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ISME J. 2016 Jan;10(1):119-29. doi: 10.1038/ismej.2015.95. Epub 2015 Jun 9.

Microbial and biochemical basis of a Fusarium wilt-suppressive soil.

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IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea.
Bioinformatics Tech Lab, SK Telecom, Sungnam, Republic of Korea.
Department of Biochemistry, University of Cambridge, Cambridge, UK.
RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea.
Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea.
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA.


Crops lack genetic resistance to most necrotrophic pathogens. To compensate for this disadvantage, plants recruit antagonistic members of the soil microbiome to defend their roots against pathogens and other pests. The best examples of this microbially based defense of roots are observed in disease-suppressive soils in which suppressiveness is induced by continuously growing crops that are susceptible to a pathogen, but the molecular basis of most is poorly understood. Here we report the microbial characterization of a Korean soil with specific suppressiveness to Fusarium wilt of strawberry. In this soil, an attack on strawberry roots by Fusarium oxysporum results in a response by microbial defenders, of which members of the Actinobacteria appear to have a key role. We also identify Streptomyces genes responsible for the ribosomal synthesis of a novel heat-stable antifungal thiopeptide antibiotic inhibitory to F. oxysporum and the antibiotic's mode of action against fungal cell wall biosynthesis. Both classical- and community-oriented approaches were required to dissect this suppressive soil from the field to the molecular level, and the results highlight the role of natural antibiotics as weapons in the microbial warfare in the rhizosphere that is integral to plant health, vigor and development.

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