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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 68, Issue 5

sp. nov., isolated from glacier ice Free

Abstract

A Gram-stain-positive strain designated MDB1-42 was isolated from ice collected from Midui glacier in Tibet, PR China. Strain MDB1-42 was catalase-positive, oxidase-negative and grew optimally at 25–28 °C and pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that MDB1-42 represented a member of the genus . The highest level of 16S rRNA gene sequence similarity (99.86 %) was found with NBRC 15319. Multilocus sequence analysis revealed low similarity of 91.93 % between MDB1-42 and NBRC 15319. Average nucleotide identity and digital DNA–DNA hybridization values between MDB1-42 and the most closely related strain, DSM 20550, were 81.36 and 24.5 %, respectively. The genomic DNA G+C content was 69.0 mol%. The major cellular fatty acids of MDB1-42 were anteiso-C and anteiso-C. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, one unidentified glycolipid and one unidentified lipid. The predominant menaquinone was MK-9(H). On the basis of results obtained using a polyphasic approach, a novel species sp. nov. is proposed, with MDB1-42 (=CGMCC 1.9772=NBRC 113088) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ANI , Arthrobacter , digital DNA-DNA hybridization , glacier and MLSA
© 2018 State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University
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2018-05-01
2025-04-18
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References

  1. Conn HJ, Dimmick I. Soil bacteria similar in morphology to Mycobacterium and Corynebacterium . J Bacteriol 1947; 54:291–303[PubMed]
     [Google Scholar]
  2. Dastager SG, Liu Q, Qin L, Tang SK, Krishnamurthi S et al. Arthrobacter enclensis sp. nov., isolated from sediment sample. Arch Microbiol 2014; 196:775–782 [View Article][PubMed]
     [Google Scholar]
  3. Hoang VA, Kim YJ, Nguyen NL, Yang DC. Arthrobacter gyeryongensis sp. nov., isolated from soil of a Gynostemma pentaphyllum field. Int J Syst Evol Microbiol 2014; 64:420–425 [View Article][PubMed]
     [Google Scholar]
  4. Kageyama A, Morisaki K, Omura S, Takahashi Y. Arthrobacter oryzae sp. nov. and Arthrobacter humicola sp. nov. Int J Syst Evol Microbiol 2008; 58:53–56 [View Article][PubMed]
     [Google Scholar]
  5. Wauters G, Charlier J, Janssens M, Delmée M. Identification of Arthrobacter oxydans, Arthrobacter luteolus sp. nov., and Arthrobacter albus sp. nov., isolated from human clinical specimens. J Clin Microbiol 2000; 38:2412–2415[PubMed]
     [Google Scholar]
  6. Funke G, Hutson RA, Bernard KA, Pfyffer GE, Wauters G et al. Isolation of Arthrobacter spp. from clinical specimens and description of Arthrobacter cumminsii sp. nov. and Arthrobacter woluwensis sp. nov. J Clin Microbiol 1996; 34:2356–2363[PubMed]
     [Google Scholar]
  7. Huang Y, Zhao N, He L, Wang L, Liu Z et al. Arthrobacter scleromae sp. nov. isolated from human clinical specimens. J Clin Microbiol 2005; 43:1451–1455 [View Article][PubMed]
     [Google Scholar]
  8. Chang HW, Bae JW, Nam YD, Kwon HY, Park JR et al. Arthrobacter subterraneus sp. nov., isolated from deep subsurface water of the South Coast of Korea. J Microbiol Biotechnol 2007; 17:1875–1879
     [Google Scholar]
  9. Margesin R, Schumann P, Zhang DC, Redzic M, Zhou YG et al. Arthrobacter cryoconiti sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:397–402 [View Article][PubMed]
     [Google Scholar]
  10. Kim KK, Lee KC, Oh HM, Kim MJ, Eom MK et al. Arthrobacter defluvii sp. nov., 4-chlorophenol-degrading bacteria isolated from sewage. Int J Syst Evol Microbiol 2008; 58:1916–1921 [View Article][PubMed]
     [Google Scholar]
  11. Liu Q, Zhou YG, Xin YH. High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing. Syst Appl Microbiol 2015; 38:578–585 [View Article][PubMed]
     [Google Scholar]
  12. Liu Q, Xin YH, Zhou YG, Chen WX. Multilocus sequence analysis of homologous recombination and diversity in Arthrobacter sensu lato named species and glacier-inhabiting strains. Syst Appl Microbiol 2018; 41:23–29 [View Article][PubMed]
     [Google Scholar]
  13. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice. Int J Syst Evol Microbiol 2015; 65:2955–2959 [View Article][PubMed]
     [Google Scholar]
  14. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
     [Google Scholar]
  15. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  16. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Wiley; 1991 pp. 115
     [Google Scholar]
  17. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
     [Google Scholar]
  18. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  19. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  20. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
     [Google Scholar]
  21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  22. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  24. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  25. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  26. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa . Arch Microbiol 1984; 137:247–249 [View Article]
     [Google Scholar]
  27. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477[PubMed]
     [Google Scholar]
  28. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [Crossref]
     [Google Scholar]
  29. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, Technical Note 101. Newark, DE: MIDI; 1990
     [Google Scholar]
  30. Ince IA, Demirbag Z, Kati H. Arthrobacter pityocampae sp. nov., isolated from Thaumetopoea pityocampa (Lep., Thaumetopoeidae). Int J Syst Evol Microbiol 2014; 64:3384–3389 [View Article][PubMed]
     [Google Scholar]
  31. Chang HW, Bae JW, Nam YD, Kwon HY, Park JR et al. Arthrobacter subterraneus sp. nov., isolated from deep subsurface water of the South Coast of Korea. J Microbiol Biotechnol 2007; 17:1875–1879[PubMed]
     [Google Scholar]
  32. Heyrman J, Verbeeren J, Schumann P, Swings J, de Vos P. Six novel Arthrobacter species isolated from deteriorated mural paintings. Int J Syst Evol Microbiol 2005; 55:1457–1464 [View Article][PubMed]
     [Google Scholar]
  33. Mullakhanbhai MF, Bhat JV. Morphogenesis in Arthrobacter species. Proc Indian Natl Sci Acad B Biol Sci 1967; 65:231–237
     [Google Scholar]
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Arthrobacter ruber sp. nov., isolated from glacier ice
Int J Syst Evol Microbiol 68, 1616 (2018); https://doi.org/10.1099/ijsem.0.002719
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