Compartmentalization Rather Than Host Tree Drives Truffle Microbiome

Abstract

Background: Truffles are some of the among the most expensive edible fungi worldwide whose value in international markets is worth billions of US dollars annually. They form ectomycorrhiza which is a symbiotic relationship with host trees and produce hypogeous ascomata. Their whole life-cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host trees are drivers for truffle microbiome is unclear.Methods: To identify and compare bacterial and fungal communities in four truffle-associated compartments (Tuber indicum bulk soil, adhering soil to peridium, peridium and gleba), associated to three host trees we sequenced their ITS (fungal) and 16S (bacterial) rDNA with Illumina MiSeq high throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Results: Tuber indicum microbiome composition was strongly driven by their associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacterial-dominated, and its bacterial community formed a substantially more complex interacting network compared with that of fungal community. Core fungal community changed from Basidiomycota-dominated (in bulk soil) to Rozellomycota-dominated (in interphase soil); while core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. At the truffle and soil interphase, an interphase-sieving process was confirmed by i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi and Planctomycetes) in gleba; ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon and Simpson indices); and iii) a substantial decrease in the complexity of the network from bulk soil, to soil-truffle interphase, to peridium and finally to gleba. The network analysis of microbiome showed a more complex and higher number of positive microbial interactions in truffle tissues than in both bulk soil and peridium-adhering soil. Cupriavidus, Bradyrhizobium, Aminobacter and Mesorhizobium were the keystone network hub genera associated to truffle gleba. Conclusion: This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing than they are more complex than previously thought.