A comprehensive China soil dataset of high-resolution microstructure, topographical characteristics and physical properties

Soil is the domain where hydro-bio-geo-chemical processes are closely coupled in the ecosystem. Soil microstructure, the arrangement of soil particles and aggregates into a porous structure, regulates the flow of resources. Soil microstructure data includes both the 3D structures of the soil and the morphological parameters characterizing their topological and physical properties, all of which are essential for understanding solute transport dynamics such as oxygen diffusion, water flow, organic matter accessibility, and nutrient availability. However, it is challenging to access high-resolution soil microstructure data, for the heterogeneity and opacity of soils, as well as the costs associated with advanced imaging techniques. In this study, we present a novel 3D soil microstructure dataset that integrates high-resolution imaging data of soils across China (CHARM3D) with comprehensive measurements of topological and physical properties to quantitatively characterize soil morphological parameters. Thirty sampling sites were selected within the Chinese Ecosystem Research Network (CERN), including six major ecosystems: forests, grasslands, deserts, agricultural lands, wetlands, and lakes. A total of 120 soil samples representing diverse soil orders were collected, reconstructed using high-resolution X-ray computed tomography (XCT), and analyzed with advanced image processing techniques via ImageJ and Avizo software. Morphological parameters are consisted of topological characteristics that describe the geometry of pore networks, and physical parameters associated with soil functions, particularly permeability and connectivity. Topological features were extracted using ImageJ combined with pore network analysis, whereas permeability-related connectivity was simulated through pore-scale modeling. A case study analyzing representative soil samples from the six ecosystems demonstrates the usefulness of the dataset in providing key parameters for reactive transport modeling in soils, such as pore connectivity, permeability, porosity distribution, as well as in characterizing the impact of soil aggregation on flow transport. This dataset provides valuable insights into soil structure variation across ecosystems and serves as a critical resource for calibrating soil hydraulic models in regional studies.