nirK

http://aem.asm.org/content/early/2011/10/14/AEM.05787-11.short?rss=1

Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil

Man-Young Jung1, Soo-Je Park1, Deullae Min2, Jin-Seog Kim2, W. Irene C. Rijpstra3, Jaap S. Sinninghe Damsté3, Geun-Joong Kim4, Eugene L. Madsen5 and Sung-Keun Rhee1

http://www.springerlink.com.proxy.lib.iastate.edu:2048/content/gj87j141m...

http://www.nature.com/ismej/journal/vaop/ncurrent/pdf/ismej2010130a.pdf

Gene transcription, nirK

Here is the updated (updated) list of primers for the 4 denitrification genes of interest. This list is very similar to Kurt's updated primer list and also works off of Ranae's primer list. The primer pairs highlighted in yellow are those that seem like the best first shot based on their use on soil samples, their reliability across studies, and if they have been used for SYBR green-based qPCR.

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.

Here's the paper I mentioned earlier today. The paper itself is kind of interesting but the methods are very detailed and give a lot more info than some of the other papers.