Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups.

Eukaryote-associated microbiomes vary across host taxa and environments but the key factors underlying their diversity and structure in fungi are still poorly understood. Here we determined the structure of bacterial communities in fungal fruitbodies in relation to the main chemical characteristics in ectomycorrhizal (EcM) and saprotrophic (SAP) mushrooms as well as in the surrounding soil. Our analyses revealed significant differences in the structure of endofungal bacterial communities across fungal phylogenetic groups and to a lesser extent across fungal guilds. These variations could be partly ascribed to differences in fruitbody chemistry, particularly the carbon-to-nitrogen ratio and pH. Fungal fruitbodies appear to represent nutrient-rich islands that derive their microbiome largely from the underlying continuous soil environment, with a larger overlap of operational taxonomic units observed between SAP fruitbodies and the surrounding soil, compared with EcM fungi. In addition, bacterial taxa involved in the decomposition of organic material were relatively more abundant in SAP fruitbodies, whereas those involved in release of minerals were relatively more enriched in EcM fruitbodies. Such contrasts in patterns and underlying processes of the microbiome structure between SAP and EcM fungi provide further evidence that bacteria can support the functional roles of these fungi in terrestrial ecosystems.