Skip to main content
SpringerLink
Log in

Geodermatophilus saharensis sp. nov., isolated from sand of the Saharan desert in Chad

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

A novel Gram-positive, aerobic, actinobacterial strain, CF5/5, was isolated from soil in the Sahara desert, Chad. It grew best at 20–35 °C and at pH 6.0–8.0 and with 0–4 % (w/v) NaCl, forming black-colored colonies. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The DNA G + C content was 75.9 mol%. The peptidoglycan contained meso-diaminopimelic acid; galactose and xylose were detected as diagnostic sugars. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol; MK-9(H4) was the dominant menaquinone. The major cellular fatty acids were: iso-C16:0 and iso-C15:0. The 16S rRNA gene showed 95.6–98.3 % sequence similarity with the other named members of the genus Geodermatophilus. Based on the polyphasic taxonomy data, the isolate is proposed to represent a novel species, Geodermatophilus saharensis with the type strain CF5/5T = DSM 45423 = CCUG 62813 = MTCC 11416.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Ahrens R, Moll G (1970) Ein neues knospendes Bakterium aus der Ostsee. Arch für Mikrobiol 70:243–265

    Article  CAS  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    Article  PubMed  CAS  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    PubMed  CAS  Google Scholar 

  • De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142

    Article  PubMed  Google Scholar 

  • DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072

    Article  PubMed  CAS  Google Scholar 

  • Giongo A, Favet J, Lapanje A, Gano KA, Kennedy S, Davis-Richardson AG, Brown C, Beck A, Farmerie WG, Cattaneo A, Crabb DB, Aung YY, Kort R, Brumsack HJ, Schnetger B, Broughton WJ, Gorbushina AA, Triplett EW (2012) Microbial hitchhikers on intercontinental dust: high—throughput sequencing to catalogue microbes in small sand samples. Aerobiologia. doi:10.1007/s10453-012-9264-0

    Google Scholar 

  • Gordon RE, Smith MM (1955) Proposed group of characters for the separation of Streptomyces and Nocardia. J Bacteriol 69:147–150

    PubMed  CAS  Google Scholar 

  • Gregersen T (1978) Rapid method for distinction of gram-negative from positive bacteria. Appl Microbiol Biotechnol 5:123–127

    Article  Google Scholar 

  • Hess PN, De Moraes Russo CA (2007) An empirical test of the midpoint rooting method. Biol J Linn Soc 92:669–674

    Article  Google Scholar 

  • Huss VAR, Fest H, Schleifer KH (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192

    Article  PubMed  CAS  Google Scholar 

  • Ishiguro EE, Wolfe RS (1970) Control of morphogenesis in Geodermatophilus: ultrastructural studies. J Bacteriol 104:566–580

    PubMed  CAS  Google Scholar 

  • Ivanova N, Sikorski J, Jando M, Munk C, Lapidus A, Del Glavina Rio T, Copeland A, Tice H, Cheng JF, Lucas S et al (2010) Complete genome sequence of Geodermatophilus obscurus type strain (G-20T). Stand Genomic Sci 2:158–167

    Article  PubMed  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger. J Liq Chromatogr 5:2359–2387

    Article  CAS  Google Scholar 

  • Kroppenstedt RM, Goodfellow M (2006) The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora. In: Dworkin M, Falkow S, Schleifer KH, Stackebrandt E (eds) The prokaryotes, vol 3, 3rd edn., Archaea and Bacteria: FirmicutesActinomycetes. Springer, New York, pp 682–724

    Chapter  Google Scholar 

  • Lechevalier MP, Lechevalier HA (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443

    Article  CAS  Google Scholar 

  • Lee C, Grasso C, Sharlow MF (2002) Multiple sequence alignment using partial order graphs. Bioinformatics 18:452–464

    Article  PubMed  CAS  Google Scholar 

  • Luedemann GM (1968) Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). J Bacteriol 96:1848–1858

    PubMed  CAS  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  • Mevs U, Stackebrandt E, Schumann P, Gallikowski CA, Hirsch P (2000) Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains). Int J Syst Evol Microbiol 50:337–346

    Article  PubMed  CAS  Google Scholar 

  • Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal K, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Montero-Calasanz MC, Göker M, Pötter G, Rohde M, Spröer C, Schumann P, Gorbushina AA, Klenk HP (2012a) Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad. Extremophiles 16:903–909

    Article  PubMed  CAS  Google Scholar 

  • Montero-Calasanz MC, Göker M, Rohde M, Schumann P, Pötter G, Spröer C, Gorbushina AA, Klenk HP (2012b) Geodermatophilus siccatus sp. nov., isolated from arid sand of the Saharan desert in Chad. Antonie van Leeuwenhoek. doi: 10.1007/s10482-012-9824-x)

  • Montero-Calasanz MC, Göker M, Pötter G, Rohde M, Spröer C, Schumann P, Klenk HP, Gorbushina AA (2012c) Geodermatophilus telluris sp. nov., a novel actinomycete isolated from Saharan desert sand in Chad. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.046888-0

  • Nie GX, Ming H, Li S, Zhou EM, Cheng J, Yu TT, Zhang J, Feng HG, Tang SK, Li WJ (2012) Geodermatophilus nigrescens sp. nov., isolated from a dry-hot valley. Antonie Van Leeuwenhoek 101:811–817

    Article  PubMed  CAS  Google Scholar 

  • Normand P (2006) Geodermatophilaceae fam. nov., a formal description. Int J Syst Evol Microbiol 56:2277–2278

    Article  PubMed  CAS  Google Scholar 

  • Normand P, Orso S, Cournoyer B, Jeannin P, Chapelon C, Dawson J, Evtushenko L, Misra AK (1996) Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int J Syst Bacteriol 46:1–9

    Article  PubMed  CAS  Google Scholar 

  • Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A (2009) How many bootstrap replicates are necessary? Lect Notes Comput Sci 5541:184–200

    Article  CAS  Google Scholar 

  • Pelczar MJ Jr (ed) (1957) Manual of Microbiological Methods. McGraw-Hill Book Co., New York, NY

    Google Scholar 

  • Rainey FA, Ward-Rainey N, Kroppenstedt RM, 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 46:28–96

    Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276–277

    Article  PubMed  CAS  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:16

    Google Scholar 

  • Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477

    PubMed  CAS  Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

    Google Scholar 

  • Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771

    Article  PubMed  Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    PubMed  CAS  Google Scholar 

  • Swofford DL (2002) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland

  • Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology. ASM Press, Washington, pp 330–393

    Google Scholar 

  • Urzì C, Brusetti L, Salamone P, Sorlini C, Stackebrandt E, Daffonchio D (2001) Biodiversity of Geodermatophilaceae isolated from stones and monuments in the Mediterranean basin. Environ Microbiol 3:471–479

    Article  PubMed  Google Scholar 

  • Vaas LAI, Sikorski J, Michael V, Göker M, Klenk HP (2012) Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE 7(4):e34846

    Article  PubMed  CAS  Google Scholar 

  • Validation List no. 147 (2012) List of new names and new combinations previously effectively, but not validly published. Int J Syst Bacteriol 62:2045–2047

    Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Zhang YQ, Chen J, Liu HY, Zhang YQ, Li WJ, Yu LY (2011) Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medical plant. Int J Syst Evol Microbiol 61:190–193

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We would like to gratefully acknowledge the help of Agathe Stricker of the International Committee of the Red Cross in Geneva, Switzerland, for organizing the collection of the sand samples from which strain 5/5T was isolated. Jocelyne Favet, Arlette Cattaneo, and William J. Broughton of the Laboratoire de Biologie Moléculaire de Plantes Supérieures (University of Geneva, Switzerland) are acknowledged for their contribution to the isolation of the strain, Bettina Sträubler and Birgit Grüm (DSMZ, Braunschweig), for their help in DNA–DNA hybridization analysis and Brian J. Tindall (DSMZ, Braunschweig) for his guidance in chemotaxonomical analyses. M.C. Montero-Calasanz is the recipient of a postdoctoral contract from European Social Fund Operational Programme (2007–2013) for Andalusia.

Author information

Authors and Affiliations

  1. Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany

    M. C. Montero-Calasanz, M. Göker, G. Pötter, C. Spröer, P. Schumann & H.-P. Klenk

  2. IFAPA-Instituto de Investigación y Formación Agraria y Pesquera, Centro Las Torres-Tomejil, Ctra. Sevilla-Cazalla de la Sierra, Km 12.2, 41200, Alcalá del Río, Sevilla, Spain

    M. C. Montero-Calasanz

  3. HZI—Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany

    M. Rohde

  4. BAM, Federal Institute for Material Research and Testing, 12205, Berlin, Germany

    A. A. Gorbushina

  5. Department of Biology, Chemistry and Pharmacy and Department of Earth Sciences, Free University of Berlin, 12249, Berlin, Germany

    A. A. Gorbushina

Authors
  1. M. C. Montero-Calasanz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Göker
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. G. Pötter
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. M. Rohde
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. C. Spröer
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. P. Schumann
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. A. A. Gorbushina
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. H.-P. Klenk
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to A. A. Gorbushina or H.-P. Klenk.

Additional information

Communicated by Erko Stackebrandt.

The INSDC accession number for the 16S rRNA gene sequence of strain CF5/5T is HE654551.

Electronic supplementary material

Below is the link to the electronic supplementary material.

203_2012_860_MOESM1_ESM.pdf

Fig. S1. The parameter “Maximum Height” estimated from the measured respiration curves as measured with the OmniLog phenotyping device and visualized as heat map using the opm package. Plates and substrates are rearranged according to their overall similarity (as depicted using the row and column dendrograms). First picture, heat map inferred from the discretized values; second picture, heat map inferred from the original “Maximum Height” measurements, standardized per row; third picture, heat map inferred from the original “Maximum Height” measurements, not standardized. (PDF 97 kb)

203_2012_860_MOESM2_ESM.tif

Fig. S2. Polar lipids profile of strain CF5/5T after separation by two-dimensional TLC. The late was sprayed with molybdatophosphoric acid for the detection of total polar lipids. DPG, diphosphatidylglycerol; PE, phosphatidylethanolamine; PC, phosphatidylcholine; PI, phosphatidylinositol; PG, phosphatidylglycerol; GL, glycolipid. (TIFF 177 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Montero-Calasanz, M.C., Göker, M., Pötter, G. et al. Geodermatophilus saharensis sp. nov., isolated from sand of the Saharan desert in Chad. Arch Microbiol 195, 153–159 (2013). https://doi.org/10.1007/s00203-012-0860-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-012-0860-8

Keywords

Search

Navigation