Quantification of syntrophic fatty acid-β-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridization

Applied and Environmental Microbiology

Volumn 65, Issue 11, 1999, Pages 4767-4774

  Hansen, Kaare H ^a,b   Ahring, Birgitte K ^b   Raskin, Lutgarde ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; BIOGAS; RIBOSOME RNA;

ARTICLE; BACTERIAL COUNT; BACTERIUM DETECTION; BIOREACTOR; CONTROLLED STUDY; FATTY ACID OXIDATION; GRAM POSITIVE BACTERIUM; METHANOGENESIS; METHANOMICROBIALES; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; RNA HYBRIDIZATION; RNA SEQUENCE;

SYNTROPHOMONAS SAPOVORANS; SYNTROPHOMONAS WOLFEI;

EID: 0032752384     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.11.4767-4774.1999     Document Type: Article

References (45)

1. Ahring, B. K. 1995. Methanogenesis in thermophilic biogas reactors. Antonie Leeuwenhoek 67:91-102.
2. Ahring, B. K., I. Angelidaki, and K. Johansen. 1992. Anaerobic treatment of manure together with industrial waste. Water Sci. Technol. 25:311-318.
3. Ahring, B. K., and P. Westermann. 1987. Thermophilic anaerobic degradation of butyrate by a butyrate-utilizing bacterium in coculture and triculture with methanogenic bacteria. Appl. Environ. Microbiol. 53:429-433.
4. Alm, E. W., and D. Stahl. Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments. Submitted for publication.
5. Alm, E. W., D. B. Oerther, N. Larsen, D. A. Stahl, and L. Raskin. 1996. The oligonucleotide probe database. Appl. Environ. Microbiol. 62:3557-3559.
6. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
7. 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.
8. Angelidaki, I., and B. K. Ahring. 1995. Establishment and characterization of an anaerobic thermophilic (55°C) enrichment culture degrading long-chain fatty acids. Appl. Environ. Microbiol. 61:2442-2445.
9. Angelidaki, I., S. P. Petersen, and B. K. Ahring. 1990. Effects of lipids on thermophilic anaerobic digestion and reduction of lipid inhibition upon addition of bentonite. Appl. Microbiol. Biotechnol. 33:469-472.
10. de los Reyes, F. L., W. Ritter, and L. Raskin. 1997. Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems. Appl. Environ. Microbiol. 63:1107-1117.
11. de los Reyes, M. F., F. L. de los Reyes, III, M. Hernandez, and L. Raskin. 1998. Quantification of Gordona amarae strains in foaming activated sludge and anaerobic digester systems with oligonucleotide hybridization probes. Appl. Environ. Microbiol. 64:2503-2512.
12. Dorsch, M., and E. Stackebrandt. 1992. Some modifications in the procedure of direct sequencing of PCR amplified 16S rDNA. J. Microbiol. Methods 16:271-279.
13. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
14. Gray, N. D., R. W. Pickup, J. G. Jones, and I. M. Head. 1997. Ecophysiological evidence that Achromatium oxaliferum is responsible for the oxidation of reduced sulfur species to sulfate in a freshwater sediment. Appl. Environ. Microbiol. 63:1905-1910.
15. Greenberg, A. E., L. S. Clesceri, and A. D. Eaton (ed.). 1992. Standard methods for the examination of water and wastewater, 18th ed. American Public Health Association, Washington, D.C.
16. Griffin, M. E., K. D. McMahon, R. I. Mackie, and L. Raskin. 1998. Methanogenic population dynamics during start-up of anaerobic digesters treating municipal solid waste and biosolids. Biotechnol. Bioeng. 57:342-355.
17. 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 rRNA sequences. Appl. Environ. Microbiol. 59:682-686.
18. Loakes, D., and D. M. Brown. 1994. 5-Nitroindole as an universal base analogue. Nucleic Acids Res. 22:4039-4043.
19. Lorowitz, W. H., H. Zhao, and M. P. Bryant 1989. Syntrophomonas wolfei subsp. saponavida subsp. nov., a long-chain fatty-acid-degrading, anaerobic, syntrophic bacterium; Syntrophomonas wolfei subsp. wolfei subsp. nov.; and emended descriptions of the genus and species. Int. J. Syst. Bacteriol. 39: 122-126.
20. Maidak, B. L., N. Larsen, M. J. McCaughey, R. Overbeek, G. J. Olsen, K. Forgel, J. Blanby, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-111.
21. McInerney, M. J., M. P. Bryant, R. B. Hespell, and J. W. Costerton. 1981. Syntrophomonas wolfei gen. nov. sp. nov., an anaerobic, syntrophic, fatty acid-oxidizing bacterium. Appl. Environ. Microbiol. 41:1029-1039.
22. McMahon, K. D., D. A. Stahl, and L. Raskin. 1998. A comparison of the use of in vitro-transcribed and native rRNA for the quantification of microorganisms in the environment. Microb. Ecol. 36:362-371.
23. Porter, K. G., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflorae. Limnol. Oceanogr. 25:943-948.
24. Postgate, J. R. 1963. Versatile medium for the enumeration of sulfate-reducing bacteria. Appl. Microbiol. 11:265-267.
25. Raskin, L., L. K. Poulsen, D. R. Noguera, B. E. Rittmann, and D. A. Stahl. 1994. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 60: 1241-1248.
26. Raskin, L., J. M. Stromley, B. E. Rittmann, and D. A. Stahl. 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1232-1240.
27. Raskin, L., D. Zheng, M. E. Griffin, P. G. Stroot, and P. Misra. 1995. Characterization of microbial communities in anaerobic bioreactors using molecular probes. Antonie Leeuwenhoek 68:297-308.
28. Raskin, L., W. C. Capman, R. Sharp, L. K. Poulsen, and D. A. Stahl. 1997. Molecular ecology of gastrointestinal ecosystems, p. 243-298. In R. I. Mackie, B. A. White, and R. E. Isaacson (ed.), Gastrointestinal microbiology, vol. 2. Gastrointestinal microbes and host interactions. Chapman & Hall, New York, N.Y.
29. Roy, F., E. Samain, H. C. Dubourguir, and G. Albagnac. 1986. Syntrophomonas sapovorans sp. nov., a new obligately proton reducing anaerobe oxidizing saturated and unsaturated long chain fatty acids. Arch. Microbiol. 145:142-147.
30. Saunders, N. A., T. G. Harrison, A. Haththotuwa, N. Kachwalla, and A. G. Taylor. 1990. A method for typing strains of Legionella pneumophila serogroup 1 by analysis of restriction fragment length polymorphism. J. Med. Microbiol. 31:45-55.
31. Schink, B. 1997. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61:262-280.
32. Sørensen, A. H., and B. K. Ahring. 1993. Measurement of the specific methanogenic activity of anaerobic digestor biomass. Appl. Microbiol. Biotechnol. 40:427-431.
33. Soto, M., R. Méndez, and J. M. Lema. 1993. Methanogenic and non-methanogenic activity tests. Theoretical basis and experimental set up. Water Res. 27:1361-1376.
34. Stahl, D. A., B. Flesher, H. R. Mansfield, and L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1079-1084.
35. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley and Sons, Ltd., New York, N.Y.
36. Svetlitshnyi, V., F. Rainey, and J. Wiegel. 1996. Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing short-and long-chain fatty acids in syntrophic coculture with a methanogenic archaeum. Int. J. Syst. Bacteriol. 46:1131-1137.
37. Tafdrup, S. 1994. Centralized biogas plants combine agricultural and environmental benefits with energy production. Water Sci. Technol. 30:133-141.
38. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 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.
39. Tijssen, P. 1993. Hybridization of nucleic acid probes, part I. Theory and nucleic acid preparation, p. 268. Elsevier Science Publishers B. V., Amsterdam, The Netherlands.
40. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703.
41. Westermann, P., B. K. Ahring, and R. A. Mah. 1989. Threshold acetate concentrations for acetate catabolism by aceticlastic methanogenic bacteria. Appl. Environ. Microbiol. 55:514-515.
42. Zhao, H., D. Yang, C. R. Woese, and M. P. Bryant. 1990. Assignment of Clostridium bryantii to Syntrophospora bryantii gen. nov., comb. nov. on the basis of a 16S rRNA sequence analysis of its crotonate-grown pure culture. Int. J. Syst. Bacteriol. 40:40-44.
43. Zhao, H., D. Yang, C. R. Woese, and M. P. Bryant. 1993. Assignment of fatty acid-β-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses. Int. J. Syst. Bacteriol. 43:278-286.
44. Zheng, D., E. W. Alm, D. A. Stahl, and L. Raskin. 1996. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol. 62:4504-4513.
45. Zheng, D., and L. Raskin. Unpublished data.