Table 1.
List of the probes used in this study, with the stringency parameters for the hybridization (formamide %) and washing (NaCl concentration) steps.
| Probes | Specificity | Reference | Probe sequence Matching rRNA sequence Reversed control strain sequence | Specificity Control |
Formamide [%] Tested | NaCl [mmol L-1] Tested | |
|---|---|---|---|---|---|---|---|
| (–)pCtrl rDNA | Accession | ||||||
| Eub338 | Domain | Amann et al., 1990 |
5′ GCT GCC TCC CGT AGG AGT 3′ 3′ CGA CGG AGG GCA UCC UCA 5′ 3′ --- --- T-- --- --- A-- 5′ |
V. spinosum | X90515 | 50,55,60,65 | 18,10,4,0 |
| EubII | Domain | Daims et al., 1999 | 5′ GCA GCC ACC CGT AGG TGT 3′ 3′ CGU CGG UGG GCA UCC ACA 5′ 3′ --A --- A-- --- --- T-- 5′ | R. denitrificans | M59063 | 50,65 | 18,0 |
| EubIII | Domain | Daims et al., 1999 | 5′ GCT GCC ACC CGT AGG TGT 3′ 3′ CGA CGG UGG GCA UCC ACA 5′ 3′ --- --- A-- --- --- T-- 5′ | R. denitrificans | M59063 | 50,55,60,65 | 18,10,4,0 |
| Gam42a | Class | Manz et al., 1992 |
5′ GCC TTC CCA CAT CGT TT 3′ 3′ TT TGC TAC ACC CTT CCG 5′ 5′ -- --- -A- --- --- --- 3′ |
H. muralis | FN257757 | 50,55 | 18,10 |
| Roseo536R | Clade | Brinkmeyer et al., 2000 | 5′ CAA CGC TAA CCC CCT CCG 3′ 3′ GCC TCC CCC AAT CGC AAC 5′ 5′ --- --- --- C-- --- --- 3′ | P. aestuarii | EF660757 | 50,55,60 | 18,10,4 |
| RoseoC536R | Competitor | Brinkmeyer et al., 2000 | 5′ CAA CGC TAG CCC CCT CCG 3′ | ||||
| Euk1209 | Domain | Giovanonni et al., 1988 |
5′ GGG CAT CAC AGA CCT G 3′ 3′ G TCC AGA CAC TAC GGG 5′ 5′ T --- --A --T --- --- 3′ |
Haloarcheon msnc14(3) | FJ868734 | 40 | 46 |
| NChlo01 | Division | Simon et al., 1995 | 5′ GCT CCA CTC CTG GTG GTG 3′ 3′ GTG GTG GTC CTC ACC TCG 5′ 5′ --- --- --- -C- --- --- 3′ | Micromonas sp. | DQ025753 | 40 | 46 |
| Chlo02 | Division | Simon et al., 2000 | 5′ CTT CGA GCC CCC AAC TTT 3′ 3′ TTT CAA CCC CCG AGC TTC 5′ 5′ --- --- --- --A --- --- 3′ | L. reticulosa | EF622539 | 40 | 46 |
| Pela01 | Class | Simon et al., 2000 | 5′ ACG TCC TTG TTC GAC GCT 3′ 3′ TCG CAG CTT GTT CCT GCA 5′ 5′ --- A-- T-C --- --- T-- 3′ | S. scintillans | Support. Info. | 40 | 46 |
| Pras04 | Class | Not et al., 2004 | 5′ CGT AAG CCC GCT TTG AAC 3′ 3′ CAA GTT TCG CCC GAA TGC 5′ 5′ --- --- --- A-- --- --- 3′ | P. subviridis | U14386 | 40 | 46 |
(–)pCtrl, negative probe control strains with mismatches. Bold means validated formamide concentrations.