Physiological, transcriptomic, and metabolomic analyses reveal that Pantoea sp. YSD J2 inoculation improves the accumulation of flavonoids in Cyperus esculentus L. var. sativus

Plant growth-promoting microorganisms (PGPMs), such as <i>Pantoea</i> sp. YSD J2, promote plant development and stress resistance, while their role in flavonoids accumulation still needs to be further understood. To investigate the complex flavonoid biosynthesis pathway of <i>Cyperus esculentus</i> L. var. sativus (tigernut), we compared <i>Pantoea</i> sp. YSD J2 inoculation (YSD J2) and water inoculation (CK) groups. YSD J2 significantly elevated the content of indole-3-acetic acid (IAA) and orientin. Furthermore, when analyzing flavonoid metabolome, YSD J2 caused increased levels of uralenol, petunidin-3-<i>O</i>-glucoside-5-<i>O</i>-arabinoside, luteolin-7-<i>O</i>-glucuronide-(2 → 1)-glucuronide, kaempferol-3-<i>O</i>-neohesperidoside, cyanidin-3-<i>O</i>-(2″-<i>O</i>-glucosyl)glucoside, kaempferol-3-<i>O</i>-glucuronide-7-<i>O</i>-glucoside, quercetin-3-<i>O</i>-glucoside, luteolin-7-<i>O</i>-glucuronide-(2 → 1)-(2″-sinapoyl)glucuronide, and quercetin-4'-<i>O</i>-glucoside, which further enhanced antioxidant activity. We then performed RNA-seq and LC-MS/MS, aiming to validate key genes and related flavonoid metabolites under YSD J2 inoculation, and rebuild the gene-metabolites regulatory subnetworks. Furthermore, the expression patterns of the trans cinnamate 4-monooxygenase (<i>CYP73A</i>), flavonol-3-<i>O</i>-L-rhamnoside-7-<i>O</i>-glucosyltransferase (<i>UGT73C6</i>), shikimate <i>O</i>-hydroxycinnamoyltransferase (<i>HCT</i>), chalcone isomerase (<i>CHI</i>), flavonol synthase (<i>FLS</i>), and anthocyanidin synthase (<i>ANS</i>) genes were confirmed by qRT-PCR. Additionally, 4 transcription factors (TF) (especially bHLH34, Cluster-37505.3) under YSD J2 inoculation are also engaged in regulating flavonoid accumulation. Moreover, the current work sheds new light on studying the regulatory effect of <i>Pantoea</i> sp. YSD J2 on tigernut development and flavonoid biosynthesis.