Abstract
For some truffle species of the Tuber genus, the symbiotic phase is often associated with the presence of an area of scant vegetation, commonly known as the brûlé, around the host tree. Previous metagenomics studies have identified the microorganisms present inside and outside the brûlé of a Tuber melanosporum truffle-ground, but the molecular mechanisms that operate in this ecological niche remain to be clarified. To elucidate the metabolic pathways present in the brûlé, we conducted a metaproteomics analysis on the soil of a characterized truffle-ground and cross-referenced the resulting proteins with a database we constructed, incorporating the metagenomics data for the organisms previously identified in this soil. The soil inside the brûlé contained a larger number of proteins and, surprisingly, more proteins from plants, compared with the soil outside the brûlé. In addition, Fisher’s Exact Tests detected more biological processes inside the brûlé; these processes were related to responses to multiple types of stress. Thus, although the brûlé has a reduced diversity of plant and microbial species, the organisms in the brûlé show strong metabolic activity. Also, the combination of metagenomics and metaproteomics provides a powerful tool to reveal soil functioning.
Highlights
Proteins from eight soil samples collected in a French truffle-ground were extracted using three extraction methods to maximize the yield of proteins (Fig. 2)
We cross-referenced all the proteins from the four replicates against a database built for this work, based on the set of organisms previously identified in this soil by metagenomics, and against the T. melanosporum database
We built a database based on our previous metagenomics data[11,12,14,15] and used it for metaproteomics analysis to link the composition of the microbial community to the ecological processes occurring in the brûlé
Summary
Firmicutes (e.g., Bacillus), several genera of Actinobacteria, and a few Cyanobacteria were more abundant inside the brûlé, whereas Pseudomonas and several genera within the family Flavobacteriaceae were more abundant outside the brûlé These metagenomics studies clearly revealed the fungal, archaeal, and bacterial community composition inside and outside the brûlé, but they did not examine the interaction and role of the different organisms. Given the promise of metaproteomics, the aim of this work was to use this tool on the same truffle-ground soils previously characterized by metagenomics[11,12,14,15], to produce a protein dataset that can help to elucidate the active metabolic pathways in organisms inside and outside the brûlé. Thanks to the availability of sequenced genomes from 2682 Eukaryota and 58252 Prokaryota (http:// www.ncbi.nlm.nih.gov/genome/browse/), including the black truffle Tuber melanosporum[1], these proteins were categorized and assigned to the organisms living in the truffle-ground, allowing us to infer metabolic processes
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