Soil Health glossary

Top terms you need to know about SOIL HEALTH

Soil Health concept is wide and complex, as it involves multiple elements and approaches. In this post, we gather some of the key elements to take into account when exploring the topic of soil health. This glossary is a live body that we will be enriching with new relevant  terms that help to shape a holistic vision of this key element in agriculture. 

Soil Health

The continued capacity of the soil to function as a vital living system, within the ecosystem and land-use boundaries, to sustain biological productivity, promote the quality of air and water environments, and maintain the plant, animal, and human health. (1)

Soil health also referred to as soil quality, is defined as the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals, and humans.
Only "living" things can have health, so viewing soil as a living ecosystem reflects a fundamental shift in the way we care for our soils. (2)

Soil health is the soil’s capacity to function in the long term as a living system, i.e. capable of insuring a plant biomass productivity compatible with long-term maintenance of the ecological functions of natural or cultivated ecosystems, and with related processes: contribution to the preservation of natural resources, that is to say, air, water, and biodiversity, quantitatively and qualitatively, and contribution to the health of plants, animals and humans by promoting the physiological processes that are involved in their self-defense systems.

This definition, by focusing on biological components and processes, has gradually emerged in the 2000s from the definition of “soil quality” which dominated in the 1990s and focused almost exclusively on the aspects of physical and chemical fertility of soils. Hence, soil health is a keystone principle in the agroecological transition perspective. (3)


Use of microorganisms having disease-suppressive capabilities to improve plant health. Disease suppression by biocontrol agents is the sustained manifestation of interactions among the plant, the pathogen, the biocontrol agent, the microbial community on and around the plant, and the physical environment (11) . In Becrop reports, this marker is based on the relative abundance of beneficial microorganisms known to perform roles of fungicide, bactericide, nematicide and insecticide biocontrol.


In BeCrop, three indexes are calculated, among them is Biosustainability. It indices are biomarkers of the ecosystem in which the parcel is based, and are related to agricultural management practices. Three indexes are calculated based on the detection of all the microorganisms in the samples. Low values may indicate of intensive management practices, while high indexes are linked to sustainable and less intensive practices.

Carbon sequestration

Carbon sequestration describes the process of capturing and long-term storing atmospheric carbon dioxide or other forms of carbon in plants, soils, geologic formations, and the ocean, to either mitigate or defer global warming and avoid dangerous climate change. It has been proposed as a way to slow the atmospheric and marine accumulation of greenhouse. (13)

In response to growing concerns about climate change resulting from increased carbon dioxide concentrations in the atmosphere, considerable interest has been drawn to the possibility of increasing the rate of carbon sequestration through changes in land use and forestry and also through geoengineering techniques such as carbon capture and storage gases, which are released by burning fossil fuels.

Crop Healthiness

Crop health according to the detected pathogens. It is calculated using epidemiological information and the vulnerability of the microbial ecosystem analyzed. Is established depending on the risk of developing diseases detected.

DNA Sequencing

Sequencing DNA means determining the order of the four chemical building blocks - called "bases" - that make up the DNA molecule. The nucleotide sequence is the most fundamental level of knowledge of a gene or genome. It is the blueprint that contains the instructions for building an organism. In other words, sequencing consists in transforming the information contained in DNA into data that can be analyzed informatically and used to identify microbes, among many other things

Plant nutrition (nutrition pathways)

Plant growth and development largely depend on the combination and concentration of mineral nutrients available in the soil. Two classes of nutrients are considered essential for plants: macronutrients and micronutrients. Macronutrients are the building blocks of crucial cellular components like proteins and nucleic acids; as the name suggests, they are required in large quantities. Nitrogen, phosphorus, magnesium, and potassium are some of the most important macronutrients. Carbon, hydrogen, and oxygen are also considered macronutrients as they are required in large quantities to build the larger organic molecules of the cell; however, they represent the non-mineral class of macronutrients.

Micronutrients, including iron, zinc, manganese, and copper, are required in very small amounts. Micronutrients are often required as cofactors for enzyme activity. Mineral nutrients are usually obtained from the soil through plant roots, but many factors can affect the efficiency of nutrient acquisition. First, the chemistry and composition of certain soils can make it harder for plants to absorb nutrients. The nutrients may not be available in certain soils, or maybe present in forms that the plants cannot use. (12)

Soil microorganisms are responsible for the cycling of many nutrients in the soil, metabolizing organic forms, and providing plants with available nutrient forms. This is especially important in providing the plant with available forms of Nitrogen, Phosphorus, Potassium, Sulfur, and Calcium among other elements. 

Plant nutrient Imbalance

Refers to an excess or a lack of nutrients (mainly nitrogen, phosphorus and potassium) in the soil as a consequence of bad land use and management. It may result in soil contamination when nutrients are in excess and in loss of inherent fertility when nutrients are mined. (FAO)

Plant nutrient mobilization

Once inside plants, nutrients are transported to where they are needed, typically to growing points. Once incorporated by the plant, some elements can be immobile while others can be remobilized. Immobile elements essentially get locked in place and that is where they stay. Those that can be remobilized can leave their original location and move to areas of greater demand.

Knowing which are mobile or immobile is helpful in diagnosing deficiency symptoms.
Since immobile elements do not easily move within the plant when deficiency symptoms occur they show up in new growth. When mobile elements become limiting, they can be scavenged from older growth and moved to where they are most needed, causing deficiency symptoms in older growth. (14)


Area of soil affected by root secretions and microorganisms

Soil biodiversity (soil biota)

Diversity of (micro- and macro-) organisms present in soil. It is assessed by calculating taxonomic diversity and converting it into a contextualized and meaningful score. (6)

Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. Lack or loss of soil biodiversity diminishes the ability of soil to provide critical ecosystem services (FAO).

The most dominant group in soil biota, both in terms of number and biomass, is represented by microorganisms (i.e., bacteria, archaea, and fungi), which show different nutrient strategies and lifestyles (saprotrophs, pathogens, symbionts).

The rhizosphere also contains nematodes, microarthropods (mites and collembola), enchytraeids, and earthworms. Nematodes are considered very important in the soil food web. Only a few nematode species are considered pest organisms, which can cause severe damage to crops (i.e., soybean), whereas others have an applicative interest for the control of insect pests without using pesticides. (7)

The biodiversity of soil microbial communities is increasingly recognized as a major factor for human health both directly, by limiting the spread of potential pathogens, and indirectly, by contributing to processes that provide clean air, water, and healthy food (3) . Soil serves as a primary reservoir for plant-colonizing bacteria (4), that play a major role in determining plant productivity (5) and preventing invasion by bacterial pathogens (6). (8)

Soil Functionality

Microorganism functionality: Capability of soil microbial communities to perform multiple functions. It is assessed based on the predicted functional profile. (9)

      • Regulating water - Soil helps control where rain, snowmelt, and irrigation water goes. Water and dissolved solutes flow over the land or into and through the soil.
      • Sustaining plant and animal life - The diversity and productivity of living things depend on soil.
      • Filtering and buffering potential pollutants - The minerals and microbes in the soil are responsible for filtering, buffering, degrading, immobilizing, and detoxifying organic and inorganic materials, including industrial and municipal by-products and atmospheric deposits.
      • Cycling nutrients - Carbon, nitrogen, phosphorus, and many other nutrients are stored, transformed, and cycled in the soil.
      • Physical stability and support - Soil structure provides a medium for plant roots. Soils also provide support for human structures and protection for archeological treasures. (10)

Soil quality / health indicator

A chemical, the physical or biological property of soil that is sensitive to disturbance and represents the performance of ecosystem function in that soil of interest. These are dynamic soil properties.

Some studies have explored how variation in the initial soil microbiome predicts future disease outcomes at the level of individual plants. (4) (5) 

Terroir characterization

Vitivinicultural “Terroir” is a concept which refers to an area in which collective knowledge of the interactions between the identifiable physical and biological environment and applied vitivinicultural practices develops, providing distinctive characteristics for the products originating from this area. “Terroir” includes specific soil, topography, climate, landscape characteristics and biodiversity features.  (15)

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(1) (Doran, Stamatiadis and Haberern, 2002). FAO and ITPS. 2015. Status of the World’s Soil Resources (SWSR) – Main Report.


(3) Jean-Pierre Sarthou. 2018. Soil health : Definition. Dictionnaire d'Agroecologie . Published on 30 October 2018

(4) NRCS


(6) BeCrop Guide

(7) Science Direct:

(8) Microbiome Journal. Coller, E., Cestaro, A., Zanzotti, R. et al. Microbiome of vineyard soils is shaped by geography and management. Microbiome 7, 140 (2019).

(9) Science Direct:


(11) The Plant Cell. Jo Handelsman‘ and Eric V. Stabb Department of Plant Pathology, University of Wisconsin.

(12) The Nature Education.

(13) Hodrien, Chris (October 24, 2008). Squaring the Circle on Coal – Carbon Capture and Storage. Claverton Energy Group Conference, Bath (vía Wikipedia).

(14) Michigan State University:,and%20role%20within%20the%20plant.&text=Once%20inside%20plants%2C%20nutrients%20are,needed%2C%20typically%20to%20growing%20points.&text=Since%20immobile%20elements%20do%20not,new%20growth%20(Photo%201).

(15) OIV definition