Antonie van Leeuwenhoek

, Volume 107, Issue 4, pp 893–900 | Cite as

Emcibacter nanhaiensis gen. nov. sp. nov., isolated from sediment of the South China Sea

  • Xiupian Liu
  • Guangyu Li
  • Qiliang Lai
  • Fengqin Sun
  • Yaping Du
  • Zongze Shao
Original Paper

Abstract

A new aerobic, Gram stain-negative, oxidase- and catalase- positive, ovoid or rod-shaped bacterial strain, designated HTCJW17T, was isolated from a sediment collected from the South China Sea and subjected to a polyphasic taxonomic characterization. The isolate forms small, creamy-white, opaque and circular colonies on agar plates. Growth occurs between 15 and 45 °C, 1–7 % (w/v) NaCl and pH 6–9. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HTCJW17T belongs to the family Kordiimonadaceae of the order Kordiimonadales, with highest sequence similarity to Kordiimonas gwangyangensis GW14-5T (91.1 %). The major fatty acids were identified to be summed feature 8 (C18:1ω7c/ω6c; 56.6 %), C14:0 (8.5 %), C14:0 2-OH (8.4 %), summed feature 3 (C16:1ω7c/C16:1ω6c; 6.2 %), and C16:0 (5.2 %). The polar lipids were determined to be phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, six unidentified glycolipids and two unidentified phospholipids. The respiratory quinone was identified as ubiquinone Q-10. The genomic DNA G+C content was determined to be 56.3 mol%. On the basis of genotypic, chemotaxonomic and phenotypic distinctness, we propose a novel genus, Emcibacter gen. nov., with Emcibacter nanhaiensis sp. nov. as the type species. The type strain is HTCJW17T (=CGMCC 1.12471T = LMG 27419T = MCCC 1A06723T).

Keywords

Emcibacter nanhaiensis gen. nov. sp. nov. The South China Sea Taxonomy Sediment 

Abbreviation

MCCC

Marine Culture Collection of China

Notes

Acknowledgments

This work was financially supported by National Infrastructure of Microbial Resources of China (No. NIMR-2014-9) and Public Welfare Project of SOA (201005032).

Supplementary material

10482_2015_381_MOESM1_ESM.docx (1 mb)
Supplementary material 1 (DOCX 1042 kb)

References

  1. Ausubel F, Brent R, Kingston R, Moore D, Seidman J, Smith J, Struhl K (1995) Short protocols in molecular biology: a compendium of methods from current protocols in molecular biology, 3rd edn. Wiley, New YorkGoogle Scholar
  2. Kates M (1986) Techniques of lipidology. Elsevier, AmsterdamGoogle Scholar
  3. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721CrossRefPubMedGoogle Scholar
  4. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  5. Kwon KK, Lee HS, Yang SH, Kim SJ (2005) Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the ‘Alphaproteobacteria’. Int J Syst Evol Microbiol 55:2033–2037CrossRefPubMedGoogle Scholar
  6. Lai Q, Yuan J, Wu C, Shao Z (2009) Oceanibaculum indicum gen. nov., sp. nov., isolated from deep seawater of the Indian Ocean. Int J Syst Evol Microbiol 59:1733–1737CrossRefPubMedGoogle Scholar
  7. Liu C, Shao Z (2005) Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 55:1181–1186CrossRefPubMedGoogle Scholar
  8. Math RK, Jeong SH, Jin HM, Park MS, Kim JM, Jeon CO (2012) Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 62:3049–3054CrossRefPubMedGoogle Scholar
  9. Mesbah M, Whitman WB (1989) Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr 479:297–306CrossRefPubMedGoogle Scholar
  10. Paramasivam N, Ben-Dov E, Arotsker L, Kushmaro A (2013) Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral Millepora dichotoma. Int J Syst Evol Microbiol 63:1880–1884CrossRefPubMedGoogle Scholar
  11. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI, NewarkGoogle Scholar
  12. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams & Wilkins, BaltimoreGoogle Scholar
  13. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  14. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefPubMedCentralPubMedGoogle Scholar
  15. Teramoto M, Nishijima M (2014) Temperatibacter marinus gen. nov., sp. nov., a mesophilic bacterium isolated from surface seawater and description of Temperatibacteraceae fam. nov. in the class Alphaproteobacteria. Int J Syst Evol Microbiol 64:3075–3080CrossRefPubMedGoogle Scholar
  16. Xu XW, Huo YY, Bai XD, Wang CS, Oren A, Li SY, Wu M (2011) Kordiimonas lacus sp. nov., isolated from a ballast water tank, and emended description of the genus Kordiimonas. Int J Syst Evol Microbiol 61:422–426CrossRefPubMedGoogle Scholar
  17. Yang SH, Kim, Seo HS, Lee SH, Lee JH, Kim SJ, Kwon KK (2013) Description of Kordiimonas aquimaris sp. nov., isolated from seawater, and emended descriptions of the genus Kordiimonas Kwon et al. 2005 emend. Xu et al. 2011 and of its existing species. Int J Syst Evol Microbiol 63:298–302CrossRefPubMedGoogle Scholar
  18. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer K-H, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Xiupian Liu
    • 1
    • 2
    • 3
  • Guangyu Li
    • 1
    • 2
    • 3
  • Qiliang Lai
    • 1
    • 2
    • 3
  • Fengqin Sun
    • 1
    • 2
    • 3
  • Yaping Du
    • 1
    • 2
    • 3
  • Zongze Shao
    • 1
    • 2
    • 3
  1. 1.Key Laboratory of Marine Biogenetic Resources, Third Institute of OceanographySOAXiamenChina
  2. 2.State Key Laboratory Breeding Base of Marine Genetic ResourcesXiamenChina
  3. 3.Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamenChina

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