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Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad

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Abstract

A novel Gram-positive, aerobic, actinobacterial strain, CF5/4T, was isolated in 2007 during an environmental screening of arid desert soil in Ouré Cassoni, Chad. The isolate grew best in a temperature range of 28–40 °C and at pH 6.0–8.5, with 0–1 % (w/v) NaCl, forming brown-coloured and nearly circular colonies on GYM agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The DNA G + C content of the novel strain was 75.9 mol %. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diaminoacid. The main phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, diphosphatidylglycerol and a small amount of phosphatidylglycerol; MK-9(H4) was identified as the dominant menaquinone and galactose as diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids: iso-C15:0 and iso-C16:0. The 16S rRNA gene showed 96.2–98.3 % sequence identity with the three members of the genus Geodermatophilus: G. obscurus (96.2 %), G. ruber (96.5 %), and G. nigrescens (98.3 %). Based on the chemotaxonomic results, 16S rRNA gene sequence analysis and DNA–DNA hybridization with the type strain of G. nigrescens, the isolate is proposed to represent a novel species, Geodermatophilus arenarius (type strain CF5/4T = DSM 45418T = MTCC 11413T = CCUG 62763T).

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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 CF5/4T 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, 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, Alcalá del Río, C.P. 41200, 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, Free University of Berlin, 12249, Berlin, Germany

    A. A. Gorbushina

  6. Department of Earth Sciences, Free University of Berlin, 12249, Berlin, Germany

    A. A. Gorbushina

Authors
  1. M. C. Montero-Calasanz
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  2. M. Göker
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  3. G. Pötter
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  4. M. Rohde
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  5. C. Spröer
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  6. P. Schumann
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  7. A. A. Gorbushina
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  8. H.-P. Klenk
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Corresponding authors

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

Additional information

Communicated by A. Oren.

The INSDC accession number for the 16S rRNA gene sequence of strain CF5/4T is HE654547.

Electronic supplementary material

Below is the link to the electronic supplementary material.

792_2012_486_MOESM1_ESM.pdf

Fig. S1. The parameter “Maximum Height” estimated from the respiration curves as measured with the OmniLog phenotyping device and visualized as heatmap using the opm package. Plates and substrates are rearranged according to their overall similarity (as depicted using the row and column dendrograms). First picture, heatmap inferred from the discretized values; second picture, heatmap inferred from the original “Maximum Height” measurements, standardized per row; third picture, heatmap inferred from the original “Maximum Height” measurements, not standardized. (PDF 36 kb)

792_2012_486_MOESM2_ESM.tif

Fig. S2. Polar lipids profile of Geodermatophilus arenarius sp. nov. CF5/4T after separation by two-dimensional TLC. Plate was sprayed with molybdatophosphoric acid for detection of total polar lipids. DPG, diphosphatidylglycerol; PE, phosphatidylethanolamine; PC, phosphatidylcholine; PI, phosphatidylinositol; PG, phosphatidylglycerol; GL, glycolipid. (TIFF 594 kb)

792_2012_486_MOESM3_ESM.docx

Table S1. Fatty acids profiles (%) of strain CF5/4T and the type strains of other Geodermatophilus species. Strains: 1, G. arenarius sp. nov. CF5/4T (DSM 45418T); 2, G. obscurus G-20T (DSM 43160T); 3, G. ruber CPCC 21356T (DSM 45317T); 4, G. nigrescens YIM 75980T (DSM 45408T). (DOCX 20 kb)

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Montero-Calasanz, M.C., Göker, M., Pötter, G. et al. Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad. Extremophiles 16, 903–909 (2012). https://doi.org/10.1007/s00792-012-0486-4

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