| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
2 Research Program for Marine Biology and Ecology, Extremobiosphere Research Center, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
Correspondence
Sang-Jin Kim
s-jkim{at}kordi.re.kr
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
-glucosidase and gelatinase activities and reduces nitrate to nitrate. The predominant cellular fatty acids are iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1
7 and C20 : 53. The DNA G+C content of strain LT17T is 38.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences places this bacterium in the class Gammaproteobacteria, within the genus Shewanella. The closest relatives of strain LT17T are Shewanella japonica (97.8 % gene sequence similarity), Shewanella pacifica (97.5 %), Shewanella olleyana (96.8 %), Shewanella frigidimarina (96.5 %) and Shewanella gelidimarina (95.4 %). The DNA–DNA hybridization levels between the novel isolate and its closest known phylogenetic relatives, S. japonica and S. pacifica, are lower than 14 %. On the basis of this polyphasic evidence, strain LT17T represents a novel species of the genus Shewanella, for which the name Shewanella donghaensis sp. nov. is proposed. The type strain is LT17T (=KCTC 10635BPT=JCM 12524T).
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain LT17T is AY326275.
A graph showing the growth rate of strain LT17T under varying pressure conditions and an extended phylogenetic tree based on 16S rRNA gene sequences are available as supplementary figures in IJSEM Online.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
). The genus Shewanella is phylogenetically affiliated to the class Gammaproteobacteria and it accommodates Gram-negative, aerobic or facultatively anaerobic and straight or curved rods. Species of the genus Shewanella have been isolated from a variety of sources including clinical samples (Nozue et al., 1992; Brink et al., 1995; Venkateswaran et al., 1999), oilfield fluids (Semple & Westlake, 1987), aquatic or marine environments (Nealson et al., 1991; Ivanova et al., 2001; Bozal et al., 2002), marine sediments (Myers & Nealson, 1988) and deep-sea sediments (Nogi et al., 1998). According to various reports, the genus Shewanella is ubiquitous in marine environments including the deep-sea. An interesting feature of species of the genus Shewanella is the ability to produce polyunsaturated fatty acids (PUFAs). Kato & Nogi (2001) proposed that deep-sea Shewanella species could be taxonomically recognized by two major subgenus branches, one group is characterized by high-pressure cold-adapted species that produce substantial amounts of eicosapentaenoic acid (EPA) and the other group is characterized by mesophilic, pressure-sensitive species that do not produce EPA or produce only scant amounts. Skerratt et al. (2002) and Ivanova et al. (2001, 2004), however, described several species, Shewanella olleyana, Shewanella japonica and Shewanella pacifica, that produce significant levels of PUFAs, such as EPA, at relatively high incubation temperatures (25–30 °C). In this study, a novel psychrophilic EPA-producing bacterium of the genus Shewanella was isolated from the deep-sea and characterized. The bacterium was isolated from sediment samples collected from the East Sea (Sea of Japan; 42° 41' N 139° 41' E; 3300 m depth) by a manned Shinkai 6500 submersible (Yokosuka 01-06 Cruise). Sediment samples were diluted with sterilized seawater and the diluted samples were spread onto marine agar 2216 (MA; Difco) on board just after sampling. Colonies were isolated after incubation at 4 °C for 2 weeks and one of them, strain LT17T, was selected for further study due to its ability to produce EPA and lipase under low temperature conditions.
Unless otherwise stated, morphological and physiological characterizations were performed as described previously (Bae et al., 2005). Cells grown at 10 °C for 7 days on MA were used to observe morphology and Gram-staining. Growth characteristics under different environmental conditions, including temperature, pH, NaCl concentration and hydrostatic pressure, were examined using marine broth 2216 (MB; Difco) as a basal medium using the same methods as described by Seo et al. (2005a).
Strain LT17T was Gram-negative, rod-shaped, motile and approximately 1.0–1.5 µm in length and 0.5–0.8 µm in width. Colonies formed on MA at 17 °C after 1 day were orange coloured, circular, opaque, convex with entire margins and 1.5–2 mm in diameter. The colour changed from orange to slightly pink after 3–4 days incubation. Strain LT17T grew optimally at 17 °C and growth was possible between 5 and 20 °C. The growth rate of strain LT17T at 5 °C was approximately half that of the optimal growth rate. No growth occurred at 22 °C or higher (Fig. 1). The novel strain grew well within the pH range 6.5–8.5 and optimally at pH 7.0–7.5. Optimal growth for strain LT17T occurred in the presence of 2.5 % (w/v) NaCl; no growth occurred at NaCl concentrations above 4.5 % or in the absence of NaCl. In addition, strain LT17T grew optimally at a hydrostatic pressure of 10 MPa. However, this strain might be ‘piezosensitive’ as no growth occurred at 50 MPa (see Supplementary Fig. S1 in IJSEM Online). Results of the other phenotypic characterizations are given in the species description and in Table 1.
|
|
. The 16S rRNA gene sequence (1539 bp) of strain LT17T was aligned manually with representative sequences of the genus Shewanella and related taxa by using known 16S rRNA secondary-structure information. Phylogenetic trees were inferred by the neighbour-joining (Saitou & Nei, 1987), maximum-likelihood (Felsenstein, 1993) and maximum-parsimony (Fitch, 1971) methods. Evolutionary-distance matrices (for the neighbour-joining method) were generated according to the model of Jukes & Cantor (1969). The trees were rooted by using Colwellia psychrerythraea (GenBank accession no. AF001375) and Alteromonas macleodii (GenBank accession no. X82145) as an outgroup. The PHYLIP package (Felsenstein, 1993) was used for all analyses. The resultant unrooted tree topology was evaluated by bootstrap analyses (1000 replicates; Felsenstein, 1985) using the neighbour-joining method. Sequence similarity analysis indicated that the closest relatives of strain LT17T were S. japonica (97.8 %), S. pacifica (97.5 %), S. olleyana (96.8 %), Shewanella frigidimarina (96.5 %) and Shewanella gelidimarina (95.4 %). Sequence similarities to all other species included in the phylogenetic analyses were <95.0 % (Fig. 2).
|
) except that the cells used were cultivated in MB at 15 °C for 1 day. Cellular fatty acids of strain LT17T ranged in carbon chain length from C12 to C20 and included saturated, unsaturated and iso-branched components (Table 2). The dominant cellular fatty acids were iso-C13 : 0 (9.8 %), iso-C15 : 0 (10.4 %), C16 : 0 (15.4 %), C16 : 17 (18.5 %) and C20 : 53 (16.2 %); a range similar to that reported for S. olleyana (Skerratt et al., 2002). Of particular note among the fatty acids of strain LT17T was C20 : 53 which is usually found in both psychrophilic and piezophilic marine bacteria (DeLong et al., 1997; Nogi et al., 1998). According to Russell & Nichols (1999), the progenitor of the genus Shewanella possessed the ability to synthesize PUFAs and this ability has disappeared on several occasions during the divergence of psychrotolerant and/or mesophilic species. Kato & Nogi (2001) proposed that two major subgenus branches of the genus Shewanella should be recognized taxonomically. Group I species were characterized as high-pressure, cold-adapted species that produce substantial amounts of EPA (11–16 %), while Group II species included mesophilic, pressure-sensitive species that do not produce or produce only low levels of EPA (3–5 %). However, in the present study, strain LT17T produces relatively higher concentrations of EPA than Group II species, but does not show any typical characteristics such as piezophily or psychrophily as found in Shewanella Group I species. There are also several contradictory descriptions reported for species of the genus Shewanella such as S. olleyana (Skerratt et al., 2002), S. japonica (Ivanova et al., 2001) and S. pacifica (Ivanova et al., 2004). These findings imply that the presence of EPA in the genus Shewanella is not just associated with psychrophily and piezophily, but is instead a more broadly distributed trait amongst Shewanella species. Production of EPA is an important physiological and descriptive component that allows differentiation between Shewanella species and it may also have an important ecological role, acting as a nutrient source for marine as well as estuarine biota that require essential fatty acids yet are unable to synthesize 3 fatty acids de novo (Skerratt et al., 2002).
|
using photobiotin-labelled DNA probes. The highest and lowest values in each sample were excluded and the remaining three values were used for calculation of the mean value. DNA–DNA reassociation values between strain LT17T and the type strains of the closely related species S. japonica and S. pacifica were lower than 14 %. This value is significantly lower than that accepted as the genotypic delineation of a species (Wayne et al., 1987). DNA G+C content was determined by using the HPLC method as described previously by Seo et al. (2005b). The DNA G+C content of the strain LT17T was 38.8 mol%, which is within the accepted range for the genus Shewanella (39–52 mol%).
Description of Shewanella donghaensis sp. nov.
Shewanella donghaensis [dong.ha.en'sis. N.L. fem. adj. donghaensis of Donghae, the Korean name for the East Sea (Sea of Japan) from which the strain was isolated].
Cells are rod-shaped, 1.0–1.5 µm in length and 0.5–0.8 µm in width, single or in chains, motile, Gram-negative and facultatively anaerobic heterotrophs. Colonies are circular, opaque, convex with entire margins and orange coloured. Growth occurs between 5 and 22 °C, with optimum growth at 17 °C. The pH range for growth is 6.5–8.5; optimum growth occurs at pH 7.0–7.5. Growth occurs between 0.5 and 4.0 % (w/v) NaCl and is optimum at 2.5 % (w/v) NaCl. The hydrostatic pressure range for growth is between 0.1 and <30 MPa, with the maximum growth rate observed at 10 MPa. Catalase- and oxidase-positive. Reduces nitrate to nitrite. Negative in tests for amylase, arginine dihydrolase, urease and -galactosidase activities, the production of indole and acidification from glucose. Exhibits gelatinase, aesculin hydrolysis (-glucosidase) and lipase activities. Does not utilize D-glucose, arabinose, D-mannose, D-mannitol, N-acetylglucosamine, maltose, D-gluconate, caprate, DL-malate, citrate or phenylacetate as sole carbon sources. Major fatty acids are iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 17 and C20 : 53. The G+C content of the DNA is 38.8 mol%.
The type strain, LT17T (=KCTC 10635BPT=JCM 12524T), was isolated from deep-sea sediment of the East Sea (3300 m depth).
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Bozal, N., Montes, M. J., Tudela, E., Jiménez, F. & Guinea, J. (2002). Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int J Syst Evol Microbiol 52, 195–205.[Abstract]
Brink, A. J., van Straten, A. & van Rensburg, A. J. (1995). Shewanella (Pseudomonas) putrefaciens bacteremia. Clin Infect Dis 20, 1327–1332.[Medline]
DeLong, E. F., Franks, D. G. & Yayanos, A. A. (1997). Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl Environ Microbiol 63, 2105–2108.[Abstract]
Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5c. Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[CrossRef]
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., Gorshkova, N. M., Bowman, J. P., Lysenko, A. M., Zhukova, N. V., Sergeev, A. F., Mikhailov, V. V. & Nicolau, D. V. (2004). Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water. Int J Syst Evol Microbiol 54, 1083–1087.
Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–32. Edited by H. N. Munro. New York: Academic Press.
Kato, C. & Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiol Ecol 35, 223–230.[CrossRef][Medline]
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.
Myers, C. R. & Nealson, K. H. (1988). Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240, 1319–1321.
Nealson, K. H., Myers, C. R. & Wimpee, B. B. (1991). Isolation and identification of manganese reducing bacteria and estimates of microbial manganese Mn(IV)-reducing potential in the Black Sea. Deep Sea Res A 38, Supplement 2, S907–S920.
Nichols, D. S., Nichols, P. D., Russell, N. J., Davies, N. W. & McMeekin, T. A. (1997). Polyunsaturated fatty acids in the psychrophilic bacterium Shewanella gelidimarina ACAM 456T: molecular species analysis of major phospholipids and biosynthesis of eicosapentaenoic acid. Biochim Biophys Acta 1347, 164–176.[Medline]
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]
Nozue, H., Hayashi, T., Hashimoto, Y., Ezaki, T., Hamasaki, K., Ohwada, K. & Terawaki, Y. (1992). Isolation and characterization of Shewanella alga from human clinical specimens and emendation of the description of S. alga Simidu et al., 1990, 335. Int J Syst Bacteriol 42, 628–634.
Russell, N. J. & Nichols, D. S. (1999). Polyunsaturated fatty acids in marine bacteria - a dogma rewritten. Microbiology 145, 767–779.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Semple, K. M. & Westlake, D. W. S. (1987). Characterization of iron reducing Alteromonas putrefaciens strains from oil field fluids. Can J Microbiol 35, 925–931.
Seo, H. J., Bae, S. S., Lee, J.-H. & Kim, S.-J. (2005a). Photobacterium frigidiphilum sp. nov., a psychrophilic, lipolytic bacterium isolated from deep-sea sediments of Edison Seamount. Int J Syst Evol Microbiol 55, 1661–1666.
Seo, H. J., Bae, S. S., Yang, S. H., Lee, J.-H. & Kim, S.-J. (2005b). Photobacterium aplysiae sp. nov., a lipolytic marine bacterium isolated from eggs of the sea hare Aplysia kurodai. Int J Syst Evol Microbiol 55, 2293–2296.
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]
Venkateswaran, K., Moser, D. P., Dollhopf, M. E., Lies, D. P., Saffarini, D. A., MacGregor, B. J., Ringelberg, D. B., White, D. C., Nishijima, M. & 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., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & 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.
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]
|
|
|
|
|
|
H.-W. Chang, S. W. Roh, K.-H. Kim, Y.-D. Nam, C. O. Jeon, H.-M. Oh, and J.-W. Bae Shewanella basaltis sp. nov., a marine bacterium isolated from black sand Int J Syst Evol Microbiol, August 1, 2008; 58(8): 1907 - 1910. [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]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
