June 15, 2004 | General


BioCycle June 2004, Vol. 45, No. 6, p. 46
Biological organisms give soil its life and energy and are responsible for driving most of the chemical reactions and transformations that occur.
Part IV
Richard Stehouwer

THE fourth and final article in this series on soil science fundamentals focuses on soil biology. Previous articles (October and November 2003 and April 2004) covered soil formation and soil physical and chemical properties and processes. By understanding soil fundamentals, composters and organics recyclers can better understand the role that organic amendments play in healthy and productive soils.
If sands and silts are the “skeleton” of the soil body, and clays and organic matter are the “muscles,” it is the biological organisms in soil that give it life and energy and are responsible for driving most of the chemical reactions and transformations that occur in soil. The array of living organisms in soil is vast. Soil organisms occupy many different niches, perform a wide variety of functions, and interact in myriad ways with other organisms and with the soil matrix. As was the case with previous topics, this brief article can only touch on some of the biological complexity and function that exists in soil. We will first survey the different types of organisms that live in soil, considering how abundant they are, the types of functions they perform, and how they make their living. We will then look at some examples of how soil organisms interact with each other, and review how soil management practices can affect soil biology.
To begin to understand the great diversity of soil organisms, it is helpful to place them into groupings of similar organisms. Such groupings could be done in many ways but here we will use size (how big the organism is) and taxonomic (genetic and functional similarities) considerations.
Soil organisms come in a wide variety of sizes. Macro organisms or large soil organisms have a diameter greater than about 2 mm (~0.1 in). They are easily visible to the human eye. Examples would include earthworms, plant roots, mice, voles, snakes, beetles, and millipedes. Meso organisms are the mid-sized organisms that range from about 2 mm down to 0.2 mm (~0.01) in diameter. These include mites, springtails, and smaller worms. Some of these organisms are visible to the naked eye, but many are difficult to see without some magnification. Finally, the microorganisms are the small ones, less than 0.2 mm in diameter. In general, these can only be seen using microscopes, though large masses of fungal filaments can sometimes be seen. Most of these organisms are truly miniscule such as the yeasts, actinomycetes, algae and bacteria. Bacteria, for example, range from 0.5 to 5 µm (~0.00002 to 0.0002 in) in diameter. To put that into perspective, about 4,000 of the smaller bacteria could line up head to tail across the head of a pin (if only they had heads and tails). This article focuses on the organisms at the smaller end of the scale because these are the most abundant and diverse organisms in soil and carry out many vital soil functions.
A healthy soil contains a very large number of different kinds of species representing every kingdom in the biological world. The species include animals, plant roots, fungi and bacteria.
Soil animals include many species that are very familiar to us because we see them all the time. Among these are:
All the familiar soil-dwelling mammals and snakes. These animals are also near the top of the food chain. They feed on plants and smaller animals.
The arthropods which include spiders, insects, and insect larvae.
The annelids which are all the various types of worms.
The mollusks which include animals such as snails and slugs.
The arthropods, worms, and mollusks are mostly herbivores and detritovores, meaning they feed on plants and parts of dead animals and plants. They perform an important function in the decay process by mixing these materials into the soil. They also break apart large pieces of material, making them more accessible to other degraders.
Nematodes are another important group of soil animals. These are very small roundworms, 4 to 100 µm (~0.002 to 0.004 in) in diameter and up to a few millimeters in length (~0.05 to 0.15 in). We usually hear about nematodes because they can be significant plant pests. Some will pierce the cells of crop roots to feed. This allows other plant pathogens to invade and cause infections that may severely damage or kill the plant. Most nematodes, however, are beneficial. They feed on insect larvae, fungi and bacteria, all of which could be plant pathogens. Since bacteria contain more nitrogen than the nematodes can use, their feeding serves to release plant available nitrogen into the soil. Nematode feeding may account for as much as 30 to 40 percent of the organic N released in some soils. Nitrogen cycling will be discussed more completely later in this article.
Soil organisms also include the roots of all the plants we are familiar with – as well as plants we are less familiar with, the algae. Plants are very important soil organisms because they are the primary producers, or autotrophs. That means they utilize water, energy from sunlight, and carbon dioxide from the atmosphere to build living tissues. All the other life in the soil, indeed all the other life on earth, depends on these organisms. Plants pump a lot of organic material into soil. Of the crops we commonly grow such as corn, wheat, beans and forages, the weight of roots left in the soil averages about 25 percent of the above ground yield.
Like the vascular plants, algae are also photosynthetic; they use sunlight as their source of energy. Most algae range in size from 2 to 20 µm (~0.0001 to 0.001 in) in diameter. The algae also add organic material to the soil. Some algae excrete sugars into the soil that help to stabilize soil structure.
In addition to adding organic matter to soil, plant roots also have a great influence on the soil biology in the volume (or zone) of soil immediately adjacent to them. This volume of soil is known as the rhizosphere and usually extends about 2 mm (0.1 in) out from the surface of living roots. Plant roots exude organic materials into this zone and slough off dead cells from growing roots. Because of this increased supply of organic carbon, microbial life in the rhizosphere may be two to ten times greater than in the surrounding soil. The net effect is beneficial for plant growth since the microbial activity tends to increase nutrient and water supply to the root. Microbial activity in the rhizosphere also appears to increase root soil contact and to lubricate root extension through the soil.
Moving down the size scale, we come to a large group of mostly microorganisms, the fungi that includes mushrooms, yeasts, mildews, molds and rusts. Although some cause significant plant diseases, many soil fungi play very important functions in overall soil and crop health. The fungi are an extremely important group of degraders in the soil ecosystem, breaking down parts of plants and animals such as cellulose, starch and lignin that bacteria have a hard time with. The fungi are very important in the process of humus formation and in nutrient cycling. The thread-like strands of fungi, called hyphae, also help to stabilize soil structure. Some fungi are predators on other organisms such as nematodes. Many fungi release chemicals into the soil that may be toxic to plants, animals and bacteria. The first modern antibiotic drug, penicillin, was obtained from the soil fungus, Penicillium. Other fungi, known as mycorrhizal fungi, live in association with and directly benefit higher plants.
The protists (protozoans) are a large group of single celled organisms. These organisms are highly mobile and “swim” about in the soil pore water. The protists are mostly predators that feed primarily on bacteria. Consequently they have a large influence on the soil bacterial population. This feeding contributes to nutrient cycling by releasing nutrients that were contained in the bacteria.
The kingdom monera includes bacteria and actinomycetes. Bacteria are an extremely diverse group of single celled organisms. Bacteria are capable of degrading a very broad array of organic compounds ranging from sugars, proteins and amino acids, to oil, diesel fuel and gasoline, to herbicides and insecticides, to highly toxic organic chemicals such as PCBs. Bacteria are vital for nitrogen cycling in soil. Some have the ability to convert nitrogen from the atmosphere into forms that plants can use (nitrogen fixation). Other bacteria convert ammonium to nitrate (nitrification), and still others convert nitrate to gaseous forms of nitrogen (denitrification).
The actinomycetes, like fungi, are filamentous and often highly branched. Actinomycetes are also able to degrade complex organic compounds such as cellulose, lignin and chitin. They tend to be most active in the final stages of organic matter decay. Actinomycetes are often abundant in humus-rich soil. They release compounds known as geosmins that account for the earthy aroma of freshly tilled land.
Diversity refers to the number of different types of organisms present in an area and abundance refers to the number of individual organisms. Both diversity and abundance are strongly influenced by soil characteristics and by climate, thus these values vary greatly from one soil to another and from one region to another. However, in a healthy soil in a moist temperate region one might reasonably expect to find several species of vertebrate animals (snakes, mice, voles, chipmunks, groundhogs), several species of earthworms, 20 to 30 species of mites, 50 to 100 species of insects, dozens of species of nematodes, hundreds of species of fungi, and thousands of species of bacteria and actinomycetes (possibly up to 5,000 species in a teaspoon of soil).
There is clearly the potential for great biological diversity in the soil environment, and the diversity becomes greater as the organisms get smaller. But it is the abundance of soil organisms that is truly staggering. Once again, as the organisms get smaller both their numbers and their weight per unit volume of soil increases dramatically. Table 1 presents the numbers and weight of various types of organisms that might be present in a healthy, moist temperate region soil.
While at first it may seem unlikely that microscopic organisms could have much of an impact on soil function, their importance becomes much more obvious when considering how many – and how many different kinds – of microbes are present. A more diverse soil ecosystem will not always mean a more healthy and productive soil, but in general this will be the case. Two reasons for the soil health connection relate to ecosystem stability and resilience. The stability of an ecosystem refers to its ability to keep on functioning if one aspect of that system breaks down. A diverse soil ecosystem has multiple ways of performing the same function so if one part of the system is lost, other parts will continue to perform that function. Resilience of the system refers to its ability to bounce back or resume functioning following a severe disturbance. An example might be the ability of a soil to resume normal functions following a severe drought.
In a diverse soil ecosystem, soil organisms are constantly interacting with each other. These interactions can occur in one of three ways. Commensalism refers to the relationship of two organisms that live side-by-side, but have no effect on each other. Parasitism refers to a relationship between two organisms where one benefits at the expense of the other. Symbiosis refers to relationships between organisms that are mutually beneficial. Soil organisms exhibit each of these relationships. In the next section we will consider some examples of organism interactions in the soil environment.
Degradation of fresh organic materials added to the soil is a complex process that involves intricate interplay of numerous species. If some of these organisms are absent, decomposition and related nutrient cycling will be much slower and may stop altogether.
Decomposition of complex organic material like plant litter begins with mixing and shredding. Earthworms and other soil arthropods are very adept at this task. Earthworms pull litter into their burrows and mix it with soil. Insects and other macro arthropods feed on the litter pulling it apart into small pieces. Mixing the material into the soil brings it into contact with other soil degraders and greatly increases the surface area exposed to them.
When fresh organic material is mixed into the soil, bacteria respond almost immediately. They begin to feed on the simple organic compounds such as sugars, proteins and amino acids. Bacterial numbers increase very rapidly in response to the food source. But the bacteria have a harder time with some of the more complex organic compounds in the litter, such as cellulose and lignin, which sometime prevent the bacteria from getting at remaining material they could degrade. This is when the activity of the fungi comes into play. Their population increases more slowly than the bacteria, but they are able to degrade the complex compounds the bacteria could not get at. The degrading work of the fungi also further breaks apart organic particles giving bacteria and other microbes access to the simple compounds they previously could not reach.
The final degraders are the actinomycetes. They are the clean-up crew and come in at the final stages of decomposition. While very similar to the fungi, actinomycetes become dominant in the final stages of decomposition because they are slower growing and because bacterial activity is slowing due to less availability of easily degradable compounds. (In compost piles, they dominate at the end also because they can’t stand the heat of thermophilic phase.) Like fungi, they are able to degrade complex compounds like cellulose, lignin, and chitin. Not to be forgotten are the protists and nematodes. These are the predators, hunting around in the soil for the organisms that got fat from eating the plant litter. They feed on the bacteria and fungi and release plant nutrients into the soil.
Organic matter decomposition is intricately linked with cycling of carbon and plant nutrients in soil. This interaction is perhaps most profound and of greatest consequence in the case of nitrogen, the nutrient plants require in the greatest quantity. Most of the nitrogen in soil is organic nitrogen (part of organic molecules) and cannot be taken up by plants. During decomposition, organic nitrogen may be converted to inorganic forms (ammonium or nitrate) that plants are able to utilize. Decomposition of organic material involves an important balance between carbon and nitrogen in the material being decomposed, in the decomposers, and in the soil. When soil microbes decompose organic material, only part of the organic carbon they consume is converted into new cell material (biomass); the remainder is given off as CO2 (respired). The efficiency of different soil microbes varies widely but on average, when fresh plant litter is added to soil, about two-thirds of the carbon consumed is used for energy and released as carbon dioxide, and only about one-third goes into building new biomass. When those microbes die and are in turn consumed by other microbes, again about two-thirds of the carbon is released. This cycle repeats over and over until the carbon remaining in the soil is converted to stable soil humus (Figure 1).
This efficiency of carbon consumption is related to nitrogen cycling because bacteria and fungi must maintain a constant ratio of carbon to nitrogen (C/N) in their cells. The exact ratio varies somewhat from one species to another, but on average is about 8:1. If fresh organic material added to soil has a C/N ratio close to 24:1, this provides exactly the ratio needed to keep the bacteria and fungi C/N ratio at 8:1. This is because with two-thirds of the carbon being lost as carbon dioxide, the C/N ratio of what the microbes actually retain is very close to 8:1 (Figure 2). In this case, none of the organic nitrogen consumed by the microbes will be released to the soil as inorganic nitrogen that could be used by plants. Neither will the microbes take up inorganic nitrogen from the soil.
However, if the added organic material has a high C/N ratio, the microbes will not be getting enough nitrogen from the material they are decomposing. For example, if the added organic material has a C/N ratio of 90:1, the microbes will be retaining material with a C/N ratio of 30:1. To maintain a C/N ratio of 8:1 the microbes need more nitrogen than they are getting from the organic material. They meet this need by scavenging inorganic nitrogen from the soil, a process called N immobilization. Because microbes are much better at taking up soil nitrogen than plants are, plants may become nitrogen deficient. In general, if organic material added to soil has a C/N ratio greater than 30:1, immobilization will result.
If added organic material has a low C/N ratio, microbes will be getting more nitrogen than they need from the material they are decomposing. For example, if the organic material has a C/N ratio of 9:1, the microorganisms will be retaining material with a C/N ratio near 3:1. This is much more N than they need, and the excess N will be released to the soil as inorganic N in a process called mineralization. This inorganic nitrogen will be available for plants to utilize. Mineralization will usually occur if the C/N ratio of added organic material is less than 20:1.
It is important to recognize that immobilized nitrogen is not lost from the soil but has been converted into organic N and is part of the soil biomass. As cycles of decomposition continue and more carbon is lost in each cycle, eventually the C/N ratio will drop low enough that microbes will again have to release inorganic N in order to maintain their desired C/N ratio. At this point, the nitrogen is again available for plant uptake.
In general, the lower the C/N ratio of the organic material being added, the more rapid and abundant the release of inorganic N. Cool season grasses (most turf) respond well to high N levels so would do well with a lower C/N ratio material. But, if the ratio is too low, high ammonia levels can injure turf. Total amount of N mineralized of course depends on the total quantity of N in the compost or whatever other organic material being added. Rates of conversion are largely limited by environmental conditions, mainly temperature and moisture as well as aeration, and then also by qualities (and quantities) of the organic material. For example, organic materials with sugars, proteins and amino acids degrade (convert) very rapidly, versus highly lignified materials, which degrade very slowly. Very generally speaking, following plow-down of a high C/N ratio material like wheat straw, corn fodder or leaves, we would expect to see a conversion from N immobilization to N mineralization in one to two months with adequate soil moisture and soil temperatures in the 60° to 80°F range.
Related to plant nitrogen availability is symbiotic nitrogen fixation, a well-known process to farmers world-wide. Many bacteria have the ability to convert nitrogen in the atmosphere into inorganic nitrogen that plants can utilize. This process, however, can be made much more efficient if the bacteria don’t have to go searching for food to keep themselves functioning.
Some species of bacteria, notably the rhizobia, have developed symbiotic relationships with the roots of leguminous plants. Rhizobia in the soil infect the host plants, forming nodules on the roots. Bacteria thrive in these nodules by growing on sugars taken from the host plant. This cost to the host plant is more than made up for by the steady supply of nitrogen supplied to the plant by the nitrogen fixing bacteria.
Another symbiotic relationship in the soil, that between plant roots and mycorrhizal fungi, may be less familiar. Although many fungi live by degrading organic material in the soil, there are also several fungal species that rely on a close association with plants for their livelihood. These are known as mycorrhizal fungi. Some of these fungi live on the external surfaces of roots, while others actually invade the root cells of the plant. This type of fungus is known as a vesicular arbuscular mycorrhizal (VAM) fungus. The VAM fungus forms arbuscules inside root cells where there is an exchange of nutrients provided by the fungus, and sugars provided by the plant. The vesicles are storage organs formed by the fungus. These types of fungal—root associations are formed with many of the important agronomic, horticultural and timber species.
The fungi benefit from the association with plant roots because they can feed on sugars produced by the plant. Therefore, the fungus does not have to compete with other soil organisms for its food. The plants benefit because in return they receive nutrients and water from the fungi. The fungal hyphae are able to reach a much greater volume of soil than the plant roots can. In many cases, they extend 5 to 10 cm beyond the reach of the roots. The hyphae also can squeeze onto soil pore spaces that are too small for root hairs to penetrate. In many cases, the fungi are better than plant roots at extracting nutrients from soils. This is especially true of phosphorus, and becomes particularly important for plant nutrition in low fertility soils. In addition to their direct benefit to plants, mycorrhizal fungi have a strong influence on soil structure. Their hyphal strands help to hold soil aggregates together, and they also excrete organic substances that help cement the aggregates.
As with all living things, the growth and activity of soil organisms are strongly influenced by environmental factors. Because soil management practices can alter the soil environment, management practices also affect soil biology.
In general, soils with higher organic matter content tend to have greater microbial growth and activity than low organic matter soils. Thus addition of organic material to soil, and management practices that maintain soil organic matter (discussed in an earlier article in this series), will tend to increase the biological activity in soil. The type of organic matter added also will have some effect on the type of microbial community in the soil. The residue of a single kind of plant (such as grass clippings) may be favored by a certain group of microorganisms. In a monoculture of that plant (such as a lawn), the favored microorganisms will predominate and may become abundant, but microorganism diversity will decrease. In general, the greater the diversity of the plant community, the greater the diversity of the microbial community. Addition of more complex organic materials such as manures and composts will tend to increase both the abundance and diversity of microorganisms.
Tilling or mixing soil temporarily stimulates microbial activity because of the influx of oxygen and exposing fresh organic materials to soil organisms. Over the long term, however, repeated tillage tends to decrease microbial activity as soil organic matter levels decrease. Tillage also destroys unique microhabitats in soil, such as plant root channels and burrows of earthworms and other soil animals. As the soil becomes more homogeneous, microorganism diversity also tends to decrease.
Most microbes that are beneficial to production of agronomic and horticultural plants are aerobic, or require oxygen. Thus management practices that affect soil drainage, porosity, and gas exchange will affect the microbial community in that soil. Aerobic organisms will not be able to thrive in a soil that is frequently flooded or saturated. To thrive, microorganisms also require adequate moisture and are most active at temperatures ranging from about 65° to 100°F. If the soil is too dry, too cold or too hot, microbial activity will slow considerably. Keeping the soil surface covered with a plant canopy or mulch will help moderate drastic fluctuations in surface soil temperature and moisture.
Overall soil fertility, especially adequate calcium and near neutral pH, will favor growth of most desirable microorganisms. Thus liming an acidic soil to increase both calcium and pH will help to increase microbial activity in that soil. Likewise, addition of fertilizer to balance soil nutrients also helps to stimulate microbial activity. Adding the nutrients in an organic form such as manure or compost has the added benefit of providing an energy source for soil microbes.
The use of pesticides (insecticides, fungicides and herbicides) has mixed effects on soil microbes. Some of these chemicals will be toxic to some species and obviously will reduce their activity and abundance until the pesticide concentration has been reduced to subtoxic levels. Use of herbicides may stimulate activity and abundance of those microbes that degrade the weed plants killed by the herbicide.
This series of articles began with a discussion of soil quality, and now at the end we will return to that concept. Soil quality was described as the ability and capacity of soil to perform functions essential to sustain not only plant growth but also to sustain the overall ecosystem that the soil is part of. In order to better understand and describe how soil can perform these myriad functions, soil was separated into its individual components of mineral, organic, air and water; and soil properties and processes were separated into physical, chemical, and biological.
Now the challenge is to put these all back together again, to think holistically about soil. It is important to remember that all the soil components and processes described individually in these articles are intricately and dynamically interrelated. Any attempt to alter a certain soil property or process will also alter many others. Management to improve soil quality requires consideration of how a given practice or amendment will affect not only the function of primary interest, but all soil functions. If a practice improves soil capacity to perform one function but others are deteriorated, then overall soil quality has not improved. Soil quality is improved only if the soil’s ability and capacity to perform all essential functions are improved or maintained.
Finally, these articles have provided a brief and highly simplified overview of soil science fundamentals. There are several texts and reference books that provide a much more in-depth and complete introduction to the fundamentals of soil science. These texts in turn provide references to more advanced treatment of specific topics in soil. Some of these soil science texts are listed below.
Richard Stehouwer is in the Crop and Soil Sciences Department at Penn State University in University Park, Pennsylvania. His email is
Brady, N.C. and R.R.Weil. 2002. Nature and Properties of Soil, 13th Ed. Prentice Hall, Upper Saddle, New Jersey.
Foth, H.D. 1990. Fundamentals of Soil Science, 8th Ed. Wiley, New York, New York.
Plaster, E.J. 2003. Soil Science and Management (4th Ed.). Delmar, New York.

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