| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 52 Oun Dong, Yusong, Daejon 305-333, Republic of Korea
2 Pacific Institute of Bioorganic Chemistry of Far-Eastern Branch of the Russian Academy of Sciences, Pr. 100 Let Vladivostoku, 159, Vladivostok, 690022, Russia
Correspondence
Seung Bum Kim
sbk01{at}kribb.re.kr
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain KMM 3905T is AY211385.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
to accommodate phylogenetically distinct actinobacteria formerly classified in the genus Micrococcus, within which heterogeneity had been suggested in earlier studies (Kloos, 1969; Ogasawara-Fujita & Sakaguchi, 1976). Kocuria is clearly separated from Micrococcus and other related Gram-positive cocci such as Arthrobacter and Rothia in phylogenetic analyses using 16S rRNA gene sequences (Stackebrandt et al., 1995).
Six species with validly published names currently comprise the genus, namely Kocuria kristinae, Kocuria palustris, Kocuria polaris, Kocuria rhizophila, Kocuria rosea and Kocuria varians (Stackebrandt et al., 1995; Kovács et al., 1999; Reddy et al., 2003). Members of Kocuria are Gram-positive, aerobic, coccoid, non-encapsulated, non-halophilic and non-endospore-forming. Their normal habitats include mammalian skin, soil, the rhizoplane and fresh water (Kloos et al., 1974; Kocur, 1986; Kovács et al., 1999). Little is known regarding their pathogenicity to humans and other mammals, but they are not considered to be a primary pathogen (Kocur, 1986; Kocur et al., 1991).
Members of Kocuria are characterized by the presence of menaquinones MK-7(H2) and MK-8(H2), lysine-based A3
-type peptidoglycan, PI-type phospholipids and saturated branched fatty acids (anteiso-C15 : 0 as the major component) in their cell envelopes (Stackebrandt et al., 1995). The G+C content of the genomic DNA ranges from 66 to 75 mol% (Bohá
ek et al., 1969; Kloos et al., 1974; Kocur et al., 1971; Kovács et al., 1999; Reddy et al., 2003).
There is no record on the isolation of strains belonging to the genus Kocuria from the marine environment, although many members exhibit tolerance to high salt concentrations (Stackebrandt et al., 1995; Kovács et al., 1999). During an investigation exploring bacterial diversity in the marine environment in the Gulf of Peter the Great, East Siberian Sea, a coccoid actinobacterial strain was isolated and designated KMM 3905T. The strain was subjected to a polyphasic investigation, and its taxonomic position is discussed below.
Strain KMM 3905T was isolated from a marine sediment sample taken from Troitsa Bay. After primary isolation and purification on marine agar 2216 (Difco) at 28 °C, the strain was subcultured on the same medium and stored at –80 °C in marine broth (Difco) supplemented with 20 % (v/v) glycerol.
The presence of enzyme activities, degradation of organic compounds, growth on NaCl, production of acid from carbohydrates, susceptibility to antibiotics and other physiological characteristics of the organism were determined as described by Han et al. (2003). DNA extraction, PCR and sequencing of 16S rRNA genes were performed according to previously described procedures (Kim et al., 1998). The 16S rRNA gene sequence obtained was aligned together with those of representative members of Kocuria using PHYDIT version 3.2 (http://plaza.snu.ac.kr/
jchun/phydit/). Phylogenetic trees were inferred using suitable programs of the PHYLIP package (Felsenstein, 1993). Phylogenetic distances were calculated from the model of Kimura (1980) and phylogenetic trees were constructed following the least-squares (Fitch & Margoliash, 1967), maximum-likelihood (Felsenstein, 1981) and neighbour-joining (Saitou & Nei, 1987) algorithms. Micrococcus luteus (M38242) was used as an outgroup to infer the root position (data not shown). Bootstrap analysis was performed with 1000 resampled datasets, using the SEQBOOT and CONSENSE programs of PHYLIP. Extraction of menaquinones and analysis by HPLC were carried out using a standard procedure (Minnikin et al., 1984). To determine fatty acid methyl esters, strains were cultivated on marine agar (Difco) at 25 °C for 24–48 h. Extraction and analysis of cellular fatty acids were performed according to the procedures for the SHERLOCK Microbial Identification System (MIDI Inc.).
Strain KMM 3905T formed aerobic, catalase-positive, coccoid, Gram-positive cells. The strain was able to grow in the presence of up to 15 % NaCl, although its presence was not required for growth (Table 1). The G+C content of the genomic DNA was 60 mol%. The cell envelope contained a major amount of 12-methyl-tetradecanoic acid (anteiso-C15 : 0), and also smaller amounts of 14-methyl hexadecanoic acid (anteiso-C17 : 0) and 14-methyl pentadecanoic acid (iso-C16 : 0; Table 2). The dominance of anteiso-C15 : 0 is consistent for Kocuria, although the test was carried out in different media than reported previously (Table 2). The morphological, phenotypic and chemotaxonomic descriptions of strain KMM 3905T are also consistent with its assignment to the genus Kocuria (Stackebrandt et al., 1995; Kovács et al., 1999).
|
|
). KMM 3905T had 16S rRNA gene sequence similarities ranging from 96·2 to 98·2 % with other species of Kocuria. KMM 3905T was most closely related to K. rhizophila DSM 11926T and K. varians DSM 20033T, and the topology of the branch for KMM 3905T and these two species was reproducible in the trees using least-squares and maximum-likelihood methods. K. rhizophila and K. varians have a close relationship with each other, sharing 98·6 % 16S rRNA gene sequence similarity and are always recovered as a single cluster group in previous analyses. However, the two species are clearly distinguished on the basis of phenotypic and genotypic data such as physiological properties and DNA–DNA relatedness (Kovács et al., 1999; Reddy et al., 2003). The high bootstrap value between KMM 3905T and the K. rhizophila–K. varians group also strongly supported the tree topology of the three taxa (Fig. 1), indicating that the branching of KMM 3905T and the K. rhizophila–K. varians group is stable. 16S rRNA gene sequence analysis clearly supports strain KMM 3905T as representing a separate phylogenetic lineage.
|
). Strain KMM 3905T showed different results in at least 11 tested characters from any other known species of Kocuria. The DNA G+C content of KMM 3905T was 60 mol%, the lowest reported among the members of the genus.
Total membrane fatty acids of members of Kocuria consist of major amounts of branched, saturated species (over 75 % of the total), with minor amounts of straight or unsaturated fatty acids. In contrast, saturated species comprise over 90 % of the total in all members (Table 2; Stackebrandt et al., 1995; Kovács et al., 1999; Reddy et al., 2003). KMM 3905T, even allowing that the data were obtained from marine 2216 agar, has a unique fatty acid profile in that anteiso-C15 : 0 comprises 74 % of the total, though this is similar to the profiles for K. rhizophila and K. varians. KMM 3905T, K. rhizophila and K. varians are also unique in that they do not contain any significant proportion of unsaturated fatty acids, whereas other species of Kocuria contain at least 7 % unsaturated components.
From the polyphasic taxonomic evidence reported here, KMM 3905T clearly merits species status within Kocuria, for which we propose the name Kocuria marina sp. nov.
Description of Kocuria marina sp. nov.
Kocuria marina (ma.ri'na. L. fem. adj. marina of the sea).
Gram-positive, aerobic, non-motile, halotolerant coccoid cells. Positive for catalase, 
-galactosidase and urease, but negative for arginine dihydrolase, lysine and ornithine decarboxylase, oxidase and alkaline phosphatase. Nitrate is reduced, but hydrogen sulphide is not produced. Production of indole and acetoin (Voges–Proskauer reaction) is negative. Growth occurs in the presence of up to 15 % NaCl, although its presence is not required for growth. Grows at 4–43 °C. Casein, gelatin and Tween 40 are hydrolysed, but agar, alginate, cellulose, DNA, starch, Tween 20 and Tween 80 are not. Glucose, lactose, mannose and sucrose are utilized as sole carbon sources, but not adonitol, L-arabinose, meso-inositol, mannitol, sorbitol, citric acid or malonic acid. Acid is produced from L-fucose, but not from acetic acid, N-acetylglucosamine, adonitol, L-arabinose, cellobiose, dulcitol, fumaric acid, galactose, glucose, glycerol, meso-inositol, lactose, malic acid, maltose, mannitol, melibiose, raffinose, rhamnose, sorbitol, sorbose, sucrose and L-xylose. Growth is inhibited by ampicillin, benzylpenicillin, carbenicillin, gentamicin, lincomycin, neomycin, oleandomycin, streptomycin and tetracycline, but not by kanamycin or polymixin B. Contains major amounts of branched, saturated fatty acids with 14 to 17 carbons, among which 12-methyl-tetradecanoic acid (anteiso-C15 : 0) is the predominant form. The G+C content of the genomic DNA is 60 mol%.
The type and only strain is KMM 3905T (=KCTC 9943T), isolated from marine sediment.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
ek, J., Kocur, M. & Martinec, T. (1969). Deoxyribonucleic acid base composition of Micrococcus roseus. Antonie van Leeuwenhoek 35, 185–188.[Medline]Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef][Medline]
Felsenstein, J. (1993). PHYLIP (Phylogenetic Inference Package), version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle, USA.
Fitch, W. M. & Margoliash, E. (1967). Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155, 279–284.
Han, S. K., Nedashkovskaya, O. I., Mikhailov, V. V., Kim, S. B. & Bae, K. S. (2003). Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. Int J Syst Evol Microbiol 53, 2061–2066.
Kim, S. B., Falconer, C., Williams, E. & Goodfellow, M. (1998). Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species isolated from soil. Int J Syst Bacteriol 48, 59–68.
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]
Kloos, W. E. (1969). Transformation of Micrococcus lysodeikticus by various members of the family Micrococcaceae. J Gen Microbiol 59, 247–255.[Medline]
Kloos, W. E., Tornabene, T. G. & Schleifer, K. H. (1974). Isolation and characterization of micrococci from human skin, including two new species: Micrococcus lylae and Micrococcus kristinae. Int J Syst Bacteriol 24, 79–101.
Kocur, M. (1986). Genus Micrococcus Cohn 1872. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1004–1008. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
Kocur, M., Bergan, T. & Mortensen, N. (1971). DNA base composition of Gram-positive cocci. J Gen Microbiol 69, 167–183.[Medline]
Kocur, M., Kloos, W. E. & Schleifer, K. H. (1991). The genus Micrococcus. In The Prokaryotes, 2nd edn, vol. 2, pp. 1300–1311. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
Kovács, G., Burghardt, J., Pradella, S., Schumann, P., Stackebrandt, E. & Màrialigeti, K. (1999). Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia). Int J Syst Bacteriol 49, 167–173.
Minnikin, D. E., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
Ogasawara-Fujita, N. & Sakaguchi, K. (1976). Classification of micrococci on the basis of deoxyribonucleic acid homology. J Gen Microbiol 94, 97–106.[Medline]
Reddy, G. S. N., Prakash, J. S. S., Prabahar, V., Matsumoto, G. I., Stackebrandt, E. & Shivaji, S. (2003). Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample. Int J Syst Evol Microbiol 53, 183–187.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Stackebrandt, E., Koch, C., Gvozdiak, O. & Schumann, P. (1995). Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 45, 682–692.
This article has been cited by other articles:
|
|
 |
|
  H. Takarada, M. Sekine, H. Kosugi, Y. Matsuo, T. Fujisawa, S. Omata, E. Kishi, A. Shimizu, N. Tsukatani, S. Tanikawa, et al. Complete Genome Sequence of the Soil Actinomycete Kocuria rhizophila J. Bacteriol., June 15, 2008; 190(12): 4139 - 4146. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Zhou, X. Luo, Y. Tang, L. Zhang, Q. Yang, Y. Qiu, and C. Fang Kocuria flava sp. nov. and Kocuria turfanensis sp. nov., airborne actinobacteria isolated from Xinjiang, China Int J Syst Evol Microbiol, June 1, 2008; 58(6): 1304 - 1307. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Mayilraj, R. M. Kroppenstedt, K. Suresh, and H. S. Saini Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1971 - 1975. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W.-J. Li, Y.-Q. Zhang, P. Schumann, H.-H. Chen, W. N. Hozzein, X.-P. Tian, L.-H. Xu, and C.-L. Jiang Kocuria aegyptia sp. nov., a novel actinobacterium isolated from a saline, alkaline desert soil in Egypt. Int J Syst Evol Microbiol, April 1, 2006; 56(Pt 4): 733 - 737. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Tvrzova, P. Schumann, I. Sedlacek, Z. Pacova, C. Sproer, S. Verbarg, and R. M. Kroppenstedt Reclassification of strain CCM 132, previously classified as Kocuria varians, as Kocuria carniphila sp. nov. Int J Syst Evol Microbiol, January 1, 2005; 55(1): 139 - 142. [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 | |
