The coculture of Fomitopsis betulina with Escherichia coli induces a nutritional stress and triggers secondary metabolism pathways

Abstract

Basidiomycete fungi are an underexplored source of specialized metabolites with significant biotechnological potential. However, the environmental cues that activate their biosynthetic pathways remain poorly understood. Here, we investigated the response of the wood-decaying fungus Fomitopsis betulina, to nutritional competition using co-cultures with Escherichia coli. On solid medium, F. betulina inhibited the bacterial growth. Using a mass spectrometry-based metabolomics approach, we identified a Sumiki’s acid derivative, calcium diformate, and sulfuric acid among the compounds enriched within the inhibition zone and hypothesized that these compounds were associated with the acidification of the medium. Although F. betulina has previously been reported to produce the antibacterial compound piptamine, neither piptamine nor related derivatives were detected under our experimental conditions. In liquid medium, the co-culture with E. coli caused the rapid depletion of the available glucose, resulting in the establishment of carbon-starvation conditions and a 44% reduction in fungal biomass. Transcriptomic analyses revealed extensive metabolic reprogramming in response to bacterial competition, including the induction of genes involved in carbon acquisition, nutrient transport, redox homeostasis, and stress adaptation. Notably, a homolog of the Velvet regulatory complex, a central regulator of fungal development and specialized metabolism, was upregulated. The co-culture induced the expression of genes associated with multiple biosynthetic gene clusters, including terpene, polyketide, and fungal RiPP. Taken together, our results demonstrate that bacterial competition acts as a potent trigger of nutritional stress and secondary metabolism in F. betulina. More broadly, fungal–bacterial co-culture represents a promising alternative to extractions to identify high-value added metabolites pathways from basidiomycetes. Importance It is now well known that basidiomycete fungi are a fantastic reservoir of yet untapped secondary metabolites and antimicrobial compounds. However, the discovery of these compounds is made difficult because the genes normally remain silent, and are only expressed under specific conditions. The co-culture of fungi and bacteria is an emerging tool to decipher interactions between microorganisms and a promising alternative to chemical extractions to identify specialized metabolites from basidiomycetes. In this study, we used a bacterial competitor to induce a nutritional stress on the birch polypore, Fomitopsis betulina. We observed that the fungus responded to the stress by regulating the carbon uptake and metabolism. Carbon starvation in presence of the bacteria also triggered the over expression of a central regulator of fungal specialized metabolism, and induced the activation of terpene, polyketide, and fungal RiPP biosynthesis.