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Morchella rotation and intercropping is a new and efficient ecological planting mode, which not only contributes to economic growth, but also promotes the sustainable development of agriculture and has high ecological benefits. Morchella sextelata is an edible mushroom that relies on soil-based cultivation. Understanding the composition and dynamics of soil fungal communities under different cropping systems is crucial for optimising its cultivation. This study investigated the fungal community characteristics of Morchella spp. under different rotation and intercropping patterns, together with the associated environmental factors. Using Illumina NovaSeq high-throughput sequencing coupled with ecological and statistical analyses, the relative abundance, alpha diversity index, beta diversity, and intergroup differences in fungal communities were assessed. Additionally, key soil physical and chemical properties were evaluated across four cultivation systems: conventional Morchella spp. cultivation, Morchella sextelata—ginger rotation, vine—Morchella sextelata intercropping, and mulberry tree—Morchella sextelata intercropping. Our results indicate that Morchella spp. cultivation leads to a significant decline in soil fungal diversity compared to uncultivated soils This indicates that cultivation with Morchella spp. simplifies the soil fungal community structure to some extent. Furthermore, distinct variations in fungal community structure were observed across the different cropping systems. Regarding major pathomycete, the relative abundance of Paecilomyces penicillatus increases in vine intercropping soil (VIS), whereas Botryotrichum atrogriseum and Paecilomyces sp. are more abundant in ginger rotation soil (GRS). Similarly, Fusarium solani and Mortierella sp. exhibit higher relative abundance in mulberry tree intercropping soil (MTIS) and fallow soil (FS) compared to natural soil (NS). Functional prediction analysis indicated a general increase in the relative abundance of potential animal and plant pathogenic fungi across all the soil samples, excluding the VIS. This increase was most pronounced in GRS. Further study revealed that the physical and chemical properties of covering soil, including pH, available potassium (AK), available phosphorus (AP), and total phosphorus (TP), significantly influence fungal community diversity and structure. A significant negative correlation was observed between pH and the relative abundance of Fusarium fungi. These findings provide valuable data for further exploration of the ecological mechanisms underlying Morchella spp. cultivation, including rotation constraints and disease dynamics. Ultimately, this research aims to support the development of sustainable and high-quality Morchella spp. production. Full article

Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis. Full article