Relationships between Arctic and Antarctic Shewanella strains evaluated by a polyphasic taxonomic approach

Polar Biology

Volumn 33, Issue 4, 2010, Pages 531-541

  Zeng, Yinxin ^a,b   Zheng, Tianling ^a   Yu, Yong ^b   Chen, Bo ^b   He, Jianfeng ^b  

^a XIAMEN UNIVERSITY   (China)

^b Yunnan Institute of Geological Environment Monitoring   (China)

Author keywords

Bipolar distribution; Polyphasic taxonomy; Shewanella frigidimarina

Indexed keywords

BACTERIUM; GENETIC ANALYSIS; MARINE ENVIRONMENT; PHENOTYPE; POLAR REGION; RNA; TAXONOMY;

BACTERIA (MICROORGANISMS); SHEWANELLA; SHEWANELLA FRIGIDIMARINA;

EID: 77952427944     PISSN: 07224060     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00300-009-0730-2     Document Type: Article

References (59)

1. Aakra A, Utåker JB, Nes IF (1999) RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach. Int J Syst Bacteriol 49: 123-130.
2. Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186: 2629-2635.
3. Allgaier M, Uphoff H, Felske A, Wagner-Döbler I (2003) Aerobic anoxygenic photosynthesis in Roseobacter clade bacteria from diverse marine habitats. Appl Environ Microbiol 69: 5051-5059.
4. An DS, Im WT, Yang HC, Lee ST (2006) Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov. Int J Syst Evol Microbiol 56: 443-448.
5. Bano N, Hollibaugh JT (2002) Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl Environ Microbiol 68: 505-518.
6. Bosshard PP, Santini Y, Grüter D, Stettler R, Bachofen R (2000) Bacterial diversity and community composition in the chemocline of the meromictic alpine Lake Cadagno as revealed by 16S rDNA analysis. FEMS Microbiol Ecol 31: 173-182.
7. Bowman JP, McCammon SA, Nichols DS, Skerratt JH, Rea SM, Nichols PD, McMeekin TA (1997) Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20: 5 omega 3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47: 1040-1047.
8. Bozal N, Montes MJ, Tudela E, Jiménez F, Guinea J (2002) Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int J Syst Bacteriol 52: 195-205.
9. Brinkmeyer R, Knittel K, Jürgens J, Weyland H, Amann R, Helmke E (2003) Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl Environ Microbiol 69: 6610-6619.
10. Chelo IM, Zé-Zé L, Tenreiro R (2007) Congruence of evolutionary relationships inside the Leuconostoc-Oenococcus-Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK. Int J Syst Evol Microbiol 57: 276-286.
11. Clarridge JE III (2004) Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17: 840-862.
12. Cohan FM (2002) What are bacterial species? Annu Rev Microbiol 56: 457-487.
13. Dolan JR (2005) An introduction to the biogeography of aquatic microbes. Aquat Microb Ecol 41: 39-48.
14. Feil EJ, Maiden MC, Achtman M, Spratt BG (1999) The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitides. Mol Biol Evol 16: 1496-1502.
15. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3. 5c. Distributed by the author. Department of Genetics. University of Washington, Seattle.
16. Fenchel T (2003) Biogeography for bacteria. Science 301: 925-926.
17. Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296: 1061-1063.
18. Gentile G, Bonasera V, Amico C, Giuliano L, Yakimov MM (2003) Shewanella sp. GA-22, a psychrophilic hydrocarbonoclastic antarctic bacterium producing polyunsaturated fatty acids. J Appl Microbiol 95: 1124-1133.
19. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3: 733-739.
20. Gounot AM (1986) Psychrophilic and psychrotrophic microorganisms. Experientia 142: 1192-1197.
21. Guo Y, Zheng W, Rong X, Huang Y (2008) A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol 58: 149-159.
22. Gürtler V, Stanisich VA (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142: 3-16.
23. Hagström Å, Pinhassi J, Zweifel UL (2000) Biogeographical diversity among marine bacterioplankton. Aquat Microb Ecol 21: 231-244.
24. Hedlund BP, Staley JT (2004) Microbial endemism and biogeography. In: Bull AT (ed) Microbial diversity and bioprospecting. American Society for Microbiology Press, Washington, D. C., pp 225-231.
25. Hollibaugh JT, Bano N, Ducklow HW (2002) Widespread distribution in polar oceans of a 16S rRNA gene sequence with affinity to Nitrosospira-like ammonia-oxidizing bacteria. Appl Environ Microbiol 68: 1478-1484.
26. Huston AL, Krieger-Brockett BB, Deming JW (2000) Remarkably low temperature optima for extracellular enzyme activity from Arctic bacteria and sea ice. Environ Microbiol 2: 383-388.
27. Jensen PR, Mafnas C (2006) Biogeography of the marine actinomycete Salinispora. Environ Microbiol 8: 1881-1888.
28. Junge K, Imhoff F, Staley T, Deming JW (2002) Phylogenetic diversity of numerically important Arctic sea-ice bacteria at subzero temperature. Microbial Ecol 43: 315-328.
29. 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.
30. Kongstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187: 6258-6264.
31. Leblond-Bourget N, Philippe H, Mangin I, Decaris B (1996) 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny. Int J Syst Bacteriol 46: 102-111.
32. Lee JV, Gibson DM, Shewan JM (1977) A numerical taxonomic study of some Pseudomonas-like marine bacteria. J Gen Microbiol 98: 439-451.
33. Lee YK, Sung KC, Yim JH, Park KJ, Chung H, Lee HK (2005) Isolation of protease-producing Arctic marine bacteria. Ocean Polar Res 27: 215-219.
34. Li WJ, Kroppenstedt RM, Wang D, Tang SK, Lee JC, Park DJ, Kim CJ, Xu LH, Jiang CL (2006) Five novel species of the genus Nocardiopsis isolated from hypersaline soils and emended description of Nocardiopsis salina Li et al. 2004. Int J Syst Evol Microbiol 56: 1089-1096.
35. Mergaert J, Verhelst A, Cnockaert MC, Tan TL, Swings J (2001) Characterization of facultative oligotrophic bacteria from polar seas by analysis of their fatty acids and 16S rDNA sequences. Syst Appl Microbiol 24: 98-107.
36. Nealson KH, Myers CR, Wimpee B (1991) Isolation and identification of manganese reducing bacteria, and estimates of microbial Mn(IV)-reducing potential in the Black Sea. Deep Sea Res 38: S907-S920.
37. Pearce DA (2008) Biodiversity of the bacterioplankton in the surface waters around Southern Thule in the Southern Ocean. Antarct Sci 20: 291-300.
38. Pearce DA, Cockell CS, Lindström ES, Tranvik LJ (2007) First evidence for a bipolar distribution of dominant freshwater lake bacterioplankton. Antarct Sci 19: 245-252.
39. Perrière G, Gouy M (1996) WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364-369.
40. Pommier T, Canbäck B, Riemann L, Boström KH, Simu K, Lundberg P, Tunlid A, Hagström A (2007) Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16: 867-880.
41. Rüger HJ, Fritze D, Spröer C (2000) New psychrophilic and psychrotolerant Bacillus marinus strains from tropical and polar deep-sea sediments and emended description of the species. Int Syst Evol Microbiol 50: 1305-1313.
42. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
43. Sambrook J, Frisch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
44. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Technical note 101. Microbial ID, Newark, DE.
45. Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68: 686-691.
46. Seldin L, Dubnau D (1985) Deoxyribonucleic acid homology among Bacillus polymyxa, Bacillus macerans, Bacillus azotofixans, and other nitrogen-fixing Bacillus strains. Int J Syst Bacteriol 35: 151-154.
47. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152-155.
48. Stackebrandt E, Goebel BM (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.
49. Staley JT, Gosink JJ (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annu Rev Microbiol 53: 189-215.
50. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
51. Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA, MacGregor BJ, Ringelberg DB, White DC, Nishijima M, Sano H, Burghardt J, Stackebrandt E, Nealson KH (1999) Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49: 705-724.
52. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (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.
53. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.
54. Yamamoto S, Harayama S (1995) PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61: 1104-1109.
55. Yamamoto S, Harayama S (1998) Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48: 813-819.
56. Yang LL, Zhi XY, Xu LH, Li WJ (2008) Phylogenetic relationships of Nocardiopsis species based on partial gyrB and 16S rRNA gene sequences. Actinomycetologica 22: 6-11.
57. Zavaleta AI, Martinez-Murcia AJ, Rodríguez-Valera F (1996) 16S-23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous. Microbiology 142: 2105-2114.
58. Zeng Y, Li H, Yu Y, Chen B, Zheng T (2007a) Phylogenetic diversity and phenotypic characterization of cultivable bacterioplankton isolated from polar oceans. Acta Oceanol Sin 26: 93-103.
59. Zeng Y, Liu W, Li H, Yu Y, Chen B (2007b) Effect of restriction endonucleases on assessment of biodiversity of cultivable polar marine planktonic bacteria by amplified ribosomal DNA restriction analysis. Extremophiles 11: 685-692.