Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Dissecting Bacterial-Fungal Interactions in the Bouteloua gracilis Rhizosphere Microbiome Using Metabolic Phenotyping


Buck Hanson1* (, Leah Johnson1, Reid Longley1, Aaron Robinson1, Justine Macalindong1, Kelli Feeser1, James Brunner1, Julia Kelliher1, Demosthenes Morales1, La Verne Gallegos-Graves1, Mary Lipton2, Guillaume Cailleau3, Saskia Bindschedler3, Pilar Junier3, Scott Baker2, Megan Korne4, Michal Babinski1, Gregory Bonito4, Patrick Chain1


1Los Alamos National Laboratory; 2Pacific Northwest National Laboratory; 3University of Neuchâtel, Switzerland; 4Michigan State University



To understand how root exudates and other carbon compounds shape bacterial-fungal interactions and their roles in ecosystem processes.


Bacteria and fungi play central roles in shaping and facilitating terrestrial ecosystem services and soil functioning. Bacterial-fungal interactions (BFIs) and interactions with other soil biota are essential to global biogeochemical cycling, soil fertility, and plant health. However, how BFIs influence these functions remains poorly understood. Researchers hypothesize that substrate utilization plays a major role in shaping BFI phenotypes (e.g., antagonistic vs. neutral); competition or substrate cross-feeding has the potential to significantly govern the distribution of bacteria and fungi in soils and rhizospheres, influence their roles in biogeochemical cycling, as well as their ability to associate and colonize plant roots. The work in the BFI Science Focus Area focuses on bacteria and fungi isolated from the heat- and drought-tolerant grass, Bouteloua gracilis (blue grama) from arid grasslands in Southwestern U.S. A framework for the efforts anticipates that blue grama-associated microbes are attracted to roots via root exudates facilitating root colonization and that blue grama benefits from these interactions (e.g., heat and drought tolerance, pathogen resistance). However, how root exudate composition influences microbial assembly and how microbial competition for root exudates contributes to successful colonization remain poorly understood. Researchers have isolated phylogenetically diverse lineages of the bacterial and fungal members of the blue grama rhizosphere (and root endophytes) and are generating preliminary data on BFI among bacterial-fungal pairs. In combination with genome sequencing, researchers have begun testing representative bacterial and fungal taxa for their potential to utilize a suite of 190 organic compounds using the Biolog Phenotype MicroArrays. Differential substrate utilization profiles document the potential for competition between isolates indicating that they may have antagonistic interactions in situ (i.e., the blue grama rhizosphere). Furthermore, antagonistic interactions may lead to niche partitioning and spatially constrained soil and root colonization. To evaluate the potential for substrate-mediated antagonistic interactions, a key goal for this work is to compare substrate utilization of individual bacterial and fungal isolates as well as assess the ability of this technology to characterize impacts of BFI in co-culture. To do this, bacterial and fungal pairs will be selected based on their individual substrate-utilization profiles, showing similar and contrasting C-source utilization and co-cultured in the Biolog plates. While the initial efforts will be focused on carbon (C) utilization, researchers will expand to other nutrients (e.g., phosphorus and nitrogen) in the future. These data provide a foundation for generating new hypotheses for investigating and understanding the ecological roles and impacts of BFI. Using the isolate genomes, next steps will be to generate a predictive understanding of substrate preference and how genetic features can be leveraged to screen for and evaluate BFI in their natural environments, leading to new tools to improve BFI-mediated soil ecosystem services (e.g., plant productivity, C sequestration).

Funding Information

This research was supported by a Science Focus Area Grant from the U.S. DOE, BER, Biological Systems Science Division (BSSD) under the grant number LANLF59T.