Tuber pseudohimalayense ascomata-compartments strongly select their associated bacterial microbiome from nearby pine forest soils independently of their maturation stage

Abstract Truffles are among the most highly prized edible fungi worldwide. They also constitute complex microhabitats harboring a high diversity of microorganisms, being therefore real holobionts. Our aim was to study whether Tuber pseudohimalayense ascomata-compartments selected their associated bacterial microbiome from that of the surrounding pine forest soil environment. We used high-throughput sequencing of V4 ribosomal DNA regions to characterize and compare the truffle-associated bacterial microbiomes across three maturation stages. Bacterial richness and diversity decreased sequentially from soil, soil adhered to peridium, peridium and gleba. Rhizobiaceae, Pseudomonadaceae, Micromonosporaceae and Bradyrhizobium were the most abundant taxa among the studied compartments. Non-metric Multidimensional Scaling (NMDS) showed that bacterial communities were similar in the truffle surrounding soils, but different from those found in the peridium and gleba, regardless of maturation stage. PICRUSt analysis showed that putative metabolic pathways recorded for terpenoids, polyketides and lipids were significantly higher in the truffles than in the surrounding soils; and increases in low temperature self-protecting proteins, amino acid transport, and substrate-binding proteins were detected during truffle maturation. Here we report for the first time the association of the superphylum Patescibacteria with a truffle and we demonstrate strong T. pseudohimalyense-peridium and gleba selection from the surrounding forest soil microbiome during the whole ascomata maturation process. This constitutes the first study of the T. pseudohimalayense microbiome and its potential ecological functions, characterizing the microbiome of one of the most highly prized fungi in China. Our study sheds some light on the ecological relevance of T. pseudohimalayense and its associated microbiome and their potential relevance in forest belowground processes in the forest ecosystems where they grow.