Soil Environment

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Microbial activity basically means the generation of microbial. It could be affected by the soil environmental and physical factors.This page explores the soil environmental factors regulating microbial activity.

Warm-up with this quote by Shuhei Ono from the Carnegie Institution's Geophysical Laboratory:

“We think that there were microbes in the oceans, before the oxygenated atmosphere, which would have used methane for energy... Oxygen first appeared on the surface of the Earth when microbes developed the capacity to split water molecules to produce O2 using the Sun's energy. This is a bit advanced biochemistry, but we think this biological revolution emerged sometime before 2.7 billion years ago," he continued.

Reuters (2006, March 22). Climate Change And The Rise Of Atmospheric Oxygen. ScienceDaily. Retrieved March 4, 2008 from

Chemical Factors


pH changes in soils is due to both biological processes in the soil that consume or release H+ through oxidation/reduction reactions and fermentation, and/or from rainfall that can leach bases [1]. The majority of soil microbes thrive in neutral pH (6-7) due to the high availability of most nutrients in this pH range, but there are examples of microbes (especially fungi) that can tolerate pH of 1 to 13 [1]. Alterations in pH can render essential microbe enzymes inactive and/or denature proteins within the cells and prevent microbial activity from occurring [2]. pH changes can also effect microbes in their access to metals and organics that react differently under varied pH régimes [2].


Oxygen levels dictate the oxidation-reduction reactions that occur and largely what microbial processes occur. In the presence of oxygen, O2 will be used for aerobic respiration, but when concentrations are low other electron acceptors are used (such as sulfur, iron, etc.) [2]. This phenomenon can be seen in flooded soils. Some microbial enzymes require O2, so the level of O2 can regulate the enzymatic activity. Some products of O2 reactions are toxic (such as superoxide radical O2-) and without the proper enzymes to inactivate these toxins microbes are susceptible to harm.

Cation Exchange Capacity (CEC)

The CEC is the total amount of exchangeable cations that a soil can hold at a specific pH [1]. The positively charged soil particles allow for charged soil microorganisms (due to charged organic molecules) to be attracted or repelled from soil. The ability to be held or repelled from the soil influences the ability of microbes to uphold their presence in the soil. The full understanding of how this mechanism works is not understood yet, but postulated mechanisms include: ion exchange attractions, weak attractive forces, coordination bonding, and hydrogen-bonding. The CEC of the soil also influences the availability of nutrients in the soil for microbial use, as charged nutrient particles also will be held or moved through the soil based on its charge [1].

Physical Factors

Soil Texture

Soil has the following types of texture:Sand (0.05-2.0 mm) Silt (0.002-0.05mm) Clay ( < 0.002mm)[1].Sands are loose and single-grained (that is, not aggregated together). They feel gritty to the touch and are not sticky. Each individual sand grain is of sufficient size that it can easily be seen and felt. Sands cannot be formed into a cast by squeezing when dry.Clay is the finest textured of all the soil classes. Clay usually forms extremely hard clods or lumps when dry and is extremely sticky and plastic when wet.[4] Soils that are coarse textured are less likely to have a well-defined structure and therefore fewer structured pore space than s soil high in clay content.S. carpocapsae (diameter=25um) move more in fine sandy loam soil than in clay soil.[5]

Soil pores

Soil pores play a major role in water and air movement. Also, soil microorganisms reside in pores. Pore space is largely determined by size and arrangement of aggregates and affects the movement of water, air, and organisms in soil.Soil pore size distribution: Macropores ( >75um) Mesopores ( 30-70um) Micropores ( 5-30um) Ultramicropores (0.1-5um) Crytopores ( <0.1um).The average particle size could be determined by knowing the soil type and the percentage of sand, clay, and silt.

Soil Structure

Aggregation of primary soil particles is a critical determinant of soil structure.Structure is strongly affected by climate, biological activity, density and continuity of surface cover, and soil management practices. Soils that are coarse textured are less likely to have a well-defined structure and therefore fewer structured pore space than s soil high in clay content. Ecological relationships among soil organisms are influenced by soil structure.

Soil water

Soil water is essential for soil microorganisms. Without some water, there is no microbial activity.Soil with large diameter particles (coarse texture) can contain less water than soil with small diameter particles (fine texture).[6]


Soil temperature greatly influences the rates of biological, physical, and chemical processes in the soil. Within a limited range, the rates of chemical reactions and biological processes double for every 10 degree increase.Soil temperature governs the rates and directions of soil physical processes and chemical reactions, and influences biological processed. Different pathogen species and strains have different thermal limits for survival, germination and infection.[5]

Soil aggregates

Soil aggregates are groups of soil particles that bind to each other more strongly than to adjacent particles. The space between the aggregates provide pore space for retention and exchange of air and water.Aggregation affects erosion, movement of water, and plant root growth.[7]

Biological Factors

growth rates (plant measurements/microbial measurements), assimilation, ect. Major Groups: viruses, bacteria, archaea, fungi, slime mold.

Soil Fauna

Soil animals are divided into macrofauna (>2 mm, earthworms), mesofauna (0.1-0.2 mm, mites and nematodes), and microfauna (<0.1 mm, protozoa). These eukaryotes have a range of effects on microbial communities:

  • Grazing: Grazing increases decomposition rates, freeing nutrients. Grazing also includes direct consumption of other organisms.
  • Nutrient cycling: Soil fauna is responsible for up to 30% of the total soil mineralizable nitrogen. Additionally, soil fauna can remobilize nutrients as waste products. This allows for increases in microbial growth.
  • Microbial community composition: Other organisms in the community are directly effected through consumption. Some soil fauna feed selectively, consuming certain organisms instead of others. This changes the makeup of the microbial community.

In addition to these direct effects, soil fauna has several indirect effects on microbes. One of these effects is habitat alteration. Earthworms especially alter the soil habitat through the formation of burroughs, which changes gas exchange, water movement, and resource locations. Microorganisms are sensitive to the presence of oxygen in their enviroment, and water is essential for microbial existence. Changes in resource locations may allow for microorganisms to colonize another area. [1]

Organism Interactions

There are several types of interactions between organisms. The table below outlines the positive, negative, and neutral aspects that each organism receives as a result of the interaction. These interactions can create environments that promote or discourage specific microbial growth.


Interaction Type


Population 1


Population 2



Mutualism (symbiosis) + + Rhizobia/legumes, mycorrhizal fungi/most plants (Bradyrhizobium), fungi/green algae, fungi/cyanobacteria (Anabaena)
Commensalism + 0 Aerobic oxygen consumption creates an anaerobic environment to support anaerobes
Synergism + + or 0 Flooded soils: fermenters provide carbon and hydrogen gas for methanogens and sulfate

reducers (Desulfosarcina), which in turn reduce toxic effects of acetate and hydrogen gas to fermenters

Amensalism - + or 0 Production of acidic or toxic chemicals
Predation - + Protozoa, nematodes, and slime molds are all major soil predators that consume bacteria
Competition (antagonism) - + Growth rates that allow for utilization of a resource before a competitor
Parasitism - + Viruses

[1, 2]


Bioavailability is a term that refers to the availability of a soil substrate (both nutrients and toxins) to an organism. The EPA lists this definition of bioavailability:

“The term bioavailability designates the state of that fraction of a chemical that is available for uptake and/or transformation by living organisms. Although associated primarily with ecotoxicology, and usually in reference to organic and metallic pollutants, the term bioavailability is also relevant to native organic material. Thus, the “problem” of bioavailability, has existed for microorganisms far longer than has the presence of xenobiotic chemicals in the environment. Sorption, insolubility, and related processes are largely responsible for controlling bioavailability of many pollutants to microorganisms in soils and sediments” [3].

Bioavailability is of special interest to environmental groups because of it's correlation with bioremediation. A common assumption made when discussing bioavailability is that only what is in solution can be metabolized. There are three major factors that effect bioavailability:

  • Sorption: how a substrate bonds to surfaces, especially charged surfaces such as clay and organic matter.
  • Solubility: the capacity for a substance to dissolve in solution. (Insolubility refers to a substance that is unable to dissolve.)
  • Chemical speciation: some substrates may be less available at certain pH or are less available because of charge [2]

Rhizodeposition, mycorrhiza, plant growth-promoting rhizobacteria (PGPR), ect.

Current Research


1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.

2. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008.

3. EPA (2003). Madsen, E.L. "Report on Bioavailability of Chemical Wastes with Resepect to the Potential for Soil Bioremediation." Washington, D.C., U.S. EPA.


5. JSTOR: Florida Entomologist Vol.75, No. 4, p.539,1991



Edited by students of Kate Scow