Journal of Microbiology and Biotechnology
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2012 ; 22(4): 457~461

AuthorAmelia-Elena Rotaru, Regina Schauer, Christina Probian, Marc Mussmann, Jens Harder
AffiliationDepartment of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
TitleVisualization of Candidate Division OP3 Cocci in Limonene-Degrading Methanogenic Cultures
PublicationInfo J. Microbiol. Biotechnol.2012 ; 22(4): 457~461
AbstractMembers of candidate division OP3 were detected in 16S rRNA gene clone libraries from methanogenic enrichment cultures that utilized limonene as a carbon and energy source. We developed probes for the visualization of OP3 cells. In situ hybridization experiments with newly designed OP3-specific probes [OP3-565 and Eub-338(VI)] revealed abundant small OP3 cocci attached to larger cells. Syntrophic Deltaproteobacteria, OP3 cells, and methanogens affiliating with Methanoculleus and Methanosaeta formed the limonenedegrading community.
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Keywordscandidate division OP3, monoterpene, limonene, hydrocarbon degradation, methanogenesis, syntrohpy
References
  1. Alfreider, A., C. Vogt, and W. Babel. 2002. Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis. Syst. Appl. Microbiol. 25: 232-240.
    Pubmed CrossRef
  2. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNAtargeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
    Pubmed Pubmed Central
  3. Boone, D. R., R. L. Johnson, and Y. Liu. 1989. Diffusion of the interspecies electron carriers H(2) and formate in methanogenic ecosystems and its implications in the measurement of K(m) for H(2) or formate uptake. Appl. Environ. Microbiol. 55: 17351741.
    Pubmed Pubmed Central
  4. Chouari, R., D. Le Paslier, P. Daegelen, P. Ginestet, J. Weissenbach, and A. Sghir. 2003. Molecular evidence for novel Planctomycete diversity in a municipal wastewater treatment plant. Appl. Environ. Microbiol. 69: 7354-7363.
    Pubmed CrossRef Pubmed Central
  5. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89: 5685-5689.
    CrossRef
  6. Glöckner, J., M. Kube, P. M. Shrestha, M. Weber, F. O. Glöckner, R. Reinhardt, and W. Liesack. 2010. Phylogenetic diversity and metagenomics of candidate division OP3. Environ. Microbiol. 12: 1218-1229.
    Pubmed CrossRef
  7. Harder, J. and S. Foss. 1999. Anaerobic formation of the aromatic hydrocarbon p-cymene from monoterpenes by methanogenic enrichment cultures. Geomicrobiol. J. 16: 295-305.
    CrossRef
  8. Harmsen, H. J., B. L. Van Kuijk, C. M. Plugge, A. D. Akkermans, W. M. De Vos, and A. J. Stams. 1998. Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfatereducing bacterium. Int. J. Syst. Bacteriol. 48: 1383-1387.
    Pubmed CrossRef
  9. Hicks, R. E., R. I. Amann, and D. A. Stahl. 1992. Dual staining of natural bacterioplankton with 4',6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S ribosomal-RNA sequences. Appl. Environ. Microbiol. 58:2158-2163.
    Pubmed Pubmed Central
  10. Holmes, D. E., K. P. Nevin, T. L. Woodard, A. D. Peacock, and D. R. Lovley. 2007. Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell. Int. J. Syst. Evol. Microbiol. 57: 701-707.
    Pubmed CrossRef
  11. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366-376.
    Pubmed Pubmed Central
  12. Hyatt, D. C., B. Youn, Y. Zhao, B. Santhamma, R. M. Coates, R. B. Croteau, and C. Kang. 2007. Structure of limonene synthase, a simple model for terpenoid cyclase catalysis. Proc. Natl. Acad. Sci. USA 104: 5360-5365.
    Pubmed CrossRef Pubmed Central
  13. Jetten, M. S. M., A. J. M. Stams, and A. J. B. Zehnder. 1990. Acetate threshold values and acetate activating enzymes in methanogenic bacteria. FEMS Microbiol. Lett. 73: 339-344.
    CrossRef
  14. Kane, M. D., L. K. Poulsen, and D. A. Stahl. 1993. Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S ribosomal-RNA sequences. Appl. Environ. Microbiol. 59: 682-686.
    Pubmed Pubmed Central
  15. Kreuzwieser, J., J. P. Schnitzler, and R. Steinbrecher. 1999. Biosynthesis of organic compounds emitted by plants. Plant Biol. 1: 149-159.
    CrossRef
  16. Loy, A., A. Lehner, N. Lee, J. Adamczyk, H. Meier, J. Ernst, et al. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68: 5064-5081.
    Pubmed CrossRef Pubmed Central
  17. Loy, A., F. Maixner, M. Wagner, and M. Horn. 2007. ProbeBase - an online resource for rRNA-targeted oligonucleotide probes:New features 2007. Nucleic Acid Res. 35: D800-D804.
    Pubmed CrossRef Pubmed Central
  18. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, et al. 2004. ARB: A software environment for sequence data. Nucleic Acid Res. 32: 1363-1371.
    Pubmed CrossRef Pubmed Central
  19. Manz, W., R. Amann, W. Ludwig, M. Vancanneyt, and K. H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142: 1097-1106.
    Pubmed CrossRef
  20. McInerney, M. J., C. G. Struchtemeyer, J. Sieber, H. Mouttaki, A. J. Stams, B. Schink, et al. 2008. Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Ann. N.Y. Acad. Sci. 1125: 58-72.
    Pubmed CrossRef
  21. Pernthaler, A., J. Pernthaler, and R. Amann. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68:3094-3101.
    Pubmed CrossRef Pubmed Central
  22. Pilhofer, M., K. Rappl, C. Eckl, A. P. Bauer, W. Ludwig, K. H. Schleifer, and G. Petroni. 2008. Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and phylogenetic comparison with rRNA genes. J. Bacteriol. 190: 3192-3202.
    Pubmed CrossRef Pubmed Central
  23. Pruesse, E., C. Quast, K. Knittel, B. M. Fuchs, W. Ludwig, J. Peplies, and F. O. Glockner. 2007. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188-7196.
    Pubmed CrossRef Pubmed Central
  24. Rautio, M., E. Eerola, M. L. Vaisanen-Tunkelrott, D. Molitoris, P. Lawson, M. D. Collins, and H. Jousimies-Somer. 2003. Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources. Syst. Appl. Microbiol. 26: 182-188.
    Pubmed CrossRef
  25. Rotaru, A. E., C. Probian, H. Wilkes, and J. Harder. 2010. Highly enriched Betaproteobacteria growing anaerobically with p-xylene and nitrate. FEMS Microbiol. Ecol. 71: 460-468.
    Pubmed CrossRef
  26. Shigematsu, T., S. Era, Y. Mizuno, K. Ninomiya, Y. Kamegawa, S. Morimura, and K. Kida. 2006. Microbial community of a mesophilic propionate-degrading methanogenic consortium in chemostat cultivation analyzed based on 16S rRNA and acetate kinase genes. Appl. Microbiol. Biotechnol. 72: 401-415.
    Pubmed CrossRef
  27. Stackebrandt, E. and J. Ebers. 2006. Taxonomic parameters revisited: Tarnished gold standards. Microbiol. Today 33: 153-156.
  28. Stahl, D. A. and R. Amann. 1991. Development and application of nucleic acid probes. In E. Stackebrandt and M. Goodfellow (eds.). Nucleic Acid Techniques in Bacterial Systematic. John Wiley & Sons Ltd, Chichester, England.
  29. Tang, Y. Q., T. Shigematsu, S. Morimura, and K. Kida. 2007. Effect of dilution rate on the microbial structure of a mesophilic butyrate-degrading methanogenic community during continuous cultivation. Appl. Microbiol. Biotechnol. 75: 451-465.
    Pubmed CrossRef
  30. Thiele, J. H. and J. G. Zeikus. 1988. Control of interspecies electron flow during anaerobic digestion: Significance of formate transfer versus hydrogen transfer during syntrophic methanogenesis in flocs. Appl. Environ. Microbiol. 54: 20-29.
    Pubmed Pubmed Central
  31. Wagner, M. and M. Horn. 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotechnol. 17: 241-249.
    Pubmed CrossRef
  32. Zellner, G., P. Messner, J. Winter, and E. Stackebrandt. 1998. Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in North-Sumatra, Indonesia. Int. J. Syst. Bacteriol. 48:1111-1117.
    Pubmed CrossRef
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