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Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodological Variability
Open accessAbstract
Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extraction and PCR amplification) and biological (inter- and intrasite) variations were evaluated by comparing the number and intensity of peaks (bands) between electrophoregrams (profiles) and by multivariate analysis. Our results showed that ARISA is a high-resolution, highly reproducible technique and is a robust method for discriminating between microbial communities. To evaluate the potential biases in community description provided by ARISA, we also examined databases on length distribution of ribosomal intergenic spacers among bacteria (L. Ranjard, E. Brothier, and S. Nazaret, Appl. Environ. Microbiol. 66:5334–5339, 2000) and fungi.
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Citations
Cited by
Garbeva, P., van Veen, J. A., & van Elsas, J. D. (2004) · Annual Review of Phytopathology · doi:10.1146/annurev.phyto.42.012604.135455 · Cited by 1,458
Role of metal-reducing bacteria in arsenic release from Bengal delta sediments
Islam, F. S., Gault, A. G., Boothman, C., Polya, D. A., Charnock, J. M., Chatterjee, D., & Lloyd, J. R. (2004) · Nature · doi:10.1038/nature02638 · Cited by 1,241
Kostka, J. E., Prakash, O., Overholt, W. A., Green, S. J., Freyer, G., Canion, A., Delgardio, J., Norton, N., Hazen, T. C., & Huettel, M. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.05402-11 · Cited by 875
Impact of wheat straw decomposition on successional patterns of soil microbial community structure.
Bastian, F., Bouziri, L., Nicolardot, B., & Ranjard, L. (2009) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2008.10.024 · Cited by 433
Self-citationRuan, Q., Dutta, D., Schwalbach, M. S., Steele, J. A., Fuhrman, J. A., & Sun, F. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl417 · Cited by 294
Metadata
- Authors
- Ranjard, L., Poly, F., Lata, J.-C., Mougel, C., Thioulouse, J., & Nazaret, S.
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2001-10
- Volume
- 67
- Issue
- 10
- Pages
- 4479-4487
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- OpenAlex
- W2142084851
- Cited by
- 480
- References
- 0
- FWCI
- 11.60
- Type
- journal article
- Language
- en
- Open access
- green
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- The paper
- Ranjard, L., Poly, F., Lata, J.-C., Mougel, C., Thioulouse, J., & Nazaret, S. (2001). Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodological Variability. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.67.10.4479-4487.2001
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