The conversion by soil organisms of inorganic nutrients such as ammonium or nitrate into organic compounds that are part of their cells. This makes the nutrients temporarily immobile in the soil and unavailable to plants. (See mineralization.)

An instrument (measurement, dataset, model, expert elicitation system) for quantifying an attribute, providing quantitative information of the system. For instance, the protocol for soil sampling and pH (KCL) measurement is an indicator for the 'soil pH', and the extraction, counting, identification of nematodes and calculation of the maturity index is an indicator for the 'nematode community in the soil system'. Note that this definition differs from the daily practice where, for example, the pH or the nematode community as such, and not the protocol, is seen as the indicator.

A quantitative or qualitative measure used to estimate soil functional capacity. Indicators should be adequately sensitive to change, accurately reflect the processes or biophysical mechanisms relevant to the function of interest, and be cost effective and relatively easy and practical to measure. Soil quality indicators are often categorized into biological, chemical, and physical indicators.

Measures of living organisms or their activity used as indicators of soil quality. Measuring soil organisms can be done in three general ways: 1) counting soil organisms or measuring microbial biomass, 2) measuring their activity (e.g. soil basal respiration, cotton strip assay, or potentially mineralizable nitrogen), or 3) measuring diversity, such as diversity of functions (e.g., biolog plates) or diversity of chemical structure (e.g. cell components, fatty acids, or DNA). Each approach provides different information.

These include tests of organic matter, pH, electrical conductivity, heavy metals, cation exchange capacity, and others.

Physical characteristics that vary with management include bulk density, aggregate stability, infiltration, hydraulic conductivity, and penetration resistance.

Accumulation of agents able to promote biological stress and subsequent loss of yield such as nematodes, weeds, microorganisms, mice, etcetera, favoured by, for instance, a too narrow crop rotation.

The movement of water passing the soil surface into the soil (as contrasted with percolation, which is movement of water through soil layers moving down to the aquifers, or out to rivers).

The maximum rate at which water can infiltrate into a soil under a given set of conditions.

The speed at which water can pass into the soil, being typically lower in wet clay than in dry sand (unless sand has become hydrophobic).