| Summary: | Fungi infestation as a disease has serious impacts on the cultivation of <i>Morchella</i> species. To investigate the effects of fungi infestation on the microbial diversity and community structure of soil when cultivating <i>Morchella sextelata</i>, we sampled soil samples of <i>Morchella</i> cultivars in the Qinghai–Xizang Platea and used metagenome sequencing technology to identify the disease fungi and analyze the differences in microbial diversity and structure between disease-infested and healthy soils. The disease fungi identified were <i>Tricharina gilva</i> and <i>Peziza lohjaoensis</i>, and the microbial diversity of <i>T. gilva</i>-infected soil was higher than that of healthy soil, while the diversity of <i>P. lohjaoensis</i>-infected soil was lower. Interestingly, whether infected with <i>T. gilva</i> or <i>P. lohjaoensis</i>, the soil microbial community was changed, and the dominant phyla and genera were different in different soil samples. When infected with <i>P. lohjaoensis</i>, the dominant phyla with relatively high abundances included Proteobacteria, Bacteroidetes, and Ascomycota, with average relative abundances of 44%, 18%, and 15%, respectively, and the dominant genera with high relative abundances encompassed <i>Pseudomonadaceae</i>, <i>Terfezia</i>, and <i>Pedobacter</i>, with average relative abundances of 8%, 9%, and 5%, respectively. Following infection with <i>T. gilva</i>, the dominant phyla with higher relative abundances were Proteobacteria, Acidobacteria, and Bacteroidetes, with average relative abundances of 46%, 15%, and 12%, respectively, and the dominant genera with high relative abundances included <i>Hydrogenophaga</i>, <i>Sphingomonas</i>, and <i>Polaromonas</i>, with average relative abundances of 9%, 3%, and 2%, respectively. Additionally, we found that lipid-metabolism-related genes were less abundant in the soil infected with <i>P. lohjaoensis</i> than in the other soil samples, and glycoside hydrolase diversity was lower in the soil infected with <i>T. gilva</i> than in other healthy soils. The results showed that the effects of different disease fungi on soil microbial communities and functional genes were different, which provided a theoretical basis for the sustainable cultivation of <i>Morchella</i>.
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