TABLE 1.
Primer selection and results of the pre-analysis in silico evaluation of all primer pairs used.
| Primer pair | Name | Primer name∗ | Sequence (5′– >3′) | Fragment size (bp) |
0 mismatch |
1 mismatch |
||||
| Archaea | Bacteria | Eukarya | Archaea | Bacteria | Eukarya | |||||
| 1 | 344F | S-D-Arch-0344-a-S-20 | ACGGGGYGCAGCAGGCGCGA | 571 | 46.1% | 0.0% | 0.0% | 67.4% | 0.0% | 0.0% |
| 915R | S-D-Arch-0911-a-A-20 | GTGCTCCCCCGCCAATTCCT | ||||||||
| 2 | 349F | S-D-Arch-0349-a-S-17 | GYGCASCAGKCGMGAAW | 566 | 71.8% | 0.0% | 0.0% | 86.1% | 0.0% | 0.0% |
| 915R | S-D-Arch-0911-a-A-20 | GTGCTCCCCCGCCAATTCCT | ||||||||
| 3 | 344F | S-D-Arch-0344-a-S-20 | ACGGGGYGCAGCAGGCGCGA | 697 | 51.5% | 0.0% | 0.0% | 72.10% | 0.0% | 0.0% |
| 1041R | S-D-Arch-1041-a-A-18 | GGCCATGCACCWCCTCTC | ||||||||
| 4 | 349F | S-D-Arch-0349-a-S-17 | GYGCASCAGKCGMGAAW | 692 | 71.2% | 0.0% | 0.0% | 88.90% | 0.0% | 0.0% |
| 1041R | S-D-Arch-1041-a-A-18 | GGCCATGCACCWCCTCTC | ||||||||
| 5 | 519F | S-D-Arch-0519-a-S-15 | CAGCMGCCGCGGTAA | 522 | 79.3% | 0.0% | 0.0% | 93.4% | 0.0% | 0.0% |
| 1041R | S-D-Arch-1041-a-A-18 | GGCCATGCACCWCCTCTC | ||||||||
| 6 | 344F | S-D-Arch-0344-a-S-20 | ACGGGGYGCAGCAGGCGCGA | 462 | 48.3% | 0.0% | 0.0% | 70.6% | 0.0% | 0.0% |
| 806R | S-D-Arch-0786-a-A-20 | GGACTACVSGGGTATCTAAT | ||||||||
| 7 | 349F | S-D-Arch-0349-a-S-17 | GYGCASCAGKCGMGAAW | 457 | 75.2% | 0.0% | 0.0% | 89.9% | 0.0% | 0.0% |
| 806R | S-D-Arch-0786-a-A-20 | GGACTACVSGGGTATCTAAT | ||||||||
| 8 | 519F | S-D-Arch-0519-a-S-15 | CAGCMGCCGCGGTAA | 287 | 85.6% | 6.8% | 0.0% | 94.9% | 90.8 | 0.1% |
| 806R | S-D-Arch-0786-a-A-20 | GGACTACVSGGGTATCTAAT | ||||||||
| 9 | 349F | S-D-Arch-0349-a-S-17 | GYGCASCAGKCGMGAAW | 170 | 79.3% | 0.0% | 0.0% | 91.7% | 0.0% | 0.1% |
| 519R | S-D-Arch-0519-a-A-16 | TTACCGCGGCKGCTG | ||||||||
| 10 | 519F | S-D-Arch-0519-a-S-15 | CAGCMGCCGCGGTAA | 266 | 88.9% | 88.8% | 0.6% | 95.1% | 94.9% | 1.2% |
| 785R | S-D-Bact-0785-b-A-18 | TACNVGGGTATCTAATCC | ||||||||
| 11 | 515F | 515F-original | GTGCCAGCMGCCGCGGTAA | 291 | 52.9% | 86.8% | 0.0% | 94.3% | 93.8% | 0.3% |
| 806uR | 806R-original | GGACTACHVGGGTWTCTAAT | ||||||||
| 12 | 515FB | 515F-modified | GTGYCAGCMGCCGCGGTAA | 291 | 85.7% | 87.7% | 0.0% | 95.1% | 93.9% | 1.4% |
| 806RB | 806R-modified | GGACTACNVGGGTWTCTAAT | ||||||||
Coverage of Archaea, Bacteria and Eukarya is given in percentages, depending on whether no or one mismatch was allowed (last base at the 3′ end excluded for mismatch). ∗According to Klindworth et al. (2013). Designated “universal” primers (primer pairs 10–12) are indicated in bold letters.