bioRxiv2025
Healthy plant leaves host both commensal bacteria, which usually do not cause harm, and opportunistic pathogens, which under the right circumstances can cause disease. Microbial and plant-derived factors can potentially govern the balance between commensals and pathogens; understanding this dynamic is crucial for developing effective biocontrol strategies. In Arabidopsis thaliana, isothiocyanates (ITCs) are toxic defense metabolites that suppress most bacteria. An important virulence factor for bacterial and fungal pathogens of A. thaliana is the ITC hydrolase SaxA, which detoxifies ITCs. To investigate microbial interactions based on SaxA-mediated ITC degradation, we used five ITC-sensitive bacterial commensals and the opportunistic pathogen Pseudomonas viridiflava 3D9 (PS). All strains were isolated from healthy A. thaliana leaves and PS degrades 4-methylsulfinylbutyl-ITC (4MSOB-ITC) with SaxA. We examined their growth in the presence of 4MSOB-ITC, both in monoculture and in coculture with PS or a saxA-deficient mutant (PSKO). Based on experimental growth data, we developed a generalizable consumer-resource mathematical model incorporating ITC toxicity, ITC degradation, and nutrient use. We predicted conditions and confirmed them experimentally under which SaxA not only benefits the pathogen but also indirectly favors commensal growth, which then can limit pathogen proliferation by competing for nutrients. In addition, we tested in silico how commensal ITC susceptibility, pathogen ITC degradation rates, and growth parameters affect the trade-off between SaxA-mediated virulence (strong pathogen growth) and high commensal rescue (commensal growth). Our findings suggest that the effects of microbial traits - traditionally viewed as either virulence or plant-beneficial factors - are context-dependent. This underscores the need to reconsider how such traits are classified in the context of plant-microbiome interactions. Author SummaryHealthy plant leaves host a variety of bacteria; these can be beneficial, but some (opportunistic pathogens) can also be harmful under certain conditions. To design effective biocontrol strategies to sustainably protect plants, it is important to understand how opportunistic pathogens thrive as part of a healthy, balanced leaf microbiome. Plant defense metabolites such as isothiocyanates (ITCs) and bacterial ITC resistance mechanisms such as the ITC hydrolase SaxA may play key roles in maintaining this balance. In this study, we explore how SaxA-mediated ITC degradation by a pathogen also benefits diverse ITC-sensitive commensals and how this in turn could shape microbiome stability and plant health. Using mathematical modeling based on growth data from PS with diverse commensals, we find that interaction dynamics can be explained by ITC detoxification and nutrient competition. We predict and experimentally confirm that conditions exist under which SaxA favors commensal growth so strongly that the pathogen is outcompeted for resources, thus not benefiting from its own virulence factor. Our findings suggest that the effects of microbial traits are context-dependent, especially when functioning as public good in a community context like SaxA. Taken together, quantitative modeling of these interactions may inform strategies to maintain healthy plant microbiomes and control disease.