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Pycnometry and WinRHIZO scans
After the laboratory tests described furtherly (Sections 2.5.1 to 2.5.3), soil was washed away to retrieve the plants individuals. Roots were placed in a pycnometer (Figure 5a), already filled with 100 mL of distilled water. The system was vibrated for 30 min to let the air bubbles come up and then, the water raised beyond the control line, due to roots immersion, was extracted with a pipette with a capacity of 0.01 mL and was assumed as roots volume.
After pycnometry, the same roots were scanned and analysed with the commercial software WinRHIZO (Regent Instruments Inc., Quebec, Canada). The software can capture and binarize images (Figure 5b) to evaluate root diameters (as projected area per length) and total length.
Water retention properties
Three root-permeated samples and one bare sample were used to determine the soil water retention curves. Matric and total suctions were assessed respectively by a ceramic tip laboratory tensiometer, up to 0.20 MPa, and a chilled mirror dew point hygrometer (WP4, Decagon Devices, Pullman, WA, USA), from 0.50 MPa on. After each drying phase during 30 min, soil samples were placed for 24 hours in glass desiccators (Figure 8a-b) with natural light, to allow suction and water content equalisation. Specimens with roots were left in the darkness for at least 2 hours to induce stomatal closure (Snyder et al. (2003)) and to completely stop the plant’s transpiration process (Howard et al. (2009)). Transpiration is in fact inducing hydraulic gradients within the matrix (Aylmore (1993)). After this period, the tensiometer was placed into the specimens up to a depth equal to their half height (35 mm).
Water content during tensiometer measurements was evaluated by oven-drying (ASTM D2216 (2019)): two soil samples of 30 g each were extracted using a spatula, one from the upper and one from the lower surface of the pots. Visual inspection before placing the samples in the oven made it possible to prevent the presence of roots inside them. This was done because the water contained in roots is not belonging anymore to soil pores (Boldrin et al. (2018); Garrigues et al. (2006); Prieto et al. (2012)). When the maximum measurable suction for tensiometer was reached, soil samples were trimmed out from the bottom part of the pots and installed in the abovementioned hygrometer, which is providing a measurement of the total suction. Results are presented in terms of water ratio (ew = ρsw/ ρw = Sre) because they are easily comparable with void ratio variations, since the two variables coincide when Sr = 1. Matric and total suctions were plotted in the same graph: indeed, according to Nam et al. (2009), osmotic effects are negligible in this kind of soil.
Volume changes upon drying
The characterization of the entire soil state and stress evolution (ew;e;s) was completed with paraffin tests (ASTM D7263 (2018)). To carry out these tests, cubes with a size of approximately 30 mm were trimmed out of fallow (5 cubes) and root-permeated pots (9 cubes) with an oil-lubricated spatula (to minimize friction with soil), and at different suctions (measured in the soil pot, by tensiometer or hygrometer, as described in Section 2.5.1) and water contents (measured in the soil pot, by oven-checking, as described in Section 2.5.1). In the case of root-permeated pots, the 9 cubes were trimmed out on plants’ vicinity. As the standard requires, the cubes were firstly weighed (with a laboratory balance with a precision of 0.1 mg) without paraffin: in the case of vegetated soil (Figure 11a), the plant’s aerial part (shoots) was cut with scissors before weighing. Soil cubes’ disturbance was evaluated by visual inspection. Samples were then immersed, face after face, in liquid paraffin at a temperature of 60°C. Once paraffin was solidified (Figure 11b), cubes were weighed again (precision 0.1 mg). Finally, soil covered by paraffin was weighed while being totally submerged in water (precision 0.1 mg). These three measurements allowed calculating the total volume of the soil cubes, with the equation: 7 = -O< 3 OP5 3 RO< 3 OSU 2N2 Q4 QT (4).
where OS is the mass of the cube without paraffin, O< is the mass of the cube covered by paraffin, OP is the submerged mass of the covered cube, Q4 and QT are the water and paraffin density respectively. Moreover, in the case of fallow soil cubes, OS consists in the sum of the masses of the liquid (O4C and the solid (OVC phases that are linked by the water content.From these two formulations, it is possible to calculate the masses of the two phases (O4 and OV) and their respective volumes (74 and 7VN*9W), which allowed estimating the void ratios.
In the case of vegetated soil cubes, the value of volume A72N2) calculated according to equation (4) included the volume of roots (as schematised in Figure 3a). As the aim of this test is to calculate the volume of voids (Vvoids) and the volume of solids (Vsolid), it was necessary to calculate the volume of roots (Vroots) and subtract it to the total volume. So, after submerged weighing, vegetated soil cubes were destroyed to recover the roots present inside them. The weight and the water content of the soil deprived of its roots were respectively measured and estimated. Then, it was possible to estimate the volume of solid particles, knowing their mass. Finally, roots volume was measured with a pycnometer, according to the procedure detailed in Section 2.4.2. Then, the volume of the pores was calculated as the difference: 7(N9WV = 72N2 3 7VN*9W 3 7$NN2V (5). With this procedure it was possible to evaluate the void ratio of the vegetated soil.
Plant effects at the microscale
It is assumed that roots affect soil structure due to different processes: pores chemical and physical clogging and soil fissuring due to roots growth and development. The domains involved by these phenomena correspond well to the porosity ranges that can be investigated by the two techniques used: Mercury Intrusion Porosimetry and X-ray microtomography.
Distribution of large-pore sizes
The images coming from the seven X-ray microtomography scans (one example is shown in Figure 14), previously analysed to determine the root volumes, have been furtherly processed to assess the effects of plants on the soil structure.
Pores and solid particles were identified through an automatic threshold operation, using ImageJ, calculated on the histogram of the grey values of the entire image stack and using the Default method. The threshold point was always close to 120 (Figure 3b). The image stack containing the roots phase (previously showed in Figure 4d) was then superimposed to the one showing solid and void phases (Figure 15a), in such a way that the roots are again virtually included into the sample (Figure 15b).
Roots effects on soil pore-size distribution
The pore size distribution (PSD) represents the cumulative void ratio occupied up to a given pore diameter, starting from the maximum diameter observed. In the case of X-ray micro-tomography, the cumulative void ratio for a given entrance pore size x* was calculated by: ‘AdeC fdgdehij 7(AdC (8) [bcF = 7V.
where Vv(x) is the volume of voids (white pixels in Figure 15b) occupied by a generic entrance pore size x and Vs is the volume of solid particles, calculated as the total volume of the black pixels in Figure 15a. In the case of the results given by MIP, the cumulative void ratio is evaluated directly from mercury intruded volume, as explained in Romero et al. (1999).
Results have been joined to make the upper end of the microtomography curve coincide with the lower end of the MIP curve (Figure 16). In the plot, there is a comparison between PSD curves obtained for bare and root-permeated soils at a water ratio equal to ew ≈ 0.33 (e ≈ 0.64, Sr ≈ 0.52). The two curves almost approached the same final cumulative void ratio but did not reach the value at which they were originally compacted. Moreover, root-permeated soil’s cumulative void ratio at 7 nm was always slightly higher than the bare soil’s one, for each water ratio tested. This means that a general increase in void ratio was observed in vegetated soil with respect to bare soil. This agrees to what observed by paraffin tests.
Table of contents :
1. Introduction and objectives
1.1 Background
1.2 Aim and objectives
1.3 Thesis content
1.4 Workshops and conference presentations:
1.5 Publications in ranked scientific journals
2. Effects of plant growth on soil microstructure and hydro-mechanical behaviour
2.1 Abstract
2.2 Introduction
2.3 Soil properties and initial state
2.4 Roots volume and structural features
2.4.1 Pycnometry and WinRHIZO scans
2.4.2 Comparison of results
2.5 Plant effects at the macroscale
2.5.1 Water retention properties
2.5.2 Volume changes upon drying
2.5.3 Saturated water permeability
2.6 Plant effects at the microscale
2.6.1 Distribution of large-pore sizes
2.6.2 Extension to the micro-pores range
2.6.3 Roots effects on soil pore-size distribution
2.7 Roots traits and soil microstructure on drying
2.8 Micro and macroscale interactions
2.9 Concluding remarks
3. Hydro-mechanical framework to predict root effects on a compacted silty soil .
3.1 Abstract
3.2 Introduction
3.3 Methods
3.3.1 Oedometer tests
3.4 Micro-scale model formulation and calibration
3.5 Macroscopic hydro-mechanical framework
3.5.1 Oedometer test results
3.5.2 Macroscopic framework development
3.6 Model validation and performance
3.7 Conclusions
4. Mechanical behaviour of a vegetated soil at different hydraulic states
4.1 Abstract
4.2 Introduction
4.3 Soil properties and compaction
4.4 Roots growth and characterization
4.5 Methodology
4.5.1 Triaxial Compression Tests
4.5.1 Direct tensile test
4.5.2 Void ratio measurements in vegetated soil
4.5.3 Constitutive laws used
4.6 Results
4.6.1 Hydraulic state and stress evolution during tests
4.6.2 Triaxial Compressions
4.7 Direct Tensile Tests
4.8 Joint interpretation of the results
4.9 Conclusions
5. Numerical analysis of a bare and a vegetated embankment
6. Conclusions
6.1 Preparation and testing protocol of samples
6.2 Roots effects on soil micro-structure
6.3 Geotechnical characterization of a vegetated soil
6.4 Constitutive model to predict a vegetated soil retention curve
6.5 Simulation of the HM response of a vegetated slope submitted to water content changes
6.6 Applications to engineering problems
6.7 Thesis contribution
6.8 Future lines of research
References
