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Abstract

A novel chemo-organoheterotroph bacterium, strain CB-286315, was isolated from a Mediterranean forest soil sampled at the Sierra de Tejeda, Almijara and Alhama Natural Park, Spain, by using the diffusion sandwich system, a device with 384 miniature diffusion chambers. 16S rRNA gene sequence analyses identified the isolate as a member of the under-represented phylum , where ‘’ KBS708, T-27 and AP64 were the closest relatives, with respective similarities of 84.4, 83.6 and 83.3 %. Strain CB-286315 was characterized as a Gram-negative, non-motile, short to long rod-shaped bacterium. Occasionally, some cells attained an unusual length, up to 35–40 μm. The strain showed positive responses for catalase and cytochrome- oxidase and division by binary fission, and exhibited an aerobic metabolism, showing optimal growth under normal atmospheric conditions. Strain CB-286315 was also able to grow under micro-oxic atmospheres, but not under anoxic conditions. The strain is a slowly growing bacterium able to grow under low nutrient concentrations. Major fatty acids included iso-Cω9, summed feature 3 (Cω7 and/or iso-C 2-OH), C and iso-C. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and three phospholipids. The major isoprenoid quinone was MK-8 and the diagnostic diamino acid was -diaminopimelic acid. The DNA G+C content was 67.0 mol%. Based on a polyphasic taxonomic characterization, strain CB-286315 represents a novel genus and species, gen. nov., sp. nov., within the phylum . The type strain of is strain CB-286315 ( = DSM 29007 = CECT 8660). In order to classify the novel taxon within the existing taxonomic framework, the family fam. nov., order ord. nov. and class classis nov. are also proposed.

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2016-05-01
2021-07-29
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References

  1. Alain K., Querellou J. 2009; Cultivating the uncultured: limits, advances and future challenges. Extremophiles 13:583–594 [View Article][PubMed]
    [Google Scholar]
  2. 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]
  3. 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]
  4. DeBruyn J. M., Nixon L. T., Fawaz M. N., Johnson A. M., Radosevich M. 2011; Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl Environ Microbiol 77:6295–6300 [View Article][PubMed]
    [Google Scholar]
  5. DeBruyn J. M., Fawaz M. N., Peacock A. D., Dunlap J. R., Nixon L. T., Cooper K. E., Radosevich M. 2013; Gemmatirosa kalamazoonesis gen. nov., sp. nov., a member of the rarely-cultivated bacterial phylum Gemmatimonadetes . J Gen Appl Microbiol 59:305–312 [View Article][PubMed]
    [Google Scholar]
  6. Hanada S., Sekiguchi Y. 2014; The phylum Gemmatimonadetes . In The Prokaryotes, 4th edn. vol. 11 pp 677–681Edited by Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., Thompson F. Berlin, Heidelberg: Springer;
    [Google Scholar]
  7. Kamagata Y. 2010; Phylum XXI. Gemmatimonadetes Zhang, Sekiguchi, Hanada, Hugenholtz, Kim, Kamagata and Nakamura 2003, 1161VP . In Bergey's Manual of Systematic Bacteriology, 2nd edn. vol. 4 pp 781–784Edited by Krieg N., Staley J., Brown D., Hedlund B., Paster B., Ward N., Ludwig W., Whitman W. New York: Springer; [View Article]
    [Google Scholar]
  8. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., other authors. 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 [View Article][PubMed]
    [Google Scholar]
  9. Kim M., Oh H. S., Park S. C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
    [Google Scholar]
  10. Ling L. L., Schneider T., Peoples A. J., Spoering A. L., Engels I., Conlon B. P., Mueller A., Schäberle T. F., Hughes D. E., other authors. 2015; A new antibiotic kills pathogens without detectable resistance. Nature 517:455–459 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. Munoz R., Yarza P., Ludwig W., Euzéby J., Amann R., Schleifer K. H., Glöckner F. O., Schleifer K.-H., Rosselló-Móra R., other authors. 2011; Release LTPs104 of the All-Species Living Tree. Syst Appl Microbiol 34:169–170 [View Article][PubMed]
    [Google Scholar]
  13. Nichols D., Cahoon N., Trakhtenberg E. M., Pham L., Mehta A., Belanger A., Kanigan T., Lewis K., Epstein S. S. 2010; Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl Environ Microbiol 76:2445–2450 [View Article][PubMed]
    [Google Scholar]
  14. Overmann J. 2013; Principles of enrichment, isolation, cultivation, and preservation of prokaryotes. In The Prokaryotes, 4th edn. vol. 1 pp 149–207Edited by Rosenberg E., DeLong E., Lory S., Stackebrandt E., Thompson F. Berlin, Heidelberg: Springer; [View Article]
    [Google Scholar]
  15. Powers E. M. 1995; Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758[PubMed]
    [Google Scholar]
  16. Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J., Glöckner F. O. 2013; The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:(D1)D590–D596 [View Article][PubMed]
    [Google Scholar]
  17. Rosselló-Móra R., Amann R. 2015; Past and future species definitions for Bacteria and Archaea . Syst Appl Microbiol 38:209–216 [View Article][PubMed]
    [Google Scholar]
  18. Salim S. M., Mandal J., Parija S. C. 2014; Isolation of Campylobacter from human stool samples. Indian J Med Microbiol 32:35–38 [View Article][PubMed]
    [Google Scholar]
  19. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  20. Schumann P. 2011; Peptidoglycan structure. Methods Microbiol 38:101–129 [View Article]
    [Google Scholar]
  21. Stackebrandt E., Goebel B. M. 1994; A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [View Article]
    [Google Scholar]
  22. 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]
  23. Tindall B. J. 1990; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  24. 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, 3rd edn. pp 330–393Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology; [View Article]
    [Google Scholar]
  25. Tittsler R. P., Sandholzer L. A. 1936; The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31:575–580[PubMed]
    [Google Scholar]
  26. 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]
  27. Zeng Y., Feng F., Medová H., Dean J., Koblížek M. 2014; Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes . Proc Natl Acad Sci U S A 111:7795–7800 [View Article][PubMed]
    [Google Scholar]
  28. Zeng Y., Selyanin V., Lukeš M., Dean J., Kaftan D., Feng F., Koblížek M. 2015; Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca . Int J Syst Evol Microbiol 65:2410–2419 [View Article][PubMed]
    [Google Scholar]
  29. Zhang H., Sekiguchi Y., Hanada S., Hugenholtz P., Kim H., Kamagata Y., Nakamura K. 2003; Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 53:1155–1163 [View Article][PubMed]
    [Google Scholar]
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