Metagenomic Insights into Disease-Induced Microbial Dysbiosis and Elemental Cycling Alterations in Morchella Cultivation Soils: Evidence from Two Distinct Regions

Soil-borne diseases represent a major constraint on the sustainable cultivation of morel mushrooms (<i>Morchella</i> spp.), yet the microbial ecological mechanisms driving disease occurrence and progression remain poorly understood. In this study, we conducted comparative metagenomic analyses of rhizosphere and root-adhering soils associated with healthy and diseased <i>Morchella</i> crops from two major production regions in China, aiming to elucidate shifts in microbial community composition, assembly processes, and functional potential. Disease conditions were linked to pronounced microbial dysbiosis, with community assembly shifting from stochastic to deterministic processes, particularly within fungal communities under host selection and pathogen pressure. Co-occurrence network analysis revealed substantial reductions in connectivity, modularity, and clustering coefficients in diseased soils, indicating the loss of ecological stability and keystone taxa. Functional annotations using CAZy, COG, and KEGG databases showed that healthy soils were enriched in genes related to carbohydrate metabolism, aerobic respiration, and ecosystem resilience, whereas diseased soils exhibited higher abundance of genes associated with stress responses, proliferation, and host defense. Furthermore, elemental cycling analysis demonstrated that healthy soils supported pathways involved in aerobic carbon degradation, nitrogen fixation, phosphate transport, and sulfur oxidation, while diseased soils favored fermentation, denitrification, phosphorus limitation responses, and reductive sulfur metabolism. Collectively, these results highlight the importance of microbial functional integrity in maintaining soil health and provide critical insights into microbiome-mediated disease dynamics, offering a foundation for developing microbiome-informed strategies for sustainable fungal crop management.