DNA analysis of soil extracts can be used to investigate fine root depth distribution of trees

Abstract

Understanding the root distribution of trees by soil coring is time -: consuming as it requires the separation of roots from soil and classification of roots into particular size classes. This labour-intensive process can limit sample throughput and therefore sampling intensity. We investigated the use of quantitative polymerase chain reaction (qPCR) on soil DNA extractions to determine live fine root DNA density (RDD, mg DNA m(-2)) for mango (Mangifera indica) trees. The specificity of the qPCR was tested against DNA extracted from 10 mango cultivars and 14 weed species. All mango cultivars and no weeds were detected. Mango DNA was successfully quantified from control soil spiked with mango roots and weed species. The DNA yield of mango root sections stored in moist soil at 23-28 °C declined after 15 days to low concentrations as roots decayed, indicating that dead root materials in moist soil would not cause false-positive results. To separate large roots from samples, a root separation method for field samples was used to target the root fragments remaining in sieved (minimum 2 mm aperture) soil for RDD comparisons. Using this method we compared the seasonal RDD values of fine roots for five mango rootstock cultivars in a field trial. The mean cultivar DNA yields by depth from root fragments in the sieved soil samples had the strongest relationship (adjusted multiple R(2) = 0.9307, P < 0.001) with the dry matter (g m(-2)) of fine (diameter <0.64 mm) roots removed from the soil by sieving. This method provides a species-specific and rapid means of comparing the distribution and concentration of live fine roots of trees in orchards using soil samples up to 500 g.

Keywords: DNA persistence; fine-roots; root DNA concentration; root DNA density (RDD).

Figure 1.

Root dry matter concentrations (0, 25, 50, 100, 300, 800 and 1600 mg kg⁻¹) of KP root tissue in control soil plotted against pg DNA (g soil)⁻¹ values (Exp. 4), with a fitted linear regression, y = 9.7666 (x), P < 0.001, adjusted multiple R² = 0.9909, standard error of coefficient 0.1769, df = 27 (Exp. 4).

Figure 2.

Results of a mango root DNA (pg DNA g⁻¹ soil) persistence experiment (Exp. 5) over 30 days for NDM (Hamilton) root tissue subjected to four treatments: sliced root in dry soil; sliced root in 75 % FC soil; 10 mm root sectioned in dry soil; 10 mm root sectioned in 75 % FC soil, df = 33, standard error of the mean = 208.1, Tukey’s HSD = 998.8.

Figure 3.

Regression results of average Class 1 (diameter <0.64 mm) mango root dry matter (DM g m⁻²) values for samples of five rootstock cultivars (see legend) sampled in November from three sample depths (0–15, 15–30 and 30–45 cm) in the rootstock trial (Exp. 6) between average mango DNA concentrations in soil (mg m⁻²) of sieved soil after root removal with fitted regression, y = 0.0062x + 0.0376.

Figure 4.

Mango DNA (mg DNA m⁻²) of sieved soil for the five cultivars (plots A–E) for three sample depths sampled in November (post-harvest) and the following February (post-wet season) in the rootstock trial (Exp. 6), df = 12 for each comparisons, HSD values shown by vertical bars.