sp. nov., a novel member of the class isolated from geothermal soil, and emended descriptions of , , and Free

Abstract

An aerobic, thermophilic and cellulolytic bacterium, designated strain WKT50.2, was isolated from geothermal soil at Waikite, New Zealand. Strain WKT50.2 grew at 53–76 °C and at pH 5.9–8.2. The DNA G+C content was 58.4 mol%. The major fatty acids were 12-methyl C and C. Polar lipids were all linked to long-chain 1,2-diols, and comprised 2-acylalkyldiol-1--phosphoinositol (diolPI), 2-acylalkyldiol-1--phosphoacylmannoside (diolP-acylMan), 2-acylalkyldiol-1--phosphoinositol acylmannoside (diolPI-acylMan) and 2-acylalkyldiol-1--phosphoinositol mannoside (diolPI-Man). Strain WKT50.2 utilized a range of cellulosic substrates, alcohols and organic acids for growth, but was unable to utilize monosaccharides. Robust growth of WKT50.2 was observed on protein derivatives. WKT50.2 was sensitive to ampicillin, chloramphenicol, kanamycin, neomycin, polymyxin B, streptomycin and vancomycin. Metronidazole, lasalocid A and trimethoprim stimulated growth. Phylogenetic analysis of 16S rRNA gene sequences showed that WKT50.2 belonged to the class within the phylum , and was most closely related to KI4 (99.6% similarity). DNA–DNA hybridization between WKT50.2 and DSM 27169 was 18.0%. Physiological and biochemical tests confirmed the phenotypic and genotypic differentiation of strain WKT50.2 from KI4 and other members of the . On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain WKT50.2 represents a novel species, for which the name sp. nov. is proposed, with the type strain WKT50.2 ( = DSM 26011 = ICMP 20042). Emended descriptions of , , and are also proposed, and include the description of a novel respiratory quinone, MK-8 2,3-epoxide (23%), in .

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2015-12-01
2024-03-29
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References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. ( 1997;). Gapped blast psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25 33893402 [View Article] [PubMed].
    [Google Scholar]
  2. Botero L. M., Brown K. B., Brumefield S., Burr M., Castenholz R. W., Young M., McDermott T. R. ( 2004;). Thermobaculum terrenum gen. nov., sp. nov.: a non-phototrophic gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green non-sulfur bacteria) and Thermomicrobia . Arch Microbiol 181 269277 [View Article] [PubMed].
    [Google Scholar]
  3. Carreto L., Moore E., Nobre M. F., Wait R., Riley P. W., Sharp R. J., Da Costa M. S. ( 1996;). Rubrobacter xylanophilus sp. nov., a new thermophilic species isolated from a thermally polluted effluent. Int J Syst Bacteriol 46 460465 [View Article].
    [Google Scholar]
  4. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. ( 1977;). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81 461466 [View Article] [PubMed].
    [Google Scholar]
  5. Chen M.-Y., Wu S.-H., Lin G.-H., Lu C.-P., Lin Y.-T., Chang W.-C., Tsay S.-S. ( 2004;). Rubrobacter taiwanensis sp. nov., a novel thermophilic, radiation-resistant species isolated from hot springs. Int J Syst Evol Microbiol 54 18491855 [View Article] [PubMed].
    [Google Scholar]
  6. Costa K. C., Navarro J. B., Shock E. L., Zhang C. L., Soukup D., Hedlund B. P. ( 2009;). Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin. Extremophiles 13 447459 [View Article] [PubMed].
    [Google Scholar]
  7. de la Torre J. R., Goebel B. M., Friedmann E. I., Pace N. R. ( 2003;). Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica. Appl Environ Microbiol 69 38583867 [View Article] [PubMed].
    [Google Scholar]
  8. Demharter W., Hensel R., Smida J., Stackebrandt E. ( 1989;). Sphaerobacter thermophilus gen. nov., sp. nov. A deeply rooting member of the Actinomycetes subdivision isolated from thermophilically treated sewage sludge. Syst Appl Microbiol 11 261266 [View Article].
    [Google Scholar]
  9. Engel A. S., Johnson L. R., Porter M. L. ( 2013;). Arsenite oxidase gene diversity among Chloroflexi and Proteobacteria from El Tatio Geyser Field, Chile. FEMS Micro Ecol 83 745756. [CrossRef]
    [Google Scholar]
  10. Giggenbach W., Sheppard D., Robinson B., Stewart M., Lyon G. ( 1994;). Geochemical structure and position of the Waiotapu geothermal field, New Zealand. Geothermics 23 599644 [View Article].
    [Google Scholar]
  11. Gladden J. M., Allgaier M., Miller C. S., Hazen T. C., VanderGheynst J. S., Hugenholtz P., Simmons B. A., Singer S. W. ( 2011;). Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Appl Environ Microbiol 77 58045812 [View Article] [PubMed].
    [Google Scholar]
  12. Grice E. A., Kong H. H., Conlan S., Deming C. B., Davis J., Young A. C., Bouffard G. G., Blakesley R. W., Murray P. R., other authors. ( 2009;). Topographical and temporal diversity of the human skin microbiome. Science 324 11901192 [View Article] [PubMed].
    [Google Scholar]
  13. Gupta R. S., Chander P., George S. ( 2013;). Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov. Antonie van Leeuwenhoek 103 99119 [View Article] [PubMed].
    [Google Scholar]
  14. Halebian S., Harris B., Finegold S. M., Rolfe R. D. ( 1981;). Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. J Clin Microbiol 13 444448 [PubMed].
    [Google Scholar]
  15. Hardy K. R., King G. M. ( 2001;). Enrichment of high-affinity CO oxidizers in Maine forest soil. Appl Environ Microbiol 67 36713676 [View Article] [PubMed].
    [Google Scholar]
  16. Hanada S., Pierson B. K. ( 2006;). The family Chloroflexaceae. In The Prokaryotes. , pp. 815842. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. New York, USA: [View Article] Springer;.
    [Google Scholar]
  17. Hugenholtz P., Stackebrandt E. ( 2004;). Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 54 20492051 [View Article] [PubMed].
    [Google Scholar]
  18. Jackson T. J., Ramaley R. F., Meinschein W. G. ( 1973;). Thermomicrobium, a new genus of extremely thermophilic bacteria. Int J Syst Bacteriol 23 2836 [View Article].
    [Google Scholar]
  19. Joynt J., Bischoff M., Turco R., Konopka A., Nakatsu C. H. ( 2006;). Microbial community analysis of soils contaminated with lead, chromium and petroleum hydrocarbons. Microb Ecol 51 209219 [View Article] [PubMed].
    [Google Scholar]
  20. Jukes T. H., Cantor C. R. ( 1969;). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21132. Edited by Munro H. N. New York:: [View Article] Academic Press;.
    [Google Scholar]
  21. Jürgens U. J., Meißner J., Fischer U., König W. A., Weckesser J. ( 1987;). Ornithine as a constituent of the peptidoglycan of Chloroflexus aurantiacus, diaminopimelic acid in that of Chlorobium vibrioforme f. thiosulfatophilum . Arch Microbiol 148 7276 [View Article].
    [Google Scholar]
  22. King C. E., King G. M. ( 2014a;). Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria . Int J Syst Evol Microbiol 64 12441251 [View Article] [PubMed].
    [Google Scholar]
  23. King C. E., King G. M. ( 2014b;). Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms. Int J Syst Evol Microbiol 64 25862592 [View Article] [PubMed].
    [Google Scholar]
  24. Kunisawa T. ( 2011;). The phylogenetic placement of the non-phototrophic, Gram-positive thermophile ‘Thermobaculum terrenum’ and branching orders within the phylum ‘Chloroflexi’ inferred from gene order comparisons. Int J Syst Evol Microbiol 61 19441953 [View Article] [PubMed].
    [Google Scholar]
  25. Lagutin K., MacKenzie A., Houghton K. M., Stott M. B., Vyssotski M. ( 2015;). Novel long-chain diol phospholipids from some bacteria belonging to the class Thermomicrobia . Lipids 50 303311 [View Article] [PubMed].
    [Google Scholar]
  26. Lesaulnier C., Papamichail D., McCorkle S., Ollivier B., Skiena S., Taghavi S., Zak D., van der Lelie D. ( 2008;). Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen. Environ Microbiol 10 926941 [View Article] [PubMed].
    [Google Scholar]
  27. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., other authors. ( 2004;). arb: a software environment for sequence data. Nucleic Acids Res 32 13631371 [View Article] [PubMed].
    [Google Scholar]
  28. MacKenzie A., Vyssotski M., Nekrasov E. ( 2009;). Quantitative analysis of dairy phospholipids by 31P NMR. J Am Oil Chem Soc 86 757763 [View Article].
    [Google Scholar]
  29. Meissner J., Krauss J. H., Jürgens U. J., Weckesser J. ( 1988;). Absence of a characteristic cell wall lipopolysaccharide in the phototrophic bacterium Chloroflexus aurantiacus . J Bacteriol 170 32133216 [PubMed].
    [Google Scholar]
  30. Merkel G. J., Durham D. R., Perry J. J. ( 1980;). The atypical cell wall composition of Thermomicrobium roseum . Can J Microbiol 26 556559 [View Article] [PubMed].
    [Google Scholar]
  31. Mesbah M., Premachandran U., Whitman W. B. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39 159167 [View Article].
    [Google Scholar]
  32. Nishijima A., Araki-Sakai M., Sano H. ( 1997;). Identification of isoprenoid quinones by frit-FAB liquid chromatography–mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Meth 28 113122. [CrossRef]
    [Google Scholar]
  33. Partanen P., Hultman J., Paulin L., Auvinen P., Romantschuk M. ( 2010;). Bacterial diversity at different stages of the composting process. BMC Microbiol 10 94 [View Article] [PubMed].
    [Google Scholar]
  34. Pati A., Labutti K., Pukall R., Nolan M., Glavina Del Rio T., Tice H., Cheng J. F., Lucas S., Chen F., other authors. ( 2010;). Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci 2 4956 [View Article] [PubMed].
    [Google Scholar]
  35. Pond J. L., Langworthy T. A., Holzer G. ( 1986;). Long-chain diols: a new class of membrane lipids from a thermophilic bacterium. Science 231 11341136 [View Article] [PubMed].
    [Google Scholar]
  36. Ronquist F., Teslenko M., van der Mark P., Ayres D. L., Darling A., Höhna S., Larget B., Liu L., Suchard M. A., Huelsenbeck J. P. ( 2012;). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61 539542 [View Article] [PubMed].
    [Google Scholar]
  37. Schleifer K. H., Kandler O. ( 1972;). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36 407477 [PubMed].
    [Google Scholar]
  38. Schumann P. ( 2011;). Peptidoglycan structure. Methods Microbiol 38 101129 [View Article].
    [Google Scholar]
  39. Sorokin D. Y., Lücker S., Vejmelkova D., Kostrikina N. A., Kleerebezem R., Rijpstra W. I., Sinninghe Damsté J. S., Le Paslier D., Muyzer G., other authors. ( 2012;). Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J 6 22452256 [View Article] [PubMed].
    [Google Scholar]
  40. Sorokin D. Y., Vejmelkova D., Lücker S., Streshinskaya G. M., Rijpstra W. I. C., Sinninghe Damsté J. S., Kleerbezem R., van Loosdrecht M., Muyzer G., Daims H. ( 2014;). Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi . Int J Syst Evol Microbiol 64 18591865 [View Article] [PubMed].
    [Google Scholar]
  41. Staneck J. L., Roberts G. D. ( 1974;). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28 226231 [PubMed].
    [Google Scholar]
  42. Stott M. B., Crowe M. A., Mountain B. W., Smirnova A. V., Hou S., Alam M., Dunfield P. F. ( 2008;). Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 10 20302041 [View Article] [PubMed].
    [Google Scholar]
  43. Sutcliffe I. C. ( 2010;). A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 18 464470 [View Article] [PubMed].
    [Google Scholar]
  44. Sutcliffe I. C. ( 2011;). Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war. Environ Microbiol 13 279282 [View Article] [PubMed].
    [Google Scholar]
  45. Suzuki K., Collins M. D., Iijima E., Komagata K. ( 1988;). Chemotaxonomic characterization of a radiotolerant bacterium, Arthrobacter radiotolerans: description of Rubrobacter radiotolerans gen. nov., comb. nov. FEMS Microbiol Lett 52 3339 [View Article].
    [Google Scholar]
  46. Vyssotski M., Ryan J., Lagutin K., Wong H., Morgan X., Stott M. ( 2012;). A novel fatty acid, 12,17-dimethyloctadecanoic acid, from the extremophile Thermogemmatispora sp. (strain T81). Lipids 47 601611 [View Article] [PubMed].
    [Google Scholar]
  47. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. ( 1987;). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 463464 [View Article].
    [Google Scholar]
  48. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991;). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 697703 [PubMed].
    [Google Scholar]
  49. Wu D., Raymond J., Wu M., Chatterji S., Ren Q., Graham J. E., Bryant D. A., Robb F., Colman A., other authors. ( 2009;). Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum . PLoS One 4 e4207 [View Article] [PubMed].
    [Google Scholar]
  50. Yabe S., Aiba Y., Sakai Y., Hazaka M., Yokota A. ( 2011;). Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria . Int J Syst Evol Microbiol 61 903910 [View Article] [PubMed].
    [Google Scholar]
  51. Ziemke F., Höfle M. G., Lalucat J., Rosselló-Mora R. ( 1998;). Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48 179186 [View Article] [PubMed].
    [Google Scholar]
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