Pseudomonas oryzagri sp. nov., isolated from a rice field soil. Issue 10 (18th October 2022)

• Record Type: Journal Article
• Authors: Huq, Md. Amdadul; Lee, Sun-Young; Ma, Juncai; Rahman, M. Mizanur; Rahman, Md. Shahedur; Park, Jong-Hyun; Akter, Shahina
• Is Part Of: International journal of systematic and evolutionary microbiology. Volume 72:Issue 10(2022)
• Publication Date: 2022-10-18
• Subjects: digital DNA–DNA hybridization -- genome sequence -- Pseudomonas oryzagri -- rice field; Microbiology -- Periodicals; Microbiology -- Classification -- Periodicals; 579
• DOI: 10.1099/ijsem.0.005534
• Languages: English
• ISSNs: 1466-5026

Abstract

Abstract : A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAHUQ-58 T, was isolated from soil sample of a rice field. The colonies were observed to be light pink-coloured, smooth, spherical and 0.6–1.0 mm in diameter when grown on nutrient agar (NA) medium for 2 days. Strain MAHUQ-58 T was found to be able to grow at 15–40 °C, at pH 5.5–10.0 and with 0–1.0 % NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, NA, MacConkey agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of Tween 20 and l -tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pseudomonas and to be closely related to Pseudomonas oryzae WM-3 T (98.9 % similarity), Pseudomonas linyingensis LYBRD3-7 T (97.7 %), Pseudomonas sagittaria JCM 18195 T (97.6 %) and Pseudomonas guangdongensis SgZ-6 T (97.2 %). The novel strain MAHUQ-58 T has a draft genome size of 4 536 129 bp (46 contigs), annotated with 4064 protein-coding genes, 60 tRNA genes and four rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-58 T and four closely related type strains were in the range of 85.5–89.5 % and 29.5–38.0 %, respectively. The genomic DNA G+C content was determined to be 67.0 mol%. The predominant isoprenoid quinone was ubiquinone 9. The major fatty acids were identified as C16:0, summed feature 3 (C16 : 1 ω 6 c and/or C16 : 1 ω 7 c ) and summed feature 8 (C18 : 1 ω 6 c and/or C18 : 1 ω 7 c ). On the basis of dDDH and ANI values, genotypic results, and chemotaxonomic and physiological data, strain MAHUQ-58 T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas oryzagri sp. nov. is proposed, with MAHUQ-58 T (=KACC 22005 T =CGMCC 1.18518 T ) as the type strain.