In situ reverse transcription, an approach to characterize genetic diversity and activities of prokaryotes

Applied and Environmental Microbiology

Volumn 63, Issue 12, 1997, Pages 4907-4913

  Chen, Feng ^a   González, José M ^a   Dustman, Wendy A ^a   Moran, Mary Ann ^a   Hodson, Robert E ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RIBOSOME RNA; SEA WATER; TOLUENE;

ARTICLE; BACTERIUM DETECTION; BIODIVERSITY; FLUORESCENCE; GENE EXPRESSION; NONHUMAN; PHYLOGENY; PROKARYOTE; PSEUDOMONAS PUTIDA; REVERSE TRANSCRIPTION; RNA ANALYSIS; RNA TRANSCRIPTION;

BACTERIA (MICROORGANISMS); MICROBULBIFER HYDROLYTICUS; PROKARYOTA; PSEUDOMONAS; PSEUDOMONAS PUTIDA; SAGITTULA STELLATA;

EID: 0342813011     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.12.4907-4913.1997     Document Type: Article

References (36)

1. Alfreider, A., J. Pernthaler, R. Amann, B. Sattler, F.-O. Glockner, A. Wille, and R. Psenner. 1996. Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Appl. Environ. Microbiol. 62:2138-2144.
2. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisolm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing a mixed microbial population. Appl. Environ. Microbiol. 56:1919-1925.
3. 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.
4. Chen, F., W. Dustman, M. A. Moran, and R. E. Hudson. In situ PCR methodologies for visualization of microscale genetic and taxonomic diversities of prokaryotic communites. In A. D. L. Akkermans, J. D. van Elsas, and F. J. DeBruijn (ed.), Molecular microbial ecology manual, suppl. 3, in press. Kluwer Academic Publishers, Dordrecht, The Netherlands.
5. Chen, F., W. A. Dustman, and R. E. Hodson. Microscopic detection of the toluene dioxygenase gene and its expression inside bacterial cells in seawater using prokaryotic in situ PCR. Submitted for publication.
6. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1362.
7. Garg, R. P., M. A. Moran, W. A. Dustman, K. Jordan, and R. E. Hudson. Detection of individual bacteria expressing nitrogen fixation genes using in situ PCR. Submitted for publication.
8. Gibson, D. T., J. R. Koch, and R. E. Kallio. 1968. Oxidative degradation of aromatic hydrocarbons by microorganisms. I. Enzymatic formation of catechol from benzene. Biochemistry 7:2653-2662.
9. Gibson, D. T., M. Hensley, H. Yoshioka, and T. J. Mabry. 1970. Formation of (+)-cis-2,3,-dihydroxy-1-methylcyclohexa-4,6-diene from toluene by Pseudomonas putida. Biochemistry 9:1626-1630.
10. Giovannoni, S. J., E. F. DeLong, G. J. Olsen, and N. R. Pace. 1988. Phylogenetic group-specific oligonucleotide probes for identification of single microbial cells. J. Bacteriol. 170:720-726.
11. González, J. M., W. B. Whitman, R. E. Hodson, and M. A. Moran. 1996. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture. Appl. Environ. Microbiol. 62:4433-4440.
12. González, J. M., W. B. Whitman, R. E. Hodson, and M. A. Moran. Variation in bacterial community structure among replicate marine microcosms as determined by 16S rRNA oligonucleotide probes. Submitted for publication.
13. Gosden, J. R. 1997. PRINS and in situ PCR protocols. Methods Mol. Biol. 71:1-165.
14. Grünewald-Janho, S., J. Keesey, M. Leous, R. V. Miltenburg, and C. Schroeder (ed.). 1996. Nonradioactive in situ hybridization application manual, 2nd ed. Boehringer Mannheim GmbH Biochemica, Mannheim, Germany.
15. Gu, J. 1997. In situ polymerase chain reaction and related technology. Eaton Publishing Co., Natick, Mass.
16. Hahn, D., R. I. Amann, and J. Zeyer. 1993. Detection of mRNA in Streptomyces cells by whole-cell hybridization with digoxigenin-labeled probes. Appl. Envrion. Microbiol. 59:2753-2757.
17. Hahn, D. R., R. I. Amann, W. Ludwig, A. D. L. Akkermans, and K.-H. Schleifer. 1992. Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labeled oligonucleotides. J. Gen. Microbiol. 138:879-887.
18. Harmsen, H. J. M., A. D. L. Akkermans, A. J. M. Stams, and W. M. De Vos. Population dynamics of propoinate-oxidizing bacteria under methanogenic and sulfidogenic conditions in anaerobic granular sludge. Appl. Environ. Microbiol. 62:2163-2168.
19. Hasse, A. T., E. F. Retzel, and K. A. Staskus. 1990. Amplification and detection of lentiviral DNA inside cells. Proc. Natl. Acad. Sci. USA 7:1874-1878.
20. 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 rRNA sequences. Appl. Environ. Microbiol. 58:2158-2163.
21. Hodson, R. E., W. A. Dustman, R. P. Garg, and M. A. Moran. 1995. In situ PCR for visualization of microscale distribution of specific genes and gene products in prokaryotic communities. Appl. Environ. Microbiol. 61:4074-4082.
22. Hönerlage, W., D. Hahn, and J. Zeher. 1995. Detection of mRNA of nprM in Bacillus megaterium ATCC 14581 grown in soil by whole-cell hybridization. Arch. Microbiol. 163:235-241.
23. Karner, M., and J. A. Fuhrman. 1997. Determination of active marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining. Appl. Environ. Microbiol. 63:1208-1213.
24. Lee, S., and P. F. Kemp. 1994. Single-cell RNA content of natuaral marine planktonic bacteria measured by hybridization with multiple 16S rRNA-targeted fluorescent probes. Limnol. Oceanogr. 39:869-879.
25. Mobarry, B. K., M. Wagner, V. Urbain, B. E. Rittmann, and D. A. Stahl. 1996. Phylegenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol. 62:2156-2162.
26. Møller, S., A. R. Pedersen, L. K. Poulsen, E. Arvin, and S. Molin. 1996. Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy. Appl. Environ. Microbiol. 62:4632-4640.
27. Patterson, B. K., M. Till, P. Otto, C. Goolsby, M. R. Furtado, L. J. McBride, and S. M. Wolinsky. 1993. Detection of HIV-1 DNA and messenger RNA in individual cells by PCR-driven in situ hybridization and flow cytometry. Science 260:976-979.
28. 2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes. Appl. Environ. Microbiol. 59: 3840-3849.
29. Ramsing, N. B., H. Fossing, T. G. Ferdelman, F. Andersen, and B. Thamdrup. 1996. Distribution of bacterial populations in a starified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl. Environ. Microbiol. 62:1391-1404.
30. Schramm, A., L. H. Larsen, N. P. Revsbech, N. B. Ramsing, R. Amann, and K.-H. Schleifer. 1996. Structure and function of a nitrifying biofilm as determined by in situ hybridization and the use of microelectrodes. Appl. Environ. Microbiol. 62:4641-4647.
31. Trebesius, K., R. Amann, W. Lugwig, K. Mühlegger, and K.-H. Schleifer. 1994. Identification of whole fixed bacterial cells with nonradioactive 23S rRNA-targeted polynucleotide probes. Appl. Environ. Microbiol. 60:3228-3235.
32. Wagner, M. R., R. Amann, H. Lemmer, and K.-H. Schleifer. 1993. Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing community structure. Appl. Environ. Microbiol. 59:1520-1525.
33. Weiss, P., B. Schweitzer, R. Amann, and M. Simon. 1996. Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow). Appl. Environ. Microbiol. 62:1998-2005.
34. Yamaguchi, N., S. Inaoka, K. Tani, T. Kenzaka, and M. Nasu. 1996. Detection of specific bacterial cells with 2-hydroxy-3-naphthoic acid-2′-phenylanilide phosphate and fast red TR in situ hybridization. Appl. Environ. Microbiol. 62:275-278.
35. Zarda, B., R. Amann, and K.-H. Schleifer. 1996. Identification of single bacterial cells using DIG-labeled oligonucleotides, p. 119-121. In S. Grünewald-Janho, J. Keesey, M. Leous, R. V. Miltenburg, and C. Schroeder (ed.). Nonradioactive in situ hybridization application manual, 2nd ed. Boehringer Mannheim GmbH Biochemica, Mannheim, Germany.
36. Zylstra, G. J., and D. T. Gibson. 1989. Toluene degradation by Pseudomonas putida F1. J. Biol. Chem. 264:14940-14946.