Metagenomic profiling of tobacco root endophytes reveals a disease-suppressive Enterobacter strain against Fusarium solani

Abstract

Background 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. Results 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. Conclusion 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.