PCR detection of genes encoding nitrite reductase in denitrifying bacteria
Sara Hallin,Per-Eric Lindgren +1 more
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Using consensus regions in gene sequences encoding the two forms of nitrite reductase (Nir), a key enzyme in the denitrification pathway, two sets of PCR primers to amplifycd1- and Cu-nir were designed and conserved.Abstract:
Using consensus regions in gene sequences encoding the two forms of nitrite reductase (Nir), a key enzyme in the denitrification pathway, we designed two sets of PCR primers to amplify cd1- and Cu-nir. The primers were evaluated by screening defined denitrifying strains, denitrifying isolates from wastewater treatment plants, and extracts from activated sludge. Sequence relationships of nir genes were also established. The cd1 primers were designed to amplify a 778 to 799-bp region of cd1-nir in the six published sequences. Likewise, the Cu primers amplified a 473-bp region in seven of the eight published Cu-nir sequences. Together, the two sets of PCR primers amplified nir genes in nine species within four genera, as well as in four of the seven sludge isolates. The primers did not amplify genes of nondenitrifying strains. The Cu primers amplified the expected fragment in all 13 sludge samples, but cd1-nir fragments were only obtained in five samples. PCR products of the expected sizes were verified as nir genes after hybridization to DNA probes, except in one case. The sequenced nir fragments were related to other nir sequences, demonstrating that the primers amplified the correct gene. The selected primer sites for Cu-nir were conserved, while broad-range primers targeting conserved regions of cd1-nir seem to be difficult to find. We also report on the existence of Cu-nir in Paracoccus denitrificans Pd1222.read more
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Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE.
TL;DR: It was demonstrated that agricultural soil harbours a substantial diversity of nirS denitrifiers by use of the new nIRS primers, which acted as broad range primers for each of the three genes.
Journal ArticleDOI
Methods for measuring denitrification: diverse approaches to a difficult problem
Peter M. Groffman,Mark A. Altabet,John Karl Böhlke,Klaus Butterbach-Bahl,Mark B. David,Mary K. Firestone,Anne E. Giblin,Todd M. Kana,Lars Peter Nielsen,Mary A. Voytek +9 more
TL;DR: Comparison of mass balance and stoichiometric approaches that constrain estimates of denitrification at large scales with point measurements (made using multiple methods), in multiple systems, is likely to propel more improvement in Denitrification methods over the next few years.
Journal ArticleDOI
Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR.
Sonia Henry,Ezékiel Baudoin,Juan C. López-Gutiérrez,Fabrice Martin-Laurent,Alain Brauman,Laurent Philippot +5 more
TL;DR: Real-time PCR was used to quantify the denitrifying nitrite reductase gene (nirK), a key enzyme of the denItrifying pathway catalyzing the reduction of soluble nitrogen oxide to gaseous form and phylogenetic analysis showed that most of environmental sequences are not related to nirK from cultivated Denitrifiers.
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The microbiology of biological phosphorus removal in activated sludge systems.
TL;DR: The history of EBPR, the currently available biochemical models, the structure of the microbial communities found in EBPR systems, possible identities of the bacteria responsible, and the evidence why these systems might operate suboptimally are looked at.
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Bacterial respiration: a flexible process for a changing environment.
TL;DR: It is amongst the Bacteria and Archaea that respiratory flexibility can be found at its most extreme and contributes to the ability of prokaryotes to colonize many of Earth’s most hostile microoxic and anoxic environments.
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