qPCR_Parameters         Probe                             Forward_primer                        Reverse_primer                     Cycling_conditions                                                                  Efficiency  Limit_of_Detection_template  Limit_of_Detection_sample  Number_plates_run  Reference                                   
Bacterial 16S rRNA      TM1389F; CTTGTACACACCGCCCGTC      BACT1369F; CGGTGAATACGTTCYCGG         PROK1492R; GGWTACCTTGTTACGACTT     94 C  2 m 35 cycles of: 94 C  15 s; 56 C  1 m; Acquisition at 56 C                  102         9.9                          920-7000                   3                  Suzuki et al. 2000                          
Thaumarchaeal 16S rRNA  TM519AR; TTACCGCGGCGGCTGGCAC      GI_334F; AGATGGGTACTGAGACACGGAC       GI_554R; CTGTAGGCCCAATAATCATCCT    94 C  2 m 40 cycles of:  94 C  15 s; 59 C  1 m; Acquisition at 59 C                 93.3        4.4                          420-3200                   2                  Suzuki et al. 2000                          
WCA amoA                WCA-amoA-P; ACTCCGCCGAACAGTATCA   WCA-amoA-F; ACACCAGTTTGGCTWCCDTCAGC   WCA-amoA-R; TCAGCCACHGTGATCAAATTG  95 C  10 m 40 cycles of: 95 C  15 s; 56 C  1 m; Acquisition at 56 C                 98.4        2.8                          270-1100                   3                  Mosier and Francis 2011                     
WCB amoA                WCB-amoA-P; CCAAAGAATATYAGCGARTG  Arch-amoAFB; CATCCRATGTGGATTCCATCDTG  WCB-amoA-R; AAYGCAGTTTCTAGYGGATC   95 C  10 m 40 cycles of: 95 C  15 s; 56 C  1 m; Acquisition at 56 C                 95.3        8.2                          780-3100                   5                  Mosier and Francis 2011; Beman et al. 2008  
Nitrospina 16S rRNA     nd                                NitSSU_130F; GGGTGAGTAACACGTGAATAA    NitSSU_282R; TCAGGCCGGCTAAMCA      94 C  15 m 50 cycles of: 84 C  15 s; 57.5 C  15 s; 72 C  30 s; Acquisition at 80 C  92.8        3.8                          360-2700                   2                  Mincer et al. 2007