Skip to main content

Paracoccus niistensis sp. nov., isolated from forest soil, India

Antonie van Leeuwenhoek volume 99, pages 501–506 (2011)Cite this article

Abstract

A Gram-negative, non-motile, catalase-positive and oxidase-positive, aerobic bacterium designated as NII-0918T was isolated from soil sample in Western ghat forest, India. 16S rRNA gene sequence analysis showed that strain NII-0918T belongs to the subclass α-Proteobacteria, being related to the genus Paracoccus, and sharing highest sequence similarity with Paracoccus chinensis NBRC 104937T (99.4%), Paracoccus marinus NBRC 100640T (97.3%), Paracoccus koreensis Ch05T (97.1%) and Paracoccus kondratievae GBT (97.0%). Other members of Paracoccus showed below 97.0% similarity. The DNA–DNA hybridization values between these four strains and NII-0918T were 44.7, 28, 32 and 41%, respectively. The major fatty acids of strain NII-0918T were summed feature 7 (C18:1 ω7c/ω 9t/ω 12t) (83.0%) and C18:0 (12.5%). Ubiquinone Q-10 was detected as the major respiratory quinone. The G+C content of genomic DNA of NII-0918T was 66.6 mol%. On the basis of physiological, morphological, chemotaxonomical and DNA–DNA hybridization data, it is proposed that strain NII-0918T should be placed as a novel species, for which we propose Paracoccus niistensis sp. nov. The type strain is NII-0918T (CCTCC AA 209055T = NCIM 5340T = KCTC 22789T).

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

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

Fig. 1

References

  • Chen MH, Sheu SY, Chen CA, Wang JT, Chen WM (2010) Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera. Int J Syst Evol Microbiol. doi:ijs.0.023333-0v1-ijs.0.023333-0

  • Chun J, Lee J-H, 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 sequence. Int J Syst Evol Microbiol 57:2259–2261

    CAS  Article  PubMed  Google Scholar 

  • Daneshvar MI, Hollis DG, Weyant RS, Steigerwalt AG, Whitney AM (2003) Paracoccus yeeii sp. nov. (formerly CDC Group EO-2), a novel bacterial species associated with human infection. J Clin Microbiol 41:1289–1294

    Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Deng ZS, Zhao LF, Xu L, Kong ZY, Zhao P, Qin W, Chang JL, Wei GH (2010) Paracoccus sphaerophysae sp. nov., a siderophore-producing, endophytic bacterium isolated from root nodules of a Sphaerophysa salsula growing in northwestern China. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.021071-0

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

    CAS  Article  PubMed  Google Scholar 

  • Felsenstein J (1985) Conference limits on phylogenies: an approach using the bootstrap. Evolution 39:783–789

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specified tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Fitch WM, Margoliash E (1967) Construction of a phylogenetic tree. Science 155:279–284

    CAS  Article  PubMed  Google Scholar 

  • Gerhardt P, Krieg NR (1981) General characterization. In: Krieg NR (ed) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 409–443

    Google Scholar 

  • Huß VAR, Festl H, Schleifer KH (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192

    Google Scholar 

  • Jahnke KD (1992) BASIC computer program for evaluation of spectroscopic DNA renaturation data from GILFORD SYSTEM 2600 spectrophotometer on a PC/XT/AT type personal computer. J Microbiol Methods 15:61–73

    Article  Google Scholar 

  • John P, Whatley FR (1975) Paracoccus denitrificans and the evolutionary origin of the mitochondrion. Nature 254:495–498

    CAS  Article  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

    Google Scholar 

  • Khan ST, Takaichi S, Harayama S (2008) Paracoccus marinus sp. nov., an adonixanthin diglucoside-producing bacterium isolated from coastal seawater in Tokyo Bay. Int J Syst Evol Microbiol 58:383–386

    CAS  Article  PubMed  Google Scholar 

  • Kim YO, Kong HJ, Park S, Kang SJ, Kim KK, Moon DY, Oh TK, Yoon JH (2010) Paracoccus fistulariae sp. nov., a lipolytic bacterium isolated from bluespotted cornetfish, Fistularia commersonii. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.021808-0

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

    CAS  Article  PubMed  Google Scholar 

  • Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP 18) and a silver loaded ion exchange as stationary phases. J Liq Chromatogr 5:2359–2387

    CAS  Article  Google Scholar 

  • Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China) and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  PubMed  Google Scholar 

  • Li H-F, Qu J-H, Yang J-S, Li J-Z, Yuan H-L (2009) Paracoccus chinensis sp. nov., isolated from sediment of a reservoir. Int J Syst Evol Microbiol 59:2670–2674

    CAS  Article  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 the genus Paracoccus Davis 1969. Int J Syst Evol Microbiol 58:257–261

    CAS  Article  PubMed  Google Scholar 

  • Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218

    CAS  Article  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

    CAS  Article  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 isoprenoid quinines and polar lipids. J Microbiol Methods 2:233–241

    CAS  Article  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 59:790–794

    CAS  Article  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:1–6

    Google Scholar 

  • Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general, molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic Note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    CAS  Article  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evolu 24:1596–1599

    CAS  Article  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 59:1924–1928

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgment

The authors would like to thank CSIR Task force network programme on Exploration of India’s Rich Microbial Diversity (NWP 0006) for providing the financial support.

Author information

Authors and Affiliations

  1. Biological Oceanography Division, National Institute of Oceanography, Dona Paula, Panaji, 403004, Goa, India

    Syed G. Dastager

  2. National Institute for Interdisciplinary Science and Technology (CSIR), Trivandrum, 695019, India

    C. K. Deepa & Ashok Pandey

  3. Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People’s Republic of China

    Wen-Jun Li & Shu-Kun Tang

Authors
  1. Syed G. Dastager
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. K. Deepa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wen-Jun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shu-Kun Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ashok Pandey
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Syed G. Dastager.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Dastager, S.G., Deepa, C.K., Li, WJ. et al. Paracoccus niistensis sp. nov., isolated from forest soil, India. Antonie van Leeuwenhoek 99, 501–506 (2011). https://doi.org/10.1007/s10482-010-9515-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-010-9515-4

Keywords

  • Paracoccus niistensis sp. nov
  • Polyphasic taxonomy
  • 16S rRNA