Pseudomonas allii sp. nov., a pathogen causing soft rot of onion in Japan

Area of Science:

• Microbiology
• Plant Pathology
• Bacteriology

Background:

• Phytopathogenic bacteria pose a significant threat to onion (Allium cepa L.) crops, causing diseases like soft rot.
• Accurate identification and characterization of bacterial pathogens are crucial for effective disease management strategies in agriculture.
• The genus Pseudomonas includes diverse species, some of which are known plant pathogens, necessitating detailed taxonomic studies.

Purpose of the Study:

• To isolate and characterize novel phytopathogenic bacteria from soft rot lesions of onion plants.
• To determine the taxonomic position of the isolated strains using polyphasic characterization, including genomic and phylogenetic analyses.
• To propose a new species within the genus Pseudomonas if the strains represent a distinct phylogenetic and phenotypic lineage.

Main Methods:

• Isolation and culturing of bacterial strains from infected onion tissues.
• Morphological, biochemical, and physiological characterization of the isolates.
• 16S rRNA gene sequencing, phylogenetic analysis based on the rpoD gene, and whole-genome sequencing for phylogenomic analysis.
• Determination of genomic DNA G+C content and cellular fatty acid composition.
• Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) calculations.

Main Results:

• Six Gram-negative, aerobic, motile, rod-shaped bacterial strains (MAFF 301512–301517) were isolated from onion soft rot lesions.
• 16S rRNA gene sequence analysis indicated affiliation with the genus Pseudomonas, with high similarity to P. poae, P. simiae, P. trivialis, and P. extremorientalis.
• Phylogenetic and phylogenomic analyses placed the strains within the Pseudomonas fluorescens subgroup, forming a distinct clade.
• ANI and dDDH values were below the thresholds for species delineation (<95.70% ANI, <65.4% dDDH) when compared to closely related species.
• The strains exhibited distinct phenotypic characteristics, pathogenicity profiles, and cellular fatty acid compositions differentiating them from known species.

Conclusions:

• The isolated strains represent a novel species within the genus Pseudomonas.
• Based on phenotypic, chemotaxonomic, and genotypic data, the novel species is proposed as Pseudomonas allii sp. nov.
• The type strain for the new species is MAFF 301514T (=ICMP 23680T), with implications for understanding onion bacterial diseases.