sp. nov., isolated from Saharan desert sand Free

Abstract

A novel Gram-reaction-positive actinobacterial strain, designated CF5/3, was isolated from a sand sample obtained in the Sahara Desert, Chad. The greenish-black-pigmented isolate was aerobic and exhibited optimal growth from 25–40 °C at pH 6.0–10.0 with 0–1 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus . The DNA G+C content of the genome of the novel strain was 75.5 mol%. The peptidoglycan contained -diaminopimelic acid as diagnostic diamino acid. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and a minor fraction of phosphatidylglycerol. MK-9(H) was the dominant menaquinone, and galactose was detected as a diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids: iso-C and iso-C. Analysis of 16S rRNA gene sequences showed 95.6–98.8 % pairwise sequence identity with the members of the genus . Based on phenotypic and chemotaxonomic properties, as well as phylogenetic distinctiveness, the isolate represents a novel species, , with the type strain CF5/3 ( = DSM 45417 = CCUG 62814 = MTCC 11412).

Funding
This study was supported by the:
  • European Social Fund Operational Programme
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.051201-0
2013-09-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/9/3437.html?itemId=/content/journal/ijsem/10.1099/ijs.0.051201-0&mimeType=html&fmt=ahah

References

  1. Castresana J. ( 2000 ). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. . Mol Biol Evol 17, 540552. [View Article] [PubMed]
    [Google Scholar]
  2. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100, 221230. [View Article] [PubMed]
    [Google Scholar]
  3. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [View Article] [PubMed]
    [Google Scholar]
  4. Giongo A., Favet J., Lapanje A., Gano K. A., Kennedy S., Davis-Richardson A. G., Brown C., Beck A., Farmerie W. G. & other authors ( 2013 ). Microbial hitchhikers on intercontinental dust: high-throughput sequencing to catalogue microbes in small sand samples. . Aerobiologia 29, 7184. [View Article]
    [Google Scholar]
  5. Gordon R. E., Smith M. M. ( 1955 ). Proposed group of characters for the separation of Streptomyces and Nocardia . . J Bacteriol 69, 147150.[PubMed]
    [Google Scholar]
  6. Gregersen T. ( 1978 ). Rapid method for distinction of Gram-negative from positive bacteria. . Appl Microbiol Biotechnol 5, 123127. [View Article]
    [Google Scholar]
  7. Hess P. N., De Moraes Russo C. A. ( 2007 ). An empirical test of the midpoint rooting method. . Biol J Linn Soc Lond 92, 669674. [View Article]
    [Google Scholar]
  8. 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, 184192. [View Article] [PubMed]
    [Google Scholar]
  9. Ishiguro E. E., Wolfe R. S. ( 1970 ). Control of morphogenesis in Geodermatophilus: ultrastructural studies. . J Bacteriol 104, 566580.[PubMed]
    [Google Scholar]
  10. Ivanova N., Sikorski J., Jando M., Munk C., Lapidus A., Glavina Del Rio T., Copeland A., Tice H., Cheng J. F. & other authors ( 2010 ). Complete genome sequence of Geodermatophilus obscurus type strain (G-20T). . Stand Genomic Sci 2, 158167. [View Article] [PubMed]
    [Google Scholar]
  11. Jin L., Lee H. G., Kim H. S., Ahn C. Y., Oh H. M. ( 2013 ). Geodermatophilus soli sp. nov. and Geodermatophilus terrae sp. nov., two novel actinobacteria isolated from grass soil. . Int J Syst Bacteriol 63, 26252629. [CrossRef]
    [Google Scholar]
  12. Kroppenstedt R. M. ( 1982 ). Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger. . J Liq Chromatogr 5, 23592367. [View Article]
    [Google Scholar]
  13. Kroppenstedt R. M., Goodfellow M. ( 2006 ). The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillospora and Thermomonospora . . In The Prokaryotes, , 3rd edn., vol. 3, pp. 682724. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E. . New York:: Springer;. [View Article]
    [Google Scholar]
  14. Lechevalier M. P., Lechevalier H. A. ( 1970 ). Chemical composition as a criterion in the classification of aerobic actinomycetes. . Int J Syst Bacteriol 20, 435443. [View Article]
    [Google Scholar]
  15. Lee C., Grasso C., Sharlow M. F. ( 2002 ). Multiple sequence alignment using partial order graphs. . Bioinformatics 18, 452464. [View Article] [PubMed]
    [Google Scholar]
  16. Luedemann G. M. ( 1968 ). Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). . J Bacteriol 96, 18481858.[PubMed]
    [Google Scholar]
  17. 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]
  18. 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, 233241. [View Article]
    [Google Scholar]
  19. 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, 903909. [View Article] [PubMed]
    [Google Scholar]
  20. Montero-Calasanz M. C., Göker M., Broughton W. J., Cattaneo A., Favet J., Pötter G., Rohde M., Spröer C., Schumann P. & other authors ( 2013a ). Geodermatophilus tzadiensis sp. nov., a UV radiation-resistant bacterium isolated from sand of the Saharan desert. . Syst Appl Microbiol 36, 177182. [View Article] [PubMed]
    [Google Scholar]
  21. Montero-Calasanz M. C., Göker M., Pötter G., Rohde M., Spröer C., Schumann P., Gorbushina A. A., Klenk H.-P. ( 2013b ). Geodermatophilus arenarius sp. nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, Validation List no. 150. . Int J Syst Evol Microbiol 63, 797798. [View Article]
    [Google Scholar]
  22. Montero-Calasanz M. C., Göker M., Pötter G., Rohde M., Spröer C., Schumann P., Gorbushina A. A., Klenk H.-P. ( 2013c ). Geodermatophilus saharensis sp. nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, Validation List no. 151. . Int J Syst Evol Microbiol 63, 15771580. [View Article]
    [Google Scholar]
  23. Montero-Calasanz M. C., Göker M., Pötter G., Rohde M., Spröer C., Schumann P., Gorbushina A. A., Klenk H.-P. ( 2013d ). Geodermatophilus saharensis sp. nov., isolated from sand of the Saharan desert in Chad. . Arch Microbiol 195, 153159. [View Article] [PubMed]
    [Google Scholar]
  24. Montero-Calasanz M. C., Göker M., Pötter G., Rohde M., Spröer C., Schumann P., Klenk H.-P., Gorbushina A. A. ( 2013e ). Geodermatophilus telluris sp. nov., an actinomycete isolated from Saharan desert sand. . Int J Syst Evol Microbiol 63, 22542259. [View Article] [PubMed]
    [Google Scholar]
  25. Montero-Calasanz M. C., Göker M., Rohde M., Schumann P., Pötter G., Spröer C., Gorbushina A. A., Klenk H.-P. ( 2013f ). Geodermatophilus siccatus sp. nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, Validation List no. 151. . Int J Syst Evol Microbiol 63, 15771580. [View Article]
    [Google Scholar]
  26. Montero-Calasanz M. C., Göker M., Rohde M., Schumann P., Pötter G., Spröer C., Gorbushina A. A., Klenk H.-P. ( 2013g ). Geodermatophilus siccatus sp. nov., isolated from arid sand of the Saharan desert in Chad. . Antonie van Leeuwenhoek 103, 449456. [View Article] [PubMed]
    [Google Scholar]
  27. 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, 811817. [View Article] [PubMed]
    [Google Scholar]
  28. Normand P. ( 2006 ). Geodermatophilaceae fam. nov., a formal description. . Int J Syst Evol Microbiol 56, 22772278. [View Article] [PubMed]
    [Google Scholar]
  29. 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, 19. [View Article] [PubMed]
    [Google Scholar]
  30. Pattengale N. D., Alipour M., Bininda-Emonds O. R. P., Moret B. M. E., Stamatakis A. ( 2009 ). How many bootstrap replicates are necessary?. In Research in Computational Molecular Biology (Lecture Notes in Computer Science vol. 5541), 184200 Edited by Batzoglou S. . Berlin:: Springer;. . [View Article]
    [Google Scholar]
  31. Pelczar M. J. Jr (editor) ( 1957 ). Manual of Microbiological Methods. New York:: McGraw-Hill;.
    [Google Scholar]
  32. 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 Nocardiopsaceae fam. nov. . Int J Syst Bacteriol 46, 10881092. [View Article] [PubMed]
    [Google Scholar]
  33. Rice P., Longden I., Bleasby A. ( 2000 ). emboss: the European molecular biology open software suite. . Trends Genet 16, 276277. [View Article] [PubMed]
    [Google Scholar]
  34. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20, 16.
    [Google Scholar]
  35. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407477.[PubMed]
    [Google Scholar]
  36. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  37. Skerman V. B. D., McGowan V., Sneath P. H. A. ( 1980 ). Approved Lists of Bacterial Names. . Int J Syst Bacteriol 30, 225420. [View Article]
    [Google Scholar]
  38. Stamatakis A., Hoover P., Rougemont J. ( 2008 ). A rapid bootstrap algorithm for the RAxML Web servers. . Syst Biol 57, 758771. [View Article] [PubMed]
    [Google Scholar]
  39. 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]
  40. Swofford D. L. ( 2002 ). paup*: Phylogenetic analysis using parsimony (and other methods), version 4.0 b10. . Sunderland, MA:: Sinauer Associates;.
    [Google Scholar]
  41. 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, 471479. [View Article] [PubMed]
    [Google Scholar]
  42. Urzì C., La Cono V., Stackebrandt E. ( 2004 ). Design and application of two oligonucleotide probes for the identification of Geodermatophilaceae strains using fluorescence in situ hybridization (FISH). . Environ Microbiol 6, 678685. [View Article] [PubMed]
    [Google Scholar]
  43. 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. [View Article] [PubMed]
    [Google Scholar]
  44. 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 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  45. 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 medicinal plant. . Int J Syst Evol Microbiol 61, 190193. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.051201-0
Loading
/content/journal/ijsem/10.1099/ijs.0.051201-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed