Phyllosphere microbes in foxtail millet primarily affect quality by modulating coloration and bitter compounds

BACKGROUND: Crop quality is influenced by crop-related factors such as varieties and metabolites, as well as by environmental conditions. Recent studies have shown the important role of rhizosphere microbes in determining crop quality and flavor, but the effects of phyllosphere (aboveground) microbes and metabolites remain unclear. Here, we examined the interaction between phyllosphere metabolites and the microbiome in three foxtail millet varieties with differing eating qualities: two high-eating-quality varieties (Yugu1, Jingu21) and one low-eating-quality variety (Daobaqi) in the field. RESULTS: Thirteen metabolites were found to be depleted in the high-eating-quality varieties, four of which were identified as bitter compounds. These depleted metabolites were negatively correlated with the abundance of two microbial genera, Curtobacterium and Pseudomonas, enriched in the high-eating-quality foxtail millet panicles. Further analyses revealed that the abundance of these microbes was significantly associated with reduced bitterness and improved viscosity in the panicles. Additionally, synthetic microbial community experiments validated that these microbes enhanced foxtail millet quality by increasing the yellow coloration and reducing levels of bitter compounds. CONCLUSIONS: In summary, the higher abundance of Curtobacterium and Pseudomonas in the panicles correlated with reduced bitter compounds and enhanced foxtail millet quality. This work provides new insights into the role of phyllosphere metabolites and microbiomes in determining crop quality.