TABLE 1.
Oligonucleotide probes used for the detection of anammox organisms and their suitability for use as PCR primers
| OPDa designation trivial name [reference] | Specificity | Sequence 5′-3′ | % Formamide/mM [NaCl]b | Tested as PCR primerc |
|---|---|---|---|---|
| S-P-Planc-0046-a-A-18 (Pla46; [26]) | Planctomycetales | GACTTGCATGCCTAATCC | 25/159 | F (58°C) |
| S-P-Planc-0886-a-A-19 (Pla 886; [26]) | Isosphaera, Gemmata, Pirellula, Plantomyces | GCCTTGCGACCATACTCCC | 30/112 | — |
| S-D-Bact-0338-b-A-18 (Eub338II; [7]) | Bacterial lineages not covered by probes EUB338 and EUB338II | GCAGCCACCCGTAGGTGT | 0/900 | — |
| S-D-Bact-0338-d-A-18d (Eub338IV) | Bacterial lineages not covered by probes EUB338, EUB338II, and EUBIII | GCAGCCTCCCGTAGGAGT | 0/900 | |
| S-*-Amx-0368-a-A-18 (36) | All anammox organisms | CCTTTCGGGCATTGCGAA | 15/338 | F/R (56°C) |
| L-*-Amx-1900-a-A-21 (35) | Genera “Ca. Brocadia” and “Ca. Kuenenia” | CATCTCCGGCTTGAACAA | 30/112 | — |
| S-*-Amx-0820-a-A-22 (AMX 820, [34]) | Genera “Ca. Brocadia” and “Ca. Kuenenia” | AAAACCCCTCTACTTAGTGCCC | 40/56 | F/R (56°C) |
| S-G-Sca-1309-a-A-21 (36) | Genus “Ca. Scalindua” | TGGAGGCGAATTTCAGCCTCC | 5/675 | R (56°C) |
| S-*-Scabr-1114-a-A-22 (36) | “Ca. Scalindua brodae” | CCCGCTGGTAACTAAAAACAAG | 20/225 | R (56°C) |
| S-*-BS-820-a-A-22 (20) | “Ca. Scalindua wagneri” | TAATTCCCTCTACTTAGTGCCC | 40/56 | R (56°C) |
| “Ca. Scalindua sorokinii” | ||||
| S-S-Kst-0157-a-A-18 (35) | “Ca. Kuenenia stuttgartiensis” | GTTCCGATTGCTCGAAAC | 25/159 | — |
| S-*-Kst-1275-a-A-20 (34) | “Ca. Kuenenia stuttgartiensis” | TCGGCTTTATAGGTTTCGCA | 25/159 | — |
| S-S-Ban-0162(B.anam.)-a-A-18 (34) | “Ca. Brocadia anammoxidans” | CGGTAGCCCCAATTGCTT | 40/56 | — |
| S-*-Amx-0156-a-A-18 (34) | “Ca. Brocadia anammoxidans” | CGGTAGCCCCAATTGCTT | 40/56 | — |
| S-*-Amx-0223-a-A-18 (34) | “Ca. Brocadia anammoxidans” | GACATTGACCCCTCTCTG | 40/56 | — |
| S-*-Amx-0432-a-A-18 (34) | “Ca. Brocadia anammoxidans” | CTTAACTCCCGACAGTGG | 40/56 | — |
| S-*-Amx-0613-a-A-22 (34) | “Ca. Brocadia anammoxidans” | CCGCCATTCTTCCGTTAAGCGG | 40/56 | — |
| S-*-Amx-0997-a-A-21 (34) | “Ca. Brocadia anammoxidans” | TTTCAGGTTTCTACTTCTACC | 20/225 | — |
| S-*-Amx-1015-a-A-18 (34) | “Ca. Brocadia anammoxidans” | GATACCGTTCGTCGCCCT | 60/14 | — |
| S-*-Amx-1154-a-A-18 (34) | “Ca. Brocadia anammoxidans” | TCTTGACGACAGCAGTCT | 20/225 | — |
| S-*-Amx-1240-a-A-23 (34) | “Ca. Brocadia anammoxidans” | TTTAGCATCCCTTTGTACCAACC | 60/14 | — |
| I-*-Ban-0071(B.anam.)-a-A-18 (35) | “Ca. Brocadia anammoxidans” | CCCTACCACAAACCTCGT | 10/450 | — |
| I-*-Ban-0108(B.anam.)-a-A-18 (35) | “Ca. Brocadia anammoxidans” | TTTGGGCCCGCAATCTCA | 10/450 | — |
| I-*-Ban-0222(B.anam.)-a-A-19 (35) | “Ca. Brocadia anammoxidans” | GCTTAGAATCTTCTGAGGG | 10/450 | — |
| I-*-Ban-0389(B.anam.)-a-A-18 (35) | “Ca. Brocadia anammoxidans” | GGATCAAATTGCTACCCG | 10/450 | — |
| I-*-Kst-0031(K.stutt.)-a-A-18 (35) | “Ca. Kuenenia stuttgartiensis” | ATAGAAGCCTTTTGCGCG | 10/450 | — |
| I-*-Kst-0077(K.stutt.)-a-A-18 (35) | “Ca. Kuenenia stuttgartiensis” | TTTGGGCCACACTCTGTT | 10/450 | — |
| I-*-Kst-0193(K.stutt.)-a-A-19 (35) | “Ca. Kuenenia stuttgartiensis” | CAGACCGGACGTATAAAAG | 10/450 | — |
| I-*-Kst-0288(K.stutt.)-a-A-20 (35) | “Ca. Kuenenia stuttgartiensis” | GCGCAAAGAAATCAAACTGG | 10/450 | — |
a
OPD, oligonucleotide probe database designation according to reference 1. Original reference is given in parentheses.
b
Percent formamide in the hybridization buffer and concentration of NaCl in the washing buffer, respectively, required for specific in situ hybridization.
c
F, forward primer; R, reverse primer. The commonly applied annealing temperature is given in parentheses. Note that probes used as forward primers are complementary and reverse to the given probe sequences. —, not determined.
d
Target sequence suggested by reference 7.