This paper reviews the current knowledge of microbial processes affecting C sequestration in agroecosystems. The microbial contribution to soil C storage is directly related to microbial community dynamics and the balance between formation and degradation of microbial byproducts. Soil microbes also indirectly influence C cycling by improving soil aggregation, which physically protects soil organic matter (SOM). Consequently, the microbial contribution to C sequestration is governed by the interactions between the amount of microbial biomass, microbial community structure, microbial byproducts, and soil properties such as texture, clay mineralogy, pore‐size distribution, and aggregate dynamics. The capacity of a soil to protect microbial biomass and microbially derived organic matter (MOM) is directly and/or indirectly (i.e., through physical protection by aggregates) related to the reactive properties of clays. However, the stabilization of MOM in the soil is also related to the efficiency with which microorganisms utilize substrate C and the chemical nature of the byproducts they produce. Crop rotations, reduced or no‐tillage practices, organic farming, and cover crops increase total microbial biomass and shift the community structure toward a more fungal‐dominated community, thereby enhancing the accumulation of MOM. A quantitative and qualitative improvement of SOM is generally observed in agroecosystems favoring a fungal‐dominated community, but the mechanisms leading to this improvement are not completely understood. Gaps within our knowledge on MOM‐C dynamics and how they are related to soil properties and agricultural practices are identified.
