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Research article

References

  1. Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS, Chen WM. 2004. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst. Appl. Microbiol. 27: 43-49.
    Pubmed CrossRef
  2. Kim BY, Weon HY, Yoo SH, Chen WM, Kwon SW, Go SJ, Stackebrandt E. 2006. Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea. Int. J. Syst. Evol. Microbiol. 56: 1761-1764.
    Pubmed CrossRef
  3. Joung Y, Lee BI, Kang H, Kim H, Joh K. 2014. Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake. Int. J. Syst. Evol. Microbiol. 64: 1123-1126.
    Pubmed CrossRef
  4. Li Y , Zh u H, L ai Q , Lei X, C hen Z , Zh ang H, et al. 2014. Chitinimonas prasina sp. nov., isolated from lake water. Int. J. Syst. Evol. Microbiol. 64: 3005-3009.
    Pubmed CrossRef
  5. Li Y , Lei X, Zhu H, Zh ang H, Guan C, C h en Z , et al. 2016. Chitinase producing bacteria with direct algicidal activity on marine diatoms. Sci. Rep. 6: 21984.
    Pubmed PMC CrossRef
  6. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60: 249-266.
    Pubmed CrossRef
  7. Padakandla SR, Chae J-C. 2017. Reclassification of Aeromonas sharmana to a new genus as Pseudaeromonas sharmana gen. nov., comb. nov and description of Pseudaeromonas pectinilytica sp. nov. isolated from a fresh water stream. Int. J. Syst. Evol. Microbiol. 67: 1018-1023.
    Pubmed CrossRef
  8. Buck JD. 1982. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol. 44: 992-993.
    Pubmed PMC
  9. Cappuccino JG, Sherman N. 1998. Microbiology – A Laboratory Manual, 4th Ed. Benjamin/Cummings Science Publishing, San Francisco, CA. USA.
  10. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, et al. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2: 233-241.
    CrossRef
  11. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. 2007. Phenotypic characterization and the principles of comparative systematics, pp. 330-393. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds.), Methods for General and Molecular Microbiology, 3rd Ed. American Society of Microbiology, Washington DC. USA.
    CrossRef
  12. Kates M. 1972. Techniques of Lipidology. Elsevier, New York. USA.
    CrossRef
  13. Oren A, Duker S, Ritter S. 1996. The polar lipid composition of Walsby’s square bacterium. FEMS Microbiol Lett. 138: 135-140.
    CrossRef
  14. Tamaoka J, Fujimura Y-K, Kuraishi H. 1983. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J. Appl. Microbiol. 54: 31-36.
    CrossRef
  15. Sasser M. 2001. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101.
  16. Marmur J. 1961. A procedure for the isolation of deoxyribonucleic acid from microorganisms. J. Mol. Biol. 3: 208-218.
    CrossRef
  17. Gonzalez JM, Saiz-Jimenez C. 2002. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ. Microbiol. 4:770-773.
    Pubmed CrossRef
  18. Padakandla SR, Lee G-W, Chae J-C. 2015. Paenibacillus gelatinilyticus sp. nov. a psychrotolerant bacterium isolated from a reclaimed soil and amended description of Paenibacillus shenyangensis. Antonie Van Leeuwenhoek. 108: 1197-1203.
    Pubmed CrossRef
  19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
    CrossRef
  20. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. 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 CrossRef
  21. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 30: 2725-2729.
    Pubmed PMC CrossRef
  22. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge. UK.
    CrossRef
  23. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
    Pubmed
  24. Fitch WM. 1972. Toward defining the course of evolution:minimum change for a specific tree topology. Syst. Zool. 20:406-416.
    CrossRef
  25. Edwards AWF, Cavalli-Sforza LL. 1963. The reconstruction of evolution. Ann. Hum. Genet. 27: 105.
  26. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464.
    CrossRef

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Article

Research article

J. Microbiol. Biotechnol. 2017; 27(7): 1300-1305

Published online July 28, 2017 https://doi.org/10.4014/jmb.1703.03075

Copyright © The Korean Society for Microbiology and Biotechnology.

Chitinimonas naiadis sp. nov., Isolated from a Freshwater River

Shalem Raj Padakandla 1 and Jong-Chan Chae 1, 2*

1Division of Biotechnology,, 2Advanced Institute of Environmental and Bioscience, Chonbuk National University, Iksan 54596, Republic of Korea

Received: March 31, 2017; Accepted: April 20, 2017

Abstract

A rod shaped, aerobic, Gram-stain-negative, and motile bacterium, strain AR2T, was isolated
from a water sample of Yeongsan river, Republic of Korea. Strain AR2T clustered closely with
the members of the genus Chitinimonas and showed the highest 16S rRNA gene sequence
similarity with Chitinimonas prasina LY03T (96.4%), Chitinimonas viridis HMD2169T (96.4%),
Chitinimonas taiwanensis cfT (96.2%), and Chitinimonas koreensis R2A43-10T (94.2%). The
predominant fatty acids of strain AR2T were identified to be summed feature 3 (comprising
C16:1ω7c and/or C16:1ω6c), C16:0, and C10:03-OH. Diphosphatidylglycerol, phosphatidylglycerol,
and phosphatidylethanolamine were found to be the major polar lipids. The genomic DNA
G+C content was 60.4 mol%. Based on the polyphasic characterization, the isolated strain AR2T
is described as a representative of a novel species in the genus Chitinimonas, for which the name
Chitinimonas naiadis sp. nov. (type strain =AR2T =KCTC 42755T =JCM 31504T) is proposed.

Keywords: Chitinimonas, polyphasic taxonomy

References

  1. Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS, Chen WM. 2004. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst. Appl. Microbiol. 27: 43-49.
    Pubmed CrossRef
  2. Kim BY, Weon HY, Yoo SH, Chen WM, Kwon SW, Go SJ, Stackebrandt E. 2006. Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea. Int. J. Syst. Evol. Microbiol. 56: 1761-1764.
    Pubmed CrossRef
  3. Joung Y, Lee BI, Kang H, Kim H, Joh K. 2014. Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake. Int. J. Syst. Evol. Microbiol. 64: 1123-1126.
    Pubmed CrossRef
  4. Li Y , Zh u H, L ai Q , Lei X, C hen Z , Zh ang H, et al. 2014. Chitinimonas prasina sp. nov., isolated from lake water. Int. J. Syst. Evol. Microbiol. 64: 3005-3009.
    Pubmed CrossRef
  5. Li Y , Lei X, Zhu H, Zh ang H, Guan C, C h en Z , et al. 2016. Chitinase producing bacteria with direct algicidal activity on marine diatoms. Sci. Rep. 6: 21984.
    Pubmed KoreaMed CrossRef
  6. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60: 249-266.
    Pubmed CrossRef
  7. Padakandla SR, Chae J-C. 2017. Reclassification of Aeromonas sharmana to a new genus as Pseudaeromonas sharmana gen. nov., comb. nov and description of Pseudaeromonas pectinilytica sp. nov. isolated from a fresh water stream. Int. J. Syst. Evol. Microbiol. 67: 1018-1023.
    Pubmed CrossRef
  8. Buck JD. 1982. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol. 44: 992-993.
    Pubmed KoreaMed
  9. Cappuccino JG, Sherman N. 1998. Microbiology – A Laboratory Manual, 4th Ed. Benjamin/Cummings Science Publishing, San Francisco, CA. USA.
  10. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, et al. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2: 233-241.
    CrossRef
  11. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. 2007. Phenotypic characterization and the principles of comparative systematics, pp. 330-393. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds.), Methods for General and Molecular Microbiology, 3rd Ed. American Society of Microbiology, Washington DC. USA.
    CrossRef
  12. Kates M. 1972. Techniques of Lipidology. Elsevier, New York. USA.
    CrossRef
  13. Oren A, Duker S, Ritter S. 1996. The polar lipid composition of Walsby’s square bacterium. FEMS Microbiol Lett. 138: 135-140.
    CrossRef
  14. Tamaoka J, Fujimura Y-K, Kuraishi H. 1983. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J. Appl. Microbiol. 54: 31-36.
    CrossRef
  15. Sasser M. 2001. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101.
  16. Marmur J. 1961. A procedure for the isolation of deoxyribonucleic acid from microorganisms. J. Mol. Biol. 3: 208-218.
    CrossRef
  17. Gonzalez JM, Saiz-Jimenez C. 2002. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ. Microbiol. 4:770-773.
    Pubmed CrossRef
  18. Padakandla SR, Lee G-W, Chae J-C. 2015. Paenibacillus gelatinilyticus sp. nov. a psychrotolerant bacterium isolated from a reclaimed soil and amended description of Paenibacillus shenyangensis. Antonie Van Leeuwenhoek. 108: 1197-1203.
    Pubmed CrossRef
  19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
    CrossRef
  20. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. 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 CrossRef
  21. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 30: 2725-2729.
    Pubmed KoreaMed CrossRef
  22. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge. UK.
    CrossRef
  23. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
    Pubmed
  24. Fitch WM. 1972. Toward defining the course of evolution:minimum change for a specific tree topology. Syst. Zool. 20:406-416.
    CrossRef
  25. Edwards AWF, Cavalli-Sforza LL. 1963. The reconstruction of evolution. Ann. Hum. Genet. 27: 105.
  26. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464.
    CrossRef