Molecular Tools for the Detection of Nitrogen Cycling Archaea

Table 1

Primer sets for the PCR amplification of archaeal genes that encode key enzymes of nitrogen metabolism.

Process in N cycle	Key enzyme	Target gene	Primer name	Primer sequence	Reference
NH4^+→NO2^−	Ammonia monooxygenase; (E.C. 1.14.99.39.)	amoA	arc-Amo-f; arc-Amo-r	5′-STAATGGTCTGGCTTAGACG-3′; 5′-GCGGCCATCCATCTGTATGT-3′	[18]
NO2^−→NH4^+	Ferredoxin nitrite reductase; (E.C. 1.7.7.1.)	nirA	arc-NirA-f; arc-NirA-r	5′-AAYMTSCCNCGGAAGTKSAA-3′; 5′-AGAACTCCBTRCCSGTRCAS-3′	This study
NO2^−→NH4^+	Ammonifying nitrite reductase; (E.C. 1.7.1.4.)	nirB	arc-NirB-f; arc-NirB-r	5′-ATGCTGAGCCATTAYATAGC-3′; 5′-CCGTTGTACTCGGCRCAGTC-3′	This study
N2O→N2	Nitrous oxide reductase; (E.C. 1.7.2.4.)	nosZ	arc-Nos-f; arc-Nos-r	5′-TGGGGHGACTMYCAYCAYCC-3′; 5′-AKGTGKCCRRSGTTGTAGTK-3′	This study
N2→NH4^+	Nitrogenase reductase; (E.C. 1.18.6.1.)	nifH	arc-Nif-f; arc-Nif-r	5′-TAYGGAAARGGNGGNATYGG-3′; 5′-CCNCCRCAGACRACRTCNCC-3′	This study
NO3^−→NO2^−	Dissimilatory nitrate reductase; (E.C.1.7.99.4.)	napA, narG	arc-Nred-f; arc-Nred-r	5′-CGACTGGTAYKCVGAYCTHC-3′; 5′-GTCRGYGTKRWACCAGTSGK-3′	This study