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Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE
Abstract
We re-evaluated PCR primers targeting nirS, nirK and nosZ genes for denaturing gradient gel electrophoresis as a tool to survey denitrifying community composition in environmental samples. New primers for both nirS and nosZ were combined with existing primers, while for nirK the previously published F1aCu:R3Cu set was chosen for denaturing electrophoresis. All three sets yielded amplicons smaller than 500 bp and amplified the correct fragment in all environmental samples. The denaturing gradient gel electrophoresis worked satisfactorily for nirK and nosZ, but not for nirS. This was probably due to the multiple melting domains in this particular nirS fragment. From the excised and sequenced bands, only sequences related to the target genes were detected and tree analysis showed that the selected primers acted as broad range primers for each of the three genes. By use of the new nirS primers it was demonstrated that agricultural soil harbours a substantial diversity of nirS denitrifiers.
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Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
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Past, present and future of soil quality indices: a biological perspective
Bastida, F., Zsolnay, A., Hernández, T., & García, C. (2008) · Geoderma · doi:10.1016/j.geoderma.2008.08.007 · Cited by 730
Petersen, D. G., Blazewicz, S. J., Firestone, M., Herman, D. J., Turetsky, M., & Waldrop, M. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02679.x · Cited by 466
Gao, B., Yao, H., Li, Y., & Zhu, Y. (2020) · Environmental Toxicology and Chemistry · doi:10.1002/etc.4916 · Cited by 430
Wei, W., Isobe, K., Nishizawa, T., Zhu, L., Shiratori, Y., Ohte, N., Koba, K., Otsuka, S., & Senoo, K. (2015) · The ISME Journal · doi:10.1038/ismej.2015.9 · Cited by 275
Pereira, E. I. P., Suddick, E. C., Mansour, I., Mukome, F. N. D., Parikh, S. J., Scow, K., & Six, J. (2015) · Biology and Fertility of Soils · doi:10.1007/s00374-015-1004-5 · Cited by 109
Metadata
- Authors
- Throbäck, I. N., Enwall, K., Jarvis, Ã., & Hallin, S.
- Venue
- FEMS Microbiology Ecology
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-09
- Volume
- 49
- Issue
- 3
- Pages
- 401-417
- ISSN
- 0168-6496 (ISSN-L)
- 1574-6941
- OpenAlex
- W2035055175
- Cited by
- 1,321
- References
- 1
- FWCI
- 17.54
- Type
- journal article
- Language
- en
- Open access
- closed
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- Throbäck, I. N., Enwall, K., Jarvis, Ã., & Hallin, S. (2004). Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology. https://doi.org/10.1016/j.femsec.2004.04.011
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