Soil biology is important for keeping agricultural systems healthy and productive. Living soil is complex. It includes creatures that cannot be seen with the naked eye, such as bacteria, fungi, actinomycetes, protozoa and nematodes, as well as creatures such as insects and earthworms. This community of organisms is bound together in a food web that affects the soil's chemical and physical properties. We care about these properties because they also affect plant growth and health.

Practices such as adding manures or composts to soil, planting cover crops and rotating crops are all aimed at rebuilding and maintaining soil organic matter, recycling and retaining nutrients, and decreasing soil diseases. These practices are usually associated with increased microbial biomass and increased soil organism diversity.

A healthy soil can contain billions of bacteria, fungi and other microorganisms in one teaspoon. Depending on soil conditions, the populations of these different microorganisms rise and fall. Some microbial populations increase quickly when fresh cover crops or other plant residues are added to the soil. For example, some microbes are able to use the readily available sources of carbon from fresh plant residues like humans use carbohydrates. These microbes decrease as the carbon sources are used up, causing other microbes that break down the less available sources of carbon like cellulose and lignin to increase. The point is that there are many native microorganisms in the soil that respond quickly when conditions are favorable for their growth.

Soil Inoculants

As we continue to recognize that soil biology plays an important part in crop production, interest in soil inoculants continues to grow. Inoculants are used for a variety of reasons. In some cases, we add soil organisms that have a known beneficial effect. For example, some bacteria, like rhizobia, form a symbiotic relationship with certain host plants, like legumes. A symbiotic relationship is one that is mutually beneficial. In return for the plant feeding it carbon from photosynthesis and giving it a home, the bacteria can "fix" atmospheric nitrogen into a form that the plant can use. Some fungi, like mycorrhizae, can also form a symbiotic relationship with plants, scavenging phosphorus and other nutrients for the plant to use. Some bacteria and fungi do not form a symbiotic relationship with plants, but, when added to soil, can promote plant growth, suppress plant pathogens or both.

The easiest way to think about soil inoculants is to divide them according to their mode of action: biofertilizers or plant growth promoters, biopesticides and plant resistance stimulants.


Biofertilizers contain live microorganisms that, when applied to the seed, plant or soil, inhabit the area around the roots (rhizosphere) or live in the roots. These microorganisms promote plant growth by increasing the supply or availability of nutrients, by stimulating root growth or by aiding other beneficial symbiotic relationships. Biofertilizers are also called plant growth promoters.

Legumes such as clover, peas and beans have root-colonizing rhizobacteria that can increase the availability of nitrogen to the plant by fixing nitrogen from the atmosphere. Each legume has a specific rhizobacteria that works best with that plant. Inoculating the legume seed with the correct bacteria ensures the legume will maximize nitrogen availability if nitrogen in the soil is low This is particularly important if you have not planted the legume species before, because the correct bacteria may not be present in the soil.

There are also free-living, nitrogen-fixing bacteria that can supply nitrogen to cereal plants such as wheat and corn. They live in the area right around the root (the rhizosphere). In general, nitrogen fixation with both the symbiotic and free-living nitrogen fixers is higher in nitrogen-poor soils.

In many soils, nutrients such as phosphorus, potassium and iron are present in large amounts but in forms that plants cannot use. Many bacteria and fungi are able to make these nutrients available to plants by secreting organic acids or other chemicals (siderophores) to dissolve the minerals. Mycorrhizal fungi that live in plant roots are well known for their ability to provide phosphorus to plants. Just like the situation with nitrogen fixers, mycorrhizal fungi are most effective when available phosphorus in the soil is low. When there are adequate nutrients available, plants do not seem to want to exchange their hard-earned products of photosynthesis for more nutrients.

Some bacteria and fungi produce plant growth hormones that can increase root growth specifically and plant growth in general. Increased root growth helps the plant utilize a larger volume of soil for nutrients and water and can help the plant to "outgrow" pathogen attacks. For example, fungi are known to produce gibberellins that are important for seed germination and cell growth, and some bacteria can reduce the amount of ethylene, which is a hormone that plants produce under stress.


There are many examples of soils that are naturally suppressive to plant pests. Suppressive soils are the result of interactions between certain microorganisms and pest organisms. Many of the most common soil inoculants are formulated with these suppressive microorganisms and are used as biopesticides or biocontrol products.

Most biopesticide organisms work by either producing a substance that inhibits or kills the pest (antagonism) or by reducing the availability of food or shelter for the pathogen (competition). The most widely used biopesticide is Bacillus thuringiensis, which produces a toxin that kills soil grubs and nematodes. Specific strains of Bacillus subtilis are widely used as a fungicide. This bacterium colonizes plant roots, competing with fungi for that niche, and prevents the rapid growth of fungal pathogens.

Protozoa and nematodes that eat bacteria are also thought to play an important role in controlling pathogens (predation). As with any ecosystem, both competition and predation tend to keep populations in balance.

Plant Resistance Stimulants

In addition to acting as a direct inhibitor of plant pathogens, some fungi and bacteria stimulate the plant to activate its own defense mechanisms. This is called induced systemic resistance. In response to chemical signals from the microorganisms, plants may change physiological responses so that there are fewer symptoms of the pathogen. This may include strengthening its cell wall to resist infection, or releasing antibiotics (such as terpenes) that reduce pathogen attack. The chemical signals that pass back and forth from microorganisms to plants are specific; consequently, microorganisms and the chemical that may cause induced systemic resistance in one plant species may not work in another.