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Int J Syst Evol Microbiol 57 (2007), 2406-2411; DOI  10.1099/ijs.0.65003-0
© 2007 International Union of Microbiological Societies

Reclassification of Marinococcus albus Hao et al. 1985 as Salimicrobium album gen. nov., comb. nov. and Bacillus halophilus Ventosa et al. 1990 as Salimicrobium halophilum comb. nov., and description of Salimicrobium luteum sp. nov.

Jung-Hoon Yoon, So-Jung Kang and Tae-Kwang Oh

Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea

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


    ABSTRACT
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 ABSTRACT
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A Gram-positive, non-motile, coccoid-shaped, non-spore-forming halophilic bacterial strain, BY-5T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated by using a polyphasic approach. The novel strain grew optimally at 37 °C and in the presence of 10 % (w/v) NaCl. Strain BY-5T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C content was 47.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BY-5T formed a coherent cluster with Bacillus halophilus and Marinococcus albus. Strain BY-5T exhibited 16S rRNA gene sequence similarity values of 98.7 and 97.4 % to the type strains of B. halophilus and M. albus, respectively. Strain BY-5T was distinguished from B. halophilus and M. albus by several phenotypic properties and DNA–DNA relatedness data. On the basis of the combined chemotaxonomic and phylogenetic data, it is proposed that M. albus, B. halophilus and strain BY-5T should be placed in a new genus as three separate species. Marinococcus albus and Bacillus halophilus are reclassified in a new genus, Salimicrobium gen. nov., as Salimicrobium album comb. nov. and Salimicrobium halophilum comb. nov., respectively. The type species of the new genus is Salimicrobium album. Strain BY-5T (=KCTC 3989T=CIP 108918T) is placed in the genus Salimicrobium as a novel species Salimicrobium luteum sp. nov.


The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain BY-5T is DQ227305.


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Moderately halophilic bacteria have been defined as micro-organisms that grow optimally in media containing 3–15 % (w/v) salt (Kushner & Kamekura, 1988Go; Ventosa et al., 1998aGo, bGo). They constitute a heterogeneous physiological group of micro-organisms which belong to different genera including Gram-positive and Gram-negative bacteria (Ventosa et al., 1998bGo). Of these bacteria, Gram-positive, moderately halophilic, coccoid-shaped taxa, e.g. members of the genera Marinococcus, Salinicoccus, Tetragenococcus, Planococcus, Jeotgalicoccus, Serinicoccus, Sinococcus and some Nesterenkonia species, have hitherto been described (Kocur et al., 1970Go; Hao et al., 1984Go; Collins et al., 1990Go; Ventosa et al., 1990Go; Stackebrandt et al., 1995Go; Yoon et al., 2003Go; Yi et al., 2004Go; Li et al., 2006Go). In this study, we describe a Gram-positive and moderately halophilic bacterial strain, BY-5T, which was isolated from a marine solar saltern in Korea. The isolate was considered to be closely related to Bacillus halophilus and Marinococcus albus on the basis of 16S rRNA gene sequence comparisons. The aim of the present study was to determine the exact taxonomic position of strain BY-5T by using a polyphasic approach.

Sediment samples collected from a marine solar saltern in Byunsan, Korea, were used as the source for the isolation of halophilic or halotolerant bacteria. Soil samples (around 50 mg) were inoculated in 50 ml of a modified liquid Sehgal–Gibbons (S–G) medium (Sehgal & Gibbons, 1960Go), which contained (l–1 distilled water) 300 g NaCl, 20 g MgSO4 . 7H2O, 2 g KCl, 3 g trisodium citrate, 10 g yeast extract (Difco) and 7.5 g Casamino acids. This medium was incubated at 25 °C on a horizontal shaker at 150 r.p.m. When turbidity was visible after incubation for several days, 1 ml of the suspension was transferred into 50 ml fresh medium and the medium was reincubated under the same conditions. After three successive transfers, the suspension was plated on the above-mentioned medium solidified with 1.5 % (w/v) agar in order to isolate pure cultures. Of the isolates obtained, strain BY-5T was selected for further study. Bacillus halophilus KCTC 3566T from the Korean Collection for Type Cultures (KCTC; Taejon, Korea) and Marinococcus albus LMG 17430T from the Laboratorium voor Microbiologie Universiteit Gent (LMG; Gent, Belgium) were used as reference strains for comparative fatty acid analysis and DNA–DNA hybridization.

The morphological properties of strain BY-5T were investigated by using routine cultivation on marine agar 2216 (MA; Difco) supplemented with 8 % (w/v) NaCl, 15 % (w/v) salt MH agar (Ventosa et al., 1982Go) and MH agar (Rodriguez-Valera et al., 1980Go) at 37 °C. Strain BY-5T was routinely cultivated on MA supplemented with 8 % (w/v) NaCl at 37 °C to investigate physiological and biochemical characteristics. Cell morphology was examined by light microscopy (E600; Nikon) and transmission electron microscopy. The presence of flagella was investigated by transmission electron microscopy using 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 ascertained in marine broth 2216 (MB; Difco) supplemented with 8 % (w/v) NaCl that was adjusted to various pH values (initial pH 4.5–10.5 at intervals of 0.5 pH units) prior to sterilization by the addition of HCl or Na2CO3. Growth in the absence of NaCl was investigated in trypticase soy broth prepared according to the formula of the Difco medium except that no NaCl was used. Growth at various NaCl concentrations (0.5 % and 1.0–30.0 %, w/v, at intervals of 1.0 %) was investigated in trypticase soy broth (Difco) or MB. Growth at various temperatures (4–50 °C) was measured on MA containing 8 % NaCl. Growth under anaerobic conditions was determined after incubation in an anaerobic chamber on 8 % NaCl MA, with or without nitrate, that had been prepared anaerobically under a nitrogen stream. Oxidase and catalase activities and hydrolysis of casein and starch were determined as described by Cowan & Steel (1965)Go. Hydrolysis of Tweens 20, 40, 60 and 80 was determined as described by Cowan & Steel (1965)Go with a modification that artificial seawater was supplemented with 7.5 % (w/v) NaCl. Hydrolysis of aesculin, gelatin and urea and nitrate reduction were determined according to Lanyi (1987)Go with a modification that artificial seawater supplemented with 7.5 % (w/v) NaCl was used for the preparation of media. The artificial seawater contained (l–1 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). H2S production was tested as described by Bruns et al. (2001)Go. Hydrolysis of hypoxanthine, tyrosine and xanthine was performed on 8 % NaCl MA (Cowan & Steel, 1965Go).

Utilization of substrates as sole carbon and energy sources was tested according to the method of Kämpfer et al. (1991)Go, with the modification that media were supplemented with 9.1 % (w/v) NaCl. Acid production from carbohydrates was determined as described by Leifson (1963)Go. Susceptibility to antibiotics was tested on 8 % NaCl MA plates using discs containing the following concentrations of antibiotics; 100 U polymyxin B, 50 µg streptomycin, 20 U penicillin G, 100 µg chloramphenicol, 10 µg ampicillin, 30 µg cephalothin, 30 µg gentamicin, 5 µg novobiocin, 30 µg tetracycline, 30 µg kanamycin, 15 µg lincomycin, 15 µg oleandomycin, 30 µg neomycin and 100 µg carbenicillin. Enzyme activity and other physiological properties were determined using the API ZYM and API 20E systems (bioMérieux); the cell suspension used to inoculate the systems was prepared by using artificial seawater supplemented with 7.5 % (w/v) NaCl.

Cell biomass of strain BY-5T for DNA extraction and for cell wall and isoprenoid quinone analyses was obtained by cultivation for 2 days in 8 % NaCl MB at 37 °C. Chromosomal DNA was isolated and purified according to the method described previously (Yoon et al., 1996Go), with the exception that RNase T1 was used in combination with RNase A to minimize contamination with RNA. The 16S rRNA gene was amplified by PCR using two universal primers as described previously (Yoon et al., 1998Go). Sequencing of the amplified 16S rRNA gene and phylogenetic analysis were performed as described by Yoon et al. (2003)Go. The isomer type of the diamino acid in the cell-wall peptidoglycan was analysed using TLC according to the method described by Komagata & Suzuki (1987)Go. Isoprenoid quinones were extracted according to the method of Komagata & Suzuki (1987)Go and analysed using reversed-phase HPLC and a YMC ODS-A (250x4.6 mm) column. For fatty acid methyl ester analysis, cell mass of strain BY-5T, B. halophilus KCTC 3566T and M. albus LMG 17430T was harvested from agar plates after incubation for 3 days at 37 °C on 8 % NaCl MA and 15 % (w/v) salt MH agar and/or MH agar. 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 a modification that DNA was hydrolysed and the resultant nucleotides were analysed by reversed-phase HPLC. DNA–DNA hybridization was performed fluorometrically by 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 means of the remaining three values were quoted as DNA–DNA relatedness values.

Cells of strain BY-5T were Gram-positive and non-spore-forming cocci on 8 % NaCl MA, MH agar and 15 % salt MH agar. Cells were 0.7–1.4 µm in diameter on 8 % NaCl MA; they were larger (1.0–2.4 µm) on MH agar and 15 % salt MH agar. Cultural, physiological and biochemical characteristics of strain BY-5T are given in the species description (see below) or are shown in Table 1Go. The almost complete 16S rRNA gene sequence of strain BY-5T, comprising 1491 nucleotides (approx. 96 % of the Escherichia coli 16S rRNA gene sequence), was determined in this study. In the neighbour-joining tree based on 16S rRNA gene sequences, strain BY-5T formed a coherent cluster with Bacillus halophilus DSM 4771T with a bootstrap resampling value of 100 % (Fig. 1Go). This cluster joined the phylogenetic lineage of Marinococcus albus DSM 20748T by a bootstrap resampling value of 100 % (Fig. 1Go). The relationships between strain BY-5T, B. halophilus and M. albus were also maintained in trees generated with the maximum-likelihood and maximum-parsimony algorithms (Fig. 1Go). Strain BY-5T exhibited 16S rRNA gene sequence similarity values of 98.7 % to B. halophilus DSM 4771T, 97.4 % to M. albus DSM 20748T and less than 95.7 % to the other sequences deposited in databases. Strain BY-5T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. It contained menaquinone-7 (MK-7) as the predominant isoprenoid quinone (approx. 80 %); a minor amount of MK-6 (approx. 12 %) was also detected. Strain BY-5T had a cellular fatty acid profile that contained large amounts of branched and straight-chain fatty acids; the major components (>10 % of total fatty acids) were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 (Table 2Go). The DNA G+C content of strain BY-5T was 47.9 mol%.


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Table 1. Differential phenotypic characteristics of strain BY-5T, Bacillus halophilus and Marinococcus albus

Species: 1, strain BY-5T; 2, B. halophilus (data from Ventosa et al., 1989Go; Arahal et al., 1999Go); 3, M. albus (Hao et al., 1984Go; Li et al., 2005Go). +, Positive; –, negative; W, weakly positive; ND, not determined. All species are positive for catalase, oxidase and utilization of glucose and all have a requirement for NaCl for growth. All species are negative for anaerobic growth, for hydrolysis of casein and starch, for activities of arginine dihydrolase, lysine decarboxylase and ornithine decarboxylase, for the Voges–Proskauer reaction and for acid production from L-arabinose, D-galactose and lactose.

 

Figure 1
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Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the positions of strain BY-5T, Bacillus halophilus, Marinococcus albus and some other related taxa. Bootstrap values (1000 replications) are shown as percentages at each node only if they are 50 % or greater. Filled circles indicate that the corresponding nodes were also recovered in the trees generated with the maximum-likelihood and maximum-parsimony algorithms. Alicyclobacillus acidocaldarius DSM 446T was used as an outgroup. Bar, 0.01 substitutions per nucleotide position.

 

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Table 2. Cellular fatty acid content (%) of strain BY-5T, Bacillus halophilus KCTC 3566T and Marinococcus albus LMG 17430T on MA supplemented with 8 % NaCl, 15 % salt MH agar and on MH agar

Strains: 1, strain BY-5T (8 % NaCl MA); 2, B. halophilus KCTC 3566T (8 % NaCl MA); 3, M. albus LMG 17430T (8 % NaCl MA); 4, strain BY-5T (15 % salt MH agar); 5, B. halophilus KCTC 3566T (15 % salt MH agar); 6, strain BY-5T (MH agar); 7, M. albus LMG 17430T (MH agar). Fatty acids that represented <0.5 % in all strains are omitted. –, Not detected.

 
The morphology of cells of strain BY-5T was similar to that of cells of M. albus. Strain BY-5T had highest 16S rRNA gene sequence similarity to B. halophilus, but it was distinguishable from B. halophilus by cell morphology. Cells of strain BY-5T are spherical, whereas cells of B. halophilus are rods (Ventosa et al., 1989Go). The peptidoglycan diamino acid and predominant menaquinone types of strain BY-5T were the same as those of B. halophilus and M. albus (Hao et al., 1984Go; Ventosa et al., 1989Go). Strain BY-5T and B. halophilus KCTC 3566T have similar fatty acid profiles, although there are differences in the contents of iso-C15 : 0 and anteiso-C17 : 0, particularly when they are grown in 15 % salt MH agar (Table 2Go). The fatty acid profile of strain BY-5T is similar to that of M. albus LMG 17430T, although there are differences in the proportions of some fatty acids, particularly anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 (Table 2Go). M. albus and B. halophilus have been found to form phylogenetic lineages that are independent of the clusters comprising the type species of the genera Marinococcus and Bacillus, respectively (Schlesner et al., 2001Go; Li et al., 2005Go; Fig. 1Go). This phylogenetic data suggest that M. albus and B. halophilus may have to be placed in a new genus or new genera. M. albus, B. halophilus and strain BY-5T are differentiated from the genus Halobacillus in the cell-wall peptidoglycan type (Spring et al., 1996Go; García et al., 2005Go). Recognized members of the genus Halobacillus have a cell-wall peptidoglycan type that is based on L-Orn–D-Asp (Spring et al., 1996Go; García et al., 2005Go). M. albus, B. halophilus and strain BY-5T are distinguishable from members of the genera Halobacillus, Thalassobacillus and Pontibacillus by fatty acid profiles, particularly in the proportions of anteiso-C17 : 0 and iso-C17 : 0, although these differences could have been caused by variations in cultivation conditions and extraction procedures (García et al., 2005Go).

Despite differences in cell morphology, it appears to be appropriate that M. albus and B. halophilus, together with strain BY-5T, should be placed in one novel genus on the basis of their phylogenetic and chemotaxonomic similarities. DNA–DNA relatedness values indicate that strain BY-5T differs genetically from M. albus and B. halophilus (Wayne et al., 1987Go). Strain BY-5T exhibited mean DNA–DNA relatedness values of 15 and 22 % to M. albus LMG 17430T and B. halophilus KCTC 3566T, respectively. Strain BY-5T is distinguishable from B. halophilus and M. albus on the basis of phenotypic properties as shown in Table 1Go. Taking into account the data presented, M. albus, B. halophilus and strain BY-5T represent three different species in a novel genus. In conclusion, we propose that Marinococcus albus and Bacillus halophilus are reclassified in a new genus, Salimicrobium gen. nov., as Salimicrobium album comb. nov. (type species) and Salimicrobium halophilum comb. nov., respectively. In addition, strain BY-5T should be placed in the genus Salimicrobium as a novel species, for which the name Salimicrobium luteum sp. nov. is proposed.

Description of Salimicrobium gen. nov.
Salimicrobium (Sa.li.mi.cro'bi.um. L. masc. n. sal salt; N.L. neut. n. microbium a microbe; N.L. neut. n. Salimicrobium a salt microbe).

Cells are Gram-positive, strictly aerobic and rods or cocci. Catalase- and oxidase-positive. NaCl is required for growth. The cell-wall peptidoglycan contains meso-diaminopimelic acid as the diagnostic diaminoacid. The predominant menaquinone is MK-7. The fatty acid profile contains large amounts of branched fatty acids. The DNA G+C content is 44.9–51.5 mol%. The type species is Salimicrobium album.

Description of Salimicrobium album (Hao et al. 1985) comb. nov.
Salimicrobium album (al'bum. L. neut. adj. album white).

Basonym: Marinococcus albus Hao et al. 1985.

The description is the same as those given by Hao et al. (1984)Go and Li et al. (2005)Go. The type strain is HK 733T (=ATCC 49811T=JCM 2574T=CIP 104820T=DSM 20748T).

Description of Salimicrobium halophilum (Ventosa et al. 1990) comb. nov.
Salimicrobium halophilum (ha.lo.phi'lum. Gr. n. halos salt; Gr. adj. philos loving; N.L. neut. adj. halophilum salt loving).

Basonym: Bacillus halophilus Ventosa et al. 1990.

The description is the same as that given by Ventosa et al. (1989)Go. The type strain is strain N23-2T (=ATCC 49085T=DSM 4771T=JCM 12305T=LMG 17942T).

Description of Salimicrobium luteum sp. nov.
Salimicrobium luteum (lu'te.um. L. neut. adj. luteum yellow).

Cells are Gram-positive, non-spore-forming cocci (0.7–2.4 µm). Colonies are smooth, circular to slightly irregular, raised, smooth, glistening, yellow and 1.0–1.5 mm in diameter after incubation for 3 days at 37 °C on 8 % NaCl MA. Optimal growth occurs at 37 °C; growth occurs at 10 and 44 °C, but not at 4 and 45 °C. Optimal pH for growth is 7.5–8.0; growth occurs at pH 6.5, but not at pH 6.0. Optimal growth occurs in the presence of 10 % (w/v) NaCl; growth does not occur in the presence of <2 % (w/v) NaCl and >27 % (w/v) NaCl. Growth does not occur under anaerobic conditions on 8 % NaCl MA, with or without nitrate. Catalase- and oxidase-positive. NaCl is required for growth. Tweens 20, 40 and 60 are hydrolysed, but hypoxanthine, xanthine and L-tyrosine are not. H2S and indole are not produced. In assays with the API ZYM system, alkaline phosphatase, esterase (C4), esterase lipase (C8), naphthol-AS-BI-phosphohydrolase and beta-galactosidase are present, but lipase (C14), leucine arylamidase, valine arylamidase, cystine arylamidase, trypsin, {alpha}-chymotrypsin, acid phosphatase, {alpha}-galactosidase, beta-glucuronidase, {alpha}-glucosidase, beta-glucosidase, N-acetyl-beta-glucosaminidase, {alpha}-mannosidase and {alpha}-fucosidase are absent. Pyruvate is utilized as a sole carbon and energy source, but L-arabinose, D-xylose, acetate, citrate, succinate, benzoate, L-malate, formate and L-glutamate are not. Acid is produced from D-mannose and D-ribose, but not from D-cellobiose, D-melezitose, melibiose, D-raffinose, L-rhamnose, myo-inositol and D-sorbitol. Susceptible to penicillin G, chloramphenicol, ampicillin, cephalothin, novobiocin, kanamycin, lincomycin, oleandomycin and carbenicillin, but not to polymyxin B, streptomycin, gentamicin, tetracycline or neomycin. The major fatty acids (>10 % of total fatty acids) are anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0. The DNA G+C content is 47.9 mol% (HPLC). Other phenotypic properties are shown in Table 1Go.

The type strain, BY-5T (=KCTC 3989T=CIP 108918T), was isolated from a marine solar saltern in Korea.


    ACKNOWLEDGEMENTS
 
This work was supported by the 21C Frontier program of Microbial Genomics and Applications (grant MG05-0401-2-0) from the Ministry of Science and Technology (MOST) of the Republic of Korea.


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