Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity

Abstract

Materials and Methods Isolation and CultivationThe novel strain CYS-02 T was isolated from soil located at Suwon, Gyeonggi-do, Republic of Korea (37º15'37'' N and 126º56'17.2'' E). A modified culture method by 6-well Transwell plates (Corning, USA) was used for isolation. The Transwell plates were incubated in a shaker at 120 ×g for 4 weeks at 28 o C. After 4 weeks, the culture was serially diluted, and 100 μl of each dilution was spread onto R2A agar plates. Colonies were individually restreaked on R2A agar plates until pure colonies were obtained. For long-term preservation, cultures were stored as suspensions in R2A broth supplemented with 20% (v/v) glycerol at -70°C. Isolation, maintenance, and preservation of strain CYS-02 T were performed following the methodology described by Dahal RH et al. [14]. A white-pigmented, non-motile, gram-negative, and rod-shaped bacterium, designated CYS-02 T , was isolated from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 20-28ºC and hydrolyzed Tween 40. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CYS-02 T formed a lineage within the family Comamonadaceae and clustered as members of the genus Variovorax. The closest members were Variovorax guangxiensis DSM 27352 T (98.6% sequence similarity), Variovorax paradoxus NBRC 15149 T (98.5%), and Variovorax gossypii JM-310 T (98.3%). The principal respiratory quinone was Q-8 and the major polar lipids contain phosphatidylethanolamine (PE), phosphatidylethanolamine (PG), and diphosphatidylglycerol (DPG). The predominant cellular fatty acids were C 16:0 , summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c) and summed feature 8 (C 18:1 ω7c and/or C 18:1 ω6c). The DNA GC content was 67.7 mol%. The ANI and dDDH values between strain CYS-02 T and the closest members in the genus Variovorax were ≤ 79.0 and 22.4%, respectively, and the AAI and POCP values between CYS-02 T and the other related species in the family Comamonadaceae were > 70% and > 50%, respectively. The genome of strain CYS-02 T showed a putative terpene biosynthetic cluster responsible for antioxidant activity which was supported by DPPH radical scavenging activity test. Based on genomic, phenotypic and chemotaxonomic analyses, strain CYS-02 T was classified into a novel species in the genus Variovorax, for which the name Variovorax terrae sp. nov., has been proposed. The type strain is CYS-02 T (= KACC 22656 T = NBRC 00115645 T ).

On requests for validation of names published in electronic material that does not provide a permanent record

“…The description of Variovorax terrae sp. nov. in the Journal of Microbiology and Biotechnology [5] contained an error in one of the culture collection accession numbers of the proposed type strain. Instead of reprinting the correct version of the protologue in a corrigendum, the online version of the paper was modified.…”