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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Bibliographic Details
Published in:Applied and environmental microbiology Vol. 71; no. 4; p. 2026
Main Authors: Rösch, Christopher, Bothe, Hermann
Format: Journal Article
Language:English
Published: United States 01.04.2005
Subjects:
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
ISSN:0099-2240
Online Access:Get more information
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Summary: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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ISSN:0099-2240
DOI:10.1128/aem.71.4.2026-2035.2005