Table 1.
Comammox amoA-targeted primers designed in this study, and in silico evaluation of the primer coverage of the target clades in our comammox amoA reference sequence database.
| Target gene | Primer name | Primer sequence (5′–3′) | Amplicon size | Target group coveragea |
|---|---|---|---|---|
| DEGENERATE PRIMER PAIRS | ||||
| Comammox Nitrospira clade A amoA | comaA-244F | TAYAAYTGGGTSAAYTA | 415 | 93/98 (95%) |
| comaA-659R | ARATCATSGTGCTRTG | |||
| Comammox Nitrospira clade B amoA | comaB-244F | TAYTTCTGGACRTTYTA | 415 | 188/228 (83%) |
| comaB-659R | ARATCCARACDGTGTG | |||
| SINGLE OLIGONUCLEOTIDES FOR EQUIMOLAR PRIMER MIXTURES | ||||
| Comammox Nitrospira clade A amoA | comaA-244f_a | TACAACTGGGTGAACTA | 415 | 93/98 (95%) |
| comaA-244f_b | TATAACTGGGTGAACTA | |||
| comaA-244f_c | TACAATTGGGTGAACTA | |||
| comaA-244f_d | TACAACTGGGTCAACTA | |||
| comaA-244f_e | TACAACTGGGTCAATTA | |||
| comaA-244f_f | TATAACTGGGTCAATTA | |||
| comaA-659r_a | AGATCATGGTGCTATG | |||
| comaA-659r_b | AAATCATGGTGCTATG | |||
| comaA-659r_c | AGATCATGGTGCTGTG | |||
| comaA-659r_d | AAATCATGGTGCTGTG | |||
| comaA-659r_e | AGATCATCGTGCTGTG | |||
| comaA-659r_f | AAATCATCGTGCTGTG | |||
| Comammox Nitrospira clade B amoA | comaB-244f_a | TAYTTCTGGACGTTCTA | 415 | 209/228 (92%) |
| comaB-244f_b | TAYTTCTGGACATTCTA | |||
| comaB-244f_c | TACTTCTGGACTTTCTA | |||
| comaB-244f_d | TAYTTCTGGACGTTTTA | |||
| comaB-244f_e | TAYTTCTGGACATTTTA | |||
| comaB-244f_f | TACTTCTGGACCTTCTA | |||
| comaB-659r_a | ARATCCAGACGGTGTG | |||
| comaB-659r_b | ARATCCAAACGGTGTG | |||
| comaB-659r_c | ARATCCAGACAGTGTG | |||
| comaB-659r_d | ARATCCAAACAGTGTG | |||
| comaB-659r_e | AGATCCAGACTGTGTG | |||
| comaB-659r_f | AGATCCAAACAGTGTG | |||
a
Indicated are the number of comammox amoA sequences in the respective target clade that fully match the primers, the total number of sequences in this target clade, and the primer coverage in percent.