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1 Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
2 DSMZ–Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
3 Department of Food and Life Science, Sungkyunkwan University, Chunchun-dong 300, Jangan-gu, Suwon, Korea
4 National Research Laboratory of Molecular Ecosystematics, Institute of Probionic, Probionic Corporation, Bio-venture Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
Correspondence
Yong-Ha Park
yhpark{at}mail.kribb.re.kr
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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, based on L-Lys–Gly3–4–L-Ala(Gly), and the predominant menaquinone is MK-7. Strains YKJ-101T and YKJ-115T have cellular fatty acid profiles containing major amounts of saturated, unsaturated and branched fatty acids; the major fatty acids are anteiso-C15 : 0 and iso-C15 : 0. The cellular polar lipids are phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipids. Strains YKJ-101T and YKJ-115T have identical DNA G+C contents of 42 mol%. The 16S rDNA similarity between strains YKJ-101T and YKJ-115T is 98 % and the mean level of DNA–DNA relatedness between the two strains is 13·4 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, it is proposed that strains YKJ-101T and YKJ-115T should be placed in a new genus, Jeotgalicoccus gen. nov., as two distinct new species, for which the names Jeotgalicoccus halotolerans sp. nov. and Jeotgalicoccus psychrophilus sp. nov. are proposed. The type strains are YKJ-101T (=KCCM 41448T =JCM 11198T) and YKJ-115T (=KCCM 41449T =JCM 11199T), respectively.
The GenBank accession numbers for the 16S rDNA sequences of strains YKJ-101T and YKJ-115T and the newly determined 16S rDNA sequence of Salinicoccus hispanicus DSM 5352T are AY028925, AY028926 and AY028927, respectively.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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with a single species, Salinicoccus roseus. Marinococcus hispanicus was later transferred to the genus Salinicoccus as Salinicoccus hispanicus (Ventosa et al., 1992). At the time of writing, there were two validly named Salinicoccus species; a third species, Salinicoccus alkaliphilus, has subsequently been described (Zhang et al., 2002). The genus Salinicoccus is chemotaxonomically characterized by having menaquinone-6 as the predominant isoprenoid quinone, a cell-wall peptidoglycan type based on L-Lys–Gly5, and a DNA G+C content of 46–51 mol% (Ventosa et al., 1992). The aim of the present study was to unravel the exact taxonomic positions of the two halotolerant or moderately halophilic cocci isolated from jeotgal, by polyphasic characterization that included phenotypic properties, phylogeny based on 16S rDNA sequences and genomic relatedness. On the basis of the data presented here, we propose that strains YKJ-101T and YKJ-115T should be placed in a new genus, Jeotgalicoccus gen. nov., as two distinct species, Jeotgalicoccus halotolerans sp. nov. and Jeotgalicoccus psychrophilus sp. nov., respectively. |
METHODS |
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Morphological characterization.
Cell morphology was examined by light microscopy and transmission electron microscopy (TEM). Flagellum type was determined by TEM using cells from an exponentially growing culture. For observation by TEM, the cells were negatively stained with 1 % (w/v) phosphotungstic acid and the grids were examined after air drying with a Philips CM-20 transmission electron microscope.
Physiological characterization.
Oxidase activity was determined by oxidation of 1 % p-aminodimethylaniline oxalate. Catalase activity was determined by bubble production with 3 % (v/v) hydrogen peroxide solution. Hydrolysis of aesculin and nitrate reduction were determined as described by Lanyi (1987). Hydrolysis of casein, starch and Tween 80 and urease activity were determined as described by Cowan & Steel (1965). Hydrolysis of hypoxanthine, tyrosine and xanthine was determined on MA with substrate concentrations as described by Cowan & Steel (1965). Acid production from carbohydrates was determined as described by Leifson (1963). Growth under anaerobic conditions was determined after incubation in an anaerobic chamber on anaerobically prepared MA. Growth at various NaCl concentrations was investigated on MA or in MB. Growth at various temperatures was measured on MA at 4–55 °C.
Chemotaxonomic characterization.
The presence or absence of diaminopimelic acid in the peptidoglycan was determined using the method described by Komagata & Suzuki (1987). Preparation of cell walls and determination of peptidoglycan structure were carried out using the methods described by Schleifer & Kandler (1972), except that TLC on cellulose sheets was used instead of paper chromatography. Menaquinones were analysed as described by Komagata & Suzuki (1987) using reversed-phase HPLC. Polar lipids were extracted as described by Minnikin et al. (1984) and identified by two-dimensional TLC followed by spraying with appropriate detection reagents (Komagata & Suzuki, 1987). For quantitative analysis of cellular fatty acid compositions, a loop of cell mass was harvested and FAMEs were prepared and identified according to the instructions of the Microbial Identification System (MIDI).
Isolation of DNA.
Chromosomal DNA was isolated and purified according to the method described previously (Yoon et al., 1996), except that ribonuclease T1 was used with ribonuclease A.
DNA base composition.
The DNA G+C content was determined using the method of Tamaoka & Komagata (1984). DNA was hydrolysed and the resultant nucleotides were analysed by reversed-phase HPLC.
16S rDNA sequencing and phylogenetic analysis.
16S rDNA was amplified by PCR using two universal primers as described previously (Yoon et al., 1998). The PCR product was purified with a QIAquick PCR purification kit (Qiagen). The sequencing of the purified 16S rDNA PCR product was performed using an ABI PRISM BigDye Terminator cycle sequencing ready reaction kit (Applied Biosystems) as recommended by the manufacturer. The purified sequencing reaction mixtures were electrophoresed on an ABI PRISM 310 DNA sequencer (Applied Biosystems). Alignment of sequences was carried out using CLUSTAL W software (Thompson et al., 1994). Gaps at the 5' and 3' ends of the alignment were omitted from further analysis. Phylogenetic trees were inferred by using three tree-making algorithms: the neighbour-joining (Saitou & Nei, 1987), maximum-likelihood (Felsenstein, 1981) and maximum-parsimony (Kluge & Farris, 1969) methods from the PHYLIP package (Felsenstein, 1993). Evolutionary distance matrices for the neighbour-joining method were calculated using the algorithm of Jukes & Cantor (1969) with the DNADIST program. The stability of relationships was assessed by bootstrap analysis, based on 1000 resamplings of the neighbour-joining dataset, by using the SEQBOOT and CONSENSE programs of the PHYLIP package.
DNA–DNA hybridization.
DNA–DNA hybridization was performed fluorometrically by the method of Ezaki et al. (1989), using photobiotin-labelled DNA probes and microdilution wells. Hybridization was performed with five replications for each sample. The highest and lowest values obtained for each sample were excluded, and the remaining three values were used to calculate similarity values. The DNA relatedness values quoted are the means of these three values.
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RESULTS |
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). After 3 days incubation on MA, colonies of both strains were smooth, glistening, low convex, circular to slightly irregular and light yellow in colour.
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, together with those of Salinicoccus roseus and Salinicoccus hispanicus.
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, based on L-Lys–Gly3–4–L-Ala(Gly), as described by Schleifer & Kandler (1972). On the chromatograms of partially hydrolysed cell walls, both the peptides D-Ala–Gly and D-Ala–L-Ala were detected. Hydrolysis of dinitrophenylated cell walls revealed high amounts of dinitrophenylated (DNP)-alanine and minor amounts of DNP-glycine, indicating that the N-terminal glycine residue of the interpeptide bridge was mostly replaced by an alanine residue. The predominant menaquinone found in strains YKJ-101T and YKJ-115T was menaquinone-7 (MK-7): they contained approximately 86 and 80 % MK-7, respectively. Strains YKJ-101T and YKJ-115T showed cellular fatty acid profiles containing large amounts of saturated, unsaturated and branched fatty acids (Table 2). The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0 (Table 2). The cellular polar lipids found in the two strains were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and unidentified phospholipids; glycolipids were not found (Fig. 2). The genomic DNA G+C contents of strains YKJ-101T and YKJ-115T were both 42 mol%.
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). The fidelity between the two phylogenetic clusters was supported by bootstrap analysis at a confidence level of 98·2 % (Fig. 3). This tree topology was also found in the trees generated by the maximum-likelihood and maximum-parsimony algorithms. Strains YKJ-101T and YKJ-115T exhibited levels of 16S rDNA similarity of 80·0–92·1 % with other species used in the phylogenetic analysis. Strains YKJ-101T and YKJ-115T exhibited two independent levels of DNA–DNA relatedness of 12·8 and 13·9 %.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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). Of these bacteria, some Gram-positive moderately halophilic cocci, e.g. the genera Marinococcus, Salinicoccus, Nesterenkonia (formerly Micrococcus halobius), Tetragenococcus and Macrococcus, have hitherto been described (Kloos et al., 1998; Ventosa et al., 1998). The result of 16S rDNA sequence analysis showed that strains YKJ-101T and YKJ-115T are most closely related to the cluster comprising the genus Salinicoccus, with a high bootstrap resampling value (Fig. 3
). However, other Gram-positive moderately halophilic cocci, such as the genera Marinococcus, Nesterenkonia and Tetragenococcus, have been shown to be phylogenetically distant from the genus Salinicoccus (Collins et al., 1990; Satomi et al., 1997; Stackebrandt et al., 1995) and strains YKJ-101T and YKJ-115T (Fig. 3). Some phenotypic characteristics show that strains YKJ-101T and YKJ-115T are clearly distinguishable from other Gram-positive halophilic cocci, as well as some phylogenetically related genera such as Salinicoccus, Staphylococcus and Macrococcus.
Strains YKJ-101T and YKJ-115T are distinguished from the genera Salinicoccus and Nesterenkonia by the types of predominant menaquinone and cell-wall peptidoglycan. The predominant menaquinone found in strains YKJ-101T and YKJ-115T is MK-7, whereas the genus Salinicoccus contains MK-6 (Ventosa et al., 1990, 1992) and the genus Nesterenkonia contains MK-8 and MK-9 (Stackebrandt et al., 1995) as the predominant menaquinones. Strains YKJ-101T and YKJ-115T have a peptidoglycan structure based on L-Lys–Gly3–4–L-Ala(Gly), whereas the genus Salinicoccus has the peptidoglycan structure L-Lys–Gly5 (Ventosa et al., 1990, 1992) and the genus Nesterenkonia has the peptidoglycan structure L-Lys–Gly–Glu (Stackebrandt et al., 1995). Strains YKJ-101T and YKJ-115T are also differentiated from Salinicoccus species in colour: YKJ-101T and YKJ-115T form light-yellow-coloured colonies, but colonies of species belonging to the genus Salinicoccus are pink-red or reddish-orange (Ventosa et al., 1990, 1992). Moreover, the genus Nesterenkonia has a high DNA G+C content (70–72 mol%) and falls into the phylogenetic radiation enclosed by the class Actinobacteria (Stackebrandt et al., 1995, 1997). Strains YKJ-101T and YKJ-115T can be differentiated from the genus Staphylococcus by the type of predominant menaquinone and G+C content: the genus Staphylococcus has MK-6, MK-7 and MK-8 as the predominant menaquinones and has a DNA G+C content of less than 40 mol% (Kloos et al., 1998; Probst et al., 1998; Stackebrandt et al., 1995). There is a difference between strains YKJ-101T and YKJ-115T and the genera Salinicoccus and Staphylococcus in the presence of lipids other than phospholipids (Kloos & Schleifer, 1986; Ventosa et al., 1992): the genera Salinicoccus and Staphylococcus contain glycolipids that were not detected in strains YKJ-101T and YKJ-115T. The genus Macrococcus is distinguished from strains YKJ-101T and YKJ-115T by its peptidoglycan type, which is based on L-Lys–Gly3–4, L-Ser (Kloos et al., 1998). Strains YKJ-101T and YKJ-115T are distinguishable from the genera Marinococcus and Tetragenococcus by the difference in cell-wall peptidoglycan type: the genus Marinococcus contains meso-diaminopimelic acid at position 3 of the peptide subunit (Ventosa et al., 1990, 1992) and the genus Tetragenococcus has the peptidoglycan type based on L-Lys–D-Asp (A4) (Satomi et al., 1997). Strains YKJ-101T and YKJ-115T show noteworthy differences from the genus Tetragenococcus in cellular fatty acid profiles and some physiological properties: while strains YKJ-101T and YKJ-115T have anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids, the genus Tetragenococcus has C18 : 1 and C16 : 0 (Satomi et al., 1997). Tetragenococcus species show no catalase or oxidase activities. The genus Tetragenococcus also contains lactic-acid-producing bacteria, and is closely related to the phylogenetic cluster comprising some lactic acid bacteria, particularly Enterococcus species (Collins et al., 1990; Satomi et al., 1997). Therefore, on the basis of the differential phenotypic and phylogenetic data, strains YKJ-101T and YKJ-115T should be classified as members of a new genus.
Strains YKJ-101T and YKJ-115T are considered to belong to different species by the results of DNA–DNA hybridization and some differences in their phenotypic properties, such as tolerance of NaCl and temperature for growth (see Table 1 for a summary). Strains YKJ-101T and YKJ-115T have approximately 30 bp (2 %) difference between their 16S rDNA sequences. The level of DNA–DNA relatedness clearly indicates that strains YKJ-101T and YKJ-115T are members of different genomic species.
On the basis of the phenotypic and phylogenetic data and the genomic distinctiveness described here, we propose a new genus, Jeotgalicoccus gen. nov., with the description of two new species, Jeotgalicoccus halotolerans sp. nov. and Jeotgalicoccus psychrophilus sp. nov., for strains YKJ-101T and YKJ-115T, respectively.
Description of Jeotgalicoccus gen. nov.
Jeotgalicoccus (je.ot.ga.li.coc'cus. Korean n. jeotgal jeotgal, traditional Korean seafood; Gr. masc. n. coccus a grain or berry; N.L. masc. n. Jeotgalicoccus coccus from jeotgal).
Gram-positive, non-motile, non-spore-forming cocci. Facultatively anaerobic. Colonies are smooth, glistening, low convex, circular to slightly irregular and light yellow in colour on MA. Optimal pH for growth is 7·0–8·0 and no growth is observed at pH 5·5. Catalase- and oxidase-positive. Urease-negative. Nitrate is not reduced to nitrite. Tyrosine is hydrolysed. Aesculin, casein, hypoxanthine, starch, Tween 80 and xanthine are not hydrolysed. Cell-wall peptidoglycan contains L-lysine at position 3 of the peptide subunit. Predominant menaquinone is MK-7. Major fatty acids are anteiso-C15 : 0 and iso-C15 : 0. DNA G+C content is 42 mol% (determined by HPLC). The type species is Jeotgalicoccus halotolerans.
Description of Jeotgalicoccus halotolerans sp. nov.
Jeotgalicoccus halotolerans (ha.lo.to'le.rans. Gr. n. hals salt; L. pres. part. tolerans tolerating, enduring; N.L. part. adj. halotolerans salt-tolerating).
Gram-positive, non-motile, non-spore-forming cocci of 0·6–1·1 µm diameter. Colonies are smooth, glistening, low convex, circular to slightly irregular and light yellow in colour on MA. Optimal growth temperature is 30–35 °C; growth occurs at 4 and 42 °C, but not above 43 °C. Optimal pH for growth is 7·0–8·0 and no growth is observed at pH 5·5. Growth occurs in the presence of 0–20 % (w/v) NaCl and not in the presence of 21 % NaCl. Optimal NaCl concentration for growth is 2–5 % NaCl. Growth occurs under anaerobic conditions on MA. Catalase- and oxidase-positive. Urease-negative. Tyrosine is hydrolysed. Aesculin, casein, hypoxanthine, starch, Tween 80 and xanthine are not hydrolysed. Nitrate is not reduced to nitrite. Acid is produced from L-arabinose, D-mannose, D-ribose and D-mannitol. Acid is not produced from D-cellobiose, D-fructose, D-galactose, D-glucose, lactose, maltose, D-melezitose, melibiose, D-raffinose, L-rhamnose, stachyose, sucrose, D-trehalose, D-xylose, adonitol, myo-inositol or D-sorbitol. Peptidoglycan type is A3 based on L-Lys–Gly3–4–L-Ala(Gly). Predominant menaquinone is MK-7. Major fatty acids are anteiso-C15 : 0 and iso-C15 : 0. DNA G+C content is 42 mol% (determined by HPLC).
Isolated from jeotgal, traditional Korean fermented seafood. Type strain is YKJ-101T, which has been deposited in the Korean Culture Center of Microorganisms as KCCM 41448T and at the Japan Collection of Microorganisms as JCM 11198T.
Description of Jeotgalicoccus psychrophilus sp. nov.
Jeotgalicoccus psychrophilus (psy.chro'phil.us. Gr. adj. psychros cold; Gr. adj. philos liking, loving; N.L. adj. psychrophilus cold-loving).
Gram-positive, non-motile, non-spore-forming cocci of 0·6–1·1 µm diameter. Colonies are smooth, glistening, low convex, circular to slightly irregular and light yellow in colour on MA. Optimal growth temperature is 20–25 °C; growth occurs at 4 and 34 °C but not at temperatures above 35 °C. The optimal pH for growth is 7·0–8·0 and no growth is observed at pH 5·5. Growth occurs in the presence of 14 % NaCl but not in the presence of 15 % NaCl. No growth occurs in the absence of NaCl. The optimal NaCl concentration for growth is 2–5 % NaCl. Growth occurs under anaerobic conditions on MA. Catalase- and oxidase-positive. Urease-negative. Tyrosine is hydrolysed. Aesculin, casein, hypoxanthine, starch, Tween 80 and xanthine are not hydrolysed. Nitrate is not reduced to nitrite. Acid is weakly produced from sucrose. Acid is not produced from L-arabinose, D-cellobiose, D-fructose, D-galactose, D-glucose, lactose, maltose, D-mannose, D-melezitose, melibiose, D-raffinose, L-rhamnose, D-ribose, stachyose, sucrose, D-trehalose, D-xylose, adonitol, D-mannitol, myo-inositol or D-sorbitol. Peptidoglycan type is A3 based on L-Lys–Gly3–4–L-Ala(Gly). Predominant menaquinone is MK-7. Major fatty acids are anteiso-C15 : 0 and iso-C15 : 0. DNA G+C content is 42 mol% (determined by HPLC).
Isolated from jeotgal, traditional Korean fermented seafood. Type strain is YKJ-115T, which has been deposited in the Korean Culture Center of Microorganisms as KCCM 41449T and at the Japan Collection of Microorganisms as JCM 11199T.
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ACKNOWLEDGEMENTS |
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