Microbial carbon use efficiency and necromass turnover drive persistent carbon formation in paddy soils under straw-returned complex rotation

Paddy soils are critical for climate change mitigation due to their substantial carbon (C) sequestration potential; however, the mechanisms underlying persistent soil organic C (SOC) accrual under diversified cropping systems remain elusive. Through the integration of a global database analysis and two field experiments, we elucidated the synergistic effects of rotation complexity and straw management on the persistence of SOC through microbial regulatory pathways. The results demonstrated that complex crop rotations reduced the SOC content by 8% when straw was removed, but increased it by 22% under full straw return compared to that of the rice monoculture systems. This transition was driven by mineral-associated organic C (MAOC) enrichment, which elevated MAOC proportions by 2.3%–7.5% in topsoil and 1.6%–2.7% in subsoil under full straw return. Mechanistically, complex crop rotations enhanced microbial C use efficiency (CUE) by up to 33.0% and accelerated microbial biomass turnover by 15.9%–47.9%, thereby stimulating necromass production, particularly in three-crop rotations. Microbial CUE and necromass content correlated strongly with MAOC, but not with particulate organic C (POC). Additionally, the necromass fractions in the SOC pools were positively correlated with the MAOC/SOC ratio and negatively correlated with the POC/SOC ratio, establishing necromass as the primary precursor for persistent MAOC formation. The enhanced contribution of fungi relative to bacteria in topsoil was facilitated by the higher redox potential and C: N ratio of the substrate input. This indicates that implementing complex crop rotations combined with full straw return in paddy ecosystems enhances microbial CUE and necromass turnover, effectively channelling C into the stable MAOC pools. This finding provides novel mechanistic insights for designing climate-smart paddy ecosystems that leverage microbial physiology to achieve durable C sequestration while safeguarding food security.