Integrated metabolomic and transcriptomic study unveils the gene regulatory mechanisms of sugarcane growth promotion during interaction with an endophytic nitrogen-fixing bacteria

BackgroundSugarcane growth and yield are complex biological processes influenced by endophytic nitrogen-fixing bacteria, for which the molecular mechanisms involved are largely unknown. In this study, integrated metabolomic and RNA-seq were conducted to investigate the interaction between an endophytic bacterial strain, Burkholderia GXS16, and sugarcane tissue culture seedlings.ResultsDuring treatment, the colonization of GXS16 in sugarcane roots were determined, along with the enhanced activities of various antioxidant enzymes. Accordingly, 161, 113, and 37 differentially accumulated metabolites (DAMs) were found in the pairwise comparisons of adjacent stages. In addition, transcriptomic analyses obtained 1,371 (IN-vs-CN), 1,457 (KN-vs-IN), and 365 (LN-vs-KN) differentially expressed genes (DEGs), which were mainly involved in the pathways of glutathione metabolism and carbon metabolism. We then assessed the pattern of metabolite accumulation and gene expression in sugarcane during GXS16 colonization. The results showed that both DAMs and DGEs in the upregulated expression profiles were involved in the flavonoid biosynthesis pathway. Overall, p-coumaroyl-CoA in sugarcane roots transferred into homoeriodictyol chalcone and 5-deoxyleucopelargonidin due to the upregulation of the expression of genes shikimate O-hydroxycinnamoyltransferase (HCT), chalcone synthase (CHS), and phlorizin synthase (PGT1).ConclusionsThis study provides insights into the gene regulatory mechanisms involved in the interaction between GXS16 and sugarcane roots, which will facilitate future applications of endophytic nitrogen-fixing bacteria to promote crop growth.

Automated summary

This study investigated the interaction between endophytic nitrogen-fixing bacteria Burkholderia GXS16 and sugarcane tissue culture seedlings using metabolomic and RNA-seq analyses. The results showed colonization of GXS16 in sugarcane roots and enhanced activities of antioxidant enzymes. Transcriptomic analyses revealed differentially expressed genes involved in glutathione metabolism and carbon metabolism pathways. The study also demonstrated that the interaction between GXS16 and sugarcane roots promoted the synthesis of flavonoids, thus promoting crop growth.