Soil Biology

Ecosystems: Places where organisms interact with each other and their abiotic environment

Soil organisms interact in many ways. For example, protozoa eat bacteria and some fungi feed on protozoa or nematodes. Other fungi are consumed by protozoa or parasitized by nematodes. Interactions among soil organisms may be very complex. They are crucial to the functioning of soils. An understanding of the nature of the organisms that live in soil is essential for understanding soil ecology. The Soil Ecology and Soil Biology components of the website are designed to complement each other. One should remember that Structure + Process ->Pattern.



Biotic soil components

Typical number or length
(in one handful of soil)

Typical biomass

Plant roots

  • Plant residues (both roots and shoots) are the ultimate source of almost all carbon (energy) for soil organisms
  • There may be 1,000 times more soil microorganisms near plant roots than in soil further away from roots

60 – 150 inches
(annual crops)

1,500 – 3,000 inches
(perennial grasses)

(annual crops)

(perennial grasses)


  • Along with fungi, are the most important group in organic matter decomposition
  • Extracellular compounds help bind soil particles into aggregates
  • Specialized groups are involved in each portion of the nitrogen cycle

300 million – 50 billion

400 – 4,000


  • The most important group involved in decomposing resistant compounds such as lignin
  • Hyphae grow extensively through soils, helping bind soil particles in aggregates
  • Some specialized fungi grow symbiotically with plant roots, increasing nutrient and water uptake and decreasing disease incidence

500,000 – 100 million

500 – 5,000


  • Type of bacteria with growth form similar to fungi; functions similar to both
  • Produce compounds that give soil its distinctive aroma

100 million – 2 billion

400 – 4,000


  • Are the most numerous animals in the soil
  • Help accelerate decomposition when they graze on bacteria, fungi and plant residues

1,000 – 10,000

5 – 50


  • Help accelerate decomposition when they graze on bacteria, fungi and plant residues

100,000 – 50 million

5 – 100


  • Help accelerate decomposition when they (mites, collembolan and other insects) graze on bacteria, fungi and plant residues
  • Collembola, shown in this photograph, are an important arthropod in plant residue decomposition

100 – 1,000

1 – 10


  • Burrowing activity mixes soils and creates macropores that increase water infiltration and flow and help aerate soil
  • Soil passage through guts increases aggregation and nutrient cycling

0 – 2

10 – 40

**Click image for larger view.


Soil-borne organisms are involved in a multitude of life processes.


Soil bacteria function as consumers and decomposers, resulting in specific patterns such as C and N immobilization.

Nematodes have a broad diversity of
feeding behaviors.

Nematodes provide many different types of ecosystem services, resulting in specific patterns such as C and N mobilization.

The highest population densities of nematodes other than the herbivores is found in the soil litter layer (O-horizon); representing a distinct pattern.

The highest population densities of flagellates, amoebae and ciliates is in the soil litter layer (O-horizon); representing a distinct pattern.

Litter layer population densities of flagellates recovered from eight cherry orchards was significantly greater in organic cherry orchards, compared to conventional orchards: representing a distinct pattern.


Nutrient Cycling Pattern

In addition to obtaining inorganic nutrients and water from soil, the root system serves as a host for various herbivores, including fungi, bacteria, nematodes, arthropods and insects. Decomposers, including fungi, bacteria, actinomycetes and earthworms, mineralize labile and resistant substrates (soil organic matter). These are referred to as first-order interactions. In second-order interactions, organisms feed on organisms involved in first order interactions. Numerous species of soil-borne organisms including nematodes, insects, mites, fungi, bacteria, and protozoa feed as carnivores, bacterivores or fungivores on the organisms involved in the previous activity level. Soil ecosystems seem to function very much the same as the aboveground pastures with which we are all more familiar.

Soil ecosystems function in accordance with the Second Law of Thermodynamics, which states that “in any energy conversion, the final product will consist of less useable energy than the original product, because of the inevitable loss of energy in the form of heat.” The amount of biomass, therefore, is less in each subsequent interaction order or trophic level.

Nematode Patterns as Indicators of Soil Quality

Soil, air and water, are basic natural resources that provide important ecosystem services. For example, soil is a carbon and nutrient cycling site and also helps clean both water and air. Much of our drinking water in Michigan is filtered through soil as it moves into ground and surface waters. Poorly managed, soils can serve as a pipeline for pollutants, such as nitrate into groundwater, silt into surface waters and nitrous oxide into the atmosphere.

Soil quality is a measure of a soil’s function, specifically, a soil’s ability to

  1. Accept, hold and release nutrients and other chemical constitutents.
  2. Accept, hold and release water to plants, streams and groundwater.
  3. Promote and sustain root growth.
  4. Maintain suitable soil biotic habitat.
  5. Respond to management.
  6. Resist degradation.

A system of nematode community structure analysis has been developed as an indicator of soil quality.

after Ferris et al.

While soil cultivations can result in soil degradation, including loss to erosion and decreased soil organic matter content, a sustainable agriculture, by definition, does not decrease soil quality.
While there is currently no consensus on which set of measures to include in an assessment of soil quality, scientists generally agree that measures of both abiotic and biotic soil components will have to be integrated in a holistic manner to assess soil quality. Balanced biodiversity is increasingly seen as an essential component of soil quality.

Soil characteristic patterns important to soil quality:

  • Soil organic matter
  • Water holding capacity
  • Water infiltration rate
  • Microbial biomass carbon and nitrogen
  • Structure
  • Texture
  • Bulk density
  • Electrical conductivity
  • Nutrient availability and release
  • pH
  • Balanced biotic diversity


Management goals for maintaining or improving soil quality include:

  1. Using renewable soil components (such as organic matter and nutrients) no faster than they can be renewed.
  2. Using nonrenewable soil components (such as soil particles) no faster than substitute resources can be developed.
  3. Generating or applying potential pollutants associated with soil management (such as manure or pesticides) only as fast as the soil system can assimilate or transform them.

Management options that increase soil quality include crop rotations and cover crops. These options can increase soil organic matter, organic nitrogen and protect against soil erosion. Ecological pest management strategies decrease the need for agricultural pesticides and also reduces soils’ exposure to toxic compounds. These management options are discussed in subsequent chapters.


Alternative orchard management practices result in different nematode community structure.

Alternate orchard management practices result in variations in nitrogen leaching into groundwater.

Three structural factors are currently recognized as indicators of soil quality and there are three major ways to approach soil quality management.

Additional reading

Coleman, D.C. and D.A. Crorsley, Jr. 1996. Fundamentals of Soil Ecology. Academic Press. N.Y. 205 pp.

Doran, J.W., D.C. Coleman, D.F. Bezdicek and B.A. Stewart. 1994. Defining soil quality for a sustainable environment. Soil Science Society of America Special Publication Number 35, ASA, Madison Wis.

Paul, P.A. and F.E. Clark. 1996. Soil Microbiology and Biochemistry. Academic Press, N.Y. 340 pp.

Soil and Water Conservation Society. 2000. Soil Biology Primer. Published in cooperation with the USDA Natural Resources Conservation Service. For more information visit their website at


© 2004 Department of Crop and Soil Sciences
Michigan State University. East Lansing, MI

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