Bacterial communities inhabiting the ascomata of the ectomycorrhizal summer truffle (Tuber aestivum)

Abstract

Abstract This paper continues the studies on the role of bacteria in the environment of summer truffle (Tuber aestivum) (soil and roots), focusing on ascomata at three sites in the Nida Basin (southern Poland). Bacterial species and the number of OTU sequences identified were determined based on analysis of peridium and gleba contamination collected in 2017 and 2018. Both the classical culture method with qualitative analyses, i.e., Sanger DNA sequencing, and next-generation sequencing (NGS) were used. In addition, the PERMANOVA test and alpha and beta biodiversity indicators were used. Of the individual bacterial colonies, 140 were used for further molecular analyses. The Sanger method identified six bacterial genera that were dominant in the community: Bacillus, Pseudomonas, Stenotrophomonas, Paenibacillus, Rhizobium, and Chryseobacterium, of which Bacillus (86.7%) and Pseudomonas (51.5%) were the most abundant. In contrast, NGS results showed the dominance (at OTUs > 10,000) of representatives of eight families, mainly Bradyrhizobiaceae, Sphingobacteriaceae, Micrococcaceae, Yersiniaceae, Sphingomonadaceae, Rhizobiaceae, Flavobacteriaceae, and Comamonadaceae. The PERMANOVA test for the Bray-Curtis and Jaccard indices showed dissimilarities between samples from sites G and W with respect to beta diversity. Significant differences were found in the bacterial communities colonising the ascomata of T. aestivum and in the root communities with T. aestivum ectomycorrhizae of the tree adjacent to the ascomata. The number of OTUs at the species level was 69 in the roots and 212 in the shoots. Our study allowed us to determine the bacterial microbiome in the ascomata of T. aestivum, leading to a better understanding of the preferences of certain groups of truffle-associated bacteria and how they relate to the presence of truffle ascomata under specific habitat conditions. The results obtained may be useful in selecting and monitoring sites suitable for the formation of ascomata of T. aestivum.