Occurrence and variability of tobacco rhizosphere and phyllosphere bacterial communities associated with nicotine biodegradation

With the aim of learning more about functional bacterial communities in the tobacco rhizosphere and phyllosphere, a total of 96 nicotine-degrading (ND) bacterial strains isolated using nicotine as the sole carbon source—56 from the rhizosphere and 40 from the phyllosphere—were quantified and analyzed phylogenetically. The ND efficiency of 19 phyllosphere strains (47.5 %) and 39 rhizosphere strains (69.6 %) exceeded 90 %. Patterns of phylogenetic relationships based on 16S rRNA gene sequences revealed a high heterogeneity of community composition and suggested the existence of microenvironment-specific communities. The phyllospheric ND bacterial community was distributed over ten genera, of which Pseudomonas spp. was the dominant population. However, the rhizospheric ND bacterial community was composed of six genera, of which Arthrobacter spp. was the major group. This is the first report of members of genera Massilia, Erwinia, Brevundimonas and Paenibacillus capable of degrading nicotine. Diversity indices were calculated provisionally using sequence data obtained from each ND bacterial library. The species richness, diversity and dominance index of the ND bacterial community of the phyllosphere were higher than that of rhizosphere community, while the evenness index of the phyllopheric community was lower compared to rhizospheric ND bacteria. Metabolic intermediate detection showed that the Pseudomonads isolates possessed all four proposed metabolic pathways of nicotine degradation while the Arthrobacter strains all had only one pyridine pathway. These results greatly enhance our knowledge of the diversity of ND bacteria and demonstrate that the tobacco-associated micro-environment contain diverse and novel ND bacteria, which might be a valuable biotechnological resource for biodegradation of nicotine.