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The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales

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Abstract

Fungi that produce their fruiting bodies underground within the soil profile are known commonly as truffles. Truffle fruiting bodies harbor a diverse but poorly understood microbial community of bacteria, yeasts, and filamentous fungi. In this study, we used next-generation 454 amplicon pyrosequencing of the V1 and V4 region of the bacterial 16S ribosomal DNA (rDNA) in order to characterize and compare effects of truffle species and geographic origin on the truffle microbiome. We compared truffle microbiomes of the glebal tissue for eight truffle species belonging to four distinct genera within the Pezizales: Tuber, Terfezia, Leucangium, and Kalapuya. The bacterial community within truffles was dominated by Proteobacteria, Bacterioides, Actinobacteria, and Firmicutes. Bacterial richness within truffles was quite low overall, with between 2–23 operational taxonomic units (OTUs). Notably, we found a single Bradyrhizobium OTU to be dominant within truffle species belonging to the genus Tuber, irrespective of geographic origin, but not in other truffle genera sampled. This study offers relevant insights into the truffle microbiome and raises questions concerning the recruitment and function of these fungal-associated bacteria consortia.

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Acknowledgments

The authors kindly acknowledge Michigan State University and AgBioResearch for research support. We are grateful to our following colleagues for helping us to obtain fresh truffles for this research: Yun Wang (T. indicum), Marcos Morcillo (T. melanosporum), Charles Lefevre (T. oregonense & T. gibbosum), Matt Trappe (Leucangium and Kalapuya), Timothy Brenneman (T. lyonii), and Khalid Hameed (Terfezia). We thank Aurélie Deveau for providing Bradyrhizobium reference sequences from the Antony-Babu study.

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  1. Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA

    Gian Maria Niccolò Benucci & Gregory M. Bonito

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  1. Gian Maria Niccolò Benucci
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  2. Gregory M. Bonito
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Correspondence to Gregory M. Bonito.

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Fig. S1

Bar-plots of all replicate samples used in the study by 454 pyrosequencing of the V1 and V4 region of the 16S bacterial gene. Two different OTUs (Operational Taxonomic Units) at 97 % sequence similarity, belonged to the bacteria genera Bradyrhizobium (within Tuber oregonense, and Tuber gibbosum) and Jantinobacterium (within Tuber oregonense), based on V1 and V4 datasets, respectively. (GIF 94 kb)

High resolution image (EPS 103 kb)

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Table S2

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Benucci, G.M.N., Bonito, G. The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales. Microb Ecol 72, 4–8 (2016). https://doi.org/10.1007/s00248-016-0755-3

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