Rhizosphere microbiome structure alters to enable wilt resistance in tomato

Min Jung Kwak; Hyun Gi Kong; Kihyuck Choi; Soon Kyeong Kwon; Ju Yeon Song; Jidam Lee; Pyeong An Lee; Soo Yeon Choi; Minseok Seo; Hyoung Ju Lee; Eun Joo Jung; Hyein Park; Nazish Roy; Heebal Kim; Myeong Min Lee; Edward M. Rubin; Seon Woo Lee; Jihyun F. Kim

doi:10.1038/nbt.4232

Rhizosphere microbiome structure alters to enable wilt resistance in tomato

Min Jung Kwak, Hyun Gi Kong, Kihyuck Choi, Soon Kyeong Kwon, Ju Yeon Song, Jidam Lee, Pyeong An Lee, Soo Yeon Choi, Minseok Seo, Hyoung Ju Lee, Eun Joo Jung, Hyein Park, Nazish Roy, Heebal Kim, Myeong Min Lee, Edward M. Rubin, Seon Woo Lee, Jihyun F. Kim

Research output: Contribution to journal › Article › peer-review

307 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	1100-1116
Number of pages	17
Journal	Nature Biotechnology
Volume	36
Issue number	11
DOIs	https://doi.org/10.1038/nbt.4232
Publication status	Published - 2018 Dec 1

Bibliographical note

Funding Information:
We would like to thank members of the laboratories of J.F.K. and S.-W.L., including B.K. Kim, K.Y. Baek, T.-H. Kang, S. Kim, H.G. Lee, S.Y. Lee, G.J. Son, S. Yoo and H. Yu, as well as KRIBB-KOBIC and NABIC, for technical support, and Y.-S. Bahn, D. Choi, S.-Y. Kwon, I. Lee, W.-J. Lee and H.-S. Pai for helpful comments and suggestions. This study was financially supported by the Strategic Initiative for Microbiomes in Agriculture and Food (914001-4 to J.F.K. and 914006-4 to J.Y.S.), the Cooperative Research Program for Agricultural Science & Technology Development (PJ01093901 to S.-W.L.), the National Research Foundation (NRF-2014M3C9A33068822 and NRF-2011-0017670 to J.F.K.), and the Next-Generation BioGreen 21 Program (PJ008201 to S.-W.L.) of the Republic of Korea. Publication was supported in part by the Brain Korea 21 PLUS program, and M.-J.K., S.-K.K. and J.L. are fellowship awardees of the program.

Publisher Copyright:
© 2018, Nature Publishing Group. All rights reserved.

All Science Journal Classification (ASJC) codes

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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10.1038/nbt.4232

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title = "Rhizosphere microbiome structure alters to enable wilt resistance in tomato",

abstract = "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.",

author = "Kwak, {Min Jung} and Kong, {Hyun Gi} and Kihyuck Choi and Kwon, {Soon Kyeong} and Song, {Ju Yeon} and Jidam Lee and Lee, {Pyeong An} and Choi, {Soo Yeon} and Minseok Seo and Lee, {Hyoung Ju} and Jung, {Eun Joo} and Hyein Park and Nazish Roy and Heebal Kim and Lee, {Myeong Min} and Rubin, {Edward M.} and Lee, {Seon Woo} and Kim, {Jihyun F.}",

note = "Funding Information: We would like to thank members of the laboratories of J.F.K. and S.-W.L., including B.K. Kim, K.Y. Baek, T.-H. Kang, S. Kim, H.G. Lee, S.Y. Lee, G.J. Son, S. Yoo and H. Yu, as well as KRIBB-KOBIC and NABIC, for technical support, and Y.-S. Bahn, D. Choi, S.-Y. Kwon, I. Lee, W.-J. Lee and H.-S. Pai for helpful comments and suggestions. This study was financially supported by the Strategic Initiative for Microbiomes in Agriculture and Food (914001-4 to J.F.K. and 914006-4 to J.Y.S.), the Cooperative Research Program for Agricultural Science & Technology Development (PJ01093901 to S.-W.L.), the National Research Foundation (NRF-2014M3C9A33068822 and NRF-2011-0017670 to J.F.K.), and the Next-Generation BioGreen 21 Program (PJ008201 to S.-W.L.) of the Republic of Korea. Publication was supported in part by the Brain Korea 21 PLUS program, and M.-J.K., S.-K.K. and J.L. are fellowship awardees of the program. Publisher Copyright: {\textcopyright} 2018, Nature Publishing Group. All rights reserved.",

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AU - Kong, Hyun Gi

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AU - Lee, Jidam

AU - Lee, Pyeong An

AU - Choi, Soo Yeon

AU - Seo, Minseok

AU - Lee, Hyoung Ju

AU - Jung, Eun Joo

AU - Park, Hyein

AU - Roy, Nazish

AU - Kim, Heebal

AU - Lee, Myeong Min

AU - Rubin, Edward M.

AU - Lee, Seon Woo

AU - Kim, Jihyun F.

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N2 - 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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Rhizosphere microbiome structure alters to enable wilt resistance in tomato

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

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