Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis

Applied and Environmental Microbiology

Volumn 63, Issue 7, 1997, Pages 2802-2813

  Godon, Jean Jacques ^a   Zumstein, Emmanuelle ^a   Dabert, Patrick ^a   Habouzit, Frédéric ^a   Moletta, René ^a  

^a LABORATOIRE DE BIOTECHNOLOGIE DE L ENVIRONNEMENT   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; RIBOSOME DNA;

ANAEROBIC BACTERIUM; ARCHAEBACTERIUM; ARTICLE; BIODIVERSITY; BIOFILM; BIOREACTOR; CONTROLLED STUDY; DNA LIBRARY; DNA SEQUENCE; FLEXIBACTERACEAE; FLUIDIZED BED; METHANOBACTERIUM; MOLECULAR CLONING; NONHUMAN; PHYLOGENY; TAXONOMY; THERMOPLASMA;

ACTINOBACTERIA (CLASS); ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDES; CHLAMYDIA; CHLOROFLEXI; CYTOPHAGA; FIRMICUTES; FLEXIBACTER; FLEXIBACTERACEAE; METHANOBACTERIUM; METHANOBACTERIUM FORMICICUM; METHANOSARCINA BARKERI; METHANOSARCINA MAZEI; OTUS; PLANCTOMYCES; POSIBACTERIA; PROKARYOTA; PROTEOBACTERIA; SYNERGISTES; THERMOPLASMA;

EID: 0030872620     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.7.2802-2813.1997     Document Type: Article

References (35)

1. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Archer, D. B., and B. H. Kirsop. 1990. The microbiology and control of anaerobic digestion, p. 43-89. In A. Wheatley (ed.), Anaerobic digestion: a waste treatment technology. Elsevier Science Publishing Ltd., London, England.
3. Boivin-Jahns, V., A. Bianchi, R. Ruimy, J. Garcin, S. Daumas, and R. Christen. 1995. Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment. Appl. Environ. Microbiol. 61:3400-3406.
4. Bond, P. L., P. Hugenholtz, J. Keller, and L. L. Blackall. 1995. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl. Environ. Microbiol. 61:1910-1916.
5. Borneman, J., P. W. Skroch, K. M. O'Sullivan, J. A. Palus, N. G. Rumjanek, J. L. Jansen, J. Nienhuis, and E. W. Triplett. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62:1935-1943.
6. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
7. Buffière, P., R. Moletta, and C. Fonade. 1995. Continuous operations of fluidized bed bioreactor for anaerobic digestion: residence time effect on degradation kinetics. Biotechnol. Lett. 17:833-838.
8. Delong, E. F., K. Y. Wu, B. B. Prézelin, and R. V. M. Jovine. 1994. High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-697.
9. Devereux, R., and G. W. Mundfrom. 1994. A phylogenetic tree of 16S rRNA sequences from sulfate-reducing bacteria in a sandy marine sediment. Appl. Environ. Microbiol. 60:3437-3439.
10. Farrelly, V., F. A. Rayney, and E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-2801.
11. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of submarine microbial communities from the Atlantic and Pacific oceans. Appl. Environ. Microbiol. 59:1294-1302.
12. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-62.
13. Hales, B. A., C. Edwards, D. A. Ritchie, G. Hall, R. W. Pickup, and J. R. Saunders. 1996. Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl. Environ. Microbiol. 62:668-675.
14. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, Inc., New York, N.Y.
15. Kopckzynski, E. D., M. M. Bateson, and D. M. Ward. 1994. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60:746-748.
16. Maidak, B. L., N. Larsen, M. J. McCaughey, R. Overbeek, G. J. Olsen, K. Fogel, J. Blandy, and C. R. Woese. 1994. The Ribosomal Database Project. Nucleic Acids Res. 22:3485-3487.
17. Moyer, C. L., F. C. Dobbs, and D. M. Karl. 1994. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60:871-879.
18. Moyer, C. L., F. C. Dobbs, and D. M. Karl. 1995. Phylogenetic diversity of the bacterial community from a microbial mat at an active hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 61:1555-1562.
19. Ng, A., W. T. Melvin, and P. N. Hobson. 1994. Identification of anaerobic digester bacteria using a polymerase chain reaction method. Bioresour. Technol. 47:73-80.
20. Ohkuma, M., and T. Kudo. 1996. Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus. Appl. Environ. Microbiol. 62:461-468.
21. Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.
22. Paster, B. J., F. E. Dewhirst, S. M. Cooke, V. Fussing, L. K. Poulsen, and J. A. Breznak. 1996. Phylogeny of not-yet-cultured spirochetes from termite guts. Appl. Environ. Microbiol. 62:347-352.
23. Rölleke, S., G. Muyzer, C. Wawer, G. Wanner, and W. Lubitz. 1996. Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 62:2059-2065.
24. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
25. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
26. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-termination inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
27. Shieh, W. K., and J. D. Keenan. 1986. Fluidized bed biofilm reactor for wastewater treatment. Adv. Biochem. Eng. Biotechnol. 33:132-186.
28. Stackebrandt, E., W. Liesack, and B. M. Goebel. 1993. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J. 7:232-236.
29. Suzuki, M. T., and S. T. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
30. Ueda, T., Y. Suga, and T. Matsuguchi. 1995. Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur. J. Soil Sci. 46:415-421.
31. Voordouw, G., S. M. Armstrong, M. F. Reimer, B. Fouts, A. J. Telang, Y. Shen, and D. Gevertz. 1996. Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria. Appl. Environ. Microbiol. 62:1623-1629.
32. Weisburg, W. G., J. G. Tully, D. L. Rose, J. P. Petzel, H. Oyaizu, D. Yang, L. Mandelco, J. Sechrest, T. G. Lawrence, J. Van Etten, J. Maniloff, and C. R. Woese. 1989. A phylogenetic analysis of the mycoplasmas: basis for their classification. J. Bacteriol. 171:6455-6467.
33. Wilson, K. H., and R. B. Blitchington. 1996. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62:2273-2278.
34. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
35. Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.