TABLE 3.
Results of PCR experiments with Mono Lake DNA extractsa
| Sample
|
Expt
|
rRNA sequence obtained
|
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Direct amplification of genomic DNA extracts with:
|
Two-stage amplification: reamplification of EUB amplification product with:
|
P2P3 amplification: reamplification of NitA-NitB amplification product with:
|
Laboratory A | Laboratory B | |||||||
| No. | Depth (m) | EUB | NitA-NitB | NitD-NitB | NitA-NitB | NitD-NitB | NOC1-NOC2 | P2P3 | N.euro* | ||
| 4.2 | 1 | + | + | − | + | + | − | + | + | ||
| 4.7 | 1 | + | − | − | + | + | − | + | + | ||
| 4.5 | 5 | + | + | + | + | + | − | + | + | 4.5PCR | 4.5-A–4.5-E |
| 4.8 | 5 | + | + | + | + | + | − | + | + | 4.8PCR | 4.8-A–4.8-E |
| 4.3 | 10 | + | + | − | + | + | − | + | + | ||
| 4.9 | 10 | + | − | − | − | + | − | + | + | ||
| 4.10 | 11 | + | − | − | + | − | − | − | |||
| 4.11 | 12 | + | − | − | + | + | − | + | + | ||
| 4.12 | 12 | + | − | ||||||||
| 4.13 | 13 | + | + | − | + | + | − | + | + | ||
| 4.14 | 15 | + | + | − | + | + | − | + | |||
| 4.15 | 15 | + | + | − | + | + | − | + | + | ||
| 4.16 | 17 | + | − | − | − | + | − | + | + | ||
| 4.17 | 20 | + | − | − | − | − | − | − | |||
| 4.20 | 20 | + | − | − | + | − | − | − | |||
| 4.18 | 23 | + | + | + | + | + | − | + | + | 4.18.4, 4.18.8 | 4.18-A–4.18-J |
| 4.19 | 25 | + | − | − | − | − | − | − | |||
| 7.6 | 1 | + | − | − | − | ND | − | ND | |||
| 7.15 | 1 | + | + | − | + | + | − | + | + | 7.15PCR | 7.15-A–7.15-J |
| 7.2 | 5 | + | + | ND | − | ND | − | ND | |||
| 7.5 | 5 | + | − | − | + | + | − | + | |||
| 7.4 | 7 | + | − | − | + | − | − | − | |||
| 7.7 | 10 | + | − | − | − | ND | − | ND | |||
| 7.13 | 10 | + | + | − | + | + | − | + | + | ||
| 7.19 | 10 | + | − | − | + | + | − | + | + | ||
| 7.3 | 12 | + | + | ND | − | ND | − | ND | |||
| 7.12 | 13 | + | − | − | + | + | − | + | |||
| 7.11 | 14 | + | − | − | + | + | − | + | |||
| 7.1 | 15 | + | + | − | − | − | − | − | |||
| 7.1 | 17 | + | − | − | + | + | − | + | |||
| 7.18 | 20 | + | + | + | + | + | − | + | + | 7.18.5, 7.18.6 | 7.18-B–7.18-H |
| 7.14 | 23 | + | + | − | + | + | − | + | + | ||
| 7.17 | 25 | + | + | − | + | + | − | + | + | ||
a
See Table 1 for primer abbreviations. The names of the rDNA sequences reflect derivation as sequenced directly from the PCR fragment (e.g., 4.5PCR) or from a cloned PCR fragment (e.g., 4.18.4). +, detection of expected size PCR fragment by agarose gel electrophoresis; −, denotes no PCR fragments detected; ND, no data due to insufficient sample to perform this analysis; N. euro*, detection of a band corresponding to the position of the N. europaea standard band in DGGE.