Rhizosphere microbiome structure alters to enable wilt resistance in tomato.

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PubMed ID: 30295674

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Kwak MJ, Kong HG, Choi K, Kwon SK, Song JY, Lee J, Lee PA, Choi SY, Seo M, Lee HJ, Jung EJ, Park H, Roy N, Kim H, Lee MM, Rubin EM, Lee SW, Kim JF

Nat Biotechnol. Oct 2018. doi: 10.1038/nbt.4232

COMMENT: In this interesting work, the authors use the tomato plant and bacterial wilt as a model system to examine how the root microbiome contributes to disease resistance.


We used S. lycopersicum var. Hawaii 7996, which is highly resistant to Ralstonia wilt, and Moneymaker, a tomato cultivar that is susceptible to the disease, to investigate the interactions between plant, pathogen and microbiota through comparative analyses of the rhizosphere microbiomes and subsequent functional evaluation of a cultured bacterium for its suppression of tomato wilt.


To complement our 16S data, we carried out shotgun sequencing of rhizosphere samples of Hawaii 7996 and Moneymaker during the growing and flowering stages (...) Among Bacteria, consistent with our amplicon sequencing data, Flavobacteriia was predominant in Hawaii 7996, whereas Bacilli and Betaproteobacteria were abundant in Moneymaker.

Hawaii 7996 plants that were either transplanted into soil that Moneymaker had grown in, or replanted into soil that Hawaii 7996 had grown in, had similar patterns of symptoms over time (...) However, the symptoms progressed more quickly in Hawaii 7996 planted in Moneymaker soil (2 d faster). In contrast, the slope of disease progression was lower and disease severity was reduced 27.7% at day 14 in Moneymaker plants that were transplanted into soil that Hawaii 7996 had grown in compared with Moneymaker plants replanted into soil that Moneymaker had grown in.

Comparing the metagenomes of rhizospheres between the resistant and susceptible varieties, the genome of an uncultured flavobacterium, termed TRM1, was assembled. That genome had a much higher coverage in the microbiome of the var. Hawaii 7996 than that of the var. Moneymaker. 

Cultivation of TRM1 was achieved (…). One of our isolates, TRM1-10, was capable of suppressing disease symptoms of Ralstonia-infected susceptible tomatoes. 


The rhizosphere microbiota may have a probiotic effect functions. Our study further supports assertions that the genetic basis of disease resistance posits the hologenome of the host and its microial counterpart(s) as an important component of plant defense. 


Raquel Ruiz-Arroyo