Microbiota in Wheat Roots, Rhizosphere and Soil in Crops Grown in Organic and Other Production Systems

Abstract Culturable microbial communities and diseases were compared in organic, integrated and conventional systems of winter wheat production and monoculture. Particular emphasis was placed on the density and diversity of cereal pathogens and their potential antagonists, and on the association of the active microbial populations with the health and productivity of wheat. In roots, rhizoplane and rhizosphere, fungi tended to be most abundant in the integrated system or monoculture, and bacteria in the organic system. The dominant fungal groups (with individual frequency >5%) included root pathogens ( Fusarium, Gibberella, Haematonectria and Ilyonectria ) and known pathogen antagonists ( Acremonium strictum , Clonostachys, Chaetomium , Gliocladium and Trichoderma spp.). The 50 subdominant species (with individual frequency 1–5%) included the pathogens Alternaria , Cladosporium (leaf spot), Gaeumannomyces graminis (take‐all), Glomerella graminicola (anthracnose), Oculimacula yallundae (eyespot), Phoma spp. (leaf spots), and Pythium and Rhizoctonia (root rot). The 40 subrecedent species (with individual frequency <1%) included minor pathogens ( Botrytis , Coniothyrium, Leptosphaeria ). Antagonists in roots, rhizoplane and rhizosphere were most frequent in the organic system and least frequent in monoculture, suggesting that these systems had the most and least disease‐suppressive habitats, respectively. The other two systems were intermediate, with microbial communities suggesting that the conventional system produced a slightly more suppressive environment than the integrated system. The highest grain yield, in the integrated system, was associated with high abundance of fungi, including fungal pathogens, lowest abundance of Arthrobacter, Pseudomonas and Streptomyces in roots, rhizoplane and soil , and relatively high stem‐base and leaf disease severity. The lowest grain yields, in the organic system and monoculture, were associated with less abundant fungi and more abundant Pseudomonas . There is no clear indication that yields were affected by diseases.