The major factors influencing soil microbiomes, namely bacteria and fungi, play crucial roles in carbon flux, nutrient cycling, and plant productivity. This project aims to uncover the fundamental principles governing bacterial:fungal interactions (BFIs), with the goal of leveraging their biotechnological potential to direct soil ecosystem functions. Over a 10-year period, the Sustainable Bioenergy Crop and Soil Carbon Sequestration Scientific Focus Area (SFA) envisions a comprehensive understanding of complex BFIs in the face of ongoing environmental changes. This knowledge will facilitate the manipulation of ecosystem functions, promoting the sustainable production of bioenergy crops and enhancing soil carbon sequestration. Currently, the focus is on exploring the biological complexities of specialized bacterial:fungal interactions. By leveraging novel bioinformatics algorithms and state-of-the-art scientific computing resources from the U.S. Department of Energy (DOE), coupled with targeted metagenomics, the SFA aims to unveil previously unknown bacterial:fungal associations. The research will explore the spectrum of BFIs under diverse abiotic environmental conditions, such as varying moisture, nutrient availability, and temperature. Furthermore, the project will elucidate the underlying mechanisms of these interactions at cellular and molecular scales, using “multi-omic” targeting and advanced in-situ imaging techniques. The ultimate goal is to provide the fundamental knowledge needed for predictive models of soil community function, thereby unlocking the biotechnological potential of the soil microbiome.

Selected publications

• Kelliher JM, Johnson LYD, Robinson AJ, Longley R, Hanson BT, Cailleau G, Bindschedler S, Junier P, Chain PSG. Fabricated devices for performing bacterial-fungal interaction experiments across scales. Front Microbiol. 2024 Aug 7;15:1380199. doi: 10.3389/fmicb.2024.1380199. PMID: 39171270; PMCID: PMC11335632.
• Périat C, Kuhn T, Buffi M, Corona-Ramirez A, Fatton M, Cailleau G, Chain PS, Stanley CE, Wick LY, Bindschedler S, Gonzalez D, Li Richter XY, Junier P. Host and nonhost bacteria support bacteriophage dissemination along mycelia and abiotic dispersal networks. Microlife. 2024 Feb 20;5:uqae004. doi: 10.1093/femsml/uqae004. PMID: 38463165; PMCID: PMC10924533.
• Cailleau G, Hanson BT, Cravero M, Zhioua S, Hilpish P, Ruiz C, Robinson AJ, Kelliher JM, Morales D, Gallegos-Graves V, Bonito G, Chain PSG, Bindschedler S, Junier P. Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp. Front Fungal Biol. 2023 Dec 13;4:1285531. doi: 10.3389/ffunb.2023.1285531. PMID: 38155707; PMCID: PMC10753826.
• Robinson AJ, House GL, Morales DP, Kelliher JM, Gallegos-Graves V, LeBrun ES, Davenport KW, Palmieri F, Lohberger A, Bregnard D, Estoppey A, Buffi M, Paul C, Junier T, Hervé V, Cailleau G, Lupini S, Nguyen HN, Zheng AO, Gimenes LJ, Bindschedller S, Rodrigues DF, Werner JH, Young JD, Junier P, Chain PSG. Widespread bacterial diversity within the bacteriome of fungi. Commun Biol. 2021 Oct 7;4(1):1168. doi: 10.1038/s42003-021-02693-y. PMID: 34621007; PMCID: PMC8497576.
• Junier P, Cailleau G, Palmieri I, Vallotton C, Trautschold OC, Junier T, Paul C, Bregnard D, Palmieri F, Estoppey A, Buffi M, Lohberger A, Robinson A, Kelliher JM, Davenport K, House GL, Morales D, Gallegos-Graves V, Dichosa AEK, Lupini S, Nguyen HN, Young JD, Rodrigues DF, Parra-Vasquez ANG, Bindschedler S, Chain PSG. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS Microbiol Ecol. 2021 Feb 11;97(2):fiab003. doi: 10.1093/femsec/fiab003. PMID: 33440006; PMCID: PMC7878174.
• Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, van Elsas JD, Wick LY. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol Rev. 2018 May 1;42(3):335-352. doi: 10.1093/femsre/fuy008. PMID: 29471481.