AGP - What is soil biodiversity

What is soil biodiversity?

What is soil biodiversity?

“Biological diversity must be treated more seriously as a global resource, used, and above all, preserved” (
Wilson, 1998). Biological diversity or "biodiversity" is described as "the variability among living organisms from all sources whether terrestrial, aquatic or marine. It includes the diversity within species (Genetic Diversity), between species (Organismal Diversity) and of ecosystems (Ecological Diversity) (see box, right).  About 1.75 million species have so far been identified, although the total number of species is likely to be much higher with conservative estimates at around 13 million.

Soil is one of the most diverse habitats on earth and contains the most diverse assemblages of living organisms (Giller et al., 1997). It is one of nature's most complex ecosystems: it contains thousands of different organisms, which interact and contribute to the global cycles that make all life possible - the life support systems. Nowhere in nature are species so densely packed as in soil communities (Hågvar, 1998). For example:


  • Over 1000 species of invertebrates may be found in a single m2 of a European beech forest (Schaefer and Schauermann, 1990)
  • Many of the world’s terrestrial insect species are soil dwellers for at least some stage of their life-cycle (Bater, 1996)
  • A single gram of soil may contain millions of individuals and several thousand species of bacteria (Torsvik et al., 1994).
  • A typical, healthy soil might contain several species of vertebrate animals, several species of earthworms, 20-30 species of mites, 50-100 species of insects, tens of species of nematodes, hundreds of species of fungi and perhaps thousands of species of bacteria and actinomycetes.
  • Soil contains the organism with the largest area. A single colony of the honey fungus Armillaria ostoyae covers 8.9 km2



Soil organisms


Soil communities are so diverse it is difficult to find one method to describe all that we find in soil. On a very basic level, size can be a useful measurement although one has to recognise the presence of juveniles or larval stages which may be very different from the parent form and be in different habitats.  More information can be gained by comparing morphology against standard or type species. This can be done at an initially gross level to describe families and later to describe genera and eventually species as more information is obtained. This level of information requires great specialist technical knowledge and a familiarity with the organisms. Many of the methods used are not transferable to other groups. For example the description of microbial species is mainly based on biochemical and physiological information rather than gross anatomy where as for arthropods, for example, the emphasis is placed on morphology and life history of the organism.  The ease at which DNA can be sequenced is making the task of assessing biodiversity easier although this is itself not without its own problems not least in defining what actually a species is.  


Soil Food Webs


The activity at one scale may affect the process occurring at another. For example, mites or collembola feeding on bacteria and fungi at the scale of a few millimetres have effects on microbial processes and their communities within a small zone of a few centimeters (Anderson, 1995). On the other hand, the feeding and burrowing behaviour of earthworms may create pores and burrows of a few millimeters in diameter that affect soil structure and hydrological processes at the scale of metres, while feeding activities of termite and ant colonies may affect soil physical and chemical processes over the scale of hectares (Swift et al., 1996). The activity of smaller organisms is therefore expressed against the background of the effects of larger organisms, which are in turn, expressed against the backdrop of climate, plant community and soil properties. In this hierarchical system, higher levels constrain activity at lower levels of spatio-temporal organization, through top-down controls (Lavelle et al., 1997). Bottom-up control (feedback) also exists, for example, the ecosystem engineers can alter ecosystem performance with effects on their own and other populations (Jones et al., 1994).


One starting point for the soil food web is to look at the energy requirements of the organisms involved. The bases of nearly every food web are autotrophic organisms. These convert the energy from solar radiation into biomass via photosynthesis or analogous processes. Examples of these are the plants and the cyanobacteria, the latter of which inhabit the first few millimetres to centimetres of soil and co-incidentally also fix atmospheric nitrogen. These traits help in the formation of soil crusts in bare soils and thus limit erosion.  Similarly, their nitrogen fixing abilities can aid soil fertility and in some cases, cyanobacteria live in intimate associations with plant roots.


The function of the soil community


In both natural and agro ecosystems, soil organisms are responsible, to a varying degree (depending on the system), for performing vital functions in the soil ecosystem (Barrios, 2007). These are carried out in a range of scales from microns to meters to kilometres.  Many of the functions performed in soil and, often controlled by the myriad of organisms, are focussed on “hot spots” of activity where biological activity may be concentrated, for example at the root/soil interface (the ”rhizosphere”) or locations where there are pools of organic matter such as areas of decaying plant material (the “detritusphere”) or, the linings of earthworm burrows (the “drilosphere”) which are covered in earthworm secretions and so are nutrient rich whilst other functions may occur in the non-rhiozosphere soil. The functions range from physical effects such as the regulation of soil structure and edaphic (in soil) water regimes, to chemical and biological processes such as degradation of pollutants, decomposition, nutrient cycling, greenhouse gas emission, carbon sequestration, plant protection and growth enhancement or suppression (click to open table). 


To make it easier to understand the complexity of the interactions between the soil biota and reduce their functions to manageable levels, soil functions can be divided into specific tasks (Barrios, 2007) with micro-organisms lying at the heart of many of the functions (click to open table). From these a direct link to ecosystem services may be made (Decaens et al., 2006). Another way is to divide the soil biota on the basis of body size or social grouping such as roots, ecosystem engineers, litter transformers, phytophages and parasites, micro-predators and microflora (click to open table). This approach can take into account the potential top-down regulatory controls of larger organisms (e.g. the ecosystem engineers) over smaller ones. For example at the top level, termites, ants and earthworms acting as ecosystem engineers, produce structures that can last long periods of time (outlasting the organisms that produced them) and affect soil organic matter dynamics and soil physical processes. At a lower level, microflora act upon organic matter and nutrient cycles, root and rhizosphere processes and plant production (with both positive and negative effects). Of course it must be remembered that the interaction may also work the way i.e. a "bottom-up" approach where the activity of microorganisms, for example, may regulate those at a higher level through feeding and release of nutrients.


Interactions within soil communities


Any community of organisms which is made up of a population of different species there is opportunity for the organisms to interact with each other (Bianchi and Bianchi, 1995). If you consider two different populations living with each other, one of the interactions may occur: (a) neutralism – population unaffected by the interaction; (b) commensalism – one partner benefits, second is unaffected; (c) mutualism or synergy – both partners may benefit  (d) predation  - one partner benefits whilst the other suffers; and (e) competition  - both partners are affected.


Which interaction occurs would depend on the nature of the resources (type and level of food and energy supply), the population density and diversity. For example commensalism favours communities with high diversity whereas neutralism is more likely in communities with a low number of individuals. Competition tends to reduce diversity where resources become limited. The interactions which occur in soil can be complex due to soils’ spatial heterogeneity. For example, many species of protozoa prey upon bacteria. Physico-chemical factors (such as amount of water, pH, and mineral surface chemistry – link to soil physical page) can affect the location, movement and binding of microorganisms to soil particles. This then affects how they are predated by predatory protozoa.



Effect of human activity on soil biodiversity


The impact of agricultural activities on biodiversity of plants and animals has a long history, which began when humans first started the domestication process over 7000 years ago (Solbrig and Solbrig, 1994). By selecting a few seemingly more useful or edible species, these ancient agriculturists began the selection process which still continues today as farmers, researchers and companies look for more productive plants and animals. This process necessarily involves a reduction and simplification of the immense biological diversity of nature, at both the species and genetic level. However, since the first farmers selected their preferred plants and cultivated their land with the few simple tools and mostly organic inputs available at a local (small) scale, their activities were, in general, of low impact or at least of a limited geographical scale. There are still examples today of cultures that continue to practice this small-scale, limited impact agriculture (Denevan, 1995; Redford and Mansour, 1996).


The growth in population and the increasing urbanization led to the need to produce larger quantities of food being transported over longer distances. Larger areas of land were dedicated to agricultural activities, using animal traction, irrigation canals and other intensification techniques. The change in land use through clearing forested or grassland for cultivation, changes in agricultural practices such as crop rotation and mixes, grazing practices, residue management, irrigation and drainage all affect the soil environment and change the range of habitats and foods for soil organisms. Treatments applied to land such as liming, fertilisers, manure and other organic materials, tillage practices, the use of pesticides and so forth, all change the physical and chemical environment.


With the urbanization of the population, proportionally less number of people were involved in food production. This led to changes in agricultural practices such as the development of modernized agricultural techniques with the use the mouldboard plough, motorized tractors, hybrid cultivars, inorganic fertilizers and pesticides. This created new pressures on the land, dramatically increasing the influence of agricultural practices on biodiversity.


Today, some 6 billion humans rely on biodiversity for its goods and services, the population having doubled since 1950. This may reach 9 billion by the year 2050. More significantly, the demands on natural resources are growing even faster, the global economy having quintupled in the last 50 years.  As the amount of land available for agricultural use continues to decrease worldwide, the demands of human populations (especially


Agriculture and soil biodiversity


Our agricultural activities exert an important influence on the soil biota, their activities and diversity (see top figure right; table). Clearing forested or grassland for cultivation drastically affects the soil environment and hence the number and kinds of soil organisms. Reducing the quantity and quality of plant residues and the number of species of higher plants leads to a reduction in the range of habitats and foods for soil organisms.


Different types of agricultural practices and systems affect the soil biota in different ways and the response (see bottom figure right) may be either positive or negative depending on which part of the soil the biota e.g. fungal or bacterial is affected. For example, organisms which are sensitive to pH will be affected by the addition of lime; the bacterial: fungal ratio will be affected by the addition of fertilisers and manures which alter the C:N ratio as will the effects of tillage. The consequences of the agricultural practice on the soil biota may be direct and far reaching. Organisms which are of benefit to agriculture and which may be affected include those responsible for;


·      organic matter decomposition and soil aggregation;

·      breakdown of toxic compounds both metabolic by-products of organisms and agrochemicals;

·      inorganic transformations that make available nitrates, sulphates, and phosphates as well as essential elements such as iron and manganese;

·      nitrogen fixation into forms usable by higher plants


High external-input agriculture can overcome specific soil constraints through the use of inorganic fertilizers, pesticides, and other amendments, in order to meet plant requirements (Sanchez, 1994; 1997). Although these practices have led to considerable increases in overall food production worldwide, they also tend to decrease or disregard the potential benefits of soil biological activities in maintaining soil fertility and enhancing plant production. However, the vast majority of the world’s farmers do not have access to, or cannot afford, the external inputs necessary to apply the principles and practices of high external input agriculture (Vandermeer et al., 1998).


Any misuse of these practices has far reaching effects and include:


·      Deterioration of soil quality and reduction in agricultural productivity due to nutrient depletion, organic matter losses, erosion and compaction

·      Pollution of soil and water through the over use of fertilizers and the improper use and disposal of animal wastes

·      Increased incidence of human and ecosystem health problems due to the indiscriminate us of pesticides and chemical fertilizers

·      Loss of biodiversity due to the use of reduced number of species being cultivated for commercial purposes

·      Loss of adaptability traits when species that grow under specific local environmental conditions become extinct

·      Loss of beneficial crop-associated biodiversity that provides ecosystem services such as pollination, nutrient cycling and regulation of pest and disease outbreaks

·      Soil salinisation, depletion of freshwater resources and reduction of water quality due to unsustainable irrigation practices throughout the world

·      Disturbance of soil physicochemical and biological processes as a result of intensive tillage and slash and burning.

Although humans generally begin their influence on soil biodiversity with naturally-present communities at a particular site (resulting essentially from ecological and evolutionary forces), they also have the ability to introduce new organisms and, through imposition of different management practices, put selective pressures on the naturally-present or introduced soil biota. This provides the opportunity to manage soil organisms and their activities to enhance soil fertility and crop growth. In theory, probably enough is known to manage these communities, yet considerable basic and applied research is needed to reach appropriate levels of biological husbandry and optimal management of these biological resources (Hendrix et al., 1990).



Soil ecosystem services


Ecosystem services are a way of putting a value on biodiversity by looking at what it does and how we value the function that the soil performs. These produce a range of services which are essential to our health and well being (IPCC 2002).


·               Clean air & water

·               Cultural, spiritual & recreational values

·               Decomposition and cycling of organic matter

·               Gas exchange and carbon sequestration

·               Maintenance of soil structure

·               Medicines

·               Plant growth control

·               Pollination

·               Production of food, fuel & energy

·               Regulation of nutrients and uptake

·               Seed dispersal

·               Soil detoxification

·               Soil formation & prevention of soil erosion

·               Suppression of pests and diseases

To provide a framework of how ecosystems provide for human lives the term “Ecosystem Approach” and “Ecosystem Services” are being used. The “Ecosystem Approach” is to assist decision makers to take full account of ecological systems and their associated biodiversity. “Ecosystem Services” describe which the process and functions, provided by the natural world, that are used by humankind for its well being.