Fungal-bacterial interactions

The study of fungal-bacterial interactions is an emerging field of biology with relevance for environmental health, medicine, and agriculture, among other sectors. The frequent co-occurrence of fungi and bacteria in many habitats has facilitated the evolution of their symbioses. Both groups are key players in host-associated microbiomes and in nutrient cycling, and these roles often intersect in dynamic ways. Interactions between fungi and bacteria can be mutualistic, commensal, or pathogenic, and they can vary in a context-dependent manner. In mutualistic interactions, fungi and bacteria can exchange nutrients, ameliorate each other's stress, enhance growth, enable dispersal, and facilitate novel niche exploration via metabolite exchange. In contrast, antagonistic interactions frequently involve competition for limited nutrients, such as iron, and active chemical warfare with secreted and bioactive compounds. Bacteria associated with fungi can occur inside of fungal cells (endosymbiotic) or on the surface of fungal hyphae (exosymbiotic). Endosymbiotic bacteria can be further differentiated into facultative symbionts, which retain the ability to enter fungal hyphae but also live independently, and obligate endosymbionts, which are always intracellular and not capable of independent life outside of hyphae. Whereas free-living bacteria can be pathogenic or mutualistic, endosymbiotic bacteria are often regarded as commensals or mutualists, although some can exhibit parasitic attributes in some conditions. A combination of molecular genetics, genomics, and microscopy has been used to study free-living bacteria. In addition to these approaches, fluorescence and electron microscopy have been used as the gold standards to study and differentiate endosymbiotic bacteria based on their intracellular location. More recently, researchers have started using systems-biology approaches to study fungal-bacterial interactions including high-throughput -omics assays. These methods produce expansive datasets that are ideally suited to artificial intelligence (AI)-based approaches to tackle long-standing questions about the basic biology and evolution of fungal-bacterial interactions. In this primer we give an overview of fungal-bacterial interactions, including their diversity, community structure, and symbiotic evolution. We highlight two research systems in particular: the intracellular endosymbionts of Mucoromycota fungi and the free-living bacteria associated with edible fungi. We focus on these systems because fungi remain understudied relative to other groups, and only a handful of fungal taxa with their bacterial symbionts are backed by large enough data sets to explore these concepts in detail. Our aim here is not to be comprehensive, but instead to use the most well-understood systems to illustrate emerging principles. We then discuss advances in using AI to infer new aspects of microbial biology and provide suggestions for how these technologies could advance research on fungal-bacterial interactions utilizing existing genomic datasets.