Table 2.
DNA extraction protocol on samples DH_1, DH_2, and CS.
| Protocola | DNA yield (ng/g)b | PCR amplification† | ||||||
|---|---|---|---|---|---|---|---|---|
| DH_1* (± SD) | DH_2 (± SD) |
CS (± SD) | Kit blankc (± SD) | DH_1 | DH_2 | CS | PCR blank | |
| 1 | BDLd | BDL | 6,633*,NS (2,310) | BDL | −d | − | +++ | − |
| 2 | BDL | 2.5*,NS (0.1) | n.d | BDL | − | − | n.d.d | − |
| 3 | 24.6* (0.2) | 31.8* (0.2) | 1517*,NS (16) | 60.1 (3) | + d | + | + | + |
| 4 | BDL | 10 (0.1) | 660* (6.4) | BDL | + | ++ d | ++ | − |
| 5 | BDL | 4.6*,NS (0.4) | n.d | BDL | − | ++ | n.d | − |
| 6 | 0.7* (0.1) | BDL | 513* (14) | BDL | +++ d | + | + | − |
| 7 | 1.1* (0.2) | 17* (0.2) | n.d | BDL | ++ | +++ | n.d | − |
† DNA templates for PCR were diluted 1:2, 1:5, and 1:10 and PCR amplifications of these dilutions were performed in triplicate. Results marked as positive yielded PCR product for all replicates; no amplification product was detected for any replicate for those marked as negative.
aDNA extraction protocols: 1 = Fast DNA SPIN kit for soil (manufacturer’s protocol), 2 = Fast DNA SPIN kit for soil (modified), 3 = OMEGA E.Z.N.A soil DNA kit (manufacturer’s protocol), 4 = Powersoil Isolation kit (manufacturer’s protocol), 5 = Powersoil Isolation kit (modified), 6 = ZymoBIOMICS DNA Microprep kit (manufacturer’s protocol), and 7 = ZymoBIOMICS DNA Microprep kit (modified).
bDNA was extracted from triplicate 1 g subsamples for DH_1 and DH_2, and triplicate 0.5 g subsamples from CS.
cMeasured in ng of DNA.
dBDL = below the detection limit, n.d. = not done, + = weak PCR band,++ = medium PCR band,+++ = strong PCR band, − = not detected.
*p < 0.05 (based on Student’s t test).
NS Not Statistically Significant (p ≥ 0.05), DH_2: Protocol 2 vs 5 and CS: Protocol 1 vs 3.