Abstract
The extent to which past disturbances influence present‐day microbial composition and assembly remains poorly understood, especially in extreme environments such as deserts. Using a phylogenetic framework of diversity partitioning, linked to soil composition, we aimed to disentangle the impacts of past disturbance on present‐day bacterial and fungal communities, where we also distinguish abundant and rare taxa. Our findings demonstrate that past agricultural activity promoted strong phylogenetic clustering and turnover, accompanied by increased phylogenetic diversity and niche width, reflecting the influence of transient resource availability and niche diversification. Conversely, long‐term disturbances reduced phylogenetic diversity and niche width while amplifying selection processes and phylogenetic turnover. These patterns indicate intensified abiotic constraints in this system, where historical contingencies—characterised by enduring drought‐wetting cycles—differentially shaped bacterial and fungal communities. Rare taxa were more sensitive to land use and deterministic, while abundant taxa showed broader niche adaptability and stochastic influences, highlighting the need for targeted conservation strategies. This work highlights the critical role of historical disturbances in shaping microbial assembly, provides actionable insights into enhancing desert ecosystem resilience and informing sustainable restoration practices. Si content—a key driver of phylogenetic turnover—could be targeted for ecosystem recovery and conservation strategies in degraded arid regions.