In his famous poem, The Auguries of Innocence, the poet William Blake wrote:

"To see a world in a grain of sand,

And a heaven in a wild flower,

Hold infinity in the palm of your hand,

And eternity in an hour."

In a similar vein, one might see the ‘biological universe' in a single gram of fertile soil, approximately a teaspoon in size, containing all the domains (Bacteria, Archaea and Eukarya) and elements of life! The majority of life on Earth is dependent upon six critical elements: hydrogen (H), carbon (C), nitrogen (N), phosphorus (P), oxygen (O), and sulfur (S) that pass through, and are transformed by, soil organisms (the soil biota). The process of biogeochemical cycling is defined as the transformation and cycling of elements between non-living (abiotic) and living (biotic) matter across land, air, and water interfaces (Madsen 2008). Biogeochemical processes are dependent upon the biota in the soil or pedosphere, the outermost layer of the Earth that is composed of soil and subject to soil formation processes. It exists at the interface of the lithosphere (rock), atmosphere (air), hydrosphere (water), and biosphere (living matter). This article addresses the role of soil biota in the pedosphere using ecological principles that link soil organisms and plants to biogeochemical processes occurring within the soil in natural and managed ecosystems.

Aggregates: Model of a Pedosphere

Soil texture (fineness or coarseness) affects plant rooting, soil structure and organic matter content. Soil texture and structure determine the pore-size distribution, soil water holding capacity and the amount of water to air-filled pore space in soil aggregates that provide habitat for soil organisms. Aggregates can be broadly classified into macroaggregates (>250 µm) and microaggregates (20-250 µm) (Six et al. 2004). An aggregate is a naturally formed assemblage of sand, silt, clay, organic matter, root hairs, microorganisms and their "glue" like secretions mucilages, extracellular polysaccharides, and hyphae (filaments) of fungi as well as the resulting pores. Soil aggregates often contain fine roots that grow into soil pores (Figure 1) associating aggregates with the rhizosphere "the zone of soil under the influence of plant roots" (Sylvia et al. 2005). Persistent binding agents like organic matter and metals stabilize microaggregates. The temporary binding agents (polysaccharides and hyphae) produced by soil organisms aid in the formation of macroaggregates contained within the more stable microaggregates. These macroaggregates function as "ecosystems or arenas of activity" (see: Arenas of Activity in the Pedosphere of a Forest) (Beare et al. 1997, Coleman et al. 2004). Thus, an aggregate is a unit of soil structure that could be considered as a very small-scale model of a pedosphere. One can visualize all the interactions of gases, water, organisms and organic and inorganic constituents at the "microscale" hence the "glimpse of the universe" in a gram of soil (Figure 1).

The Soil Biota

Soil biota consist of the micro-organisms (bacteria, fungi, archaea and algae), soil animals (protozoa, nematodes, mites, springtails, spiders, insects, and earthworms) and plants (Soil Quality Institute 2001) living all or part of their lives in or on the soil or pedosphere. Millions of species of soil organisms exist but only a fraction of them have been cultured and identified. Microorganisms (fungi, archaea, bacteria, algae and cyanobacteria) are members of the soil biota but are not members of the soil fauna. The soil fauna is the collection of all the microscopic and macroscopic animals in a given soil. Soil animals can be conventionally grouped by size classes: macrofauna (cm; enchytraeids, earthworms, macroarthropods), mesofauna (mm; microarthropods, mites and collembolan), and microfauna (µm; protozoa, nematodes) (Figure 2). The size of a soil organism can restrict its location in the soil habitat. Smaller members of the microfauna like nematodes are basically aquatic organisms that live in the thin water films or capillary pores of aggregates preying or grazing on other aquatic microfauna such as amoebas (Figure 1). Soil protozoa are also land-adapted members of aquatic microfauna that can dwell in water films in field moist soils. Water films are created by the adsorption of water to soil particles. Soil has a direct effect on the environmental conditions, habitat and nutrient sources available to the soil biota. The term pedosphere is often used interchangeably with soil and captures the concept that the soil is a habitat where the integration of spheres occurs. These spheres include the lithosphere, atmosphere, hydrosphere, and the biosphere (Brady & Weil 2002) (Figure 3). Numerous biogeochemical processes regulated by soil biota occur in the pedosphere. Studies of the pedosphere range in scale from the field (km) to a soil aggregate (µm to nm).

Soil organisms serve numerous roles in the pedosphere. Their most critical function is the regulation of biogeochemical transformations (Table 1). Five functions mediated by the soil biota are 1) the formation and turnover of soil organic matter (OM) that includes mineralization and sequestration of C, 2) nutrient cycling, 3) disease transmission and prevention, 4) pollutant degradation, and 5) improvement of soil structure (Gupta et al. 1997) (Figure 2). The byproducts of metabolic oxidation or reduction of C and N compounds in soils include GHG (Madsen 2008). The dominant soil GHGs consist of: carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). Soil management practices such as N fertilization and tillage can stimulate specific microbial activities such as autotrophic nitrification, denitrification and mineralization that regulate GHG emissions (Greenhouse Gas Working Group 2010) by the oxidation and reduction of C and N.

Table 1 Examples of physiological processes catalyzed by microorganisms in biosphere habitats.
Process		Process
Carbon cycle	Nature of process	Nitrogen cycle	Nature of process
Photosynthesis	Light-driven CO2 fixation into biomass	N2 fixation	N2 gas becomes NH3
C Respiration	Oxidation of organic C to CO2	NH4+ oxidation	NH3 becomes NO2-, NO3-
Cellulose decomposition	Depolymerization, respiration	Anaerobic NH4+ oxidation	NO2- and NH3 becomes N2 gas
Methanogenesis	CH4 production	Denitrification	NO3- is used as an electron acceptor and converted to N2 gas
Aerobic CH4 oxidation	CH4 becomes CO2
Anaerobic CH4 oxidation	CH4 becomes CO2
		Sulphur cycle	Nature of process
		S2 oxidation	S2- and S0 become SO42-
		SO42- reduction	SO42- is used as an electron acceptor and converted to N2 gas
Biodegradation	Nature of process	Other elements	Nature of process
Synthetic organic compounds	Decomposition, CO2 formation	H2 oxidation	H2 is oxidized to H+, electrons reduce other substances
Petroleum hydrocarbons	Decomposition, CO2 formation	Hg methylation & reduction	Organic Hg is formed & Hg2+ is converted to Hg
Fuel additives (MTBE)	Decomposition, CO2 formation	(per)chlorate reduction	Oxidants in rocket fuel & other sources are converted to chloride
Nitroaromatics	Decomposition, CO2 formation	U reduction	U oxyanion is used as an electron acceptor, therefore immobilized
Pharmaceuticals, personal care products	Decomposition	As reduction	As oxyanion is used as an electron acceptor; therefore toxicity is diminished
Chlorinated solvents	Compounds are chlorinated through respiration in anaerobic habitats	Fe oxidation, acid mine drainage	FeS ores are oxidized, strong acidity is generated
As, arsenic; C, carbon; CH4, methane; CO2, carbon dioxide; Fe, iron; FeS, Iron sulphide; H, hydrogen; Hg, mercury; Hg2+, mercuric ion; MTBE, methyl tertiary butyl ether; N2, nitrogen; NH3, ammonia; NH4+, ammonium; NO2-, nitrite; NO3-, nitrate; S0, elemental sulphur; S2-, sulphide; SO42-, sulphate; U, uranium.
Table 1 Modified from Madsen, E. L. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nature Reviews Microbiology 3, 1740-1526 (2005).

The size and composition of the microbial biomass (the combined mass of micro-organisms in the soil) is dependent upon soil properties and the source(s) of C available for energy and cell synthesis. Carbon inputs to the soil vary in their biochemical composition (e.g., their ability to be decomposed) and nutrient content. Carbon turnover, decomposition and microbial activity often lead to increases in OM and soil aggregation (see Aggregates: Model of a Pedosphere). Different ecosystems vary in their potential to support soil organisms (Table 2) and sequester C in OM. Organic C constitutes the chemical backbone of OM and is the energy source for most soil organisms. Microbial decomposition of plant residues and OM provides access to C and nutrients such as N and P required by the majority of living organisms. Mineralization of organic N to ammonium (NH₄⁺) and additions of N fertilizers that contain NH₄⁺ stimulate nitrification a process driven by nitrifying bacteria and archaea that transform NH₄⁺ to nitrate (NO₃^-) (Maier et al. 2009, van Elsas et al. 2007). Nitrate can then undergo an additional microbially mediated step, denitrification. Denitrifiers include bacteria and archaea (Maier et al. 2009, van Elsas et al. 2007). Both nitrification and denitrification are pathways that produce nitrous oxide (N₂O).

The soil food web consists of the community of organisms that live all or part of their lives in the pedosphere and mediate the transfer of nutrients among the living (biotic) and non-living (abiotic) components of the pedosphere through a series of conversions of energy and nutrients as one organism and or substance is consumed by other organisms (Sylvia et al. 2005). The mesofauna (collembolan, mites) play a role in nutrient turnover by shredding materials into smaller pieces with higher surface area providing greater access for microfauna (bacteria, fungi, mycorrhizae) that recycle the majority of C (Figure 2). All food webs contain several trophic levels or feeding positions in a food chain (Figure 2). The term grazing is used when organic C is obtained from living things. Soil organisms are part of the detrital food chain if their organic C is derived from dead materials. The detrital food chain creates new soil organic matter and cycles nutrients from existing OM. Biological systems and organisms contain fairly constant elemental ratios of carbon:nitrogen:phosphorus:sulfur (C:N:P:S). These ratios and mass balances (net change = input + output + internal change) allow scientists to determine biochemical shifts between organisms or ecosystems.

Most members of the soil fauna are chemoheterotrophs, meaning they obtain C and energy by oxidizing (metabolizing) organic compounds (Sylvia et al. 2005). Carbon sequestration limits the process of mineralization mediated by chemoheterotrophs that produce CO₂. The byproducts of the mineralization process are metabolites, heat and CO₂, a GHG. The production of CO₂ can reduce O₂ concentrations creating anoxic sites within microaggregates that result in microenvironments that differ in their content of nutrients and oxygen (van Elsas et al. 2007). These microsites are environments in which CO₂ is converted to CH₄⁺ a GHG via anaerobic respiration by archaea known as methanogens. Methane can undergo oxidation to CO₂ in adjacent microsites. This process is regulated by a group of bacteria known as methanotrophs that transform CH₄⁺ back to CO₂ all in the same aggregate.

The ability of microorganisms to recycle C can provide indirect health benefits to plant communities. Soils that contain larger amounts of OM and microbial biomass tend to have higher rates of microbial activity and as such, some organisms may have the ability to out compete other organisms including plant pathogens. This type of suppression of plant pathogens is known as general suppression (Sylvia et al. 2005). Soils that contain high levels of OM may also support specific antagonistic microorganisms that have an explicit means of suppressing pathogens such as the production of antibiotics. This is an example of specific suppression. Soils that exhibit such properties are termed suppressive soils.

Microorganisms also interact directly with plants through symbiotic relationships that provide nutrients to plants while supplying C to the microorganism(s). An example of a symbiotic relationship between a soil microbe and a higher plant is the interaction of the bacterium known as a rhizobium that induces the formation of nodules on roots of soybean plants in which it fixes N for the plant using carbohydrate supplied by the plant.

Soil is a heterogeneous environment containing limited resources and multiple ecosystems ranging in size between a forest floor, the rhizosphere of a tree, an aggregate, or a single pore of an aggregate (Figure 4). These ecosystems contain areas or arenas of activity rich in detritus or plant matter representing approximately 10% of the total soil volume (Beare et al. 1995, Coleman et al. 2004). These "hot spots" of activity are widely dispersed in space and time but contain a rich biodiversity of organisms that control the biogeochemical cycling and release of nutrients transferred from one ecosystem to another by their movement (Figure 4). The link between biodiversity and biogeochemical cycling is not always evident. Many organisms in a soil are redundant and serve a similar purpose (e.g., the heterotrophs involved in C cycling). Other "keystone" organisms have greater influence on soil processes than their numbers would indicate. Nitrifiers are "keystone" organisms that control transformations in a portion of the N cycle but constitute less than 1% of the total microbial population.

As an example of the linkages and transport of nutrients among ecosystems in a forest consider the following scenario. Leaves fall to the forest floor. This is followed by the physical breakdown of the leaf by the shredding action mediated by the members of the mesofauna (e.g., mites, collembolans) and subsequent further decomposition by microorganisms. Overtime, the decaying leaf passes through the gut of a worm and is deposited in the drilosphere. Remaining leaf matter in the drilosphere located within an aggregate and additional organic materials contained within the aggregate replenish the supply of N, P, and OM used by soil organisms. These organisms decompose and mineralize detritus and OM providing a source of nutrients to plants when aggregates are part of the rhizosphere of a tree root. The mucilages that are produced by the active microorganisms feeding on detrital leaf matter and other organic materials increase the size and stability of the aggregate ecosystem. In this way, soil organisms release, transform, and relocate resources found in arenas of activity throughout the pedosphere via a number of biogeochemical cycles.

Summary

Soil, or the pedosphere, is a heterogeneous environment containing limited resources widely dispersed in space and time across a continuum of ecosystems ranging in size from the microscopic to landscape scale. The interaction of soil organisms within food webs results in the release, transformation and relocation of elements throughout the pedosphere by several biogeochemical processes. Soil organisms influence soil structure by physically binding soil particles together and increasing the number and size of aggregates that provide habit for microfauna. Visualizing all the interactions of gases, water, organisms and organic and inorganic constituents in an aggregate at the "microscale" provides us with a "glimpse of the universe" in a gram of soil.

Aggregates: The arrangement or structure of soil particles held in a single mass or cluster. Aggregates are defined by their shape size and distinctness. (Brady & Weil 2002)

Anaerobic: Cellular respiration that occurs without oxygen.

Anoxic: Without oxygen.

Archaea: A group of prokaryotes (single celled organisms) phylogenetically distinct from bacteria.

Autotrophic nitrification: Carried out by nitrifying bacteria and archaea. It is aprocess in which ammonium is oxidized and converted to nitrite and nitrite is converted to nitrate. Inorganic N serves as the energy source. Nitrous oxide is a by-product of this process. (Sylvia 2005)

Biogeochemical cycling: The transformation and cycling of elements between non-living (abiotic) and living (biotic) matter across land, air, and water interfaces. (Madsen 2008)

Collembolan are microarthropods: Wingless insects a few millimeters in length and 0.2 to 2 mm in width. They are found on or near the surface of the soil and in plant litter. Populations range between 10³ m^-2 in agricultural soils to 10⁶ m^-2 in forest soils. (Sylvia et al. 2005)

Chemoheterotrophs: Organisms that obtain energy and carbon from the oxidation of organic compounds (Sylvia et al. 2005)

Denitrification: A form of anaerobic respiration that results in the conversion of NO₃^- to primarily N₂O and elemental N (N₂) (Sylvia et al. 2005)

Drilosphere: The portion of the soil volume influenced by secretions of earthworms . (Coleman et al. 2004)

Earthworms: Oligochaeta that dwell in soil. These worms have a segmented body structure. Through their activities, earthworms can stimulate microbial activity, mix soils and aide in the formation of soil structure, and translocate plant material from the surface to lower soil strata. Oligochaete is a particular class of segmented worms, including the earthworms, which have few (oligo) body bristles (chaeta). (Sylvia et al. 2005)

Enchytraeids: Small (10- 20 mm in length) unpigmented terrestrial oligochaeta referred to as pot worms. (Coleman et al. 2004)

Field moisture capacity or field moist soil: The moisture content of a soil, expressed as a percentage of the oven dry weight, after the gravitational, or free, water has drained away; the field moisture content 2 or 3 days after a soaking rain; also called normal field capacity, normal moisture capacity, or capillary capacity. Glossary of Soil Science Terms. (Madison, WI: ASA, CSSA, and SSSA 2010).

General suppression: Competition from fungi and bacteria in root fragments, which reduces the inoculum density of the pathogen. (Sylvia 2005)

Hyphae: Long and often branched tubular filament that constitutes the vegetative body of many fungi and fungus like organisms. (Sylvia 2005)

Keystone organisms: Species that have a disproportionate effect on their environment relative to their biomass. (Paine 1995)

Macroarthropod: Larger insects and spiders are examples of this group of organisms. Typical body lengths range 10 mm to as much as 15 cm. (Coleman et al. 2004)

Macrofauna: Earthworms, termites, and dungbeetles, etc., are important biological agents fragmenting organic residues and causing a large surface area to be exposed. They also help the formation of soil aggregates and soil pores. (Gupta et al. 1997)

Microbial biomass: Total mass of micro-organisms alive in a given volume or mass of soil. (Sylvia 2005)

Microflora: Bacteria and fungi have diverse metabolic capabilities and are the principle agents for the cycling of nutrients (e.g., nitrogen, phosphorous, and sulphur). They may be free living or symbiotic and active in the decomposition or build-up of organic matter. They also help in the formation of stable soil aggregates. (Gupta et al. 1997)

Microfauna: Protozoa and nematodes are a crucial link between microflora and larger fauna. They regulate the populations of bacteria and fungi and play a major role in the mineralization of nutrients. (Gupta et al. 1997)

Microarthropods: Arthropods that are micrometers in size, have segmented bodies, jointed legs, and a cuticle that acts as an exoskeleton. The two most abundant groups of soil microarthropods are collembolan and mites. (Sylvia et al. 2005)

Mineralization: Conversion of an element from an organic form to an inorganic state as a result of microbial decomposition. (Sylvia et al. 2005)

Mites: Microarthropods with oval bodies, four pairs of legs, and a cuticle that acts as an exoskeleton. (Sylvia et al. 2005)

Mesofauna: Mites and collembola feed on litter and help fragment organic residues. They are predators of fungi and microfauna, playing an important role in regulating microbial populations and nutrient turnover. (Gupta et al. 1997)

Mucilages: Gelatinous secretions and exudates produced by plant roots and many microorganisms. (Sylvia 2005)

Nematodes: also known as roundworms, are cylindrical, unsegmented worms with tapered ends. They are small enough (100 to 1000 µm in length and 5 to 100 µm in diameter) to fit within existing pores of aggregates. (Sylvia 2005)

Pedology: "The study of soils as natural bodies, the properties of soil horizons, and the relationships among soils within a landscape" (Brady & Weil 2002). The term was coined by F.A. Fallow in 1862 but was popularized by Vasily Dokuchaev who founded the discipline of pedology. (Simonson 1999)

Pedosphere: Used interchangeably with soil and captures the concept that the soil is a habitat where the integration of rock (lithosphere), air (atmosphere), water (hydrosphere), and living things (the biosphere) occurs. (Brady & Weil 2002)

Protozoa: Unicellular eukaryotic microorganism that moves by either protoplasmic flow (amoeba), flagella (flagellates), or cilia (ciliates). Most species feed on bacteria, fungi, or detrital particles. (Sylvia 2005)

Rhizosphere: The zone of soil under the influence of plant roots. (Sylvia et al. 2005)

Soil: The naturally occurring unconsolidated material on the surface of the earth that has been influenced by parent material, climate (including the effects of moisture and temperature), macro- and micro-organisms, and relief, all acting over a period of time to produce soil that may differ from the material from which it was derived in many physical, chemical, mineralogical, biological, and morphological properties. Glossary of Soil Science Terms. (Madison, WI: ASA, CSSA, and SSSA 2010).

Soil biota: Consists of the micro-organisms (bacteria, fungi, and algae), soil animals (protozoa, nematodes, mites, springtails, spiders, insects, and earthworms) and plants living all or part of their lives in or on the soil or pedosphere.

Soil fauna: The collection of all the micro- and macroscopic animals in a given soil.

Soil food web: Consists of the community of organisms that live all or part of their lives in the pedosphere and mediate the transfer of nutrients among the living (biotic) and non-living (abiotic) components of the pedosphere through a series of conversions of energy and nutrients as one organism and or substance is consumed by other organisms. (Sylvia et al. 2005)

Soil organic matter: Organic fraction of the soil exclusive of the undecayed plant and animal residue (Sylvia 2005)

Soil structure: The arrangement of soil particles into small clumps, called peds. Much like ingredients in a cake batter bind together to form a cake, soil particles (sand, silt, clay, and even organic matter) bind together to form peds. Peds have various shapes depending on their "ingredients" and on the conditions in which the peds formed: getting wet and drying out or freezing and thawing-or even people walking on or farming the soil. Ped shapes roughly resemble balls, blocks, columns, and plates. Between the peds are spaces, or pores, in which air, water, and organisms can move. The sizes of pores and their shapes vary from soil structure to soil structure. Glossary of Soil Science Terms. (Madison, WI: ASA, CSSA, and SSSA 2010).

Soil texture: The particles that make up soil are categorized into three groups by size-sand, silt, and clay. Sand particles are the largest and clay particles the smallest. Although a soil could be all sand, all clay, or all silt, that is rare. Instead most soils are a combination of the three. The relative percentages of sand, silt, and clay are what give soil its texture. A loamy texture soil, for example, has nearly equal parts of sand, silt, and clay. Glossary of Soil Science Terms. (Madison, WI: ASA, CSSA, and SSSA 2010).

Specific suppression: Antagonistic microorganisms in the rhizosphere and in young root lesions, which limit infection and secondary spread of the pathogen by runner hyphae along the roots. (Sylvia 2005)

Soil water holding capacity: The ratio of the volume of water which the porous medium, after being saturated, will retain against the pull of gravity to the volume of the porous medium (Lohman et al. 1972).

Trophic levels: Levels of the food chain. The first trophic level includes photosynthesizers that get energy from the sun. Organisms that eat photosynthesizers make up the second trophic level. Third trophic level organisms eat those in the second level, and so on. It is a simplified way of thinking of the food web. In fact, some organisms eat members of several trophic levels. Natural Resource Conservation Service (NRCS) Soil Biology website 2000. (verified 20 July 2011) (http://www.soils.usda.gov/sqi/concepts/)