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Soil biology and soil management

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.

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 deverse 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.

How to encourage healthy soil biology

Supply organic matter

  • maximize crop residue
  • apply compost or manure
  • plant cover crops

Increase variety

  • create a diverse landscape
  • rotate crops

Protect the habitat of soil organisms

  • reduce tillage
  • minimize compaction
  • minimize fallow periods
  • minimize the use of pesticides
  • improve water drainage

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

  • Compost inoculates the soil with a wide variety of organisms and provides them with a high quality food source. Some species thrive in both compost and in the soil, but many do not. For example, the redworms (Eisenia fetida) that thrive in worm compost do poorly in soil.
  • Animal manure: Manure patties provide food and habitat for larger soil organisms, and manure in any form is a significant source of nutrients. Manure and plant matter each support different mixes of soil organisms.
  • Sludge: Like manure, sludge can be an excellent food source for organisms. However, high levels of metals in some sludge will kill some organisms.

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 pesicides

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:

  • inoculate soil or seeds with nitrogen-fixing bacteria,
  • introduce bacteria, nematodes, or insects that are predators of pest organisms,
  • add nitrification inhibitors to reduce the activity of specific bacteria that convert ammonium to nitrate.

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.

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:

  • decomposition: turning organic compounds into other organic compounds
  • mineralization: turning organic matter into inorganic compounds that may be used by plants
  • immobilization: turning inorganic compounds into organic compounds. Farmers depend on bacteria for one more transformation:
  • mineral transformation: turning inorganic matter into other inorganic compounds

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.

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’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).

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.

(Source – http://www.extension.umn.edu/agriculture/tillage/soil-management/soil-management-series/soil-biology-and-soil-management/)

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