Soil management strategies shape bacterial and eukaryotic community structure in organic and inorganic systems of Malus × domestica production

Understanding the temporal dynamics of soil microbial communities is crucial for assessing the stability of orchard soils. We analyzed bacterial and eukaryotic communities in the rhizosphere of apple trees under seven mulching treatments across two growing seasons (2020 and 2023). To account for potential batch effects between separate sequencing runs, results from each year were juxtaposed to identify recurring microbial patterns. High-throughput 16S and ITS sequencing revealed that management-specific signatures persisted over time despite inter-run variability. Bacterial alpha diversity varied significantly among individual treatments, while beta diversity consistently distinguished management regimes across both years. Fungal alpha diversity remained largely unaffected, but beta diversity revealed significant compositional shifts between organic and inorganic groups. Organic mulching (shredded Miscanthus straw and spent mushroom compost) consistently enriched bacterial families linked to organic matter turnover (Sphingomonadaceae, Flavobacteriaceae, Moraxellaceae), whereas inorganic systems favored Comamonadaceae and Nitrosomonadaceae. Organic soils were also enriched in saprotrophic fungi (Lasiosphaeriaceae) and broader eukaryotes (Ciliophora), while inorganic - Mortierellaceae. Network analyses identified a cohesive bacterial core, whereas fungal/eukaryotic communities were more modular and responsive to mulching type. These findings demonstrate that sustained organic mulching promotes stable microbial configurations associated with soil functioning, highlighting the consistency of management-associated microbial signatures under long-term agricultural practices.