Shewanella electrodiphila sp. nov., a psychrotolerant bacterium isolated from Mid-Atlantic Ridge deep-sea sediments

International Journal of Systematic and Evolutionary Microbiology

Volumn 65, Issue 9, 2015, Pages 2882-2889

  Zhang, Jinwei ^a,b   Burgess, J Grant ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; CARBOHYDRATE; CARBON; FATTY ACID; FERRIC ION; NITRATE; PEPTONE; RNA 16S; SEA WATER;

ANAEROBIC CAPACITY; ANAEROBIC GROWTH; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATION; DEEP SEA; DNA CONTENT; DNA DNA HYBRIDIZATION; ELECTRODE; GENE SEQUENCE; MICROBIAL FUEL CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; SEDIMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SHEWANELLA; SHEWANELLA ELECTRODIPHILA; TYPE STRAIN; UNITED STATES; ATLANTIC OCEAN; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION;

ATLANTIC OCEAN; BASE COMPOSITION; DNA, BACTERIAL; FATTY ACIDS; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SHEWANELLA;

EID: 84943576662     PISSN: 14665026     EISSN: 14665034     Source Type: Journal    
DOI: 10.1099/ijs.0.000345     Document Type: Article

References (60)

1. Amiri-Jami, M., Wang, H., Kakuda, Y. & Griffiths, M. W. (2006). Enhancement of polyunsaturated fatty acid production by Tn5 transposon in Shewanella baltica. Biotechnol Lett 28, 1187-1192.
2. Bowman, J. P., McCammon, S. A., Brown, M. V., Nichols, D. S. & McMeekin, T. A. (1997a). Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl Environ Microbiol 63, 3068-3078.
3. Bowman, J. P., McCammon, S. A., Nichols, D. S., Skerratt, J. H., Rea, S. M., Nichols, P. D. & McMeekin, T. A. (1997b). Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20: 5ω3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47, 1040-1047.
4. 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.
5. 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.
6. Christie, W. W. (1989). The analysis of fatty acids. In Gas Chromatography and Lipids: a Practical Guide, pp. 64-84. Edited by W. W. Christie. Ayr: The Oily Press.
7. Coates, J. D., Ellis, D. J., Gaw, C. V. & Lovley, D. R. (1999). Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 49, 1615-1622.
8. DeLong, E. F. (1992). Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89, 5685-5689.
9. Delong, E. F. & Yayanos, A. A. (1986). Biochemical function and ecological significance of novel bacterial lipids in deep-sea procaryotes. Appl Environ Microbiol 51, 730-737.
10. 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.
11. Deming, J. W., Hada, H., Colwell, R. R., Luehrsen, K. R. & Fox, G. E. (1984). The ribonucleotide sequence of 5S rRNA from two strains of deep-sea barophilic bacteria. J Gen Microbiol 130, 1911-1920.
12. DiLella, A. G. & Woo, S. L. (1987). Cloning large segments of genomic DNA using cosmid vectors. Methods Enzymol 152, 199-212.
13. Dos Santos, J. P., Iobbi-Nivol, C., Couillault, C., Giordano, G. & Méjean, V. (1998). Molecular analysis of the trimethylamine Noxide (TMAO) reductase respiratory system from a Shewanella species. J Mol Biol 284, 421-433.
14. El-Naggar, M. Y., Wanger, G., Leung, K. M., Yuzvinsky, T. D., Southam, G., Yang, J., Lau, W. M., Nealson, K. H. & Gorby, Y. A. (2010). Electrical transport along bacterial nanowires from Shewanella oneidensis MR-1. Proc Natl Acad Sci U S A 107, 18127-18131.
15. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
16. Felsenstein, J. (1985). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
17. Gorby, Y. A. & Beveridge, T. J. (2005). Composition, reactivity, and regulation of extracellular metal-reducing structures (nanowires) produced by dissimilatory metal reducing bacteria. Proceedings of the Annual NABIR PI Meeting, Warrenton, VA, USA, 18-20 April 2005. Available at http://www.osti.gov/em52/2005NABIRpresentations/ 1024844pres.pdf
18. Hirota, K., Nodasaka, Y., Orikasa, Y., Okuyama, H. & Yumoto, I. (2005). Shewanella pneumatophori sp. nov., an eicosapentaenoic acidproducing marine bacterium isolated from the intestines of Pacific mackerel (Pneumatophorus japonicus). Int J Syst Evol Microbiol 55, 2355-2359.
19. 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.
20. 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 acidproducing bacterium isolated from sea water. Int J Syst Evol Microbiol 54, 1083-1087.
21. Kato, C. & Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiol Ecol 35, 223-230.
22. Kim, H., Park, H., Hyun, M., Chang, I., Kim, M. & Kim, B. (2002). A mediator-less microbial fuel cell using a metal reducing bacterium, Shewanella putrefaciens. Enzyme Microb Technol 30, 145-152.
23. 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.
24. Komagata, K. & Suzuki, K. (1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161-207.
25. Leonardo, M. R., Moser, D. P., Barbieri, E., Brantner, C. A., MacGregor, B. J., Paster, B. J., Stackebrandt, E. & Nealson, K. H. (1999). Shewanella pealeana sp. nov., a member of the microbial community associated with the accessory nidamental gland of the squid Loligo pealei. Int J Syst Bacteriol 49, 1341-1351.
26. Lovley, D. R. (2006). Bug juice: harvesting electricity with microorganisms. Nat Rev Microbiol 4, 497-508.
27. 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.
28. Makemson, J. C. & Hastings, J. W. (1979). Glutamate functions in osmoregulation in a marine bacterium. Appl Environ Microbiol 38, 178-180.
29. Miyazaki, M., Nogi, Y., Usami, R. & Horikoshi, K. (2006). Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan. Int J Syst Evol Microbiol 56, 1607-1613.
30. Myers, C. R. & Nealson, K. H. (1990). Respiration-linked proton translocation coupled to anaerobic reduction of manganese(IV) and iron(III) in Shewanella putrefaciens MR-1. J Bacteriol 172, 6232-6238.
31. Nealson, K. H. & Scott, J. (2006). Ecophysiology of the genus Shewanella. In The Prokaryotes, vol. 3, 3rd edn. pp. 1133-1151. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer.
32. T: molecular species analysis of major phospholipids and biosynthesis of eicosapentaenoic acid. Biochim Biophys Acta 1347, 164-176.
33. Nogi, Y., Kato, C. & Horikoshi, K. (1998). Taxonomic studies of deepsea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol 170, 331-338.
34. Rainey, F. A., Ward-Rainey, N., Kroppenstedt, R. M. & Stackebrandt, E. (1996). The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 46, 1088-1092.
35. Reguera, G., McCarthy, K. D., Mehta, T., Nicoll, J. S., Tuominen, M. T. & Lovley, D. R. (2005). Extracellular electron transfer via microbial nanowires. Nature 435, 1098-1101.
36. Reid, W. D. K., Wigham, B. D., McGill, R. A. R. & Polunin, N. V. C. (2012). Elucidating trophic pathways in benthic deep-sea assemblages of the Mid-Atlantic Ridge north and south of the Charlie-Gibbs Fracture Zone. Mar Ecol Prog Ser 463, 89-103.
37. Russell, N. J. & Nichols, D. S. (1999). Polyunsaturated fatty acids in marine bacteria-a dogma rewritten. Microbiology 145, 767-779.
38. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
39. Satomi, M., Oikawa, H. & Yano, Y. (2003). Shewanella marinintestina sp. nov., Shewanella schlegeliana sp. nov. and Shewanella sairae sp. nov., novel eicosapentaenoic-acid-producing marine bacteria isolated from sea-animal intestines. Int J Syst Evol Microbiol 53, 491-499.
40. 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.
41. Sly, L. I., Blackall, L. L., Kraat, P. C., Tian-Shen, T. & Sangkhobol, V. (1986). The use of second derivative plots for the determination of mol% guanine plus cytosine of DNA by the thermal denaturation method. J Microbiol Methods 5, 139-156.
42. 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.
43. 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.
44. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
45. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
46. Valentine, R. C. & Valentine, D. L. (2004). Omega-3 fatty acids in cellular membranes: a unified concept. Prog Lipid Res 43, 383-402.
47. 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.
48. von Canstein, H., Ogawa, J., Shimizu, S. & Lloyd, J. R. (2008). Secretion of flavins by Shewanella species and their role in extracellular electron transfer. Appl Environ Microbiol 74, 615-623.
49. Watson, V. J. & Logan, B. E. (2010). Power production in MFCs inoculated with Shewanella oneidensis MR-1 or mixed cultures. Biotechnol Bioeng 105, 489-498.
50. Woulds, C., Cowie, G. L., Levin, L. A., Andersson, J. H., Middleburg, J. J., Vandewiele, S., Lamont, P. A., Larkin, K. E., Gooday, A. J. & other authors (2007). Oxygen as a control on sea floor biological communities and their roles in sedimentary carbon cycling. Limnol Oceanogr 52, 1698-1709.
51. Xiao, X., Wang, P., Zeng, X., Bartlett, D. H. & Wang, F. (2007). Shewanella psychrophila sp. nov. and Shewanella piezotolerans sp. nov., isolated from west Pacific deep-sea sediment. Int J Syst Evol Microbiol 57, 60-65.
52. Yang, S. H., Lee, J. H., Ryu, J. S., Kato, C. & Kim, S. J. (2007). 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 57, 208-212.
53. Yano, Y., Nakayama, A., Ishihara, K. & Saito, H. (1998). Adaptive changes in membrane lipids of barophilic bacteria in response to changes in growth pressure. Appl Environ Microbiol 64, 479-485.
54. Yazawa, K., Watanabe, K., Ishikawa, C., Kondo, K. & Kimura, S. (1992). Production of eicosapentaenoic acid from marine bacteria. In Industrial Applications of Single Cell Oils, pp. 29-51. Edited by D. J. Kyle & C. Ratledge. Urbana, IL: AOCS Press.
55. Yilmaz, G., Aydin, K., Bektas, D., Caylan, R., Caylan, R. & Koksal, I. (2007). Cerebellar abscess and meningitis, caused by Shewanella putrefaciens and Klebsiella pneumoniae, associated with chronic otitis media. J Med Microbiol 56, 1558-1560.
56. Yoon, J. H., Kang, K. H., Oh, T. K. & Park, Y. H. (2004). Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea. Int J Syst Evol Microbiol 54, 487-491.
57. Zhang, J. W. & Zeng, R. Y. (2008). Molecular cloning and expression of a cold-adapted lipase gene froman Antarctic deep sea psychrotrophic bacterium Pseudomonas sp. 7323. Mar Biotechnol (NY) 10, 612-621.
58. Zhang, J., Zhang, E., Scott, K. & Burgess, J. G. (2012). Enhanced electricity production by use of reconstituted artificial consortia of estuarine bacteria grown as biofilms. Environ Sci Technol 46, 2984-2992.
59. Ziemke, F., Höfle, M. G., Lalucat, J. & Rosselló-Mora, R. (1998). Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48, 179-186.
60. ZoBell, C. (1946). Marine Microbiology. Waltham, MA: Chronica Botanica.