Variovorax beijingensis sp. nov., a novel plant-associated bacterial species with plant growth-promoting potential isolated from different geographic regions of Beijing, China

• Published in: Systematic and applied microbiology 2020-11, Vol.43 (6), p.126135-126135, Article 126135
• Main Authors: Gao, Jun-lian, Sun, Yu-chen, Xue, Jing, Sun, Pengbo, Yan, Hui, Khan, Mohammad Sayyar, Wang, Li-wei, Zhang, Xiuhai, Sun, Jian-guang
• Format: Article
• Language: English
• Subjects: Bacterial Typing Techniques; Base Composition; Beijing; Comamonadaceae - classification; Comamonadaceae - isolation & purification; DNA, Bacterial - genetics; Fatty Acids - chemistry; Genes, Bacterial; Genome; Lycopersicon esculentum - microbiology; Nucleic Acid Hybridization; Phospholipids - chemistry; Phylogeny; Plant associated bacteria; Plant growth-promoting potential; Plant Roots - microbiology; Polyphasic approach; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; Ubiquinone - chemistry; Variovorax beijingensis; Zea mays - microbiology
• ISSN: 0723-2020; 1618-0984
• DOI: 10.1016/j.syapm.2020.126135

Two plant-associated bacterial strains were isolated from Beijing, China. The two strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. The average nucleotide identity (ANI) value and the digital DNA-DNA hybridization (dDDH) value between the two strains were 99.4% and 94.7%, respectively, suggesting that they belonged to the same species. The 16S rRNA gene phylogeny analysis indicated that the two strains belonged to the genus Variovorax and were closely related to V. paradoxus NBRC 15149T and V. boronicumulans BAM-48T. Their phylogenetic relationship were confirmed in both phylogenetic trees constructed with house-keeping gene sequences and concatenated core genes of the genome. The ANI and dDDH comparisons among 502T and the most related type strains showed values below the accepted threshold for species discrimination. The genome sizes of strains 502T and T529 were 6.76 and 6.69 Mbp, respectively. The strain 502T had 6,227 predicted genes with DNA G+C content of 67.4 %. The respiratory quinone was ubiquinone-8 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphospatidylglycerol. The major fatty acids of strain 502T were C10: 03-OH (26.2%), C16:0 (12.9%), C17:0 cyclo (14.5%) and summed feature 3 (21.4%). Furthermore, both strains showed the potential of plant growth promotion. Based on these results, the two isolates could be considered to represent a novel species of the genus Variovorax, for which the name Variovorax beijingensis sp. nov., is proposed, with 502T (= DSM 106862T = CGMCC 1.16560T) as the type strain.