Fungi and bacteria form different types of associations that are central to numerous environmental processes. Similar to human dysbioses and microbiome manipulation via antibiotics and probiotic remediation, it may be possible to steer agricultural ecosystem function by altering soil environmental parameters to select for desired microbes and traits. As a first step, we wish to investigate and characterize bacterial interactions with fungi at a fundamental level, to establish the types of interactions, their breadth both phylogenetically and functionally, and later, to characterize these interactions at the molecular level. Prior work suggests that bacteria and fungi exploit each other both on the surfaces of fungal mycelial networks, as well as within mycelia. We begin by exploring the diverse nature of these associations by screening both genomic databases as well as culture collections. Available fungal genome projects are screened for the presence of bacterial genomic signatures that may have been inadvertently sequenced. Challenges in this field of taxonomy classification and bacterial identification will be discussed. In addition, we screen diverse fungal collections for bacterial signatures using an approach based on sequencing of the 16S rRNA gene combined with microscopic confirmation of the presence of endohyphal bacteria. For some isolates, we explore some of the interactions phenotypically, by monitoring growth during confrontation assays. We have used devices dubbed ‘fungal highway’ columns, to isolate bacteria capable of utilizing fungal mycelia as a dispersal mechanism, and are testing a 3D fabrication of this type of device for routine exploration of such interactions. Growth phenotypes of some of these bacterial and fungal isolates, as well as known interacting bacterial-fungal pairs, are being examined. Collectively, these studies begin to shed light into the diversity, and range of interactions that occur among these dominant microbial players.  

https://github.com/LANL-Bioinformatics
https://genomicscience.energy.gov/research/sfas/lanlbfi.shtml
This study was supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research Division, under award numbers LANLF59T and LANLF59C.

Learning objectives:
1. Metagenomic analysis is already complex, and complicated further by incomplete and non-standardized databases of known organisms
2. fungi may have their own 'microbiomes', as we discover signatures of bacteria both within and on the surface of fungal hyphae