The soil-borne pathogen Setophoma terrestris is the causal agent of pink root of onion, one of the most challenging diseases in onion production. Conventional approaches for managing the disease like solarization, soil fumigation and crop rotation have not been proven effective enough. In this work, we evaluated the biocontrol capacity of Bacillus subtilis ALBA01 (BsA01) against S. terrestris, in a highly susceptible onion cultivar, both under greenhouse and field conditions. Disease incidence and severity were evaluated together with growth, photosynthesis among other physiological variables, and yield parameters. When compared with plants infected with the pathogen, those plants co-inoculated with BsA01 showed significantly less damage and levels of biocontrol above 50%. With regard to physiological parameters, plants challenged with S. terrestris and inoculated with BsA01 performed as well as the control non-infected plants revealing a growth promotion effect of BsA01 on onion plants.

Soil microorganisms coexist and interact showing antagonistic or mutualistic behaviors. Here, we show that an environmental strain of Bacillus subtilis undergoes heritable phenotypic variation upon interaction with the soil fungal pathogen Setophoma terrestris (ST). Metabolomics analysis revealed differential profiles in B. subtilis before (pre-ST) and after (post-ST) interacting with the fungus, which paradoxically involved the absence of lipopeptides surfactin and plipastatin and yet acquisition of antifungal activity in post-ST variants. The profile of volatile compounds showed that 2-heptanone and 2-octanone were the most discriminating metabolites present at higher concentrations in post-ST during the interaction process. Both ketones showed strong antifungal activity, which was lost with the addition of exogenous surfactin. Whole-genome analyses indicate that mutations in ComQPXA quorum-sensing system, constituted the genetic bases of post-ST conversion, which rewired B. subtilis metabolism towards the depletion of surfactins and the production of antifungal compounds during its antagonistic interaction with S. terrestris.

Soil-borne pathogen Setophoma terrestris is the causal agent of pink root of onion, one of the most challenging diseases in onion production. Conventional approaches for managing the disease like solarization, soil fumigation and crop rotation have not been proven effective enough. In this work, we evaluated the biocontrol capacity of Bacillus subtilis ALBA01 (BsA01) against S. terrestris , in a highly susceptible onion cultivar, both under greenhouse and field conditions. Disease incidence and severity were evaluated together with growth, photosynthesis among other physiological variables and yield parameters. When compared with plants infected with the pathogen, those plants co-inoculated with BsA01 showed significantly less damage and levels of biocontrol above 50%. With regard to physiological parameters, plants challenged with S terrestris and inoculated with BsA01 performed as well as the control non-infected plants revealing a growth promotion effect of BsA01 on onion plants.

The soil-borne fungal plant pathogen Verticillium dahliae can infect more than 300 plant species including important economic crops, causing great economic loses. V. dahliae can persist and survive more than 14 years in the soil by resistance structures, known as microsclerotia, which constitute the primary inoculum in the field. In vitro mass production of microsclerotia is essential for performing many pathological assays. Nevertheless to harvest the microsclerotia is not an easy task and several protocols have been described although none of them is completely satisfying for different reasons. here we present a new protocol that is reproducible, robust, simple and fast allows to overcome the difficulties for obtaining massive amounts of microsclerotia. In summary, we developed a new culture medium that we called Pluronic Potato Medium (PPM) because it is essentially potato dextrose media with the hydrogel, Pluronic F127 as a solidifying agent. The microsclerotia collected in form PPM were infectious in tomato plants were they were able to reproduce the disease and we recovered and quantitated V. dahliae in infected plants.

Metabolic exchange may define adaptation to the changes imposed by microbial interactions. We found that antifungal activity of cell-free supernatants of Bacillus subtilis ALBA01 is acquired after interacting with the soil fungus Setophoma terrestris (ST). Here we evaluated different traits of B. subtilis ALBA01 before (pre-ST) and after (post-ST) interacting with the fungus in co-cultures and inquired about the molecular mechanisms underlying this inter-kingdom interaction dependent antagonistic activity. Apart from the high fungal inhibition activity, we observed that the ability to form robust biofilms in vitro was a prevailing feature of post-ST and that biofilm formation was positively correlated to biocontrol efficacy. Moreover, nuclear magnetic resonance and mass spectrometry analysis revealed a differential metabolomics profile in post-ST variants, including the unexpected absence of surfactin or plipastatin production. Disruption of the srfAA gene implicated in surfactin synthesis resulted in an abolition of the ST-driven antifungal activity and ST growth inhibition levels similar to those observed for post-ST variants. The post-ST phenotype was stable after several passages on solid media, indicating that a mutation-based process underlies this phenotypic adaptation process. In fact, whole genome comparison revealed mutations that converge in genes of the ComQPXA quorum sensing system in post-ST variants. Altogether, our results suggest a role for a still unknown quorum sensing regulated pathway, which by classical antimicrobial lipopeptide abrogation mediates B. subtilis ALBA01 adaptive phenotypic variation and that may be responsible for the antagonistic behavior it exerts on S. terrestris.