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

Springer Science and Business Media LLC - Tập 10 - Trang 285-294 - 2006
Debora Frigi Rodrigues1, Johan Goris1, Tatiana Vishnivetskaya2,3, David Gilichinsky2, Michael F. Thomashow4, James M. Tiedje1
1NASA Astrobiology Institute, Center for Microbial Ecology, Michigan State University, East Lansing, USA
2Institute for Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
3Food Science Department, North Carolina State University, Raleigh, USA
4DOE Plant Research Laboratory, NASA Astrobiology Institute, Michigan State University, East Lansing, USA

Tóm tắt

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.

Tài liệu tham khảo

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 Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230 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 Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. Cambridge University Press, London Desoete G (1983) On the construction of optimal phylogenetic trees. Z Naturforsch C J Biosci 38:156–158 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 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 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 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 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 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 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 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 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 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 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 40:2653–2658 Koneman E, Allen S, Dowell V, Sommers H (1979) Color atlas and text book of diagnostic microbiology. Lippincott, Philadelphia 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 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 MacKenzie SL (1987) Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 70:151–160 Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218 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 McKay CP, Friedmann EI, Meyer MA (1991) From Siberia to Mars. Planet Rep Mar–Apr:8–11 Miller L, Berger T (1984) Bacterial identification by gas chromatography and whole cell fatty acids. Hewlett-Packard, Palo Alto, pp. 228–241 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 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 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 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 Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425 Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156 Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477 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 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 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 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 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 Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976–978 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 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 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 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 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