Experiment 3: rhizosphere soil architecture analysis
To study soil architecture of the rhizosphere using micro-CT scan, three
chickpea genotypes were planted in the PVC tubes (5 cm diameter × 30 cm
height to fit the micro-CT scanner) using the same 5 soils with the same
soil bulk density and growing conditions to Experiment 1. At 16 DAP, a
period when no roots were observed at the bottom of every PVC tube,
plant shoots were cut off, and the tube with soil and roots was used for
micro-CT scanning. The PVC tubes with chickpea roots were scanned using
X-ray microtomography (Phoenix|X-ray, GE Sensing & Inspection,
Wunstorf, Germany) at 160 kV and 200 µA with a voxel resolution of
~16 µm to extract the 3D root system and measure the
pore architecture of the rhizosphere and bulk soil (Rabbi et al., 2018;
Rabbi et al., 2021). The top and bottom 1 cm-long roots were considered
as the basal and apical roots, respectively. The roots were extracted
from 3D image slices using ROOT1 (Flavel et al., 2017) plug-in for Fiji
(Schindelin et al., 2012). The segmentation of soils in pores and solids
were performed with the image thresholding algorithm in Fiji. The pores
within 0 to 1 mm (defined as rhizosphere) and from 1 to 2 mm (defined as
bulk soil) from the root surface were extracted and analysed using
RHIZOSPHERE macro (Rabbi et al., 2018) developed for Fiji.