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Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi – 110007, India
Correspondence
Rup Lal
duzdel{at}vsnl.com
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ABSTRACT |
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and defined as a group of Gram-negative, rod-shaped, chemoheterotrophic, strictly aerobic bacteria that possess ubiquinone 10 as the major respiratory quinone, contain glycosphingolipids in their cell envelopes and typically produce yellow-pigmented colonies. The genus is a dynamic group of bacterial isolates with respect to taxonomy and phylogeny, metabolic diversity and the ability to produce extracellular gellan-like polysaccharides (sphingans). Although members of the genus Sphingomonas have created much interest for biotechnological applications in the fields of novel catalysts, bioremediation, fossil fuel desulfurization, novel enzymes and biotin and polysaccharide production (Sutherland, 1999), reorganization of the genus Sphingomonas has also long been a subject of discussion for many taxonomists (Takeuchi et al., 2001; Yabuuchi et al., 2002). Many Gram-negative organisms previously classified as members of the genera Beijerinckia (Khan et al., 1996), Flavobacterium (Yabuuchi et al., 1990) and Pseudomonas (Yrjala et al., 1998), and even Gram-positive organisms from the genus Arthrobacter, have been reclassified as members of the genus Sphingomonas. As a result, the number of species represented by the genus Sphingomonas has increased and this has created quite a diverse group of sphingomonads as far as their ecological, physiological and phylogenetic properties are concerned. Thus, a re-evaluation of the species belonging to the genus Sphingomonas was carried out by Takeuchi et al. (2001). On the basis of phylogenetic analysis, polyamine patterns, fatty acid profiling and nucleotide signature sequences, the genus Sphingomonas was subdivided into four separate genera: Sphingomonas sensu stricto, Sphingobium, Novosphingobium and Sphingopyxis. By and large, this scheme of classification of sphingomonads has been accepted and is in operation (Pal et al., 2005). Currently, the genera Sphingomonas sensu stricto, Sphingobium, Novosphingobium and Sphingopyxis respectively contain 31, 8, 11 and 7 species with validly published names. However, there are still some discrepancies and a few sphingomonads have not yet been re-evaluated in the light of the classification proposed by Takeuchi et al. (2001) and are still represented in literature by the genus Sphingomonas (Stolz et al., 2000; Fujii et al., 2001; Lee et al., 2001; Yabuuchi et al., 2002). These discrepancies are largely due to the fact that at the time the four new genera were created from the genus Sphingomonas, some of the papers that had already been submitted for publication were not available to Takeuchi et al. (2001).
In this paper, we analyse the current status of species of the genus Sphingomonas with validly published names on the basis of the information available in the literature on 16S rRNA gene sequences, fatty acid profiling, 16S rRNA signature nucleotides and polyamine patterns. On the basis of our findings, we propose 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, according to the scheme of Takeuchi et al. (2001). The reclassification of Sphingomonas cloacae (Fujii et al., 2001) has already been taken up by O. Prakash & R. Lal (unpublished). The reclassification of ‘Sphingomonas agrestis’ has not been undertaken as it is not a species with a validly published name. The taxonomic positioning of the species Sphingomonas ursincola (synonym Blastomonas ursincola; Hiraishi et al., 2000) and Sphingomonas suberifaciens (Yabuuchi et al., 1999) has been debated in the past. These two species have been reported to show some characteristics of the sphingomonads, such as ubiquinone 10, the presence of spermidine and glycosphingolipids (Yabuuchi et al., 2002); however, phylogenetic analysis reveals that the two species do not fall in any cluster of the four sphingomonad genera and form distinct sublines (Fig. 1).
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) and [Sphingomonas] taejonensis DSM 15583T (1443 nt) (Lee et al., 2001), as well as the sequence of Rhodanobacter lindaniclasticus RP 5557T (Nalin et al., 1999), were retrieved from the GenBank database at NCBI (http://www.ncbi.nlm.nih.gov/). The 16S rRNA gene sequences of [Sphingomonas] xenophaga DSM 6383T and [Sphingomonas] taejonensis DSM 15583T were aligned with the 16S rRNA gene sequences of representative sphingomonads that encompass the four distinct sphingomonad genera by using CLUSTAL_X (version 1.8b; Thompson et al., 1997). Gaps at the 5' and 3' ends of the alignment were omitted from further analysis. Evolutionary distance matrices were calculated using the method of Jukes & Cantor (1969) with the DNADIST program within the PHYLIP package (Felsenstein, 1993). A phylogenetic tree was constructed by using the neighbour-joining method (Saitou & Nei, 1987). The stability of the relationships was assessed by bootstrap analysis of 1000 datasets with SEQBOOT and CONSENSE programs in the PHYLIP package (Fig. 1
). An identical phylogenetic tree was obtained by the maximum-parsimony method (data not shown). On the basis of the 16S rRNA gene sequence analysis, strains [Sphingomonas] xenophaga DSM 6383T and [Sphingomonas] taejonensis DSM 15583T formed distinct clades within the evolutionary radiations of the genera Sphingobium and Sphingopyxis, respectively, and the positions were supported by high levels of bootstrap confidence. The 16S rRNA gene sequence placed [Sphingomonas] xenophaga DSM 6383T in the neighbourhood of Sphingobium yanoikuyae GIFU 9882T (Yabuuchi et al., 1990). The highest 16S rRNA gene sequence similarities, of 96·5 and 94·8 %, were found between [Sphingomonas] xenophaga DSM 6383T and Sphingobium amiense JCM 11777T (Ushiba et al., 2003) and Sphingobium chungbukense KCTC 2955T (Kim et al., 2000; Pal et al., 2005), respectively. In the case of [Sphingomonas] taejonensis DSM 15583T (Lee et al., 2001), the highest gene sequence similarities, of 98·7 and 98·2 %, were with Sphingopyxis chilensis DSM 14889T (Godoy et al., 2003) and Sphingopyxis alaskensis DSM 13593T (Vancanneyt et al., 2001), respectively. Additionally, the 16S rRNA gene sequences of [Sphingomonas] xenophaga DSM 6383T (Stolz et al., 2000) and [Sphingomonas] taejonensis DSM 15583T (Lee et al., 2001) contained the signature nucleotides specific for the genera Sphingobium cluster II and Sphingopyxis cluster IV (Takeuchi et al., 2001), respectively, confirming that the strains should be reclassified in the genera Sphingobium and Sphingopyxis, respectively.
The chemical properties of strains [Sphingomonas] xenophaga DSM 6383T (Stolz et al., 2000) and [Sphingomonas] taejonensis DSM 15583T (Lee et al., 2001), nitrate reduction, polyamine pattern and fatty acid profiling, also indicate that the strains show a strong associations with members of the genera Sphingobium and Sphingopyxis, respectively. [Sphingomonas] xenophaga DSM 6383T has been reported to contain 2-hydroxymyristic acid (2-OH 14 : 0) as the dominant hydroxylated fatty acid (Stolz et al., 2000), whereas [Sphingomonas] taejonensis DSM 15583T contains 2-OH 14 : 0, 2-OH 15 : 0 and 2-OH 16 : 0 (Lee et al., 2001). These fatty acids are characteristic for the genera Sphingobium and Sphingopyxis, respectively. For [Sphingomonas] xenophaga DSM 6383T, the major polyamine has been reported to be spermidine (Stolz et al., 2000). This clearly distinguishes [Sphingomonas] xenophaga DSM 6383T from members of the genus Sphingomonas sensu stricto, as they contain homospermidine as the major polyamine (Takeuchi et al., 2001). Both [Sphingomonas] xenophaga DSM 6383T and [Sphingomonas] taejonensis DSM 15583T are negative for nitrate reduction, a characteristic of the genera Sphingobium and Sphingopyxis, unlike the genera Sphingomonas and Novosphingobium, in which members are positive for nitrate reduction. This further confirms the taxonomic positions of the two species as determined by 16S rRNA gene sequence analysis. The G+C contents of DNA for [Sphingomonas] xenophaga DSM 6383T and [Sphingomonas] taejonensis DSM 15583T were reported to be 62·1±0·2 mol% (Stolz et al., 2000) and 63 mol% (Lee et al., 2001), respectively. There are differences in some phenotypic properties between strains [Sphingomonas] xenophaga DSM 6383T and [Sphingomonas] taejonensis DSM 15583T with respect to other members of the genera Sphingobium and Sphingopyxis, respectively, and a comparative account of some of these characteristics is given in Table 1. Based on these data, we propose 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.
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) comb. nov.. Sphingobium xenophagum [xe.no'pha.gum. Gr. adj. xenos foreign; Gr. v. phagein to eat; N.L. neut. n. xenophagum eater of foreign (xenobiotic) compounds].
The description is identical to the description given for Sphingomonas xenophaga by Stolz et al. (2000). The type strain is BN6T (=DSM 6383T=CIP 107206T).
Description of Sphingopyxis taejonensis (Lee et al. 2001) comb. nov.
Basonym: Sphingomonas taejonensis Lee et al. 2001.
Sphingopyxis taejonensis (tae.jon.en'sis. N.L. fem. adj. taejonensis referring to Taejon, Korea, the geographical origin of the type strain).
The description is identical to the description given for Sphingomonas taejonensis by Lee et al. (2001). The type strain is JSS54T (=DSM 15583T=KCTC 2884T=KCCM 41068T).
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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