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Int J Syst Evol Microbiol 55 (2005), 1007-1013; DOI  10.1099/ijs.0.63464-0
© 2005 International Union of Microbiological Societies

Psychrobacter aquimaris sp. nov. and Psychrobacter namhaensis sp. nov., isolated from sea water of the South Sea in Korea

Jung-Hoon Yoon1, Choong-Hwan Lee1, Soo-Hwan Yeo2 and Tae-Kwang Oh1

1 Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
2 The Center for Traditional Microorganism Resources, Keimyung University, Shindang-Dong, Dalseo-gu, Daegu, Korea

Correspondence
Jung-Hoon Yoon
jhyoon{at}kribb.re.kr


    ABSTRACT
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Two Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strains, SW-210T and SW-242T, were isolated from sea water of the South Sea in Korea, and were characterized taxonomically by means of a polyphasic approach. The two isolates grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. Strains SW-210T and SW-242T contained Q-8 as the predominant respiratory lipoquinone and C18 : 1{omega}9c as the major fatty acid. The DNA G+C contents of strains SW-210T and SW-242T were 43·2 and 45·3 mol%, respectively. The 16S rRNA gene sequences of strains SW-210T and SW-242T were 98·9 % similar, and the mean DNA–DNA relatedness value between them was 24 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains SW-210T and SW-242T form distinct phylogenetic lineages within the radiation of the cluster comprising Psychrobacter species, having 16S rRNA gene sequence similarity levels of 95·9–99·2 % with respect to the type strains of Psychrobacter species. The levels of DNA–DNA relatedness between the two isolates and the type strains of 15 phylogenetically related Psychrobacter species were well below 70 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains SW-210T and SW-242T were classified in the genus Psychrobacter as representing two distinct novel species, for which the names Psychrobacter aquimaris sp. nov. (type strain, SW-210T=KCTC 12254T=DSM 16329T) and Psychrobacter namhaensis sp. nov. (type strain, SW-242T=KCTC 12255T=DSM 16330T) are proposed, respectively.


Published online ahead of print on 3 December 2004 as DOI 10.1099/ijs.0.63464-0.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains SW-210T and SW-242T are AY722804 and AY722805, respectively.


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The genus Psychrobacter was proposed by Juni & Heym (1986)Go, and, at the time of writing, the genus comprises at least 18 species with validly published names: Psychrobacter immobilis (Juni & Heym, 1986Go), Psychrobacter frigidicola, Psychrobacter urativorans and Psychrobacter phenylpyruvicus (Bowman et al., 1996Go), Psychrobacter glacincola (Bowman et al., 1997Go), Psychrobacter pacificensis (Maruyama et al., 2000Go), Psychrobacter proteolyticus (Denner et al., 2001Go), Psychrobacter submarinus and Psychrobacter marincola (Romanenko et al., 2002Go), Psychrobacter faecalis (Kämpfer et al., 2002Go), Psychrobacter pulmonis (Vela et al., 2003Go), Psychrobacter jeotgali (Yoon et al., 2003Go), Psychrobacter luti and Psychrobacter fozii (Bozal et al., 2003Go), Psychrobacter okhotskensis (Yumoto et al., 2003Go), Psychrobacter maritimus and Psychrobacter arenosus (Romanenko et al., 2004Go) and Psychrobacter alimentarius (Yoon et al., 2005Go). In this study, we report on the detailed taxonomic characterization of two Psychrobacter-like bacterial strains, SW-210T and SW-242T, which were isolated from sea water of the South Sea in Korea.

Sea water collected from the South Sea in Korea was used as source for the isolation of bacterial strains. Strains SW-210T and SW-242T were isolated by using the usual dilution plating technique on marine agar 2216 (MA; Difco) at 30 °C. The type strains of 15 Psychrobacter species were used as reference strains for DNA–DNA hybridization. P. faecalis DSM 14664T, P. frigidicola DSM 12411T, P. glacincola DSM 12194T, P. immobilis DSM 7229T, P. marincola DSM 14160T, P. proteolyticus DSM 13887T, P. submarinus DSM 14161T and P. urativorans DSM 14009T were obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany. P. okhotskensis JCM 11840T was obtained from the Japan Collection of Microorganisms, Saitama, Japan. P. fozii CECT 5889T, P. luti CECT 5885T and P. pulmonis CECT 5989T were obtained from the Colección Española de Cultivos Tipo, Valencia, Spain. P. jeotgali KCCM 41559T and P. alimentarius JG-100T were obtained and described in the studies of Yoon et al. (2003Go, 2005)Go. P. maritimus KMM 3646T was obtained from Dr O. I. Nedashkovskaya and Dr L. A. Romanenko, Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia. Cell morphology was examined by light microscopy (E600 microscope; Nikon) and transmission electron microscopy (CM-20 apparatus; Philips). Transmission electron microscopy was also used to determine if flagella were present in cells from exponentially growing cultures. The Gram reaction was determined by using the bioMérieux Gram stain kit according to the manufacturer's instructions. The pH range for growth was determined in marine broth 2216 (MB; Difco) that was adjusted to various pH values (pH 4·5–9·5 at intervals of 0·5 pH units). Growth in the absence of NaCl was investigated in trypticase/soy broth (Difco) lacking NaCl. Growth at various NaCl concentrations was investigated in MB or trypticase/soy broth. Growth at various temperatures (4–45 °C) was measured on MA. 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. Catalase and oxidase activities and hydrolysis of casein, starch and Tweens 20, 40, 60 and 80 were determined as described by Cowan & Steel (1965)Go. Hydrolysis of aesculin and nitrate reduction were determined as described previously (Lanyi, 1987Go). Hydrolysis of gelatin and urea was determined as described by Lanyi (1987)Go, with the modification that artificial sea water was used instead of distilled water. The artificial sea water contained (per litre of distilled water) 23·6 g NaCl, 0·64 g KCl, 4·53 g MgCl2.6H2O, 5·94 g MgSO4.7H2O and 1·3 g CaCl2.2H2O (Bruns et al., 2001Go). Hydrolysis of hypoxanthine, tyrosine and xanthine was investigated on MA with the substrate concentrations described previously (Cowan & Steel, 1965Go). H2S production was tested as described previously (Bruns et al., 2001Go). Acid production from carbohydrates was determined as described by Leifson (1963)Go. Enzyme activity was determined by using the API ZYM system (bioMérieux). Utilization of substrates as sole carbon and energy sources was tested according to the method of Baumann & Baumann (1981)Go using supplementation with 2 % (v/v) Hutner's mineral base (Cohen-Bazire et al., 1957Go) and 1 % (v/v) vitamin solution (Staley, 1968Go). Requirements for yeast extract and vitamins for growth were investigated in liquid medium (Yurkov et al., 1994Go), omitting yeast extract and vitamin B12 but supplementing with 0·1 % (w/v) acetate as the sole carbon and energy source. Yeast extract and vitamins were added to the medium at the following concentrations (l–1): yeast extract, 0·005 g; p-aminobenzoic acid, 1 mg; biotin, 10 µg; thiamine hydrochloride, 1 mg; and vitamin B12, 1 mg. Susceptibility to antibiotics was detected on MA plates using antibiotic discs with the following concentrations: polymyxin B, 100 U; streptomycin, 50 µg; penicillin G, 20 U; chloramphenicol, 100 µg; ampicillin, 10 µg; cephalothin, 30 µg; gentamicin, 30 µg; novobiocin, 5 µg; erythromycin, 15 µg; and tetracycline, 30 µg. Other physiological tests were performed with the API 20E system (bioMérieux).

Cell biomass for respiratory lipoquinone analysis and for DNA extraction was obtained from cultivation in MB at 30 °C. Respiratory lipoquinones were analysed as described by Komagata & Suzuki (1987)Go, using reversed-phase HPLC. Chromosomal DNA was isolated and purified according to the method described previously (Yoon et al., 1996Go), with the exception that ribonuclease T1 was used together with ribonuclease A to minimize the contamination of RNA. For fatty acid methyl ester analysis, cell mass of strains SW-210T and SW-242T was harvested from agar plates after incubation for 3 days at 30 °C on MA. The fatty acid methyl esters were extracted and prepared according to the standard protocol of the MIDI/Hewlett Packard Microbial Identification System (Sasser, 1990Go). The DNA G+C content was determined by the method of Tamaoka & Komagata (1984)Go, with the modification that DNA was hydrolysed and the resultant nucleotides were analysed by reversed-phase HPLC. 16S rRNA genes were amplified by the PCR method, using two universal primers as described previously (Yoon et al., 1998Go). Sequencing of the amplified 16S rRNA genes and phylogenetic analysis were performed as described by Yoon et al. (2003)Go. DNA–DNA hybridization was performed fluorometrically according to the method of Ezaki et al. (1989)Go, using photobiotin-labelled DNA probes and microdilution wells. Hybridization was performed with five replications for each sample. The highest and lowest values obtained in each sample were excluded and the remaining three values were used to calculate similarity values. The DNA relatedness values quoted are the means of the three values.

Cells of strains SW-210T and SW-242T were cocci or short rods on MA. Strains SW-210T and SW-242T did not require yeast extract or vitamins for growth in minimal salts medium (Yurkov et al., 1994Go). However, both strains grew better when yeast extract was added to the medium. Benzoate was utilized by strain SW-242T but not by strain SW-210T. Strain SW-210T was sensitive to penicillin G but strain SW-242T was not. Other morphological, cultural, physiological and biochemical characteristics of strains SW-210T and SW-242T are given in the species description (see below) and are shown in Table 1Go together with those of some Psychrobacter species. The predominant respiratory lipoquinone found in strains SW-210T and SW-242T was Q-8, at a peak area ratio of approximately 84–86 %. The major components of the fatty acids detected in strains SW-210T and SW-242T were C18 : 1{omega}9c and C17 : 1{omega}8c (Table 2Go). These fatty acid profiles were similar to those determined previously for other Psychrobacter species, although there were differences in the proportions of some fatty acids, perhaps because of differences in cultivation conditions, e.g. cultivation media (Maruyama et al., 2000Go; Romanenko et al., 2002Go, 2004Go; Bozal et al., 2003Go; Yumoto et al., 2003Go; Yoon et al., 2005Go). The DNA G+C contents of strains SW-210T and SW-242T were 43·2 and 45·3 mol%, respectively.


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Table 1. Differential phenotypic characteristics of Psychrobacter species

1, P. aquimaris (n=1); 2, P. namhaensis (n=1); 3, P. immobilis (n=20), data from Juni & Heym (1986)Go, Bowman et al. (1996)Go and Romanenko et al. (2002)Go; 4, P. frigidicola (n=4), Bowman et al. (1996)Go and Romanenko et al. (2002)Go; 5, P. urativorans, Bowman et al. (1996)Go and Romanenko et al. (2002)Go; 6, P. glacincola (n=4), Bowman et al. (1997)Go and Romanenko et al. (2002)Go; 7, P. proteolyticus (n=1), Denner et al. (2001)Go and Bozal et al. (2003)Go; 8, P. submarinus (n=1), Romanenko et al. (2002)Go; 9, P. marincola (n=1), Romanenko et al. (2002)Go; 10, P. faecalis (n=1), Kämpfer et al. (2002)Go; 11, P. jeotgali (n=2), Yoon et al. (2003)Go; 12, P. pulmonis (n=2), Vela et al. (2003)Go; 13, P. okhotskensis (n=1), Yumoto et al. (2003)Go; 14, P. luti (n=1), Bozal et al. (2003)Go; 15, P. fozii (n=2), Bozal et al. (2003)Go; 16, P. alimentarius (n=2), Yoon et al. (2005)Go; 17, P. maritimus (n=3), Romanenko et al. (2004)Go; 18, P. phenylpyruvicus (n=1), Bowman et al. (1996)Go and Romanenko et al. (2002)Go; 19, P. pacificensis (n=6), Maruyama et al. (2000)Go. +, Positive reaction; –, negative reaction; ND, not determined; W, weakly positive reaction; V, variable reaction. Data in parentheses relate to the type strain; n, number of strains. All species are positive for catalase and oxidase. All species are negative for Gram stain, spore formation, motility, hydrolysis of aesculin, acid production from D-mannitol, utilization of D-glucose, arginine dihydrolase, lysine decarboxylase and ornithine decarboxylase.

 

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Table 2. Cellular fatty acid composition (%) of strain SW-210T and strain SW-242T on MA

Fatty acids representing less than 0·5 % in each of the two strains were omitted. –, Not detected.

 
The almost-complete 16S rRNA gene sequences of strains SW-210T and SW-242T determined in this study each comprised 1494 nt, representing approximately 96 % of the Escherichia coli 16S rRNA sequence. There were 17 bp sequence differences (i.e. 98·9 % identity) between the 16S rRNA gene sequence of strain SW-210T and that of strain SW-242T. Comparative analysis revealed that strains SW-210T and SW-242T had the highest 16S rRNA gene sequence similarities to members of the genus Psychrobacter. Phylogenetic trees based on 16S rRNA gene sequences showed that the two isolates fall within the evolutionary radiation encompassed by the genus Psychrobacter (Fig. 1Go). Strains SW-210T and SW-242T exhibited 16S rRNA gene sequence similarity levels of 96·0–99·2 % and 95·9–98·9 %, respectively, with respect to the type strains of Psychrobacter species with validly published names. The 16S rRNA gene sequence similarities of the two isolates with respect to other species included in the phylogenetic analysis were below 92·5 % (Fig. 1Go). DNA–DNA hybridization was performed to determine the level of genetic relatedness between strain SW-210T and strain SW-242T and also those between each of the two strains and the type strains of some Psychrobacter species that exhibited 16S rRNA gene sequence similarity values above 97 % with respect to the two novel isolates. Strains SW-210T and SW-242T exhibited a mean level of DNA–DNA relatedness of 24 % when their DNAs were used individually as labelled DNA probes for cross-hybridization. Levels of DNA–DNA relatedness between two strains and the type strains of 15 Psychrobacter species were in the range 6–35 %.



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Fig. 1. Neighbour-joining tree, based on 16S rRNA gene sequences, showing the phylogenetic positions of strains SW-210T and SW-242T and representatives of some other related taxa. Bootstrap values (expressed as percentages of 1000 replications) greater than 50 % are shown at the branch points. Pseudomonas aeruginosa DSM 50071T was used as the outgroup. Scale bar represents 0·01 substitution per nucleotide position.

 
In the neighbour-joining tree, inferred from comparison of 16S rRNA gene sequences, the cluster comprising the two isolates and Psychrobacter species was distinguishable from the genus Moraxella at a bootstrap confidence level of 100 % (Fig. 1Go). The thermal tolerance and chemotaxonomic data (the predominant respiratory lipoquinone, the cellular fatty acid profile and the DNA G+C content) for strains SW-210T and SW-242T are similar to those for Psychrobacter species (Bøvre, 1984Go; Kodjo et al., 1995Go, 1997Go; Bowman et al., 1997Go; Maruyama et al., 2000Go; Yoon et al., 2003Go; Bozal et al., 2003Go; Yumoto et al., 2003Go). Strains SW-210T and SW-242T are similar to each other in terms of most phenotypic characteristics (Table 1Go). However, the two strains differ from each other phylogenetically and genetically. Strains SW-210T and SW-242T are distinguishable from phylogenetically related Psychrobacter species by differences in physiological and biochemical characteristics (Table 1Go). The level of DNA relatedness, together with differential phenotypic properties and 16S rRNA gene sequence similarity data, justifies the taxonomic discrimination of strains SW-210T and SW-242T from all Psychrobacter species (Wayne et al., 1987Go; Stackebrandt & Goebel, 1994Go). Therefore, on the basis of the data presented, strains SW-210T and SW-242T should be placed in the genus Psychrobacter as representing two distinct novel species, for which the names Psychrobacter aquimaris sp. nov. and Psychrobacter namhaensis sp. nov., respectively, are proposed.

Description of Psychrobacter aquimaris sp. nov.
Psychrobacter aquimaris (a.qui.ma'ris. L. n. aqua water; L. gen. n. maris of the sea; N.L. gen. n. aquimaris of the water of the sea).

Cells are cocci or short rods (1·0–1·2x1·4–2·5 µm). On MA, colonies are smooth, glistening, raised, circular to slightly irregular, cream in colour and 1·5–2·5 mm in diameter after incubation for 3 days at 30 °C. Growth occurs at 4 and 34 °C but not at 35 °C. Optimal pH for growth is 6·5–7·5; growth occurs at pH 5·0 but not at 4·5. Growth occurs in the presence of 0–12 % (w/v) NaCl, with an optimum of 2–3 % (w/v). Yeast extract, biotin, p-aminobenzoic acid, thiamine hydrochloride and vitamin B12 are not required for growth. Tyrosine is hydrolysed, but hypoxanthine is not. Indole and H2S are not produced. In assays with the API ZYM system, lipase (C8) and leucine arylamidase are present, but trypsin, {alpha}-chymotrypsin, {alpha}-galactosidase, {beta}-galactosidase, {beta}-glucuronidase, {alpha}-glucosidase, {beta}-glucosidase, N-acetyl-{beta}-glucosaminidase, {alpha}-mannosidase and {alpha}-fucosidase are absent. L-Arabinose, D-cellobiose, D-fructose, D-galactose, lactose, maltose, D-mannose, sucrose, D-trehalose, D-xylose, benzoate, formate and L-glutamate are not utilized. Acid is produced from D-cellobiose, D-mannose, melibiose and D-ribose. Acid is not produced from D-melezitose, D-raffinose, sucrose, D-trehalose, adonitol, myo-inositol or D-sorbitol. Sensitive to cephalothin (30 µg), chloramphenicol (100 µg) and penicillin G (20 U) but not to novobiocin (5 µg). The predominant respiratory lipoquinone is Q-8. The major fatty acid is C18 : 1{omega}9c. The DNA G+C content is 43·2 mol% (HPLC). Other characteristics are shown in Table 1Go.

The type strain, SW-210T (=KCTC 12254T=DSM 16329T), was isolated from sea water of the South Sea in Korea.

Description of Psychrobacter namhaensis sp. nov.
Psychrobacter namhaensis (nam.ha.en'sis. N.L. masc. adj. namhaensis of Namhae, the Korean name for the South Sea in Korea, where the organism was isolated).

Cells are cocci or short rods (1·0–1·2x1·4–2·5 µm). On MA, colonies are smooth, glistening, raised, circular to slightly irregular, cream in colour and 1·5–2·5 mm in diameter after incubation for 3 days at 30 °C. Growth occurs at 4 and 37 °C but not at 38 °C. Optimal pH for growth is 6·5–7·5; growth occurs at pH 5·0 but not at pH 4·5. Growth occurs in the presence of 0–13 % (w/v) NaCl, with an optimum of 2–3 % (w/v). Yeast extract, biotin, p-aminobenzoic acid, thiamine hydrochloride and vitamin B12 are not required for growth. Tyrosine is hydrolysed, but hypoxanthine is not. Indole and H2S are not produced. In assays with the API ZYM system, lipase (C8) and leucine arylamidase are present, but trypsin, {alpha}-chymotrypsin, {alpha}-galactosidase, {beta}-galactosidase, {beta}-glucuronidase, {alpha}-glucosidase, {beta}-glucosidase, N-acetyl-{beta}-glucosaminidase, {alpha}-mannosidase and {alpha}-fucosidase are absent. Benzoate is utilized. L-Arabinose, D-cellobiose, D-fructose, D-galactose, lactose, maltose, D-mannose, sucrose, D-trehalose, D-xylose, formate and L-glutamate are not utilized. Acid is produced from D-cellobiose, D-mannose, melibiose and D-ribose. Acid is not produced from D-melezitose, D-raffinose, sucrose, D-trehalose, adonitol, myo-inositol or D-sorbitol. Sensitive to cephalothin (30 µg) and chloramphenicol (100 µg) but not to novobiocin (5 µg) or penicillin G (20 U). The predominant respiratory lipoquinone is Q-8. The major fatty acid is C18 : 1{omega}9c. The DNA G+C content is 45·3 mol% (HPLC). Other characteristics are shown in Table 1Go.

The type strain, SW-242T (=KCTC 12255T=DSM 16330T), was isolated from sea water of the South Sea in Korea.


    ACKNOWLEDGEMENTS
 
This work was supported by the 21C Frontier Program of Microbial Genomics and Applications (grant MG02-0401-001-1-0-0) from the Ministry of Science and Technology (MOST) of the Republic of Korea.


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