Skip to main content
Log in

Members of the Candidate Division OP10 are spread in a variety of environments

  • Short Communication
  • Published:
World Journal of Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Our planet holds a huge bacterial diversity. Most of these bacteria have only been detected by their 16S rRNA gene sequences remaining to be cultured. Many are classified within Candidate Divisions. One them is the Candidate Division OP10. Analysis of environmental 16S rRNA gene sequences available in public repositories revealed the existence of numerous sequences clustering within the Candidate Division OP10 but currently unclassified or assigned to other bacterial phyla. Newly proposed 16S rRNA sequences multiply several fold the reported sequences for the Candidate Division OP10. This study showed that the Candidate Division OP10 is a diverse and broadly distributed bacterial phylum and represents a stable microbial component in different natural environments.

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

Access this article

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  • Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  Google Scholar 

  • Ashelford KE, Chuzhanova NA, Fry JC et al (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71:7724–7736. doi:10.1128/AEM.71.12.7724-7736.2005

    Article  CAS  Google Scholar 

  • Benson DA, Karsh-Mizrachi I, Lipman DJ et al (2000) GenBank. Nucleic Acids Res 28:15–18. doi:10.1093/nar/28.1.15

    Article  CAS  Google Scholar 

  • Bond PL, Hugenholtz P, Keller J et al (1995) Bacterial community structure of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol 61:1910–1916

    CAS  Google Scholar 

  • Chow ML, Radomski CC, McDermott JM et al (2002) Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol Ecol 42:347–357. doi:10.1111/j.1574-6941.2002.tb01024.x

    Article  CAS  Google Scholar 

  • Cole J, Chai B, Marsh T (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443. doi:10.1093/nar/gkg039

    Article  CAS  Google Scholar 

  • Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99:10494–10499. doi:10.1073/pnas.142680199

    Article  CAS  Google Scholar 

  • Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005) Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21:333–337. doi:10.1093/bioinformatics/bti008

    Article  CAS  Google Scholar 

  • Hugenholtz P, Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53:289–293. doi:10.1099/ijs.0.02441-0

    Article  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace N (1998) Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    CAS  Google Scholar 

  • Hughes JB, Hellmann JJ, Ricketts TH et al (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406. doi:10.1128/AEM.67.10.4399-4406.2001

    Article  CAS  Google Scholar 

  • Inagaki F, Nunoura T, Nakagawa S et al (2005) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean margin. Proc Natl Acad Sci USA 103:2815–2820. doi:10.1073/pnas.0511033103

    Article  Google Scholar 

  • Kanakratana P, Chanapan S, Pootanakit K (2004) Diversity and abundance of bacteria and archaea in the Bor Khlueng hot spring in Thailand. J Basic Microbiol 44:430–444. doi:10.1002/jobm.200410388

    Article  Google Scholar 

  • Kanz C, Aldebert P, Althorpe N et al (2005) The EMBL nucleotide sequence database. Nucleic Acids Res 33:D29–D33. doi:10.1093/nar/gki098

    Article  CAS  Google Scholar 

  • Lesaulnier C, Papamichail D, McCorkle S et al (2008) Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen. Environ Microbiol 10:926–941. doi:10.1111/j.1462-2920.2007.01512.x

    Article  CAS  Google Scholar 

  • Ley RE, Harris JK, Wilcox J et al (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 72:3685–3695. doi:10.1128/AEM.72.5.3685-3695.2006

    Article  CAS  Google Scholar 

  • Liles MR, Manske BF, Bintrim SB et al (2003) A census of rRNA genes and linked genomic sequences within soil metagenomic library. Appl Environ Microbiol 69:2684–2691. doi:10.1128/AEM.69.5.2684-2691.2003

    Article  CAS  Google Scholar 

  • Ludwig W, Strunk O, Klugbauer S et al (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554–568. doi:10.1002/elps.1150190416

    Article  CAS  Google Scholar 

  • Nogales B, Moore ERB, Llobet-Brossa E et al (2001) Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 67:1874–1884. doi:10.1128/AEM.67.4.1874-1884.2001

    Article  CAS  Google Scholar 

  • Pruesse E, Quast C, Knittel K et al (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196. doi:10.1093/nar/gkm864

    Article  CAS  Google Scholar 

  • Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394. doi:10.1146/annurev.micro.57.030502.090759

    Article  Google Scholar 

  • Stott MB, Crowe MA, Mountain BW et al (2008) Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 10:2030–2041. doi:10.1111/j.1462-2920.2008.01621.x

    Article  CAS  Google Scholar 

  • Strimmer K, von Haeseler A (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969

    CAS  Google Scholar 

  • Sugawara H, Ogasawara O, Okubo K (2008) DDBJ with new system and face. Nucleic Acids Res 36:D22–D24. doi:10.1093/nar/gkm889

    Article  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix-choice. Nucleic Acids Res 22:4673–4680. doi:10.1093/nar/22.22.4673

    Article  CAS  Google Scholar 

  • Urbach E, Vergin KL, Young L et al (2001) Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnol Oceanogr 46:557–572

    CAS  Google Scholar 

  • von Wintzingerode F, Slent B, Hegemann W (1999) Phylogenetic analysis of an anaerobic, trichlorobenzene-transforming microbial consortium. Appl Environ Microbiol 65:283–286

    Google Scholar 

  • Walker JJ, Pace NR (2007) Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems. Appl Environ Microbiol 73:3497–3504. doi:10.1128/AEM.02656-06

    Article  CAS  Google Scholar 

  • Wu X, Xi W, Ye W et al (2007) Bacterial community composition of a shallow hypertrophic freshwater lake in China, revealed by 16S rRNA gene sequences. FEMS Microbiol Ecol 61:85–96. doi:10.1111/j.1574-6941.2007.00326.x

    Article  CAS  Google Scholar 

Download references

Acknowledgment

The authors acknowledge funding from the Government of Andalusia (BIO288).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to J. M. Gonzalez.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Portillo, M.C., Gonzalez, J.M. Members of the Candidate Division OP10 are spread in a variety of environments. World J Microbiol Biotechnol 25, 347–353 (2009). https://doi.org/10.1007/s11274-008-9895-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11274-008-9895-z

Keywords

Navigation