Plant toxin becomes a food source for microbes

July 27, 2026

Discovery of the role of nicotine produced by tobacco plants in shaping the root microbiome

A research group from Hokkaido University, RIKEN CSRS, and Kyoto University has revealed that toxic compounds produced by plants also contribute to the formation of the root microbiome.
Recent research has shown that the root microbiome plays a critical role in plant growth by alleviating stresses such as diseases and drought, as well as promoting nutrient uptake. Therefore, the mechanisms underlying how plants establish and regulate their root microbiomes have attracted increasing attention.

In this study, the researchers discovered that a specific root-associated bacterium, Arthrobacter, gained a competitive advantage within the root microbiome by degrading and utilizing nicotine, a toxic alkaloid produced by tobacco plants. Furthermore, although nicotine exhibits strong toxicity toward insects, it did not inhibit the growth of many root-associated microorganisms, including Arthrobacter. These findings suggest that nicotine has distinct physiological functions above and below ground, acting as a defense compound against insects in aerial tissues while serving as a nutrient source for certain root-associated microorganisms. Moreover, comparative genomic analyses of Arthrobacter strains isolated from diverse environments revealed that Arthrobacter acquired nicotine-degrading genes through horizontal gene transfer. This finding demonstrates that dynamic genome rearrangements in root-associated bacteria play an important role in interactions with host plants.

These findings are expected to contribute to the development of sustainable agricultural technologies that use plant metabolites to control root microbiome functions and thereby harness the power of microorganisms.

Original article: Microbiome　DOI: 10.1186/s40168-026-02466-x; T. Shimasaki, Y. Nose, S. Masuda, A. Shibata, T. Shoji, S. Yabe, M. Furubayashi, Y. Kikuchi, K. Shirasu, K. Yazaki, Y. Ichihashi, A. Sugiyama, R. T. Nakano,; "Horizontal acquisition of nicotine catabolism gene cluster enhances Arthrobacter fitness within tobacco root microbiota".
Contact: Sachiko Masuda; Research Scientist
Ken Shirasu; Group Director
Plant Immunity Research Group
Yasunori Ichihashi; Team Director
Holobiont and Resilience Research Team