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1 School of Biological Sciences and Institute of Microbiology, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
2 Institute of Molecular Biology and Genetics, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
Correspondence
Jongsik Chun
jchun{at}snu.ac.kr
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ABSTRACT |
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-hydroxybutyrateThe polar lipid compositions of the type strains of Ruegeria atlantica, Silicibacter lacuscaerulensis and Silicibacter pomeroyi are shown in a supplementary figure in IJSEM Online.
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MAIN TEXT |
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TOPABSTRACTMAIN TEXTREFERENCES |
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to accommodate three species previously assigned as Agrobacterium atlanticus (Rüger & Höfle, 1992), Agrobacterium gelatinovorum (Rüger & Höfle, 1992) and Roseobacter algicola (Lafay et al., 1995). Recently, Ruegeria gelatinovorans and Ruegeria algicola were transferred to other genera as Thalassobius gelatinovorus (Arahal et al., 2005) and Marinovum algicola (Martens et al., 2006), respectively. Therefore, at present Ruegeria atlantica is the type and only species of the genus Ruegeria. The genus Silicibacter, with the type species Silicibacter lacuscaerulensis, was created by Petursdottir & Kristjansson (1997) to describe mesophilic, moderately halophilic alphaproteobacteria isolated from the Blue Lagoon geothermal lake in Iceland. An additional Silicibacter species, Silicibacter pomeroyi, was subsequently described by González et al. (2003).
However, several subsequent taxonomic studies (González et al., 2003; Macián et al., 2005; Martínez-Cánovas et al., 2004; Yi & Chun, 2004) have demonstrated that the genera Ruegeria and Silicibacter show a close phylogenetic relationship in which members of both genera have always formed a monophyletic clade. In this study, we present a critical taxonomic evaluation of the members of the two genera and propose the combination of the genus Silicibacter with the genus Ruegeria, since Ruegeria has nomenclatural priority.
R. atlantica KCTC 12017T, S. lacuscaerulensis DSM 11314T and S. pomeroyi DSM 15171T were obtained from the respective culture collections and maintained on marine agar 2216 (MA; Difco).
Phylogenetic analysis was carried out using the previously published 16S rRNA gene sequences (Fig. 1). The sequences were aligned manually based on bacterial 16S rRNA secondary structure using the jPHYDIT program (Jeon et al., 2005). The regions available for all sequences (positions 52–1437; Escherichia coli numbering system), excluding positions likely to show ambiguous alignment (positions 62–88 and 994–1026), were used to generate phylogenetic trees. Evolutionary distance matrices for the neighbour-joining (Saitou & Nei, 1987) tree were generated according to the model of Jukes & Cantor (1969). Maximum-likelihood (Felsenstein, 1981) and maximum-parsimony (Fitch, 1971) trees were created using the PAUP* 4.0b10 program with the heuristic search algorithm (Swofford, 2002). The confidence levels of the branching points were determined by 1000 bootstrap replicates for the neighbour-joining tree (Felsenstein, 1985). The members of the genera Ruegeria and Silicibacter formed a monophyletic clade with 98 % bootstrap support and were readily differentiated from other genera in the suprageneric Roseobacter-clade (Fig. 1). The pairwise sequence similarity values within this clade ranged from 96.9 to 98.2 % (Table 1), which are typical for species that are members of the same genus.
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following the modification of Yi & Chun (2006). The DNA–DNA relatedness values among the test strains were all below 70 % (Table 1
), which confirms that these taxa merit their separate species status (Wayne et al., 1987).
The temperature range for growth (between 5 °C and 55 °C, with intervals of 5 °C) was determined on MA. A requirement for sea salts or NaCl was determined using modified ZoBell medium [ZoBell, 1941; 5 g Bacto peptone (Difco); 1 g yeast extract (Difco); 0.1 g ferric citrate; 1 l distilled water] containing 3.24 g MgSO4 l–1. Growth under anaerobic conditions was determined in an anaerobic chamber (10 % CO2, 10 % H2, 80 % N2; Sheldon Manufacturing). Standard physiological and biochemical tests were performed as described previously (Smibert & Krieg, 1994). R. atlantica was grown on MA at 25 °C, S. lacuscaerulensis at 35 °C and S. pomeroyi at 30 °C, respectively. Hydrolysis of high molecular mass compounds was tested using MA as the basal medium. Poly--hydroxybutyrate (PHB) accumulation was investigated by using Nile blue A staining. Other enzymic activities were determined using API 20NE and API ZYM kits (bioMérieux). Strips were inoculated with a heavy bacterial suspension in half-strength artificial seawater (Sigma). The biochemical and physiological properties are given in the species descriptions and Table 2.
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. Thalassobacter stenotrophicus LMG 22015, Roseobacter denitrificans NBRC 15277T and Staleya guttiformis LMG 19755T were used as positive controls according to Yi & Chun (2004). Marinovum algicola NBRC 16653T, Octadecabacter antarcticus CIP 106731T and Thalassobius gelatinovorus NBRC 15761T were used as negative controls. As pufLM genes were not amplified from species of the genera Ruegeria or Silicibacter, this implies the absence of aerobic anoxygenic photosynthesis in these strains.
Fatty acid methyl esters were prepared from biomass scraped from MA after 3 days of incubation and analysed by GC according to the instructions for the Microbial Identification System (MIDI). The predominant cellular fatty acids in the test strains were C18 : 1
7c and C18 : 111 methyl 7c, although R. atlantica contained a smaller amount of C18 : 17c (Table 3). Phospholipids were extracted, purified and identified as described by Minnikin et al. (1984). The polar lipid compositions of the three type strains were very similar, as shown in Supplementary Fig. S1 (available in IJSEM Online). All of the Ruegeria and Silicibacter strains contained phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and three or four unidentified phospholipids.
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). The genus name Silicibacter was effectively published in 1997 (Petursdottir & Kristjansson, 1997) and Ruegeria in 1998 (Uchino et al., 1998). However, the name Ruegeria has nomenclatural priority over Silicibacter as it was validly published in Validation List No. 68 (Uchino et al., 1999) whereas Silicibacter appeared in Validation List No. 71 (Petursdottir & Kristjansson, 1999). On the basis of polyphasic evidence presented in this and earlier studies, we propose that Silicibacter lacuscaerulensis and Silicibacter pomeroyi be transferred to the genus Ruegeria as Ruegeria lacuscaerulensis comb. nov. and Ruegeria pomeroyi comb. nov., respectively.
Emended description of the genus Ruegeria
Ruegeria (Rue.ge'ria. N.L. fem. n. Ruegeria honouring Rueger, a German microbiologist, for his contribution to the taxonomy of marine species of Agrobacterium).
Gram-negative, oxidase- and catalase-positive. Ovoid or rod-shaped cells are motile by a polar flagellum or non-motile. Colonies are convex, opaque, butyrous, circular with entire margins and beige-coloured on MA after 2–3 days. Spores are not formed. Accumulate PHB. Require sea salts for growth. Strict aerobes. Genetic potential for aerobic anoxygenic photosynthesis is not detected. Bacteriochlorophyll a is absent. Major isoprenoid quinone is ubiquinone 10. Predominant cellular fatty acids are C18 : 17c and C18 : 1 11 methyl 7c. The polar lipids are phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and three or four unidentified phospholipids. DNA G+C content is 55–68 mol%. The type species is Ruegeria atlantica.
Emended description of Ruegeria atlantica
Ruegeria atlantica (at.lan'ti.ca. L. fem. adj. atlantica pertaining to the Atlantic Ocean as the locality).
The description remains that given by Uchino et al. (1998) with the following modifications and additions. Reduces nitrate to nitrogen and requires sea salts for growth. Growth occurs at 10–35 °C (optimum, 25–30 °C). Decomposes aesculin, L-tyrosine, xanthine and hypoxanthine, but not casein, carboxymethylcellulose, gelatin, starch or Tween 80. Positive reaction for -galactosidase (API 20NE) and negative reactions for arginine dihydrolase and urease. Does not produce acid from glucose or indole from tryptophan. With API ZYM kits, alkaline phosphatase and leucine arylamidase are positive, valine arylamidase and 
-glucosidase are weakly positive and esterase (C4) and esterase lipase (C8), lipase (C14), cystine arylamidase, trypsin, -chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, -galactosidase, -galactosidase, -glucuronidase, -glucosidase, N-acetyl--glucosaminidase, -mannosidase and -fucosidase are negative. The cellular fatty acid content is shown in Table 3.
The type strain is 1480T (=IAM 14463T=DSM 5823T).
Description of Ruegeria lacuscaerulensis comb. nov.
Ruegeria lacuscaerulensis (la.cus.cae.ru.len'sis. L. masc. n. lacus lake; L. adj. caeruleus blue; N.L. fem. adj. lacuscaerulensis pertaining to the blue lake).
Basonym: Silicibacter lacuscaerulensis Petursdottir and Kristjansson 1999.
The description is as given by Petursdottir & Kristjansson (1997) with the following modifications and additions. Reduces nitrate to nitrogen. Does not grow on media supplemented with NaCl only and requires sea salts for growth. Growth occurs at 10–45 °C (optimum, 35–40 °C). Decomposes aesculin, L-tyrosine, Tween 80, xanthine and hypoxanthine, but not carboxymethylcellulose or gelatin. Positive reaction for -galactosidase (API 20NE) and negative reactions for arginine dihydrolase and urease. Does not produce acid from glucose or indole from tryptophan. With API ZYM kits, alkaline phosphatase, leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and -glucosidase are positive, esterase (C4), esterase lipase (C8), valine arylamidase and -galactosidase are weakly positive and lipase (C14), cystine arylamidase, trypsin, -chymotrypsin, -galactosidase, -glucuronidase, -glucosidase, N-acetyl--glucosaminidase, -mannosidase and -fucosidase are negative. The cellular fatty acid content is shown in Table 3.
The type strain is ITI-1157T (=DSM 11314T=KCTC 2953T).
Description of Ruegeria pomeroyi comb. nov.
Ruegeria pomeroyi (po.me.roy'i. N.L. masc. gen. n. pomeroyi of Pomeroy, named after Lawrence R. Pomeroy, a marine microbial ecologist who first elucidated the role of bacteria in the marine food web).
Basonym: Silicibacter pomeroyi González et al. 2003.
The description remains that given by González et al. (2003) with the following modifications and additions. Does not grow on media supplemented with NaCl only, requires sea salts for growth and hydrolyses Tween 80. Decomposes L-tyrosine, xanthine and hypoxanthine, but not casein or aesculin. Negative reactions for -galactosidase, arginine dihydrolase and urease. Does not produce acid from glucose or indole from tryptophan. Alkaline phosphatase and leucine arylamidase are positive; esterase lipase (C8) is weakly positive; esterase (C4), lipase (C14), valine arylamidase, cystine arylamidase, trypsin, -chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, -galactosidase, -galactosidase, -glucuronidase, -glucosidase, -glucosidase, N-acetyl--glucosaminidase, -mannosidase and -fucosidase are negative in API ZYM kits.
The type strain is DSS-3T (=ATCC 700808T=DSM 15171T).
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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Arahal, D. R., Macian, M. C., Garay, E. & Pujalte, M. J. (2005). Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov. Int J Syst Evol Microbiol 55, 2371–2376.
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef][Medline]
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[Abstract]
González, J. M., Covert, J. S., Whitman, W. B., Henriksen, J. R., Mayer, F., Scharf, B., Schmitt, R., Buchan, A., Fuhrman, J. A. & other authors (2003). Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol 53, 1261–1269.
Huß, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184–192.
Jeon, Y.-S., Chung, H., Park, S., Hur, I., Lee, J.-H. & Chun, J. (2005). jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 21, 3171–3173.
Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
Lafay, B., Ruimy, R., Rausch de Traubenberg, C., Breittmayer, V., Gauthier, M. J. & Christen, R. (1995). Roseobacter algicola sp. nov., a new marine bacterium isolated from the phycosphere of the toxin-producing dinoflagellate Prorocentrum lima. Int J Syst Bacteriol 45, 290–296.
Macián, M. C., Arahal, D. R., Garay, E., Ludwig, W., Schleifer, K. H. & Pujalte, M. J. (2005). Jannaschia rubra sp. nov., a red-pigmented bacterium isolated from sea water. Int J Syst Evol Microbiol 55, 649–653.
Martens, T., Heidorn, T., Pukall, R., Simon, M., Tindall, B. J. & Brinkhoff, T. (2006). Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1998 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera. Int J Syst Evol Microbiol 56, 1293–1304.
Martínez-Cánovas, M. J., Quesada, E., Martínez-Checa, F., del Moral, A. & Béjar, V. (2004). Salipiger mucescens gen. nov., sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium isolated from hypersaline soil, belonging to the -Proteobacteria. Int J Syst Evol Microbiol 54, 1735–1740.
Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athayle, M., Schaal, A. & Parlett, J. H. (1984). An integrated procedure for the extraction of isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
Petursdottir, S. K. & Kristjansson, J. K. (1997). Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland. Extremophiles 1, 94–99.[CrossRef][Medline]
Petursdottir, S. K. & Kristjansson, J. K. (1999). Silicibacter lacuscaerulensis gen. nov., sp. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 71. Int J Syst Bacteriol 49, 1325–1326.
Rüger, H. J. & Höfle, M. G. (1992). Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev. Int J Syst Bacteriol 42, 133–143.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
Swofford, D. L. (2002). PAUP* - Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sunderland, MA: Sinauer Associates.
Uchino, Y., Hirata, A., Yokota, A. & Sugiyama, J. (1998). Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J Gen Appl Microbiol 44, 201–210.[CrossRef][Medline]
Uchino, Y., Hirata, A., Yokota, A. & Sugiyama, J. (1999). Ruegeria algicola (basonym Roseobacter algicola) comb. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 68. Int J Syst Bacteriol 49, 1–3.
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
Yi, H. & Chun, J. (2004). Comparative phylogeny of Roseobacter clade bacteria based on gyrB, pufL and 16S rRNA gene sequences. In Proceedings of the International Meeting of the Federation of Korean Microbiological Societies, abstract A019, p. 167. Seoul, Korea: Federation of Korean Microbiological Societies.
Yi, H. & Chun, J. (2006). Thalassobius aestuarii sp. nov., isolated from tidal flat sediment. J Microbiol 44, 171–176.[Medline]
ZoBell, C. E. (1941). Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 4, 42–75.
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