Harnessing the genomic diversity of Pseudomonas strains against lettuce bacterial pathogens

Lettuce is a major vegetable crop worldwide that is affected by numerous bacterial pathogens, including pv. , , and . 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 strains retrie...

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Published inFrontiers in microbiology Vol. 13; p. 1038888
Main Authors Zboralski, Antoine, Biessy, Adrien, Ciotola, Marie, Cadieux, Mélanie, Albert, Daphné, Blom, Jochen, Filion, Martin
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 22.12.2022
Subjects
lettuce
Microbiology
pathogen
Pectobacterium
PGPR
Pseudomonas
Xanthomonas
genome
pathogen
Pectobacterium
PGPR
Pseudomonas
biocontrol
lettuce
Xanthomonas
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Summary:Lettuce is a major vegetable crop worldwide that is affected by numerous bacterial pathogens, including pv. , , and . 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 strains retrieved from agricultural soils for their antagonistic capabilities against the three bacterial pathogens under study. Thirty-five strains significantly inhibited some or all three pathogens. Their genomes were fully sequenced and annotated. These strains belong to the . and . 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 . group displayed on average better inhibition abilities than strains in the . 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 genome databases, including quality genome sequences on some poorly represented species.
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Reviewed by: Kanika Bansal, Institute of Microbial Technology (CSIR), India; Sanjeet Kumar, Max Planck Institute for the Science of Human History (MPI-SHH), Germany
Edited by: Marco Scortichini, Council for Agricultural and Economics Research (CREA), Italy
These authors have contributed equally to this work and share first authorship
This article was submitted to Microbe and Virus Interactions with Plants, a section of the journal Frontiers in Microbiology
ISSN:1664-302X
1664-302X
DOI:10.3389/fmicb.2022.1038888