Recognition of individual genes in diverse microorganisms by cycling primed in situ amplification

Applied and Environmental Microbiology

Volumn 71, Issue 11, 2005, Pages 7236-7244

  Kenzaka, Takehiko ^a   Tamaki, Shigeru ^a   Yamaguchi, Nobuyasu ^a   Tani, Katsuji ^a   Nasu, Masao ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; ESCHERICHIA COLI; FLUORESCENCE; MICROBIOLOGY; MICROORGANISMS; RNA;

A. HYDROPHILLA; IN SITU AMPLIFICATION; PERMEABILIZED MICROBIAL CELLS;

GENES;

CHLORAMPHENICOL ACETYLTRANSFERASE; FRESH WATER; GELATIN; LAKE WATER; POLYCARBONATE; RIVER WATER; RNA 16S; SINGLE STRANDED DNA;

GENE;

AEROMONAS; AEROMONAS HYDROPHILA; AEROMONAS SOBRIA; AMPLICON; ANIMAL CELL; ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIOPLANKTON; BACTERIUM DETECTION; CELL COUNT; CELL PERMEABILIZATION; CYCLING PRIMED IN SITU AMPLIFICATION FLUORESCENT IN SITU HYBRIDIZATION; ESCHERICHIA COLI; FLUORESCENCE IN SITU HYBRIDIZATION; FRESHWATER ENVIRONMENT; GENE AMPLIFICATION; GRAM NEGATIVE BACTERIUM; NONHUMAN; PENICILLIN RESISTANCE; RPOD GENE; WATER SAMPLING;

BACTERIAL PROTEINS; DNA, BACTERIAL; DNA, SINGLE-STRANDED; DNA-DIRECTED RNA POLYMERASES; FRESH WATER; GRAM-NEGATIVE BACTERIA; IN SITU HYBRIDIZATION, FLUORESCENCE; PRIMED IN SITU LABELING; SIGMA FACTOR;

AEROMONAS; AEROMONAS HYDROPHILA; AEROMONAS SOBRIA; ANIMALIA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 32044444305     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.11.7236-7244.2005     Document Type: Article

References (43)

1. Alfreider, A., J. Pernthaler, R. Amann, B. Sattler, F. O. Glöckner, 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. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
4. 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.
5. Araujo, R. M., R. Pares, and F. Lucena. 1990. The effect of terrestrial effluents on the incidence of Aeromonas spp. in coastal waters. J. Appl. Bacteriol. 69:439-444.
6. Chen, F., B. Binder, and R. E. Hodson. 2000. Flow cytometric detection of specific gene expression in prokaryotic cells using in situ RT-PCR. FEMS Microbiol. Lett. 184:291-296.
7. Cinti, C., S. Santi, and N. M. Maraldi. 1993. Localization of single copy gene by PRINS technique. Nucleic Acids Res. 21:5799-5800.
8. Faude, U. C., and M. G. Hofle. 1997. Development and application of monoclonal antibodies for in situ detection of indigenous bacterial strains in aquatic ecosystems. Appl. Environ. Microbiol. 63:4534-4542.
9. Goni-Urriza, M., M. Capdepuy, C. Arpin, N. Raymond, P. Caumette, and C. Quentin. 2000. Impact of an urban effluent on antibiotic resistance of riverine Enterobacteriaceae and Aeromonas spp. Appl. Environ. Microbiol. 66:125-132.
10. Gosden, J., and D. Lawson. 1994. Rapid chromosome identification by oligonucleotide-primed in situ DNA synthesis (PRINS). Hum. Mol. Genet. 3:931-936.
11. Gupta, R. S. 1998. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev. 62:1435-1491.
12. 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.
13. Holmstrom, K., T. Tolker-Nielsen, and S. Molin. 1999. Physiological states of individual Salmonella typhimurium cells monitored by in situ reverse transcription-PCR. J. Bacteriol. 181:1733-1738.
14. Ivanova, E. P., N. V. Zhukova, N. M. Gorshkova, and E. L. Chaikina. 2001. Characterization of Aeromonas and Vibrio species isolated from a drinking water reservoir. J. Appl. Microbiol. 90:919-927.
15. Iwamoto, T., K. Tani, K. Nakamura, Y. Suzuki, M. Kitagawa, M. Eguchi, and M. Nasu. 2000. Monitoring impact of in situ biostimulation treatment on groundwater bacterial community by DGGE. FEMS Microbiol. Ecol. 32: 129-141.
16. Jacobs, D., M. L. Angles, A. E. Goodman, and B. A. Neilan. 1997. Improved methods for in situ enzymatic amplification and detection of low copy number genes in bacteria. FEMS Microbiol. Lett. 152:65-73.
17. Janda, J. M. 1991. Recent advances in study of the taxonomy, pathogenicity, and infectious syndromes associated with the genus Aeromonas. Clin. Microbiol. Rev. 4:397-410.
18. Jishage, M., A. Iwata, S. Ueda, and A. Ishihama. 1996. Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intercellular levels of four species of sigma subunit under various growth conditions. J. Bacteriol. 178:5447-5451.
19. Kenzaka, T., N. Yamaguchi, K. Tani, and M. Nasu. 1998. rRNA-targeted fluorescent in situ hybridization analysis of bacterial community structure in river water. Microbiology 144:2085-2093.
20. Kenzaka, T., N. Yamaguchi, B. Prapagdee, E. Mikami, and M. Nasu. 2001. Bacterial community composition and activity in urban rivers in Thailand and Malaysia. J. Health Sci. 47:353-361.
21. Kurokawa, K., K. Tani, M. Ogawa, and M. Nasu. 1999. Abundance and distribution of bacteria carrying sltII gene in natural river water. Lett. Appl. Microbiol. 61:405-410.
22. Lanoil, B. D., and S. J. Giovannoni. 1997. Identification of bacterial cells by chromosomal painting. Appl. Environ. Microbiol. 63:1118-1123.
23. Maruyama, A., and M. Sunamura. 2000. Simultaneous direct counting of total and specific microbial cells in seawater, using a deep-sea microbe as target. Appl. Environ. Microbiol. 66:2211-2215.
24. 2 gene by in situ loop-mediated isothermal amplification. Appl. Environ. Microbiol. 69:5023-5028.
25. Niki, H., and S. Hiraga. 1998. Polar localization of the replication origin and terminus in Escherichia coli nucleoids during chromosome partitioning. Genes Dev. 12:1036-1045.
26. Normark, B. H., and S. Normark. 2002. Evolution and spread of antibiotic resistance. J. Intern. Med. 252:91-106.
27. Ochman, H., and A. C. Wilson. 1987. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26:74-86.
28. Pernthaler, A., C. M. Preston, J. Pernthaler, E. F. DeLong, and R. Amann. 2002. Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea. Appl. Environ. Microbiol. 68:661-667.
29. 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.
30. Pernthaler, A., J. Pernthaler, M. Schattenhofer, and R. Amann. 2002. Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl. Environ. Microbiol. 68:5728-5736.
31. Sawada, H., F. Suzuki, I. Matsuda, and N. Saitou. 1999. Phylogenetic analysis of Pseudomonas syringae pathovars suggests the horizontal gene transfer of argK and the evolutionary stability of hrp gene cluster. J. Mol. Evol. 49:627-644.
32. Schönhuber, W., B. Fuchs, S. Juretschko, and R. Amann. 1997. Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl. Environ. Microbiol. 63:3268-3273.
33. Tani, K., K. Kurokawa, and M. Nasu. 1998. Development of a direct in situ PCR method for detection of specific bacteria in natural environments. Appl. Environ. Microbiol. 64:1536-1540.
34. Tani, K., M. Muneta, K. Nakamura, K. Shibuya, and M. Nasu. 2002. Monitoring of Ralstonia eutropha KT1 in groundwater in an experimental bioaugmentation field by in situ PCR. Appl. Environ. Microbiol. 68:412-416.
35. Terkelsen, C., J. Koch, S. Kolvraa, J. Hindkjaer, S. Pedersen, and L. Bolund. 1993. Repeated primed in situ labeling: formation and labeling of specific DNA sequences in chromosomes and nuclei. Cytogenet. Cell Genet. 63:235-237.
36. Teuber, M. 2001. Veterinary use and antibiotic resistance. Curr. Opin. Microbiol. 4:493-499.
37. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
38. Tolker-Nielsen, T., A. B. Christensen, K. Holmstrom, L. Eberl, T. B. Rasmussen, C. Sternberg, A. Heydorn, S. Molin, and M. Givskov. 2000. Assessment of flhDC mRNA levels in Serratia liquefaciens swarm cells. J. Bacteriol. 182:2680-2686.
39. Villari, P., M. Crispino, P. Montuori, and S. Boccia. 2003. Molecular typing of Aeromonas isolates in natural mineral waters. Appl. Environ. Microbiol. 69:697-701.
40. Weinbauer, M. G., and M. G. Höfle. 1998. Distribution and life strategies of two bacterial populations in a eutrophic lake. Appl. Environ. Microbiol. 64:3776-3783.
41. Yamaguchi, N., and M. Nasu. 1997. Flow cytometric analysis of bacterial respiratory and enzymatic activity in the natural aquatic environment. J. Appl. Microbiol. 83:43-52.
42. Yamamoto, S., H. Kasai, D. L. Arnold, R. W. Jackson, A. Vivian, and S. Harayama. 2000. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146:2385-2394.
43. Zwirglmaier, K., W. Ludwig, and K. H. Schleifer. 2004. Recognition of individual genes in a single bacterial cell by fluorescence in situ hybridization-RING-FISH. Mol. Microbiol. 51:89-96.