Comparative Transcriptome Profiling of Gaeumannomyces graminis var. tritici in Wheat Roots in the Absence and Presence of Biocontrol Bacillus velezensis CC09

This study aimed to explore potential biocontrol mechanisms involved in the interference of antagonistic bacteria with fungal pathogenicity in planta. To do this, we conducted a comparative transcriptomic analysis of the “take-all” pathogenic fungus Gaeumannomyces graminis var. tritici (Ggt) by examining Ggt-infected wheat roots in the presence or absence of the biocontrol agent Bacillus velezensis CC09 (Bv) compared with Ggt grown on potato dextrose agar (PDA) plates. A total of 4,134 differentially expressed genes (DEGs) were identified in Ggt-infected wheat roots, while 2,011 DEGs were detected in Bv+Ggt-infected roots, relative to the Ggt grown on PDA plates. Moreover, 31 DEGs were identified between wheat roots, respectively infected with Ggt and Bv+Ggt, consisting of 29 downregulated genes coding for potential Ggt pathogenicity factors – e.g., para-nitrobenzyl esterase, cutinase 1 and catalase-3, and two upregulated genes coding for tyrosinase and a hypothetical protein in the Bv+Ggt-infected roots when compared with the Ggt-infected roots. In particular, the expression of one gene, encoding the ABA3 involved in the production of Ggt’s hormone abscisic acid, was 4.11-fold lower in Ggt-infected roots with Bv than without Bv. This is the first experimental study to analyze the activity of Ggt transcriptomes in wheat roots exposed or not to a biocontrol bacterium. Our results therefore suggest the presence of Bv directly and/or indirectly impairs the pathogenicity of Ggt in wheat roots through complex regulatory mechanisms, such as hyphopodia formation, cell wall hydrolase, and expression of a papain inhibitor, among others, all which merit further investigation.