Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome Bridget L. Hansen, a Rita de Cassia Pessotti, a Monika S. Fischer, a Alyssa Collins, b Laila El-Hifnawi, b Mira D. Liu, c Matthew F. Traxler a a Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA b Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, USA c Department of Chemistry, University of California, Berkeley, Berkeley, California, USA ABSTRACT Microbiomes associated with various plant structures often contain members with the potential to make specialized metabolites, e.g., molecules with antibacterial, antifungal, or siderophore activities. However, when and where mi- crobes associated with plants produce specialized metabolites, and the potential role of these molecules in mediating intramicrobiome interactions, is not well under- stood. Root nodules of legume plants are organs devoted to hosting symbiotic bac- teria that fix atmospheric nitrogen and have recently been shown to harbor a rela- tively simple accessory microbiome containing members with the ability to produce specialized metabolites in vitro. On the basis of these observations, we sought to de- velop a model nodule microbiome system for evaluating specialized microbial me- tabolism in planta. Starting with an inoculum derived from field-grown Medicago sa- tiva nodules, serial passaging through gnotobiotic nodules yielded a simplified accessory community composed of four members: Brevibacillus brevis, Paenibacillus sp., Pantoea agglomerans, and Pseudomonas sp. Some members of this community exhibited clear cooperation in planta, while others were antagonistic and capable of disrupting cooperation between other partners. Using matrix-assisted laser desorp- tion ionization–imaging mass spectrometry, we found that metabolites associated with individual taxa had unique distributions, indicating that some members of the nodule community were spatially segregated. Finally, we identified two families of molecules produced by B. brevis in planta as the antibacterial tyrocidines and a novel set of gramicidin-type molecules, which we term the britacidins. Collectively, these results indicate that in addition to nitrogen fixation, legume root nodules are likely also sites of active antimicrobial production. KEYWORDS antibiotic, microbial interactions, microbiome, root nodule, specialized metabolism P lants harbor distinct microbial communities associated with their roots (1–3), stems (2–4), leaves (2–5), and flowers (6, 7). These communities can influence host phenotypes in a variety of ways that are beneficial, including enhanced growth (6, 8), drought tolerance (2, 3, 9), and disease resistance (2, 3, 6). The content of these microbiomes is thought to be shaped by a combination of historical contingency (i.e., the order of arrival of strains) (10), microbial interspecies interactions (11, 12), and nutrients or other compounds exuded by the plants themselves that may select for microbes with beneficial characteristics (13, 14). Specialized metabolites produced by microbes, including molecules with antibacterial, antifungal, and siderophore activities, have been hypothesized to play a role in shaping plant microbiomes. For example, specialized metabolites may influence interactions between members of plant micro- biomes (15–17) and may be a mechanism of protection from pathogen invasion (7, 17). Citation Hansen BL, Pessotti RDC, Fischer MS, Collins A, El-Hifnawi L, Liu MD, Traxler MF. 2020. Cooperation, competition, and specialized metabolism in a simplified root nodule microbiome. mBio 11:e01917-20. https://doi .org/10.1128/mBio.01917-20. Editor Deborah A. Hogan, Geisel School of Medicine at Dartmouth Copyright © 2020 Hansen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Matthew F. Traxler, mtrax@berkeley.edu. Received 15 July 2020 Accepted 20 July 2020 Published RESEARCH ARTICLE Ecological and Evolutionary Science crossm July/August 2020 Volume 11 Issue 4 e01917-20 ® mbio.asm.org 1 25 August 2020 Downloaded from https://journals.asm.org/journal/mbio on 15 February 2022 by 3.239.57.10.