Root-associated microbial community dynamics in tobacco following topping: implications for nicotine degradation

Agricultural topping is followed by rapid nicotine synthesis in tobacco roots, which may pose environmental risks due to nicotine accumulation in soil. Microbial degradation offers a promising remediation strategy, but the temporal associations between nicotine accumulation and root-associated microbiomes remain unclear. Here, we integrated multi-omics analysis and experimental validation to characterize the post-topping temporal dynamics of tobacco root-associated microbiomes and their potential roles in nicotine degradation. Amplicon sequencing revealed distinct temporal shifts in bacterial communities in bulk soil and rhizosphere (explaining 2.84% of bacterial variance), as well as the fungal community in the root endosphere following topping. Notably, this included enrichment of key nicotine-degrading microorganisms such as Paenarthrobacter , Streptomyces , Arthrobacter , Ensifer , and Nocardioides . Metabolomic profiling showed increased levels of nicotine, its biosynthetic precursor (putrescine), and microbial degradation products (6-hydroxynicotinine and 6-hydroxy-N-methylmyosmine) following topping. Integrated microbiome-metabolome analysis highlighted strong correlations between rhizosphere bacteria and nicotine-related alkaloids, particularly with nicotine-degrading genera such as Paenarthrobacter , Streptomyces , Arthrobacter , Ensifer , and Nocardioides . High-throughput cultivation yielded 221 and 197 nicotine-utilizing bacteria from rhizosphere and root, respectively. Functional validation of five representative strains demonstrated exceptional degradation efficiency, notably in Ensifer sp. A4 and Pseudomonas sp. B11. Given the absence of matched untopped controls in the field sampling scheme, our findings should be interpreted as temporal post-topping associations rather than causal evidence of topping effects. This study provides novel insights into the ecological patterns and temporal dynamics of tobacco root-associated microbiomes following topping, highlighting the potential role of specific microbes in nicotine degradation.