Rice (Oryza sativa) is usually grown under flooded conditions, leading to anoxic periods in the soil. Rice plants transport oxygen via aerenchyma from the atmosphere to the roots. Driven by O2 release into the rhizosphere, radial gradients of ferric Fe and co-precipitated organic substances are formed. Our study aimed at elucidating the composition and spatial extension of those gradients. Air-dried soil aggregates from a paddy field were embedded in epoxy resin, cut, and polished to produce cross sections. Reflected-light microscopy was used to identify root channels. With nano-scale secondary ion mass spectrometry (NanoSIMS), we investigated transects from root channels into the soil matrix and detected 12C−, 16O−, 12C14N−, 28Si−, 27Al16O−, and 56Fe16O− to distinguish between embedding resin, organic matter, oxides, and silicates. Image analyses reveal high occurrences of 56Fe16O− within and in close proximity of oxide-encrusted root cells, followed by a thin layer with high occurrences of 27Al16O− and 12C14N−. In two of the three transects, 28Si− only occurs at distances larger than approximately 10 µm from the root surface. Thus, we can distinguish distinct zones: the inner zone is composed of oxide encrusted root cells and their fragments. A thin intermediate zone may occur around some roots and comprises (hydr)oxides and organic matter. This can be distinguished from a silicate-dominated outer zone, which reflects the transition from the rhizosphere to the bulk soil.

Some soils have serious physical and chemical limitations to cultivation. They are problem soils. These soils need special management for satisfactory crop production. Physical limitations can be managed by irrigation, drainage, mulching, manuring, tillage, and soil conservation measures such as terracing, contouring, and cover crops whichever is appropriate. Use and disturbance of soils on steep slopes and in wetlands should be avoided because of the risk of their degradation. They should be left under natural conditions. Saline soils are managed through adequate irrigation, leaching, draining, and growing salt-tolerant crops. Sodic soil management needs chemical amendments such as application of sulfur and gypsum along with leaching and draining. Management of acid soils involves liming, leaching, and safe disposal of acid-wash water along with cultivating acid-tolerant crops.

Physical properties of soil include color, texture, structure, porosity, density, consistence, temperature, and air. Colors of soils vary widely and indicate such important properties as organic matter, water, and redox conditions. Soil texture, structure, porosity, density, and consistence are related with types of soil particles and their arrangement. There are two types of soil particles—primary and secondary. Primary particles include sand, silt, and clay, categorized on the basis of their effective diameter. There are important differences in physical, chemical, and mineralogical properties of these fractions. Their relative proportion in a soil is called soil texture. It is a fundamental property of soil. It is not easily altered. There are 12 textural classes ranging from sand to clay. Soil structure is the arrangement of soil particles into different geometric patterns. It is classified into different types on shape, classes on size, and grades on stability. Soil structure is amenable. Soil texture and structure together regulate porosity, density, compactness, retention, and movement of water and air in soil. Soil temperature is slightly higher than air temperature in a place. It influences life processes of soil biota including plants. Soil air is retained in soil pores; its composition is variable, and it contains higher carbon dioxide and moisture and lower oxygen concentration than atmospheric air. Soil air has a great role in respiration of plant roots and microorganisms and transformation of mineral and organic matter.