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Antonie van Leeuwenhoek

, Volume 101, Issue 3, pp 469–478 | Cite as

Kocuria sediminis sp. nov., isolated from a marine sediment sample

  • Monu Bala
  • Chandandeep Kaur
  • Ishwinder Kaur
  • Fazlurrahman Khan
  • Shanmugam Mayilraj
Original Paper

Abstract

A Gram-positive, pinkish-orange pigmented, coccoid strain, FCS-11T was isolated from a marine sediment sample taken from Kochi fort area, Kerala, India and subjected to polyphasic taxonomic study. The 16S rRNA gene sequence of the strain was determined and the results of 16S rRNA gene sequence analysis showed that the strain FCS-11T should be assigned to the genus Kocuria. The chemotaxonomic data supported this taxonomic placement i.e. menaquinones MK-7(H2), MK-8(H2) and MK-9(H2); major fatty acids anteiso C15:0 and iso-C15:0 and phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG) as major polar lipids. Further phylogenetic analysis of the 16S rRNA gene sequence confirmed that the strain FCS-11T belonged to the genus Kocuria and is closely related to Kocuria turfanensis MTCC 10790T (99.4%) followed by Kocuria polaris MTCC 3702T (98.2%), Kocuria rosea MTCC 2522T (98.2%), Kocuria flava MTCC 10971T (98.2%), Kocuria aegyptia MTCC 10791T (98.0%), Kocuria himachalensis MTCC 7020T (97.5%) and Kocuria atrinae MTCC 10972T (97.1%). However, the DNA–DNA hybridisation values obtained between strain FCS-11T and other related strains were well below the threshold that is required for the proposal of a novel species. The G+C content of the genomic DNA was 60.7 mol%. The phenotypic and genotypic data showed that the strain FCS-11T merits the recognition as a representative of a novel species of the genus Kocuria. It is proposed that the isolate should be classified in the genus Kocuria as a novel species, Kocuria sediminis sp. nov. The type strain is FCS-11T (= MTCC 10969T = JCM 17929T).

Keywords

DNA–DNA hybridisation Fatty acid methyl ester Biolog 16S rRNA gene sequencing 

Notes

Acknowledgments

We thank Mr Malkit Singh for his excellent technical assistance. This work was supported by CSIR (net work project NWP006) Government of India. This is IMTECH communication number 43/2011.

Supplementary material

10482_2011_9654_MOESM1_ESM.docx (13.9 mb)
Supplementary material (DOCX 14191 kb)

References

  1. Barrow GI, Feltham RKA (1993) Cowan and steel’s manual for the identification of medical bacteria, 3rd edn. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  2. Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917PubMedCrossRefGoogle Scholar
  3. 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
  4. Kaur C, Kaur I, Raichand R, Bora TC, Mayilraj S (2011) Description of a novel actinobacterium Kocuria assamensis sp. nov., isolated from a water sample collected from the river Brahmaputra. Assam, India. Antonie Van Leeuwenhoek 99:721–726CrossRefGoogle Scholar
  5. Kim SB, Nedashkovskaya OI, Mikhailov VV, Han SK, Kim KO, Rhee MS, Bae KS (2004) Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 54:1617–1620PubMedCrossRefGoogle Scholar
  6. Komagata K, Suzuki K (1987) Lipid and cell-wall systematics in bacterial systematics. Methods Microbiol 19:161–207CrossRefGoogle Scholar
  7. Kovacs G, Burghardt J, Pradella S, Schumann P, Stackebrandt E, Marialigeti K (1999) Kocuria palustris sp. nov. and K. rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia). Int J Syst Bacteriol 49:167–173PubMedCrossRefGoogle Scholar
  8. Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367CrossRefGoogle Scholar
  9. Lányi B (1988) Classical and rapid identification methods for medically important bacteria. In: Colwell RR, Grigorova R (eds) Methods Microbiol 19:1–67Google Scholar
  10. Li WJ, Zhang YQ, Schumann P, Chen HH, Hozzein WN, Tian XP, Xu LH, Jiang CL (2006) Kocuria aegyptia sp. nov., a novel actinobacterium isolated from a saline, alkaline desert soil in Egypt. Int J Syst Evol Microbiol 56:733–737PubMedCrossRefGoogle Scholar
  11. Mandel M, Marmur J (1968) Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195–206CrossRefGoogle Scholar
  12. Mayilraj S, Kroppenstedt RM, Suresh K, Saini HS (2006) Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas. Int J Syst Evol Microbiol 56:1971–1975PubMedCrossRefGoogle Scholar
  13. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 2:233–241CrossRefGoogle Scholar
  14. Pandey KK, Mayilraj S, Chakrabarti T (2002) Pseudomonas indica sp. nov., a novel butane-utilising species. Int J Syst Evol Microbiol 52:1559–1567PubMedCrossRefGoogle Scholar
  15. Park EJ, Kim MS, Roh SW, Jung MJ, Bae JW (2010a) Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood. Int J Syst Evol Microbiol 60:914–918PubMedCrossRefGoogle Scholar
  16. Park EJ, Roh SW, Kim MS, Jung MJ, Shin KS, Bae JW (2010b) Kocuria koreensis sp. nov., isolated from fermented seafood. Int J Syst Evol Microbiol 60:140–143PubMedCrossRefGoogle Scholar
  17. Rainey FA, Nobre MF, Schumann P, Stackebrandt E, da Costa MS (1997) Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison. Int J Syst Bacteriol 47:510–514PubMedCrossRefGoogle Scholar
  18. Reddy GS, Prakash JS, Prabahar V, Matsumoto GI, Stackebrandt E, Shivaji S (2003) Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample. Int J Syst Evol Microbiol 53:183–187PubMedCrossRefGoogle Scholar
  19. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. MIDI Inc, NewarkGoogle Scholar
  20. Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156CrossRefGoogle Scholar
  21. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477PubMedGoogle Scholar
  22. Seo YB, Kim DE, Kim GD, Kim HW, Nam SW, Kim YT, Lee JH (2009) Kocuria gwangalliensis sp. nov., an actinobacterium isolated from seawater. Int J Syst Evol Microbiol 59:2769–2772PubMedCrossRefGoogle Scholar
  23. Smibert RM, Krieg NR (1994) Phenotypic characterisation. In: Gerhard P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654Google Scholar
  24. Smith NR, Gordan RE, Clark FE (1952) Aerobic spore forming bacteria. Agricultural monograph no.16 Washington. US Department of agriculture, DCGoogle Scholar
  25. Stackebrandt E, Woese C (1979) A phylogenetic dissection of the family micrococcaceae. Current Microbiology 2:317–322CrossRefGoogle Scholar
  26. Stackebrandt E, Koch C, Gvozdiak O, Schumann P (1995) Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., Micrococcus Cohn 1872 gen.emend. Int J Syst Bacteriol 45:682–692PubMedCrossRefGoogle Scholar
  27. 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 doi:  10.1093/molbev/msr121
  28. Tang SK, Wang Y, Lou K, Mao PH, Xu LH, Jiang CL, Kim CJ, Li WJ (2009) Kocuria halotolerans sp. nov., an actinobacterium isolated from a saline soil in China. Int J Syst Evol Microbiol 59:1316–1320PubMedCrossRefGoogle Scholar
  29. Tourova TP, Antonov AS (1988) Identification of microorganisms by rapid DNA–DNA hybridisation. Methods Microbiol 19:333–355CrossRefGoogle Scholar
  30. Tvrzova L, Schumann P, Sedlacek I, Pacova Z, Sproer C, Verbarg S, Kroppenstedt RM (2005) Reclassification of strain CCM 132, previously classified as Kocuria varians, as K. carniphila sp. nov. Int J Syst Evol Microbiol 55:139–142PubMedCrossRefGoogle Scholar
  31. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, other authors (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  32. Yun JH, Roh SW, Jung MJ, Kim MS, Park EJ, Shin KS, Nam YD, Bae JW (2011) Kocuria salsicia sp. nov., isolated from salt-fermented seafood. Int J Syst Evol Microbiol 61:286–289PubMedCrossRefGoogle Scholar
  33. Zhou G, Luo X, Tang Y, Zhang L, Yang Q, Qiu Y, Fang C (2008) Kocuria flava sp. nov. and K. turfanensis sp. nov., airborne actinobacteria isolated from Xinjiang, China. Int J Syst Evol Microbiol 58:1304–1307PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Monu Bala
    • 1
  • Chandandeep Kaur
    • 1
  • Ishwinder Kaur
    • 1
  • Fazlurrahman Khan
    • 1
  • Shanmugam Mayilraj
    • 1
  1. 1.Microbial Type Culture Collection & Gene Bank (MTCC)Institute of Microbial Technology (IMTECH)ChandigarhIndia

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