Pedobacter glucosidilyticus sp. nov., isolated from dry riverbed soil

Abstract

Two Gram-staining-negative, rod-shaped, non-spore-forming bacterial strains, 1-2 T and 1-4 were isolated from dry riverbed soil collected from the Xietongmen area of Tibet, China. On the basis of 16S rRNA gene sequence similarity, the novel strains were shown to belong to the genus Pedobacter, sharing ,95 % sequence similarity with all recognized species of the genus Pedobacter. The major respiratory quinone was MK-7 and the predominant cellular fatty acids were iso-C15 : 0, iso-C 17 : 0 3-OH and summed feature 3 (comprising iso-C 16 : 1 v7c and/or C 16 : 1 v6c). The DNA G+C contents were 37.2-37.6 mol%. Chemotaxonomic data supported the affiliation of the two new isolates to the genus Pedobacter and the results of physiological and biochemical tests confirmed that the new strains differed significantly from the recognized species of the genus Pedobacter. Therefore, the new isolates represent a novel species within the genus Pedobacter, for which the name Pedobacter glucosidilyticus sp. nov. is proposed. The type strain is 1-2 T (5CCTCC AB 206110 T 5KCTC 22438 T ).At the time the family Sphingobacteriaceae and the genus Pedobacter were proposed by Steyn et al. (1998), the genus comprised only four recognized species: Pedobacter heparinus, Pedobacter piscium, Pedobacter africanus and Pedobacter saltans. Many novel species have been recovered from various environments and, at the time of writing, the genus Pedobacter contained 26 recognized species (Steyn et al., 1998;Margesin et al., 2003;Shivaji et al., 2005;Vanparys et al., 2005;Gallego et al., 2006;Hwang et al., 2006; Ten et al., 2006;Baik et al., 2007; Kwon et al., 2007;Muurholm et al., 2007;Yoon et al., 2006Yoon et al., , 2007aAn et al., 2009;Roh et al., 2008;Lee et al., 2009). The description of the genus Pedobacter has also been emended recently (Vanparys et al., 2005;Gallego et al., 2006;Hwang et al., 2006).In the course of a study of the cultivable microbial community of Tibet, China, a soil sample was collected from a dry riverbed in the Xietongmen area and used as a source for the isolation of bacterial strains. Over 50 colonies were isolated by means of the standard dilution plating technique at 28 u C on plates of 10-fold diluted tryptic soy agar (TSA, Difco). All strains were preserved as lyophilized cultures. Two cream to pink coloured, raised, translucent and slimy colonies developed on the plates inoculated with the terminal dilutions of the soil suspension. They were picked up and purified and were designated strains 1-2 T and 1-4. The strains were routinely grown on 0.16TSA at 28 u C. Bacterial cells were observed by light and phase-contrast microscopy (BX51; Olympus) to ascertain their morphology. Gliding motility was assessed as described previously (Bowman, 2000). Cells were Gram-staining-negative, non-motile rods that occurred singly or in chains (see Supplementary Fig. S1 available at IJSEM online).The genomic DNA of strains 1-2 T and 1-4 was isolated using a bacteria genomic kit (CASarray Co., Ltd). The fragments comprising the 16S rRNA ...

Pedobacter bauzanensis sp. nov., isolated from soil

“…Phenotypic characteristics that differentiate strain BZ42 T from its closest phylogenetic neighbours and the type strain of the type species of the genus Pedobacter Strains: 1, Pedobacter bauzanensis sp. nov. BZ42 T ; 2, P. daechungensis Dae 13 T (data from An et al, 2009); 3, P. lentus DS-40 T (Yoon et al, 2007); 4, P. terricola DS-45 T (Yoon et al, 2007); 5, P. glucosidilyticus KCTC 22438 T (Luo et al, 2010); 6, P. heparinus DSM 2366 T (data from this study and Steyn et al, 1998;Takeuchi & Yokota, 1992;Yoon et al, 2007). All strains were positive for aerobic growth, aesculin hydrolysis, activities of catalase, oxidase, alkaline phosphatase and esterase lipase (C8) and assimilation of D-mannose and maltose.…”

Pedobacter lotistagni sp. nov. isolated from lotus pond water

“…Mostly Pedobacter species have been reported from soils (Yoon et al 2007;Luo et al 2010;Zhou et al 2012;Oh et al 2013). Members of this genus are ubiquitous in nature and some species have been reported from various environments such as a waterfall (Chung et al 2014), Hina Singh and Juan Du have contributed equally to this work.…”

Pedobacter pituitosus sp. nov., isolated from a waterfall

“…T (Urios et al, 2013;93.4 %) and Pedobacter glucosidilyticus 1-2 T (Luo et al, 2010;93.4 %). The phylogenetic tree reconstructed by the neighbour-joining method ( Fig.…”