Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles

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 brule, around the host tree. Previous metagenomics studies have identified the microorganisms present inside and outside the brule 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 brule, 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 brule contained a larger number of proteins and, surprisingly, more proteins from plants, compared with the soil outside the brule. In addition, Fisher's Exact Tests detected more biological processes inside the brule; these processes were related to responses to multiple types of stress. Thus, although the brule has a reduced diversity of plant and microbial species, the organisms in the brule show strong metabolic activity. Also, the combination of metagenomics and metaproteomics provides a powerful tool to reveal soil functioning.