Journal of Microbiology

, Volume 51, Issue 1, pp 36–42 | Cite as

Bhargavaea indica sp. nov., a member of the phylum Firmicutes, isolated from Arabian Sea sediment

  • Pankaj Verma
  • Chi Nam Seong
  • Prashant Kumar Pandey
  • Ramesh Ramchandra Bhonde
  • Cathrin Spröer
  • Manfred Rohde
  • Yogesh Shreepad Shouche
Microbial Systematics and Evolutionary Microbiology

Abstract

A Gram-positive, aerobic, coccoid-rod shaped, non-motile, catalase- and oxidase-positive bacterium, designated strain KJW98T, was isolated from the marine sediment of Karwar jetty, west coast of India. The strain was β-haemolytic, non-endospore-forming and grew with 0–8.5% (w/v) NaCl, at 15–48°C and at pH 6.5–9.0, with optimum growth with 0.5% (w/v) NaCl, at 42°C and at pH 7.0–8.0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences showed that strain KJW98T forms a lineage within the genus Bhargavaea. The G+C content of the genomic DNA was 55 mol%. The DNA-DNA relatedness values of strain KJW98T with B. beijingensis DSM 19037T, B. cecembensis LMG 24411T and B. ginsengi DSM 19038T were 43.2, 39 and 26.5%, respectively. The major fatty acids were anteiso-C15:0 (37.7%), iso-C15:0 (19.7%), anteiso-C17:0 (17.0%) and iso-C16:0 (11.1%). The predominant menaquinone was MK-8 and the cell-wall peptidoglycan was of A4α type with L-lysine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The phenotypic, genotypic and DNA-DNA relatedness data indicate that strain KJW98T should be distinguished from the members of the genus Bhargavaea, for which the name Bhargavaea indica sp. nov. is proposed with the type strain KJW98T (=KCTC 13583T =LMG 25219T).

Keywords

Bhargavaea indica Firmicutes 16S rRNA gene gyrB 

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References

  1. Altschul, S.F., Madden, T.L., Schaeffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res.25, 3389–3402.PubMedCrossRefGoogle Scholar
  2. Chun, J., Lee, J.-H., Jung, Y., Kim, M., Kim, S., Kim, B.K., and Lim, Y.W. 2007. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol.57, 2259–2261.PubMedCrossRefGoogle Scholar
  3. Collins, M.D., Pirouz, T., Goodfellow, M., and Minnikin, D.E. 1977. Distribution of menaquinones in Actinomycetes and Corynebacteria. J. Gen. Microbiol.100, 221–230.PubMedGoogle Scholar
  4. De Ley, J., Cattoir, H., and Reynaerts, A. 1970. The quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem.12, 133–142.PubMedCrossRefGoogle Scholar
  5. Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool.20, 406–416.CrossRefGoogle Scholar
  6. Groth, I., Schumann, P., Weiss, N., Martin, K., and Rainey, F.A. 1996. Agrococcus jenensis gen. nov., sp. nov., a new genus of Actinomycetes with diaminobutyric acid in the cell wall. Int. J. Syst. Bacteriol.46, 234–239.PubMedCrossRefGoogle Scholar
  7. Hauben, L., Vauterin, L., Swings, J., and Moore, E.R.B. 1997. Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int. J. Syst. Bacteriol.47, 328–335.PubMedCrossRefGoogle Scholar
  8. Huss, V.A.R., Festl, H., and Schleifer, K.H. 1983. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst. Appl. Microbiol.4, 184–192.PubMedCrossRefGoogle Scholar
  9. Kämpfer, P., Rossello-Mora, R., Falsen, E., Busse, H.J., and Tindall, B.J. 2006. Cohnella thermotolerans gen. nov., sp. nov., and classification of ‘Paenibacillus hongkongensis’ as Cohnella hongkongensis sp. nov. Int. J. Syst. Evol. Microbiol.56, 781–786.PubMedCrossRefGoogle Scholar
  10. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol.16, 111–120.PubMedCrossRefGoogle Scholar
  11. Kovacs, N. 1956. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature178, 703.PubMedCrossRefGoogle Scholar
  12. Logan, N.A., Berge, O., Bishop, A.H., Busse, H.-J., De Vos, P., Fritze, D., Heyndrickx, M., Kämpfer, P., Rabinovitch, L., Salkinoja-Salonen, M.S., andet al. 2009. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int. J. Syst. Evol. Microbiol.59, 2114–2121.PubMedCrossRefGoogle Scholar
  13. MacKenzie, S.L. 1987. Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J. Assoc. Off. Anal. Chem.70, 151–160.PubMedGoogle Scholar
  14. Manorama, R., Pindi, P.K., Reddy, G.S.N., and Shivaji, S. 2009. Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos-Laccadive ridge system in the Indian Ocean. Int. J. Syst. Evol. Microbiol.59, 2618–2623.PubMedCrossRefGoogle Scholar
  15. Mesbah, M., Premachandran, U., and Whitman, W.B. 1989. Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int. J. Syst. Bacteriol.39, 159–167.CrossRefGoogle Scholar
  16. Pike, E.B., Carringtoen, E.G., and Ashburner, A.P. 1972. An evaluation of procedures for enumerating bacteria in activated sludge. J. Appl. Bacteriol.35, 309–321.PubMedCrossRefGoogle Scholar
  17. Qiu, F., Zhang, X., Liu, L., Sun, L., Schumann, P., and Song, W. 2009. Bacillus beijingensis sp. nov. and Bacillus ginsengi sp. nov., isolated from ginseng root. Int. J. Syst. Evol. Microbiol.59, 729–734.PubMedCrossRefGoogle Scholar
  18. Rzhetsky, A. and Nei, M. 1992. A simple method for estimating and testing minimum evolution trees. Mol. Biol. Evol.9, 945–967.Google Scholar
  19. Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4, 406–425.PubMedGoogle Scholar
  20. Schleifer, K.H. 1985. Analysis of the chemical composition and primary structure of murein. Methods Microbiol.18, 123–156.CrossRefGoogle Scholar
  21. Schleifer, K.H. and Kandler, O. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol. Rev.36, 407–477.PubMedGoogle Scholar
  22. Tamaoka, J. and Komagata, K. 1984. Determination of DNA base composition by rever-sed-phase high-performance liquid chromatography. FEMS Microbiol. Lett.25, 125–128.CrossRefGoogle Scholar
  23. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol.28, 2731–2739.PubMedCrossRefGoogle Scholar
  24. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res.25, 4876–4882.PubMedCrossRefGoogle Scholar
  25. Tindall, B.J. 1990a. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst. Appl. Microbiol.13, 128–130.CrossRefGoogle Scholar
  26. Tindall, B.J. 1990b. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol. Lett.66, 199–202.CrossRefGoogle Scholar
  27. Verma, P., Pandey, P.K., Gupta, A.K., Seong, C.N., Park, S.C., Choe, H.N., Baik, K.S., Patole, M.S., and Shouche, Y.S. 2012. Reclassification of Bacillus beijingensis and Bacillus ginsengi Qiu et al., 2009 as Bhargavaea beijingensis comb. nov. and Bhargavaea ginsengi comb. nov. and emended description of the genus Bhargavaea. Int. J. Syst. Evol. Microbiol.62, 2495–2504.PubMedCrossRefGoogle Scholar
  28. Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., andet al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol.37, 463–464.CrossRefGoogle Scholar
  29. Xia, X. and Xie, Z. 2001. DAMBE: Data analysis in molecular biology and evolution. J. Hered.92, 371–373.PubMedCrossRefGoogle Scholar
  30. Yamamoto, S. and Harayama, S. 1995. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl. Environ. Microbiol.61, 1104–1109.PubMedGoogle Scholar
  31. Yamamoto, S. and Harayama, S. 1998. Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int. J. Syst. Bacteriol.48, 813–819.PubMedCrossRefGoogle Scholar
  32. Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. 2000. A greedy algorithm for aligning DNA sequences. J. Comput. Biol.7, 203–214.PubMedCrossRefGoogle Scholar
  33. Zuckerkandl, E. and Pauling, L. 1965. Evolutionary divergence and convergence in proteins, pp. 97–166 in Evolving Genes and Proteins. In Bryson, V. and Vogel, H.J. (eds.). Academic Press, New York, N.Y., USA.Google Scholar

Copyright information

© The Microbiological Society of Korea and Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Pankaj Verma
    • 1
  • Chi Nam Seong
    • 2
  • Prashant Kumar Pandey
    • 1
  • Ramesh Ramchandra Bhonde
    • 3
  • Cathrin Spröer
    • 4
  • Manfred Rohde
    • 5
  • Yogesh Shreepad Shouche
    • 1
    • 6
  1. 1.Molecular Biology UnitNational Centre for Cell SciencePuneIndia
  2. 2.Department of Biology, College of Life Science and Natural ResourcesSunchon National UniversitySuncheonRepublic of Korea
  3. 3.Manipal Institute of Regenerative MedicineBangaloreIndia
  4. 4.Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweigGermany
  5. 5.BraunschweigGermany
  6. 6.Microbial Culture CollectionNational Centre for Cell SciencePuneIndia

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