Microbial Diversity and Metabolite Changes in Greenhouse Soil Continuously Cropped with Morchella

True morels (Morchella spp., Morchellaceae, Ascomycota) are a rare and highly valuable edible fungus. As the morel cultivation scale has expanded, obstacles to continuous cropping have come to the fore. This study investigates the specific biological mechanisms that may hinder the continuous cropping of Morchella by means of microbiome and metabolome analysis of the soil. Using amplicon sequencing-based microbiome analysis, 5288 bacterial operational taxonomic units (OTUs) and 1847 fungal OTUs were identified. Bacterial genera such as Arthrobacter, Tychonema, Rhodanobacter, Luteimonas, and Streptomyces, along with pathogenic fungi, likely play specific roles in hindering continuous cropping of Morchella. Metabolomic analysis revealed 368 metabolites, including lipids and lipid-like molecules, organic acids and derivatives, benzene-containing compounds, and heterocyclic compounds. Eighteen metabolites showed significant differences between Morchella continuous cropping and control soil, including toxic compounds such as 2,4,5-Trichloro-6-Hydroxybenzene-1,3-Dicarbonitrile, 2,4-Dichloro-6-nitrophenol, and Aflatoxin B2. These results indicate that alterations in soil microbial structure and toxic metabolites secreted by Morchella collectively contribute to the hindrance of continuous cropping.