Soil Health – Applications And Opportunities For Climatesmart Farming, Food Security And Environmental Integrity

Written by Neil Douglas Fuller of the Atlas Sustainable Soil Programme

Soil health is a product of interactions between plant roots and the living fraction of the soil, operating within the constraints of the physical, chemical and climatic parameters of the soil environment.

In part, soil health is determined by the inherent, effectively fixed, properties of underlying geology, topography and landscape processes. Of equal importance are the dynamic soil properties that are influenced by land use and soil management practices, each of which can induce incremental changes to the functional characteristics of soil. Defining those characteristics, and developing the associated metrics and measurements required to effectively monitor and manage them, is fundamental to achieving sustainable farming and food production.

Society’s foundation

Soil is often considered to be the foundation for agricultural productivity, food security and environmental integrity. The majority of our air, water, fibre and nutrition is derived from soilbased eco-systems. History illustrates the social, economic and political importance of soil, and the role that soil degradation has played in the downfall of many a civilisation, both ancient and modern. Right now, soil provides a cornerstone for the global response to climate change and occupies the centre-ground for strategies designed to reverse global warming.

UK strategies

In 2019 the UK became the first major economy to declare a “Net Zero Carbon” agenda, to be realised by 2050. Coupled with the promise of a “Green Brexit”, the requirements of the “25 year plan” and the clear intent to replace Common Agricultural Policy support mechanisms with an Environmental Land Management Scheme, that fully integrates the twin objectives of food production and environmental protection, soil health is now firmly in the political spotlight. Yet despite all this, the wonderfully diverse, intricate and incredibly complex array of soil-based ecosystems that constitute the agricultural and environmental heart of the United Kingdom are in steady decline. On average, the total carbon reservoir in arable soils in England has been returning to the atmosphere at rate of around 0.6% per annum since the introduction of artificial nitrogen fertiliser and the four-furrow reversible plough.

Global issue

The global situation is very similar, with some studies estimating that the carbon stocks of agricultural soils have reduced by half, releasing around 140 billion tonnes CO2e back into the atmosphere. As carbon is synonymous with life on this planet, the implications for this, in terms of soil life processes and the degradation of soil health, could be considerable. This loss of soil carbon presents a major threat, both directly, on farm performance, food quality and soil resilience. Indirectly it impacts biodiversity, natural capital and eco-system service provision and regulation. Land managers, strategists and policy-makers are becoming more aware of this, and a whole suite of regenerative soil and crop management practices, have been designed to move carbon from the atmosphere, where it is causing problems, and place it safely into the soil, where it belongs. However, their deployment is being delayed, frustrated and compromised by one overarching limitation – the measurement, evaluation and quantification of soil health. 

Soil health

Essentially, health is a function of life processes. As such, associating the concept of health to soil, implies that this vital, but fragile, global resource is, in fact, alive. This is in stark contrast to the more mechanistic view that soil is basically a mix of weathered rock and plant residue; or the pragmatic belief that soil is primarily a growing media, the functionality of which depends on the need for soil to be cultivated, fertilised, tempered and conditioned. Classifying soil as a living eco-system is a paradigm shift for many agronomists, farmers and land managers. And with this shift comes a knowledge gap, both in terms of quantifying appropriate soil life processes and in evaluating the incremental impact that discriminatory management practices may transfer onto those processes.


Traditionally, focus has been placed on inherent soil qualities; the content of sand, silt and clay; the effect of underlying geology on acidity, nutrient status and water movement; the impact of aspect, topography and climate on plant performance. As a result, the success of land management practices was most often noted in terms of biomass production, soil nutrient status, alkalinity and conductivity. More recently, soil quality metrics have been introduced as part of the evaluation process, incorporating factors such as visual assessments of soil structure and earthworm populations; observational assessment of compaction and erosion risk; in-field measures for water infiltration, aggregate stability and soil bulk density.

Carbon measurement

One fundamental component, routinely omitted from soil analysis and quality metrics, is measurement of one of the building blocks of terrestrial life processes – carbon. Despite the requirement under Cross Compliance, routine soil testing in the UK continues to omit any direct or indirect measurement of this vital soil constituent. The situation is further compounded by the current lack of any standardised analytical procedure for the basic metric, soil organic matter content, as determined by the most commonly used method, Loss on Ignition (LOI). With a large coefficient of variation, dependent on protocol, even the best laboratories may struggle to deliver suitably repeatable results using LOI.

With the Action Plan of the Paris Agreement only seeking to achieve an annual increase in soil Carbon of 0.4% in order to halt climate change, it is possible that current soil analytics will be unable to detect positive, or negative, change sufficiently accurately to be able to inform, monitor, validated or reward the regenerative Carbon Farming practices that are now forming agriculture’s Net Zero Initiative. If soil health is going to inform agricultural policy and influence farm management practices, decisionmakers need to have access to robust, reproducible, reliable systems of measurement that can detect the incremental changes that land management practices have on the dynamics and functionality of individual soil systems.

Defining the soil health space

A brief literature search will reveal a wide range of terms and definitions used to outline the working premise of “soil health” and “soil quality”. These two terms appear to be interchangeable, although they do convey different operational parameters. In simplest form, health equates to absence of illness, while quality equates to specific attributes, one of which could be health. While both terms relate to functionality, soil health implies that the physical, chemical and biological components of soil combine to create dynamic, living, processes.

The Journal of Environmental Quality (Meanings of Environmental Terms) describes soil quality as “… a measure of the condition of soil relative to the requirements of one or more biotic species and/or to any human need or purpose”. This is taken a stage further by Doran and Zeiss (2000), who define Soil health as, “the capacity of a specific kind of soil to function, within natural or managed ecosystem boundaries, to sustain plant and animal productivity, maintain or enhance water and air quality, and support human health and habitation”.

The concept of health is also central to the applied definition proposed by Kibblewhite et al. (2008) which determines that “… healthy agricultural soil is capable of supporting the production of food and fibre to a level, and with a quality, sufficient to meet human requirements, and deliver ecosystem services essential to maintain environmental quality, quality of life for humans, animals, plants and conservation of biodiversity”. However, Toth et al. (2007) defines soil quality in slightly different terms, being “… an account of the soil’s ability to provide ecosystem and social services through its capacities to perform its functions under changing conditions”.

The ability to define those functions, and effectively measure the impact of management practices on the outcomes of those functions, is fundamental to sustainable soil management and, by implication, the impact this has on future food security and environmental integrity.

Soil health is imbued with transferable performance-enhancing characteristics that influence plant, animal and human health. Not just in terms of the nutritional bio-chemistry that supports healthy growth, development and the expression of genetic traits; but also functional metabolite-related, elicitor-induced and microbe-mediated disease resistance, abiotic stress factor mitigation, and associative adaption. Each individual attribute has specific physical, chemical and biological frames of reference.

Physical soil health

The relative content of sand, silt and clay, traditionally referred to as the fine earth fraction, defines the texture, or “feel”, of a soil. However, it is the orientation, alignment and aggregation of these soil particles that define its structure, or function. Part of this definition relates to the size and distribution of pore space, which regulates:

• water movement, retention and availability

• infiltration and drainage

• air exchange and anaerobic-aerobic balance

• soluble nutrient retention

• root development and

• primary root-microbe interactions

In essence, physical soil health defines the abiotic parameters, or hard landscape, of the rhizosphere and its associative microbial habitat.

Health vs Structure

As physical soil health declines, structural integrity declines. As pore space distribution shifts from macro (large) to meso (small) dominated, the volume of soil occupied by hygroscopic water (which is inaccessible to most plant roots and soil microbes) increases. Such water tends to extend the plasticine limits of soil consistency, elevating the risk of erosion, compaction, impaired drainage, localised saturation and run-off. This can result in the formation of anaerobic zones within the soil profile that influence carbon-nitrogen transformation and associated nitrous oxide emissions. Changes in soil microbial population dynamics can also be induced, not just within the soil around the roots, but throughout the soil profile, often detected by changes in the relative ratios of protozoa and the balance between total and active, or live, biomass of indicator microbes.

Agriculturally, this can lead to:

• significant changes in the ability of beneficial microbes to suppress pathogens

• performance limitations related to water and nutrient availability and

• reductions in the activity of rhizosphere microbes that both feed and protect plants.

Delays in seed germination and plant emergence can occur, leading to reduced expression of genetic yield potential and impaired tolerance to abiotic stresses, particularly drought, temperature and photo-oxidative stress. This, in turn, can impact yield, quality and response to inputs. Declining physical soil health can also extended the dormancy, germination and population dynamics of grass weeds, affecting the efficacy and application of selective herbicides. Sustainable improvements in physical soil health are most often associated with elevated activity in biological processes that transform carbon; mainly derived from the decomposition of complex plant residues, root exudates and microbial mucilage, which stabilise soil aggregates, maintain pore space, encourage root development and facilitate plant-microbe interactions.

Key performance indicators of this process, relative to particle size distribution, include:

• water infiltration, retention and drainage rates

• soil bulk density and shear strength

• carbon flux and carbon to clay ratio

• carbon respiration and • nitrous oxide evolution.

Additional metrics are being generated by advances in electromagnetic and hyper-spectral scanning; remote sensing of moisture, temperature and aerobic-anaerobic balance through the soil profile; and digital image analysis of soil structure to determine aggregate and pore space distribution. Penetrometer measurements to determine shear strength and structural limitations to root development are also providing useful in-field data, particularly in determining the requirements for, and working depth of, primary cultivation practices. Although shear strength often increases as a result of the improved carbon dynamics associated with bio-pore formation, this is usually offset by decreases in soil bulk density, delivering a net positive gain to physical soil health.

Chemical soil health

Although chemistry has been the focus of soil husbandry guidelines for decades, much of the nutrient availability recognised as delivering agronomic benefit to the growing plant could not be achieved without appropriate physical and biological support. Traditionally, only soil pH and the “easily extractable”, or “readily available”, levels of phosphorous, potassium and magnesium have featured in the chemical soil health toolbox. However, since the turn of the century, a steady increase in the complexity, cost and implied value of more detailed soil analysis has added depth and breadth to applied soil chemistry. The determination of soil particle size distribution and clay chemistry; the inclusion of anion-cation exchange and base saturation ratios; measurements for electro-conductivity, salinity, functional carbon dynamics and respiration-evolution rates; can all now be added to an array of major and micro-nutrient assessments. 

Key nutrients

In that same time frame, focus has moved to two key nutrients, both of which have significant agronomic and environmental impact. The first of these is phosphorous; the nutrient that essentially drives root development and plant-microbe interactions. Phosphorous is strongly anionic (negatively charged) and is readily adsorbed to the cationic (positive) charge associated with humic polymers, organic matter and dominant cations (calcium, magnesium). This gives it really low mobility and uptake characteristics. However, phosphorous associated with erodible or diffusible soil particulates can enter water courses, leading to eutrophication (nutrient enrichment) and oxygen depletion of aquatic eco-systems.

As chemical soil health declines, phosphorous movement from labile, organic and biological reservoirs within the rhizosphere can also decline. In response, plant root systems may be smaller, architecturally simpler and less adventurous. This can lead to decreased root exudate production and associated microbial activity. In addition there may be a decline in bio-pore formation and soil structural integrity and increased risk of erosion, compaction and aggregate destabilisation.

All of these can have a direct impact on photosynthetic efficiency, carbon partitioning, stress response and disease resistance. An extra interaction, specific only to legumes, is a reduction in biological nitrogen fixation; a process that is very phosphorous-dependent. An uplift in physical soil health can alleviate much of this.

The second nutrient to receive increased attention is nitrogen, which essentially drives protein production, plant growth and yield. The introduction of nitrogen fertiliser has generated an increase in global food production of around 45%. However, the manufacture and application of nitrogen fertiliser can account for up to 80% of the production emissions of arable crops. Routine application of nitrogen fertiliser also provides a selection pressure for soil microbial communities, which often shift population dynamics away from symbiotic and non-symbiotic nitrogen fixing organisms, placing greater reliance on fertiliser.

In addition, current nitrogen use efficiency is low, with significant levels of nitrogen entering the environment rather than being taken up by plants. Part of the issue relates to the rapid movement through the soil profile of nitrogen in the nitrate form. On its own, nitrate entering ground or surface water represents a significant threat to water quality. But once at depth in the soil, if it encounters anaerobic conditions, nitrate can be converted into the potent Greenhouse Gas nitrous oxide.

Selective ion sensor arrays, generating real-time data for nitrate movement, soil moisture deficit and carbon dioxideoxygen levels; coupled with weather data and hyperspectral determination of both soil and plant nutrient status; are advancing predictive nitrogen modelling and decision support tools. The result is not only seen in performance uplifts and operational savings but also in reduced global warming potential and enhanced levels of environmental protection. Plants often deploy positive feedback mechanisms in response to a decline in chemical soil health, adjusting root exudate composition in order to stimulate the activity of specific rhizobacteria, promote nutrient uptake, combat abiotic stress factors and prime disease resistance mechanisms.

Biological soil health

Although often viewed as a new and emerging horizon in soil health, studies into the biological functionality of soil have a long history. However, unlike physical and chemical soil health metrics, the biological metrics currently under consideration have to contend with increased levels of spatial and temporal variability. The introduction of a conceptual framework for the soil microbial food web and associated laboratory techniques for evaluating microbial population dynamics is providing a greater insight into biological soil health.

Supported by more generic soil enzyme assays; functional carbonnitrogen determinations; the detection and evaluation of pathogen-mediated elicitor and signature molecules; and the deployment of rapid gene sequencing techniques; the biological soil health toolbox is progressively expanding. However, the inherent variability of both the composition and distribution of soil microbial communities continues to exert practical limitations on sampling and analytical protocols. Specific analytical focus has been applied to the biological processes of atmospheric nitrogen fixation by symbiotic microbes that occupy the rhizosphere or the intracellular space of plant leaf tissue. The biochemistry of converting nitrogen gas into microbial protein and plant-available ammonium is reliant on phosphorous, magnesium, manganese and iron.

The process is energy-intense, timeconsuming and often host-specific, but the commercialisation and application of nitrogen-fixing microbes would be transformative in terms of sustainability, food security and environmental impact. However, results to date clearly illustrate the importance of establishing physical, chemical and biological soil health prior to deploying this emerging technology.

One area of particular interest, outside the plant health sphere, is the role of biological soil health in carbon sequestration and transformation. Seen as instrumental to climate change mitigation, the ability for plants to move carbon from atmosphere to soil, and for soil processes to safeguard the storage of this carbon, has the potential to halt, and reverse, global warming. Realising this potential resides, at least in part, on our ability to evaluate, verify and monitor soil carbon dynamics.


Soil health is a prerequisite for the health-related characteristics expressed by plants, animals, humans and ultimately, the planet. Monitoring soil health is fundamental to the effective management of this globally significant resource. The processes involved in regulating, maintaining and enhancing soil health are complex. As a result, no one single metric has, as yet, proven to be the definitive soil health metric. Technological advances in the realms of physical, chemical and biological analytics, coupled with innovations in sensor design and geo-bio-chemical data acquisition; evaluation of microbial population dynamics and target metabolite functionality; observational data sets generated by in-field soil assessments; determination of carbon sequestration and transformation rates; all provide valuable insight into the effective measurement, monitoring and management of soil health.