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Int J Syst Evol Microbiol 56 (2006), 2229-2233; DOI  10.1099/ijs.0.64283-0
© 2006 International Union of Microbiological Societies

Idiomarina homiensis sp. nov., isolated from seashore sand in Korea

Soon-Wo Kwon1, Byung-Yong Kim1, Hang-Yeon Weon2, Youn-Kyung Baek1, Bon-Sung Koo1 and Seung-Joo Go1

1 Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea
2 Applied Microbiology Division, National Institute of Agricultural Science and Technology, Rural Development Administration, Suwon 441-707, Korea

Correspondence
Byung-Yong Kim
kimby{at}rda.go.kr


   ABSTRACT
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A halophilic, aerobic bacterium, designated PO-M2T, was isolated from seashore sand, from Pohang, Korea and characterized on the basis of physiological and biochemical features. Phylogenetic analysis of 16S rRNA gene sequences revealed a clear affiliation of the novel strain with members of the genus Idiomarina. Sequence similarities between strain PO-M2T and the type strains of species belonging to the genus Idiomarina ranged from 94.3 to 95.5 %. Cells of strain PO-M2T were straight or slightly curved rods and formed light-yellow colonies on marine agar medium. The major isoprenoid quinone was ubiquinone (Q-8) and the predominant cellular fatty acids were C15 : 0 iso (19.3 %), C17 : 1{omega}9c iso (11.9 %), C17 : 0 iso (10.9 %), C18 : 1{omega}7c (10.4 %), C16 : 0 (9.0 %) and C16 : 1{omega}7c and/or C15 : 0 iso 2-OH (7.2 %). The G+C content of the DNA was 45.1 mol%. Based on physiological, biochemical and chemotaxonomic traits and comparative 16S rRNA gene sequence analysis, it is demonstrated that the isolate represents a novel species of the genus Idiomarina, for which the name Idiomarina homiensis sp. nov. is proposed. The type strain is PO-M2T (=KACC 11514T=DSM 17923T).

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain PO-M2T is DQ342238.


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The genus Idiomarina was first proposed by Ivanova et al. (2000)Go to accommodate two marine bacteria, Idiomarina abyssalis and Idiomarina zobellii. Since the description of the genus, the names of the species Idiomarina baltica (Brettar et al., 2003Go), Idiomarina loihiensis (Donachie et al., 2003Go), Idiomarina fontislapidosi (Martínez-Cánovas et al., 2004Go), Idiomarina ramblicola (Martínez-Cánovas et al., 2004Go) and Idiomarina seosinensis (Choi & Cho, 2005Go) have been validly published. Features that distinguish members of the genus Idiomarina from other marine bacteria are their high content of iso-branched fatty acids and their physiological properties, in particular their ability to grow within a broad range of temperatures, pH values and NaCl concentrations (Martínez-Cánovas et al., 2004Go). In this study, we report on the taxonomic characterization of a novel Idiomarina bacterial strain, PO-M2T, which was isolated from Homi Cape, near Pohang, Korea.

Strain PO-M2T was isolated from a seashore sand sample by using a dilution plating technique on marine agar 2216 (MA; Difco). Colonial properties were observed on MA medium. Cell morphology was observed using light microscopy and transmission electron microscopy (TEM) (Fig. 1Go). Flagellum type was also determined by TEM. Gram staining, KOH test and L-alanine aminopeptidase assay were performed according to the manufacturer's instructions by using a Gram stain kit (Difco), 3 % (w/v) KOH (Buck, 1982Go) and Bactident aminopeptidase (Merck), respectively. Phenotypic tests were performed using standard procedures (Smibert & Krieg, 1994Go). Hydrolysis of carboxymethylcellulose (0.1 %; Sigma), alginic acid (0.5 %, w/v), chitin from crab shells (1 %, w/v), pectin (0.5 %, w/v) and tyrosine (0.5 %, w/v) was also tested. Growth at different salinities was tested in 0, 1, 3, 5, 7, 10, 15, 20 and 25 % NaCl in half-strength marine broth. The temperature range for growth was assessed at 4, 10, 15, 20, 25, 30, 35, 40, 45, 50 and 55 °C on MA. Marine broth adjusted to initial pH values of 4, 5, 6, 7, 8, 9 and 10 with citrate/phosphate buffer or Tris/HCl buffer (Breznak & Costilow, 1994Go) was used to test the ability of the strain to grow at different pH values. API 20NE, API 50 CH and API ZYM test strips (bioMérieux) were used according to the manufacturer's instructions. To investigate the utilization of carbon substrates, Biolog GN2 plates were used with both 0.85 % NaCl solution and artificial seawater for cell suspension.


Figure 1
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  		Fig. 1. Electron micrograph of a negatively stained cell of PO-M2T. Bar, 500 nm.

 
The following chemotaxonomic characteristics were analysed: isoprenoid quinone (as described by Groth et al., 1996Go), fatty acids (according to the standard protocol of the MIDI/Hewlett Packard microbial identification system; Sasser, 1990Go) and G+C content of the DNA (Mesbah et al., 1989Go).

The 16S rRNA gene sequence of strain PO-M2T was analysed as described by Kwon et al. (2003)Go. Phylogenetic analysis was performed by using MEGA, version 3.1 (Kumar et al., 2004Go), after multiple alignment of the data using CLUSTAL W (Thompson et al., 1994Go). Distances were obtained using options according to the Kimura two-parameter model (Kimura, 1980Go) and clustering was performed by using neighbour-joining (Saitou & Nei, 1987Go) and maximum-parsimony (Fitch, 1971Go) methods. Bootstrap values with 1000 replications were used to determine the confidence level of the branches (Felsenstein, 1985Go).

Strain PO-M2T had a 16S rRNA gene sequence similarity range of 94.3–95.5 % with sequences of the type strains of species within the genus Idiomarina, with the highest sequence similarities to I. loihiensis L2-TRT (95.5 %) and I. fontislapidosi F23T (95.5 %). The phylogenetic tree clearly showed that strain PO-M2T formed a robust clade separate from other related genera, which was supported by a high bootstrap value (Fig. 2Go). A maximum-parsimony tree also confirmed the stable positioning of strain PO-M2T within the genus Idiomarina (data not shown).


Figure 2
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  		Fig. 2. Neighbour-joining tree showing the position of strain PO-M2T and some other related taxa on the basis of 16S rRNA gene sequences. Numbers at branch points indicate bootstrap confidence values (%) of 1000 resamplings; only values greater than 60 % are shown. Bar, 0.01 substitutions per nucleotide position.

 
Cells of strain PO-M2T were aerobic, Gram-negative, motile, straight or slightly curved rods, 0.4–0.6 µm in width and 0.7–2.0 µm in length. Colonies formed on MA medium were light-yellow and convex. The strain was oxidase- and catalase-positive. It did not grow anaerobically. Strain PO-M2T grew at 4–45 °C, with optimum growth occurring at 25–30 °C. The pH range for growth was 6.0–9.0. Strain PO-M2T was also positive for the KOH test and hydrolysis of tyrosine, gelatin, DNA and Tween 80. H2S was produced from cysteine. Growth occurred in MA medium containing 15 % (w/v) NaCl. Details of various characteristics that differentiated strain PO-M2T from phylogenetically related species are given in Table 1Go; other characteristics determined are given in the species description.


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  		Table 1. Characteristics that distinguish Idiomarina homiensis sp. nov. from other Idiomarina species

Strains: 1, strain PO-M2T; 2, I. seosinensis CL-SP19T; 3, I. abyssalis KMM 227T; 4, I. zobellii KMM 231T; 5, I. baltica OS145T; 6, I. loihiensis L2-TRT; 7, I. fontislapidosi F23T; 8, I. ramblicola R22T. Data from Choi & Cho (2005)Go, Martínez-Cánovas et al. (2004)Go, Brettar et al. (2003)Go, Ivanova et al. (2000)Go and this study. ND, No data available; +, positive response; –, negative response; W, weak response.

 
The major respiratory lipoquinone of strain PO-M2T (Q-8) supported the affiliation of the strain to the genus Idiomarina. The fatty acid profile and DNA G+C content of strain PO-M2T were similar to those of other species of the genus Idiomarina. The predominant fatty acids of strain PO-M2T were iso-branched fatty acids, which is characteristic of the genus Idiomarina (Table 2Go). The detailed fatty acid profile was C15 : 0 iso (19.3 %), C17 : 1{omega}9c iso (11.9 %), C17 : 0 iso (10.9 %), C18 : 1{omega}7c (10.4 %), C16 : 0 (9.0 %) and C16 : 1{omega}7c and/or C15 : 0 iso 2-OH (7.2 %). The G+C content of the genomic DNA was 45.1 mol%. The chemotaxonomic results supported the phylogenetic analysis, indicating that strain PO-M2T belongs to the genus Idiomarina.


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  		Table 2. Fatty acid composition of Idiomarina homiensis sp. nov. and other Idiomarina species

Strains: 1, strain PO-M2T (data from this study); 2, I. seosinensis CL-SP19T (Choi & Cho, 2005Go); 3, I. abyssalis KMM 227T (Ivanova et al., 2000Go); 4, I. zobellii KMM 231T (Ivanova et al., 2000Go); 5, I. baltica OS145T (Brettar et al., 2003Go); 6, I. loihiensis L2-TRT (Donachie et al., 2003Go); 7, I. fontislapidosi F23T (Martínez-Cánovas et al., 2004Go); 8, I. ramblicola R22T (Martínez-Cánovas et al., 2004Go). Values are percentages of total fatty acids. –, Not detected or <1 %.

 
On the basis of phylogenetic, biochemical and physiological data, we propose that isolate PO-M2T should be classified as representing the type strain of a novel species, Idiomarina homiensis sp. nov.

Description of Idiomarina homiensis sp. nov.
Idiomarina homiensis (ho.mi.en'sis. N.L. fem. adj. homiensis referring to the Homi Cape in Korea, where the type strain was isolated).

Cells are aerobic, straight or slightly curved rods, approximately 0.4–0.6 µm in width and 0.7–2.0 µm in length. Motile by means of a single polar flagellum. On MA solid medium, colonies are light-yellowish, round and convex. Growth occurs within the temperature range 4–45 °C (optimum growth at 25–30 °C) and at pH values between 6 and 9. Growth occurs in 1–15 % (w/v) NaCl (optimum growth at 3–5 %). Does not grow anaerobically. Cells are Gram-negative by Gram-stain test, KOH test and aminopeptidase test. Positive for oxidase, catalase, KOH test, production of H2S from cysteine and hydrolysis of tyrosine, DNA, gelatin and Tween 80. Negative for indole production, Voges–Proskauer test, phenylalanine deamination and hydrolysis of casein, starch, chitin, lecithin, cellulose, pectin and urea. Does not degrade alginic acid. In API 20NE tests, cells are positive for nitrate reductase activity and hydrolysis of aesculin, but negative for other reactions. In API ZYM tests, cells are positive for acid and alkaline phosphatase, esterase (C4 and C8), leucine arylamidase, valine arylamidase, cystine arylamidase, trypsin, {alpha}-chymotrypsin and naphthol phosphohydrolase activities, but negative for {alpha}-galactosidase, beta-galactosidase, beta-glucuronidase, {alpha}-glucosidase, beta-glucosidase, N-acetyl-beta-glucosaminidase, {alpha}-mannosidase and {alpha}-fucosidase activities. No reactions are observed in API 50 CH and Biolog tests. The DNA G+C content is 45.1 mol%. Ubiquinone-8 is the main respiratory lipoquinone. Major fatty acids are C15 : 0 iso (19.3 %), C17 : 1{omega}9c iso (11.9 %), C17 : 0 iso (10.9 %), C18 : 1{omega}7c (10.4 %), C16 : 0 (9.0 %) and C16 : 1{omega}7c and/or C15 : 0 iso 2-OH (7.2 %) when grown on MA for 48 h.

The type strain is PO-M2T (=KACC 11514T=DSM 17923T), which was isolated from seashore sand in Pohang, Korea.


   ACKNOWLEDGEMENTS
 
This study was supported by the Agricultural Research & Promotion Center, Republic of Korea. We thank Seung-Hee Yoo and Young-Ju Lee for their excellent technical assistance.


   REFERENCES
TOP
 ABSTRACT
 MAIN TEXT
 REFERENCES
 
Brettar, I., Christen, R. & Höfle, M. G. (2003). Idiomarina baltica sp. nov., a marine bacterium with a high optimum growth temperature isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 53, 407–413.[Abstract/Free Full Text]

Breznak, J. A. & Costilow, R. N. (1994). Physicochemical factors in growth. In Methods for General and Molecular Bacteriology, pp. 137–154. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.

Buck, J. D. (1982). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993.[Abstract/Free Full Text]

Choi, D. H. & Cho, B. C. (2005). Idiomarina seosinensis sp. nov., isolated from hypersaline water of a solar saltern in Korea. Int J Syst Evol Microbiol 55, 379–383.[Abstract/Free Full Text]

Donachie, S. P., Hou, S., Gregory, T. S., Malahoff, A. & Alam, M. (2003). Idiomarina loihiensis sp. nov., a halophilic {gamma}-Proteobacterium from the Lo'ihi submarine volcano, Hawai'i. Int J Syst Evol Microbiol 53, 1873–1879.[Abstract/Free Full Text]

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.[CrossRef]

Groth, I., Schumann, P., Weiss, N., Martin, K. & Rainey, F. A. (1996). Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46, 234–239.[Abstract/Free Full Text]

Ivanova, E. P., Romanenko, L. A., Chun, J. & 7 other authors (2000). Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov. Int J Syst Evol Microbiol 50, 901–907.[Abstract]

Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef][Medline]

Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[Abstract/Free Full Text]

Kwon, S. W., Kim, J. S., Park, I. C., Yoon, S. H., Park, D. H., Lim, C. K. & Go, S. J. (2003). Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. Int J Syst Evol Microbiol 53, 21–27.[Abstract/Free Full Text]

Martínez-Cánovas, M. J., Béjar, V., Martínez-Checa, F., Páez, R. & Quesada, E. (2004). Idiomarina fontislapidosi sp. nov. and Idiomarina ramblicola sp. nov., isolated from inland hypersaline habitats in Spain. Int J Syst Evol Microbiol 54, 1793–1797.[Abstract/Free Full Text]

Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.

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, MIDI Technical Note 101. Newark, DE: MIDI Inc.

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.

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.[Abstract/Free Full Text]




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