Winter rye cover crops shelter competent squash phyllosphere bacteria to reduce Pseudomonas syringae pv. lachrymans growth and angular leaf spot symptoms.

Cover crops, a soil conservation practice, can contribute to reducing disease pressure caused by Pseudomonas syringae, considered one of the most important bacterial plant pathogens. We recently demonstrated that phyllosphere (leaf surface) bacterial community structure changed when squash (Cucurbita pepo) was grown with a rye (Secale cereale) cover crop treatment, followed by a decrease of angular leaf spot (ALS) disease symptoms on squash caused by P. syringae pv. lachrymans. Application of biocontrol agents is a known agricultural practice to mitigate crop losses due to microbial disease. In this study, we tested the hypothesis that some phyllosphere bacteria promoted when squash are grown on cover crops could be isolated and used as a biocontrol agent to decrease ALS symptoms. We grew squash during a two-year field experiment using four agricultural practices: bare soil, cover crops, chemically terminated cover crops, and plastic cover. We sampled squash leaves at 3 different dates each year and constructed a collection of cultivable bacterial strains isolated from squash leaves and rye cover crop material. Each isolated strain was identified by 16S rRNA gene sequencing and used in in vitro (Petri dish) pathogen growth and in vivo (greenhouse) symptom control assays. Four bacterial isolates belonging to the genera Pseudarthrobacter, Pseudomonas, Delftia and Rhizobium were shown to inhibit P. syringae pv. lachrymans growth and ALS symptom development. Strikingly, the symptom control efficacy of all strains was stronger on older leaves. This study sheds light on the importance of bacterial isolation from cover crops sources to promote disease control.

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

Lettuce is an economically major leafy vegetable that is affected by numerous diseases. One of the most devastating diseases of lettuce is white mold caused by Sclerotinia sclerotiorum. Control methods for this fungus are limited due to the development of genetic resistance to commonly used fungicides, the large number of hosts and the long-term survival of sclerotia in soil. To elaborate a new and more sustainable approach to contain this pathogen, 1,210 Pseudomonas strains previously isolated from agricultural soils in Canada were screened for their antagonistic activity against S. sclerotiorum. Nine Pseudomonas strains showed strong in vitro inhibition in dual-culture confrontational assays. Whole genome sequencing of these strains revealed their affiliation with four phylogenomic subgroups within the Pseudomonas fluorescens group, namely Pseudomonas corrugata, Pseudomonas asplenii, Pseudomonas mandelii, and Pseudomonas protegens. The antagonistic strains harbor several genes and gene clusters involved in the production of secondary metabolites, including mycin-type and peptin-type lipopeptides, and antibiotics such as brabantamide, which may be involved in the inhibitory activity observed against S. sclerotiorum. Three strains also demonstrated significant in planta biocontrol abilities against the pathogen when either inoculated on lettuce leaves or in the growing substrate of lettuce plants grown in pots. They however did not impact S. sclerotiorum populations in the rhizosphere, suggesting that they protect lettuce plants by altering the fitness and the virulence of the pathogen rather than by directly impeding its growth. These results mark a step forward in the development of biocontrol products against S. sclerotiorum.

Genome Sequences of Two Plant-Beneficial Chryseobacterium Strains Isolated from Agricultural Soils in the Province of Quebec, Canada.

Two Chryseobacterium strains, B21-013 and B21-037, were isolated from agricultural soils located in the province of Quebec, Canada, as part of a screening for plant-beneficial bacteria able to suppress Xanthomonas hortorum pv. vitians and other lettuce bacterial pathogens. Here, we report the genome sequences of these two organisms.

Genome Sequences of Two Soil-Dwelling Bacteria Belonging to the Family Comamonadaceae.

Members of the family Comamonadaceae are rod-shaped betaproteobacteria found in various environments. Here, we report the genome sequences of 2 bacteria belonging to this family. They were isolated from agricultural soils located in the Montérégie region (Quebec, Canada) and display biocontrol activity against various lettuce bacterial pathogens.

Complete Genome Sequences of Five Burkholderia Strains with Biocontrol Activity against Various Lettuce Pathogens.

Numerous bacterial strains from the Burkholderia cepacia complex display biocontrol activity. Here, we report the complete genome sequences of five Burkholderia strains isolated from soil. Biosynthetic gene clusters responsible for the production of antimicrobial compounds were found in the genome of these strains, which display biocontrol activity against various lettuce pathogens.

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 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.

Rapid identification of Erwinia amylovora and Pseudomonas syringae species and characterization of E. amylovora streptomycin resistance using quantitative PCR assays.

Erwinia amylovora and Pseudomonas syringae are bacterial phytopathogens responsible for considerable yield losses in commercial pome fruit production. The pathogens, if left untreated, can compromise tree health and economically impact entire commercial fruit productions. Historically, the choice of effective control methods has been limited. The use of antibiotics was proposed as an effective control method. The identification of these pathogens and screening for the presence of antibiotic resistance is paramount in the adoption and implementation of disease control methods. Molecular tests have been developed and accepted for identification and characterization of these disease-causing organisms. We improved existing molecular tests by developing methods that are equal or superior in robustness for identifying E. amylovora or P. syringae while being faster to execute. In addition, the real-time PCR-based detection method for E. amylovora provided complementary information on the susceptibility or resistance to streptomycin of individual isolates. Finally, we describe a methodology and results that compare the aggressiveness of the different bacterial isolates on four apple cultivars. We show that bacterial isolates exhibit different behaviors when brought into contact with various apple varieties and that the hierarchical clustering of symptom severity indicates a population structure, suggesting a genetic basis for host cultivar specificity.