Soil Microorganisms

Microorganisms are very small forms of life that can sometimes live as single cells, although many also form colonies of cells. A microscope is usually needed to see individual cells of these organisms. Many more microorganisms exist in topsoil, where food sources are plentiful, than in subsoil. They are especially abundant in the area immediately next to plant roots (called the rhizosphere), where sloughed-off cells and chemicals released by roots provide ready food sources. These organisms are primary decomposers of organic matter, but they do other things, such as provide nitrogen through fixation to help growing plants, detoxify harmful chemicals (toxins), suppress disease organisms, and produce products that might stimulate plant growth. Soil microorganisms have had another direct importance for humans—they are the source of most of the antibiotic medicines we use to fight diseases.


Bacteria live in almost any habitat. They are found inside the digestive system of animals, in the ocean and fresh water, in compost piles (even at temperatures over 130°F), and in soils. Although some kinds of bacteria live in flooded soils without oxygen, most require well-aerated soils. In general, bacteria tend to do better in neutral pH soils than in acid soils.

In addition to being among the first organisms to begin decomposing residues in the soil, bacteria benefit plants by increasing nutrient availability. For example, many bacteria dissolve phosphorus, making it more available for plants to use. Bacteria are also very helpful in providing nitrogen to plants, which they need in large amounts but is often deficient in agricultural soils. You may wonder how soils can be deficient in nitrogen when we are surrounded by it—78% of the air we breathe is composed of nitrogen gas. Yet plants as well as animals face a dilemma similar to that of the Ancient Mariner, who was adrift at sea without fresh water: “Water, water, everywhere nor any drop to drink.” Unfortunately, neither animals nor plants can use nitrogen gas (N2) for their nutrition. However, some types of bacteria are able to take nitrogen gas from the atmosphere and convert it into a form that plants can use to make amino acids and proteins. This conversion process is known as nitrogen fixation.

Some nitrogen-fixing bacteria form mutually beneficial associations with plants. One such symbiotic relationship that is very important to agriculture involves the nitrogen-fixing rhizobia group of bacteria that live inside nodules formed on the roots of legumes. These bacteria provide nitrogen in a form that leguminous plants can use, while the legume provides the bacteria with sugars for energy.

People eat some legumes or their products, such as peas, dry beans, and tofu made from soybeans. Soybeans, alfalfa, and clover are used for animal feed. Clovers and hairy vetch are grown as cover crops to enrich the soil with organic matter, as well as nitrogen, for the following crop. In an alfalfa field, the bacteria may fix hundreds of pounds of nitrogen per acre each year. With peas, the amount of nitrogen fixed is much lower, around 30 to 50 pounds per acre.

The actinomycetes, another group of bacteria, break large lignin molecules into smaller sizes. Lignin is a large and complex molecule found in plant tissue, especially stems, that is difficult for most organisms to break down. Lignin also frequently protects other molecules like cellulose from decomposition. Actinomycetes have some characteristics similar to those of fungi, but they are sometimes grouped by themselves and given equal billing with bacteria and fungi.


Fungi are another type of soil microorganism. Yeast is a fungus used in baking and in the production of alcohol. Other fungi produce a number of antibiotics. We have all probably let a loaf of bread sit around too long only to find fungus growing on it. We have seen or eaten mushrooms, the fruiting structures of some fungi. Farmers know that fungi cause many plant diseases, such as downy mildew, damping-off, various types of root rot, and apple scab. Fungi also initiate the decomposition of fresh organic residues. They help get things going by softening organic debris and making it easier for other organisms to join in the decomposition process. Fungi are also the main decomposers of lignin and are less sensitive to acid soil conditions than bacteria. None are able to function without oxygen. Low soil disturbance resulting from reduced tillage systems tends to promote organic residue accumulation at and near the surface. This tends to promote fungal growth, as happens in many natural undisturbed ecosystems.

Many plants develop a beneficial relationship with fungi that increases the contact of roots with the soil. Fungi infect the roots and send out root-like structures called hyphae (see figure 4.2). The hyphae of these mycorrhizal fungi take up water and nutrients that can then feed the plant. The hyphae are very thin, about 1/60 the diameter of a plant root, and are able to exploit the water and nutrients in small spaces in the soil that might be inaccessible to roots. This is especially important for phosphorus nutrition of plants in low-phosphorus soils. The hyphae help the plant absorb water and nutrients, and in return the fungi receive energy in the form of sugars, which the plant produces in its leaves and sends down to the roots. This symbiotic interdependency between fungi and roots is called a mycorrhizal relationship. All things considered, it’s a pretty good deal for both the plant and the fungus. The hyphae of these fungi help develop and stabilize larger soil aggregates by secreting a sticky gel that glues mineral and organic particles together.


Algae, like crop plants, convert sunlight into complex molecules like sugars, which they can use for energy and to help build other molecules they need. Algae are found in abundance in the flooded soils of swamps and rice paddies, and they can be found on the surface of poorly drained soils and in wet depressions. Algae may also occur in relatively dry soils, and they form mutually beneficial relationships with other organisms. Lichens found on rocks are an association between a fungus and an alga.


Protozoa are single-celled animals that use a variety of means to move about in the soil. Like bacteria and many fungi, they can be seen only with the help of a microscope. They are mainly secondary consumers of organic materials, feeding on bacteria, fungi, other protozoa, and organic molecules dissolved in the soil water. Protozoa—through their grazing on nitrogen-rich organisms and excreting wastes—are believed to be responsible for mineralizing (releasing nutrients from organic molecules) much of the nitrogen in agricultural soils.


This Page Was Created Utilizing Text And Images From These Sources:

Sustainable Agriculture Research & Education Learning Center, Soil Microorganisms Page

Natural Resources Conservation Service Soil Health Campaign Flickr Account

Photo Credit: USDA-ARS, Electron & Confocal Microscopy Unit, Beltsville, MD USA


Soil Macro Fauna



While the most well‐known nematodes are pests occupying and feeding on plant roots (such as the lesion nematode and the soybean cyst nematode), in fact most nematodes are beneficial organisms. Nematodes are extremely important because they consume a diverse array of food sources, which places them at multiple trophic levels in the soil food web. Nematodes are mostly microscopic and occupy water pores in soil but also rely on air pores for diffusion. Nematodes are a diverse group of animals and can be found in almost all soil types and climates including Antarctica. Some nematodes consume bacteria and others fungi. Like protozoa, nematodes have a role in nitrogen mineralization, disease control of microbes, and root growth stimulation. Still other nematodes are opportunistic or omnivorous and feed on a variety of food sources including protozoa. Specific nematodes are used in biological application to consume the larvae of invertebrate pests (e.g. Japanese beetles). Still other nematodes are specifically predators, feeding exclusively on other nematodes. Due to this nature, scientists use nematodes as biological indicators in soil. Nematode community measures are related to the structure of the entire food web and also reflect both chemical and physical disturbances.


Earthworms have many benefits and are also the easiest indicator of biology because they do not require a microscope for observation. Earthworm burrows create increased soil structure and porosity, and habitat for other soil organisms. Earthworms digest substantial quantities of organic matter, turning it into more available nutrients. Different earthworms occupy different places in the soil profile; therefore earthworm diversity is important in maintaining soil health.

Other Soil Organisms:

Other soil fauna include arthropods, potworms (also called enchytraeids) and water bears (also called tardigrades). Soil arthropods may spend all or only a part of their life in the soil. While some are pests, many are strictly shredders, breaking down plant litter as they feed on microbes, and like earthworms, enhance soil structure with their fecal pellets and burrows. Some also have a role in nitrogen mineralization (e.g., collebolans). Larger, mobile arthropods actually function to move smaller soil organisms around, dispersing them into new settings where they can then assist in decomposition. Potworms are native, somewhat common, small, light colored worms and serve similar functions to earthworms, but affect smaller pore structure. Like nematodes, water bears live in soil water and through a unique kind of suspended metabolism (crytobiosis) can withstand substantial stresses of moisture loss, temperature extremes, high pressure and even the vacuum of space. They feed on plant residues, algae and small invertebrates, playing a role in nutrient turnover.

How Management Practices Can Impact & Enhance Soil Biota:

The great news is that the actions we take to remediate phosphorus pollution or enhance nitrogen uptake can also benefit soil biology. Both physical and chemical disturbances can affect the abundance and diversity of soil organisms, and in particular soil fauna that are higher up on the food web. The complexity and type of a soil food web can vary substantially from one soil and management practice to another. Generally speaking agricultural soils tend to have a greater population of bacteria, and therefore more soil organisms that feed on bacteria, in comparison to forest soils, which tend to have a greater number of fungi and soil organisms that feed on fungi. However, within agricultural soils, management practices can shift the dynamics of the soil food web over time in either direction. Complexity is an important concept in studying soil biology, because it relates to how many kinds and groups of organisms there are. More complex and diverse food webs usually confer more benefits to plants.

Increasing quantity and complexity of soil habitat and food sources and maintaining water‐air balance generally increases biological complexity. For example, providing a diverse array of food sources from organic matter applications, plant rotations and cover crops allows for more diversity in soil biota that feed on the organic matter. Similarly, decreasing compaction and increasing soil structure encourages soil biota. This is both due to increased water infiltration and to diversity in soil pores – allowing for a range of pore sizes that support a range of soil biota. Owing to the fact that soil organisms are so tiny and soil is complex, physical space is a really important piece of maintaining soil biology. Places of high biological activity in soil are mainly near plant roots, in plant litter and earthworm and arthropod burrows. Therefore, increasing soil quality for root growth development can also benefit soil biota. Also, if your soils are permanently saturated only anaerobic organisms‐ those that do not need oxygen to survive – will be able to live there. This is important for nitrogen cycling because if affects how well nitrogen is mineralized. Many organisms, including nematodes, live in water films; if you have a soil that is in serious drought conditions on a regular basis, many will die, or go into a kind of temporary stasis until more water is available. Soil organisms can also be sensitive to chemical disturbances and low pH to differing degrees by species; however earthworms and other soil animals are usually more sensitive.

While tillage can lead to a bloom of soil activity as organic matter is incorporated into the soil, this activity is generally bacterial in nature and short lived. Every time you till the soil, you are shifting back the soil community either by direct damage or by homogenization of the habitat. Reducing tillage can have positive effects on biology and in particular fungi and larger animals. Reducing tillage leaves more roots intact, and allows more stable, slowly decomposing organic matter and physical structure to develop through time. While a no‐till system might not be ideal or practical in all farming situations, reduction and better management of tillage can benefit soil biology. Research has suggested that reducing tillage and increasing plant residues may be a mechanism for suppression of plant disease by supporting a complex food web with organisms that compete with or control the pest of concern.

In summary:

Practices that increase quantity and quality of organic matter and physical habitat have beneficial impacts on soil biota. A diverse array of foods and habitats generally leads to a more complex and stable food web. Supply diverse organic matter – which provides both food and habitat for soil biota. Practices that increase diversity of food sources, encourage beneficial biota, and interrupt pest cycles include:

  • applying compost & manure
  • planting cover crops and legumes (consider inoculation)
  • crop rotation
  • planting a diversity of crops or forages
  • maximizing plant residues
  • reducing tillage

Protect the soil habitat. Soil organisms need space to live, and they need a balance of air & water. Soil organisms also need intact root structures. Practices that can preserve and improve soil habitat include:

  • minimizing compaction
  • reducing tillage
  • improving drainage (in wet soils) or supplying moisture or cover (in dry soils)
  • minimizing/managing pesticides & inorganic fertilizer use (IPM & NMP)
  • optimizing pH (as with agronomic crops)
  • managing grazing to increase plant root biomass

Developing healthy soil biota in your soil is a feedback process on your farm. When conditions are more favorable for soil biota they will begin to sustain and enhance their own habitat and provide conditions more conducive to other organisms. The long term biological goals on agricultural soils would be to establish a set of management practices that maintain a semi‐stable condition for soil biota, so that the community is less affected by more extreme conditions that farmers cannot control – like a drought or flood. Management would focus first on the farm or field specific soil properties that are most limiting for soil biota. A healthy soil community – just like a healthy agricultural community – will be more capable of bouncing back from a disturbance than one that is already highly stressed before the disturbance occurs.


This Page Was Created Utilizing Text And Images From These Sources:

UVM Extension Fact Sheet, The Living Breathing Soil: Farming With Soil Biology

Natural Resources Conservation Service Soil Health Campaign Flickr Account

Photo Credit: USDA-ARS, Electron & Confocal Microscopy Unit, Beltsville, MD USA

South Dakota Natural Resources Conservation Service Flickr Account

Particulate Organic Matter


Particulate organic matter (POM) fraction referred to in this document comprises all soil organic matter (SOM) particles less than 2 mm and greater than 0.053 mm in size (Cambardella and Elliot, 1992). POM is biologically and chemically active and is part of the labile (easily decomposable) pool of soil organic matter (SOM). Figure 1 shows tiny debris of POM (0.25 mm < POM size < 0.5 mm) at different stages of decomposition isolated from soil under no-till management. Studies have shown that POM accounts for few to large amounts of soil C (20% and more) in some soils of Eastern Canada and the USA depending upon agroecosystems and management practices (Table1).


Relationship to Soil Function

As perhaps the most easily decomposable fraction of nonliving SOM after microbial biomass, POM fulfills many soil functions mediated by OM. It is a source of food/energy for microorganisms and soil animals as well as nutrients for plant growth. Particulate organic matter enhances aggregate stability, water infiltration and soil aeration; it increases cation exchange capacity and buffering pH. It also binds environmental pollutants such as heavy metals and pesticides. Particulate organic matter may play an important role in the suppression of soil borne diseases (e.g. damping off of cucumber) by compost. This may be explained by the fact that POM is an important source of food/energy in the compost for microorganisms responsible of disease suppression.

POM and Poor Soil Function

In poorly managed soils, the transport by erosion of sediments rich in POM into rivers and other water bodies can result in alteration of water quality and aquatic life. Build up and mineralization of those organic materials lead to the eutrophication of lakes and rivers. Incomplete mineralization of POM C in very poorly drained soils can lead to the formation of methane, which escapes into the atmosphere and contributes to ozone depletion.

Improving POM Levels

Management that affects SOM accumulation also affects POM content in soil (figs 2 and 3). More POM in the soil means that carbon and other nutrients are being stored in the intermediately available pool and are not subjected to losses (e.g., leaching) yet are available when needed.


The following practices enhance POM levels:


  • Tillage management (no-till, strip till, and ridge till)
  • Crop rotation, cover crops, and cropping frequency (reduction in fallow frequency)
  • Application of manure/compost and organic byproducts
  • Pasture and hay land management (e.g., rotational grazing and haying)


This Page Was Created Utilizing Text And Images From These Sources:

Particulate Organic Matter, Soil Quality Indicators Fact Sheet- USDA Natural Resources Conservation Service

Total Organic Carbon

Total organic carbon (TOC) is the carbon (C) stored in soil organic matter (SOM). Organic carbon (OC) enters the soil through the decomposition of plant and animal residues, root exudates, living and dead microorganisms, and soil biota. SOM is the organic fraction of soil exclusive of nondecomposed plant and animal residues. Nevertheless, most analytical methods do not distinguish between decomposed and non-decomposed residues. SOM is a heterogeneous, dynamic substance that varies in particle size, C content, decomposition rate, and turnover time.

Soil organic carbon (SOC) is the main source of energy for soil microorganisms. The ease and speed with which SOC becomes available is related to the SOM fraction in which it resides. In this respect, SOC can be partitioned into fractions based on the size and breakdown rates of the SOM in which it is contained (table 1). The first three fractions are part of the active pool of SOM. Carbon sources in this pool are relatively easy to break down.

SOM contains approximately 58% C; therefore, a factor of 1.72 can be used to convert OC to SOM. There is more inorganic C than TOC in calcareous soils. TOC is expressed as percent C per 100 g of soil.

Relationship to Soil Function

SOC is one of the most important constituents of the soil due to its capacity to affect plant growth as both a source of energy and a trigger for nutrient availability through mineralization. SOC fractions in the active pool, previously described, are the main source of energy and nutrients for soil microorganisms. Humus participates in aggregate stability, and nutrient and water holding capacity.

OC compounds, such as polysaccharides (sugars) bind mineral particles together into microaggregates. Glomalin, a SOM substance that may account for 20% of soil carbon, glues aggregates together and stabilizes soil structure making soil resistant to erosion, but porous enough to allow air, water and plant roots to move through the soil. Organic acids (e.g., oxalic acid), commonly released from decomposing organic residues and manures, prevents phosphorus fixation by clay minerals and improve its plant availability, especially in subtropical and tropical soils. An increase in SOM, and therefore total C, leads to greater biological diversity in the soil, thus increasing biological control of plant diseases and pests. Data also reveals that interaction between dissolved OC released from manure with pesticides may increase or decrease pesticide movement through soil into groundwater.

Problems with Poor Carbon Levels

A direct effect of poor SOC is reduced microbial biomass, activity, and nutrient mineralization due to a shortage of energy sources. In non-calcareous soils, aggregate stability, infiltration, drainage, and airflow are reduced. Scarce SOC results in less diversity in soil biota with a risk of the food chain equilibrium being disrupted, which can cause disturbance in the soil environment (e.g., plant pest and disease increase, accumulation of toxic substances).

Improving Carbon Levels

Compiled data shows that farming practices have resulted in the loss of an estimated 4.4×109 tons of C from soils of the United States, most of which is OC. To compensate for these losses, practices such as no-till may increase SOC (figure 1). Other practices that increase SOC include continuous application of manure and compost, and use of summer and/or winter cover crops. Burning, harvesting, or otherwise removing residues decreases SOC.


This Page Was Created Utilizing Text And Images From These Sources:

Total Organic Carbon, Soil Quality Indicators Fact Sheet- USDA Natural Resources Conservation Service




Soil Enzymes

Soil enzymes increase the reaction rate at which plant residues decompose and release plant available nutrients. The substance acted upon by a soil enzyme is called the substrate. For example, glucosidase (soil enzyme) cleaves glucose from glucoside (substrate), a compound common in plants. Enzymes are specific to a substrate and have active sites that bind with the substrate to form a temporary complex. The enzymatic reaction releases a product, which can be a nutrient contained in the substrate.

Sources of soil enzymes include living and dead microbes, plant roots and residues, and soil animals. Enzymes stabilized in the soil matrix accumulate or form complexes with organic matter (humus), clay, and humus-clay complexes, but are no longer associated with viable cells. It is thought that 40 to 60% of enzyme activity can come from stabilized enzymes, so activity does not necessarily correlate highly with microbial biomass or respiration. Therefore, enzyme activity is the cumulative effect of long term microbial activity and activity of the viable population at sampling. However, an example of an enzyme that only reflects activity of viable cells is dehydrogenase, which in theory can only occur in viable cells and not in stabilized soil complexes.

Relationship to Soil Function

Enzymes respond to soil management changes long before other soil quality indicator changes are detectable. Soil enzymes play an important role in organic matter decomposition and nutrient cycling (table 1). Some enzymes only facilitate the breakdown of organic matter (e.g., hydrolase, glucosidase), while others are involved in nutrient mineralization (e.g., amidase, urease, phosphatase, sulfates). With the exception of phosphatase activity, there is no strong evidence that directly relates enzyme activity to nutrient availability or crop production. The relationship may be indirect considering nutrient mineralization to plant available forms is accomplished with the contribution of enzyme activity.

Problems with Poor Activity

Absence or suppression of soil enzymes prevents or reduces processes that can affect plant nutrition. Poor enzyme activity (e.g., pesticide degrading enzymes) can result in an accumulation of chemicals that are harmful to the environment; some of these chemicals may further inhibit soil enzyme activity.

Improving Enzyme Activity

Organic amendment applications, crop rotation, and cover crops have been shown to enhance enzyme activity (figs 1 and 2). The positive effect of pasture (fig 2) is associated with the input of animal manure and less soil disturbance. Agricultural methods that modify soil pH (e.g., liming) can also change enzyme activity.




This Page Was Created Utilizing Text And Images From These Sources:

Soil Enzymes, Soil Quality Indicators Fact Sheet- USDA Natural Resources Conservation Service

Soil Respiration

Carbon dioxide (CO2) release from the soil surface is referred to as soil respiration. This CO2 results from several sources, including aerobic microbial decomposition of soil organic matter (SOM) to obtain energy for their growth and functioning (microbial respiration), plant root and faunal respiration, and eventually from the dissolution of carbonates in soil solution. Soil respiration is one measure of biological activity and decomposition. The rate of CO2 release is expressed as CO2-C lbs/acre/day (or kg/ha/d). It can be measured by simple field methods (e.g. fig. 1) or more sophisticated field and laboratory methods. During the decomposition of SOM, organic nutrients contained in organic matter (e.g., organic phosphorus, nitrogen, and sulfur) are converted to inorganic forms that are available for plant uptake. This conversion is known as mineralization. Soil respiration is also known as carbon mineralization.

Relationship to Soil Function

Soil respiration reflects the capacity of soil to support soil life including crops, soil animals, and microorganisms. It describes the level of microbial activity, SOM content and its decomposition. In the laboratory, soil respiration can be used to estimate soil microbial biomass and make some inference about nutrient cycling in the soil. Soil respiration also provides an indication of the soil’s ability to sustain plant growth. Excessive respiration and SOM decomposition usually occurs after tillage due to destruction of soil aggregates that previously protected SOM and increased soil aeration. Depleted SOM, reduced soil aggregation, and limited nutrient availability for plants and microorganisms can result in reduced crop production in the absence of additional inputs. The threshold between accumulation and loss of organic matter is difficult to predict without knowledge of the amount of carbon added.

Problems with Poor Function

Reduced soil respiration rates indicate that there is little or no SOM or aerobic microbial activity in the soil. It may also signify that soil properties that contribute to soil respiration (soil temperature, moisture, aeration, available N) are limiting biological activity and SOM decomposition. With reduced soil respiration, nutrients are not released from SOM to feed plants and soil organisms. This affects plant root respiration, which can result in the death of the plants. Incomplete mineralization of SOM often occurs in saturated or flooded soils, resulting in the formation of compounds that are harmful to plant roots, (e.g. methane and alcohol). In such anaerobic environments, denitrification and sulfur volatilization usually occur, contributing to greenhouse gas emissions and acid deposition.

Improving Soil Respiration

The rate of soil respiration under favorable temperature and moisture conditions is generally limited by the supply of SOM. Agricultural practices that increase SOM usually enhance soil respiration. The following practices have the potential to significantly improve SOM and indirectly soil respiration when other factors are at an optimum:

  • Conservation tillage (no-till, strip-till, mulch till, etc.)
  • Application of manure and other organic by-products
  • Rotations with high residue and deep-rooted crops
  • Cover and green manure crops
  • Irrigation or drainage
  • Controlled traffic


This Page Was Created Utilizing Text And Images From These Sources:

Soil Respiration , Soil Quality Indicators Fact Sheet- USDA Natural Resources Conservation Service

Comparative Measurements of Arbuscular Mycorrhizal Fungal Responses to Agricultural Management Practices

R. Michael Lehman, Shannon L. Osborne, Wendy I. Taheri, Jeffrey S. Buyer, Bee Khim Chim