Pedobacter terrae sp. nov., isolated from soil

Abstract

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-57 T , was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated using a polyphasic approach. It grew optimally at 25 6C and in trypticase soy broth without NaCl and trypticase soy broth with 0.5 % NaCl. Strain DS-57 T contained MK-7 as the predominant menaquinone and iso-C 15 : 0 , C 16 : 1 v7c and/or iso-C 15 : 0 2-OH and iso-C 17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-57 T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae, clustering coherently with Pedobacter suwonensis, Pedobacter roseus and Pedobacter sandarakinus. Strain DS-57 T exhibited 16S rRNA gene sequence similarity values of 99.2, 97.9 and 97.2 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively, and values less than 95.6 % with respect to the type strains of other Pedobacter species. Strain DS-57 T exhibited levels of DNA-DNA relatedness of 45, 17 and 15 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively. Differential phenotypic properties, together with the phylogenetic distinctiveness and the DNA-DNA relatedness data, were sufficient to allow the classification of strain DS-57 T as a species that is separate from recognized Pedobacter species. On the basis of phenotypic properties and phylogenetic distinctiveness, therefore, strain DS-57 T represents a novel species of the genus Pedobacter, for which the name Pedobacter terrae sp. nov. is proposed. The type strain is DS-57 T (5KCTC 12762 T 5DSM 17933 T ).

Mechanism of the rice hull‐induced germination of Monochoria vaginalis seeds in darkness

“…; Yoon et al . ). Therefore, it is most likely that bacteria‐mediated Monochoria seed germination occurs in the field.…”

“…The germination stimulatory activity of the bacteria tended to be varied, presumably because of their changeable viability ( Table 5). All of these bacteria are Gram-negative and frequently have been isolated from soil, plants and/or airborne dust (Leys et al 2004;Zhang et al 2005;Vilain et al 2006;Cruz et al 2007;Yoon et al 2007). Therefore, it is most likely that bacteria-mediated Monochoria seed germination occurs in the field.…”

Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil

“…The genus Pedobacter was initially described by Steyn et al (1998) and, at the time of writing, included 23 species: Pedobacter heparinus, P. piscium, P. africanus and P. saltans (Steyn et al, 1998), P. cryoconitis (Margesin et al, 2003), P. himalayensis (Shivaji et al, 2005), P. caeni (Vanparys et al, 2005), P. sandarakinus (Yoon et al, 2006), P. roseus (Hwang et al, 2006), P. aquatilis (Gallego et al, 2006), P. ginsengisoli (Ten et al, 2006), P. panaciterrae (Yoon et al, 2007a), P. suwonensis (Kwon et al, 2007), P. insulae (Yoon et al, 2007b), P. lentus and P. terricola (Yoon et al, 2007c), P. koreensis (Baik et al, 2007), P. duraquae, P. westerhofensis, P. metabolipauper, P. hartonius and P. steynii (Muurholm et al, 2007) and P. terrae (Yoon et al, 2007d). All of these species are aerophilic or microaerophilic, Gram-negative rods with MK-7 as the predominant isoprenoid quinone and a DNA G+C content of 36-45 mol% (T m ).…”

Solitalea koreensis gen. nov., sp. nov. and the reclassification of [Flexibacter] canadensis as Solitalea canadensis comb. nov.

“…The Table 1. Differential phenotypic characteristics among Solitalea gen. nov. and related genera of the family Sphingobacteriaceae Taxa: 1, Solitalea gen. nov.; 2, Mucilaginibacter (data from Pankratov et al, 2007); 3, Nubsella zeaxanthinifaciens TDMA-5 T (Asker et al, 2008); 4, Olivibacter (4 species) (Ntougias et al, 2007;Wang et al, 2008); 5, Parapedobacter (2 species) (Kim et al, , 2008; 6, Pedobacter (20 species) (Baik et al, 2007;Hwang et al, 2006;Gallego et al, 2006;Kwon et al, 2007;Muurholm et al, 2007;Shivaji et al, 2005;Steyn et al, 1998;Ten et al, 2006b;Vanparys et al, 2005;Yoon et al, 2006Yoon et al, , 2007a; 7, Sphingobacterium (7 species) (Kim et al, 2006;Shivaji et al, 1992;Steyn et al, 1998;Takeuchi & Yokota, 1992). +, Positive; -, negative; V, variable; ND, no data available.…”

“…Solitalea gen. nov. (Ntougias et al, 2007;Wang et al, 2008); 5, Parapedobacter (2 species) (Kim et al, , 2008; 6, Pedobacter (20 species) (Baik et al, 2007;Hwang et al, 2006;Gallego et al, 2006;Kwon et al, 2007;Muurholm et al, 2007;Shivaji et al, 2005;Steyn et al, 1998;Ten et al, 2006b;Vanparys et al, 2005;Yoon et al, 2006Yoon et al, , 2007a; 7, Sphingobacterium (11 species) (Liu et al, 2008;Mehnaz et al, 2007;Steyn et al, 1998;Ten et al, 2006a;Yoo et al, 2007). Values are percentages of total fatty acids.…”