Digital, Three-Dimensional Visualization of Root Systems in Peat

Abstract

Belowground plant structures are inherently difficult to observe in the field. Sedge peat that mainly consists of partly decayed roots and rhizomes offers a particularly challenging soil matrix to study (live) plant roots. To obtain information on belowground plant morphology, research commonly relies on rhizotrons, excavations, or computerized tomography scans (CT). However, all of these methods have certain limitations. For example, CT scans of peat cores cannot sharply distinguish between plant material and water, and rhizotrons do not provide a 3D structure of the root system. Here, we developed a low-cost approach for 3D visualization of the root system in peat monoliths. Two large diameter (20 cm) peat cores were extracted, frozen and two smaller peat monoliths (47 × 6.5 × 13 cm) were taken from each core. Slices of 0.5 mm or 1 mm were cut from one of the frozen monoliths, respectively, using a paper block cutter and the freshly cut surface of the monolith was photographed after each cut. A 3D model of the fresh (live) roots and rhizomes was reconstructed from the resulting images of the thinner slices based on computerized image analysis, including preprocessing, filtering, segmentation and 3D visualization using the open-source software Fiji, Drishti, and Ilastik. Digital volume measurements on the models produced similar data as manual washing out of roots from the adjacent peat monoliths. The constructed 3D models provide valuable insight into the three-dimensional structure of the root system in the peat matrix.