| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
Correspondence
Jung-Hoon Yoon
jhyoon{at}kribb.re.kr
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
7c and/or iso-C15 : 0 2-OH. The DNA G+C contents of the three strains were 34·7–34·9 mol%. The phylogenetic tree based on 16S rRNA gene sequences revealed that the three strains form one distinct evolutionary lineage supported by a bootstrap value of 100 % within the family Flavobacteriaceae. The three strains exhibited 16S rRNA gene sequence similarity levels of 93·8–94·9 % to the nearest phylogenetic neighbours, the genera Algibacter, Bizionia and Formosa. On the basis of differences in phenotypic characteristics and phylogenetic distinctiveness, strains SMK-12T, SMK-36 and SMK-45 were classified in a novel genus and species, for which the name Gaetbulibacter saemankumensis gen. nov., sp. nov. is proposed. The type strain for the novel species is SMK-12T (=KCTC 12379T=DSM 17032T).
Published online ahead of print on 22 April 2005 as DOI 10.1099/ijs.0.63738-0.
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains SMK-12T, SMK-36 and SMK-45 are AY883937, AY883938 and AY883939, respectively.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
and included in the first edition of Bergey's Manual of Systematic Bacteriology (Reichenbach, 1989). The family Flavobacteriaceae forms an evolutionary lineage of descent within the domain Bacteria, together with the families Bacteroidaceae, Cytophagaceae, Sphingobacteriaceae, Spirosomaceae and several taxa unaffiliated to any family (Woese et al., 1985; Bernardet et al., 1996; Bernardet et al., 2002). The family Flavobacteriaceae accommodates bacteria that are motile by gliding or non-motile, chemo-organotrophic, Gram-negative and rod-shaped, and contain menaquinone-6 as the major isoprenoid quinone (Bernardet et al., 1996, 2002; Nedashkovskaya et al., 2004b). Currently, the family Flavobacteriaceae comprises more than 20 genera, including the recently described genera Formosa (Ivanova et al., 2004), Ulvibacter (Nedashkovskaya et al., 2004a), Algibacter (Nedashkovskaya et al., 2004b), Winogradskyella (Nedashkovskaya et al., 2005a) and Bizionia (Nedashkovskaya et al., 2005b). Recently, three Gram-negative, slightly halophilic, yellow-pigmented bacterial strains, SMK-12T, SMK-36 and SMK-45, were isolated from a tidal flat sediment in Korea. Comparison of 16S rRNA gene sequence revealed that the three strains were phylogenetically affiliated to the family Flavobacteriaceae. The aim of the present work is to establish the taxonomic positions of strains SMK-12T, SMK-36 and SMK-45 by using a polyphasic taxonomic approach.
Tidal flat sediment collected from Saemankum, Pyunsan, Korea, was used as the source for isolation of bacterial strains. Strains SMK-12T, SMK-36 and SMK-45 were isolated by the usual dilution plating technique on marine agar 2216 (MA; Difco) at 30 °C. Growth at various temperatures from 4 to 45 °C was measured on MA, and growth at various pH and tolerance to various NaCl concentrations were measured in marine broth 2216 (MB; Difco). Growth under anaerobic conditions was determined after incubation in an anaerobic chamber on MA and on MA supplemented with nitrate, both of which had been prepared anaerobically using nitrogen. Cell morphology and presence of flagella were examined by light microscopy (Nikon E600) and transmission electron microscopy using cells grown on MA. Gliding motility was determined as described by Bowman (2000). Presence of flexirubin pigment was investigated as described by Reichenbach (1992). Gram reaction was determined by using the bioMérieux Gram Stain kit according to the manufacturer's instructions. Catalase activity was determined by bubble production in a 3 % (v/v) hydrogen peroxide solution on MA. Oxidase activity was determined by oxidation of 1 % (w/v) p-aminodimethylaniline oxalate. Hydrolysis of casein and starch was determined as described by Cowan & Steel (1965). Hydrolysis of hypoxanthine, tyrosine and xanthine was performed on MA with the substrate concentrations described previously (Cowan & Steel, 1965). Hydrolysis of Tweens 20, 40, 60 and 80 was determined as described by Cowan & Steel (1965) with the modification that artificial sea water (containing 23·6 g NaCl, 0·64 g KCl, 4·53 g MgCl2.6H2O, 5·94 g MgSO4.7H2O and 1·3 g CaCl2.2H2O per litre distilled water; Bruns et al., 2001) was used for the preparation of media. Hydrolysis of aesculin and urea and nitrate reduction were studied as described by Lanyi (1987) with the modification that artificial sea water was used for the preparation of media. The production of H2S was tested as described previously (Bruns et al., 2001). Acid production from carbohydrates was determined as described by Leifson (1963). Utilization of various substrates for growth was determined as described by Yurkov et al. (1994). The API ZYM system (bioMérieux) was used to determine enzyme activity. Antibiotic sensitivity was tested by spreading bacterial suspension on MA and applying discs impregnated with the following antibiotics (concentration per disc): ampicillin (10 µg), carbenicillin (25 µg), lincomycin (15 µg), gentamicin (10 µg), oleandomycin (15 µg), benzylpenicillin (10 U), polymyxin B (300 U), streptomycin (30 µg), tetracycline (30 µg) and neomycin (15 µg).
Cell biomass for isoprenoid quinone analysis and for DNA extraction was obtained after cultivation for 3 days in MB at 30 °C. Isoprenoid quinones were analysed as described previously (Komagata & Suzuki, 1987), using reversed-phase HPLC. For fatty acid methyl ester (FAME) analysis, cell biomass of strains SMK-12T, SMK-36 and SMK-45 was harvested from agar plates after cultivation for 3 days on MA at 30 °C. The FAMEs were extracted and prepared according to the standard protocol of the MIDI/Hewlett Packard Microbial Identification System (Sasser, 1990). Chromosomal DNA was extracted and purified by the procedure described previously (Yoon et al., 1996). The DNA G+C content was determined by the method of Tamaoka & Komagata (1984) with a modification that DNA was hydrolysed and the resultant nucleotides were analysed by reversed-phase HPLC. DNA–DNA relatedness was determined by the microplate hybridization method (Ezaki et al., 1989) using photobiotin-labelled DNA probes.
16S rRNA gene amplification was performed according to the method described previously using two universal primers (Yoon et al., 1998). Sequencing of the amplified 16S rRNA gene was performed as described by Yoon et al. (2003). Alignment of sequences was carried out with CLUSTAL W program (Thompson et al., 1994) and gaps at the 5' and 3' ends of the alignment were omitted from further analysis. The evolutionary distances were calculated using the Kimura two-parameter correction with the CLUSTAL W package (Thompson et al., 1994). A phylogenetic tree was constructed by using the neighbour-joining method (Saitou & Nei, 1987) on the basis of distance matrix data. The reliability of grouping was assessed by 1000 bootstrap resamplings of the neighbour-joining dataset by using the CLUSTAL W package.
Morphological, cultural, physiological and biochemical characteristics of strains SMK-12T, SMK-36 and SMK-45 are shown in Table 1 or are given in the genus and species descriptions. The predominant menaquinone detected in the three strains was MK-6, at peak area ratios of greater than 90 %. Cellular fatty acid profiles of strains SMK-12T, SMK-36 and SMK-45 are summarized in Table 2. The fatty acids profiles were characterized by a common core of straight-chain, branched, unsaturated and hydroxy fatty acids in similar amounts; the major components were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH and C16 : 17c and/or iso-C15 : 0 2-OH. The DNA G+C contents of strains SMK-12T, SMK-36 and SMK-45 were 34·8, 34·7 and 34·9 mol%, respectively.
|
|
). In the phylogenetic tree based on the neighbour-joining algorithm, the cluster comprising strains SMK-12T, SMK-36 and SMK-45 joined the phylogenetic lineage comprising the genus Algibacter by a bootstrap resampling value of 82·3 % (Fig. 1). The 16S rRNA gene sequence similarity values between strains SMK-12T, SMK-36, SMK-45 and members of three phylogenetically related genera were 94·9 % (Algibacter lectus KMM 3902T), 94·5 % (Bizionia paragorgiae KMM 6029T) and 93·8 % (Formosa algae KMM 3553T). Sequence similarities to all other species included in the phylogenetic analysis were lower than 93·1 %. Mean DNA–DNA relatedness values of strains SMK-12T, SMK-36 and SMK-45 were 83–106 % when their DNAs were used individually as labelled DNA probes for cross-hybridization. These values indicated that strains SMK-12T, SMK-36 and SMK-45 were members of the same genomic species (Wayne et al., 1987).
|
). In particular, nitrate reduction and hydrolysis of gelatin distinguish the three strains from the genera Algibacter, Bizionia and Formosa. Sensitivity of these three strains to several antibiotics differed from that of members of the genera Algibacter and Formosa (Table 1). The three strains were clearly distinguishable from the genus Bizionia in phenotypic properties, including gliding motility, acid production from carbohydrates, H2S production and hydrolysis of some substrates (Table 1). There were noteworthy differences between the fatty acid profiles of the three strains and the three phylogenetically related genera Algibacter, Bizionia and Formosa, particularly in the proportion of some fatty acids (Table 2). Therefore, on the basis of phenotypic, phylogenetic and genetic data, strains SMK-12T, SMK-36 and SMK-45 should be classified as members of a novel genus and species, for which the name Gaetbulibacter saemankumensis gen. nov., sp. nov. is proposed.
Description of Gaetbulibacter gen. nov.
Gaetbulibacter (Gaet.bu.li.bac'ter. N.L. n. gaetbulum -i gaetbul, the Korean name for a tidal flat; N.L. masc. n. bacter from Gr. neut. n. baktron rod; N.L. masc. n. Gaetbulibacter rod isolated from a tidal flat).
Cells are aerobic, Gram-negative, non-flagellated, non-spore-forming and rod-shaped. Growth also occurs under anaerobic conditions on MA and on MA with nitrate. Motile by means of gliding. Catalase- and oxidase-positive. Flexirubin pigments are absent. The predominant menaquinone is MK-6. Phylogenetically, the genus is a member of the family Flavobacteriaceae. The type species is Gaetbulibacter saemankumensis.
Description of Gaetbulibacter saemankumensis sp. nov.
Gaetbulibacter saemankumensis (sae.man.kum.en'sis. N.L. masc. adj. saemankumensis of Saemankum, from where the organism was originally isolated).
Exhibits the following properties in addition to those given in the genus description. Cells are 0·4–0·5x3·0–4·5 µm. Optimal pH for growth is 7·0–8·0; growth occurs weakly at pH 5·5, but not at 5·0. Optimal growth occurs in the presence of 2–5 % (w/v) NaCl; growth occurs in the presence of 7 % (w/v) NaCl, but not in the presence of >8 % NaCl. Aesculin, tyrosine and Tween 20 are hydrolysed, but hypoxanthine, xanthine and Tweens 40, 60 and 80 are not. Using the API ZYM system (bioMérieux), alkaline phosphatase, esterase (C4), esterase lipase (C8), lipase (C14), leucine arylamidase, valine arylamidase, cystine arylamidase, acid phosphatase, 
-glucosidase and N-acetyl-
-glucosaminidase are present. Naphthol-AS-BI phosphohydrolase, -galactosidase, -galactosidase, -glucuronidase, -mannosidase, -fucosidase and trypsin are absent; -chymotrypsin and -glucosidase activities are variable (absent for type strain). D-Cellobiose, D-fructose, D-galactose, D-glucose, D-xylose and L-rhamnose are utilized as sole carbon and energy sources. L-Alanine, L-asparagine, D-gluconic acid, glycerol, L-malic acid, melibiose, propionic acid, pyruvic acid, D-raffinose, succinic acid, D-sorbitol, L-serine and D-trehalose are not utilized. Utilization of maltose, L-proline and sucrose is variable (positive for type strain). Acid is produced from D-cellobiose, D-galactose, lactose and maltose. Acid is not produced from L-arabinose, D-fructose, D-mannitol, D-melezitose, melibiose, myo-inositol, D-raffinose, D-ribose, D-sorbitol, D-trehalose and D-xylose. Acid production from D-glucose and sucrose (positive for type strain), D-mannose and L-rhamnose (negative for type strain) is variable. The major cellular fatty acids are iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH and C16 : 17c and/or iso-C15 : 0 2-OH. The DNA G+C content is 34·7–34·9 mol%.
The type strain, SMK-12T (=KCTC 12379T=DSM 17032T), was isolated from a tidal flat sediment at Saemankum, Pyunsan, Korea.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Bernardet, J.-F., Nakagawa, Y. & Holmes, B. (2002). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52, 1049–1070.[Abstract]
Bowman, J. P. (2000). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50, 1861–1868.
Bruns, A., Rohde, M. & Berthe-Corti, L. (2001). Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 51, 1997–2006.[Abstract]
Cowan, S. T. & Steel, K. J. (1965). Manual for the Identification of Medical Bacteria. London: Cambridge University Press.
Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.
Ivanova, E. P., Alexeeva, Y. V., Flavier, S., Wright, J. P., Zhukova, N. V., Gorshkova, N. M., Mikhailov, V. V., Nicolau, D. V. & Christen, R. (2004). Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 54, 705–711.
Jooste, P. J. (1985). The taxonomy and significance of Flavobacterium –Cytophaga strains from dairy sources. PhD thesis, University of the Orange Free State, Bloemfontein, South Africa.
Komagata, K. & Suzuki, K. (1987). Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207.
Lanyi, B. (1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1–67.
Leifson, E. (1963). Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 85, 1183–1184.
Nedashkovskaya, O. I., Kim, S. B., Han, S. K., Rhee, M. S., Lysenko, A. M., Falsen, E., Frolova, G. M., Mikhailov, V. V. & Bae, K. S. (2004a). Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata. Int J Syst Evol Microbiol 54, 119–123.
Nedashkovskaya, O. I., Kim, S. B., Han, S. K. & 7 other authors (2004b). Algibacter lectus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from green algae. Int J Syst Evol Microbiol 54, 1257–1261.
Nedashkovskaya, O. I., Kim, S. B., Han, S. K. & 9 other authors (2005a). Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae. Int J Syst Evol Microbiol 55, 49–55.
Nedashkovskaya, O. I., Kim, S. B., Lysenko, A. M., Frolova, G. M., Mikhailov, V. V. & Bae, K. S. (2005b). Bizionia paragorgiae gen. nov., sp. nov, a novel member of the family Flavobacteriaceae isolated from the soft coral Paragorgia arborea. Int J Syst Evol Microbiol 55, 375–378.
Reichenbach, H. (1989). Order I. Cytophagales Leadbetter 1974. In Bergey's Manual of Systematic Bacteriology, vol. 3, pp. 2011–2013. Edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. G. Holt. Baltimore: Williams & Wilkins.
Reichenbach, H. (1992). The order Cytophagales. In The Prokaryotes, 2nd edn, vol. 4, pp. 3631–3687. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer. Berlin: Springer.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Sasser, M. (1990). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. Newark, DE: MIDI Inc.
Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed phase high performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.
Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 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.
Woese, C. R., Stackebrandt, E., Macke, T. J. & Fox, G. E. (1985). A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 6, 143–151.[Medline]
Yoon, J.-H., Kim, H., Kim, S.-B., Kim, H.-J., Kim, W. Y., Lee, S. T., Goodfellow, M. & Park, Y.-H. (1996). Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. Int J Syst Bacteriol 46, 502–505.
Yoon, J.-H., Lee, S. T. & Park, Y.-H. (1998). Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rRNA sequences. Int J Syst Bacteriol 48, 187–194.
Yoon, J.-H., Kang, K. H. & Park, Y.-H. (2003). Psychrobacter jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 53, 449–454.
Yurkov, V., Stackebrandt, E., Holmes, A. & 7 other authors (1994). Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 44, 427–434.
This article has been cited by other articles:
|
|
 |
|
  D.-H. Lee, H.-Y. Kahng, Y. S. Lee, J. S. Jung, J. M. Kim, B. S. Chung, S. K. Park, and C. O. Jeon Jejuia pallidilutea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from seawater Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2148 - 2152. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bercovich, S. C. Vazquez, P. Yankilevich, S. H. Coria, M. Foti, E. Hernandez, A. Vidal, L. Ruberto, C. Melo, S. Marenssi, et al. Bizionia argentinensis sp. nov., isolated from surface marine water in Antarctica Int J Syst Evol Microbiol, October 1, 2008; 58(10): 2363 - 2367. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Barbeyron, S. L'Haridon, G. Michel, and M. Czjzek Mariniflexile fucanivorans sp. nov., a marine member of the Flavobacteriaceae that degrades sulphated fucans from brown algae Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2107 - 2113. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, S.-J. Kang, Y.-T. Jung, and T.-K. Oh Aestuariicola saemankumensis gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from tidal flat sediment Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2126 - 2131. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-J. Yang and J.-C. Cho Gaetbulibacter marinus sp. nov., isolated from coastal seawater, and emended description of the genus Gaetbulibacter Int J Syst Evol Microbiol, February 1, 2008; 58(2): 315 - 318. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-Y. Jung, H.-S. Kim, J. J. Song, S.-G. Lee, T.-K. Oh, and J.-H. Yoon Aestuariimicrobium kwangyangense gen. nov., sp. nov., an LL-diaminopimelic acid-containing bacterium isolated from tidal flat sediment Int J Syst Evol Microbiol, September 1, 2007; 57(9): 2114 - 2118. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. D. Lee Tamlana crocina gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae, isolated from beach sediment in Korea Int J Syst Evol Microbiol, April 1, 2007; 57(4): 764 - 769. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z.-P. Liu, B.-J. Wang, X. Dai, X.-Y. Liu, and S.-J. Liu Zhouia amylolytica gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from sediment of the South China Sea Int J Syst Evol Microbiol, December 1, 2006; 56(12): 2825 - 2829. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Einen and L. Ovreas Flaviramulus basaltis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from seafloor basalt. Int J Syst Evol Microbiol, October 1, 2006; 56(Pt 10): 2455 - 2461. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. K. Kwon, H.-S. Lee, H.-B. Jung, J.-H. Kang, and S.-J. Kim Yeosuana aromativorans gen. nov., sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae, isolated from estuarine sediment of the South Sea, Korea. Int J Syst Evol Microbiol, April 1, 2006; 56(Pt 4): 727 - 732. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. I. Nedashkovskaya, S. B. Kim, M. Vancanneyt, C. Snauwaert, A. M. Lysenko, M. Rohde, G. M. Frolova, N. V. Zhukova, V. V. Mikhailov, K. S. Bae, et al. Formosa agariphila sp. nov., a budding bacterium of the family Flavobacteriaceae isolated from marine environments, and emended description of the genus Formosa Int J Syst Evol Microbiol, January 1, 2006; 56(1): 161 - 167. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
