Abstract

Were-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 by 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. (C) 2004 Published by Elsevier B.V. on behalf of the Federation of European Microbiological Societies

Published in

FEMS Microbiology Ecology
2004, Volume: 49, number: 3, pages: 401-417
Publisher: ELSEVIER SCIENCE BV

SLU Authors

• Hallin, Sara

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Jarvis, Åsa

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Throbäck, Ingela

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Enwall, Karin

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Environmental Sciences related to Agriculture and Land-use


Publication identifier

DOI: https://doi.org/10.1016/j.femsec.2004.04.011

Permanent link to this page (URI)

https://res.slu.se/id/publ/4852