Table 1. PCR primers and FISH probes for small subunit rRNA used in this study.
| Target taxon | Primer/probe | Sequence (5′→3′) | Annealing/formamide | Reference |
|---|---|---|---|---|
| For PCR | ||||
| Bacteria | 27F-mix | AGRGTTTGATYMTGGCTCAG | 50 °C | Hongoh et al. (2007a) |
| 1390R | ACGGGCGGTGTGTACAA | |||
| 1492R | GGHTACCTTGTTACGACTT | |||
| Eukarya | E23F3 | ACYTGGTTGATYCTGCC | 50 °C | This study |
| E1511R4 | CWDCBGCAGGTTCWCCWAC | 50 °C | This study | |
| Verrucomicrobia subdivisions 1–4 and 6 | Verr-61F | GCGTGGYTAAGACATGCAAG | 72 °C | This study |
| Verr-361F | ACGGGTGGCAGCAGTTTC | |||
| Verr-1351R | GYCRTAGCTGATRCGCCA | |||
| For FISH | ||||
| Bacteria except Verrucomicrobia | EUB338 | GCTGCCTCCCGTAGGAGT | 60 °C | Amann et al. (1990) |
| Mainly Verrucomicrobia | EUB338-III | GCTGCCACCCGTAGGTGT | 60 °C | Daims et al. (1999) |
| Verrucomicrobia ‘termite cluster' | V-RsD37-130 | CGAGCTATCCCCAACTAA | 50 °C | This study |
| RsTaN-K1 | Verr-K1-181 | CATGCAGAACGAAACCAC | 50 °C+20% | This study |
| helper-K1 | ATTCGGTATTAATTCGCCTT | |||
| RsTaN-K2 | Verr-K2-181 | CATGCGAAAAGAAATCAC | 48 °C | This study |
| helper-K2 | ATTCGGTATTAATTCACC | |||