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

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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).

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References

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool.20, 406–416.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Kovacs, N. 1956. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature178, 703.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • MacKenzie, S.L. 1987. Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J. Assoc. Off. Anal. Chem.70, 151–160.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Rzhetsky, A. and Nei, M. 1992. A simple method for estimating and testing minimum evolution trees. Mol. Biol. Evol.9, 945–967.

    CAS  Google Scholar 

  • Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4, 406–425.

    PubMed  CAS  Google Scholar 

  • Schleifer, K.H. 1985. Analysis of the chemical composition and primary structure of murein. Methods Microbiol.18, 123–156.

    Article  CAS  Google Scholar 

  • Schleifer, K.H. and Kandler, O. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol. Rev.36, 407–477.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Tindall, B.J. 1990a. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst. Appl. Microbiol.13, 128–130.

    Article  CAS  Google Scholar 

  • Tindall, B.J. 1990b. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol. Lett.66, 199–202.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Xia, X. and Xie, Z. 2001. DAMBE: Data analysis in molecular biology and evolution. J. Hered.92, 371–373.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. 2000. A greedy algorithm for aligning DNA sequences. J. Comput. Biol.7, 203–214.

    Article  PubMed  CAS  Google Scholar 

  • 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 

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Author notes

  1. Pankaj Verma

    Present address: National Institute of Ocean Technology, Pallikaranai, Chennai, 600 100, Tamil Nadu, India

Authors and Affiliations

  1. Molecular Biology Unit, National Centre for Cell Science, Pune, 411 007, Maharashtra, India

    Pankaj Verma, Prashant Kumar Pandey & Yogesh Shreepad Shouche

  2. Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 540-742, Republic of Korea

    Chi Nam Seong

  3. Manipal Institute of Regenerative Medicine, Bangalore, 560 071, Karnataka, India

    Ramesh Ramchandra Bhonde

  4. Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124, Braunschweig, Germany

    Cathrin Spröer

  5. Helmholtz-Zentrum für Infektionsforschung GmbH, D-38124, Braunschweig, Germany

    Manfred Rohde

  6. Microbial Culture Collection, National Centre for Cell Science, Pune, 411 007, Maharashtra, India

    Yogesh Shreepad Shouche

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  1. Pankaj Verma
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Correspondence to Chi Nam Seong or Yogesh Shreepad Shouche.

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Verma, P., Seong, C.N., Pandey, P.K. et al. Bhargavaea indica sp. nov., a member of the phylum Firmicutes, isolated from Arabian Sea sediment. J Microbiol. 51, 36–42 (2013). https://doi.org/10.1007/s12275-013-2488-z

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  • DOI: https://doi.org/10.1007/s12275-013-2488-z

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