Seasonal Dynamics of Various Scab-Causing Streptomyces Genotypes Among Potato Fields on Prince Edward Island.

Potato common scab is an important bacterial plant disease caused by numerous Streptomyces species and strains. A better understanding of the genetic diversity and population dynamics of these microorganisms in the field is crucial to develop effective control methods. Our research group previously studied the genetic diversity of scab-causing Streptomyces spp. in Prince Edward Island, one of Canada's most important potato-growing provinces. Fourteen distinct Streptomyces genotypes were identified and displayed contrasting aggressiveness toward potato tubers. To better understand the distribution and occurrence of these genotypes over time under field conditions, the population dynamics were studied in nine commercial potato fields throughout a growing season. A comparative genomic-driven approach was used to design genotype-specific primers and probes, allowing us to quantify, using quantitative polymerase chain reaction, the abundance of each of the 14 genotypes in field soil. Thirteen of the previously identified genotypes were detected in at least one soil sample, with various frequencies and population sizes across the different fields under study. Interestingly, weakly virulent genotypes dominated, independent of time or location. Among them, three genotypes accounted for more than 80% of the genotypes' combined population. Although the highly virulent genotypes were detected in lower relative abundance than the weakly virulent ones, an increase in the highly virulent genotypes' population size was observed over the growing season in most fields. The results will ultimately be useful for the development of targeted common scab control strategies.

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.

Combining Desirable Traits for a Good Biocontrol Strategy against Sclerotinia sclerotiorum.

The fungal pathogen Sclerotinia sclerotiorum (Helotiales: Sclerotiniaceae) causes white mold, a disease that leads to substantial losses on a wide variety of hosts throughout the world. This economically important fungus affects yield and seed quality, and its control mostly relies on the use of environmentally damaging fungicides. This review aimed to present the latest discoveries on microorganisms and the biocontrol mechanisms used against white mold. A special focus is put on the identification of biocontrol desirable traits required for efficient disease control. A better understanding of the mechanisms involved and the conditions required for their action is also essential to ensure a successful implementation of biocontrol under commercial field conditions. In this review, a brief introduction on the pathogen, its disease cycle, and its main pathogenicity factors is presented, followed by a thorough description of the microorganisms that have so far demonstrated biocontrol potential against white mold and the mechanisms they use to achieve control. Antibiosis, induced systemic resistance, mycoparasitism, and hypovirulence are discussed. Finally, based on our actual knowledge, the best control strategies against S. sclerotiorum that are likely to succeed commercially are discussed, including combining biocontrol desirable traits of particular interest.

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.

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.

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.