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Front. Microbiol. | doi: 10.3389/fmicb.2019.00342

Long-term organic farming manipulated rhizospheric microbiome and Bacillus antagonism against Pepper blight (Phytophthora capsici)

huixiu li1, Xiaoxu Cai1, jingyang gong1, Ting Xu1, 2,  Guo-chun Ding2, 3* and Ji Li1, 2
  • 1College of Resources and Environmental Sciences, China Agricultural University, China
  • 2Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, China
  • 3Institute for Epidemiology and Pathogen Diagnostics, China Agricultural University, China

Soil-borne diseases are often less severe in organic farms, possibly because of the recruitment of beneficial microorganisms by crops. Here, the suppressiveness of soils from organic, integrated, and conventional farming systems to pepper blight (Phytophthora capsici) were studied in growth chamber experiments. Disease incidence was 41.3% and 34.1% lower in the treatment with soil from the organic farming system than either from the integrated or conventional farming system, respectively. Beta-diversity of rhizospheric microbial communities differed among treatments, with enrichment of Bacillus, Sporosarcina, Acidobacteria Gp5, Gp6, Gp22, and Ignavibacterium by the organic soil. Cultivation-dependent analysis indicated that 50.3% of in vitro antagonists of P. capsici isolated from the rhizosphere of healthy peppers were affiliated to Bacillus. An integration of in vitro antagonists and metagenomic analysis indicated that Bacillus antagonists were higher in the rhizosphere of pepper treated by the organic soil. A microbial consortium of 18 in vitro Bacillus antagonists significantly increased the suppressiveness of soil from the integrated farming system against pepper blight. Overall, soil microbiome under the long-term organic farming system was more suppressive to pepper blight, possibly due to Bacillus antagonism in the rhizosphere. This study provided insights into microbiome management for disease suppressions under greenhouse conditions.

Keywords: Organic farming, Disease-suppressive soil, soil microbiome, Capsicum annuum L, Phytophthora capsici, rhizosphere, Bacillus

Received: 02 Dec 2018; Accepted: 08 Feb 2019.

Edited by:

Holger Heuer, Julius Kühn-Institut, Germany

Reviewed by:

Qi-Lin Zhang, Kunming University of Science and Technology, China
Kang Qiao, Provincial Key Laboratory of Pesticide Toxicology and Applied Technology, Shandong Agricultural University, China  

Copyright: © 2019 li, Cai, gong, Xu, Ding and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Guo-chun Ding, China Agricultural University, Institute for Epidemiology and Pathogen Diagnostics, Beijing, D38104, China,