Pectobacterium nicotianae sp. nov., a novel pathogen causing tobacco hollow stalk disease, is phylogenetically distinct from P. brasiliense

Abstract

Five Gram-negative, facultatively anaerobic bacteria were isolated from the hollow stalk tissues of tobacco plants in Yunnan, China. Based on polyphasic taxonomic data, they were identified as a new Pectobacterium species. Phylogenetic analyses of 16S rRNA and the concatenated dnaX-leuS-recA genes grouped them into a distinct monophyletic clade. Genome analyses showed high average nucleotide identity (ANIb 96.96–97.63%) and digital DNA-DNA hybridization (dDDH 76.2–80.1%) values, supporting their classification as a single species. However, three indices, including lower dDDH (67.9%), borderline ANIb (95.89%), and phylogenomic separation with 99% support, differentiate them from Pectobacterium brasiliense IPO 3540T. Comparative genomics across 24 reference strains revealed differences in virulence factors and specific plant cell wall-degrading enzyme profiles, highlighting adaptations to different hosts. Biochemical tests showed that all isolates lacked β-glucosidase and exhibited unique carbon utilization patterns; chemotaxonomically, strain 21LCBS03T produced only menaquinone MK-8. Pathogenicity experiments confirmed that four strains caused severe soft rot and hypersensitive responses on various hosts, while strain BSHS4, with a dDDH of 76.2% relative to 21LCBS03T, showed reduced virulence—possibly a subspecies. Reanalysis of 633 Pectobacterium genomes from NCBI reclassified 121 strains into this new species, exposed common misidentifications, and identified 9 candidate novel species awaiting phenotypic validation. Combining phylogenomic, virulence, phenotypic, and pathogenic data, we propose Pectobacterium nicotianae sp. nov., with 21LCBS03T (=GDMCC 1.3317T = CCTCC AB2022131T = JCM 35650T) designated as the type strain.