Fusarium Head Blight is one of the most devastating fungal diseases of cereals worldwide, causing significant yield losses and affecting grain quality. The predominant role of the interactions within the Fusarium communities as well as with members of the phytomicrobiome in disease onset and development has gained increasing attention. Understanding the diversity and dynamics of bacterial and fungal communities across different substrates colonized by Fusarium spp. in wheat fields can provide valuable insights into disease ecology and lead to the discovery of native microorganisms with biocontrol potential. In this study, the bacterial and fungal communities associated with soil, maize residues, and wheat grains, were studied based on metabarcoding sequencing of 16S rRNA and ITS2 regions in six wheat fields over two years and characterized by different levels of FHB disease pressure and mycotoxin contamination. Overall, the diversity and composition of microbial communities were primarily influenced by substrate type followed by geographic origins of fields and sampling time, notably for grains and residues while the soil microbiome was less impacted by environmental fluctuations. Notably, our findings suggest that crop residues function as a transient substrate between soil and wheat microbiomes. In addition, we found several taxa either strongly negatively correlated to Fusarium spp. and/or to levels of Fusarium DNA or mycotoxins in grains or residues, including Cladosporium, Epicoccum, Paenibacillus, Curtobacterium, Pseudomonas, Pantoea, and Sphingomonas, which could be potential antagonistic agents against Fusarium spp. Altogether, these findings provide novel insights into the field microbiome functioning and their complex interactions with the Fusarium communities.
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