Soil Biodiversity


The Convention on Biological Diversity (CBD) defined the soil biodiversity as "the variation in soil life, from genes to communities, and the ecological complexes of which they are part, that is from soil micro-habitats to landscapes".

In other terms the soil biodiversity represents the variety of life belowground. The concept is conventionally used in a genetic sense and denotes the number of distinct species (richness) and their proportional abundance (evenness) present in a system, but may be extended to encompass phenotypic (expressed), functional, structural or trophic diversity. The total biomass belowground generally equals or exceeds that aboveground, whilst the biodiversity in the soil always exceeds that on the associated surface by orders of magnitude, particularly at the microbial scale.

Some numbers describe well the soil biodiversity: a teaspoon of soil (about one gram) may typically contain one billion bacterial cells (corresponding to about ten thousand different bacterial genomes), up to one million individual fungi, about one million cells of protists, and several hundred of nematodes. Beside microorganisms and microfauna, soil harbours different species of meso and macro/megafauna represented by arthropods, earthworms and mammals.

The soil biota plays many fundamental roles in delivering key ecosystem goods and services. 

Ecosystems goods provided by soil biota are:

  • food production;
  • fibre production;
  • fuel production;
  • provision of clean water;
  • provision of secondary compounds (e.g. pharmaceuticals and agrochemicals).

Ecosystems services provided by soil biota:

  • driving nutrient cycling and regulation of water flow and storage;
  • regulation of soil and sediment movement and biological regulation of other biota (including pests and diseases);
  • soil structure maintenance;
  • detoxification of xenobiotics and pollutants and regulation of atmospheric composition.

In the image, you may view a round up of soil dwellers.




Methods for studying SOIL BIODIVERSITY – The HOW

Soil organisms are extremely variegated in terms of morphology, quantity and lifestyle: we move from microorganisms invisible to the naked eye (e.g., bacteria and fungi) to invertebrates (e.g., earthworms) and vertebrates (e.g., mammals). Therefore, surveys on soil biodiversity require specific tools depending on which group of organism is studied.

Three ways are feasible for studying microbial diversity:

  • direct observation and counting: some microbes can be grown in vitro by using specific growth media and then identified through microscopy. Problem is that only a tiny percentage of microorganisms are capable of growing in artificial conditions;
  • functional assays: different biochemical techniques allow to detect functional activities carried out by specific enzymes of soil microorganisms;
  • molecular fingerprinting: this approach represents the new age in studying of soil biodiversity. It relies on direct extraction of DNA from soil and identification of microorganisms through the sequencing of some portions (barcode regions) of their genomes. This strategy is recently grown thanks to the new sequencing technologies (next generation sequencing - NGS) allowing to obtain an unprecedented amount of data (number of DNA sequences) in a short time. This technique has led to observe a microbial soil biodiversity higher than expected.

Investigations are more straightforward for animals and many invertebrates living in soils. Indeed, their taxonomic identification is relatively easier: what can be seen can be identified and counted. Due to their importance in soil quality assessment, standard guidelines are nowadays available for sampling of some soil invertebrates such as earthworms. Furthermore, it has been recently observed that molecular fingerprinting could be successfully applied to identify vertebrates and plants living below- and aboveground (A et al., 2011).

The identification of soil organisms is the first step to comprehend the role of soil biodiversity. Indeed, once you know the soil inhabitants you have to understand what they are doing, that means studying the function of soil biodiversity. Functional assays and analysis of genes expressed by the organisms, targeting soil RNA instead of DNA, help in replying this question.

Last step is the comprehension of large-scale effects coming from the interactions of different organisms in soil. That is the task of the ecology. Ecological experiments, such as set up of microcosms and in-field observations and measurements, allow to assess the soil function and impact as environmental service.

In the image, you can view an approximate number and diversity of organisms typically found in a handful of grassland soil (KR & JJIM). Because of their various features (quality and quantity), each group of organisms has its specific survey strategy.


soil biodiversity

Role of SOIL BIODIVERSITY in soil system – The WHERE

A healthy soil biota needs an appropriate habitat. In soil, this is essentially the space denoted by the complex architecture of the pore network, and the associated supply and dynamics of gases, water, solutes and substrates that this framework supports.

In such a complex system, the relationships between biodiversity and function are intricate and somewhat poorly understood, even in aboveground situations. The exceptional complexity of belowground communities further confounds our understanding of soil systems. However, it is possible to define three important mechanisms underlying relationships between organisms and functions carried out in soil system:

  • repertoire: for a biologically-mediated process to occur, organisms that carry out that process must be present;
  • interactions: most soil organisms have the capacity to directly or indirectly influence other organisms, either positively or negatively;
  • redundancy: the more organisms there are that can carry out a function in a particular soil, the more likely it is that if some are incapacitated or removed the process will remain unaffected, as those that remain fill the gap.

Richness per se is of little consequence; rather it is the functional repertoire of the soil biota that is critical. For processes such as decomposition, there is a clear and high degree of redundancy at a microbial level. Other processes, such as nitrification (the oxidation of ammonium), are carried out by a narrower range of bacteria with less functional redundancy, whereas for highly specific symbiotic associations, such as orchid mycorrhizas (association between orchids and certain fungi), there is a total dependence and hence zero redundancy.

A depletion of biodiversity will therefore have differing consequences in relation to the functional repertoire: processes with high redundancy and weak interactions among organisms (e.g., decomposition) can be easily replaced, while the loss of a strong and specific link (e.g., one of the actors of orchid mycorrhizas) can alter the stability of the community. In some circumstances it has been demonstrated that there are threshold levels of soil diversity below which processes are impaired, although these are usually related to narrow processes and are manifest under experimentally constructed systems of exceptionally low levels of diversity, as opposed to natural systems.

In the image, you may view a simplified soil food web. Interactions and links are present among all of different trophic levels with energy and nutrient elements transferred from one level to another. Note that the chain is cyclic with a continual movement of material from all trophic levels back to the detritus/organic matter pool and the base of the series (modified from Tugel, A.J. & A.M. Lewandowski, eds., Soil Biology Primer).


food web

Brief history of SOIL BIODIVERISITY and European Union – The WHEN

European Commission (EC) complies with the Convention on Biological Diversity (CBD) of United Nations, entered into force in 1993. The main aims of CBD are: 1) conservation of biological diversity; 2) sustainable use of biological diversity; 3) fair sharing of benefits coming from biological diversity.

At the European level the importance of preserving nature and biodiversity is well recognized and led to develop specific environmental policies over the years: from the EU's Bird Directive in 1979 to the Biodiversity Strategy in 1998.

In 2006 the soil theme becomes crucial for EU, with the adoption of the Soil Thematic Strategy in order to guarantee a high level of soil protection across the EU. In this frame the EC recognises the importance of soil biodiversity and undertakes to improve the knowledge of its function as environmental service. Indeed, in 2008 a soil biodiversity expert group is born in the Action SOIL of Joint Research Centre, aiming at providing and supporting the EC's decisions and policies on this topic.

The increasing relevance of soil themes, including biodiversity, at both global and European levels, is confirmed by recent international events as the Global Soil Week (November 18th-22nd, 2012 - and the World Soil Day 2012 (December 5th). Furthermore, the Global Soil Biodiversity Initiative ( involving different organizations, included the Joint Research Centre as key participant, has been launched in 2012.


Value and importance of studying SOIL BIODIVERSITY – The WHY

Ecosystem services were defined as the benefits supplied to people by the ecosystems. In this frame, soil biodiversity carries a range of values to humankind that depend on the perspective from which they are being considered. These include:

  • functional value, relating to the natural services that the soil biota provides, the associated preservation of ecosystem structure and integrity, and ultimately the functioning of the planetary system via connections with the atmosphere and hydrosphere;
  • utilitarian ("direct use") value, which covers the commercial and subsistence benefits of soil organisms to humankind;
  • intrinsic ("non-use") value, which comprises social, aesthetic, cultural and ethical benefits;
  • bequest ("serependic") value, relating to future planetary function or generations of humankind. It is yet unknown

The overall ecological value of soil biota is increasingly appreciated, as we understand more about its origins and consequences. Soil biodiversity has also a monetary value in term of contribution to ecosystem services: estimates ranging from 1.5 to 13 trillion US Dollars (VdP, 2004).

Decline in soil biodiversity is the reduction of forms of life living in soils, both in terms of quantity and variety.

Soil biodiversity is more and more under pressure because of threats to soil, such as erosion, contamination, salinization and sealing. These events threaten soil biodiversity by compromising or destroying the habitat of the soil biota. Management practices that reduce the deposition or persistence of organic matter in soils, or bypass biologically-mediated nutrient cycling also tend to reduce the size and complexity of soil communities. It is however notable that even polluted or severely disturbed soils still support relatively high levels of microbial diversity at least. It has been observed that specific groups may be more susceptible to certain pollutants or stresses than others (e.g., nitrogen-fixing bacteria that are symbiotic to legumes are particularly sensitive to copper). Additional studies on the negative effects of direct and indirect soil threats on specific organisms are required.

Any loss of biodiversity is surely undesirable. However, given our limited state of understanding of the consequences of soil biodiversity, further efforts will be necessary to know potential risks. At the moment, it is common sense that a strong precautionary principle needs to be applied before making any decision.

Potential threats to soil biodiversity

A recently published JRC article maps the potential threats to three categories of soil biodiversity(namely soil microorganisms, fauna and biological functions) in the EU, and gives guidelines for identifying soils that are potentially at risk. Ranking the threats to soil biodiversity based on the knowledge of 107 soil experts from 21 different countries, the study found the potential risk to soil biodiversity to be remarkably high. According to the findings, intensive human use / exploitation poses the greatest  potential threat, while agricultural genetically modified organisms(GMOs) pose the least threat. The authors set out to develop unbiased, normalised indices of potential risk to soil biodiversity based on assessments of the threat associated to 13 possible stressors: climate change, land - use change, habitat fragmentation, intensive human exploitation, soil organic matter decline, industrial pollution, nuclear pollution, soil compaction, soil erosion, soil sealing, soil salinisation, the use of GMOs in agriculture, and invasive species. They used these indices to design maps of potential risk to soil biodiversity in Europe, and compared them with the spatial distributions of different types of land cover, biogeographic regions and protected areas to identify the most sensitive soils and common spatial patterns. The maps show that most European countries contain soils that are at high risk.This risk is higher in agricultural areas and the Danube floodplain than in forest and boreal areas.The authors suggest that the distribution of protected areas should be revised to include soils at high risk, and that land cover should be considered when identifying areas most urgently in need of interventions.

The public user can download the soil biodiversity threats (soil microorganisms, fauna, and biological functions) plus 13 input layers.

On-line publications


Working group

The JRC has created in middle 2008 a Biodiversity expert group to provide it with advice and assistance regarding its scientific and technical activities in support to EU soil policy making and research. Find more information about:

  • Terms of reference
  • Members

Many initiatives dedicated to soil biodiversity are taking place in Member States, but they are not coordinated at European scale. A first initiative coming from Joint Research Centre, SOIL Action is to invite experts to participate in the implementation of a Soil Biodiversity Inventory in Europe (Evaluate ongoing soil biodiversity monitoring activities in the Member States in various scales). In case of interest, we would be pleased to be informed about on-going activities (Databases, Data Collection, Reports, Maps, etc) that National, Regional or Local Institutes perform in relation to Soil Biodiversity. 



1st Experts Meeting (Ispra, 19-20 June 2008) 
The Joint Research Centre (JRC) of the European Commission organised an experts meeting (Ispra, 19-20 June 2008) in support of its contribution to the Soil Biodiversity component of the EU's Soil Thematic Strategy and the Proposal for a Soil Framework Directive.
Find the presentations of the meeting.

What lives below? The soil is alive! 
public awareness event organised by the European Commission on the occasion of World Biodiversity Day (22nd May 2008) at the Ninth Meeting of the Parties to the Convention on Biological Diversity (CBD) 
Forenzelt "Campus", Plaza der Vielfalt (in front of Maritim Hotel), Bonn, Germany. Find more information.......


Contact Points

Alberto Orgiazzi
Tel: +39 0332 789671, fax +39-0332-786394



Soil biodiversity: functions, threats and tools for policy makers 
Did you know that every year soil organisms process an amount of organic matter equivalent in weight to 25 cars on a surface area as big as a soccer field? Or that one hectare of soil can contain the equivalent in weight of two cows of bacteria? Or that some fungi are extremely big and can reach a length of several hundred metres? 

If you are interested in all that, plus the relationship between worms and erosion, microbes and clean water, or why soil organisms are important for antibiotic production, you will find a wealth of information in the report Soil biodiversity: functions, threats and tools for policy makers now available at A press release issued on this occasion is attached below. The report has been prepared by a consortium formed by BIO Intelligence Service, IRD (Institut de recherche pour le développement) and NIOO-KNAW (Netherlands Institute of Ecology) on behalf of the Environment Directorate-General of the European Commission. 

One of the authors of the report (professor Van der Putten) had intervened at Green Week in the session 'The soil life we walk on: does it matter?'  held in Brussels on Wednesday 2 June 2010.

Displaying 1 - 2 of 2 |

Title: Soil microbial biomass and respiration
Resource Type: Datasets, Soil Threats Data
Registration requested: Request Form
Year: 2021

Title: Biodiversity factor in soil erosion.
Resource Type: Datasets, Soil Threats Data
Registration requested: Request Form
Year: 2018
Publisher: Joint Research Centre of the European Commission
Language: en
Displaying 1 - 1 of 1 |

Title: Atlas of Soil Biodiversity
Resource Type: Maps & Documents, Atlases
Year: 2010
Language: en