Cover crops (CC) are promoted to enhance soil structure and aggregation, but little is known about their impact on the spatial variability of soil microstructure. This study was conducted to assess the effects of medium-term (4-yr) annual CC systems, including oat (Avena sativa L.), winter cereal rye (rye; Secale cereale L.), oilseed radish (OSR; Raphanus sativus L. var. oleoferus Metzg. Stokes), as well as a mixture of OSR and winter cereal rye (OSR + Rye), against a control (no cover crop, no-CC), on topsoil microstructure utilizing 3D semivariance analysis, as influenced by soil depth (0–5 and 5–10 cm) in a tile-drained Orthic Humic Gleysol in Ridgetown, Ontario, Canada. Replicate undisturbed topsoil core samples were collected manually in plexiglass tubes from each plot. All soil cores were dried at 40 °C, then imaged at 20 μm pixel size using GE MS8-130× CT scanner (120kv, 0.5 mm Cu filter). The whole core greyscale imagery (representing radiodensity on the Hounsfield Scale) was subjected to a three-phase segmentation (solids, voids, and remaining soil matrix). For the whole soil and the soil matrix imagery, 16-bit histograms and 3D orthogonal semivariograms were generated. Directional anisotropy and four semivariogram parameters close to the origin, including the ratio between the values of the total variance and the semivariance at first lag (RVF), the ratio between semivariance values at second and first lag (RSF), first derivative near the origin (FDO), and second derivative at the third lag (SDT), were calculated to explain spatial variability in the soil microstructure. The results exhibited lower radiodensities for whole soil samples from the 0–5 cm than 5–10 cm layers. All CCs, other than oats, showed lower radiodensities than the control (no-CC). For both the whole soil and soil matrix, more variability was encountered in the vertical than the horizontal dimensions of all soils. Comparing the whole soil and the soil matrix in different CC systems and layers, more anisotropy was pronounced in the soil matrix than the whole soil imagery. The highest and the lowest anisotropy, calculated for the whole soil and soil matrix of different CC systems, were observed in oat and rye plots, respectively. There were no significant differences among CCs systems in terms of RVF, RSF, and SDT values, suggesting similarity of the structure at the scale slightly above image resolution. The results illustrated that soils under different CC systems showed only significant differences in the whole soil for FDO values (P ≤ 0.08). All four near-origin semivariogram parameters showed significant differences between 0 and 5 and 5–10 cm layers in both the whole soil and the soil matrix, suggesting more complexity in the microstructure of the uppermost soil layers.
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