Skip to main content

Advertisement

SpringerLink
Log in

Paracoccus pacificus sp. nov., isolated from the Western Pacific Ocean

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A Gram-stain negative, short rod-shaped, non-motile, catalase- and oxidase-positive, aerobic bacterium, designated F14T, was isolated from the Western Pacific Ocean. Phylogenetic and phenotypic properties of the organism supported that it belongs to the genus Paracoccus. The levels of 16S rRNA gene sequences similarity between strain F14T and other type strains of recognized members of the genus Paracoccus were 93.6–96.5 %. Growth of strain F14T was observed at 4–40 °C (optimum, 28–30 °C), pH 6.0–10.0 (optimum, pH 7.0–8.0) and in the presence of 0–7 % (w/v) NaCl (optimum, 1–2 %). The major cellular fatty acid was summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major respiratory quinone was ubiquinone-10. The polar lipid pattern indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and three unknown lipids. The DNA G+C content was 61.4 mol%. On the basis of polyphasic characterization, strain F14T represents a novel species, for which the name Paracoccus pacificus sp. nov. is proposed. The type strain is F14T (=CGMCC 1.12755T=LMG 28106T=MCCC 1A09947T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Bruns A, Rohde M, Berthe-Corti L (2001) Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 51(6):1997–2006. doi:10.1099/00207713-51-6-1997

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100(2):221–230. doi:10.1099/00221287-100-2-221

    Article  CAS  PubMed  Google Scholar 

  • Davis DH, Doudoroff M, Stanier RY, Mandel M (1969) Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int J Syst Bacteriol 19(4):375–390. doi:10.1099/00207713-19-4-375

    Article  Google Scholar 

  • Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P, Murray RGE, Costilow RN et al (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 21–33

    Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376. doi:10.1007/BF01734359

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791. doi:10.2307/2408678

    Article  Google Scholar 

  • Ghosh W, Mandal S, Roy P (2006) Paracoccus bengalensis sp. nov., a novel sulfur-oxidizing chemolithoautotroph from the rhizospheric soil of an Indian tropical leguminous plant. Syst Appl Microbiol 29(5):396–403. doi:10.1016/j.syapm.2005.10.004

    Article  CAS  PubMed  Google Scholar 

  • Kampfer P, Lai WA, Arun AB, Young CC, Rekha PD, Martin K, Busse HJ, Chen WM (2012) Paracoccus rhizosphaerae sp. nov., isolated from the rhizosphere of the plant Crossostephium chinense (L.) Makino (Seremban). Int J Syst Evol Microbiol 62(Pt 11):2750–2756. doi:10.1099/ijs.0.039057-0

    Article  CAS  PubMed  Google Scholar 

  • Katayama Y, Hiraishi A, Kuraishi H (1995) Paracoccus thiocyanatus sp. nov., a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of Thiobacillus versutus to the genus Paracoccus as Paracoccus versutus comb. nov. with emendation of the genus. Microbiology 141(Pt6):1469–1477. doi:10.1099/13500872-141-6-1469

    Article  CAS  PubMed  Google Scholar 

  • Kelly DP, Rainey FA, Wood AP (2006) The genus Paracoccus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria, vol 5, 3rd edn. Springer, New York, pp 232–249

    Chapter  Google Scholar 

  • 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(Pt 3):716–721. doi:10.1099/ijs.0.038075-0

    Article  CAS  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120. doi:10.1007/BF01731581

    Article  CAS  PubMed  Google Scholar 

  • Lee M-J, Lee S-S (2013) Paracoccus limosus sp. nov., isolated from activated sludge in a sewage treatment plant. Int J Syst Evol Microbiol 63(Pt 4):1311–1316. doi:10.1099/ijs.0.035212-0

    Article  CAS  PubMed  Google Scholar 

  • Lee M, Woo SG, Park G, Kim MK (2011) Paracoccus caeni sp. nov., isolated from sludge. Int J Syst Evol Microbiol 61(Pt 8):1968–1972. doi:10.1099/ijs.0.017897-0

    Article  CAS  PubMed  Google Scholar 

  • Li WJ, Xu LH, Liu ZH, Jiang CL (2007) Actinomycete systematic—principle, methods and practice. Science Press, Beijing

    Google Scholar 

  • Li HF, Qu JH, Yang JS, Li ZJ, Yuan HL (2009) Paracoccus chinensis sp. nov., isolated from sediment of a reservoir. Int J Syst Evol Microbiol 59(Pt 11):2670–2674. doi:10.1099/ijs.0.004705-0

    Article  CAS  PubMed  Google Scholar 

  • Liu ZP, Wang BJ, Liu XY, Dai X, Liu YH, Liu SJ (2008) Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969. Int J Syst Evol Microbiol 58(Pt 1):257–261. doi:10.1099/ijs.0.65237-0

    Article  CAS  PubMed  Google Scholar 

  • Ludwig W, Mittenhuber G, Friedrich CG (1993) Transfer of Thiosphaera pantotropha to Paracoccus denitrificans. Int J Syst Bacteriol 43(2):363–367. doi:10.1099/00207713-43-2-363

    Article  CAS  PubMed  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (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 

  • 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 Methods 2(5):233–241. doi:10.1016/0167-7012(84)90018-6

    Article  CAS  Google Scholar 

  • Rainey FA, Kelly DP, Stackebrandt E, Burghardt J, Hiraishi A, Katayama Y, Wood AP (1999) A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov. Int J Syst Bacteriol 49(Pt 2):645–651. doi:10.1099/00207713-49-2-645

    Article  PubMed  Google Scholar 

  • Roh SW, Nam YD, Chang HW, Kim KH, Kim MS, Shin KS, Yoon JH, Oh HM, Bae JW (2009) Paracoccus aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 59(Pt 4):790–794. doi:10.1099/ijs.0.65759-0

    Article  CAS  PubMed  Google Scholar 

  • Rzhetsky A, Nei M (1992) Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 35(4):367–375. doi:10.1007/BF00161174

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning:a laboratory manual, vol 2. Cold Spring Harbor Laboratory, New York

    Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Technical note no. 101. Newark MIDI Inc., Newark

  • Sun LN, Zhang J, Kwon SW, He J, Zhou SG, Li SP (2013) Paracoccus huijuniae sp. nov., an amide pesticide-degrading bacterium isolated from activated sludge of a wastewater biotreatment system. Int J Syst Evol Microbiol 63(Pt 3):1132–1137. doi:10.1099/ijs.0.044180-0

    Article  CAS  PubMed  Google Scholar 

  • 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(10):2731–2739. doi:10.1093/molbev/msr121

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wang Y, Tang SK, Lou K, Mao PH, Jin X, Jiang CL, Xu LH, Li WJ (2009) Paracoccus saliphilus sp. nov., a halophilic bacterium isolated from a saline soil. Int J Syst Evol Microbiol 59(Pt 8):1924–1928. doi:10.1099/ijs.0.005918-0

    Article  CAS  PubMed  Google Scholar 

  • Yoon JH, Lee ST, Park YH (1998) Inter-and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 48(Pt 1):187–194. doi:10.1099/00207713-48-1-187

    Article  CAS  PubMed  Google Scholar 

  • Zhu S, Zhao Q, Zhang G, Jiang Z, Sheng H, Feng H, An L (2013) Paracoccus tibetensis sp. nov., isolated from Qinghai–Tibet Plateau permafrost. Int J Syst Evol Microbiol 63(Pt 5):1902–1905. doi:10.1099/ijs.0.041905-0

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was financially supported by COMRA program (No. DY125-15-R-01) and National Natural Science Foundation of China (41206160).

Author information

Authors and Affiliations

  1. Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, People’s Republic of China

    Gaiyun Zhang, Yanliu Yang & Shuang Wang

  2. Laboratory of Ocean & Coast Geology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, People’s Republic of China

    Xijie Yin

Authors
  1. Gaiyun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yanliu Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xijie Yin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shuang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gaiyun Zhang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 973 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, G., Yang, Y., Yin, X. et al. Paracoccus pacificus sp. nov., isolated from the Western Pacific Ocean. Antonie van Leeuwenhoek 106, 725–731 (2014). https://doi.org/10.1007/s10482-014-0242-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-014-0242-0

Keywords

Search

Navigation