Genomic Analysis, Metabolite Characterization, and Wheat Seedling Growth Promotion of Variovorax Endophyticus sp....

A bacterial strain CY25R-8^T (= CGMCC 1.16908^T = KACC 21250^T) was isolated from the root tissues of wheat. It is aerobic, motile (with a single flagellum), Gram-negative, rod-shaped and yellow, and capable of growing at 10-40 ℃, pH 3.0-10.0 and NaCl 0.0-5.0%; its major fatty acids were C_16:0, C_17:0 cyclo, summed feature 8 and 3; its genomic DNA G + C content was 69.5%. Its respiratory quinone was ubiquinone-8 and major polar lipids were phosphatidylethanolamine, phosphatidylglycerol diphospatidylglycerol and unidentified aminophospholipid. Strain CY25R-8^T exhibited the highest 16S rRNA gene sequence similarity (99.0%-99.6%) with the type strains of several Variovorax species. However, the dDDH and ANI values between strain CY25R-8^T with these type strains were 28.6%-29.5% and 84.65%-86.0%, respectively. These values indicated that strain CY25R-8^T represents a novel species of the genus Variovorax. The name Variovorax endophyticus sp. nov. is proposed. Furthermore, genomic comparisons with uncharacterized isolates and uncultured strains (metagenome-assembled genomes) revealed no close relatives of CY25R-8^T, suggesting this species is novel and potentially aquatic. Through LC-MS, NMR, and MS data, 25 metabolites were identified in strain CY25R-8^T, with cyclo (L-Phe-L-Ser), cyclo (L-Phe-D-4-OH-Pro), H-_DPro-β³-Glu-NH₂ 1-ααβ and pGlu-His-Pro-OH being the major compounds. Notably, strain CY25R-8^T is the first reported natural producer of H-_DPro-β³-Glu-NH₂ 1-ααβ. As an endophyte of wheat, strain CY25R-8^T also demonstrated the ability to enhance wheat seedling growth by promoting main root elongation in vivo. These findings suggest that V. endophyticus CY25R-8^T has potential applications in biotechnology and agriculture.