Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6

Abstract

Plant-growth promotion has been linked to the Pseudomonas genus since the beginning of this research field. In this work, we mined the genome of an Argentinean isolate of the recently described species P. donghuensis. Strain SVBP6, isolated from bulk soil of an agricultural plot, showed a broad antifungal activity and several other plant-probiotic activities. As this species has been recently described, and it seems like some plant-growth promoting (PGP) traits do not belong to the classical pseudomonads toolbox, we decide to explore the SVBP6 genome via an bioinformatic approach. Genome inspection confirmed our previous in vitro results about genes involved in several probiotic activities. Other genetic traits possibly involved in survival of SVBP6 in highly competitive environments, such as rhizospheres, were found. Tn5 mutagenesis revealed that the antifungal activity against the soil pathogen Macrophomina phaseolina was dependent on a functional gacS gene, from the regulatory cascade Gac-Rsm, but it was not due to volatile compounds. Altogether, our genomic analyses and in vitro tests allowed the phylogenetic assignment and provided the first insights into probiotic properties of the first P. donghuensis isolate from the Americas.

7‐hydroxytropolone is the main metabolite responsible for the fungal antagonism of Pseudomonas donghuensis strain SVBP6

“…A thorough mining of SVBP6 draft genome did not reveal obvious gene clusters related to production of soluble secondary metabolites typical of other biocontrol pseudomonads, such as 2,4-diacetylphloroglucinol, pyrrolnitrin, pyoluteorin, cyclic or linear lipopeptides, phenazines, 2-hexyl 5-propyl resorcinol or mupirocin (Haas and Keel, 2003;Loper et al, 2012;Paterson et al, 2017;Biessy et al, 2019). We observed, however, that alike production of most of the aforementioned compounds, the antagonistic activity of strain SVBP6 is strongly dependent on the Gac-Rsm global regulatory system (Lapouge et al, 2008;Agaras et al, 2018). In this context, the goal of this work was the identification of the compound(s) responsible for the in vitro fungal antagonism displayed by P. donghuensis SVBP6, by a combination of genetic, physiological and chemical approaches.…”

“…1 (Fig 2B, C). Interestingly, the supernatant of a gacS::Tn5 clone from our library, previously reported as unable to inhibit 12 different phytopathogenic fungal isolates (Agaras et al, 2018), also lost the UV peaks of the wild-type SVBP6 supernatant (Fig 2A-C). In line with this observation, we found three sequences within the locus as shown in Fig.…”

“…S2). Strain SVBP6 also displays a diffusible and Gac-Rsm-dependent inhibitory activity against Bacillus subtilis and Escherichia coli (Agaras et al, 2018). However, all the Tn5 mutants that lost the ability to restrict growth of different fungi and that did not produce the UV-absorbing compound still retained their antibacterial activity (Fig.…”

“…In order to get insights into the molecular basis underlying the broad antifungal activity displayed by P. donghuensis strain SVBP6, we screened a Tn5 mutant library (Agaras et al, 2018) for clones showing a strong reduction in the in vitro antagonism against a local isolate of the fungal phytopathogen Macrophomina phaseolina (Table S1). Among a set of nearly 60 selected mutants with reduced antagonism for which the Tn5 insertion site was determined, we found six independent clones whose Tn5 hits mapped close to each other within a 16-kb region in scaffold 5.1 of the SVBP6 draft genome (Fig.…”

“…We have recently isolated from an agricultural soil in Argentina, strain SVBP6-a member of the lately defined Pseudomonas donghuensis species (Jiang et al, 2016)-as a bacterium with a remarkable broad-spectrum in vitro antifungal activity (Agaras et al, 2015;Agaras et al, 2018), which is due to diffusible, but not volatile, compounds (Agaras et al, 2018). A thorough mining of SVBP6 draft genome did not reveal obvious gene clusters related to production of soluble secondary metabolites typical of other biocontrol pseudomonads, such as 2,4-diacetylphloroglucinol, pyrrolnitrin, pyoluteorin, cyclic or linear lipopeptides, phenazines, 2-hexyl 5-propyl resorcinol or mupirocin (Haas and Keel, 2003;Loper et al, 2012;Paterson et al, 2017;Biessy et al, 2019).…”