A comparison of the use of in vitro-transcribed and native rRNA for the quantification of microorganisms in the environment

Microbial Ecology

Volumn 36, Issue 3, 1998, Pages 362-371

  McMahon, K D ^a,c   Stahl, D A ^b   Raskin, L ^a  

^a University of Illinois at Urbana Champaign   (United States)

^b Northwestern University   (United States)

^c Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DENATURATION; ENVIRONMENT; MICROORGANISM; OLIGONUCLEOTIDE PROBE; QUANTITATIVE HYBRIDIZATION; RIBOSOMAL RNA;

METHODOLOGY; MICROORGANISM; POPULATION ESTIMATION;

EID: 0032412331     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002489900122     Document Type: Article

References (38)

1. Alm EW, Oerther DB, Larsen N, Stahl DA, Raskin L (1996) The oligonucleotide probe database. Appl Environ Microbiol 62:3557-3559
2. Alm EW, Stahl DA Evaluation of key parameters for extraction of native rRNA from different environmental matrices. In preparation
3. Aim EW, Zheng D, Raskin L The presence of humic substances and DNA in RNA extracts affects quantitative hybridization results. In preparation
4. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919-1925
5. Amann RI, Ludwig W, Schleifer K (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
6. 2 or formate uptake. Appl Environ Microbiol 55:1735-1741
7. DeLong EF, Wu KY, Prezelin BB, Jovine RVM (1994) High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-697
8. de los Reyes FL, Ritter W, Raskin L (1997) Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems. Appl Environ Microbiol 63:1107-1117
9. Griffin ME, McMahon KD, Mackie RI, Raskin L (1998) Methanogenic population dynamics during startup of anaerobic digesters treating municipal solid waste and biosolids. Biotech Bioengr 57:342-355
10. Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD (1997) Oligonucleotide microchips of genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63:2397-2402
11. Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58:10-26
12. Hansen KH, Ahring BK, Raskin L Importance of syntrophic fatty acid-beta-oxidizing bacteria in a mesophilic biogas reactor determined by oligonucleotide probe hybridizations. In preparation
13. Harmsen HJM, Akkermans ADL, Stams AJM, deVos WM (1996) Population dynamics of propionate-oxidizing bacteria under methanogenic and sulfidogenic conditions in anaerobic granular sludge. Appl Environ Microbiol 62:2163-2168
14. Harmsen HJM, Kengen HMP, Akkermans ADL, Stams AJM (1995) Phylogenetic analysis of two syntrophic propionate-oxidizing bacteria in enrichment cultures. Syst Appl Microbiol 18:67-73
15. Harmsen HJM, Kengen HMP, Akkermans ADL, Stams AJM, deVos WM (1996) Detection and localization of syntrophic propionate-oxidizing bacteria in granular sludge by in situ hybridization using 16S rRNA-based oligonucleotide probes. Appl Environ Microbiol 62:1656-1663
16. Hovanec TA, DeLong E (1996) Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria. Appl Environ Microbiol 62:2888-2896
17. Kane MD, Poulsen LK, Stahl D (1993) Monitoring the enrichment and isolation of sulfate-reducing bacteria using oligonucleotide probe hybridization probes designed from environmental derived 16S rRNA sequences. Appl Environ Microbiol 59:682-686
18. Kowalak JA, Bruenger E, Hashizume T, Peitier JM, Ofengand J, McCloskey JA (1996) Structural characterization of U*-1915 in domain IV from Escherichia coli 23S ribosomal RNA as 3-methylpseudouridine. Nucleic Acids Res 24:688-693
19. MacGregor BJ, Moser DP, Alm EW, Nealson KH, Stahl DA (1997) Crenarchaeota in Lake Michigan sediment. Appl Environ Microbiol 63:1178-1181
20. Massana R, Murray AE, Preston CM, DeLong EF (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel. Appl Environ Microbiol 63:50-56
21. McMahon KD, Stroot PG, Mackie RI, Raskin L (1998) Anaerobic co-digestion of municipal solid waste and biosolids under various mixing conditions - II. Microbial population dynamics. Submitted for publication
22. McMahon KD, Raskin L Microbial population dynamics linked to performance during startup of anaerobic digesters treating municipal solid waste and sewage sludge. In preparation
23. Oerther DB, Raskin L Use of 5-nitroindole in universal oligonucleotide probe design for quantitative molecular microbial ecology studies. In preparation
24. Oerther DB, de los Reyes FL, Raskin L (1998) Interfacing phylogenetic oligonucleotide probe hybridizations with representations of microbial populations in mathematical models of activated sludge processes. Modelling and Microbiology of Activated Sludge Processes, Kollekolle, Denmark, March 16-18
25. Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by ribosomal rRNA sequences. In: Marshall KC (ed) Advances in Microbial Ecology, Vol 9, Plenum Press, pp 1-55
26. Polz MF, Cavanaugh CM (1997) A simple method for quantification of uncultured microorganisms in the environment based on in vitro transcription of 16S rRNA. Appl Environ Microbiol 63:1028-1033
27. Raskin L, Capman WC, Sharp R, Poulsen LK, Stahl DA (1997) Molecular ecology of gastrointestinal ecosystems. In: Mackie RI, White BA, Isaacson RE (eds) Gastrointestinal Microbiology, Vol 2, Gastrointestinal Microbes and Host Interactions, Chapman & Hall, pp 243-298
28. Raskin L, Stromley JM, Rittmann BE, Stahl DA (1994) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol 60: 1232-1240
29. Raskin L, Zheng D, Griffin ME, Stroot PG, Misra P (1995) Characterization of microbial communities in anaerobic bioreactors using molecular probes. Antonie van Leeuwenhoek 68:297-308
30. Saunders NA, Harrison TG, Haththotuwa A, Kachwalla N, Taylor AG (1990) A method for typing strains of Legionella pneumophila serogroup 1 by analysis of restriction fragment length polymorphisms. J Med Microbiol 31:45-55
31. Stahl DA, Flesher B, Mansfield HR, Montgomery L (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl Environ Microbiol 54:1079-1084
32. Stams AJM (1994) Metabolic interactions between anaerobic bacteria in methanogenic environments. Antonie van Leeuwenhoek 66:271-294
33. Stams AJM, van Dijk JB, Dijkema C, Plugge CM (1993) Growth of syntrophic propionate-oxidizing bacteria with fumarate in the absence of methanogenic bacteria. Appl Environ Microbiol 59:1114-1119
34. Triana-Alonso FJ, Dabrowski M, Wadzack J, Nierhaus KH (1995) Self-coded 3′-extension of run-off transcripts produces aberrant products during in vitro transcription with T7 RNA polymerase. J Biol Chem 270:6298-6307
35. Wallrabenstein C, Hauschild E, Schink B (1995) Syntrophobacter pfennigii sp. nov., new syntrophically propionate-oxidizing anaerobic growing in pure culture with propionate and sulfate. Arch Microbiol 164:346-352
36. Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. In: Marshall KC (ed) Advances in Microbial Ecology, Vol 12, Plenum Press, pp 219-286
37. Zhao H, Yang D, Woese CR, Bryant MP (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
38. Zheng D, Alm EW, Stahl DA, Raskin L (1996) Characterization of universal small subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 62:4504-4513