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

Assessing Bacterial-Fungal Interactions Across Experimental Scales

Authors:

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

Institutions:

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

URLs:

Goals

To characterize bacterial-fungal interaction (BFI) mechanisms and the impacts of BFIs on their environments under conditions relevant to future climate scenarios.

Abstract

Bacteria and fungi are often dominant constituents of environmental microbial communities, and interactions between these groups can impact microbial functions within their environments, such as nutrient cycling, and plant and soil health. While there have been important advancements in identifying bacterial-fungal interactions (BFIs) and their roles, there is still much to be discovered regarding the underlying interaction mechanisms. It is additionally not well understood how these interactions may shift under changing climate conditions, and how BFIs may contribute to the resilience of soil communities and plant hosts. Through expansive characterization of BFI across experimental scales, the BFI Science Focus Area team seeks to develop foundational knowledge regarding the drivers of BFI and to provide to the broader research community an integrated suite of publicly available resources as the field rapidly expands. Here, researchers focus on bacteria and fungi isolated from the rhizosphere of the highly stress tolerant grass, Bouteloua gracilis, from the arid grassland sites at the Sevilleta Long Term Ecological Research Station in New Mexico. Grasslands have been estimated to store up to 33% of soil carbon globally (Bai and Cotrufo 2022), and the grassland sites from which the team samples experience stressors relevant to future climate scenarios, such as drought and extreme heat. Researchers hypothesize that microbes associated with B. gracilis in the arid grasslands may leverage inter-microbial interactions to respond and adapt to these stressors, providing a useful model ecosystem to understand how BFI will respond as environments become hotter and drier. Using co-occurrence networks built from amplicon sequencing datasets from a large geographical survey, researchers have predicted bacterial and fungal partners that are likely to interact based on co-occurrence rates and which may have greater influence on their ecological contributions due to the prevalence of their interactions. The novel approach will evaluate the ability of co-occurrence models to predict interactions between bacteria and fungi and utilize laboratory-based investigations of interactions to help develop more accurate interaction models based on sequencing and interaction feature data. Several bacterial and fungal isolates were selected for initial laboratory investigations based on network analyses and abundance in sequencing and culture-based surveys. Researchers have conducted preliminary investigations of how environmental conditions such as nutrient availability and temperature impact these BFIs. Phenotyping data indicates that some interactions appear to be more strongly impacted by changing environmental conditions, while other interactions are more stable. Researchers have conducted preliminary comparative genomics analyses of genomic differences that may contribute to the distinct responses underlying BFI phenotypes such as pigmentation and growth. Researchers aim to further characterize the underlying molecular mechanisms using a multi-omics approach to identify relevant molecular markers for BFIs, and which may eventually be applied to understanding the relevance of functional features found in broader-scale datasets (e.g., metagenomics, metatranscriptomics). This data will be made publicly available through the Bacterial-Fungal Interactions Portal (https://:sfa- bfi.edgebioinformatics.org/about), which was developed to provide a centralized resource of BFI research, including known BFI and their associated studies (Robinson et al 2023).

References

Bai, Y., and M. F. Cotrufo. 2022. “Grassland Soil Carbon Sequestration: Current Understanding, Challenges, and Solutions,” Science 377, 603–608.

Robinson, A., et al. 2023. “A Centralized Resource for Bacterial–Fungal Interactions Research,” Fungal Biology 127, 1005–09.

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.