Comparative analysis of soil prokaryotic community structure and function in Ethiopian Church Forests and adjacent habitats

Abstract

Abstract Soil microorganisms are central to ecosystem functioning, yet how habitat degradation affects their community structure and functional potential in dry Afromontane forests (DAFs) remains poorly understood. This study investigated soil prokaryotic communities across five habitats representing a disturbance gradient in Ethiopian DAFs: Church forest, State forest, Community-managed forest, Shrubland, and Cropland. Using next-generation sequencing, we examined prokaryotic community composition, diversity, assembly processes, and predicted functional profiles. Actinobacteriota and Crenarchaeota were more abundant in less disturbed forests, whereas disturbed habitats showed shifts toward taxa associated with stressed conditions. Alpha diversity was lower in Church and State forests than in shrubland and cropland, indicating environmental filtering and dominance of habitat specialists. Community composition differed significantly among habitats and was associated with soil properties, stand attributes, and indicator trees. Deterministic processes explained most community turnover (81%), indicating strong environmental structuring, with homogeneous selection more evident in forests and mixed deterministic–stochastic processes in disturbed habitats. Predicted functional profiles suggest shifts in nitrogen-related processes, particularly ammonia oxidation and nitrification, although not directly measure microbial activity. Overall, habitat degradation is associated with changes in prokaryotic community structure and assembly, highlighting the importance of conserving intact forests and supporting restoration efforts in dryland ecosystems.