Fungal communities associated with durum wheat production system: A characterization by growth stage, plant organ and preceding crop

Fungal diversity in soil and durum wheat was studied in relation to durum, oilseed and pulse preceding crops, durum growth stages and plant organs. Fungi isolated from soil and plant samples were classified in 258 operational taxonomical units (OTUs) followed by the PCR amplification and sequencing of the internal transcribed spacer (ITS) rDNA and elongation factor EF-1 alpha gene. Most of the 46 identified fungal species belong to Ascomycota and few isolates to Basidiomycota and Zygomycota phyla. Penicillium, Fusarium and Geomyces spp. were abundant throughout growth stages and plant organs. Seventeen species were potential pathogens on durum wheat and, among them, Fusarium taxa are the most abundant. Other pathogenic taxa recovered belong to Pyrenophora, Alternaria, Nigrospora, Microdochium, Bipolaris, Phaeosphaeria, Arthrinium and Cladosporium taxa. Crop rotation significantly impacted the dominance of two fungal pathogens: Bipolaris sorokiniana (teleomorph: Cochliobolus sativus) was less abundant in durum following a year of pea, whereas Fusarium torulosum was less abundant in durum following canola crops. Principal component analysis combined with persistence index of spatio-temporal species distribution showed that the occurrence of fungi such as Acremonium, Chaetomium, Epicoccum, Kabatiella, Penicillium and Trichoderma were negatively related to the Fusarium and Bipolaris isolates, and therefore, they may be potential antagonists or biocontrol candidates against both pathogens. This study provides a basis for screening beneficial fungal species associated to durum wheat in wheat-based cropping systems of the Canadian Prairies. Assessing the biodiversity is crucial for the development of effective integrated management strategies, including biocontrol agents for the suppression of fungal diseases.

► Fungal antagonists confer benefits to their wheat host.
► Fungal diversity shows dramatic shifts in relation to different crop rotation systems.
► Beneficial fungi are more efficient when different species are combined.
► Improved crop protection strategy relies on fungal assemblage in rotation system.