Proposal to reclassify [Sphingomonas] xenophaga Stolz et al. 2000 and [Sphingomonas] taejonensis Lee et al. 2001 as Sphingobium xenophagum comb. nov. and Sphingopyxis taejonensis comb. nov., respectively

Abstract

The sphingomonad group contains bacterial isolates that are quite diverse in terms of their phylogenetic, ecological and physiological properties. Thus, the genus Sphingomonas was divided into four distinct genera, Sphingomonas sensu stricto, Sphingobium, Novosphingobium and Sphingopyxis on the basis of 16S rRNA gene sequence phylogenetic analysis, signature nucleotides, fatty acid profiles and polyamine patterns and this classification is currently widely accepted. In this study, a complete analysis of the 16S rRNA gene sequences of all the members of the group of sphingomonads encompassed in the genera Sphingomonas sensu stricto, Sphingobium, Novosphingobium and Sphingopyxis was inferred by using tree-making algorithms. [Sphingomonas] xenophaga DSM 6383T was found to form a distinct clade with the members of the genus Sphingobium, whereas [Sphingomonas] taejonensis DSM 15583T forms a clade with the members of the genus Sphingopyxis. The respective positions of these strains were also supported by the data for signature nucleotides, 2-hydroxy fatty acid profiles, polyamine patterns and the nitrate reduction properties of the strains. We therefore propose the reclassification of [Sphingomonas] xenophaga and [Sphingomonas] taejonensis as Sphingobium xenophagum comb. nov. (type strain DSM 6383T=CIP 107206T) and Sphingopyxis taejonensis comb. nov. (type strain DSM 15583T=KCTC 2884T=KCCM 41068T), respectively.

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

“…In this work, we test three of these species, Novosphingobium aromaticivorans DSM 12444 ( 7 , 8 ), Novosphingobium sp. PP1Y ( 9 ), and Sphingobium xenophagum NBRC 107872 ( 10 , 11 ), for the ability to break the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE 2 ; Fig. 1 ) and find that N. aromaticivorans most rapidly and completely metabolizes GGE.…”

Sphingopyxis italica sp. nov., isolated from Roman catacombs

“…The genus Sphingopyxis was proposed by Takeuchi et al (2001) to include the type species Sphingopyxis macrogoltabida and Sphingopyxis terrae , which Takeuchi et al (1993) had previously described as Sphingomonas macrogoltabidus and Sphingomonas terrae . At the time of writing, the genus Sphingopyxis comprises 16 species: Sphingopyxis macrogoltabida (Takeuchi et al , 1993, 2001), Sphingopyxis terrae (Takeuchi et al , 1993, 2001), Sphingopyxis alaskensis (Vancanneyt et al , 2001; Godoy et al , 2003), Sphingopyxis taejonensis (Lee et al , 2001; Pal et al , 2006), Sphingopyxis witflariensis (Kämpfer et al , 2002), Sphingopyxis chilensis (Godoy et al , 2003), Sphingopyxis baekryungensis (Yoon et al , 2005), Sphingopyxis granuli (Kim et al , 2005), Sphingopyxis panaciterrae (Lee et al , 2008a), Sphingopyxis ginsengisoli (Lee et al , 2008b), Sphingopyxis ummariensis (Sharma et al , 2010), Sphingopyxis panaciterrulae (Srinivasan et al , 2010), Sphingopyxis bauzanensis (Zhang et al , 2010), Sphingopyxis soli (Choi et al , 2010), Sphingopyxis rigui (Baik et al , 2013) and Sphingopyxis wooponensis (Bai...…”

Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil

“…At the time of writing, 23 species of the genus Sphingopyxis have been taxonomically classified. The members of this genus have been isolated from a wide range of habitats such as soil (Lee et al , 2008; Srinivasan et al , 2010; Choi et al , 2010), hexachlorocyclohexane (HCH)-contaminated soil (Sharma et al , 2010; Jindal et al , 2013), a sludge blanket (Kim et al , 2005), a wastewater treatment plant (Kämpfer et al , 2002), the river subsurface (Godoy et al , 2003), a mineral water source (Pal et al , 2006), hydrocarbon-contaminated soil (Zhang et al , 2010) and seawater (Yoon & Oh, 2005). Strains belonging to the genus Sphingopyxis are distinctly yellow to brown, Gram-negative, aerobic, non-spore-forming and non-fermenting, with DNA G+C contents in the range 58–69.2 mol% (Takeuchi et al , 2001).…”

“…Further, signature sequences in the 16S rRNA gene sequence of strain R11H T were analysed and observed to share all positions with the pattern characteristic for the genus Sphingomonas sensu stricto (Takeuchi et al , 2001). These nucleotides were G at position 359, T at 593, G : C at 987 : 1218 and T : G at 990 : 1215, based on Escherichia coli numbering (Brosius et al , 1978; Pal et al , 2006). The phylogenetic analysis and signature sequence pattern provided additional support that strain R11H T belongs to the genus Sphingopyxis.…”