An Online Public Resource for Bacterial-Fungal Interaction Research
Aaron Robinson, Julia Kelliher, Buck Hanson, Reid Longley, Demosthenes Morales, and Patrick Chain* (firstname.lastname@example.org)
Los Alamos National Laboratory (LANL)
As part of the LANL Science Focus Area (SFA) on Bacterial-Fungal Interactions (BFIs), researchers are developing novel bioinformatic and experimental tools and resources for the identification and characterization of BFIs that occur within complex natural microbiomes. The theoretical framework of this project is built upon gaining a more comprehensive understanding of how bacteria and fungi sense, respond to, and co-evolve with one another using multiomics-based interrogations. A more complete understanding of the molecular mechanisms underlying BFIs allows interrogation of how the dynamics of these relationships are altered in the context of environmental change (e.g., nutrient availability, temperature). Through these studies, the team hopes to gain a predictive understanding of how these interactions impact microbiome function and how they may be altered to steer the function of soil ecosystems and increase resilience to climate change and other environmental perturbations.
The burgeoning field of BFI research is quickly gaining interest in broader fields such as microbial ecology and evolution. This is at least partially due to the fact that current knowledge on BFIs suggests that interactions between these two kingdoms are quite common (Robinson et al. 2021). Furthermore, it has been demonstrated that BFIs can have direct impacts on the ecological functions performed by participating bacterial and fungal partners, suggesting that BFIs play an important role in the ecology and evolution of environmental microbiomes (Deveau et al. 2018; Pierce et al. 2021). However, it is currently very challenging to assess the state of the field, particularly with respect to what bacterial and fungal taxa have been previously reported as participants in BFIs. This is due to non-standardized methods and even format in which BFIs are reported in literature, as different descriptors (BFIs, endofungal, symbiotic, etc.) are often used, and some interactions are only reported in tables and/or figures. To address this problem, the BFI SFA has performed a comprehensive search to establish a database containing current knowledge on BFIs and which bacterial and fungal taxa participate in them. This database has been integrated into the BFI Research Portal (https://sfa-bfi.edgebioinformatics.org/search), which can be queried using specific taxa to identify if any known BFIs involving that taxa have been previously reported in the literature. The database is a dynamic resource that will be updated as new BFI descriptions are published and allows users to submit any descriptions of BFIs not presently represented in the database after internal review. Additionally, the team is continually analyzing non-published fungal sequencing data from the National Center for Biotechnology Information Sequence Read Archive to find potential bacterial associates/interactions. Interactive visual outputs allow users to expand upon their initial queries to gain insights as to the diversity of BFIs related to their taxa or lineages of interest. This centralized resource will continually be developed to allow researchers in the field the ability to conduct BFI relevant analyses using custom bioinformatic workflows and enable the BFI database to be integrated into any analyses performed within the portal.
Deveau, A., et al. 2018. “Bacterial–Fungal Interactions: Ecology, Mechanisms and Challenges,” FEMS Microbiology Reviews 42(3), 335–52.
Pierce, E. C., et al. 2021. “Bacterial–Fungal Interactions Revealed by Genome-Wide Analysis of Bacterial Mutant Fitness,” Nature Microbiology 6(1), 87–102.
Robinson, A. J., et al. 2021. “Widespread Bacterial Diversity Within the Bacteriome of Fungi,” Communications Biology 4(1), 1168.
This research was supported by an SFA Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER) Program, Biological Systems Science Division (BSSD) under grant number LANLF59T.