Taxonomic classification of Anoxybacillus isolates from geothermal regions in Turkey by 16S rRNA gene sequences and ARDRA, ITS-PCR, Rep-PCR analyses

• Autorzy: Cihan A.C.
• Języki publikacji: EN

Abstrakty

EN

A total of 115 endospore-forming bacilli were taken for 16S rRNA gene sequence analyses and clustered among 7 genera. In this paper, the most abundant thermophiles belonging to genus Anoxybacillus with its 53 isolates are presented. The Anoxybacillus species, some of which were producing biotechnologically valuable enzymes, mostly displayed amylolytic and glucosidic activities and the ability of carbohydrate degradation made them superior in number among the other bacilli in these extreme habitats. In comparative sequence analyses, similarities ranged from 91.1% to 99.9% between the isolates and the type strains. Isolates were clustered into eight phylogenetic lineages within the type strains of A. kamchatkensis, A. flavithermus, A. kamchatchensis subsp. asaccharedens, and A.salavatliensis. In addition, C161ab and A321 were proposed as novel species which displayed <97.0% similarities to their closest relatives. Moreover, their individual AluI, HaeIII, and TaqI ARDRA restriction patterns, ITS-, (GTG)₅-, and BOX-PCR fingerprintings generated 27, 28, 31, 35, 40, and 41 clusters, respectively. The twelve type strains and 35 of the isolates showed unique distinctive patterns from all the others at least in two of these analyses. These phenotypic and genomic characters allowed us to differentiate their genotypic diversity from the reference strains.

Słowa kluczowe

EN

taxonomic classification; Anoxybacillus; isolate; geothermal region; Turkey [geogr.]; 16S rRNA gene; gene sequence; amplified rDNA restriction analysis; ARDRA zob.amplified rDNA restriction analysis; polymerase chain reaction

• Wydawca: -
• Czasopismo: Polish Journal of Microbiology
• Rocznik: 2013
• Tom: 62
• Numer: 2
• Opis fizyczny: p.149-163,fig.,ref.

Twórcy

autor

Cihan A.C.

• Biology Department, Faculty of Science, Ankara University, 06100, Tandogan, Ankara, Turkey

Bibliografia

• Atanassova M., A. Derekova, R. Mandeva, C. Sjøholm and M. Kambourova. 2008. Anoxybacillus bogrovensis sp. nov., a novel thermophilic bacterium isolated from a hot spring in Dolni Bogrov, Bulgaria. Int. J. Syst. Evol. Microbiol. 58: 2359–2362.
• Adiguzel A, H. Ozkan, O. Barıs, K. Inan, M. Gulluce and F. Sahin. 2009 Identification and characterization of thermophilic bacteria isolated from hot spring in Turkey. J. Microbiol. Methods. 79: 321–328.
• Belduz A.O., S. Dulger and Z. Demirbag. 2003. Anoxybacillus gonensis sp. nov., a moderately thermophilic, xylose-utilizing, endospore-forming bacterium. Int. J. Syst. Evol. Microbiol. 53: 1315–1320.
• Caccamo D., T.L. Maugeri and C. Guglisndolo. 2001. Identification of thermohilic and marine bacilli from shallow thermal vents by restriction analysis of their amplified 16S rRNA. J. Appl. Microbiol. 91: 520–524.
• Cihan A.C., C. Cokmus and B. Ozcan. 2009. Characterization of thermostable α-glucosidases from newly isolated Geobacillus sp. A333 and thermophilic bacterium A343. World J. Microbiol. Biotechnol. 25: 2205–2217.
• Cihan A.C., B. Ozcan and C. Cokmus 2011. Anoxybacillus salavatliensis sp. nov., an α-glucosidase producing, thermophilic bacterium isolated from Salavatli, Turkey. J. Basic Microbiol. 51: 136–146.
• Claus D. and C.W. Berkeley. 1986. The genus Bacillus In: Bergey’s Manual of Systematic Bacteriology. Volume 2. Sneath pHA (Ed.) Williams, Wilkins, Baltimore, ISBN: 0-683-07893-934, pp. 1105–1139.
• Colak A., D. Sisik, N. Saglam, S. Güner, S. Canakci and A.O. Belduz. 2005. Characterization of a thermoalkalophilic esterase from a novel thermophilic bacterium, Anoxybacillus gonensis G2. Bioresour. Technol. Mar. 96: 625–631.
• Coleri A., C. Cokmus, B. Ozcan, N. Akkoc and M. Akcelik. 2009. Isolations of α-glucosidase-producing thermophilic bacilli from hot springs of Turkey. Microbiol. 78: 56–66.
• Coorevits A., A.E., Dinsdale, G. Halket, L. Lebbe, P. De-Vos, A. Van-Landschoot and N.A. Logan. 2012. Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G.stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly ‘thermoglucosidasius’); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov. Int. J. Syst. Evol. Microbiol. 62: 1470–1485.
• Daffonchio D., A. Cherif, L. Brusetti, A. Rizzi, D. Mora, A. Boudabous and S. Borin. 2003. Nature of polymorphisms in 16S–23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera. Appl. Environ. Microbiol. 69: 5128–5137.
• Dai J., Y. Liu, Y. Lei, Y. Gao, F. Han, Y. Xiao and H. Peng. 2011. A new subspecies of Anoxybacillus flavithermus ssp. yunnanensis ssp. nov. with very high ethanol tolerance. FEMS Microbiol. Lett. 320: 72–78.
• De Clerck E., M. Rodríguez-Díaz, T. Vanhoutte, J. Heyrman, N.A. Logan and P. De Vos. 2004. Anoxybacillus contaminans sp. nov. and Bacillus gelatini sp. nov., isolated from contaminated gelatin batches. Int. J. Syst. Evol. Microbiol. 54: 941–946.
• Demirjian D.C., F. Moris-Varas and C.S. Cassidy. 2001. Enzymes from extremophiles. Curr. Oppinion Chem. Biol. 5: 144–151.
• Derekova A., C. Sjøholm, R. Mandeva and M. Kambourova. 2007. Anoxybacillus rupiensis sp. nov., a novel thermophilic bacterium isolated from Rupi basin (Bulgaria). Extremophiles 11: 577–583.
• Derekova A., R. Mandeva and M. Kambourova. 2008. Phylogenetic diversity of thermophilic carbohydrate degrading bacilli from Bulgarian hot springs. World J. Microbiol. Biotechnol. 24: 1697–1702.
• Dulger S., Z. Demirbag and A.O. Belduz. 2004. Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov. Int. J. Syst. Evol. Microbiol. 54: 1499–1503.
• Ertunga N.S., A. Colak, A.O. Belduz, S. Canakci, H. Karaoglu and C. Sandalli. 2007. Cloning, Expression, Purification and characterization of Fructose-1,6-bisphosphate Aldolase from Anoxybacillus gonensis G2. J. Biochem. 141: 817–825.
• Gul-Guven R., K. Guven, A. Poli and B.J. Nicolaus. 2008. Anoxybacillus kamchatkensis subsp. asaccharedens subsp. nov., a thermophilic bacterium isolated from a hot spring in Batman. J. Gen. Appl. Microbiol. 54: 327–334.
• Inan K., A.O. Belduz and S. Canakci. 2012. Anoxybacillus kaynarcensis sp. nov., a moderately thermophilic, xylanase producing bacterium. J. Basic Microbiol. doi: 10.1002/jobm.201100638.
• Jukes T.H. and C.R. Cantor. 1969. Evolution of protein molecules. In: Munro HN (ed) Mammalian Protein Metabolism, Academic Press, New York, pp. 21–132.
• Kacagan M., S. Canakci, C. Sandalli, K. Inan, D.N. Colak and A.O. Belduz. 2008. Characterization of a xylanase from a thermophilic strain of Anoxybacillus pushchinoensis A8. Biologia 63: 599–606.
• Kevbrin V.V., K. Zengler, A.M. Lysenko and J. Wiegel. 2005. Anoxybacillus kamchatkensis sp. nov., a novel thermophilic facultative aerobic bacterium with a broad pH optimum from the Geyser valley, Kamchatka. Extremophiles 9: 391–398.
• Kim O.S., Y.J. Cho, K. Lee, S.H. Yoon, M. Kim, H. Na, S.C. Park, Y.S. Jeon, J.H. Lee, H. Yi, S. Won and J. Chun. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62: 716–721.
• Kuisiene N., R. Jomantiene, D. Valiunas and D. Chitavichius. 2002. Characterization of thermophilic proteolytic spore-forming bacteria from a geothermal site in Lithuania based on 16S rRNA RFLP and ITS-PCR analyses. Microbiol. 71: 712–716.
• Lavrenteva E.V., A.P. Shagzhina, O.B. Babasanova, Y.E. Dunaevsky, Z.B. Namsaraev and D.D. Barkhutova. 2009. The study of two alkaliphilic thermophile bacteria of the Anoxybacillus genus as producers of extracellular proteinase. Appl. Biochem. Micro. 45: 484–488.
• Logan N.A. O. Berge, A.H. Bishop, H.J. Busse, P. De Vos, D. Fritze, M. Heyndrickx, P. Kämpfer, L. Rabinovitch, M.S. Salkinoja-Salonen and others. 2009. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int. J. Syst. Evol. Microbiol. 59: 2114–2121.
• Ludwig W and K.H. Schleifer. 1999. Phylogeny of Bacteria beyond the 16S rRNA standard. ASM News 65: 752–757.
• Mora D.M., M.G. Fortina, G. Nicastro, C. Parini and P.L. Manachini. 1998. Genotypic characterization of thermophilic bacilli: a study of new soil isolates and several reference strains. Res. Microbiol. 149: 711–722.
• Namsaraev Z.B., O.B. Babasanova, Y.E. Dunaevsky, V.N Akimov, D.D Barkhutova, V.M. Gorlenko and B.B. Namsaraev. 2010. Anoxybacillus mongoliensis sp. nov., a novel thermophilic proteinase producing bacterium isolated from alkaline hot spring, central Mongolia. Microbiol. 79: 491–499.
• Pikuta E., A. Lysenko, N. Chuvilskaya, U. Mendrock, H. Hippe, N. Suzina, D. Nikitin, G. Osipov and K. Laurinavichius. 2000. Anoxybacillus pushchinensis gen. nov., sp. nov., a novel anaerobic, alkaliphilic, moderately thermophilic bacterium from manure, and description of Anoxybacillus flavithermus comb. nov. Int. J. Syst. Evol. Microbiol. 50: 2109–2117.
• Pikuta E., D. Cleland and J. Tang 2003. Aerobic growth of Anoxybacillus pushchinoensis K1T: emended descriptions of A. pushchinoensis and the genus Anoxybacillus. Int. J. Syst. Evol. Microbiol. 53: 1561–1562.
• Poli A., E. Esposito, L. Lama, P. Orlando, G. Nicolaus, F. De Appolonia, A. Gambacorta and B. Nicolaus. 2006. Anoxybacillus amylolyticus sp. nov., a thermophilic amylase producing bacterium isolated from Mount Rittmann (Antarctica). Syst. Appl. Microbiol. 29: 300–307.
• Poli A., I. Romano, P. Cordella, P. Orlando, B. Nicolaus and C.C. Berrini. 2009. Anoxybacillus thermarum sp. nov., a novel thermophilic bacterium isolated from thermal mud in Euganean hot springs, Abano Terme, Italy. Extremophiles. 13: 867–874.
• Rodas A.M, S. Ferrer and I. Pardo. 2003. 16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine. Syst. Appl. Microbiol. 26: 412–422.
• Rosselló-Mora R. 2005. Updating prokaryotic taxonomy. J. Bacteriol. 187: 6255–6257.
• Saitou N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
• Schäffer C., W.L. Franck, A. Scheberl, P. Kosma, T.R. Mcdermott and P. Messner. 2004. Classification of isolates from locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov. Int. J. Syst. Evol. Microbiol. 54: 2361–2368.
• Stackebrandt E. and B.M. Goebel. 1994. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. System. Bacteriol. 44: 846–849.
• Stackebrandt E., W. Fredericksen G.M. Garrity, P.A.D. Grimont, P. Kämpfer, M.C.J. Maiden, X. Nesme, R. Rossello-Mora, J. Swings, H.G. Trüper, L. Vauterin, A.C. Ward and W.B. Whitman. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 1043–1047.
• Suzuki Y., T. Kishigami and S. Abe. 1976. Production of extracellular α-glucosidase by a thermophilic Bacillus species. Appl. Environ. Microbiol. 31: 807–812.
• Tamura K., J. Dudley, M. Nei and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol .Biol. Evol. 24: 1596–1599.
• Tekin N., A.C. Cihan, Z.S. Takac, C.Y. Tuzun, K. Tunc and C. Cokmus. 2012. Alkaline protease production of Bacillus cohnii APT5. Turk. J. Biol. 36: 430–440.
• Vaneechoutte M., R. Rossau, P. De Vos, M. Gills, D. Janssens, N. Paepe, A. De Rouck, T. Fiers, G. Claeys and K. Kersters. 1992 Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol. Letts. 93: 227–234.
• Versalovic J., M. Schneider, F.J. De Bruijn and J.R. Lupski. 1994. Genomic fingerprinting of bacteria using repetitive sequence based PCR (rep-PCR). Meth. Cell. Mol. Biol. 5: 25–40.
• White D., R.J. Sharp and F.G. Priest. 1993. A polyphasic taxonomic study of thermophilic bacilli from a wide geographical area. Antonie van Leeuwenhoek. 64: 357–386.
• Yumoto I., K. Hirota, T. Kawahara, Y. Nodasaka, H. Okuyama, H. Matsuyama, Y. Yokota, K. Nakajima and T. Hoshino. 2004. Anoxybacillus voinovskiensis sp. nov., a moderately thermophilic bacterium from a hot spring in Kamchatka. Int. J. Syst. Evol. Microbiol. 54: 1239–1242.
• Zhang C.M., X.W. Huang, W.Z. Pan, J. Zhang, K.B. Wei, H.P. Klenk, S.K. Tang, W.J. Li and K.Q. Zhang. 2010. Anoxybacillus tengchongensis sp. nov. and Anoxybacillus eryuanensis sp. nov., two novel facultatively anaerobic, alkalitolerant bacteria from hot springs in Yunnan, China. Int. J. Syst. Evol. Microbiol. 61: 118–122.