Effects of continuous cropping on microbial−metabolite interactions in the rhizosphere soil of tobacco (Nicotiana tabacum) plants

Context Continuous cropping restricts the quality and yield of tobacco (Nicotiana tabacum), yet interactions between microorganisms and metabolites in rhizosphere soil remain poorly understood. Aims To show how continuous cropping duration influences the accumulation of allelopathic substances and shapes rhizosphere microbial communities in tobacco. Methods Rhizosphere soil samples were collected from two tobacco cultivars, Chuxue 80 (CX80) and Chuxue 81 (CX81), under continuous cropping. Metagenomic and metabolomic analyses were used to profile microbial communities and accumulated metabolites. Key results After 4 years of continuous cropping, mycophenolic acid (MPA) in the rhizosphere soil of CX80-4 and CX81-4 increased by 97.1 and 143.1 times, respectively, and 1-(4-nitrophenyl) piperidine increased by 224.8 and 497.4 times, respectively. At the phylum level, Acidobacteriota bacteria showed a marked reduction, declining to 7.6% in CX80-5, whereas that of Pseudomonadota reached a relative abundance of 15.1% in CX81-4. At the genus level, the relative abundances of the functional genera Sphingomonas and Lysobacter increased by 65.9% and 190.8% compared with the control, while the relative abundance of the potential pathogen Escherichia increased by 370.9 times and 135.4 times, respectively. Correlation analysis indicated a significant positive relationship between MPA and the viral pathogen Kochitakasuvirus (r = 0.99, P < 0.01), and a positive correlation between 1-(4-nitrophenyl) piperidine and Leptolyngbya. Conclusions Continuous cropping of tobacco resulted in a substantial accumulation of allelopathic compounds and structural and functional reorganisation of the rhizosphere microbial community. Implications These results suggest that toxic metabolites may promote the proliferation of pathogens by reshaping microbial community structure.