Vogesella oryzagri sp. nov., isolated from the rhizosphere of rice and in silico genome mining for the prediction of biosynthetic gene clusters.

Abstract

A Gram-stain-negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-64^T, was isolated from the rhizosphere of rice. The colonies were observed to be creamy white-coloured, smooth, spherical and 0.5-1.1 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAHUQ-64^T was able to grow at 10-40 °C, at pH 5.0-9.5 and in the presence of 0-2.0% NaCl (w/v). The strain was positive for both catalase and oxidase tests. The strain was positive for hydrolysis of l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Vogesella and is closely related to Vogesella oryzae L3B39^T (98.6% sequence similarity) and Vogesella facilis TTM-24^T (98.2%). The novel strain MAHUQ-64^T has a draft genome size of 3 827 146 bp (22 contigs), annotated with 3612 protein-coding genes, 74 tRNA and 4 rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-64^T and its closest member V. oryzae L3B39^T were 86.5 and 33.4%, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAHUQ-64^T. The genomic DNA G+C content was determined to be 63.4 mol%. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as summed feature 3 (comprising C_{16  :  1} ω7c and/or C_{16  :  1} ω6c) and C_{16  :  0}. Based on dDDH, ANI value, genotypic analysis and chemotaxonomic and physiological data, strain MAHUQ-64^T represents a novel species within the genus Vogesella, for which the name Vogesella oryzagri sp. nov. is proposed, with MAHUQ-64^T (=KACC 22245^T=CGMCC 1.19000^T) as the type strain.