|
|
||||||||
1 Coastal Marine Laboratory/Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
2 Division of Environmental Science and Engineering, The National University of Singapore, Singapore
3 Department of Biology, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong SAR, People's Republic of China
4 Microbial Ecology and Biogeochemistry Group, Laboratoire d'Océanographie de Villefranche-sur-Mer, Villefranche-sur-Mer, France
Correspondence
Pei-Yuan Qian
boqianpy{at}ust.hk
| ABSTRACT |
|---|
|
|
|---|
8c and summed feature 3 (comprising i15 : 0 2-OH and/or 16 : 1
7c), altogether representing 56.9 % of the total. The DNA G+C content was 39.9 mol%. The strain could be differentiated from other Shewanella species by its inability to reduce nitrate or produce H2S and by 1022 additional phenotypic characteristics. On the basis of the phylogenetic and phenotypic data presented in this study, strain UST040317-058T represents a novel species in the genus Shewanella, for which the name Shewanella irciniae sp. nov. is proposed. The type strain is UST040317-058T (=JCM 13528T=NRRL B-41466T).
A scanning electron micrograph of cells of strain UST040317-058T is available as a supplementary figure in IJSEM Online.
| MAIN TEXT |
|---|
|
|
|---|
Strain UST040317-058T was isolated using a standard dilution plating technique on a marine agar medium containing 3 g yeast extract (Oxoid), 5 g peptone (Oxoid) and 12 g bacteriological agar (Oxoid) in 1 l 0.22 µm-filtered seawater at 32
salinity after 48 h incubation at 28 °C. Unless otherwise indicated, all characteristics described hereafter are based on cultures grown on marine agar under these conditions. Colonies of strain UST040317-058T were milky, raised and circular (0.81.5 mm in diameter) with entire edges and a smooth surface (as observed under a Leica MZ6 light microscope at 40x magnification). Gram stain was determined using light microscopy according to Smibert & Krieg (1994)
. Cell morphology was examined using scanning electron microscopy (6700F; JEOL) according to Neu et al. (2001)
and the presence of flagella was determined by transmission electron microscopy according to Allan et al. (2002)
. Gliding motility was observed under a phase-contrast light microscope (BX51; Olympus) at 100x magnification using cells grown on quarter-strength marine broth 2216 (Oxoid) solidified with 1.2 % agar according to Bowman (2000)
. Strain UST040317-058T comprised Gram-negative, rod-shaped cells that were motile by means of a single polar flagellum (see Supplementary Fig. S1 available in IJSEM Online).
The almost-complete 16S rRNA gene sequence of strain UST040317-058T (1462 bp) was obtained bidirectionally with three replicates, as described by Lau et al. (2004)
. Comparative analysis of the 16S rRNA gene sequence with sequences deposited in GenBank using BLAST indicated that the strain belonged to the family Shewanellaceae and showed the highest sequence similarity (95.0 %) with Shewanella algae IAM 14159T (Simidu et al., 1990
). The 16S rRNA gene sequence was automatically, and then manually, aligned with a database of >30 000 previously aligned 16S rRNA gene sequences by using the ARB software package (Ludwig et al., 2004
). Phylogenetic trees were constructed using three different methods: neighbour-joining, maximum-likelihood and maximum-parsimony. The neighbour-joining phylogenetic tree (Fig. 1
) placed strain UST040317-058T within a cluster of two undescribed bacteria which were also isolated from marine sponges: an unidentified sponge bacterium, strain Ex6 (Wichels et al., 2006
), and Shewanella species strain HJ039 (GenBank accession no. DQ167234). This cluster, together with the recognized species S. algae IAM 14159T, formed a distinct clade that clustered robustly with another clade comprising six other Shewanella species with validly published names, including Shewanella amazonensis SB2BT (Venkateswaran et al., 1998
), Shewanella waksmanii KMM 3823T (Ivanova et al., 2003
), Shewanella aquimarina SW-120T (Yoon et al., 2004b
), Shewanella marisflavi SW-117T (Yoon et al., 2004b
), Shewanella colwelliana ATCC 39565T (Coyne et al., 1989
) and Shewanella affinis KMM 3587T (Ivanova et al., 2004b
). These species shared 91.693.8 % 16S rRNA gene sequence similarity with strain UST040317-058T. The maximum-likelihood and maximum-parsimony trees based on cladistic methods (i.e. character-based) showed similar topography for the novel strain and the Shewanella species. These results support the inclusion of UST040317-058T as a novel species in the genus Shewanella.
|
8c (13.3 %) and summed feature 3 (comprising i15 : 0 2-OH and/or 16 : 1
7c) (16.5 %), which together constituted 56.9 % of the total fatty acid content (Table 1
7c (Table 1
|
|
salinity before inoculation (MacDonell et al., 1982
salinity (Nedashkovskaya et al., 2003
Strain UST040317-058T can be differentiated from its closest relative, S. algae IAM 14159T, by means of several phenotypic characteristics, including the inability of the novel strain to reduce nitrate, produce H2S, grow at 8 % NaCl and 40 °C, produce lipase or utilize D-maltose, DL-lactate, DL-malate, succinate, fumarate and L-serine and its ability to utilize D-galactose, D-glucose, D-mannitol and D-sorbitol as sole carbon sources. The novel strain is differentiated from other selected Shewanella species in Table 2
. On the basis of the phylogenetic evidence together with the phenotypic characteristics presented in this study, strain UST040317-058T represents a novel species within the genus Shewanella, for which the name Shewanella irciniae sp. nov. is proposed.
Description of Shewanella irciniae sp. nov.
Shewanella irciniae (ir.ci'ni.ae. N.L. gen. n. irciniae of/from Ircinia, isolated from the marine sponge Ircinia dendroides).
Cells are Gram-negative, short, straight rods (1.32.0 µm in length and 0.5 µm in width) and are motile by means of a single polar flagellum. Facultatively anaerobic. When cultivated on marine agar at 28 °C for 48 h, colonies are milky, 0.81.5 mm in diameter, circular and raised with a smooth surface and an entire edge. Does not produce diffusible pigments. Optimal growth occurs at 2028 °C, but no growth occurs at temperatures lower than 12 °C or higher than 36 °C. Growth occurs at pH 610, but no growth occurs at or below pH 5. Requires NaCl (2.06.0 %; optimum, 2.04.0 %) for growth. MK-7, Q-7 and Q-8 are the predominant respiratory quinones detected. The predominant fatty acids are i15 : 0, 16 : 0, 17 : 1
8c and summed feature 3 (comprising i15 : 0 2-OH and/or 16 : 1
7c), together constituting 56.9 % of the total. Susceptible to 1.0 µg benzylpenicillin, 1.0 µg chloramphenicol, 1.0 µg ampicillin, 10.0 µg tetracycline and 100.0 µg streptomycin, but resistant to kanamycin (up to 100.0 µg tested). Gelatin is hydrolysed, but casein, agar, starch, chitin, cellulose and Tweens 20, 40 and 80 are not. Acetoin, indole and H2S are not produced. Nitrate is not reduced. Citrate is not utilized. Positive for haemolytic activity, DNase, oxidase, catalase, alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and
-fucosidase. Negative for urease, lipase (C14), cystine arylamidase, trypsin,
-chymotrypsin,
- and
-galactosidases,
-glucuronidase,
- and
-glucosidases, N-acetyl-
-glucosaminidase,
-mannosidase, arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase and tryptophan deaminase. Utilizes glycerol, D-glucose, sucrose, D-mannitol, D-galactose, starch, D-sorbitol, D-arabinose and D-melibiose as sole carbon sources on agar medium supplemented with 4 % (w/v) carbon source. Utilizes D-glucose, L-arabinose, aesculin ferric citrate and potassium 2-ketogluconate in the API 50 CH and 20NE systems. Utilizes
- and
-hydroxybutyric acids, methyl pyruvate and D-psicose in the MicroLog 3 system. Other carbon sources included in the MicroLog 3, API 20NE and 50 CH systems are not utilized. No acid production is observed from the carbon sources in the API 50 CH and 20E systems.
The type strain, UST040317-058T (=JCM 13528T=NRRL B-41466T), was isolated from the surface of a marine sponge (Ircinia dendroides) associated with Posidonia sea-grass in the Bay of Villefranche, Mediterranean Sea.
| ACKNOWLEDGEMENTS |
|---|
| REFERENCES |
|---|
|
|
|---|
Allan, V. J. M., Callow, M. E., Macaskie, L. E. & Paterson-Beedle, M. (2002). Effect of nutrient limitation on biofilm formation and phosphatase activity of a Citrobacter sp. Microbiology 148, 277288.
Baumann, P. & Baumann, L. (1981). The marine gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas and Alcaligenes. In The Prokaryotes, vol. 1, pp. 13021331. Edited by M. P. Starr, H. Stolp, H. G. Trüper, A. Balows & H. Schlegel. Berlin: Springer.
Bowman, J. P. (2000). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50, 18611868.[Abstract]
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 : 5
3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47, 10401047.
Collins, M. D. (1994). Isoprenoid quinones. In Chemical Methods in Prokaryotic Systematics, pp. 265310. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: Wiley.
Coyne, V. E., Pillidge, C. J., Sledjeski, D. D., Hori, H., Ortiz-Conde, B. A., Muir, D. G., Weiner, R. M. & Colwell, R. R. (1989). Reclassification of Alteromonas colwelliana to the genus Shewanella by DNA-DNA hybridization, serology and 5S ribosomal RNA sequence data. Syst Appl Microbiol 12, 275279.
Debois, J., Degreef, H., Vandepitte, J. & Spaepen, J. (1975). Pseudomonas putrefaciens as a cause of infection in humans. J Clin Pathol 28, 993996.
Gao, M., Liu, H., Yang, M., Hu, J. & Shao, B. (2004). Indirect identification of isoprenoid quinones in Escherichia coli by LC-MS with atmospheric pressure chemical ionization in negative mode. J Basic Microbiol 44, 424429.[CrossRef][Medline]
Holmes, B., Lapage, S. P. & Malnick, H. (1975). Strains of Pseudomonas putrefaciens from clinical material. J Clin Pathol 28, 149155.
Isnansetyo, A. & Kamei, Y. (2003). Pseudoalteromonas phenolica sp. nov., a novel marine bacterium that produces phenolic anti-methicillin-resistant Staphylococcus aureus substances. Int J Syst Evol Microbiol 53, 583588.
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, 10271033.[Abstract]
Ivanova, E. P., Nedashkovskaya, O. I., Zhukova, N. V., Nicolau, D. V., Christen, R. & Mikhailov, V. V. (2003). Shewanella waksmanii sp. nov., isolated from a sipuncula (Phascolosoma japonicum). Int J Syst Evol Microbiol 53, 14711477.
Ivanova, E. P., Gorshkova, N. M., Bowman, J. P., Lysenko, A. M., Zhukova, N. V., Sergeev, A. F., Mikhailov, V. V. & Nicolau, D. V. (2004a). Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water. Int J Syst Evol Microbiol 54, 10831087.
Ivanova, E. P., Nedashkovskaya, O. I., Sawabe, T., Zhukova, N. V., Frolova, G. M., Nicolau, D. V., Mikhailov, V. V. & Bowman, J. P. (2004b). Shewanella affinis sp. nov., isolated from marine invertebrates. Int J Syst Evol Microbiol 54, 10891093.
Ivanova, E. P., Flavier, S. & Christen, R. (2004c). Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol 54, 17731788.
Jensen, M. J., Tebo, B. M., Baumann, P., Mandel, M. & Nealson, K. H. (1980). Characterization of Alteromonas hanehai (sp. nov.), a nonfermentative luminous species of marine origin. Curr Microbiol 3, 311315.[CrossRef]
Lau, S. C. K., Tsoi, M. M. Y., Li, X., Plakhotnikova, I., Wu, M., Wong, P. K. & Qian, P. Y. (2004). Loktanella hongkongensis sp. nov., a novel member of the
-Proteobacteria originating from marine biofilms in Hong Kong waters. Int J Syst Evol Microbiol 54, 22812284.
Lee, J. V., Gibson, D. M. & Shewan, J. M. (1981). Alteromonas putrefaciens sp. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 6. Int J Syst Bacteriol 31, 215218.
Levin, R. E. (1972). Correlation of DNA base composition and metabolism of Pseudomonas putrefaciens isolates from food, human clinical specimens, and other sources. Antonie van Leeuwenhoek 38, 121127.[CrossRef][Medline]
Ludwig, W., Strunk, O., Westram, R. & 29 other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 13631371.
MacDonell, M. T. & Colwell, R. R. (1985). Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella. Syst Appl Microbiol 6, 171182.
MacDonell, M. T., Singleton, F. L. & Hood, M. A. (1982). Diluent composition for use of API 20E in characterizing marine and estuarine bacteria. Appl Environ Microbiol 44, 423427.
Mesbah, M., Premachandran, U. & Whitman, W. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159167.
Myers, C. R. & Nealson, K. H. (1988). Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240, 13191321.
Nakagawa, Y. & Yamasato, K. (1993). Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J Gen Microbiol 139, 11551161.
Nedashkovskaya, O. I., Kim, S. B., Hans, S. K. & 7 other authors (2003). Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm. Int J Syst Evol Microbiol 53, 19671971.
Neu, B., Voigt, A., Mitlohner, R. & 7 other authors (2001). Biological cells as templates for hollow microcapsules. J Microencapsul 18, 385395.[CrossRef][Medline]
Norris, J. R., Ribbons, D. W. & Varma, A. K. (editors) (1985). Methods in Microbiology, vol. 18. London: Academic Press.
Petrovskis, E. A., Vogel, T. M. & Adriaens, P. (1994). Effects of electron acceptors and donors on transformation of tetrachloromethane by Shewanella putrefaciens MR-1. FEMS Microbiol Lett 121, 357364.[CrossRef][Medline]
Russell, N. J. & Nichols, D. S. (1999). Polyunsaturated fatty acids in marine bacteria a dogma rewritten. Microbiology 145, 767779.
Semple, K. M. & Westlake, D. W. S. (1987). Characterization of iron-reducing Alteromonas putrefaciens from oil field fluids. Can J Microbiol 33, 366371.
Simidu, U., Kita-Tsukamoto, K., Yasumoto, K. & Yotsu, M. (1990). Taxonomy of four marine bacterial strains that produce tetrodotoxin. Int J Syst Bacteriol 40, 331336.
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, 21012106.[Abstract]
Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characteristics. In Methods for General and Molecular Biology, pp. 607654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
Steyn, P. L., Segers, P., Vancanneyt, M., Sandra, P., Kersters, K. & Joubert, J. J. (1998). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48, 165177.
Venkateswaran, K., Dollhopf, M. E., Aller, R., Stackebrandt, E. & Nealson, K. H. (1998). Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds. Int J Syst Bacteriol 48, 965972.
Wichels, A., Würtz, S., Döpke, H., Schütt, C. & Gerdts, G. (2006). Bacterial diversity in the breadcrumb sponge Halichondria panicea (Pallas). FEMS Microbiol Ecol 56, 102118.[CrossRef][Medline]
Xu, M., Guo, J., Cen, Y., Zhong, X., Cao, W. & Sun, G. (2005). Shewanella decolorationis sp. nov., a dye-decolorizing bacterium isolated from activated sludge of a waste-water treatment plant. Int J Syst Evol Microbiol 55, 363368.
Yoon, J. H., Kang, K. H., Oh, T. K. & Park, Y. H. (2004a). Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea. Int J Syst Evol Microbiol 54, 487491.
Yoon, J. H., Yeo, S. H., Kim, I. G. & Oh, T. K. (2004b). Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 54, 23472352.
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] |
||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |