sp. nov., sp. nov., sp. nov. and sp. nov., novel acidobacteria from tundra soil Free

Abstract

Four aerobic bacteria, designated MP5ACTX2, MP5ACTX8, MP5ACTX9 and S6CTX5A, were isolated from tundra soil of north-western Finland (69° 03′ N 20° 50′ E). Cells of all isolates were Gram-negative, non-motile rods. Phylogenetic analysis indicated that they belonged to the genus of subdivision 1 of the phylum . 16S rRNA gene sequence similarity between the new isolates and the type strains of , , and ranged from 94 to 99 %. Analysis of the RNA polymerase beta subunit () gene sequence indicated that the isolates represented novel species of the genus (<92 % sequence similarity between the isolates and members of the genus ). This was also confirmed by low DNA–DNA relatedness (31 %) between strain S6CTX5A and the type strain of , which exhibited 99.1 % 16S rRNA gene sequence similarity and 91.7 % gene sequence similarity. The isolates grew at pH 3.5–6.5 and at 4–26 °C. Sugars were the preferred growth substrates. The major cellular fatty acids were iso-C, Cω7 and C and the major isoprenoid quinone was MK-8. The DNA G+C content was 56–60 mol%. On the basis of phylogenetic analysis and chemotaxonomic and physiological data, the isolates represent four novel species of the genus , for which the names MP5ACTX2 ( = ATCC BAA-1858 = DSM 23128), MP5ACTX8 ( = ATCC BAA-1857 = DSM 23137), MP5ACTX9 (ATCC BAA-1859 = DSM 23138) and S6CTX5A ( = LMG 26174 = DSM 23136) are proposed. An emended description of the genus is also presented.

Funding
This study was supported by the:
  • Academy of Finland (Award 123725 and 106208)
  • National Science Foundation (Award IPY 0732956)
  • Lapland Regional Fund of the Finnish Cultural Foundation
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2012-09-01
2024-03-28
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References

  1. Adékambi T., Shinnick T. M., Raoult D., Drancourt M. 2008; Complete rpoB gene sequencing as a suitable supplement to DNA–DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Microbiol 58:1807–1814 [View Article][PubMed]
    [Google Scholar]
  2. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [View Article][PubMed]
    [Google Scholar]
  3. Barns S. M., Cain E. C., Sommerville L., Kuske C. R. 2007; Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73:3113–3116 [View Article][PubMed]
    [Google Scholar]
  4. Bazzola J. J., Russel L. D. 1991 Electron Microscopy. Principles and Techniques for Biologists Boston, London, Singapore: Jones and Bartlett Publishers;
    [Google Scholar]
  5. Campbell B. J., Polson S. W., Hanson T. E., Mack M. C., Schuur E. A. 2010; The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ Microbiol 12:1842–1854 [View Article][PubMed]
    [Google Scholar]
  6. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. 1977; A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466 [View Article][PubMed]
    [Google Scholar]
  7. Coates J. D., Ellis D. J., Gaw C. V., Lovley D. R. 1999; Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 49:1615–1622 [View Article][PubMed]
    [Google Scholar]
  8. Davis K. E. R., Joseph S. J., Janssen P. H. 2005; Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 71:826–834 [View Article][PubMed]
    [Google Scholar]
  9. Dedysh S. N., Kulichevskaya I. S., Serkebaeva Y. M., Mityaeva M. A., Sorokin V. V., Suzina N. E., Rijpstra W. I., Damsté J. S. 2012; Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008. Int J Syst Evol Microbiol 62:654–664 [View Article][PubMed]
    [Google Scholar]
  10. Eichorst S. A., Breznak J. A., Schmidt T. M. 2007; Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria . Appl Environ Microbiol 73:2708–2717 [View Article][PubMed]
    [Google Scholar]
  11. Eichorst S. A., Kuske C. R., Schmidt T. M. 2011; Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria . Appl Environ Microbiol 77:586–596 [View Article][PubMed]
    [Google Scholar]
  12. Fukunaga Y., Kurahashi M., Yanagi K., Yokota A., Harayama S. 2008; Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum ‘Acidobacteria’. Int J Syst Evol Microbiol 58:2597–2601 [View Article][PubMed]
    [Google Scholar]
  13. Galtier N., Gouy M., Gautier C. 1996; seaview and phylo_win: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543–548[PubMed]
    [Google Scholar]
  14. Hayt M. A. 1981 Fixation for Electron Microscopy New York: Academic Press;
    [Google Scholar]
  15. Huß V. A. R., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [View Article]
    [Google Scholar]
  16. Janssen P. H. 2006; Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728 [View Article][PubMed]
    [Google Scholar]
  17. Jones R. T., Robeson M. S., Lauber C. L., Hamady M., Knight R., Fierer N. 2009; A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3:442–453 [View Article][PubMed]
    [Google Scholar]
  18. Kishimoto N., Kosako Y., Tano T. 1991; Acidobacterium capsulatum gen. nov., sp. nov. an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol 22:1–7 [View Article]
    [Google Scholar]
  19. Koch I. H., Gich F., Dunfield P. F., Overmann J. 2008; Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. Int J Syst Evol Microbiol 58:1114–1122 [View Article][PubMed]
    [Google Scholar]
  20. Kulichevskaya I. S., Suzina N. E., Liesack W., Dedysh S. N. 2010; Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria . Int J Syst Evol Microbiol 60:301–306 [View Article][PubMed]
    [Google Scholar]
  21. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp. 115–175 Edited by Stackebrant E., Goodfellow M. London: John Wiley & Sons;
    [Google Scholar]
  22. Liesack W., Bak F., Kreft J. U., Stackebrandt E. 1994; Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Arch Microbiol 162:85–90 [View Article][PubMed]
    [Google Scholar]
  23. Männistö M. K., Häggblom M. M. 2006; Characterization of psychrotolerant heterotrophic bacteria from Finnish Lapland. Syst Appl Microbiol 29:229–243 [View Article][PubMed]
    [Google Scholar]
  24. Männistö M. K., Tiirola M., Häggblom M. M. 2007; Bacterial communities in Arctic fjelds of Finnish Lapland are stable but highly pH-dependent. FEMS Microbiol Ecol 59:452–465 [View Article][PubMed]
    [Google Scholar]
  25. Männistö M. K., Tiirola M., Häggblom M. M. 2009; Effect of freeze-thaw cycles on bacterial communities of arctic tundra soil. Microb Ecol 58:621–631 [View Article][PubMed]
    [Google Scholar]
  26. Männistö M. K., Tiirola M., McConnell J., Häggblom M. M. 2010; Mucilaginibacter frigoritolerans sp. nov., Mucilaginibacter lappiensis sp. nov. and Mucilaginibacter mallensis sp. nov., isolated from soil and lichen samples. Int J Syst Evol Microbiol 60:2849–2856 [View Article][PubMed]
    [Google Scholar]
  27. Männistö M. K., Rawat S., Starovoytov V., Häggblom M. M. 2011; Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil. Int J Syst Evol Microbiol 61:1823–1828 [View Article][PubMed]
    [Google Scholar]
  28. 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 39:159–167 [View Article]
    [Google Scholar]
  29. Miller, L. & Berger, T. (1985). Bacterial identification by gas chromatography of whole cell fatty acids, Hewlett-Packard application note 228-41. Palo Alto, CA: Hewlett-Packard Co.
  30. Murray R. G. E., Doetsch R. N., Robinow C. F. 1994; Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology pp. 683–700 Edited by Gerhardt P. , Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  31. Okamura K., Kawai A., Yamada T., Hiraishi A. 2011; Acidipila rosea gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum Acidobacteria . FEMS Microbiol Lett 317:138–142 [View Article][PubMed]
    [Google Scholar]
  32. Pankratov T. A., Dedysh S. N. 2010; Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs. Int J Syst Evol Microbiol 60:2951–2959 [View Article][PubMed]
    [Google Scholar]
  33. Pankratov T. A., Serkebaeva Y. M., Kulichevskaya I. S., Liesack W., Dedysh S. N. 2008; Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat. ISME J 2:551–560 [View Article][PubMed]
    [Google Scholar]
  34. Pankratov T. A., Kirsanova L. A., Kaparullina E. N., Kevbrin V. V., Dedysh S. N. 2012; Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991. Int J Syst Evol Microbiol 62:430–437 [View Article][PubMed]
    [Google Scholar]
  35. Sait M., Hugenholtz P., Janssen P. H. 2002; Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4:654–666 [View Article][PubMed]
    [Google Scholar]
  36. Stackebrandt E., Ebers J. 2006; Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
    [Google Scholar]
  37. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. 2011; mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  38. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  39. Ward N. L., Challacombe J. F., Janssen P. H., Henrissat B., Coutinho P. M., Wu M., Xie G., Haft D. H., Sait M. other authors 2009; Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75:2046–2056 [View Article][PubMed]
    [Google Scholar]
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