Target gene Primers Primer Sequence (5’-3’) Amplicon size (base pair, bp) Primers Reference
Bacterial 16S rRNA gene 349F AGG CAG CAG TDR GGA AT ~460 (Takai & Horikoshi, 2000)
806R GGA CTA CYV GGG TAT CTA AT
ITS ITS3 CAH CGA TGA AGA ACG YRG ~430 (Frey et al., 2016; Tedersoo et al., 2014)
ITS4 TCC TSC GCT TAT TGA TAT GC
mcrA ML-F(mcrA)32 GGT GGT GTM GGA TTC ACA CAR TAY GCW ACA GC ~476 (Luton et al., 2002)
ML-R(mcrA)23 TTC ATT GCR TAG TTW GGR TAG TT
pmoA A189F GGN GAC TGG GAC TTC TGG ~532 (Holmes et al., 1995)
A682r GAA SGC NGA GAA GAA SGC
nifH PolF_115 TGC GAY CCS AAR GCB GAC TC ~362 (Poly et al., 2001)
PolR_457 ATS GCC ATC ATY TCR CCG GA
nosZ nosZ-1F WCS YTG TTC MTC GAC AGC CAG ~249 (Henry et al., 2006)
nosZ_1R ATG TCG ATC ARC TGV KCR TTY TC
archaeal amoA Arch-amoAF CTG AYT GGG CYT GGA CAT C ~635 (Francis et al., 2005)
Arch-amoAR TTC TTC TTT GTT GCC CAG TA
bacterial amoA amoA-1F GGG GHT TYT ACT GGT GGT ~491 (Rotthauwe et al., 1997)
amoA-2R CCC CTC KGS AAA GCC TTC TTC
nirS cd3AF GTS AAC GTS AAG GAR ACS GG ~425 (Throback et al., 2004)
R3cd GAS TTC GGR TGS GTC TTG A
nirK nirK_F1aCu ATC ATG GTS CTG CCG CG ~473 (Hallin & Lindgren, 1999)
nirK_R3Cu GCC TCG ATC AGR TTG TGG TT
nxrB nxrB169f TAC ATG TGG TGG AAC A ~485 (Pester et al., 2014)
nxrB638r CGG TTC TGG TCR ATC A
norB qnorB2F GGN CAY CAR GGN TAY GA ~260 (Braker & Tiedje, 2003)
qnorB5R ACC CAN AGR TGN ACN ACC CAC CA
phoD
phoD-F733
TGG GAY GAT CAY GAR GT
~363
(Ragot et al., 2015)
phoD-R1083 CTG SGC SAK SAC RTT CCA