The goal of this project is to unravel the mechanisms that underlie functioning and stability of associations between early divergent fungi in the phylum Mucoromycota and their endosymbiotic bacteria (EB) as well as the role of EB in the evolution of the Mucoromycota fungi and in ecological structuring of their communities. Mucoromycota are ubiquitous plant-associated soil fungi with global distribution and immense ecological and economical significance. Unlike other fungi, Mucoromycota are commonly involved in ancient and highly coevolved symbioses with EB. To address our overall goal, we will focus on two levels of biological organization: (1) the symbiosis of the fungus Rhizopus microsporus (Rm, Mucoromycotina) with the Mycetohabitans sp. bacterium (Beta-proteobacteria) and (2) natural and experimental communities of Mucoromycota representing two biomes across the U.S. and South Africa, which we are studying in the NSF-funded project Dimensions of Biodiversity (DoB). (1) Using the Rm-Mycetohabitans symbiosis we will assess the molecular underpinnings of fungal-bacterial symbioses, focusing on the function of 6-methyladenine (6mA) DNA modifications shared by these organisms, and the role of EB in phylogenic diversification of fungi. (2) The environmental rhizosphere and root samples of focal plants from the DoB project will be used for metagenomic and metatranscriptomic analyses aimed at testing hypotheses concerning the roles of dispersal, environmental and biotic filtering in determining the biodiversity of Mucoromycota. The metatranscriptomic and metabolomic analyses of the experimental Mucoromycota communities will test the hypothesis that EB have a role in shaping these communities by competitive exclusion due to EB-produced secondary metabolites. Genomic sequences of novel holobionts (host fungi and their EB) discovered in the DoB project will reveal evolutionary innovations represented by these symbioses.