Harnessing the genomic diversity of Pseudomonas strains against lettuce bacterial pathogens

Abstract

Lettuce is a major vegetable crop worldwide that is affected by numerous bacterial pathogens, including Xanthomonas hortorum pv. vitians, Pseudomonas cichorii, and Pectobacterium carotovorum. Control methods are scarce and not always effective. To develop new and sustainable approaches to contain these pathogens, we screened more than 1,200 plant-associated Pseudomonas strains retrieved from agricultural soils for their in vitro antagonistic capabilities against the three bacterial pathogens under study. Thirty-five Pseudomonas strains significantly inhibited some or all three pathogens. Their genomes were fully sequenced and annotated. These strains belong to the P. fluorescens and P. putida phylogenomic groups and are distributed in at least 27 species, including 15 validly described species. They harbor numerous genes and clusters of genes known to be involved in plant-bacteria interactions, microbial competition, and biocontrol. Strains in the P. putida group displayed on average better inhibition abilities than strains in the P. fluorescens group. They carry genes and biosynthetic clusters mostly absent in the latter strains that are involved in the production of secondary metabolites such as 7-hydroxytropolone, putisolvins, pyochelin, and xantholysin-like and pseudomonine-like compounds. The presence of genes involved in the biosynthesis of type VI secretion systems, tailocins, and hydrogen cyanide also positively correlated with the strains’ overall inhibition abilities observed against the three pathogens. These results show promise for the development of biocontrol products against lettuce bacterial pathogens, provide insights on some of the potential biocontrol mechanisms involved, and contribute to public Pseudomonas genome databases, including quality genome sequences on some poorly represented species.

Identification and genomic characterization of Pseudomonas spp. displaying biocontrol activity against Sclerotinia sclerotiorum in lettuce

“…Genome sequencing of the nine Pseudomonas strains that displayed antagonistic activity against S. sclerotiorum uncovered their phylogenomic affiliation to the group, subgroup, and sometimes species levels within the Pseudomonas genus ( Supplementary Figure 1 ). Figure 2 shows the phylogenomic relationships between the antagonistic strains and non-antagonistic Pseudomonas strains isolated from the same collection of 1,210 strains ( Zboralski et al, 2022 ). The antagonistic strains all clustered within the P. fluorescens group and are subdivided into the four following subgroups: six strains belong to the Pseudomonas corrugata , one strain to the Pseudomonas mandelii , one strain to the Pseudomonas asplenii , and one strain to the Pseudomonas protegens subgroup.…”

“…This analysis included 35 other Pseudomonas spp. characterized in a previous study ( Zboralski et al, 2022 ; Supplementary Table 1 ), which are non-antagonistic against S. sclerotiorum . This comparative approach aimed to identify differences in gene distribution between antagonistic and non-antagonistic strains, which could point to genetic determinants involved in S. sclerotiorum ’s inhibition.…”

“…To better understand the mechanism(s) leading to biocontrol under in planta conditions in our study, we explored the diversity of secondary metabolites potentially produced by these antagonistic Pseudomonas strains by identifying genes and BGCs involved in antibiotic biosynthesis in their genomes that are mostly absent from the genomes of 35 other Pseudomonas strains, non-antagonistic against S. sclerotiorum ( Zboralski et al, 2022 ; listed in Supplementary Table 1 ).…”

“…A collection of 1,210 Pseudomonas strains was assessed for their in vitro antagonistic abilities against S. sclerotiorum . These strains were previously isolated from agricultural soils in the province of Québec, Canada, and screened against three lettuce bacterial pathogens ( Zboralski et al, 2022 ). A single pathogenic strain of S. sclerotiorum called Ss2019-1 was used in this study.…”

Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato

“…Moreover, the assembled genome of Flavobacteria, called the TRM1 strain, was associated with carbohydrate metabolism [18], and specific monosaccharide transporters indicate that TRM1 can reduce the availability of sugars that R. solanacearum lectin binds to, thereby reducing disease pressure [18,99]. Increasing the soil pH to 6.45 reduces R. solanacearum in tomatoes and increases beneficial microbiomes, including bacteria of Firmicutes such as Bacillus Paenibacillus and others such as Flavobacterium (Bacteroidetes) and Pseudomonas (Pseudomonadota) [100,101]. This suggests that changes in soil pH directly affect the spread of BW disease among tomatoes.…”