Table 1 HOPE primers used to target the different ammonia- and nitrite-oxidizing bacterial groups
| Â | Target | Primer sequence (5'-3') | Extended ddNTP | PolyA-tail (nt) | Reference |
|---|---|---|---|---|---|
NOB tube 1: Nitrospira | |||||
 27F | Most Bacteria | AGAGTTTGATCCTGGCTCAG | A | 0 | [38] |
 Ntspa712 | 4451 out of 8171 members of Nitrospirae; also targets comammox bacteria Candidatus N. inopinata | CGCCTTCGCCACCGGCCTTCC | T | 0 | [39] |
 Ntspa572 | 1835 out of 8171 members of Nitrospirae; also targets comammox bacteria Candidatus N. inopinata | AACCGCCTACGCTCCCTG | T | 0 | This study |
 Ntspa1429 | 107 out of 8171 members of Nitrospirae; Nitrospira cluster II | TGGCTTGGGCGACTTCAG | G | 6 | Modified from [37] |
NOB tube 2: Nitrobacter | |||||
 Eub338Ia | Most Bacteria | GCTGCCTCCCGTAGGAG | T | 8 | [12] |
 Nit1017 | 107 out of 195 genus Nitrobacter | TGC TCC GAA GAG AAG GTC ACA | T | 6 | Modified from [40] |
 Nit1000 | 117 out of 195 genus Nitrobacter | TGC GAC CGG TCA TGG | A | 0 | [41] |
AOB tube 1: Nitrosomonas and Nitrosospira | |||||
 27F | Most Bacteria | AGAGTTTGATCCTGGCTCAG | A | 0 | [38] |
 NmoCL6a | 379 out of 7530 members of order Nitrosomonadales, Nitrosomonas cluster 6a; mainly targeting unclassified Nitrosomonadaceae | AAGCATAAGGTCTTTCGATCCCCT | G | 3 | Modified from [42] |
 NmoCL6b | 1749 out of 7530 members of order Nitrosomonadales, Nitrosomonas cluster 6b; Major coverage also includes other non-AOB and NOB groups | GGATCAGGCTTGCGCCC | A | 0 | [42] |
AOB tube 2: Nitrosomonas and Nitrosospira | |||||
 Eub338Ia | Most Bacteria | GCTGCCTCCCGTAGGAG | T | 8 | [12] |
 Nso190 | 1295 out of 7530 members of order Nitrosomonadales | CGATCCCCTGCTTTTCTC | C | 9 | [41] |
 Nmo218 | 321 out of 897 members of unclassified Nitrosomonadaceae | CGGCCGCTCCAAAAGCAT | A | 0 | [43] |
 Nse1472 | 208 out of 911 members of genus Nitrosomonas | ACCCCAGTCATGACCCCC | A | 6 | [44] |
 Nsv443 | 934 out of 5714 members of genus Nitrosospira | CCGTGACCGTTTCGTTCCGGC | T | 0 | [41] |