1887

Abstract

A novel Gram-positive, multiloculated thalli-forming, aerobic, actinobacterial strain, CF9/1/1, was isolated in 2007 during environmental screening for xerophilic fungi in arid desert soil from the Sahara desert, Chad. The isolate grew best at a temperature range of 20–35 °C and at pH 6.0–8.5 and with 0–4 % (w/v) NaCl, forming black-coloured and irregular colonies on GYM agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus . The DNA G+C content of the novel strain was 75.4 mol%. The peptidoglycan contained -diaminopimelic acid as a diagnostic diamino acid. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, a not yet structurally identified aminophospholipid and a small amount of phosphatidylglycerol; MK-9(H) was identified as the dominant menaquinone and galactose was a diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids: iso-C and iso-C. The 16S rRNA gene sequence of the isolate showed 94.6–97.0 % sequence similarities with those of five members of the genus: DSM 45317 (94.6 %), DSM 43160 (94.8 %), DSM 45419 (96.2 %), DSM 45408 (96.7 %) and DSM 45418 (97.0 %). Based on the evidence from this polyphasic taxonomic study, a novel species, sp. nov., is proposed; the type strain is CF9/1/1 ( = DSM 45421 = CCUG 62764).

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2013-06-01
2019-10-22
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References

  1. Altschul S. F. , Gish W. , Miller W. , Myers E. W. , Lipman D. J. . ( 1990; ). Basic local alignment search tool. . J Mol Biol 215:, 403–410.[PubMed] [CrossRef]
    [Google Scholar]
  2. Castresana J. . ( 2000; ). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. . Mol Biol Evol 17:, 540–552. [CrossRef] [PubMed]
    [Google Scholar]
  3. Collins M. D. , Pirouz T. , Goodfellow M. , Minnikin D. E. . ( 1977; ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100:, 221–230.[PubMed] [CrossRef]
    [Google Scholar]
  4. De Ley J. , Cattoir H. , Reynaerts A. . ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142. [CrossRef] [PubMed]
    [Google Scholar]
  5. DeSantis T. Z. , Hugenholtz P. , Larsen N. , Rojas M. , Brodie E. L. , Keller K. , Huber T. , Dalevi D. , Hu P. , Andersen G. L. . ( 2006; ). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. . Appl Environ Microbiol 72:, 5069–5072. [CrossRef] [PubMed]
    [Google Scholar]
  6. Euzéby J. . ( 2012; ). Geodermatophilus nigrescens sp. nov. In List of new names and new combinations previously effectively, but not validly published, list no. 147. . Int J Syst Evol Microbiol 62:, 2045–2047. [CrossRef]
    [Google Scholar]
  7. Euzéby J. . ( 2013a; ). Geodermatophilus arenarius sp. nov. In List of new names and new combinations previously effectively, but not validly published, list no. 150. . Int J Syst Evol Microbiol 63:, 797–798. [CrossRef]
    [Google Scholar]
  8. Euzéby J. . ( 2013b; ). Geodermatophilus siccatus sp. nov. In List of new names and new combinations previously effectively, but not validly published, list no. 151. . Int J Syst Evol Microbiol 62:, 1577–1580. [CrossRef]
    [Google Scholar]
  9. Giongo A. , Favet J. , Lapanje A. , Gano K. A. , Kennedy S. , Davis-Richardson A. G. , Brown C. , Beck A. , Farmerie W. G. et al. ( 2013; ). Microbial hitchhikers on intercontinental dust: high-throughput sequencing to catalogue microbes in small sand samples. . Aerobiologia. 29:, 71–84. [CrossRef]
    [Google Scholar]
  10. Gordon R. E. , Smith M. M. . ( 1955; ). Proposed group of characters for the separation of Streptomyces and Nocardia . . J Bacteriol 69:, 147–150.[PubMed]
    [Google Scholar]
  11. Gregersen T. . ( 1978; ). Rapid method for distinction of Gram-negative from positive bacteria. . Appl Microbiol Biotechnol 5:, 123–127. [CrossRef]
    [Google Scholar]
  12. Hess P. N. , De Moraes Russo C. A. . ( 2007; ). An empirical test of the midpoint rooting method. . Biol J Linn Soc Lond 92:, 669–674. [CrossRef]
    [Google Scholar]
  13. 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. [CrossRef] [PubMed]
    [Google Scholar]
  14. Ivanova N. , Sikorski J. , Jando M. , Munk C. , Lapidus A. , Glavina Del Rio T. , Copeland A. , Tice H. , Cheng J. F. et al. ( 2010; ). Complete genome sequence of Geodermatophilus obscurus type strain (G-20). . Stand Genomic Sci 2:, 158–167. [CrossRef] [PubMed]
    [Google Scholar]
  15. Kroppenstedt R. M. . ( 1982; ). Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger. . J Liq Chromatogr 5:, 2359–2367. [CrossRef]
    [Google Scholar]
  16. Kroppenstedt R. M. , Goodfellow M. . ( 2006; ). The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora . . In The Prokaryotes, Archaea and Bacteria: Firmicutes, Actinomycetes, , 3rd edn., vol. 3, pp. 682–724. Edited by Dworkin M. , Falkow S. , Schleifer K. H. , Stackebrandt E. . . New York:: Springer;. [CrossRef]
    [Google Scholar]
  17. Lechevalier M. P. , Lechevalier H. A. . ( 1970; ). Chemical composition as a criterion in the classification of aerobic actinomycetes. . Int J Syst Bacteriol 20:, 435–443. [CrossRef]
    [Google Scholar]
  18. Lee C. , Grasso C. , Sharlow M. F. . ( 2002; ). Multiple sequence alignment using partial order graphs. . Bioinformatics 18:, 452–464. [CrossRef] [PubMed]
    [Google Scholar]
  19. Luedemann G. M. . ( 1968; ). Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). . J Bacteriol 96:, 1848–1858.[PubMed]
    [Google Scholar]
  20. 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. [CrossRef]
    [Google Scholar]
  21. Minnikin D. E. , O'Donnell A. G. , Goodfellow M. , Alderson G. , Athalye M. , Schaal K. , Parlett J. H. . ( 1984; ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2:, 233–241. [CrossRef]
    [Google Scholar]
  22. Montero-Calasanz M. C. , Göker M. , Pötter G. , Rohde M. , Spröer C. , Schumann P. , Gorbushina A. A. , Klenk H. P. . ( 2012; ). Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad. . Extremophiles 16:, 903–909. [CrossRef] [PubMed]
    [Google Scholar]
  23. Montero-Calasanz M. C. , Göker M. , Rohde M. , Schumann P. , Pötter G. , Spröer C. , Gorbushina A. A. , Klenk H. P. . ( 2013; ). Geodermatophilus siccatus sp. nov., isolated from arid sand of the Saharan desert in Chad. . Antonie van Leeuwenhoek 103:, 449–456. [CrossRef] [PubMed]
    [Google Scholar]
  24. Nie G. X. , Ming H. , Li S. , Zhou E. M. , Cheng J. , Yu T. T. , Zhang J. , Feng H. G. , Tang S. K. , Li W. J. . ( 2012; ). Geodermatophilus nigrescens sp. nov., isolated from a dry-hot valley. . Antonie van Leeuwenhoek 101:, 811–817. [CrossRef] [PubMed]
    [Google Scholar]
  25. Normand P. . ( 2006; ). Geodermatophilaceae fam. nov., a formal description. . Int J Syst Evol Microbiol 56:, 2277–2278. [CrossRef] [PubMed]
    [Google Scholar]
  26. Normand P. , Orso S. , Cournoyer B. , Jeannin P. , Chapelon C. , Dawson J. , Evtushenko L. , Misra A. K. . ( 1996; ). Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae . . Int J Syst Bacteriol 46:, 1–9. [CrossRef] [PubMed]
    [Google Scholar]
  27. Pattengale N. D. , Alipour M. , Bininda-Emonds O. R. P. , Moret B. M. E. , Stamatakis A. . ( 2009; ). How many bootstrap replicates are necessary?. Lect Notes Comput Sci 5541:, 184–200. [CrossRef]
    [Google Scholar]
  28. Pelczar M. J. Jr . (editor) ( 1957; ). Manual of Microbiological Methods. New York, NY:: McGraw-Hill Book Co;.
    [Google Scholar]
  29. Rainey F. A. , Ward-Rainey N. , Kroppenstedt R. M. , Stackebrandt E. . ( 1996; ). The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsiaceae fam. nov.. Int J Syst Bacteriol 46:, 1088–1092. [CrossRef]
    [Google Scholar]
  30. Rice P. , Longden I. , Bleasby A. . ( 2000; ). EMBOSS: the European Molecular Biology Open Software Suite. . Trends Genet 16:, 276–277. [CrossRef] [PubMed]
    [Google Scholar]
  31. Sasser M. . ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20:, 16.
    [Google Scholar]
  32. Schleifer K. H. , Kandler O. . ( 1972; ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36:, 407–477.[PubMed]
    [Google Scholar]
  33. Shirling E. B. , Gottlieb D. . ( 1966; ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16:, 313–340. [CrossRef]
    [Google Scholar]
  34. Stamatakis A. , Hoover P. , Rougemont J. . ( 2008; ). A rapid bootstrap algorithm for the RAxML Web servers. . Syst Biol 57:, 758–771. [CrossRef] [PubMed]
    [Google Scholar]
  35. Staneck J. L. , Roberts G. D. . ( 1974; ). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol 28:, 226–231.[PubMed]
    [Google Scholar]
  36. Swofford, D. L. (2002). paup*: Phylogenetic analysis using parsimony (and other methods), version 4. Sunderland, MA: Sinauer Associates.
  37. Tindall B. J. , Sikorski J. , Smibert R. A. , Krieg N. R. . ( 2007; ). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology, pp. 330–393. Edited by Beveridge T. J. , Breznak J. A. , Marzluf G. A. , Schmidt T. M. , Snyder L. R. . . Washington:: American Society for Microbiology;.
    [Google Scholar]
  38. Urzì C. , Brusetti L. , Salamone P. , Sorlini C. , Stackebrandt E. , Daffonchio D. . ( 2001; ). Biodiversity of Geodermatophilaceae isolated from altered stones and monuments in the Mediterranean basin. . Environ Microbiol 3:, 471–479. [CrossRef] [PubMed]
    [Google Scholar]
  39. Vaas L. A. I. , Sikorski J. , Michael V. , Göker M. , Klenk H. P. . ( 2012; ). Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. . PLoS ONE 7:, e34846. [CrossRef] [PubMed]
    [Google Scholar]
  40. 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; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  41. Zhang Y.-Q. , Chen J. , Liu H.-Y. , Zhang Y.-Q. , Li W.-J. , Yu L.-Y. . ( 2011; ). Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medical plant. . Int J Syst Evol Microbiol 61:, 190–193. [CrossRef] [PubMed]
    [Google Scholar]
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