Cultivating macrofungi is an important management measure to develop economy in shady forest areas; however, its effect on soil ecology, especially microbial abundance and structure, remains insufficiently studied. Herein, in a subtropical forestland, soil chemical and enzyme analyses, metagenomic sequencing and quantitative real-time PCR were employed to evaluate the impact of Stropharia rugosoannulata cultivation on soil microbiomes in three niches: soil below fungal beds, soil from furrows, and control forest soil with no influence from mushroom cultivation. Nutrients were accumulated in the soil below fungal beds with a significant increase (p < 0.05) in SOC, total C, total N, available P, and the activities of glucosidase and cellobiosidase. Non-metric multidimensional scaling and PERMANOVA results indicated that the structure of the microbiomes had been significantly (p < 0.05) shaped among the different niches. Soil furrows were microbial hotspots characterized by the higher microbial diversity and richness. Moreover, the increased microbiome abundance (assessed through qPCR) and the high number of significant stimulated functional types (based on MetaCyc genome database) indicated an enhanced functional capacity in furrows. Together, these results provide a comprehensive understanding of the microbial assemblies and the differently influenced soil properties in mushroom cultivation areas.

The uniquely compartmentalized fruiting body structure of the ectomycorrhizal fungus (EMF) Tricholoma matsutake, is a hotspot of microbial habitation and interaction. However, microbial diversity within this microniche structure of the EMF is rarely investigated. Furthermore, there is limited information concerning microbiomes associated with sporomes belonging to the ubiquitous fungal phylum Basidiomycota, particularly with respect to fungus-EMF interactions. In this study, we conducted high throughput sequencing, using ITS (fungal) and 16S rRNA (bacterial) marker genes to characterize and compare fruiting body microbiomes in the outer (pileipellis and stipitipellis) and inner layers (pileum context, stipe context, and lamellae) of the fruiting body of T. matsutake. Our results show the number of unique bacterial operational taxonomic units (OTUs) among the different compartments ranged from 410 to 499 and was more than double that of the shared/common OTUs (235). Micrococcales, Bacillales, Caulobacter, and Sphingomonas were the primary significant bacterial taxa within the different compartments of the dissected T. matsutake fruiting body. Non-parametric multivariate analysis of variance showed significant compartmental differences for both the bacterial and the fungal community structure within the T. matsutake fruiting body. The metabolic profiling revealed putative metabolisms (of amino acids, carbohydrates, and nucleotides) and the biosynthesis of secondary metabolites to be highly enriched in outer layers; in the inner parts, the metabolisms of energy, cofactors, vitamins, and lipids were significantly higher. This study demonstrates for the first time the distinct compartmentalization of microbial communities and potential metabolic function profiles in the fruiting body of an economically important EMF T. matsutake.