| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Industrial Research Institute, Swinburne University of Technology, PO Box 218, Hawthorn, Vic 3122, Australia
2 Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Pr. 100 Let Vladivostoku 159, 690022 Vladivostok, Russia
3 Department of Agricultural Science, University of Tasmania, Hobart, Tasmania, Australia
4 Institute of Microbiology of the Russian Academy of Sciences, 117811 Moscow, Russia
5 Institute of Marine Biology of the Far-Eastern Branch of the Russian Academy of Sciences, Palchevskogo Str. 17, 690041 Vladivostok, Russia
6 Pacific Oceanological Institute of the Far-Eastern Branch of the Russian Academy of Sciences, Baltiiskaya Str. 43, 690017 Vladivostok, Russia
Correspondence
Elena P. Ivanova
eivanova{at}swin.edu.au
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
7 (14·8±1·1). The fatty acid 20 : 53, formed at 28 °C, was present at up to 5·3 % total fatty acids. The major isoprenoid quinones were Q7 (21–41 %) and Q8 (50–59 %). The phylogenetic, genetic and physiological properties of the six strains placed them within a novel species, Shewanella pacifica sp. nov., the type strain of which is R10SW1T (=KMM 3597T=CIP 107849T).
Published online ahead of print on 19 December 2003 as DOI 10.1099/ijs.0.02993-0.
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains KMM 3597T, KMM 3590 and KMM 3506 are AF500076, AF500075 and AY366086, respectively.
Tables showing the S. pacifica cellular fatty acid and isoprenoid quinone compositions and comparative fatty acid compositions of S. pacifica and related species are available in IJSEM Online.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
-Proteobacteria (MacDonell & Colwell, 1985
; Gauthier et al., 1995; Venkateswaran et al., 1999; Garrity & Holt, 2001). One of the striking features of these bacteria is the ability of some recently described species to produce polyunsaturated fatty acids (PUFAs) at relatively high incubation temperatures (25–30 °C; Ivanova et al., 2001, 2003a; Skerratt et al., 2002), which contradicts the notion that only barophilic or cold-adapted species are able to produce significant levels of PUFAs such as eicosapentaenoic acid (EPA, 20 : 53c; Russell & Nichols, 1999; Nogi et al., 1998).
In this study, a novel mesophilic, PUFA-producing bacterium of the genus Shewanella was characterized. The bacterium was isolated from sea water samples collected in Chazhma Bay (Sea of Japan, Pacific Ocean) and was able to form EPA at relatively high incubation temperatures. This work was part of a taxonomic survey of free-living microbial populations of the Bay in the North-West Pacific Ocean, sediments of which have been contaminated by radionuclides. During the course of this work, 70 presumptive Shewanella strains of different phenotypes were isolated. The majority of the strains had a few phenotypic features (e.g. agar-digesting and haemolytic activities, PUFA production) that were similar to those of a previously described species, Shewanella japonica (Ivanova et al., 2001), and also showed a high level of 16S rRNA gene sequence similarity (99 %) to the 16S rRNA gene of S. japonica. However, further detailed taxonomic investigation revealed a number of atypical phenotypic traits, such as different proportions of cellular fatty acids and low levels of genetic identity (45–50 %) with S. japonica KMM 3299T. It is therefore concluded that this group of strains constitutes a novel species, for which the name Shewanella pacifica sp. nov. is proposed.
Water samples were collected in October/November 2000 from depths of 1 m and 9–13 m (salinity 32 
; temperature 13·6 °C) using a standard hydrological plastic bathometer in different locations in Chazhma Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean. Samples were kept at 4 °C and processed within 4–8 h. A portion of sea water (0·1 ml) was plated onto marine agar 2216 (Difco) or medium B (Ivanova et al., 2004). Plates were incubated aerobically at room temperature (about 22–25 °C) for 5, 7 and 10 days. Isolation and purification of the bacterial strains have been described elsewhere (Ivanova et al., 1996). Strains were stored at –80 °C in marine broth 2216 (Difco) supplemented with 20 % (v/v) glycerol.
Unless otherwise indicated, phenotypic characteristics were studied using standard procedures (Baumann et al., 1972; Smibert & Krieg, 1994) described previously (Ivanova et al., 1996, 1998, 2003a; Sawabe et al., 1998). The following physiological and biochemical properties were examined: oxidation/fermentation of glucose, denitrification, catalase and oxidase activities, gelatin liquefaction, arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase, indole and H2S production, and the ability to hydrolyse starch, alginate, chitin, elastin, Tween 80 and casein. The medium used to study Na+ ion requirements is described by Ivanova et al. (2004). Tests for salt tolerance, dissimilatory iron reduction, haemolytic activity and antimicrobial activities were carried out as described by Ivanova et al. (2004). Phenotypic analysis showed that all isolates were essentially identical to each other and differed only in their ability to grow at 33 °C. Morphological and physiological properties are listed in Table 1 and given in the species description.
|
. The cellular fatty acid profile was genus-specific and included saturated, monoenoic, monounsaturated, straight-chain and iso-branched components (complete cellular fatty acid and isoprenoid quinone compositions are available as supplementary material in IJSEM Online). The high proportion of i15 : 0 (up to 36 %) and 20 : 53 (EPA; up to 5·3 %) produced during growth at 28 °C are characteristic features of the novel strains. The mean fatty acid contents (%±SD) were as follows: i13 : 0, 9·3±1·1; i15 : 0, 33·9±1·5; 16 : 0, 8·9±1·6; and 16 : 17, 14·8±1·1.
The 16S rRNA gene sequences of KMM 3597T and KMM 3590 were amplified and sequenced as described elsewhere (Ivanova et al., 2001, 2003a, b). The 16S rRNA gene sequences of KMM 3590, KMM 3597T and KMM 3605 were aligned and compared to the GenBank nucleotide database using an online BLAST search. Analyses of 16S rRNA gene sequences were done using PHYLIP version 3.57c (Felsenstein, 1993). DNADIST was used to determine sequence similarities using the maximum-likelihood algorithm option. Phylogenetic trees were constructed with the neighbour-joining method using the program NEIGHBOR. The outgroup on the Shewanella trees was Psychromonas antarctica DSM 10704T (GenBank accession no. Y14697). According to our phylogenetic analysis, strains KMM 3597T, KMM 3590 and KMM 3605 formed a cluster with S. japonica and shared high (99 %) 16S rRNA gene sequence similarity (Fig. 1).
|
. DNA–DNA hybridization was performed spectrophotometrically and initial renaturation rates were recorded as described elsewhere (Marmur & Doty, 1962; De Ley et al., 1970). The DNA G+C content was 39·5–40·5 (±0·4) mol% (Table 2). DNA–DNA hybridization data revealed high levels of DNA relatedness among the six strains (83–96 %). DNA from S. japonica KMM 3299T showed intrageneric relatedness with the newly isolated strains of 45–50 % (Table 2). This clearly indicated that the strains from Chazhma Bay belong to the same genospecies, but constitute a distinct Shewanella species (Wayne et al., 1987; Stackebrandt & Goebel, 1994). Strains of the novel species can be phenotypically, chemotaxonomically and genetically distinguished from other species, in particular from S. japonica, by a combination of phenotypic traits listed in Table 1
(e.g. obligate requirement for Na+ ions, tolerance to 6 % NaCl, the ability to grow at 4 °C, different carbon source utilization patterns, lower DNA G+C content, and higher proportions of i15 : 0 and EPA).
|
Cells are rod-shaped, 1·0–2·0x0·6–0·8 µm, motile with a single polar flagellum and Gram-negative. Facultatively anaerobic chemoheterotroph. Does not form endospores. Anaerobic growth occurs by fermentation of D-glucose by anaerobic respiration of nitrate. Colonies on marine agar 2216 are slightly pink, circular, smooth and convex with an entire edge. Organic growth factors are not required. Has absolute requirement for Na+ ions and grows in 0·5–6·0 % NaCl. No growth detected at 8 % NaCl. The temperature growth range is 4–33 °C; optimum growth occurs at 20–25 °C and no growth is detected at 35 °C. Oxidase- and catalase-positive. Reduces nitrate to nitrite. Arginine dihydrolase and lysine decarboxylase are not observed. Haemolytic, produces amylase, esterase (Tween 20, 40, 80), proteinase (gelatinase), alginase (depending on strain) and agarase. Chitin is not hydrolysed. H2S is formed from thiosulfate anaerobically. Indole is not formed from L-tryptophan. Voges–Proskauer test is negative. D-Glucose is utilized as sole source of carbon. Does not utilize D-galactose, D-fructose, N-acetylglucosamine, succinate, D-mannose, lactose, fumarate or L-tyrosine. The following substrates (according to Biolog) are utilized: dextrin, Tween 40 and 80, L-arabinose, D-cellobiose, maltose, -hydroxybutyric acid, 
-ketobutyric acid, -ketoglutaric acid, -ketovaleric acid, D-saccharic acid, succinic acid, L-alanine, L-alanyl-glycine, L-aspartic acid, L-glutamic acid, glycyl-L-aspartic acid, glycyl-L-glutamic acid, L-ornithine, L-proline, L-pyroglutamic acid, L-serine, L-threonine, DL-carnitine, -aminobutyric acid, urocanic acid, putrescine, 2-aminoethanol, 2,3-butanediol, glycerol, DL--glycerol phosphate, -D-glucose 1-phosphate and D-glucose 6-phosphate. Major cellular fatty acids are i13 : 0, i15 : 0, 16 : 0 and 16 : 17 (60–70 % of total), and 20 : 53 (4–5 %). The major isoprenoid quinones are Q7 (21–41 %) and Q8 (50–59 %). Isolated from the sea water of Chazhma Bay, Sea of Japan, Pacific Ocean. The DNA G+C content is 39·5–40·5 mol%.
Type strain is R10SW1T (=KMM 3597T=CIP 107849T).
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Baumann, L., Baumann, P., Mandel, M. & Allen, R. D. (1972). Taxonomy of aerobic marine eubacteria. J Bacteriol 110, 402–429.
Bowman, J. P., McCammon, S. A., Nichols, D. S., Skerratt, J. H., Rea, S. M., Nichols, P. D. & McMeekin, T. A. (1997). Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20 : 53) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47, 1040–1047.
De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 143–153.[Medline]
Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5c. Department of Genetics, University of Washington, Seattle, USA.
Garrity, G. M. & Holt, J. G. (2001). The road map to the Manual. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, p. 119–166. Edited by D. R. Boone & R. W. Castenholz. New York: Springer.
Gauthier, G., Gauthier, M. & Christen, R. (1995). Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations. Int J Syst Bacteriol 45, 755–761.
Ivanova, E. P., Kiprianova, E. A., Mikhailov, V. V., Levanova, G. F., Garagulya, A. D., Gorshkova, N. M., Yumoto, N. & Yoshikawa, S. (1996). Characterization and identification of marine Alteromonas nigrifaciens strains and emendation of the description. Int J Syst Bacteriol 46, 223–228.
Ivanova, E. P., Kiprianova, E. A., Mikhailov, V. V. & 8 other authors (1998). Phenotypic diversity of Pseudoalteromonas citrea from different marine habitats and emendation of the description. Int J Syst Bacteriol 48, 247–256.
Ivanova, E. P., Sawabe, T., Gorshkova, N. M., Svetashev, V. I., Mikhailov, V. V., Nicolau, D. V. & Christen, R. (2001). Shewanella japonica sp. nov. Int J Syst Evol Microbiol 51, 1027–1033.[Abstract]
Ivanova, E. P., Nedashkovskaya, O. I., Zhukova, N. V., Nicolau, D. V., Christen, R. & Mikhailov, V. V. (2003a). Shewanella waksmanii sp. nov., isolated from a sipuncula (Phascolosoma japonicum). Int J Syst Evol Microbiol 53, 1471–1477.
Ivanova, E. P., Sawabe, T., Zhukova, N. V. & 8 other authors (2003b). Occurrence and diversity of mesophilic Shewanella strains isolated from the North-West Pacific Ocean. Syst Appl Microbiol 26, 293–301.[CrossRef][Medline]
Ivanova, E. P., Nedashkovskaya, O. I., Sawabe, T., Zhukova, N. V., Frolova, G. M., Nicolau, D. V., Mikhailov, V. V. & Bowman, J. P. (2004). Shewanella affinis sp. nov., isolated from marine invertebrates. Int J Syst Evol Microbiol 54, 1089–1093.
MacDonell, M. T. & Colwell, R. R. (1985). Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella. Syst Appl Microbiol 6, 171–182.
Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.
Marmur, J. & Doty, P. (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 4, 109–118.
Nogi, Y., Kato, C. & Horikoshi, K. (1998). Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol 170, 331–338.[CrossRef][Medline]
Russell, N. J. & Nichols, D. S. (1999). Polyunsaturated fatty acids in marine bacteria – a dogma rewritten. Microbiology 145, 767–779.
Sawabe, T., Makino, H., Tatsumi, M., Nakano, K., Tajima, K., Iqbal, M. M., Yumoto, I., Ezura, Y. & Christen, R. (1998). Pseudoalteromonas bacteriolytica sp. nov., a marine bacterium that is the causative agent of red spot disease of Laminaria japonica. Int J Syst Bacteriol 48, 769–774.
Skerratt, J. H., Bowman, J. P. & Nichols, P. D. (2002). Shewanella olleyana sp. nov., a marine species isolated from a temperate estuary which produces high levels of polyunsaturated fatty acids. Int J Syst Evol Microbiol 52, 2101–2106.[Abstract]
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.
Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.
Venkateswaran, K., Moser, D. P., Dollhopf, M. E. & 10 other authors (1999). Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49, 705–724.
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
Weiner, R. M., Coyne, V. E., Brayton, P., West, P. & Raiken, S. F. (1988). Alteromonas colwelliana sp. nov., an isolate from oyster habitats. Int J Syst Bacteriol 38, 240–244.
This article has been cited by other articles:
|
|
 |
|
  S. C. Park, K. S. Baik, M. S. Kim, D. Kim, and C. N. Seong Shewanella marina sp. nov., isolated from seawater Int J Syst Evol Microbiol, August 1, 2009; 59(8): 1888 - 1894. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hosoya, S. Suzuki, K. Adachi, S. Matsuda, and H. Kasai Paramoritella alkaliphila gen. nov., sp. nov., a member of the family Moritellaceae isolated in the Republic of Palau Int J Syst Evol Microbiol, February 1, 2009; 59(2): 411 - 416. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Kim, K. S. Baik, M. S. Kim, B.-M. Jung, T.-S. Shin, G.-H. Chung, M. S. Rhee, and C. N. Seong Shewanella haliotis sp. nov., isolated from the gut microflora of abalone, Haliotis discus hannai Int J Syst Evol Microbiol, December 1, 2007; 57(12): 2926 - 2931. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-H. Yang, J.-H. Lee, J.-S. Ryu, C. Kato, and S.-J. Kim Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments Int J Syst Evol Microbiol, February 1, 2007; 57(2): 208 - 212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. O. Lee, S. C. K. Lau, M. M. Y. Tsoi, X. Li, I. Plakhotnikova, S. Dobretsov, M. C. S. Wu, P.-K. Wong, M. Weinbauer, and P.-Y. Qian Shewanella irciniae sp. nov., a novel member of the family Shewanellaceae, isolated from the marine sponge Ircinia dendroides in the Bay of Villefranche, Mediterranean Sea Int J Syst Evol Microbiol, December 1, 2006; 56(12): 2871 - 2877. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Gao, A. Obraztova, N. Stewart, R. Popa, J. K. Fredrickson, J. M. Tiedje, K. H. Nealson, and J. Zhou Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1911 - 1916. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-S. Zhao, D. Manno, C. Leggiadro, D. O'Neil, and J. Hawari Shewanella halifaxensis sp. nov., a novel obligately respiratory and denitrifying psychrophile Int J Syst Evol Microbiol, January 1, 2006; 56(1): 205 - 212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-S. Zhao, D. Manno, C. Beaulieu, L. Paquet, and J. Hawari Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment Int J Syst Evol Microbiol, July 1, 2005; 55(4): 1511 - 1520. [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 | |
