Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter

Abstract

A Gram-stain-negative, halotolerant bacterium designated as PTR5(T) was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38 & DEG;C (optimum 30 & DEG;C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5(T) based on 16 S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C-16:0, C-18:1 omega 7c 11-methyl and summed feature 8 (comprising C-18:1 omega 7c/C-18:1 omega 6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5(T) was 3,689,283 bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5(T) and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5(T) was able to produce siderophore and indole acetic acid (IAA) in the presence of l-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5(T), this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5(T) using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5(T) is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5(T) (KCTC 82691(T) = TBRC 15163(T)) is proposed.