Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov.

Extremophiles

Volumn 10, Issue 4, 2006, Pages 285-294

  Rodrigues, Debora Frigi ^a   Goris, Johan ^a   Vishnivetskaya, Tatiana ^b,c   Gilichinsky, David ^b   Thomashow, Michael F ^a   Tiedje, James M ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b INSTITUTE OF PHYSICOCHEMICAL AND BIOLOGICAL PROBLEMS IN SOIL SCIENCE   (Russian Federation)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

Exiguobacterium; Exiguobacterium sibiricum sp. nov.; Polyphasic taxonomy; Siberian permafrost

Indexed keywords

ARTICLE; BACILLACEAE; CLASSIFICATION; CYTOLOGY; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; RUSSIAN FEDERATION;

BACILLACEAE; ECOSYSTEM; PHYLOGENY; SIBERIA; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); EXIGUOBACTERIUM; EXIGUOBACTERIUM ANTARCTICUM; EXIGUOBACTERIUM UNDAE; POSIBACTERIA;

EID: 33748299372     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-005-0497-5     Document Type: Article

References (42)

1. Chen ML, Tsen HY (2002) Discrimination of Bacillus cereus and Bacillus thuringiensis with 16S rRNA and gyrB gene based PCR primers and sequencing of their annealing sites. J Appl Microbiol 92:912-919
2. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221-230
3. Collins MD, Lund BM, Farrow JAE, Schleifer KH (1983) Chemotaxonomic study of an alkalophilic bacterium, Exiguobacterium aurantiacum gen-nov., sp-nov. J Gen Microbiol 129:2037-2042
4. Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. Cambridge University Press, London
5. Desoete G (1983) On the construction of optimal phylogenetic trees. Z Naturforsch C J Biosci 38:156-158
6. Eden PA, Schmidt TM, Blakemore RP, Pace NR (1991) Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA. Int J Syst Bacteriol 41:324-325
7. 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
8. Francis KP, Stewart GS (1997) Detection and speciation of bacteria through PCR using universal major cold-shock protein primer oligomers. J Ind Microbiol Biotechnol 19:286-293
9. Fruhling A, Schumann P, Hippe H, Straubler B, Stackebrandt E (2002) Exiguobacterium undae sp. nov. and Exiguobacterium antarcticum sp. nov. Int J Syst Evol Microbiol 52:1171-1176
10. Fukushima M, Kakinuma K, Kawaguchi R (2002) Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol 40:2779-2785
11. Gilichinsky D, Rivkina E, Shcherbakova V, Laurinavichuis K, Tiedje J (2003) Supercooled water brines within permafrost - an unknown ecological niche for microorganisms: a model for astrobiology. Astrobiology 3:331-341
12. Goris J, Suzuki K, Vos dP, Nakase T, Kersters K (1998) Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44:1148-1153
13. Groth I, Schumann P, Weiss N, Martin K, Rainey FA (1996) Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46:234-239
14. Kim W, Song MO, Song W, Kim KJ, Chung SI, Choi CS, Park YH (2003) Comparison of 16S rDNA analysis and rep-PCR genomic fingerprinting for molecular identification of Yersinia pseudotuberculosis. Antonie Van Leeuwenhoek 83:125-133
15. Kim IG, Lee MH, Jung SY, Song JJ, Oh TK, Yoon JH (2005) Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 55:885-889
16. Ko KS, Lee HK, Park MY, Lee KH, Yun YJ, Woo SY, Miyamoto H, Kook YH (2002) Application of RNA polymerase betasubunit gene (rpoB) sequences for the molecular differentiation of Legionella species. J Clin Microbiol 40:2653-2658
17. Koneman E, Allen S, Dowell V, Sommers H (1979) Color atlas and text book of diagnostic microbiology. Lippincott, Philadelphia
18. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, West Sussex, England, pp 115-175
19. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A et al (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371
20. MacKenzie SL (1987) Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 70:151-160
21. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208-218
22. Matsumoto GI, Friedmann EI, Gilichinsky DA (1995) Geochemical characteristics of organic compounds in a permafrost sediment core sample from northeast Siberia, Russia. Proc NIPR Symp Antarct Meteorites 8:258-267
23. McKay CP, Friedmann EI, Meyer MA (1991) From Siberia to Mars. Planet Rep Mar-Apr:8-11
24. Miller L, Berger T (1984) Bacterial identification by gas chromatography and whole cell fatty acids. Hewlett-Packard, Palo Alto, pp. 228-241
25. Minnikin DE, Collins MD, Goodfellow M (1979) Fatty-acid and polar lipid-composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87-95
26. Olsen GJ, Matsuda H, Hagstrom R, Overbeek R (1994) FastDNAml - a tool for construction of phylogenetic trees of DNA-sequences using maximum-likelihood. Comput Appl Biosci 10:41-48
27. Rademaker JLW, Louws FJ, Bruijn FJ (1998) Characterisation of diversity of ecologically important microbes by rep-PCR fingerprinting. In: Akkermans ADL, van Elsas JD, Bruijn FJ (eds) Molecular microbial ecology manual, supplement 3. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 1-26
28. Riley MS, Cooper VS, Lenski RE, Forney LJ, Marsh TL (2001) Rapid phenotypic change and diversification of a soil bacterium during 1000 generations of experimental evolution. Microbiology 147:995-1006
29. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
30. Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123-156
31. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407-477
32. Seurinck S, Verstraete W, Siciliano SD (2003) Use of 16S-23S rRNA intergenic spacer region PCR and repetitive extragenic palindromic PCR analyses of Escherichia coli isolates to identify nonpoint fecal sources. Appl Environ Microbiol 69:4942-4950
33. Shi T, Reeves RH, Gilichinsky DA, Friedmann EI (1997) Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing. Microb Ecol 33:169-179
34. Versalovic J, Koeuth T, Lupski JR (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823-6831
35. Vishnivetskaya T, Kathariou S, McGrath J, Gilichinsky D, Tiedje JM (2000) Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments. Extremophiles 4:165-173
36. Watanabe K, Nelson J, Harayama S, Kasai H (2001) ICB database: the gyrB database for identification and classification of bacteria. Nucleic Acids Res 29:344-345
37. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976-978
38. 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
39. Yamamoto S, Bouvet PJ, Harayama S (1999) Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization. Int J Syst Bacteriol 49:87-95
40. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A, Harayama S (2000) Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146:2385-2394
41. Yumoto I, Hishinuma-Narisawa M, Hirota K, Shingyo T, Takebe F, Nodasaka Y, Matsuyama H, Hara I (2004) Exiguobacterium oxidotolerans sp. nov., a novel alkaliphile exhibiting high catalase activity. Int J Syst Evol Microbiol 54:2013-2017
42. Zvyagintsev DG, Gilichinsky DA, Blagodatskii SA, Vorobyeva EA, Khlenikovan GM, Arkhangelov AA, Kudryavtseva NN (1985) Survival time of microorganisms in permanently frozen sedimentary rock and buried soils. Microbiology 54:155-161