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Ornithinimicrobium cavernae sp. nov., an actinobacterium isolated from a karst cave

Abstract

A novel actinobacterium, designated strain CFH 30183T, was isolated from a soil sample collected from a karst cave in Luoyang, Henan Province. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of strain CFH 30183T were observed to be Gram-stain positive, motile, asporogenous and coccoid to rod shaped. The strain was found to be aerobic and oxidase positive. On the basis of 16S rRNA gene sequence analysis, strain CFH 30183T was found to be closely related to Ornithinimicrobium murale 01-Gi-040T (97.8% sequence identity). The ANIb/ANIm values between strain CFH 30183T and O. murale DSM 22056T were found to be 80.3%/85.9%. Strain CFH 30183T was found to grow optimally at 28–32 °C, at pH 8.0–9.0 and in the presence of up to 7% NaCl (w/v). Whole cell hydrolysates of strain CFH 30183T contained l-ornithine as the diagnostic diamino acid, and arabinose, glucose, mannose and rhamnose as whole cell sugars. The respiratory quinone was determined to be MK-8(H4), while the major fatty acids were found to consist of iso-C15:0 and iso-C16:0. The polar lipids profile was found to include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid, an unidentified phosphoglycolipid and four unidentified lipids. The DNA G + C content of strain CFH 30183T was calculated to be 70.9%. Based on the phenotypic, genotypic and phylogenetic data obtained, strain CFH 30183T is considered to represent a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium cavernae sp. nov. is proposed. The type strain is CFH 30183T (= KCTC 49018T = CGMCC 1.16393T).

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References

  1. Atlas RM (1993) Handbook of microbiological media. CRC Press, Boca Raton

    Google Scholar 

  2. Buck JD (1982) Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ (2011) Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol 60(2):117

    Article  CAS  PubMed  Google Scholar 

  4. Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diaminobutyric acid. J Appl Bacteriol 48:459–470

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  6. Edgar RC (2004) MUSCLE multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Fang XM, Yan D, Bai JL, Su J, Liu HY, Ma BP, Zhang YQ, Yu LY (2017) Ornithinimicrobium flavum sp. nov., isolated from the leaf of Paris polyphylla. Int J Syst Evol Microbiol 67:4541–4545

    Article  CAS  PubMed  Google Scholar 

  8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  10. Finn RD, Coggil P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279–D285

    Article  CAS  PubMed  Google Scholar 

  11. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416

    Article  Google Scholar 

  12. Gordon RE, Barnett DA, Handerhan JE, Pang CHN (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63

    Article  Google Scholar 

  13. Groth I, Schumann P, Weiss N, Schuetze B, Augsten K, Stackebrandt E (2001) Ornithinimicrobium humiphilum gen. nov., sp. nov., a novel soil actinomycete with l-ornithine in the peptidoglycan. Int J Syst Evol Microbiol 51:81–87

    Article  CAS  PubMed  Google Scholar 

  14. Harrison P, Strulo B (2000) SPADES—a process algebra for discrete event simulation. J Log Comput 10:3–42

    Article  Google Scholar 

  15. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119

    Article  CAS  Google Scholar 

  16. Kampfer P, Glaeser SP, Schafer J, Lodders N, Martin K, Schumann P (2013) Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds. Int J Syst Evol Microbiol 63:119–123

    Article  CAS  PubMed  Google Scholar 

  17. Kanehisa FM, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361

    Article  CAS  Google Scholar 

  18. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  Google Scholar 

  19. Kimura M (1985) The neutral theory of molecular evolution. Evol Genes Prot 241:98–100

    Google Scholar 

  20. Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367

    Article  CAS  Google Scholar 

  21. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp.nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  PubMed  Google Scholar 

  23. Liu XY, Wang BJ, Jiang CY, Liu SJ (2008) Ornithinimicrobium pekingense sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 58:116–119

    Article  CAS  PubMed  Google Scholar 

  24. Liu LZ, Liu Y, Chen Z, Liu HC, Zhou YG, Liu ZP (2013) Ornithinimicrobium tianjinense sp. nov., isolated from a recirculating aquaculture system. Int J Syst Evol Microbiol 63:4489–4494

    Article  CAS  PubMed  Google Scholar 

  25. Locci R (1989) Streptomyces and related genera. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2451–2508

    Google Scholar 

  26. Mayilraj S, Saha P, Suresh K, Saini HS (2006) Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas. Int J Syst Evol Microbiol 56:1657–1661

    Article  CAS  Google Scholar 

  27. Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM, Feng HG, Tang SK, Li WJ (2012) Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 102:297–305

    Article  CAS  PubMed  Google Scholar 

  28. Ming H, Yin YR, Li S, Nie GX, Yu TT, Zhou EM, Liu L, Dong L, Li WJ (2014) Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area. Int J Syst Evol Microbiol 64:650–656

    Article  CAS  PubMed  Google Scholar 

  29. Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95

    Article  CAS  Google Scholar 

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

    CAS  Google Scholar 

  31. Ramaprasad EVV, Sasikala C, Ramana CV (2015) Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva. Int J Syst Evol Microbiol 65:4627–4631

    Article  CAS  PubMed  Google Scholar 

  32. Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Antonie Van Leeuwenhoek 110:455–456

    Article  PubMed  Google Scholar 

  33. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  Google Scholar 

  34. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. Microbial ID, Inc., Newark

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

    Article  Google Scholar 

  36. Stackebrandt E, Rainey FA, Wardrainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491

    Article  Google Scholar 

  37. Stamatakis A (2006) Raxml-vi-hpc: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688

    Article  CAS  Google Scholar 

  38. Tamaoka J, Katayama-Fujimura Y, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36

    Article  CAS  Google Scholar 

  39. Tang SK, Wang Y, Chen Y, Lou K, Cao LL, Xu LH, Li WJ (2009) Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 59:2025–2031

    Article  CAS  PubMed  Google Scholar 

  40. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Waksman SA (1967) The actinomycetes. A summary of current knowledge. Ronald Press, New York

    Google Scholar 

  43. Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2452–2492

    Google Scholar 

  44. Wu M, Scott AJ (2012) Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28:1033

    Article  CAS  PubMed  Google Scholar 

  45. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    Article  CAS  PubMed  Google Scholar 

  46. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by National Key Research and Development Program of China (2017YFD0200503), National Natural Science Foundation of China (Nos. 31600015, 31500004), Innovation Scientists and Technicians Troop Construction Projects of Henan Province (CXTD2016043), National Fundamental Fund Project Subsidy Funds of Personnel Training of China (No. J1310025) and Henan Province University youth researcher support project (2017GGJS106). W.-J. Li was also supported by Guangdong Province Higher Vocational Colleges and Schools Pearl River Scholar Funded Scheme (2014). The authors are grateful to Rüdiger Pukall (DSMZ, Germany) for kindly providing the reference type strain.

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LYZ, HM, WJL and GXN designed research and project outline. LYZ, BZF, HM and XLM performed isolation, deposition and identification. JYJ, NS and XTZ performed genome analysis. LYZ, BZF and WJL drafted the manuscript. All authors read and approved the final manuscript.

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Correspondence to Wen-Jun Li or Guo-Xing Nie.

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Zhang, LY., Ming, H., Meng, XL. et al. Ornithinimicrobium cavernae sp. nov., an actinobacterium isolated from a karst cave. Antonie van Leeuwenhoek 112, 179–186 (2019). https://doi.org/10.1007/s10482-018-1141-6

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Keywords

  • Ornithinimicrobium cavernae sp. nov.
  • Karst cave
  • Polyphasic taxonomy