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This is a list of the most commonly used primers for genes nirK, nirS, norB and nosZ in literature articles we have looked at so far. All primers listed except for the norB primers have been assessed in the paper by Throback et al (Microbiology Ecology 2004). Some of the primers on the list are the same primers that Kurt has on the list he generated.
Here is a list of the primers that seem to work the best. The nirS from Throbeck 2004 seems to be the most widely used for nirS but rdeitzel seemed to have problems getting it to work so I don't if you guys want to try a different nirS primer set. Take a look at the list and let me know if you have any better suggestions.
There isn't a lot on norB primers out there. This paper by Braker and Tiedje is the only one I could find that developed norB primers for use in environmental samples. The Dandie group (three papers under denitrifcation genes/ first look at functional genes) developed primers from culturable bacteria and applied them to ag fields, but as they are focused on culturable microbes it's hard to tell how well those primers would work in finding other species.
Here are some primers I considered. At first I was trying cloning to create standards for qPCR, so I used the primers recommended by Throback. As I moved towards qPCR, I was looking for shorter primers.