TABLE 3.
Efficacy of DNA extraction procedures evaluated on the basis of DNA yield and cell lysis
| Procedure | Chemical treatmenta | Physical treatmentb | DNA yield (μg g [dry wt]−1)c
|
% Cell lysis with wetland sediment (mean ± SE)d | ||
|---|---|---|---|---|---|---|
| Agricultural soil | Forest soil | Wetland sediment | ||||
| 1 | SDS | B | 7.0 ± 0.5 | 26 ± 4 | 32 ± 1 | 68 ± 4 |
| 2 | SDS-phenol | B | 7.8 ± 0.2 | 31 ± 5 | 40 ± 4 | 77 ± 5 |
| 3 | SDS-chloroform | B | 7.9 ± 1.2 | 35 ± 7 | 53 ± 8 | 81 ± 4 |
| 4 | SDS-Chelex 100 | B | 6.2 ± 0.3 | 19 ± 5 | 32 ± 2 | 68 ± 7 |
| 5 | Lysozyme-SDS | FT | 1.5 ± 0.7 | 4 ± 3 | 6 ± 1 | 65 ± 4 |
| 6 | GTC | FT | <0.1 | <0.1 | 0.2 ± 0.3 | 64 ± 3 |
| 7 | SDS | FT | 2.7 ± 0.8 | 6 ± 3 | 6 ± 1 | 63 ± 6 |
| 8 | Lysozyme-SDS | B | 1.5 ± 1.2 | 9 ± 4 | 7 ± 4 | 69 ± 2 |
| 9 | GTC | B | <0.1 | <0.1 | <0.1 | 67 ± 4 |
a
See Table 2, footnotes a and b.
b
See Table 2, footnote c.
c
Calculated from the average density of ethidium bromide-stained DNA bands by using NIH Image software. The values are averages ± standard errors based on three or four independent extractions.
d
Estimated from the DAPI direct counts of bacterial cells per microscope field before and after DNA extraction. The values are average percentages of cells lysed ± standard errors based on three independent DNA extractions performed by using the same DNA extraction procedure.