Contrast-enhanced repacked soil cores as a proxy for soil organic matter spatial arrangement

Soil organic matter (SOM) plays a key role in soil structure formation, although the bidirectional relationship between SOM and the soil pore network is complex and needs further investigation. Despite great advances provided by X-ray computed microtomography (mu CT), it has only been used in a few studies to investigate the organic matter 3D-arrangement within the soil matrix. Results are based on the X-ray linear attenuation coefficient (alpha), and mixtures of organic and mineral soil fractions could imply overlapping of information that makes any segmentation procedure difficult. The aim of this study was to visualise, segment, and quantify the particulate organic matter fraction (POM) within the soil matrix through X-ray mu CT in combination with contrast agents (phosphomolybdic acid and silver nitrate). Two series of repacked soil cores, dry' and wet', were scanned through X-ray mu CT at a 7-mu m resolution. Different segmentation approaches were tested to separate POM from other soil phases: manual, global, and local thresholding methods. Reported algorithms were also compared with a supervised grey value-based (GV) approach followed by morphological operations. Results showed contrast agents increased alpha of POM, simplifying its identification and the following segmentation on dry cores. The POM was discriminated from the mineral fraction and its content correctly estimated. This was particularly accurate when applying manual thresholding or GV approach with respect to indicator kriging, suggesting that operator-based ability to set threshold level is still the best solution for accurate POM segmentation. Beyond single-phase accounting, different thresholding algorithms and morphological operations also affected POM morphological characteristics. In particular, the simpler was an object shape, the easier was its segmentation. Improvements are thus required to increase the efficiency of automated thresholding algorithms. Moreover, wet cores were exposed to washing-out phenomena that compromised any digital image processing and further POM quantification, implying that more effort should be made to find other suitable staining agents.