Comparison of Bacterial Endophytes in Barley Grains Infected and Non‐Infected With Fusarium Head Blight Using Metabarcoding

Endophytes are organisms that maintain an intimate relationship with the plant host as they are adapted to the niche of internal plant tissues and are mutually beneficial in these interactions. Plant diseases can potentially alter the endophytic community structure, negatively affecting plant development and defence mechanisms. Fusarium head blight (FHB) is a complex and devastating barley disease that could induce such changes. Investigating the structure of the bacterial endophytic community of barley grains with FHB may provide valuable information about the disease development, the resistance of the plant to FHB and the impact of endophytes on pathogen(s) development. We sequenced amplicons of the 16S rRNA gene from barley grains and compared the endophytic bacterial profiles under Fusarium graminearum‐ infected and disease‐free conditions. In addition, we tested microbiome responses to barley genotype (moderately resistant, intermediate or susceptible toward FHB), plant growth stage (mid‐dough stage vs. physiological maturity stage) and year (years 2021 vs. 2022). This study demonstrated significant changes in the overall bacterial endophytic microbiome with FHB and the plant growth stage. Xanthomonas spp. were predominantly detected in the barley grain endosphere. In addition, bacterial amplicon sequence variants (ASVs) significantly associated with FHB‐infected samples (ASV0016; Kosakonia cowanii ), physiological maturity stage (ASV0001; Xanthomonas sp.) and genotypes moderately resistant to FHB (ASV0292; Weeksellaceae chryseobacterium ) were identified. An accumulation of bacterial ASVs was observed over the years. The study's findings may be used to predict conditions that could either induce or control FHB in the host through bacterial microbiome interaction.