Loss of Soil Biodiversity

What is Loss of Soil Biodiversity? 


Soil biodiversity is generally defined as the variability of living organisms in soil and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems1. The threat - decline in Soil Biodiversity - has been described as a reduction of forms of life living in soils (both in terms of quantity and variety) and of related functions2.

Soils are a globally important reservoir of biodiversity. They contain at least one quarter to one-third of all living organisms on the planet yet little is known about them, as only around 1% of soil microorganisms have been identified compared to 80% of plants3. At its simplest, the vast biodiversity of the soil can be divided into four major groups:

  • Microbes and microfauna with body widths of less than 100 micrometres
  • Mesofauna with body widths between 100 micrometres and 2 millimetres
  • Macrofauna, which are larger than 2 millimetres than 2 millimetres

Where does it occur?

In general and geographical terms, the state of soil biodiversity has been well described in the European Atlas of Soil Biodiversity3. Soil biodiversity decline is usually related to some other deterioration in soil quality and at local levels, it is clear that biodiversity is in decline. For example, soil sealing (the permanent covering of soil with hard surfaces, such as roads and buildings) causes the death of the soil biota by cutting off water and carbon and nutrient inputs. In other cases, soil biodiversity decline can be linked with erosion, organic matter depletion, salinization, contamination and compaction.

What causes it?


Simple model showing the effect of a perturbation on the resistance and resilience of a soil biological function or property. Higher biodiversity is thought to correspond to high resistance and resilience. A loss of biodiversity is thought lead to a soil with lower resistance to a perturbation and lower capacity to recover.  

Soil biodiversity is subject to considerable disturbances through any number of threats. The soil biota has its own unique capacity to resist events that cause disturbance or change and a certain capacity to recover from these perturbations. The capacity to recover from change is considered a key attribute of biodiversity. The figure below provides a simple schematic that describes the concept of Resistance and Resilience.

Land Management
Land management can have varying effects on belowground biodiversity. A primary driver of this is the close link between soil biodiversity and soil organic matter, although the relationship is not fully understood. As the source of energy underpinning food-webs, carbon losses from organic matter may lead to reduced biodiversity. Coupled with this, the general use of fertilizers, pesticides and herbicides as part of agricultural intensification are a significant cause of soil biodiversity loss. The agricultural techniques/management that lead to loss of soil biodiversity are monoculture cropping, removal of residues, soil erosion, soil compaction (both due to degradation of the soil structure) and repeated application of pesticides 4.

Climate change leading to flooding and subsequent lack of oxygen and compaction, loss of organic matter through enhanced oxidation, and prolonged periods of drought (in typically un-droughted landscapes) are the drivers of biodiversity loss in soil. Many of these factors link with, and may be compounded by, local and regional land management practices.

For Europe, the main pressures have been recognised for three levels of biodiversity:

Ecosystem-level - the main pressures are thought to derive from land use change, overuse and exploitation, a change of climatic and hydrological regime and change of geochemical properties.
Level of species of organism in the soil - the main pressures on biodiversity are thought to derive from a change in environmental conditions of geochemistry, competition with invasive species and ecotoxins.
Genetic level - the main pressures are thought to derive from a change of environmental conditions, ecotoxins and “Genetic pollution” 3.

How can it be measured or assessed?

 The table below lists key and/or proxy indicators for loss of soil biodiversity identified by RECARE and ENVASSO projects. 

Soil threatRECARE indicatorsEVASSO indicators
Decline in soil biodiversity TOP3 indicators by ENVASSO
  • earthworms diversity & fresh biomass (number m-2, g fresh weight m-2
  • Collembola diversity (number m-2, g fresh weight m-2)
  • microbial respiration (g CO2 kg-1 soil)

The table below lists key indicators of a decline in soil biodiversity, the purpose of the indicator and methods used for measuring or assessing a decline in soil biodiversity

Earthworms diversity

Determine earthworms/collemboia diversity based on soil descriptions (depth, pH, nutrient) and site descriptions (climate, land use, vegetation)

  • Soil type should follow WRB 2006 classification (ftp://ftp.fao.org/agl/agll/docs/wsrr103e.pdf),
  • Land management, land use and vegetation type should follow FAO 2006 classification (ftp://ftp.fao.org/agl/agll/docs/guidel_soil_descr.pdf) 3, 4, 5
Collembola diversity
Microbial respiration (substrate induced)

Measuring CO2 respiration responses from soil

Multiple substrate induced respiration 6,7

How can it be prevented or remediated?

There are a number of different measures that can be taken to prevent the loss of soil biodiversity or remediate damage, but broadly it does not decline independent of other factors and is usually related to some other deterioration in soil quality.

Agronomic measuresVegetative measuresStructural measures Management measures
Applying conservation tillage Increasing soil organic matter Creating buffer zones: blue and green veining Established regional or national strategies
Sequential cropping      
Limiting application of inorganic pesticides, herbicides & fertilizers      

Case Study Experiments

How does it interact with other soil threats?


The decline in soil biodiversity is usually related to other deteriorations in soil quality and can be linked with other threats like erosion, organic matter depletion, salinization, contamination and compaction. An expert group weighted the potential threat – for a selection of possible soil threats - to soil biodiversity3. This illustrates that soil biodiversity is highly influenced by the other threats.

How does it affect soil functions?

As the figure shows, the activities of the soil biota are essential to all of the soil functions. The primary services that soil biota undertake include (i) nutrient cycling; (ii) regulation of water flow and storage (iii) regulation of soil and sediment movement; (iv) biological regulation of other biota (including pests and diseases); (v) soil structural development and maintenance; (vi) the detoxification of xenobiotics and pollutants; and (vii) the regulation of atmospheric gases.


1 UNEP (1992) Global Biodiversity Strategy. Washington, DC: WRI.
2 Huber, S., Prokop, G., Arrouays, D., Banko, G., Bispo, A., Jones, R., Kibblewhite, M., Lexer, W.,Möller, A., Rickson, J., Shishkov, T., Stephens, M., Van den Akker, J., Varallyay, G., Verheijen, F., 2008. Indicators and Criteria report. ENVASSO Project (Contract 022713) coordinated by Cranfield University, UK, for Scientific Support to Policy, European Commission 6th Framework Research Programme.
3 Jeffery S, Gardi C, Jones A, Montanarella L, Marmo L, Miko L, Ritz K Peres G, Römbke, J & Van der Putten W. (2010). European Atlas of Soil Biodiversity. Publications Office of the European Union.
4 Wachira, PM, Kimenju JW, Okoth SA, Kiarie JW. 2014. Conservation and Sustainable Management of Soil Biodiversity for Agricultural Productivity . Sustainable Living with Environmental Risks. , Japan: Springer
5 Jones, R.J.A., Verheijen, F.G.A., Reuter, H.I., Jones, A.R., 2008. Environmental Assessment of Soil for Monitoring Volume V : Procedures & Protocols.
6 Van Straalen, N. M. 1998. Evaluation of bioindicator systems derived from soil arthropod communities. Applied Soil Ecology, 9(1), 429-437.
7 Degens, B. P., & Harris, J. A., 1997. Development of a physiological approach to measuring the catabolic diversity of soil microbial communities. Soil Biology and Biochemistry, 29(9), 1309-1320.
8 Campbell, C. D., Chapman, S. J., Cameron, C. M., Davidson, M. S., & Potts, J. M. 2003. A rapid microtiter plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil. Applied and environmental microbiology, 69(6), 3593-3599.Ceccato, P., Flasse, S., Tarantola, S., Jacquemoud, S., Grégoire, J.-M., 2001. Detecting vegetation leaf water content using reflectance in the optical domain. Remote sensing of environment 77, 22–33.
9 Wall, D. Neilsen, U. Six, J. 2015. Soil biodiversity and human health. Nature 528, 69-76.

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