Ramlibacter terrae sp. nov. and Ramlibacter montanisoli sp. nov., Isolated from Soil

Abstract

The genus Ramlibacter, a new genus of the family Comamonadaceae in the class Betaproteobacteria, was first proposed by Heulin et al. with Ramlibacter tataouinensis as the type species, which was isolated from subdesert soil [1]. At the time of writing, the genus comprises 10 validly published species (https://lpsn.dsmz.de/genus/ ramlibacter) isolated primarily from soil habitats, such as subdesert soil [1], ginseng soil [2, 3], forest soil [4-6], and garden soil [7,8]. An exception is Ramlibacter aquaticus LMG 30558 T , which was isolated from a water environment [9]. The genus Ramlibacter includes gram-negative, catalase-positive, oxidase-variable, aerobic, and non-motile (by flagella) rod or coccoid bacteria containing ubiquinone-8 (Q-8) and C 16:0 , cyclo-C 17:0 , and summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c) as the major respiratory quinone and fatty acids, respectively [1][2][3][4][5][6][7][8][9]. The DNA G+C content of Ramlibacter species ranges from 62.0-70.6 mol%. In this study, we isolated two strains, presumably representing novel species of the genus Ramlibacter, from soil samples collected from different areas in South Korea and taxonomically characterized them using a polyphasic approach. Material and Methods Isolation and CultivationStrains H242 T and B156 T were isolated from flatland near a river (37°15′04.2′′N, 128°32′26.3′′E) and mountain (37°15′38.7′′N, 128°36′28.6′′E), respectively, in Gangwon Province of South Korea, according to a previously described procedure [10]. In brief, soil samples were collected in sterile plastic tubes and stored in an icebox for transport. The soil samples were resuspended and serially diluted in phosphate-buffered saline (137 mM NaCl, 2.7 mM KCl, 10 mM Na 2 HPO 4 , 2 mM KH 2 PO 4 , pH 7.2). The serially diluted aliquots (100 μl) were spread on R2A agar (BD, USA), and the agar plates were incubated aerobically at 30 °C for 3 d. The 16S rRNA genes of colonies grown on R2A agar were PCR-amplified using the universal primers F1 (5′-AGA GTT TGA TCM TGG CTC AG-3′) and R13 (5′-TAC GGY TAC CTT GTT ACG ACT T-3′) and double-digested with HaeIII and HhaI. The representative PCR amplicons of 16S rRNA genes showing different fragment patterns were partially sequenced using the universal primer 340F (5′-CCT ACG GGA GGC AGC AG-3′) at Macrogen (Korea). The resulting sequences were compared with all validly reported type strains using the Nucleotide Similarity Search program on Two gram-negative, catalase-positive, strictly aerobic, and white colony-forming bacteria, strains H242 T and B156 T , were isolated from soil in South Korea. Cells of strain H242 T were oxidase-positive and non-motile short rods, while those of strain B156 T were oxidase-negative and long non-motile rods. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. C 16:0 , cyclo-C 17:0 , and summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c) and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were identified in both strains as the major cellular fatty acids an...

Ramlibacter paludis sp. nov., isolated from wetland

“…At the time of this writing, fifteen species had been described, based on the List of Prokaryotic names with Standing in Nomenclature (LPSN): Ramlibacter agri, Ramlibacter algicola, Ramlibacter alkalitolerans, Ramlibacter aquaticus, Ramlibacter ginsenosidimutans, Ramlibacter henchirensis, Ramlibacter humi, Ramlibacter lithotrophicus, Ramlibacter montanisoli, Ramlibacter monticola, Ramlibacter pinisoli, Ramlibacter rhizophilus, Ramlibacter solisilvae, Ramlibacter tataouinensis and Ramlibacter terrae. All of these 15 species were isolated from different soil samples collected in subdesert [2], forest [3–6], rhizosphere [7], ginseng [8, 9], garden [10], agriculture [11], freshwater [12] and water [13]. Members of the genus Ramlibacter are Gram-stain-negative, aerobic, rod-shaped and contain ubiquinone (Q-8) as a major respiratory quinone and a high G+C content of 66.6–69.9 mol%.…”