Background: Paddy soils used to cultivate Oryza sativa (rice) cover about 155 million hectares around the world, providing a vital link between agricultural production and sustainable environmental systems. In rice-based systems, soil organic matter (SOM) dynamics are regulated by a multitude of complex interactions involving hydrologic (water-related), mineralogical, microbial (bacterial) activity and plant inputs. Flooded (anaerobic) versus aerobic cultivation creates an opposite combination of redox (chemical oxidation-reduction) conditions that dramatically change SOM transformation pathways, organo-mineral dynamic interactions and GHG emissions.
Objective: This review offers a detailed examination of the mechanisms that are responsible for the long-term maintenance of SOM and its relationship to minerals in flooded and aerobic rice cultivation systems, with emphasis on the interactions between SOM and mineral materials primarily related to the presence of Fe/Al oxides and clay minerals, the role of microbial necromass, and the implications of various water management strategies such as AWD, which alter the biogeochemical processes within these environments.
Methods: We conducted an organized assessment of articles published within the peer-reviewed academic literature from 2010 through 2025. The integration used literature related to 3 types of methods that have been used in the soil fractionation process (i.e., density, particle size, and chemical), isotopic tracing (i.e., 13C and 15N), spectroscopic methods (i.e., NMR, FTIR, and XPS) and tools to study microbiological communities (i.e., metagenomics and enzyme activities) and the synthesis of comparative data with long-term (10+ years) field studies across rice (Oryza sativa) producing countries.
Results: Flooding greatly increases the amount of SOM (soil organic matter) by reducing oxidative breakdown (decomposition) processes, reducing Fe oxide solubility which releases OC (organic carbon) that was previously bound, and increasing the accumulation of microbial carcasses. Mineral-associated OC (MAOC) comprise 60% to 75% of the total OC found in flooded paddy soils primarily bound to amorphous Fe phases. Aerobic systems usually have faster SOM turnover compared to anaerobic systems but also provide higher aggregate stability, enhanced nitrogen mineralization and greater oxidative enzyme activity. Alternate Wetting-Drying (AWD) is an effective management tool for accomplishing both the reduction of CH4 (methane) emissions by 30-50%, while having little to no impact on SOM stocks. However, it is possible that N2O (nitrous oxide) emissions could be increased as a result of using AWD methods.
Conclusion: The dynamic balance between microbial interactivity with soil organic matter, mineral stabilization of organic matter and redox-driven transformations determines the persistence of soil organic matter (SOM) in paddy soils. Integrated management of organic additions, optimized hydrology and site-specific mineral conditions will result in effective carbon sequestration of SOC in paddy agroecosystems. Future research will focus on determining the long-term stability of MAOM under changing climate-induced hydrology and quantifying the contribution of MAOM from microbial necromass to long-lived SOC pools.