TABLE 5.
Efficacy of DNA purification procedures as evaluated by DNA recovery and inhibition of the PCR
| Purification method | % DNA recovery (mean ± SE)a
|
No. of successful PCR amplifications with the following dilutions of extractb:
|
|||||
|---|---|---|---|---|---|---|---|
| Agricultural soil | Forest soil | Wetland sediment | 100 | 10−1 | 10−2 | 10−3 | |
| No purification | 100 ± 7 | 100 ± 9 | 100 ± 15 | 0 | 0 | 0 | 2f |
| SpinBind column | 83 ± 3 | 80 ± 5 | 41 ± 8 | 0 | 1c | 3 | 3 |
| Gel electrophoresis | 40 ± 12 | 38 ± 12 | 10 ± 1 | 0 | 2d | 3 | 3 |
| Ammonium acetate precipitation | 85 ± 4 | 76 ± 9 | 69 ± 6 | 0 | 0 | 0 | 3 |
| Sephadex G-200 column | 80 ± 7 | 95 ± 6 | 80 ± 8 | 0 | 2e | 3 | 3 |
a
DNA yield was calculated by using the average density of ethidium bromide-stained DNA bands analyzed with NIH Image software.
b
DNA from each soil or sediment was diluted, spiked with purified DNA, PCR amplified, and scored on the basis of the presence of a 215-bp BG8 amplicon as described in Materials and Methods.
c
PCR amplification was successful only from forest soil DNA.
d
PCR amplification was successful only from forest soil and wetland sediment DNA.
e
PCR amplification was successful only from agricultural soil and wetland sediment DNA.
f
PCR amplification was successful only from agricultural soil and forest soil DNA.