Improved assessment of denitrifying, N2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes
A database of terminal restriction fragments (tRFs) of the 16S rRNA gene was set up utilizing 13 restriction enzymes and 17,327 GenBank sequences. A computer program, termed TReFID, was developed to allow identification of any of these 17,327 sequences by means of polygons generated from the specifi...
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| Veröffentlicht in: | Applied and environmental microbiology Jg. 71; H. 4; S. 2026 |
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01.04.2005
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| ISSN: | 0099-2240 |
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| Abstract | A database of terminal restriction fragments (tRFs) of the 16S rRNA gene was set up utilizing 13 restriction enzymes and 17,327 GenBank sequences. A computer program, termed TReFID, was developed to allow identification of any of these 17,327 sequences by means of polygons generated from the specific tRFs of each bacterium. The TReFID program complements and exceeds in its data content the Web-based phylogenetic assignment tool recently described by A. D. Kent, D. J. Smith, B. J. Benson, and E. W. Triplett (Appl. Environ. Microb. 69:6768-6766, 2003). The method to identify bacteria is different, as is the region of the 16S rRNA gene employed in the present program. For the present communication the software of the tRF profiles has also been extended to allow screening for genes coding for N2 fixation (nifH) and denitrification (nosZ) in any bacterium or environmental sample. A number of controls were performed to test the reliability of the TReFID program. Furthermore, the TReFID program has been shown to permit the analysis of the bacterial population structure of bacteria by means of their 16S rRNA, nifH, and nosZ gene content in an environmental habitat, as exemplified for a sample from a forest soil. The use of the TReFID program reveals that noncultured denitrifying and dinitrogen-fixing bacteria might play a more dominant role in soils than believed hitherto. |
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| AbstractList | A database of terminal restriction fragments (tRFs) of the 16S rRNA gene was set up utilizing 13 restriction enzymes and 17,327 GenBank sequences. A computer program, termed TReFID, was developed to allow identification of any of these 17,327 sequences by means of polygons generated from the specific tRFs of each bacterium. The TReFID program complements and exceeds in its data content the Web-based phylogenetic assignment tool recently described by A. D. Kent, D. J. Smith, B. J. Benson, and E. W. Triplett (Appl. Environ. Microb. 69:6768-6766, 2003). The method to identify bacteria is different, as is the region of the 16S rRNA gene employed in the present program. For the present communication the software of the tRF profiles has also been extended to allow screening for genes coding for N2 fixation (nifH) and denitrification (nosZ) in any bacterium or environmental sample. A number of controls were performed to test the reliability of the TReFID program. Furthermore, the TReFID program has been shown to permit the analysis of the bacterial population structure of bacteria by means of their 16S rRNA, nifH, and nosZ gene content in an environmental habitat, as exemplified for a sample from a forest soil. The use of the TReFID program reveals that noncultured denitrifying and dinitrogen-fixing bacteria might play a more dominant role in soils than believed hitherto. A database of terminal restriction fragments (tRFs) of the 16S rRNA gene was set up utilizing 13 restriction enzymes and 17,327 GenBank sequences. A computer program, termed TReFID, was developed to allow identification of any of these 17,327 sequences by means of polygons generated from the specific tRFs of each bacterium. The TReFID program complements and exceeds in its data content the Web-based phylogenetic assignment tool recently described by A. D. Kent, D. J. Smith, B. J. Benson, and E. W. Triplett (Appl. Environ. Microb. 69:6768-6766, 2003). The method to identify bacteria is different, as is the region of the 16S rRNA gene employed in the present program. For the present communication the software of the tRF profiles has also been extended to allow screening for genes coding for N2 fixation (nifH) and denitrification (nosZ) in any bacterium or environmental sample. A number of controls were performed to test the reliability of the TReFID program. Furthermore, the TReFID program has been shown to permit the analysis of the bacterial population structure of bacteria by means of their 16S rRNA, nifH, and nosZ gene content in an environmental habitat, as exemplified for a sample from a forest soil. The use of the TReFID program reveals that noncultured denitrifying and dinitrogen-fixing bacteria might play a more dominant role in soils than believed hitherto.A database of terminal restriction fragments (tRFs) of the 16S rRNA gene was set up utilizing 13 restriction enzymes and 17,327 GenBank sequences. A computer program, termed TReFID, was developed to allow identification of any of these 17,327 sequences by means of polygons generated from the specific tRFs of each bacterium. The TReFID program complements and exceeds in its data content the Web-based phylogenetic assignment tool recently described by A. D. Kent, D. J. Smith, B. J. Benson, and E. W. Triplett (Appl. Environ. Microb. 69:6768-6766, 2003). The method to identify bacteria is different, as is the region of the 16S rRNA gene employed in the present program. For the present communication the software of the tRF profiles has also been extended to allow screening for genes coding for N2 fixation (nifH) and denitrification (nosZ) in any bacterium or environmental sample. A number of controls were performed to test the reliability of the TReFID program. Furthermore, the TReFID program has been shown to permit the analysis of the bacterial population structure of bacteria by means of their 16S rRNA, nifH, and nosZ gene content in an environmental habitat, as exemplified for a sample from a forest soil. The use of the TReFID program reveals that noncultured denitrifying and dinitrogen-fixing bacteria might play a more dominant role in soils than believed hitherto. |
| Author | Rösch, Christopher Bothe, Hermann |
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| References | 11709853 - Curr Issues Intest Microbiol. 2001 Mar;2(1):17-25 9254694 - Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 9464425 - Appl Environ Microbiol. 1998 Feb;64(2):795-9 12147477 - Appl Environ Microbiol. 2002 Aug;68(8):3818-29 9595664 - FEMS Microbiol Lett. 1998 May 1;162(1):61-8 11243261 - Environ Microbiol. 2000 Feb;2(1):39-50 1987160 - J Bacteriol. 1991 Jan;173(2):697-703 9396791 - Nucleic Acids Res. 1997 Dec 15;25(24):4876-82 7683183 - Appl Environ Microbiol. 1993 Mar;59(3):695-700 12823187 - Environ Microbiol. 2003 Jul;5(7):539-54 9925556 - Appl Environ Microbiol. 1999 Feb;65(2):374-80 9361437 - Appl Environ Microbiol. 1997 Nov;63(11):4516-22 14532052 - Appl Environ Microbiol. 2003 Oct;69(10):5974-82 14602639 - Appl Environ Microbiol. 2003 Nov;69(11):6768-76 9924826 - Syst Appl Microbiol. 1998 Dec;21(4):579-87 10353797 - J Microbiol Methods. 1999 May;36(1-2):29-33 10441703 - Microb Ecol. 1999 Aug;38(2):93-113 8902363 - Comput Appl Biosci. 1996 Aug;12(4):357-8 2317046 - Appl Environ Microbiol. 1990 Mar;56(3):782-7 7535888 - Microbiol Rev. 1995 Mar;59(1):143-69 |
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| SubjectTerms | Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Bacteria - metabolism Bacterial Proteins - genetics Bacterial Proteins - metabolism Databases, Genetic DNA Restriction Enzymes - metabolism DNA, Bacterial - analysis DNA, Bacterial - genetics Ecosystem Nitrites - metabolism Nitrogen Fixation Oxidoreductases - genetics Polymorphism, Restriction Fragment Length RNA, Ribosomal, 16S - genetics Software Soil Microbiology |
| Title | Improved assessment of denitrifying, N2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes |
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