sequestration through changes in soil properties and microbial community structure

Rubber monoculture (RM) often causes soil degradation and loss of ecosystem functioning. In contrast, rubber-based agroforestry systems (RAFs) can enhance soil organic carbon (SOC); however, the mechanisms regulating SOC fractions and microbial communities remain poorly understood. This study examined six RAFs comprising Hevea brasiliensis intercropped with Alpinia katsumadai (AKH), Alpinia oxyphylla (AOM), Coffea arabica (CAA), Cinnamomum cassia (CCA), Pandanus amaryllifolius (PAR), and Theobroma cacao (TCA), compared with RM. We quantified SOC fractions (mineral-associated organic carbon, MAOC; particulate-organic carbon, POC), soil properties, enzyme activities, microbial community structure, and microbial co-occurrence networks. After nine years, RAFs significantly increased SOC by 16.3–75.8% (8.96 ± 1.96 g. kg −1 ) relative to RM, with similar gains in MAOC (18.4–82%), POC (26.5–61.6%), and microbial biomass carbon (MBC; 21.9–47.9%). In the 0–20 cm layer, SOC and MAOC stocks were 18.3–30.8 Mg. ha −1 and 13.7–24.3 Mg. ha −1 , respectively, compared with 18.4 and 14.5 Mg. ha −1 in RM. Using RM as the baseline, CAA, CCA, AOM, and AKH accumulated SOC at rates of 1.38, 0.83, 0.59, and 0.43 Mg. C ha −1 yr −1 , respectively. RAFs also increased soil pH, reduced bulk density, and enhanced carbon-, nitrogen-, and phosphorus-acquiring enzyme activities. Microbial richness rose in AOM (bacteria, 19.9%) and CCA (fungi, 93.4%). Co-occurrence network analysis showed higher modularity (48%) and fewer antagonistic (2–27%) associations in bacteria, while fungal networks exhibited greater connectivity (18–109%) and clustering (65–190%) than RM. Partial least squares path modeling identified soil properties, MBC, and enzyme activities as significant mediators of SOC fractions. These results suggest that RAFs not only enhance soil fertility and enrich SOC pool but also restructure belowground microbial interactions toward more cooperative networks. Integrating diverse trees, shrubs, and herbs within rubber plantations thus offers a promising strategy to increase ecosystem services, climate resilience, and long-term sustainability in tropical rubber production landscapes.