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Soil-borne diseases are often less severe in organic farms, possibly because of the recruitment of beneficial microorganisms by crops. Here, the suppressiveness of organic, integrated, and conventionally managed soils to pepper blight ( Phytophthora capsici ) was studied in growth chamber experiments. Disease incidence was 41.3 and 34.1% lower in the soil from an organic farming system than in either the soil from the integrated or from the conventional farming systems, 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 bacterial diversity analyses 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, the soil microbiome under the long-term organic farming system was more suppressive to pepper blight, possibly owing to  Bacillus  antagonism in the rhizosphere. This study provided insights into microbiome management for disease suppression under greenhouse conditions.

Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight (Phytophthora capsici)