Advertisement

Antonie van Leeuwenhoek

, Volume 101, Issue 3, pp 641–647 | Cite as

Echinicola shivajiensis sp. nov., a novel bacterium of the family “Cyclobacteriaceae” isolated from brackish water pond

  • T. N. R. Srinivas
  • B. Kailash Tryambak
  • P. Anil Kumar
Original Paper

Abstract

Strain AK12T, an orange pigmented Gram-negative, rod shaped, non-motile bacterium, was isolated from a mud sample collected from a brackish water pond at Rampur of West Bengal, India. The strain was positive for oxidase, catalase and phosphatase. The predominant fatty acids were iso-C15:0 (42.7%), iso-C17:0 3OH (13.2%), C16:1ω7c/C16:1ω6c (summed feature 3) (8.0%), iso-C17:1 I/anteiso-C17:1 B (summed feature 4) (6.1%) and iso-C17:1ω9c/C16:0 10-methyl (summed feature 9) (9.4%). Strain AK12T contained MK-7 as the major respiratory quinone and phosphatidylethanolamine, one unidentified aminophospholipid and six unidentified lipids as the polar lipids. The G + C content of DNA of the strain AK12T was 46.2 mol%. The 16S rRNA gene sequence analysis indicated that strain AK12T was member of the genus Echinicola and closely related to Echinicola vietnamensis, Echinicola pacifica and Echinicola jeungdonensis with pair-wise sequence similarity of 96.8, 96.3 and 96.0% respectively. Phylogenetic analyses indicated that the strain AK12T clustered with E. vietnamensis and together with E. pacifica and E. jeungdonensis with a phylogenetic distance of 5.1, 6.3 and 6.6% (94.9, 93.7 and 93.4% similarity) respectively. Based on data from the current polyphasic study, strain AK12T is proposed as a novel species of the genus Echinicola, for which the name Echinicola shivajiensis sp. nov. is proposed. The type strain of E. shivajiensis is AK12T (= MTCC 11083T = JCM 17847T).

Keywords

Echinicola shivajiensis 16S rRNA gene based phylogeny Bacteroidetes 

Notes

Acknowledgments

We thank Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology, Government of India for financial assistance. We would like to thank Mr. Deepak for his excellent help in sequencing DNA. The laboratory facility was extended by MMRF of NIO, RC, Kochi funded by the Ministry of Earth Sciences, New Delhi. TNRS is thankful to CSIR SIP projects (SIP1302 and SIP1308) for providing facilities and funding respectively.

Supplementary material

10482_2011_9679_MOESM1_ESM.docx (153 kb)
Supplementary Fig. S1. Phase contrast photograph of cells of strain AK12T. Bar, 5.0 μm (DOCX 153 kb)
10482_2011_9679_MOESM2_ESM.docx (337 kb)
Supplementary Fig. S2. Two-dimensional thin-layer chromatogram of polar lipids of the strains AK12T (a), LMG 23350T (b) and LMG 23754T (c). Detection of total lipids by molybdatophosphoric acid. Abbreviations: PE, phosphatidylethanolamine; AL, unidentified aminolipid; AP, unidentified aminophospholipid; L, unidentified lipid. (DOCX 336 kb)

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Mol Biol 215:403–410Google Scholar
  2. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261PubMedCrossRefGoogle Scholar
  3. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in Actinomycetes and Corynebacteria. J Gen Microbiol 100:221–230PubMedGoogle Scholar
  4. Groth I, Schumann P, Rainey FA, Martin K, Schuetze B, Augsten K (1997) Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 47:1129–1133PubMedCrossRefGoogle Scholar
  5. Guindon S, Lethiec F, Duroux P, Gascuel O (2005) PHYML Online: a web server for fast maximum likelihood-based phylogenetic inference. Nucl Acids Res 33:W557–W559PubMedCrossRefGoogle Scholar
  6. Kim H, Joung Y, Ahn TS, Joh K (2011) Echinicola jeungdonensis sp. nov., isolated from a solar saltern. Int J Syst Evol Microbiol 61:2065–2068PubMedCrossRefGoogle Scholar
  7. Komagata K, Suzuki K (1987) Lipid and cell wall analysis in bacterialsystematictics. Methods Microbiol 19:161–206CrossRefGoogle Scholar
  8. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Chichester, Wiley, pp 115–175Google Scholar
  9. Lányί B (1987) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67CrossRefGoogle Scholar
  10. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218CrossRefGoogle Scholar
  11. Nedashkovskaya OI, Kim SB, Vancanneyt M, Lysenko AM, Shin DS, Park MS, Lee KH, Jung WJ, Kalinovskaya NI, Mikhailov VV, Bae KS, Swings J (2006) Echinicola pacifica gen. nov., sp. nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 56:953–958PubMedCrossRefGoogle Scholar
  12. Nedashkovskaya OI, Kim SB, Hoste B, Shin DS, Beleneva IA, Vancanneyt M, Mikhailov VV (2007) Echinicola vietnamensis sp. nov., a member of the phylum Bacteroidetes isolated from seawater. Int J Syst Evol Microbiol 57:761–763PubMedCrossRefGoogle Scholar
  13. Sly LI, Blackall LL, Kraat PC, Tian-Shen T, Sangkhobol V (1986) The use of second derivative plots for the determination of mol% guanine plus cytosine of DNA by the thermal denaturation method. J Microbiol Methods 5:139–156CrossRefGoogle Scholar
  14. 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 607–654Google Scholar
  15. Thompson JD, Higgins DG, 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. Nucl Acids Res 25:4876–4882PubMedCrossRefGoogle Scholar
  16. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438PubMedGoogle Scholar
  17. ZoBell CE (1941) Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 4:42–75Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • T. N. R. Srinivas
    • 1
  • B. Kailash Tryambak
    • 3
  • P. Anil Kumar
    • 2
  1. 1.National Institute of Oceanography (CSIR), Regional CentreKochiIndia
  2. 2.Microbial Type Culture Collection and Gene BankInstitute of Microbial Technology (CSIR)ChandigarhIndia
  3. 3.Institute of Microbial Technology (CSIR)ChandigarhIndia

Personalised recommendations