Microbial communities inhabiting the surface and gleba of white (<i>Tuber magnatum</i>) and black (<i>Tuber macrosporum</i>) truffles from Russia

The complex symbiotic relationships between truffles and their microbiota, coupled with their obligate mycorrhizal lifestyle, present significant challenges for obtaining axenic mycelium and achieving controlled cultivation. This study aimed to characterize the microbial communities within the surface and gleba of truffle ascomata using 16S and 18S rRNA gene sequencing and identify the taxonomic composition and ecological roles of these microbiota. Specimens of <i>Tuber magnatum</i> (white truffle) and <i>Tuber macrosporum</i> (smooth black truffle) were collected, with <i>T. magnatum</i> representing the first documented discovery of this species in Russia. Metabarcoding profiling identified both species-specific and shared microbial taxa, with the yeast-like fungus <i>Geotrichum</i> spp. emerging as a core symbiont in both truffle species. Its consistent detection in surface and gleba tissues suggests a critical role in mycorrhizal establishment and spore dispersal, potentially mediated by sulfur volatiles that attract mycophagous fauna. In <i>T. magnatum</i>, the bacterial community was dominated by Proteobacteria, particularly Alphaproteobacteria and Gammaproteobacteria, with the nitrogen-fixing genus <i>Bradyrhizobium</i> being especially abundant. The truffle microbiota predominantly comprised soil-derived microorganisms (<i>e.g.</i>, nitrogen-fixing <i>Rhizobiaceae</i> spp., phenol-degrading <i>Mycoplana</i> spp.) and plant-associated symbionts (<i>e.g.</i>, ectomycorrhizal <i>Sebacina</i> spp.), implicating these communities in nutrient cycling, xenobiotic degradation, and host plant interactions. By elucidating the taxonomic and functional profiles of truffle-associated microbiota, this study provides foundational insights into their ecological contributions. Chemical differences align with tissue-specific microbial communities, suggesting microenvironmental specialization in bioactive compound synthesis. These findings advance efforts to replicate critical symbiotic interactions <i>in vitro</i>, a prerequisite for developing sustainable cultivation protocols for <i>T. magnatum</i> and <i>T. macrosporum</i> under controlled conditions.