Tobacco root rot, caused by
Fusarium
species, is a persistent soil-borne disease that threatens tobacco production. To identify endophytic contributors to disease suppression, this study compared the root endophytic microbiomes of healthy and diseased tobacco plants using metagenomic sequencing and isolated functional bacteria from healthy roots.
Metagenomic analysis of 30 root samples (223 Gb) generated 2.9 million non-redundant genes and identified 1,953 core genera. Healthy plants contained distinct endophytic microbial communities enriched in bacterial taxa and pathways associated with secondary metabolite biosynthesis, siderophore production, chemotaxis, biofilm formation, and carbohydrate metabolism. This microbiome-guided approach identified TM-1, an endophytic
Enterobacter
strain that significantly inhibited
Fusarium solani
by 62.29% in a dual-culture assay. Transcriptome profiling revealed that TM-1 treatment broadly altered
F. solani
gene expression, with prominent effects on ribosome function, amino acid biosynthesis, carbon metabolism, and glycolysis. TM-1 disrupted sugar transporter-related gene expression, and deletion of five representative genes significantly restricted fungal mycelial growth, with the strongest inhibition (66.47%) observed for the hexose transporter homolog MRS44_010803.
These results indicate that healthy tobacco roots harbor disease-suppressive endophytic microorganisms and suggest that TM-1 may suppress
F. solani
by interfering with sugar transport and carbon acquisition. These findings provide a potential biocontrol resource for the sustainable management of tobacco root rot.
Tian-Miao Li, Xiao-Yu Zhou, Fei Xiong et al.· Frontiers in Microbiology· 0 citations
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.
Can-Hua Lu, Xiaofang Lu, Hou-Fa Zhou et al.· Frontiers in Plant Science· 0 citations
