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The Living Soil

By Ember Morrissey, Ph.D.

It is easy to mistake soil for an inert, lifeless substance like the rock that so often lies beneath. Although we may not see it, soil is teeming with life. Over a billion individual microorganisms can inhabit a single gram of soil. This abundance of life is made up of a diverse assemblage of bacteria, fungi and a cohort of microscopic animals, insects and worms. Most soils are inhabited by over a thousand different types (or species) of organisms, all of which play a part in determining how the soil functions—including its ability to support plant growth.

The soil food web

The primary job of soil microorganisms is to break down organic matter. If microbes went on strike, the Earth would quickly be buried under a giant layer of leaves and brush. Plants are the primary producers of organic matter entering soil, and thus form the base of the food web that support soil life.

The decomposition of plant remains begins with bacteria and fungi. These organisms release enzymes into the soil that break down large particles of plant material into small bits they consume for energy and growth. The next trophic level includes both microscopic and visible organisms that feed mainly on bacteria and fungi. Too small for the eye to see are amoeba, roundworms (nematodes) and tiny bugs (micro-arthropods), such as mites. Larger fungal and bacteria feeders include the familiar earth worms. At the top of the soil food web live the predators, which encompass different species of nematodes and arthropods, including some centipedes. In addition to feeding on other soil organisms, the worms and arthropods stimulate decomposition by breaking organic matter into smaller pieces and agitating the soil, both of which stimulate bacterial and fungal activity.

At every step in this food web, some of the carbon that was previously bound up in plant material is released into the atmosphere as carbon dioxide as the organisms breathe. Similarly, the nutrients (such as nitrogen and phosphorus) are released into the soil. In this way, soil micro-organisms ‘recycle’ nutrients, releasing essential elements from the dead so that they can be used by the living once again.

For farmers, this decomposition process is critical to sustaining soil fertility. Adding organic inputs, such as manure, compost and plant residues, ensures nutrients are returned to the soil so that it does not become exhausted of key elements over time.

Microbes and soil structure

Improving soil structure has many benefits. Plants benefit directly from healthy soil structure, as roots are able to penetrate the soil more easily and a greater proportion of seedlings emerge after planting. Soils with healthy structure also have enhanced water infiltration and retention, as well as reduced erosion risk.

Bacteria and fungi play a critical role in maintaining and building healthy soil structure. As microorganisms go about their job of breaking down plant debris, they simultaneously build soil organic matter, improving soil structure. While live microbes only account for about four percent of the organic material in soil, an estimated 80 percent is derived from microorganisms. This microbially processed organic matter is composed of molecules excreted by microorganisms and the remains of dead microbial cells. Microbially processed organic matter is more stable than plant residue because it is thoroughly integrated into the soil. To under-stand why this is the case we must consider the physical structure of soil.

If you look closely at your soil, you will notice it is composed of seemingly endless little crumbs known as aggregates. A healthy soil has a high degree of aggregate stability, meaning the little clumps do not fall apart easily. Soil aggregates are assemblages of tiny, often microscopic, soil particles all stuck together. Microorganisms live in, around and between these little clumps. While aggregates provide a home for microbes, these bacteria and fungi are not passive inhabitants. In fact, you can think of microbes as tiny builders who construct and maintain soil aggregates. Bacteria within aggregates produce compounds to adhere to soil particles and remain in a favorable habitat. This molecular glue that keeps microbes in their favored environment also holds soil particles together.

Fungi contribute to the formation of larger soil aggregates. Long, hair-like fungi weave threads around and through soil particles, holding them together. Because soil bacteria and fungi are so well integrated into soil aggregates, the organic matter they produce is less likely to be eroded away or decomposed. In this way, microorganisms build soil organic matter and help hold aggregates together, improving soil structure.

Beneficial plant-microbe interactions

Plants and microorganisms have been living together for hundreds of millions of years. Over this long evolutionary history, many plants have become reliant on microbial partners and vice versa. Generally, these ‘symbiotic’ relationships involve sharing resources, where the plant provides carbon to microorganisms in return for nutrients.

The oldest and most prevalent of these symbioses is between plants and root-associated fungi known as mycorrhizae. This relationship is ancient, estimated to have begun around 400 million years ago when early land plants transitioned from an aquatic to a terrestrial environment. Because this symbiosis coevolved with land plants, the majority (over 80 percent) of terrestrial plants, including most agricultural crops, participate in this mutually beneficial relationship.

Mycorrhizal fungi form an extensive web of microscopic tubes known as ‘hyphae’ that are extremely thin, approximately one tenth the size of fine root hairs. These hyphae extend from the plant root out through the soil, far beyond the plant’s rooting zone. In this way, the fungi increase the plant’s access to water and vital nutrients, such as nitrogen and phosphorus. This type of symbiosis is particularly critical for the establishment and success of corn and most cereal crops; it also greatly benefits flax, potatoes, sunflowers and soybeans. Mycorrhizal fungi are generally present in the soil, and so it is usually not necessary to inoculate when planting. In order to maintain a healthy symbiosis between plants and mycorrhizal fungi, producers should be careful to limit the use of phosphorous fertilizer.

Fungi are not the only microorganisms that intimately associate with plant roots. Symbiotic bacteria, most notably nitrogen-fixing Rhizobia, engage in a relationship that is central to maintaining soil fertility. Rhizobia live within the roots of legumes, such as alfalfa, beans and clovers. This beneficial ‘infection’ leads to the formation of spherical growths on the roots known as nodules. Within these odd-looking structures, bacteria are busy at work converting atmospheric nitrogen into bioavailable nitrogen. Much of this nitrogen is shared with the plant and, in return, the plant provides the bacteria with sugar, a source of food and energy. Because this relationship requires an investment from the plant, nodule formation will not occur when excess nitrogen is available from fertilizer.

Integrating legumes into crop rotations or pastures can naturally and sustainably increase nitrogen availability in soil. Legumes incorporate nitrogen into the soil as they grow and when their residues are added to the soil. For instance, nitrogen from a tilled-in legume cover crop will be slowly released by microorganisms and made available to plants gradually over the growing season.

Microbes and nutrient management

Soil microorganisms can be allies or enemies in the struggle to sustainably enhance or maintain soil fertility. The Rhizobia discussed above are certainly allies that improve soil fertility. However, there are also organisms that contribute to the loss of nutrients—particularly nitrogen—from agroecosystems.

Nitrogen is generally lost from agricultural systems when nitrate is leached into the watershed or converted into atmospheric nitrogen by soil microorganisms during a process called de-nitrification. Typically, nitrogen enters the soil in the form of ammonium following nitrogen fixation (see legume-Rhizobium association above) or fertilizer addition. Ammonium is usually well retained in soil because it adheres to soil particles. However, excess ammonium is rapidly converted to nitrate by specialized bacteria in a process known as nitrification. In one sense, this is valuable because nitrate is the preferred nitrogen source of many crops, and thus may stimulate plant growth. But nitrate is also highly soluble and is often leached during heavy rains. Saturated soil also enhances nitrate loss through denitrification. Wet soil limits soil oxygen availability, and under these circumstances denitrifying bacteria use nitrate to respire, converting it to atmospheric nitrogen.

A variety of strategies can be employed to ork with—and not against—microbes to retain added nutrients:

  • Add fertilizer when plants are actively growing and taking in nitrogen. This will limit ammonium accumulation, nitrification and nitrate loss.
  • Avoid fertilizing during or immediately prior to seasons of heavy rain. Much of the added nitrogen would be lost through nitrification and leaching, or denitrification.
  • Add fertilizer along with hay, straw or non-legume crop residues. This will cause the nitrogen to be taken up into microbial biomass as they decompose the plant matter, and it will be released more slowly over the course of the growing season.

Maintaining biological soil health

Just like you, soil microbes need a safe place to live and a balanced diet to thrive. To maintain a healthy soil biota, it is important to maintain soil structure and add organic matter into the soil.

Best practices for crop production including minimizing tillage, using crop rotations, and planting cover crops. Cover crops prevent soil erosion, and also bring organic matter into the soil to sustain the soil community. In pastures, soil can benefit from rotational grazing, avoiding high stocking densities (particularly following heavy rains), and planting deep-rooting perennial forages. The diversity of crop rotations and pastures positively influences diversity in the soil community, and diverse soil communities are associated with lower incidence of crop disease. These positive practices all serve to maintain soil structure and increase organic matter inputs into the soil, which feed soil microorganisms and support soil function.

Dr. Ember Morrissey is Assistant Professor of Environmental Microbiology at Davis College of Agriculture, Natural Resources & Design, West Virginia University.


The Soil Biology Primer (2002) offers an excellent introduction to soil life and how it contributes to agricultural productivity and air and water quality. Available from the Soil and Water Conservation Society at




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