Skip to content



This is a huge topic and despite growing knowledge there remains many gaps in our understanding of the living system in our soils. This section attempts to introduce the major topics and some assessments you can do on your own soils to get an indication of your soil ecosystem and functioning.

It is essential to keep in mind that the soil is a dynamic system of interactions and it is these relationships and interfaces between physical and biological elements that drives the health of the whole. No single physical parameter or species tells the story, it is the dynamic interactions that are key, and any interventions need to consider the impact on the whole.

However, these are hard to measure and fully elucidate, so some humility is required in our assumptions and interpretation.

So what? The benefits of healthy soil ecology

The 2020 UNFAO State of Knowledge of Soil Biodiversity reported: In the United Kingdom of Great Britain and Northern Ireland, soil biological activity has huge importance for the delivery of the following services: production of food, fuel and fibre (nutrient cycling and fixation, water supply, soil structure formation, pest and disease control); climate regulation (carbon storage, methane production and consumption, nitrous oxide fluxes); flood risk mitigation (rebuilding and maintaining soil structure, water storage); water supply and quality (crop water holding capacity, biological treatment of water pollutants, mycorrhizal supply to crop roots); biodiversity support (soils as part of all terrestrial ecosystems; note that soils also represent a vast biodiversity resource in themselves); climate change adaptation (both in support of natural habitats, improving, linking and expanding and in terms of soil resource use for agriculture); waste/resource recycling (for example, sewage, crop residues, green waste); decontamination (organic pollutants, metals); and regulating air quality (generation of ammonia emissions, NOx gases, particulate matter). Soil genetic diversity has huge potential to yield compounds of medicinal and industrial value but is largely unexplored.

In a healthy system, diverse soil organisms will interact with each other and their physical surroundings to perform important ecological functions:

Carbon cycling

Every organism in the soil is involved in cycling organic (carbon containing) compounds, from plants exuding carbon sugars via their roots that they have manufactured from sunlight in order to ‘pay’ for fungi and bacteria services, through to little critters like mites and centipedes eating each other. Isopods, certain myriapods, earthworms, springtails, many species of mites, and the larvae and adults of many insects feed on the organic remains in soil. For example, of the 400g/m2 leaf litter found in temperate forests about 250 g/m2 is ingested by earthworms and enchytraeids (potworms), 30-40 g/m2 by mites and 50-60 g/m2 by springtails (Menta, 2012).

It all helps build organic matter, and ultimately create more soil. The more the merrier in this regard, all keeping each other in balance.

Mineral cycling and supply

It is now understood that in nature fungi and bacteria are the kings of nitrogen and phosphorous mining, fixing and supply, which are the key components of chemical fertilizers. Some soil experts state that it is very rare for soils to lack these minerals, but plants cannot access the full potential without microbes unlocking the supply. Once in the system, these are recycled as living organisms uptake the elements, or consume others with the elements, and dead residues release them back or are consumed by others organisms.

Nitrogen is often considered the limiting growth factor for crops. Symbiotic and free-living (non-symbiotic) nitrogen fixing bacteria, found in most (particularly undisturbed) soil types, can convert atmospheric nitrogen to ammonia, which nitrifiers convert into nitrate, both of which can be readily assimilated by plants.

Many fungi and bacteria have associations with plant roots. They make minerals available from parent and organic soil material in exchange for carbon sugars exuded (exudates) from the plant roots. Other organisms get involved, eating the bacteria and fungi and then excreting nutrient rich deposits making it available to others. The reach of fungal hyphae enables a much wider range for sourcing nutrients and fungi collaborate with bacteria to extract nitrogen, phosphorous, potassium and calcium from these distant regions to then bring back to root zones.

In addition, earthworms, particularly anecic burrowing worms, ingest large quantities of mineral substances from deeper layers and bring these to the surface in casts, performing a vertical cycling service. Earthworms and other soil invertebrates also contribute to the increase in the amount of nitrogen present in the ground through the excretion of ammonia and urea, forms that are also directly useable by plants.

Fungi and bacteria can also access other trace minerals like iron, boron, copper, zinc, magnesium, manganese which are supplied to plants, and these include important elements for healthy development and synthesis of disease and pest defence compounds. Many believe that a good supply also increases crop micronutrient content, and therefore health benefits of our foods, and research is underway to demonstrate this.

Soil aggregation

An aggregate is a naturally formed assemblage of sand, silt, clay, organic matter, root hairs. Various physical and chemical (organomineral complexing) processes contribute to aggregate formation, but microorganisms also have a biochemical role to play. Their “glue” like secretions of mucilages, extracellular polysaccharides, stick soil particles together and hyphae (filaments) of fungi literally bind them together. Certain fungal root symbionts known as arbuscular mycorrhizae fungi produce a sticky glycoprotein material known as glomalin (still to be fully elucidated) which helps the hyphae move through soil particles. Glomalin material is very resiliant and can be stable for over 40 years depending on conditions and helps superglue the soil together in aggregates. Earthworms also form water stable aggregates, and the mucus from worms and molluscs, as well as other soil fauna, has a cementing effect.

Good soil aggregation reduces soil erosion, creates a porous soil which helps with aeration (important for beneficial organisms), moisture retention and infiltration, reduces compaction, encourages healthy deep root growth, and sequesters carbon in the soil.  

Water management: holding, infiltration, and delivery

In addition to aggregates, other creatures, like earthworms, also provide aeration that helps reduce compacted layers up to several meters deep and improves the porosity of the ground by 20-30%. Other species also create cavities such as millipedes, ants, beetle larvae, mole-crickets, scarab beetles etc. In terms of holding water, organic matter will absorb 10 times its weight in water, providing a useful reservoir in droughts and flood events.

Carbon sequestration

Plants capture CO2 and convert it to simple sugars. The primary purpose is to create building blocks for the plant’s own growth. However, a significant proportion of this is exuded out through the roots to stimulate fungi and bacterial growth.

Glomalin secreted from arbuscular mycorrhizal fungi (see aggregates above) contains as much as 40% carbon, representing about a third of carbon storage in soils worldwide. In addition, higher CO2 levels appear to stimulate fungi to produce more glomalin.

Soils in England and Wales store 2.4 billion tonnes of carbon, of which 58% is in the top 30 cm of soil (Defra 2011). The conversion of grassland to arable cropland was the largest contributor to soil carbon losses from land use change in the UK between 1990 and 2000 (Ostle et al 2009), but careful management practices applied to arable soils can help reverse this decline, and restore ecosystem functioning.

Young plant growth & health

A benefit from the combined functioning of a biologically healthy soil is that young plants have a better chance of establishing and enjoying vigorous, productive growth with reduced chemical inputs due to the access to macronutrients, trace minerals and plant growth promoting factors from the bacteria-fungi-plant interrelationships. Access to optimal moisture levels is also more likely in carbon rich, spongy soil, with healthy aggregates and fungal transportation.

Mitigates/Remedies soil compaction

As mentioned under water management, various fauna provide aeration which helps reduce compacted layers. Burrowing earthworms can go down to 2.5 meters deep and improve the porosity of the ground by 20-30%. Other species also create cavities such as millipedes, beetle larvae, mole-crickets, scarabs etc. Their activities also mix the soil of different horizons.

Temperature tolerance in plants

Arbuscular mycorrhizal symbiosis has been shown to improve tolerance to temperature stress in plants.  In addition, soil that has debris or living plant cover can be 10oC cooler in extreme heat e.g. 30oC vs 40oC of bare soils between crop rows, and reduces evaporation losses.

Increased lipid and protein availability

Lipids and proteins are made available within soil via predation and digestion of soil animals. A soil with plenty of thriving fauna will contain higher protein levels, all of which are circulated as those organisms die and degrade, making nitrogen, and amino acids available to plants (yes, plants can uptake intact amino acids, but seem to prefere mineralised N where available).  

Arbuscular mycorrhizal fungi store lipids within their structures within root cells of plants. After approximately seven days these structures are closed down and disintegrate within the plant, and these lipids and proteins from the fungal membranes become available to the plant.

Improved resilience e.g. to climate change

Diversity in the soil means there are more options for the system to continue to function if some elements (e.g. species) start to struggle. Other parts may be able to provide sufficient buffering or could take over their job, preventing collapse.

In addition, a soil that is already functioning well in terms of water management, aeration, carbon and nutrient cycling is likely to be able to support life in more extreme conditions: literally able to weather the changes.

Plant systemic disease resistance

In part at least, a plants inherent pest and disease resistance are enabled by improved trace element availability from bacteria and fungi, and from good macronutrient availability, such as amino acids and lipids, which are needed for enzyme co-factors and molecules for healthy development, cell growth and specialist defence chemicals and waxy cuticles in plants.

Pest and disease suppression

“Species are to ecosystems what rivets are to a plane’s wing. Losing one might not be a disaster, but each loss adds to the likelihood of a serious problem” Conservationists Paul and Anna Ehrlich.

In a diverse, healthy system pests and diseases will still exist but they will not get a chance to get much of a foothold due to balancing predators and plant health factors. Where there are many different species occupying different ecological niches there is higher competition for space, and this means there is reduced risk of a pathogen or pest becoming dominant enough to create a serious problem. Think of it like a paining with hundreds of colours and shades occupying the paper – it would be a lot harder for one colour to find space to dominate and take over.

For example, arbuscular mycorrhizal symbiosis has been shown to stimulate immune resistance to viruses in plants and certain strains of the soil bacteria Pseudomonas fluorescens have anti-fungal activity that inhibits some plant pathogens, and actinomycetes secrete antibiotics that will keep pathogenic attackers away.

If pests and diseases start to dominate, it may indicate that the system is out of balance and some aspect needs attention.

The underlying mechanisms of the impact of arbuscular mycorrhizal (AM) symbiosis on infection by viral pathogens, including modulated plant tolerance, the manipulation of induced systemic resistance, and altered vector pressure. SA= salicylic acid; JA= jasmonic acid.
Source: Review of Arbuscular Mycorrhizal Symbiosis Affects Plant Immunity to Viral Infection and Accumulation. Zhipeng Hao, Wei Xie and Baodong Chen, Viruses 2019, 11, 534; doi:10.3390/v11060534

Pollution bioremediation

A complex food web includes organisms that consume and degrade a wide range of pollutants under various environmental conditions. For example, various bacterial decomposers can break down or immobilise pesticides and pollutants in soil.

Summary Overview of Soil Ecological Services

A DEFRA project which reviewed the biological indicators of soil quality for soil monitoring summarised the role of soil biota in the table below.

Food and Fibre Production
C CyclingMicrobial biomass, methanogens
Decomposition of organic mattermicroarthropods, saprotrophic fungi
N cyclingAll organisms. Nitrifiers, denitrifiers for mineralisation and N2 processes
P cyclingphosphatase, mycorrhiza
S cyclingSulphur-reducting bacteria
N fixationrhizobia
Primary (microbial) activitymicrobial community structure & activity
Soil food web transfersmicrobial community & food web structure
Disease & pest transmission/suppressionpredators, pathogens
Nutrient supply from symbiosesmycorrhiza, N-fixers
Redistribution by bioturbationearthworms, ants
Bio-aggregation of soilfungi, worms
Environmental Interactions Between Soils, Air & Water
Degredation/immobilisation of pollutantsfungi, worms
C retention/releasemicrobial biomass, methanogens
N retention/releasenitrifiers, denitrifiers
P retention/releasemicrobial activity, mycorrhiza
Tolerance/Resistance (toxins)soil community structure and activity
S retention/releasesulphur-reducing bacteria
Redistribution by bioturbationearthworms, ants
Bio-aggregation of soilfungi, worms
Supporting Ecological Habitats & Biodiversity
Habitat for rare soil specieswax cap fungi, Wood Ant
Germination zone for plantsplant roots, mycorrhiza
Nutrient supply from symbiosesmycorrhiza
Food source (above ground)fungi, insects
Reservoir for soil biodiversity (taxonomic)soil species and diversity
Reservoir for soil biodiversity (genetic)community DNA & RNA
Reservoir for soil biodiversity (functional)nitrifiers, trophic structure, worms
Source: H.I.J. Black et al, 2006, SQID: Prioritising biological indicators of soil quality for deployment in a national-scale soil monitoring scheme, Summary report, Defra Project No. SP0529

YOUR Soil biology: DIY assessments

Soil Organism RespirationThe soil respiration test is a way to measure how much biological activity is occurring in your soil. When soil respires carbon dioxide is released by microbes, plant roots and soil fauna. However, guidance on interpretation of results is currently limited.  
Find out how:
Solvita Soil Life Test Kit from NRM Laboratories                        
Soil Mentor explains how to use Solvita test kit
‘Shovelomics’: phenotyping crop developmentThe basic idea of evaluating the root crown of field crops to estimate the growth, development, and architecture of principal roots near the base of the shoot. Digging up the crop with the top 20–30 cm of soil, the soil is then washed off, revealing the roots for assessment. Root angle, seminal root number, nodal root number, branching density and root biomass are all measured. Root angle is associated with increased root biomass in deeper soil layers, and root number or branching density can be indicative of improved establishment.  
Find out how:
Penn State University USA, Methodology                          
AHDB GreatSoils Project Soil Health Scorecard mentions it                          
Lancaster University Wheat Method                          
Nottingham University 3D imaging in field  
Soil Aggregation & Water InfiltrationWater infiltration is related to run-off, flooding and water storage capacity. It is related to biological activity as good soil aggregation from high biology results in the soil acting like a sponge. In addition, good root structure and mesofauna can help with water infiltration.  
Find out how:
Innovation for Agriculture to test water holding                          
Soil Mentor guide to infiltration rate test  
Earthworm CountsGood indicator for overall soil structure and health as well as soil biology and biodiversity  
Find out how:
AHDB Recording sheet                           
Soil Mentor Earthworm Count Method                          
OPAL earthworm ID guide (some issues with this on accuracy)  
Soil MesofaunaDiscover the world of soil nutrient cyclers such as mites and springtails and how they impact your crop, grasslands or habitat ecology. Requires some specialist equipment and a basic low magnification microscope would be useful.  
Find out how:
Innovation for Agriculture bug assessment method videos                          
Chaos of Delight for introduction to different mesofauna  
Soil MicrobesCovering organisms such as bacteria, fungi, protozoa and nematodes, this will require a decent microscope, costing a few hundred GBP, following the specification guidance of Elaine Ingram (see intro video below). Microbiometer claim to have a device that can be used on-site to determine F:B ratio.  
Find out how:
Elaine Ingram Soil Microscopy Introduction videos                          
Elaine Ingram Soil Food Web site                          
Meridith Leith Assessing Soil Health Using a Microscope                           
SoilBioLab conduct analysis  
GeneralAHDB GreatSoils Project summary of different soil assessment methods
AHDB GreatSoils Project Soil Health Scorecard and Guide Notes
AHDB GreatSoils Project Summary of Biological Tests for Soil Health
USDA Natural Resource Conservation Service Soil Test interpretation guide (p51 onwards) Comprehensive soil health analysis, including chemical, biological and physical parameter such as Bioscene test used by Leake et al. (2013), or the SSM (Sustainable Soil Management) test offered by the Glenside Group/NRM  

NB: references to specific organisations or tests are not recommendations but represent players in the space.


  1. Cristina Menta (August 29th 2012). Soil Fauna Diversity – Function, Soil Degradation, Biological Indices, Soil Restoration, Biodiversity Conservation and Utilization in a Diverse World, Gbolagade Akeem Lameed, IntechOpen, DOI: 10.5772/51091. Available from: (Open source)
  2. Michael Philips, Mycorrhizal Planet: How symbiotic fungi work with roots to support plant health and build soil fertility, 2017. Chelsea Green Publishing, White River Junction, Vermont
  3. AHDB Soil Food Web
  4. The Soil Biota, Wageningen University & Research, The Netherlands
  5. Chaos of Delight: mesofauna information and photography
  6. Global Soil Biodiversity Initiative
  7. Global Soil Health, FAO SOILS PORTAL, Food and Agriculture Organization of the United Nations
  8. Dr Elaine Ingham Soil Food Web
  9. Nature Education, The Soil Biota By: Ann-Marie Fortuna (Dept. of Crop & Soil Sciences, Washington State University)  2012 Nature Education
  10. Fortuna, A. (2012) The Soil Biota. Nature Education Knowledge 3(10):1
  11. eOrganic, Oregon State University
  12. David C. Coleman, Chapter: Soil Biota, Soil Systems, and Processes. Encyclopedia of Biodiversity, 2001
  13. Łukasz Gajda et al, Food preferences of enchytraeids June 2017, Pedobiologia 63. DOI: 10.1016/j.pedobi.2017.06.002
  14. H.I.J. Black et al, 2006, SQID: Prioritising biological indicators of soil quality for deployment in a national-scale soil monitoring scheme, Summary report, Defra Project No. SP0529
  15. OSTLE, N., LEVY, P.E., EVANS, C.D. & SMITH, P. 2009. UK land use and soil carbon sequestration. Land Use Policy, 26, S274–S283.
  16. DEFRA. 2011. Review of the evidence base for the status and change of soil carbon below 15 cm from the soil surface in England and Wales. Sub-Project iii of Defra Project SP1106: Soil carbon: studies to explore greenhouse gas emissions and mitigation. Department for Environment, Food and Rural Affairs, Research project final report.
  17. Natural England Access to Evidence Information Note EIN012. Summary of evidence: Soils EIN012. First edition 19 May 2015.
  18. Essaid Ait Barka et al. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev. 2016 Mar; 80(1): 1–43. Published online 2015 Nov 25. doi: 10.1128/MMBR.00019-15 PMCID: PMC4711186 PMID: 26609051
  19. Hazelton PA, Murphy BW (2007) Interpreting Soil Test Results: What Do All The Numbers Mean?. CSIRO Publishing: Melbourne.
  20. Cations and Cation Exchange Capacity Fact Sheet, Soil Quality collaboration, Australia
  21. Cornell University Cooperative Extension Fact Sheet Cation Exchange Capacity
  22. Dr Alan Smith, Ethylene production by bacteria in reduced microsites in soil and some implications to agriculture, Journal of Soil Biology and Biochemistry, Volume 8, Issue 4, 1976, Pages 293-298 and summarised by Dr Smith in