Pedobacter composti sp. nov., isolated from compost

Lee, Hyung-Gwan; Kim, Song-Gun; Im, Wan‐Taek; Oh, Hee‐Mock; Lee, Sung‐Taik

doi:10.1099/ijs.0.003061-0

Cited by 40 publications

(25 citation statements)

References 15 publications

(11 reference statements)

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“…P. saltans strain 113 T was isolated from soil in Iceland; several more strains belonging to the species were isolated from soil in Iceland, Belgium (Brussels) and Germany (Rüdesheim) [1]. Members of the genus Pedobacter were isolated from various environments including different soils [1,6-10], water [11-13], a nitrifying inoculum [14], glaciers [15,16], fish [1] and compost [17]. Here we present a summary classification and a set of features for P. saltans strain 113 T , together with the description of the complete genome sequence and the genome annotation.…”

Section: Introductionmentioning

confidence: 99%

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113T)

Liolios

Sikorski

et al. 2011

Stand. Genomic Sci.

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Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

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Section: Introductionmentioning

confidence: 99%

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113T)

Liolios

Sikorski

et al. 2011

Stand. Genomic Sci.

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“…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).…”

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confidence: 99%

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

Luo

Wang

Dai

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

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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 ...

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“…glacial cryonite (Margesin et al 2003), glacial water (Qui et al 2014), food (Derichs et al 2014) and compost (Lee et al 2009). Currently, there are 45 species of the genus Pedobacter with validly published names (http://www.bacterio.net/pedobacter.html).…”

Section: Introductionmentioning

confidence: 98%

Pedobacter lotistagni sp. nov. isolated from lotus pond water

Singh

Ngo

et al. 2015

Antonie van Leeuwenhoek

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A light-yellow coloured, Gram-stain negative, rod-shaped, aerobic, non-motile bacterium, designated THG-DN6.8(T), was isolated from a lotus pond near Donghaksa temple in Daejeon, South Korea. The strain was found to grow well on nutrient agar, optimally at pH 6.0-7.5, at temperature 25-28 °C and in the presence of 0.5 % NaCl. Based on 16S rRNA gene sequence analysis, strain THG-DN6.8(T) was found to share the highest sequence similarity with Pedobacter koreensis KCTC 12536(T), followed by Pedobacter glacialis CCTCC AB 2012941(T), Pedobacter kyungheensis KACC 16221(T), Pedobacter caeni LMG 22862(T), Pedobacter insulae KCTC 12820(T) and Pedobacter boryungensis KCTC 23344 (T). The DNA G+C content was determined to be 36.8 mol%. In DNA-DNA hybridization tests, the DNA relatedness between strain THG-DN6.8(T) and its closest phylogenetic neighbour P. koreensis was found to be below 10 %. The predominant isoprenoid quinone was identified as menaquinone MK-7 and the major polar lipid as phosphatidylethanolamine. The major fatty acids of strain THG-DN6.8(T) were identified as iso-C15:0, C16:0, C18:0 and C16:1 ω6c and/or C16:1 ω7c (summed feature 3). On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain THG-DN6.8(T) is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter lotistagni sp. nov. is proposed. The type strain is THG-DN6.8(T) (= KCTC 42229(T) = JCM 30354(T)).

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Pedobacter composti sp. nov., isolated from compost

Cited by 40 publications

References 15 publications

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113T)

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113T)

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

Pedobacter lotistagni sp. nov. isolated from lotus pond water

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