TABLE 1.
PCR primers and FISH probes used in this study
| Purpose and target | Primer name | Fluorescent label | Formamide concn (%) | Sequence (5′–3′) | Reference(s) |
|---|---|---|---|---|---|
| PCR | |||||
| 18S rRNA of eukaryotes | 18S-42F | CTCAARGAYTAAGCCATGCA | 44 | ||
| 18S-1520R | CYGCAGGTTCACCTAC | 44 | |||
| 16S rRNA of bacteria | Eub11fa | TGRGTTTGATCMTGGCTYAG | 8 | ||
| Eub1511r | TGGDTACCTTGTTACGACTT | 8 | |||
| 16S rRNA of archaea | Ar109f | AMDGCTCAGTAACACGT | 46 | ||
| Ar1490Ra | GGHTACCTTGTTACGACTT | 45 | |||
| Colony PCR and sequencing | |||||
| Cloning vector pCR2.1 | pCR2.1f | GTAATACGACTCACTATAGGG | This study | ||
| pCR2.1r | ATTACGCCAAGCTTGGTACC | This study | |||
| Sequencing | |||||
| 18S rRNA of eukaryotes | EK-555F | AGTCTGGTGCCAGCAGCCGC | 44 | ||
| 16S rRNA of bacteria | Eub920r | CCGYCAATTCCTTTGAGTTT | 8 | ||
| 16S rRNA of archaea | Arc1000r | TCTCGCTCGTTGCCTGACT | 8, 47 | ||
| FISH | |||||
| 16S rRNA of endosymbiotic Methanoregula (Met1) of GW7 | GW7Met1 | Alexa 488 | 20 | CAGCCCGACTATCATTCAGCTG | This study |
| 16S rRNA of Methanosaeta spp. (used for detecting Met2) | MX825 | Alexa 488 | 0 | TCGCACCGTGGCCGACACCTAGC | 54 |
| 16S rRNA of the bacterial candidate (Bac1) of GW7 | GW7Bac1 | Alexa 568 | 0 | ACAATAACACTTGCTCACAA | This study |
| 16S rRNA of endosymbiotic “Candidatus Hydrogenosomobacter endosymbioticus” (Bac2) of GW7 | GW7Bac2 | Alexa 568 | 20 | CTCTGTTTCCAGAGCCCTCGAT | This study |
| 16S rRNA of the bacterial candidate (Bac3) of GW7 | GW7Bac3 | Alexa 568 | 0 | CCGACTGGTTACTTTCATAACC | This study |
| 16S rRNA of archaea | ARC915 | Alexa 488/Alexa 568 | 20/35 | GTGCTCCCCCGCCAATTCCT | 55 |
| 16S rRNA of most bacteria | EUB338 | Alexa 488/Alexa 568 | 20/35 | GCTGCCTCCCGTAGGAGT | 56 |
| 16S rRNA of Verrucomicrobia | EUB338III | Alexa 488 | 0 | GCTGCCACCCGTAGGTGT | 54 |
a
In the respective references, the primers are named Eub8f and 1490R.