Perennial cropping systems alter microbial resource limitations and promote soil carbon storage

Converting conventional cropping systems from annual to perennial has been proposed as a strategy to enhance soil organic carbon (SOC) input and storage, due to larger root systems and reduced soil disturbance. The mechanisms underlying SOC sequestration are fundamentally mediated by soil microorganisms, which play dual roles: they assimilate labile plant-derived C into microbial biomass that can stabilize as soil organic matter (SOM); and they simultaneously regulate the mineralization of SOM to provision plants with nutrients. These microbial processes are constrained by resource availability, which is mediated by plant-soil-microbe interactions. To understand microbial resource limitation under different crops, we collected soil from annual and perennial cropping systems in 0-30 cm and 30-60 cm depths, and assessed whether carbon (C), nitrogen (N), or phosphorus (P) limited microbial growth and respiration. Microbial biomass and turnover time were also estimated to assess how resource limitation influenced microbial contributions to C accumulation. We found that perennial systems alleviated the microbial C limitation and simultaneously strengthened the secondary N limitation in the topsoil. Perennial systems also increased microbial biomass and shifted the microbial community to higher fungal dominance. Higher SOC concentrations were also observed under perennial systems, increasing by approximately 11% in the topsoil and 43% in the subsoil. Together, these findings suggest that perennial cropping reshaped microbial resource limitations, physiology and community structure, creating conditions for altered microbial processing of plant-derived C and enhanced SOC formation. The strengthened microbial secondary N limitation observed in the topsoil may also have increased microbial demand for N, potentially priming the microbial decomposition of SOM to target N. This was consistent with our finding of dampened SOC increase in topsoil compared to subsoil. Our findings support microbial resource limitation as a useful framework for understanding how perennial cropping systems may influence SOC accumulation.