1887

Abstract

A Gram-stain-negative, aerobic, non-motile and coccus-shaped bacterium, designated strain FeSDHB5-19, was isolated from a biofilm sample collected from a radioactive thermal spring (Budapest, Hungary), after exposure to 5 kGy gamma radiation. A polyphasic approach was used to study the taxonomic properties of strain FeSDHB5-19, which had highest 16S rRNA gene sequence similarity to Deinococcus antarcticus G3-6-20 (96.5 %). The 16S rRNA gene sequence similarity to type strains of other Deinococcus species were 93.0 % or lower. The DNA G+C content of the draft genome sequence, consisting of 3.9 Mb, was 63.9 mol%. Strain FeSHDB5-19 was found to grow at temperatures of 10–32 °C (optimum, 28 °C) and pH 5–10 (pH 6.5–7.5) and tolerated up to 1.5 % NaCl (w/v) with optimum growth at 0–0.5 % NaCl. The predominant fatty acids (>10 %) were C16 : 0 and C16 : 1ω7c. The cell-wall peptidoglycan type was A3β l-Orn–Gly1-2. The whole-cell sugars were glucose and low amounts of galactose. Strain FeSDHB5-19 possessed MK-8 as the predominant respiratory quinone, typical of the genus Deinococcus . The polar lipid profile contained unidentified phosphoglycolipids and unidentified glycolipids. The isolate was found to be highly resistant to gamma (D10<8 kGy) and UV (D10~800 J m) radiation. According to its genotypic, phenotypic and chemotaxonomic characteristics, strain FeSDHB5-19 represents a novel species in the genus Deinococcus , for which the name Deinococcus fonticola sp. nov. is proposed. The type strain is FeSDHB5-19 (=NCAIM B.02639=DSM 106917).

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2019-04-30
2020-01-22
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References

  1. Anderson AW, Nordan HC, Cain RF, Parrish G, Duggan D. Studies on a radio-resistant micrococcus. I. The isolation, morphology, cultural characteristics and resistance to gamma radiation. Food Technol 1956;10575–10577
    [Google Scholar]
  2. Brooks BW, Murray RGE. Nomenclature for "Micrococcus radiodurans" and other radiation-resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Syst Bacteriol 1981;31:353–360 [CrossRef]
    [Google Scholar]
  3. Sun Joo E, Jin Lee J, Kang MS, Lim S, Jeong SW et al. Deinococcus actinosclerus sp. nov., a novel bacterium isolated from soil of a rocky hillside. Int J Syst Evol Microbiol 2016;66:1003–1008 [CrossRef][PubMed]
    [Google Scholar]
  4. De Groot A, Chapon V, Servant P, Christen R, Saux MF et al. Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol 2005;55:2441–2446 [CrossRef][PubMed]
    [Google Scholar]
  5. Asker D, Awad TS, Beppu T, Ueda K. Deinococcus aquiradiocola sp. nov., isolated from a radioactive site in Japan. Int J Syst Evol Microbiol 2009;59:144–149 [CrossRef][PubMed]
    [Google Scholar]
  6. Lee JJ, Lee YH, Park SJ, Lim S, Jeong SW et al. Deinococcus sedimenti sp. nov. isolated from river sediment. J Microbiol 2016;54:802–808 [CrossRef][PubMed]
    [Google Scholar]
  7. Shashidhar R, Bandekar JR. Deinococcus piscis sp. nov., a radiation-resistant bacterium isolated from a marine fish. Int J Syst Evol Microbiol 2009;59:2714–2717 [CrossRef][PubMed]
    [Google Scholar]
  8. Kobatake M, Tanabe S, Hasegawa S. [New Micrococcus radioresistant red pigment, isolated from Lama glama feces, and its use as microbiological indicator of radiosterilization]. C R Seances Soc Biol Fil 1973; 1973;167:1506–1510[PubMed]
    [Google Scholar]
  9. Asker D, Awad TS, Beppu T, Ueda K. Deinococcus misasensis and Deinococcus roseus, novel members of the genus Deinococcus, isolated from a radioactive site in Japan. Syst Appl Microbiol 2008;31:43–49 [CrossRef][PubMed]
    [Google Scholar]
  10. Asker D, Awad TS, McLandsborough L, Beppu T, Ueda K. Deinococcus depolymerans sp. nov., a gamma- and UV-radiation-resistant bacterium, isolated from a naturally radioactive site. Int J Syst Evol Microbiol 2011;61:1448–1453 [CrossRef][PubMed]
    [Google Scholar]
  11. Makk J, Tóth EM, Anda D, Pál S, Schumann P et al. Deinococcus budaensis sp. nov., a mesophilic species isolated from a biofilm sample of a hydrothermal spring cave. Int J Syst Evol Microbiol 2016;66:5345–5351 [CrossRef][PubMed]
    [Google Scholar]
  12. Wang W, Mao J, Zhang Z, Tang Q, Xie Y et al. Deinococcus wulumuqiensis sp. nov., and Deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil. Int J Syst Evol Microbiol 2010;60:2006–2010 [CrossRef][PubMed]
    [Google Scholar]
  13. Battista JR, Rainey FA. Deinococcus. Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Inc., in association with Bergey’s Manual Trust; 2015
    [Google Scholar]
  14. Thornley MJ, Horne RW, Glauert AM. The fine structure of Micrococcus radiodurans. Arch Mikrobiol 1965;51:267–289 [CrossRef][PubMed]
    [Google Scholar]
  15. Suresh K, Reddy GS, Sengupta S, Shivaji S. Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India. Int J Syst Evol Microbiol 2004;54:457–461 [CrossRef][PubMed]
    [Google Scholar]
  16. Anda D, Büki G, Krett G, Makk J, Márialigeti K et al. Diversity and morphological structure of bacterial communities inhabiting the Diana-Hygieia Thermal Spring (Budapest, Hungary). Acta Microbiol Immunol Hung 2014;61:329–346 [CrossRef][PubMed]
    [Google Scholar]
  17. Enyedi NT, Anda D, Borsodi AK, Szabó A, Pál SE et al. Radioactive environment adapted bacterial communities constituting the biofilms of hydrothermal spring caves (Budapest, Hungary). J Environ Radioact 2019;203:8–17 [CrossRef][PubMed]
    [Google Scholar]
  18. Erőss A. Characterization of fluids and evaluation of their effects on karst development at the Rózsadomb and Gellért Hill, Buda Thermal Karst, Hungary. Ph.D. Dissertation 2010
    [Google Scholar]
  19. Dobosy P, Sávoly Z, Óvári M, Mádl-Szőnyi J, Záray G, Gy Z. Microchemical characterization of biogeochemical samples collected from the Buda Thermal Karst System, Hungary. Microchemical Journal 2016;124:116–120 [CrossRef]
    [Google Scholar]
  20. Erőss A, Mádl-Szőnyi J, Surbeck H, Horváth Ákos, Goldscheider N et al. Radionuclides as natural tracers for the characterization of fluids in regional discharge areas, Buda Thermal Karst, Hungary. J Hydrol 2012;426-427:124–124–137137 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef][PubMed]
    [Google Scholar]
  22. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 2003
    [Google Scholar]
  23. Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 1953;66:24–26[PubMed]
    [Google Scholar]
  24. Schumann P. Peptidoglycan structure. Methods Microbiol 2011;38:101–129
    [Google Scholar]
  25. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389–3402 [CrossRef][PubMed]
    [Google Scholar]
  26. 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 [CrossRef][PubMed]
    [Google Scholar]
  27. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  28. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  30. Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010; Available online at. http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  31. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  32. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013;29:1072–1075 [CrossRef][PubMed]
    [Google Scholar]
  33. Bushnell B. BBMap: a fast, accurate, splice-aware aligner. 2014; Available online at. https://sourceforge.net/projects/bbmap/
  34. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017;67:2053–2057 [CrossRef][PubMed]
    [Google Scholar]
  35. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  36. Peng F, Zhang L, Luo X, Dai J, An H et al. Deinococcus xinjiangensis sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2009;59:709–713 [CrossRef][PubMed]
    [Google Scholar]
  37. Kim DU, Lee H, Lee JH, Ahn JH, Lim S et al. Deinococcus metallilatus sp. nov. and Deinococcus carri sp. nov., isolated from a car air-conditioning system. Int J Syst Evol Microbiol 2015;65:3175–3182 [CrossRef][PubMed]
    [Google Scholar]
  38. Dong N, Hr L, Yuan M, Zhang XH, Yu Y et al. Deinococcus antarcticus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015;65:331–335
    [Google Scholar]
  39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
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