Interactive roles of mineralogy, microbial community composition and litter quality in regulating organic matter turnover

Soils are often treated as chemically defined reactors, yet the physical architecture of minerals, organic inputs, and microbiomes jointly shapes where and how carbon turns over. We used a factorial microcosm experiment to test how clay mineralogy (fibrous palygorskite vs. swelling bentonite), clay content (0–20%), calcium carbonate (7.5–15%), litter quality (recalcitrant wheat vs. labile alfalfa), and microbiome origin (native soil vs. a synthetic fungi + bacteria consortium) interact to control respiration kinetics and microbial biomass carbon over 90 days. Clay type and amount acted as primary filters: increasing clay generally raised cumulative mineralized C, but palygorskite produced higher C₀, faster mineralization (higher k or lower t₀, steeper n), and stronger late-stage biomass recovery than bentonite, indicating a colonizable, catalytic habitat rather than a purely protective matrix. Litter chemistry modulated this filter: N-rich alfalfa shifted the system toward facilitation, with rapid, high-amplitude mineralization and large biomass peaks, whereas high-C:N wheat slowed mineralization, increased sensitivity to clay content, and emphasized protection and diffusion limitation. Microbiome composition added a third control: native communities generated higher cumulative C loss but lower rate constants, while the synthetic consortium drove faster mineralization and higher biomass on palygorskite. Calcium carbonate acted as a tuner, enhancing C₀, k and biomass in wheat systems and shifting mineralization timing in alfalfa systems. Together, these results support a hierarchical framework where mineral pore architecture sets the habitat filter, litter quality and microbial traits determine its exploitation, and Ca availability adjusts the balance between facilitation and protection.