Advertisement

Extremophiles

, Volume 10, Issue 4, pp 285–294 | Cite as

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

  • Debora Frigi RodriguesEmail author
  • Johan Goris
  • Tatiana Vishnivetskaya
  • David Gilichinsky
  • Michael F. Thomashow
  • James M. Tiedje
Original Paper

Abstract

Three Gram-positive bacterial strains, 7-3, 255-15 and 190-11, previously isolated from Siberian permafrost, were characterized and taxonomically classified. These microorganisms are rod-shaped, facultative aerobic, motile with peritrichous flagella and their growth ranges are from −2.5 to 40°C. The chemotaxonomic markers indicated that the three strains belong to the genus Exiguobacterium. Their peptidoglycan type was A3α L-Lys-Gly. The predominant menaquinone detected in all three strains was MK7. The polar lipids present were phosphatidyl-glycerol, diphosphatidyl-glycerol and phosphatidyl-ethanolamine. The major fatty acids were iso-C13:0, anteiso-C13:0, iso-C15:0, C16:0 and iso-C17:0. Phylogenetic analysis based on 16S rRNA and six diverse genes, gyrB (gyrase subunit B), rpoB (DNA-directed RNA polymerase beta subunit), recA (homologous recombination), csp (cold shock protein), hsp70 (ClassI-heat shock protein—chaperonin) and citC (isocitrate dehydrogenase), indicated that the strains were closely related to Exiguobacterium undae (DSM 14481T) and Exiguobacterium antarcticum (DSM 14480T). On the basis of the phenotypic characteristics, phylogenetic data and DNA–DNA reassociation data, strain 190-11 was classified as E. undae, while the other two isolates, 7-3 and 255-15, comprise a novel species, for which the name Exiguobacterium sibiricum sp. nov. is proposed.

Keywords

Exiguobacterium Exiguobacterium sibiricum sp. nov. Polyphasic taxonomy Siberian permafrost 

Notes

Acknowledgment

This work was supported by a cooperative agreement with NASA Astrobiology Institute number NCC2-1274.

References

  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 92:912–919CrossRefPubMedGoogle Scholar
  2. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230PubMedGoogle Scholar
  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 129:2037–2042Google Scholar
  4. Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. Cambridge University Press, LondonGoogle Scholar
  5. Desoete G (1983) On the construction of optimal phylogenetic trees. Z Naturforsch C J Biosci 38:156–158Google Scholar
  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 41:324–325PubMedGoogle Scholar
  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 39:224–229Google Scholar
  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 19:286–293CrossRefPubMedGoogle Scholar
  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 52:1171–1176CrossRefPubMedGoogle Scholar
  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 40:2779–2785CrossRefPubMedGoogle Scholar
  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 3:331–341CrossRefPubMedGoogle Scholar
  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 44:1148–1153CrossRefGoogle Scholar
  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 46:234–239PubMedGoogle Scholar
  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 83:125–133CrossRefPubMedGoogle Scholar
  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 55:885–889CrossRefPubMedGoogle Scholar
  16. Ko KS, Lee HK, Park MY, Lee KH, Yun YJ, Woo SY, Miyamoto H, Kook YH (2002) Application of RNA polymerase beta-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species. J Clin Microbiol 40:2653–2658CrossRefPubMedGoogle Scholar
  17. Koneman E, Allen S, Dowell V, Sommers H (1979) Color atlas and text book of diagnostic microbiology. Lippincott, PhiladelphiaGoogle Scholar
  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 115–175Google Scholar
  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 32:1363–1371CrossRefPubMedGoogle Scholar
  20. MacKenzie SL (1987) Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 70:151–160PubMedGoogle Scholar
  21. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218CrossRefGoogle Scholar
  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 8:258–267PubMedGoogle Scholar
  23. McKay CP, Friedmann EI, Meyer MA (1991) From Siberia to Mars. Planet Rep Mar–Apr:8–11Google Scholar
  24. Miller L, Berger T (1984) Bacterial identification by gas chromatography and whole cell fatty acids. Hewlett-Packard, Palo Alto, pp. 228–241Google Scholar
  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 47:87–95Google Scholar
  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 10:41–48PubMedGoogle Scholar
  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 1–26Google Scholar
  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 147:995–1006PubMedGoogle Scholar
  29. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  30. Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156CrossRefGoogle Scholar
  31. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477PubMedGoogle Scholar
  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 69:4942–4950CrossRefPubMedGoogle Scholar
  33. Shi T, Reeves RH, Gilichinsky DA, Friedmann EI (1997) Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing. Microb Ecol 33:169–179CrossRefPubMedGoogle Scholar
  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 19:6823–6831PubMedCrossRefGoogle Scholar
  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 4:165–173CrossRefPubMedGoogle Scholar
  36. Watanabe K, Nelson J, Harayama S, Kasai H (2001) ICB database: the gyrB database for identification and classification of bacteria. Nucleic Acids Res 29:344–345CrossRefPubMedGoogle Scholar
  37. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976–978CrossRefPubMedGoogle Scholar
  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 48:813–819PubMedGoogle Scholar
  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 49:87–95PubMedCrossRefGoogle Scholar
  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 146:2385–2394PubMedGoogle Scholar
  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 54:2013–2017CrossRefPubMedGoogle Scholar
  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 54:155–161Google Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Debora Frigi Rodrigues
    • 1
    Email author
  • Johan Goris
    • 1
  • Tatiana Vishnivetskaya
    • 2
    • 4
  • David Gilichinsky
    • 2
  • Michael F. Thomashow
    • 3
  • James M. Tiedje
    • 1
  1. 1.NASA Astrobiology Institute, Center for Microbial EcologyMichigan State UniversityEast LansingUSA
  2. 2.Institute for Physicochemical and Biological Problems in Soil ScienceRussian Academy of SciencesPushchinoRussia
  3. 3.DOE Plant Research Laboratory, NASA Astrobiology InstituteMichigan State UniversityEast LansingUSA
  4. 4.Food Science DepartmentNorth Carolina State UniversityRaleighUSA

Personalised recommendations