Rothia marina sp. nov., isolated from an intertidal sediment of the South China Sea

Abstract

A novel non-sporulating, non-motile, catalase-positive, oxidase-negative, facultatively anaerobic, Gram-positive coccus, designated strain JSM 078151T, was isolated from an intertidal sediment sample collected from Naozhou Island in the South China Sea, China. Growth was found to occur in the presence of 0–15 % (w/v) NaCl (optimum 0.5–3 % (w/v) NaCl), at pH 6.5–10.5 (optimum pH 7.0–8.0) and at 5–35 °C (optimum 25–30 °C). The peptidoglycan type was determined to be A3a, containing lysine, glutamic acid and alanine. The major cellular fatty acid identified was anteiso-C15:0 and the predominant menaquinones are MK-7 and MK-8. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unidentified phospholipid. The genomic DNA G+C content of strain JSM 078151T was determined to be 55.2 mol%. A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 078151T should be assigned to the genus Rothia, and was most closely related to Rothia nasimurium CCUG 35957T (98.3 % sequence similarity), followed by Rothia amarae J18T (97.5 %) and Rothia terrae L-143T (97.3 %). A combination of phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the suggestion that strain JSM 078151T represents a novel species of the genus Rothia, for which the name Rothia marina sp. nov. is proposed. The type strain is JSM 078151T (= DSM 21080T = KCTC 19432T).

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References

  1. Atlas RM (1993) In: Parks LC (ed) Handbook of microbiological media. CRC Press, Boca Raton, pp 666–672

    Google Scholar 

  2. Bergan T, Kocur M (1982) Stomatococcus mucilaginosus gen. nov., sp. nov., ep. rev, a member of the family Micrococcaceae. Int J Syst Bacteriol 32:374–377

    Article  CAS  Google Scholar 

  3. Chen YG, Cui XL, Pukall R, Li HM, Yang YL, Xu LH, Wen ML, Peng Q, Jiang CL (2007) Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 57:2327–2332

    PubMed  Article  CAS  Google Scholar 

  4. Chen YG, Zhang YQ, Huang K, Tang SK, Cao Y, Shi JX, Xiao HD, Cui XL, Li WJ (2009) Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment. Int J Syst Evol Microbiol 59:521–525

    PubMed  Article  CAS  Google Scholar 

  5. Chou YJ, Chou JH, Lin KY, Lin MC, Wei YH, Arun AB, Young CC, Chen WM (2008) Rothia terrae sp. nov. isolated from soil in Taiwan. Int J Syst Evol Microbiol 58:84–88

    PubMed  Article  CAS  Google Scholar 

  6. Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. John Wiley & Sons, Chichester, pp 265–309

    Google Scholar 

  7. Collins MD, Hutson RA, Baverud V, Falsen E (2000) Characterization of a Rothia-like organism from a mouse: description of Rothia nasimurium sp. nov. and reclassification of Stomatococcus mucilaginosus as Rothia mucilaginosa comb. nov. Int J Syst Evol Microbiol 50:1247–1251

    PubMed  Article  CAS  Google Scholar 

  8. Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. Cambridge University Press, London

    Google Scholar 

  9. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP, Xu LH, Jiang CL (2001) Streptomonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51:357–363

    PubMed  CAS  Google Scholar 

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

    PubMed  Article  Google Scholar 

  11. Embley TM, Wait R (1994) Structural lipids of eubacteria. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. John Wiley & Sons, Chichester, pp 121–161

    Google Scholar 

  12. Fan Y, Jin Z, Tong J, Li W, Pasciak M, Gamian A, Liu Z, Huang Y (2002) Rothia amarae sp. nov., from sludge of a foul water sewer. Int J Syst Evol Microbiol 52:2257–2260

    PubMed  Article  CAS  Google Scholar 

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

    PubMed  Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  15. Felsenstein J (2002) PHYLIP (phylogeny inference package) version 3.6a. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA

  16. Fitch WM (1972) Toward defining the course of evolution: minimum change for a species tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  17. Georg LK, Brown JM (1967) Rothia gen. nov., an aerobic genus of the family Actinomycetaceae. Int J Syst Bacteriol 17:79–88

    Article  Google Scholar 

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

    Article  Google Scholar 

  19. Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ, Kieser HM, Lydiate DJ, Smith CP, Ward JM (1985) Preparation of chromosomal, plasmid and phage DNA. In: Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ, Kieser HM, Lydiate DJ, Smith CP, Ward JM, Schrempf H (eds) Genetic manipulation of Streptomyces: a laboratory manual. F. Crowe and Sons, Norwich, pp 79–80

    Google Scholar 

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

    PubMed  Article  Google Scholar 

  21. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    PubMed  Article  CAS  Google Scholar 

  22. 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

    PubMed  Article  CAS  Google Scholar 

  23. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163

    PubMed  Article  CAS  Google Scholar 

  24. Lesher RJ, Gerencser MA, Gerencser VF (1974) Morphological, biochemical, and serological characterization of Rothia dentocariosa. Int J Syst Bacteriol 24:154–159

    Article  Google Scholar 

  25. Li Y, Kawamura Y, Fujiwara N, Naka T, Liu H, Huang X, Kobayashi K, Ezaki T (2004) Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov., Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir. Int J Syst Evol Microbiol 54:827–835

    PubMed  Article  CAS  Google Scholar 

  26. Liu ZX, Chen J, Tang SK, Zhang YQ, He JW, Chen QH, Li WJ, Chen YG (2011) Jeotgalicoccus nanhaiensis sp. nov., isolated from intertidal sediment of the South China Sea, and emended description of the genus Jeotgalicoccus. Int J Syst Evol Microbiol 61:2029–2034

    Google Scholar 

  27. 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 

  28. Møller V (1955) Simplified tests for some amino acid decarboxylases and for the arginine dihydrolase system. Acta Pathol Microbiol Scand 36:158–172

    PubMed  Article  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  30. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Newark

    Google Scholar 

  31. Schaal KP (1992) The genera Actinomyces, Arcanobacterium, and Rothia. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd edn. Springer, New York, pp 850–905

    Google Scholar 

  32. Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156

    Article  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  34. Schumann P, Kämpfer P, Busse HJ, Evtushenko LI, Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes (2009) Proposed minimal standards for describing new genera and species of the suborder Micrococcineae. Int J Syst Evol Microbiol 59:1823–1849

    Article  Google Scholar 

  35. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654

    Google Scholar 

  36. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  38. Tang ST, 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 59:2025–2032

    PubMed  Article  CAS  Google Scholar 

  39. 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

    PubMed  Article  CAS  Google Scholar 

  40. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by Grants from the National Basic Research Program of China (2010CB833800), National Natural Science Foundation of China (NSFC) (30970007), Construct Program of the Key Discipline in Hunan Province (JSU071312Z01), Aid Program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province (201208Z01), the Education Department of Hunan Province (12K108) and Jiugui Liquor Co. Ltd. (JGKJ 2012-JD03).

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Correspondence to Yi-Guang Chen.

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Liu, ZX., Yang, LL., Huang, Y. et al. Rothia marina sp. nov., isolated from an intertidal sediment of the South China Sea. Antonie van Leeuwenhoek 104, 331–337 (2013). https://doi.org/10.1007/s10482-013-9955-8

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Keywords

  • Rothia marina sp. nov.
  • South China Sea
  • Sediment