Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea

Abstract

The non-fluorescent pseudomonads, Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed), are closely related species that cause pith necrosis, a disease of tomato that causes severe crop losses. However, they also show strong antagonistic effects against economically important pathogens, demonstrating their potential for utilization as biological control agents. In addition, their metabolic versatility makes them attractive for the production of commercial biomolecules and bioremediation. An extensive comparative genomics study is required to dissect the mechanisms that Pcor and Pmed employ to cause disease, prevent disease caused by other pathogens, and to mine their genomes for genes that encode proteins involved in commercially important chemical pathways. Here, we present the draft genomes of nine Pcor and Pmed strains from different geographical locations. This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison. All examined strains were able to trigger symptoms in tomato plants but not all induced a hypersensitive-like response in Nicotiana benthamiana. Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains. The lack of a type III secretion system appears to be unique among the plant pathogenic pseudomonads. Several gene clusters coding for type VI secretion system were detected in all genomes. Genome-mining also revealed the presence of gene clusters for biosynthesis of siderophores, polyketides, non-ribosomal peptides, and hydrogen cyanide. A highly conserved quorum sensing system was detected in all strains, although species specific differences were observed. Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

Microbial taxa and functional genes shift in degraded soil with bacterial wilt

“…Ralstonia solanacearum is a pathogenic agent of bacterial wilt23; Pseudomonas syringae, P. aeruginosa, P. corrugate and P. mediterranea are economically important plant pathogens242526; Rhizoctonia solani is a soil-borne fungal pathogen that causes disease in a wide range of plants including tobacco27; Fusarium contains many plant pathogens such as F. oxysporumi for infection of tomato and F. solani for infection of pea28. It is possible that these pathogenic microorganisms may cause serious plant diseases in the degraded soils, consistent with the high disease index of tobacco bacteria wilt in the degraded soils (Table 2).…”

Friend or foe? Exploring the fine line between Pseudomonas brassicacearum and phytopathogens

“…As seen in other non-pathogenic and pathogenic pseudomonads, a mangotoxin-like biosynthetic cluster is conserved in P. brassicacearum, P. corrugata and P. mediterranea (Fig. 1) [20,41,52,53]. Despite its name, the product of this mangotoxin-like cluster is thought to act as a regulator of SMs rather than a toxin [41,54,53].…”

Microbial community dynamics in the recirculating nutrient solution of tomato plug seedlings cultivated under ebb-and-flow system

“…P. mediterranea, a pathogen responsible for pith necrosis, was detected predominantly in winter, with decreasing in the nutrient solution but increasing in the substrate. Pith necrosis is a disease of tomato that causes severe crop losses [31,32]. Additionally, some potentially pathogenic fungi including F. oxysporum and A. alternate, were increased considerably in the nutrient solution or substrate samples.…”