Table 2.

Details of primers and PCR cycling conditions used in this study.

Target gene	Primer	Sequence (5′-3′)	Reference	Cycling conditions
Bacterial 16S rRNA	27f1492r	AGAGTTTGGATCMTGGCTCAGGYYACCTTGTTACGACTT	Lane (1991) Nicol et al. (2008)	95°C 5 min; 10 cycles of 94°C 30 s, 55°C 30 s, 72°C 2 min; 25 cycles of 92°C 30 s, 55°C 30 s, 72°C 2 min; 72°C 5 min
Fungal 18S rRNA	Fung5fFF390r	GGGAACCAGGACTTTTACGAGGTCTCGTTCGTTATCG	Smit et al. (1999) Vainio and Hantula (2000)	95°C 5 min; 10 cycles of 94°C 30 s, 55°C 30 s, 72°C 50 s; 25 cycles of 92°C 30 s, 55°C 30 s, 72°C 50 s; 72°C 5 min
Archaeal 16S rRNA	A109F 1492r	ACKGCTCAGTAACACGT GYYACCTTGTTACGACTT	Grosskopf, Janssen and Liesack (1998) Nicol et al. (2008)	95°C 5 min; 10 cycles of 94°C 30 s, 55°C 30 s, 72°C 2 min; 25 cycles of 92°C 30 s, 55°C 30 s, 72°C 2 min; 72°C 5 min
Thaumarchaeal amoA	CrenamoA23fCrenamoA616r	ATGGTCTGGCTWAGACGGCCATCCATCTGTATGTCCA	Tourna et al. (2008) Tourna et al. (2008)	95°C 5 min; 10 cycles of 94°C 30 s, 55°C 30 s, 72°C 1 min; 25 cycles of 92°C 30 s, 55°C 30 s, 72°C 1 min; 72°C 5 min
Nitrosotalea sp. Nd2 amoA gene cluster	Nd2F1Nd2R2	GATACTTGCAGTGATACCTACCCCAGATATTCTTGTTTCAACAGAGG	This studyThis study	95°C 5 min; 35 cycles of 94°C 30 s, 52°C 30 s, 72°C 4 min; 72°C 10 min