Stochastic Processes Dominate Prokaryotic Community Assembly Yet Decouple From Nitrogen Cycling in Mediterranean Soils

ABSTRACT Understanding interactions between pedo‐climatic properties and soil microbial communities is crucial for predicting ecosystem responses to environmental change. However, the ecological processes governing prokaryotic community assembly and whether compositional shifts predict soil functioning, with focus on nitrogen cycling, in Mediterranean ecosystems remain poorly understood. We characterized soil properties, prokaryotic communities (16S rRNA), and net N mineralization rates across 22 sites spanning agricultural and natural land uses, two soil depths (0–15, 15–30 cm), and three consecutive years at Koiliaris Critical Zone Observatory, east from the city of Chania, Crete, Greece. Despite substantial environmental heterogeneity (SOC: 0.59%–5.54%; TN: 0.05%–0.40%; elevation: 0–1100 m), land use, soil depth, and sampling year explained only 8.1% of β‐diversity variance (PERMANOVA). Shannon diversity correlated negatively with SOC ( r = −0.32, p < 0.01) and positively with pH ( r = 0.31, p < 0.05) in agricultural soils only. Prokaryotic communities were enriched in stress‐responsive taxa (particularly Actinobacteria), with differential abundance analysis revealing consistent taxa clusters across land uses that may serve as soil health indicators. iCAMP framework revealed stochastic processes dominated community assembly (81%–85%) with drift and dispersal limitation as primary mechanisms. Agricultural soils showed higher stochasticity than natural ecosystems. Net N mineralization rates (−3.5 to 3.1 mgN kg −1 d −1 ; CV = 388%) showed no significant correlations with soil properties, α‐diversity, or community turnover (βNTI). This structure–function decoupling challenges deterministic ecosystem models and suggests that functional redundancy buffers process rates against compositional stochasticity in Mediterranean soils. Trait‐based, probabilistic frameworks may provide more reliable predictions for these climate‐sensitive ecosystems.