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Nat Biotechnol. 2018 Oct 8. doi: 10.1038/nbt.4232. [Epub ahead of print]

Rhizosphere microbiome structure alters to enable wilt resistance in tomato.

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Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea.
Department of Applied Biology, Dong-A University, Busan, Republic of Korea.
C&K Genomics, Seoul, Republic of Korea.
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Department of Energy Joint Genome Institute (DOE JGI) and Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Strategic Initiative for Microbiomes in Agriculture and Food (iMAF), Yonsei University, Seoul, Republic of Korea.


Tomato variety Hawaii 7996 is resistant to the soil-borne pathogen Ralstonia solanacearum, whereas the Moneymaker variety is susceptible to the pathogen. To evaluate whether plant-associated microorganisms have a role in disease resistance, we analyzed the rhizosphere microbiomes of both varieties in a mesocosm experiment. Microbiome structures differed between the two cultivars. Transplantation of rhizosphere microbiota from resistant plants suppressed disease symptoms in susceptible plants. Comparative analyses of rhizosphere metagenomes from resistant and susceptible plants enabled the identification and assembly of a flavobacterial genome that was far more abundant in the resistant plant rhizosphere microbiome than in that of the susceptible plant. We cultivated this flavobacterium, named TRM1, and found that it could suppress R. solanacearum-disease development in a susceptible plant in pot experiments. Our findings reveal a role for native microbiota in protecting plants from microbial pathogens, and our approach charts a path toward the development of probiotics to ameliorate plant diseases.

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