1887

Abstract

Three novel strains of the phylum (Ac_11_E3, Ac_12_G8 and Ac_16_C4) were isolated from Namibian semiarid savanna soils by a high-throughput cultivation approach using low-nutrient growth media. 16S rRNA gene sequence analysis placed all three strains in the order of the class ( subdivision 4). However, 16S rRNA gene sequence similarities to their closest relative K22 were ≤90 %. Cells of strains Ac_11_E3, Ac_12_G8 and Ac_16_C4 were Gram-staining-negative and non-motile and divided by binary fission. Ac_11_E3 and Ac_16_C4 formed white colonies, while those of Ac_12_G8 were orange-yellowish. All three strains were aerobic chemoorganoheterotrophic mesophiles with a broad pH range for growth. All strains used a very limited spectrum of carbon and energy sources for growth, with a preference for complex proteinaceous substrates. The major respiratory quinone was MK-8. The major shared fatty acid was iso-C. The DNA G+C contents of strains Ac_11_E3, Ac_12_G8 and Ac_16_C4 were 55.9 mol%, 66.9 mol% and 54.7 mol%, respectively. Based on these characteristics, the two novel genera gen. nov. and gen. nov. are proposed, harboring the novel species sp. nov. (Ac_11_E3=DSM 27934=LMG 28618), sp. nov. (Ac_16_C4=DSM 29892=LMG 28995) and sp. nov. (Ac_12_G8=DSM 26556=LMG 29166), respectively. Since these novel genera are only distantly related to established families, we propose the novel family fam. nov. that accommodates the proposed genera and the genus ).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001199
2016-09-01
2021-07-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/9/3355.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001199&mimeType=html&fmt=ahah

References

  1. Barns S. M., Takala S. L., Kuske C. R. 1999; Wide distribution and diversity of members of the bacterial kingdomAcidobacterium in the environment. Appl Environ Microbiol 65:1731–1737[PubMed]
    [Google Scholar]
  2. Barrow G. I, Feltham R. K. A. 1993 Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge & New York: Cambridge University Press; [CrossRef]
    [Google Scholar]
  3. Beveridge T. J., Lawrence J. R., Murray R. G. E. 2007; Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology , pp. 19–33 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  4. Bligh E. G., Dyer W. J. 1959; A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917 [View Article][PubMed]
    [Google Scholar]
  5. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci USA 75:4801–4805 [View Article]
    [Google Scholar]
  6. Bryant D. A., Costas A. M., Maresca J. A., Chew A. G., Klatt C. G., Bateson M. M., Tallon L. J., Hostetler J., Nelson W. C. et al. 2007; Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium. Science 317:523–526 [View Article][PubMed]
    [Google Scholar]
  7. Buck J. D. 1982; Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993[PubMed]
    [Google Scholar]
  8. 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]
  9. Collins M. D., Jones D. 1981; Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354[PubMed]
    [Google Scholar]
  10. Crowe M. A., Power J. F., Morgan X. C., Dunfield P. F., Lagutin K., Rijpstra W. I., Rijpstra I. C., Vyssotski G. N., Sinninghe Damste J. S. et al. 2014; Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylumAcidobacteria from geothermal soils. Int J Syst Evol Microbiol 64:220–227 [View Article][PubMed]
    [Google Scholar]
  11. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [View Article][PubMed]
    [Google Scholar]
  12. Foesel B. U., Rohde M., Overmann J. 2013; Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil – the first described species ofAcidobacteria subdivision 4. Syst Appl Microbiol 36:82–89 [View Article][PubMed]
    [Google Scholar]
  13. Foesel B. U., Nägele V., Naether A., Wüst P. K., Weinert J., Bonkowski M., Lohaus G., Polle A., Alt F. et al. 2014; Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils. Environ Microbiol 16:658–675 [View Article][PubMed]
    [Google Scholar]
  14. Foesel B. U., Mayer S., Luckner M., Wanner G., Rohde M., Overmann J. 2016; Occallatibacter riparius gen. nov., sp. nov. andO. savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the familyAcidobacteriaceae . Int J Syst Evol Microbiol 66:219–229 [View Article][PubMed]
    [Google Scholar]
  15. Garcia Costas A. M., Tsukatani Y., Rijpstra W. I., Schouten S., Welander P. V., Summons R. E., Bryant D. A. 2012; Identification of the bacteriochlorophylls, carotenoids, quinones, lipids, and hopanoids of ‘Candidatus Chloracidobacterium thermophilum’. J Bacteriol 194:1158–1168 [View Article][PubMed]
    [Google Scholar]
  16. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. 1994 Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;
    [Google Scholar]
  17. Huber K. J., Wüst P. K., Rohde M., Overmann J., Foesel B. U. 2014; Aridibacter famidurans gen. nov., sp. nov. andAridibacter kavangonensis sp. nov., two novel members of subdivision 4 of theAcidobacteria isolated from semiarid savannah soil. Int J Syst Evol Microbiol 64:1866–1875 [View Article][PubMed]
    [Google Scholar]
  18. Huss V. A., 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][PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Kolinko S., Wanner G., Katzmann E., Kiemer F., Fuchs B. M., Schüler D. 2013; Clone libraries and single cell genome amplification reveal extended diversity of uncultivated magnetotactic bacteria from marine and freshwater environments. Environ Microbiol 15:1290–1301 [View Article][PubMed]
    [Google Scholar]
  22. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics , pp. 115–175 Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  23. Lee K. C., Morgan X. C., Power J. F., Dunfield P. F., Huttenhower C., Stott M. B. 2015; Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22T . Stand Genomic Sci 10:101 [View Article][PubMed]
    [Google Scholar]
  24. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. et al. 2004; ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. Naether A., Foesel B. U., Naegele V., Wüst P. K., Weinert J., Bonkowski M., Alt F., Oelmann Y., Polle A. et al. 2012; Environmental factors affect Acidobacterial communities below the subgroup level in grassland and forest soils. Appl Environ Microbiol 78:7398–7406 [View Article][PubMed]
    [Google Scholar]
  27. Pascual J., Wüst P. K., Geppert A., Foesel B. U., Huber K. J., Overmann J. 2015; Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4. Syst Appl Microbiol 38:534–544 [View Article][PubMed]
    [Google Scholar]
  28. Sasser M. 1990 Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. Technical Note No 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  29. Sinninghe Damsté J. S., Rijpstra W. I., Hopmans E. C., Foesel B. U., Wüst P. K., Overmann J., Tank M., Bryant D. A., Dunfield P. F. et al. 2014; Ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4. Appl Environ Microbiol 80:5207–5218 [View Article][PubMed]
    [Google Scholar]
  30. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [View Article]
    [Google Scholar]
  31. Tank M., Bryant D. A. 2015; Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium. Int J Syst Evol Microbiol 65:1426–1430 [View Article][PubMed]
    [Google Scholar]
  32. Tindall B. J. 1990; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  33. Tindall B. J., Sikorski J., Smibert R. M., Krieg N. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology , pp. 330–393 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  34. Wanner G., Vogl K., Overmann J. 2008; Ultrastructural characterization of the prokaryotic symbiosis in ‘Chlorochromatium aggregatum’. J Bacteriol 190:3721–3730 [View Article][PubMed]
    [Google Scholar]
  35. 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. et al. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  36. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R. 2008; The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250 [View Article][PubMed]
    [Google Scholar]
  37. Yarza P., Yilmaz P., Pruesse E., Glöckner F. O., Ludwig W., Schleifer K. H., Whitman W. B., Euzéby J., Amann R., Rosselló-Móra R. 2014; Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001199
Loading
/content/journal/ijsem/10.1099/ijsem.0.001199
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error