Soil ecology

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Soil ecology is the study of the interactions among soil organisms, and between biotic and abiotic aspects of the soil environment. [1] It is particularly concerned with the cycling of nutrients, formation and stabilization of the pore structure, the spread and vitality of pathogens, and the biodiversity of this rich biological community.



Soil is made up of a multitude of physical, chemical, and biological entities, with many interactions occurring among them. Soil is a variable mixture of broken and weathered minerals and decaying organic matter. Together with the proper amounts of air and water, it supplies, in part, sustenance for plants as well as mechanical support.

The diversity and abundance of soil life exceeds that of any other ecosystem. Plant establishment, competitiveness, and growth is governed largely by the ecology below-ground, so understanding this system is an essential component of plant sciences and terrestrial ecology.

Features of the ecosystem

Soil fauna

Soil fauna is crucial to soil formation, litter decomposition, nutrient cycling, biotic regulation, and for promoting plant growth. Yet soil organisms remain underrepresented in studies on soil processes and in existing modeling exercises. This is a consequence of assuming that much below ground diversity is ecologically redundant and that soil food webs exhibit a higher degree of omnivory. However, evidence is accumulating on the strong influence of abiotic filters, such as temperature, moisture and soil pH, as well as soil habitat characteristics in controlling their spatial and temporal patterns. [2]

Soils are complex systems and their complexity resides in their heterogeneous nature: a mixture of air, water, minerals, organic compounds, and living organisms. The spatial variation, both horizontal and vertical, of all these constituents is related to soil forming agents varying from micro to macro scales. [3] Consequently, the horizontal patchy distribution of soil properties (soil temperature, moisture, pH, litter/nutrient availability, etc.) also drives the patchiness of the soil organisms across the landscape, [4] and has been one of the main arguments for explaining the great diversity observed in soil communities. [5] Because soils also show vertical stratification of their elemental constituents along the soil profile as result of microclimate, soil texture, and resource quantity and quality differing between soil horizons, soil communities also change in abundance and structure with soil depth. [6] [2]

The majority of these organisms are aerobic, so the amount of porous space, pore-size distribution, surface area, and oxygen levels are crucial to their life cycles and activities. The smallest creatures (microbes) use the micropores filled with air to grow, whereas other bigger animals require bigger spaces, macropores, or the water film surrounding the soil particles to move in search for food. Therefore, soil textural properties together with the depth of the water table are also important factors regulating their diversity, population sizes, and their vertical stratification. Ultimately, the structure of the soil communities strongly depends not only on the natural soil forming factors but also on human activities (agriculture, forestry, urbanization) and determines the shape of landscapes in terms of healthy or contaminated, pristine or degraded soils. [2]


Soil macrofauna, climatic gradients and soil heterogeneity
Historical factors, such as climate and soil parent materials, shape landscapes above and below ground, but the regional/local abiotic conditions constraint biological activities. These operate at different spatial and temporal scales and can switch on and off different organisms at different microsites resulting in a hot moment in a particular hotspot. As a result, trophic cascades can occur up and down the food web.
Soil invertebrates are shown. Ellipses indicate hot (red) or cold spots (blue), with the curved arrows giving some examples of the factors that could switch on/off a hot moment and the straight black arrows (continuous black line = on, dashed = off) showing the implications for soil processes along the soil profile. In the boxes, the main ecosystem characteristics are listed. Soil fauna, climatic gradients and soil heterogeneity.jpg
Soil macrofauna, climatic gradients and soil heterogeneity
Historical factors, such as climate and soil parent materials, shape landscapes above and below ground, but the regional/local abiotic conditions constraint biological activities. These operate at different spatial and temporal scales and can switch on and off different organisms at different microsites resulting in a hot moment in a particular hotspot. As a result, trophic cascades can occur up and down the food web.
Soil invertebrates are shown. Ellipses indicate hot (red) or cold spots (blue), with the curved arrows giving some examples of the factors that could switch on/off a hot moment and the straight black arrows (continuous black line = on, dashed = off) showing the implications for soil processes along the soil profile. In the boxes, the main ecosystem characteristics are listed.

Since all these drivers of biodiversity changes also operate above ground, it is expected that there must be some concordance of mechanisms regulating the spatial patterns and structure of both above and below ground communities. In support of this, a small-scale field study revealed that the relationships between environmental heterogeneity and species richness might be a general property of ecological communities. [5] In contrast, the molecular examination of 17,516 environmental 18S rRNA gene sequences representing 20 phyla of soil animals covering a range of biomes and latitudes around the world indicated otherwise, and the main conclusion from this study was that below-ground animal diversity may be inversely related to above-ground biodiversity. [7] [2]

The lack of distinct latitudinal gradients in soil biodiversity contrasts with those clear global patterns observed for plants above ground and has led to the assumption that they are indeed controlled by different factors. [8] For example, in 2007 Lozupone and Knight found salinity was the major environmental determinant of bacterial diversity composition across the globe, rather than extremes of temperature, pH, or other physical and chemical factors. [9] In another global scale study in 2014, Tedersoo et al. concluded fungal richness is causally unrelated to plant diversity and is better explained by climatic factors, followed by edaphic and spatial patterns. [10] Global patterns of the distribution of macroscopic organisms are far poorer documented. However, the little evidence available appears to indicate that, at large scales, soil metazoans respond to altitudinal, latitudinal or area gradients in the same way as those described for above-ground organisms. [11] In contrast, at local scales, the high diversity of microhabitats commonly found in soils provides the required niche portioning to create “hot spots” of diversity in just a gram of soil. [8] [2]

Not only spatial patterns of soil biodiversity are difficult to explain, but also its potential linkages to many soil processes and the overall ecosystem functioning remains under debate. For example, while some studies have found that reductions in the abundance and presence of soil organisms results in the decline of multiple ecosystem functions, [12] others concluded that above-ground plant diversity alone is a better predictor of ecosystem multi-functionality than soil biodiversity. [13] Soil organisms exhibit a wide array of feeding preferences, life-cycles and survival strategies and they interact within complex food webs. [14] Consequently, species richness per se has very little influence on soil processes and functional dissimilarity can have stronger impacts on ecosystem functioning. [15] Therefore, besides the difficulties in linking above and below ground diversities at different spatial scales, gaining a better understanding of the biotic effects on ecosystem processes might require incorporating a great number of components together with several multi-trophic levels [16] as well as the much less considered non-trophic interactions such as phoresy, passive consumption. [17] ) In addition, if soil systems are indeed self-organized, and soil organisms concentrate their activities within a selected set of discrete scales with some form of overall coordination, [18] there is no need for looking for external factors controlling the assemblages of soil constituents. Instead we might just need to recognize the unexpected and that the linkages between above and below ground diversity and soil processes are difficult to predict. [2]


Recent advances are emerging from studying sub-organism level responses using environmental DNA [19] and various omics approaches, such as metagenomics, metatranscriptomics, proteomics and proteogenomics, are rapidly advancing, at least for the microbial world. [20] Metaphenomics has been proposed recently as a better way to encompass the omics and the environmental constraints. [21] [2]

Soil food web

An incredible diversity of organisms make up the soil food web. They range in size from the tiniest one-celled bacteria, algae, fungi, and protozoa, to the more complex nematodes and micro-arthropods, to the visible earthworms, insects, small vertebrates, and plants. As these organisms eat, grow, and move through the soil, they make it possible to have clean water, clean air, healthy plants, and moderated water flow.

There are many ways that the soil food web is an integral part of landscape processes. Soil organisms decompose organic compounds, including manure, plant residues, and pesticides, preventing them from entering water and becoming pollutants. They sequester nitrogen and other nutrients that might otherwise enter groundwater, and they fix nitrogen from the atmosphere, making it available to plants. Many organisms enhance soil aggregation and porosity, thus increasing infiltration and reducing surface runoff. Soil organisms prey on crop pests and are food for above-ground animals.


Research interests span many aspects of soil ecology and microbiology, Fundamentally, researchers are interested in understanding the interplay among microorganisms, fauna, and plants, the biogeochemical processes they carry out, and the physical environment in which their activities take place, and applying this knowledge to address environmental problems.

Example research projects are to examine the biogeochemistry and microbial ecology of septic drain field soils used to treat domestic wastewater, the role of anecic earthworms in controlling the movement of water and nitrogen cycle in agricultural soils, and the assessment of soil quality in turf production. [22]

Of particular interest as of 2006 is to understand the roles and functions of arbuscular mycorrhizal fungi in natural ecosystems. The effect of anthropic soil conditions on arbuscular mycorrhizal fungi, and the production of glomalin by arbuscular mycorrhizal fungi are both of particular interest due to their roles in sequestering atmospheric carbon dioxide.

Related Research Articles

Ecology Scientific study of the relationships between living organisms and their environment

Ecology is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystems, and biosphere level. Ecology overlaps with the closely related sciences of biogeography, evolutionary biology, genetics, ethology and natural history. Ecology is a branch of biology, and it is not synonymous with environmentalism.

Ecosystem Community of living organisms together with the nonliving components of their environment

An ecosystem consists of all the organisms and the physical environment with which they interact. These biotic and abiotic components are linked together through nutrient cycles and energy flows. Energy enters the system through photosynthesis and is incorporated into plant tissue. By feeding on plants and on one another, animals play an important role in the movement of matter and energy through the system. They also influence the quantity of plant and microbial biomass present. By breaking down dead organic matter, decomposers release carbon back to the atmosphere and facilitate nutrient cycling by converting nutrients stored in dead biomass back to a form that can be readily used by plants and microbes.

Food web Natural interconnection of food chains

A food web is the natural interconnection of food chains and a graphical representation of what-eats-what in an ecological community. Another name for food web is consumer-resource system. Ecologists can broadly lump all life forms into one of two categories called trophic levels: 1) the autotrophs, and 2) the heterotrophs. To maintain their bodies, grow, develop, and to reproduce, autotrophs produce organic matter from inorganic substances, including both minerals and gases such as carbon dioxide. These chemical reactions require energy, which mainly comes from the Sun and largely by photosynthesis, although a very small amount comes from bioelectrogenesis in wetlands, and mineral electron donors in hydrothermal vents and hot springs. These trophic levels are not binary, but form a gradient that includes complete autotrophs, which obtain their sole source of carbon from the atmosphere, mixotrophs, which are autotrophic organisms that partially obtain organic matter from sources other than the atmosphere, and complete heterotrophs that must feed to obtain organic matter.

Landscape ecology Science of relationships between ecological processes in the environment and particular ecosystems

Landscape ecology is the science of studying and improving relationships between ecological processes in the environment and particular ecosystems. This is done within a variety of landscape scales, development spatial patterns, and organizational levels of research and policy. Concisely, landscape ecology can be described as the science of landscape diversity as the synergetic result of biodiversity and geodiversity.

Urban ecology Scientific study of living organisms

Urban ecology is the scientific study of the relation of living organisms with each other and their surroundings in the context of an urban environment. The urban environment refers to the environments dominated by high-density residential and commercial buildings, paved surfaces, and other urban-related factors that create a unique landscape dissimilar to most previously studied environments in the field of ecology. The goal of urban ecology is to achieve a balance between human culture and the natural environment.

This glossary of ecology is a list of definitions of terms and concepts in ecology and related fields. For more specific definitions from other glossaries related to ecology, see Glossary of biology, Glossary of evolutionary biology, and Glossary of environmental science.

The metabolic theory of ecology (MTE) is an extension of Metabolic Scaling Theory and Kleiber's law. It posits that the metabolic rate of organisms is the fundamental biological rate that governs most observed patterns in ecology. MTE is part of a larger set of theory known as metabolic scaling theory that attempts to provide a unified theory for the importance of metabolism in driving pattern and process in biology from the level of cells all the way to the biosphere.

Freshwater ecosystems are a subset of Earth's aquatic ecosystems. They include lakes, ponds, rivers, streams, springs, bogs, and wetlands. They can be contrasted with marine ecosystems, which have a larger salt content. Freshwater habitats can be classified by different factors, including temperature, light penetration, nutrients, and vegetation. There are three basic types of freshwater ecosystems: Lentic, lotic and wetlands. Freshwater ecosystems contain 41% of the world's known fish species.

Arbuscular mycorrhiza Symbiotic penetrative association between a fungus and the roots of a vascular plant

An arbuscular mycorrhiza(AM) is a type of mycorrhiza in which the symbiont fungus penetrates the cortical cells of the roots of a vascular plant forming arbuscules.

Bioturbation Reworking of soils and sediments by organisms.

Bioturbation is defined as the reworking of soils and sediments by animals or plants. These include burrowing, ingestion, and defecation of sediment grains. Bioturbating activities have a profound effect on the environment and are thought to be a primary driver of biodiversity. The formal study of bioturbation began in the 1800s by Charles Darwin experimenting in his garden. The disruption of aquatic sediments and terrestrial soils through bioturbating activities provides significant ecosystem services. These include the alteration of nutrients in aquatic sediment and overlying water, shelter to other species in the form of burrows in terrestrial and water ecosystems, and soil production on land.

Soil food web

The soil food web is the community of organisms living all or part of their lives in the soil. It describes a complex living system in the soil and how it interacts with the environment, plants, and animals.

Ecosystem service Benefits provided by healthy nature, forests and environmental systems

Ecosystem services are the many and varied benefits to humans provided by the natural environment and from healthy ecosystems. Such ecosystems include, for example, agroecosystems, forest ecosystems, grassland ecosystems and aquatic ecosystems. These ecosystems, functioning in healthy relationship, offer such things like natural pollination of crops, clean air, extreme weather mitigation, and human mental and physical well-being. Collectively, these benefits are becoming known as 'ecosystem services', and are often integral to the provisioning of clean drinking water, the decomposition of wastes, and resilience and productivity of food ecosystems.

Functional ecology

Functional ecology is a branch of ecology that focuses on the roles, or functions, that species play in the community or ecosystem in which they occur. In this approach, physiological, anatomical, and life history characteristics of the species are emphasized. The term "function" is used to emphasize certain physiological processes rather than discrete properties, describe an organism's role in a trophic system, or illustrate the effects of natural selective processes on an organism. This sub-discipline of ecology represents the crossroads between ecological patterns and the processes and mechanisms that underlie them. It focuses on traits represented in large number of species and can be measured in two ways – the first being screening, which involves measuring a trait across a number of species, and the second being empiricism, which provides quantitative relationships for the traits measured in screening. Functional ecology often emphasizes an integrative approach, using organism traits and activities to understand community dynamics and ecosystem processes, particularly in response to the rapid global changes occurring in earth's environment.

River ecosystem Type of aquatic ecosystem with flowing freshwater

River ecosystems are flowing waters that drain the landscape, and include the biotic (living) interactions amongst plants, animals and micro-organisms, as well as abiotic (nonliving) physical and chemical interactions of its many parts. River ecosystems are part of larger watershed networks or catchments, where smaller headwater streams drain into mid-size streams, which progressively drain into larger river networks. The major zones in river ecosystems are determined by the river bed's gradient or by the velocity of the current. Faster moving turbulent water typically contains greater concentrations of dissolved oxygen, which supports greater biodiversity than the slow-moving water of pools. These distinctions form the basis for the division of rivers into upland and lowland rivers.

Soil biology

Soil biology is the study of microbial and faunal activity and ecology in soil. Soil life, soil biota, soil fauna, or edaphon is a collective term that encompasses all organisms that spend a significant portion of their life cycle within a soil profile, or at the soil-litter interface. These organisms include earthworms, nematodes, protozoa, fungi, bacteria, different arthropods, as well as some reptiles, and species of burrowing mammals like gophers, moles and prairie dogs. Soil biology plays a vital role in determining many soil characteristics. The decomposition of organic matter by soil organisms has an immense influence on soil fertility, plant growth, soil structure, and carbon storage. As a relatively new science, much remains unknown about soil biology and its effect on soil ecosystems.

Microbial loop

The microbial loop describes a trophic pathway where, in aquatic systems, dissolved organic carbon (DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. In soil systems, the microbial loop refers to soil carbon. The term microbial loop was coined by Farooq Azam, Tom Fenchel et al. in 1983 to include the role played by bacteria in the carbon and nutrient cycles of the marine environment.

Community (ecology) Associated populations of species in a given area

In ecology, a community is a group or association of populations of two or more different species occupying the same geographical area at the same time, also known as a biocoenosis, biotic community, biological community, ecological community, or life assemblage. The term community has a variety of uses. In its simplest form it refers to groups of organisms in a specific place or time, for example, "the fish community of Lake Ontario before industrialization".

Soil biodiversity refers to the relationship of soil to biodiversity and to aspects of the soil that can be managed in relation to biodiversity. Soil biodiversity relates to some catchment management considerations.

Plant litter Dead plant material that has fallen to the ground

Litterfall, plant litter, leaf litter, tree litter, soil litter, or duff, is dead plant material that have fallen to the ground. This detritus or dead organic material and its constituent nutrients are added to the top layer of soil, commonly known as the litter layer or O horizon. Litter is an important factor in ecosystem dynamics, as it is indicative of ecological productivity and may be useful in predicting regional nutrient cycling and soil fertility.

Nutrient cycle Set of processes exchanging nutrients between parts of a system

A nutrient cycle is the movement and exchange of inorganic and organic matter back into the production of matter. Energy flow is a unidirectional and noncyclic pathway, whereas the movement of mineral nutrients is cyclic. Mineral cycles include the carbon cycle, sulfur cycle, nitrogen cycle, water cycle, phosphorus cycle, oxygen cycle, among others that continually recycle along with other mineral nutrients into productive ecological nutrition.


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