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Soil biology and soil management

Ann Lewandowski


While you work long hours to produce tons of hay or corn from each acre of land, tons of bacteria, fungi, insects, and other organisms are working underground, making farming possible. They decompose organic matter and transform nutrients into forms your crops can use. They help build good soil tilth, enhance crop growth, and control pests.

How can you benefit from better management of the soil biological community

Reduced input costs. Less fertilizer may be needed if nutrient cycling becomes more efficient and less fertilizer is lost from the rooting zone. Fewer pesticides are needed where a diverse set of pest-control organisms are active. As soil structure improves, tillage becomes easier and potentially less costly.

Pollution prevention. Soil organisms filter and detoxify chemicals and absorb the excess nutrients that would otherwise become pollutants when they reach groundwater or surface water.


A night crawler has pulled a dead corn leaf into its burrow. Earthworms are some of the most visible members of the soil community, but tons of bacteria, fungi, and other organisms are also essential to soil productivity.

Improved yield and crop quality. Soil organisms are key to forming good soil structure or tilth. Good tilth promotes better root development and water storage. Many microorganisms enhance crop growth or reduce the activity of disease organisms that can degrade the quality of food and feed.

How well are you taking care of your underground "herd"?

Your land management choices help determine what lives in your soil and how well your soil works for you. This publication will help you consider the effects of management decisions on the soil community.

Soil manager

Aim for diversity

Soil performance generally improves when the complexity, or diversity, of the soil biological community increases. (See p. 11 for an explanation of complexity.) There is a limit to the amount of diversity that is economically and agronomically beneficial, but trying to increase diversity may be a useful way to manage soil biology.

How do I encourage a diverse soil community?

The next few pages will describe common ways to encourage healthy soil biology, and explain why some farm practices affect soil organisms.

If you ask others for suggestions, keep in mind that what works in one place might not work in another. To manage the soil biological community, be a careful observer of the changes on your farm.

Managing for soil biology

Supply organic matter

Most soil organisms rely on organic matter for food. Each source of organic matter favors a different mix of organisms, so a variety of sources generally supports a variety of organisms. The location of the organic matter - whether at the surface or mixed in the soil - also makes a difference.

Maximize crop residue

Crop residue is a convenient and valuable source of organic matter. Corn harvested for grain will grow 3 to 4 tons of surface residue per acre and 1 to 2 tons of root biomass. Dense, sod-type crops produce generous amounts of root biomass. Soybeans generate notoriously little surface residue.

Surface residue encourages the decomposers - especially fungi - and increases food web complexity. Fungi increase because they have some advantage over bacteria in digesting surface residue, though greener and younger plant residues are easy for bacteria to use. Residue provides food and habitat for surface feeders (such as some earthworms) and surface dwellers (such as some arthropods). It also changes the moisture and temperature of the soil surface. Some pathogens will be increased by the residue, others will be decreased.

Apply compost or manure
Plant cover crops

Cover crops extend the growing season and increase the amount of roots and above-ground growth that becomes part of soil. As with other crops, the rhizosphere (the area immediately surrounding roots) of a cover crop provides food for bacteria when food sources would otherwise be scarce. Because of each crop's unique physiology, populations of certain pathogens will decline under specific cover crops.

Increase variety

Create a diverse landscape

Diverse habitats support complex mixes of soil organisms. Diversity can be achieved with crop rotations, vegetated fence rows, buffer strips, strip cropping, and small fields.

Rotate crops

Crop rotation puts a different food source into the soil each year. This encourages a wider variety of organisms and prevents the build-up of a single pest species. Cover crops increase the variety of plants in a field each year.

Protect the habitat of soil organisms

Large and small soil organisms need air, moisture, a constant food supply, and room to move in a protected place. Reduced tillage, lack of compaction, constant ground cover, and minimum disruption by chemicals protect the environment of soil organisms.

Reduce tillage

Tillage enhances bacterial growth in the short-term by aerating the soil and by thoroughly mixing the organic matter with bacteria and soil. The bacterial activity increases the loss of carbon as CO2, and triggers explosions of bacterial predators such as protozoa. A single tillage event is generally inconsequential to microorganisms, but repeated tillage eventually reduces the amount of soil organic matter that fuels the soil food web.

The mechanical action of tillage can kill individual organisms and tends to temporarily reduce populations of fungi, earthworms, nematodes, and arthropods. Over the long term with repeated tillage, these populations may decline as a result of lack of food (i.e., surface residue), rather than because of the mechanical action of tillage.

No-till: The environment for soil organisms can differ significantly in no-till compared to conventionally tilled soils. No-till soils are more likely to have anaerobic environments, soil may be cooler in spring because of surface cover, there can be more macropores, and organic matter is not evenly mixed throughout the top-soil.

The result is a lower rate of organic matter decomposition. In addition, the lack of disturbance and the presence of surface residue encourages fungi and relatively large organisms such as arthropods and earthworms. No-till soils generally have a higher ratio of fungi-to-bacteria.

Minimize compaction

Compaction reduces the space available for larger organisms to move through the soil. This favors bacteria and small predators over fungi and the larger predators. Arthropods are severely affected. Among nematodes, the predatory species are most sensitive to compaction, followed by fungal-feeders and bacterial-feeders. Root-feeding nematodes are the least sensitive to compaction - perhaps because they do not need to move through soil in search of food.

Compaction changes the movement of air and water through soil, and may cause a switch from aerobic to more anaerobic organisms.

Minimize fallow periods

During long fallow periods, most arthropods will emigrate or die of starvation. Mycorrhizal fungi (fungi that need to form associations with plant roots and are critical to the growth of most crops) also "starve" during a fallow period and recover slowly after the fallow period ends. Cover crops help maintain or build arthropod populations and diversity by reducing the length of fallow periods at the beginning and end of growing seasons. Cover crops also affect the biological habitat by changing temperature and moisture levels.

Minimize the use of pesticides

All pesticides will impact some non-target organisms. Pesticides feed some organisms and harm others. Labels generally do not list the non-target organisms affected by a product, and few pesticides have been studied for their effect on a wide range of soil organisms, so the net effect of moderate pesticide use is not well understood. Heavy pesticide use probably reduces soil biological complexity.

Herbicides may not affect many organisms directly, but the weed loss changes the food sources and habitats available to organisms.

Improve water drainage

Good water drainage improves microbial habitats by increasing oxygen availability.

Inorganic fertilizers

Fertilizers provide some of the nutrients needed by organisms and will favor those species that can best use these forms of nutrients. The pH and salt effect of some fertilizers (e.g. ammonium nitrate, ammonium sulfate, and urea formaldehyde) reduces populations of fungi, nematodes, and probably protozoa, at least temporarily. It is not clear how long this effect lasts in different situations.

Because fertilizer use increases plant growth, and therefore organic inputs into the soil, biological activity may be higher in fertilized soil than in soil with low levels of plant nutrients.

Soil inoculants

So far, this publication has described how soil management practices change the environment that supports soil organisms. Another approach to managing soil biology is to inoculate the soil with desired species or reduce the activity of undesired species. For example, products are available that allow farmers to:

Many of these products are effective and valuable, but there are limits to what can be accomplished with a management approach that targets specific organisms. Inoculants will have little effect or only a temporary effect if the organisms cannot compete in their new environment. Furthermore, some benefits of soil organisms come from a mix of organisms, not from a few specific species.

Your farm

In the Introduction to soil management, you started a list of your soil-friendly management practices. After reading this section, try to estimate the effect of your practices on soil biology. Which ones promote a healthy, complex community? Which ones are most damaging? Should you consider changing them?

Soil scientist

To understand why management practices make a difference to soil life, it helps to back up and examine the vast diversity of micro- and macro-organisms living in the soil and the critical roles they play in agriculture.

What lives in your soil?

The soil ecosystem is tremendously varied - more-so than many above-ground plant and animal food webs. Each species has slightly different requirements. Aerobic microbes require oxygen. Anaerobes require the absence of oxygen. Some prefer either a high or a low pH, or high or low moisture. Many organisms can digest simple sugars, while only a few species have the enzymes to digest lignin, a major component of woody tissue.

At the microscopic level, soil conditions can change drastically from one point to the next, so a variety of organisms may be present in a single soil sample. Aerobes may live near anaerobes. Organisms requiring high pH may live near those preferring low pH.

Microbes differ greatly in how they get their energy. Most soil organisms are heterotrophs that get their energy and carbon from breaking down organic compounds. In contrast, the autotrophs use inorganic carbon (carbon dioxide). There are two groups of autotrophs. Phototrophs, such as plants and a few soil organisms, get their energy from light. Chemotrophs are a small, but important, group of soil bacteria that get their energy from oxidizing inorganic compounds including ammonium, nitrite, and sulfur compounds.

Macro-organisms, such as mites, beetles, and earthworms, are also tremendously varied in what they eat, their life cycle, and what agricultural conditions they will or will not tolerate. Each plays a different role in eating and breaking down plant residue and their fellow soil organisms.

What do soil organisms do?

Healthy soil is a jungle of rapacious organisms devouring everything in sight (including each other), processing their prey or food through their innards, and then excreting it. The value of these creatures to farmers lies in:

Nutrient cycling

One of the important functions of the soil biological community is managing nutrients. Soil organisms continually transform nutrients among many organic and inorganic forms. (Organic compounds contain carbon. Inorganic compounds do not.) Plants primarily need simple inorganic forms of each nutrient. Soil organisms create many of these plant-available nutrients and help store nutrients in the soil as organic compounds.

Decomposition is the breakdown of plant and animal residue into different organic and inorganic compounds. Soil organisms decompose organic matter more quickly under warm, moist conditions than under cold or dry conditions. This is why it is easier to build up soil organic matter levels in the Midwest than in the southeastern part of the United States, where decomposition is rapid.

As part of the decomposition process, many bacteria and fungi produce humic acids. In the soil, these acids chemically combine with each other to form large molecules of stabilized organic matter. This formation of large molecules is both a biological and chemical process.

When soil organisms convert organic matter into inorganic, plant-available nutrients, they are said to be mineralizing nutrients. Protozoa and nematodes mineralize and excrete several hundred pounds of ammonium (NH4+) per acre per day. Most is snatched up by other soil organisms, but some is used by plants.

The reverse of mineralization is immobilization - the conversion of inorganic compounds into organic compounds. Soil organisms consume inorganic molecules and incorporate them into their cells. Because immobilized nutrients are parts of soil organisms, they do not move easily through the soil and are unavailable to plants. Bacteria and fungi are responsible for large amounts of immobilization.

The previous paragraphs described three kinds of transformations performed by many soil organisms:

Bacteria that perform mineral transformations are important in nitrogen cycling. The roots of legumes host nitrogen-fixing bacteria that convert large amounts of dinitrogen (N2) from the atmosphere into forms that plants can use. Some nitrogen-fixing bacteria live free in the soil.

Nitrifying bacteria convert ammonia (NH3) into nitrate (NO3-). Plants prefer nitrate, but nitrate is easily leached from the soil. Some farmers apply "nitrification inhibitors" which reduce the activity of nitrifying bacteria and prevent the loss of fertilizer nitrogen from the soil.

Denitrifying bacteria convert nitrate into gases that are lost into the atmosphere. These species are anaerobic so denitrification occurs only in places in the soil where there is little or no oxygen. Anaerobic conditions are more common in compacted soils and in no-till soils.

Other soil bacteria are important for similar mineral transformations of sulfur, iron, and manganese.

Forming soil structure

Most crops grow best in crumbly soil that roots can easily grow through and that allows in water and air. Soil organisms play an important role in the formation of a good soil structure.

As spring turns to summer and the soil heats up, fungi grow long filaments called hyphae that surround soil particles and hold them together in soil aggregates. Some bacteria produce sticky substances that also help bind soil together.

Many soil aggregates between the diameters of 1/1000 and 1/10 of an inch (the size of the period at the end of this sentence) are fecal pellets. Arthropods and earthworms consume soil, digest the bacteria, and excrete a clump of soil coated with secretions from the gut. As beetles and earthworms chew and bury plant residue and burrow through the soil, they aerate the soil and create nutrient-lined channels for roots and water to move through.

Controlling disease and enhancing growth

Soil organisms have many methods for controlling disease-causing organisms. Protozoa, nematodes, insects, and other predatory organisms help control the population levels of their prey and prevent any single species from becoming dominant. Some bacteria and fungi generate compounds that are toxic to other organisms. Some organisms compete with harmful organisms for food or a location on a root.

In addition to protecting plants from disease, some organisms produce compounds that actually enhance the growth of plants. Plant roots may excrete compounds that attract such beneficial organisms.

How do soil organisms and plants get along?

The lives of plants and soil organisms are closely intertwined. Some plant and microbe species have developed symbioses, or mutually beneficial relationships. Rhizobium and other bacteria can invade roots and get sugars from the plant. In return, they fix atmospheric nitrogen into a form that plants can use.

Another group of friendly root-invaders are the mycorrhizal fungi. The fungal hyphae extend from inside the root, out into the soil, and often greatly expand the plant's access to nutrients and (perhaps) water. Mycorrhizae improve phosphorus nutrition by producing acids that convert phosphorus into plant-available forms and transport the phosphorus back to the root. Most crop species depend on or benefit greatly from mycorrhizal associations.

Not all plant/microbe interactions are invasions. The rhizosphere (the narrow region surrounding each root) is rich in biological activity as bacteria and other microbes feed on the carbon compounds exuded by roots. Plants may exude compounds that attract certain species to the rhizosphere that protect the roots from disease-causing species.

When microbes and plants compete for soil nutrients, microbes have an advantage because they are often suspended in the soil solution while plants must pull the soil solution towards their roots.

In an ideal situation, microbes will tie-up (immobilize) nitrogen and prevent its loss from the rooting zone when plants are not growing, and then will release (mineralize) nitrogen when crops are actively growing. See Organic matter management for more information about competition between microbes and plants for nitrogen.

When do soil organisms do their work?

The activity of organisms is constantly changing with temperature, moisture, pH, food supply, and other environmental conditions. Different species prefer different conditions, so even at maximum total activity levels only a minority of soil microbes are busily eating and respiring. The highest total activity is in late spring/early summer and in late summer/early fall when the soil is warm and moist. In early spring, some farmers see nutrient deficiency symptoms in their plants because not enough microbes are warm enough to convert organic compounds into plant-available nutrients. Leaching of excess nitrate often happens in early spring when the soil is too cool for either plants or microbes to grow and immobilize the nitrogen.

What lives in the soil and what are they doing?

Each type of organism fills a unique niche and plays a different role in the cycling of nutrients, the structure of soil, and in pest dynamics.

Table 1. Description of soil organisms, their size, diet, and role in soil.

Description Size Diet Typical amt in ag soils Action in soil
Usually one-celled
1 um (0.001 mm) Organic matter, especially simple carbon compounds 100 mil. to 1 bil. in a teaspoon Decompose organic matter. Immobilize nutrients in the rooting zone.
Rhizobium and other genera fix nitrogen from air.
Convert ammonium to nitrate, and nitrate to nitrogen gasses.
Actinomycetes, which grow as filaments, are important in decomposition at moderate-to-high pH. Create substances that help bind soil aggregates.
Grow in long filaments calleed hyphae
A few um wie, yards or miles long Organic matter, especially simple carbon compounds. Also, living plants Several yards in a teaspoon Decompose organic matter. Immobilize nutrients in the rooting zone. Mycorrhizal fungi form mutually beneficial associations with roots. They release acids that help make phosphorus more available to plants. Help stabilize soil aggregates.
One-celled animals
5-500 um Bacteria, primarily Several thousand in a teaspoon Stimulate and control growth of bacteria.
Release ammonium.
Roundworms. Not segmented as are earthworms
50 um wide, 1 mm long Bacteria, fungi, protozoa, other nematodes, and roots Ten to twenty in a teaspoon Control many disease-causing organisms.
Root-feeders may cause root diseases. Release ammonium.
Include insects, mites, spiders, springtails, & millipedes
Microscopic to inches All other organisms Several hundred in a cubic foot Shred plant residue, making it more accessible to bacteria and fungi.
Enhance soil structure by creating fecal pellets, and by burrowing.
Control populations of other organisms
Earthworms Inch or more long Bacteria, fungi, and organic matter Five to thirty in a cubic foot Shred plant residue.
Enhance soil structure by burrowing, mixing, and creating fecal pellets.
Transport and stimulate growth of bacteria.

Why is diversity important?

Like the above-ground ecosystem, the soil community is not just a collection of individual species, but a complex, interacting food web. Decomposition of a single compound may require several organisms. The creation of aggregates involves a mix of physical and chemical processes and the activity of many types of organisms.

As the complexity of the food web increases, productivity of the soil tends to increase. It is not clear how much complexity is needed, but there are several reasons why complexity is thought to be beneficial.

First, the soil system may be more stable and resilient. If many organisms perform a similar role, the system is not dependent on just a few for that function. A soil disturbance (such as drought or tillage) might reduce the activity of some organisms, but in a complex system others will perform the same functions (such as providing ammonium or degrading a particular compound).

Other benefits of complexity may include improved nutrient cycling, decomposition, and disease control. When many different kinds of organisms are present, many organic compounds and potential pollutants can be degraded, and many competitors and predators are present to control pest populations.

Nematodes: Good guys or bad guys?

Nematodes are a group of tiny roundworms that demonstrate the wide diversity and the inextricable food web that exists in a healthy soil. Twenty thousand species have been described, but half a million species may exist. Most soil nematodes eat bacteria, fungi, protozoa, and other nematodes, making them important in nutrient cycling. Others are plant parasites and cause disease symptoms such as malformed or dwarfed plants, or root structures with deformities such as galls and cysts.

The root knot nematode, for instance, stimulates parasitized plants to form root galls. The galls choke off the flow of water and nutrients to the above-ground portion of the plant. Plants infected by root gall nematodes may live through the season but crop yields will be dramatically reduced.

One way to respond to nematode problems is to rotate crops to remove the nematodes' food source. Another highly effective approach is to build up soil organic matter. The increased organic matter might initially increase nematode populations, but it will also create an explosion of nematode predators such as fungi, mites, and other nematodes.

Fungi prey on nematodes in a number of ways. They trap them with their sticky appendages or squeeze them (like a boa constrictor) in fungal mechanical ring traps. Some fungi exude a toxin to quiet their struggling prey. (Think of these vicious dramas next time you are riding safely in your tractor cab!)

Some nematodes eat undesirable residents of farm fields. Cut worms, for instance, are hunted down by one species of carnivorous nematode. These nematodes (N. carpocapsae) are available from some biological supply catalogues to control cut worms and other crop-damaging underground caterpillars and beetle larva.

Nematodes are not simply pests, but a diverse group of species that play many roles in the soil system.

What's next?

Several guidelines for managing soil biology were introduced in this chapter - encourage diversity, feed organisms frequently, don't destroy habitat with excessive pesticides or tillage. But there were no strict numbers for how many arthropods you need, or a list of species that are essential, or a precise set of practices that will generate the "ideal" mix of soil organisms. This means that good observation skills are important to assessing the effects of practices on your farm.


Each farmer notices a unique set of changes as soil biological activity rises. One might notice more birds picking out earthworms behind the plow. Another might see manure pies disappearing more quickly, or reduced ponding after a rain. It takes practice to observe the activities of soil organisms. Observations such as these are essential, but there are also more systematic ways to monitor soil biology.

Assessing soil life on your farm

Soil life can be measured in three general ways: the amount of organisms, their activity, and the soil processes they influence.

The amount of organisms can be measured by directly counting them under a microscope or by estimating biomass using several laboratory methods. Activity is often monitored by measuring soil respiration (the amount of carbon dioxide given off) or decomposition rates.

The biomass (amount of organisms) does not change drastically from day to day, but activity levels respond rapidly to changes in temperature, moisture, and food. Because activity levels can change quickly, it is important to note temperature and moisture conditions when sampling.

In addition to directly measuring the organisms or their activity, it can be useful to monitor the processes they influence. These include the stability of soil aggregates, rate of water infiltration into the soil, the rate of decomposition, pest activity, and soil nitrate levels.

On-farm tests

The Monitoring Tool Box describes a soil respiration test that measures carbon dioxide, and a cotton strip test that measures the rate of degradation of a buried piece of cloth. The Tool Box also describes tests of aggregate stability and percolation (infiltration).

A simple on-farm respiration test is available from Woods End Research Laboratory (207-293-2457,

Biological activity can be observed more informally by noting how long it takes for manure or residue to disappear from a field.

Lab tests

A few commercial labs will test the number or activity of organisms in your soil. Some consultants are developing recommendations based on such tests, but the research basis for interpreting biological measures is still weak.

The future of soil biology management

There is much to learn about managing soil biology. Researchers are only beginning to understand the specific biologic mechanisms of many management practices. As research accumulates, farmers may increasingly use practices such as:

Your farm: Practice seeing soil organisms

Take half an hour for a little investigation. If you have a wooded lot, go there. Or go to an unpastured, untilled fence line or meadow. Take along a shovel or spade. Kneel down on the leaf mold. Maybe you'll see a frog, toad, or shrew. You'll probably see small spiders and beetles immediately. Peel away a few leaves. You'll probably see more spiders, beetles, and a millipede or two. These creatures are busily devouring each other and the dry leaves. They are carrying out life functions such as breeding and defecating. Dig a little further and you'll find white fungus roots or mycelium wrapping around skeletonized leaves and little chunks of wood. As you gently dig deeper you'll find earthworms and their burrows. The material you find now will begin to look like soil but will be in little crumbly balls and pellets. Some of it will be earthworm castings, which will be further broken down by fungi and by organisms too small to see, and some of it will be glued together by mucous from microbes. Among all this you will no doubt see threads of plant and tree roots taking advantage of the rich chemical environment that is generated by the teeming life on the forest floor.

In a few square feet of forest floor and leaf mold there are spiders, millipedes, snails, slugs, beetle larva and pupae, and countless other small creatures. Scientists say that a single gram of soil from the forest floor can contain up to a kilometer of fungal hyphae. Without all this crunching, munching, and processing of living things down to the basic elements, plants simply couldn't grow.

Now take a trip to one of your farm fields. What do you see that's different?


Deborah Allan, professor, Department of Soil, Water, and Climate, University of Minnesota
Jay Dorsey, (former) research associate, Department of Soil, Water, and Climate, University of Minnesota
Thomas Hansmeyer, graduate student, Department of Soil, Water, and Climate, University of Minnesota
David Huggins, (former) professor, Department of Soil, Water, and Climate, University of Minnesota
Maggie Jones, consultant, Blue Earth Agronomics
Bob Olson, Washington County Extension, University of Minnesota Extension
Jean Peterson, farmer, Delano
Mark Zumwinkle, Energy and Sustainable Agriculture Program, Minnesota Department of Agriculture

Series Editor
Debra Elias Morse, Minnesota Institute for Sustainable Agriculture

Kathleen Cleberg, copy editor, Press 1 Production
Roxanne Madison, product manager, Communication and Educational Technology Services, University of Minnesota Extension
John Molstad, Studio 31 Graphics, Inc., designer

Jim Anderson, Department of Soil, Water, and Climate, University of Minnesota
Barb Bakken, farmer, Alden
Carmen Fernholz, farmer, Madison
Dennis Gibson, farmer, Montevideo
Peter Graham, Department of Soil, Water, and Climate, University of Minnesota
Ken Matzdorf, Natural Resources Conservation Service, United States Department of Agriculture
Steve Potter, farmer, Sauk Centre
Linda Schroeder, Schroeder Communications
Russ Severson, West Polk County Extension, University of Minnesota Extension

Funding for this project approved by the Minnesota Legislature, 1995 Minnesota Laws, Ch. 220 Sec. 7, Subd. 2.

Additional funding provided by the Soil Quality Institute, Natural Resources Conservation Service, United States Department of Agriculture


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