Soil Microbes and Nutrient Uptake

Ag, Soil

Soil Microbes and Nutrient Uptake

Improvement in crop growth obtained from crop and soil management practices is the result of increased activity of microbes in the vicinity of plant roots (the rhizosphere). There is still much unknown in the relationship of roots and microbes because of the complexity of this symbiotic relationship.

Vesicular-arbuscular mycorrhizal (VAM) fungi are critically important for virtually all crop plants. Research has shown that the lack of VAM can result in poor plant growth. Most crop fields have adequate VAM spores present if crop residue, compost, or liquid humic substance (Humega®) is placed back into fields.

Intensive pesticide use, or intense fertilizer use will reduce VAM so low that plant growth will be in jeopardy.

The mycorrhizae linkage between plants and soil fungi varies greatly. Some types of plants do not use the fungi for nutrient uptake, while other plants have trouble even surviving without mycorrhizae. Clearly, the evolutionary process over millions of years has led different plants down different paths.

It is known, that the zone of soil next to plant roots support a much higher population of microbes than the soil even a short distance away from the roots. The number of microbes near the roots (rhizosphere) is from 10 to 100 times greater than 1/4″ away.

Plants often exude from 25 to 50% of their photosynthates to attract and feed those mycorrhizal fungi. Why?

Microbes digest chemical compounds and make them available to the plants.

Colonization by VAM fungi can limit root-feeding nematode attacks of the root system.

Microbes receive nutrition from plants and soil organic matter and convert them to humus storage for plant use.

Rhizosphere fungi provide a protective coating on roots that buffer the negative effects of salts and other toxic compounds in the soil.

The greater the diversity and number of microbes, the higher the fertility of the soil.

Maintenance of an environment around the plant roots, which is favorable for the good growth of beneficial microbes, will result in increased fertilizer efficiency and higher crop yields.


Heterotrophic Bacteria (Aerobic Bacteria)

The functional group of bacteria utilizes oxygen in their growth and represents a very diverse and important cross-section of soil microorganisms. The heterotrophic bacteria enumeration is a good indicator of general soil conditions with the number of these bacteria decreasing with the increasing depth in the soil.

Yeasts and Molds (Fungi)

Soil fungi are primarily in the top 4-6 inches of soil and are most abundant in well-aerated soil. While some fungi are pathogenic to plants, many contribute to soil fertility by breaking down organic compounds including cellulose, lignin, and pectin as well as increasing phosphate uptake in plants.

Fungi are also important in binding together fine soil particles to form water-stable aggregates thereby improving the soil crumb structure. Fungi typically tolerate a low soil pH making them particularly significant in acidic soils.

Nitrogen Fixing Bacteria

Nitrogen fixing bacteria are able to convert atmospheric nitrogen into nitrogen compounds used by plants to synthesize plants. These bacteria can be free living or associated with certain plant roots, although the nitrogen-fixing bacteria enumerated at BBC Laboratories are free-living bacteria.

There are bacteria of many genera in the soil that are capable of nitrogen fixation and the number of these bacteria will fluctuate.


Actinomycetes comprise a significant proportion of the bacterial population in agricultural soils. They are capable of degrading many complex chemical substances including chitin. They favor alklaine or neutral soil pH and are intolerant of waterlogged soils.

Actinomycetes are responsible for the musty or earthy odor of a freshly plowed field and are helpful in improving soil crumb structure. Most soil actinomycetes are streptomycetes, which are well known for the production of antibiotics.

Although the presence of antibiotic substances in the soil can rarely be detected, it is possible they are present and active in a microenvironment.

Anaerobic Bacteria

Anaerobic bacteria are capable of growth without oxygen. The anaerobic bacteria enumeration is predominantly a count of facultative anaerobes, or those organisms that have the ability to live and grow both with and without oxygen.

High numbers of anaerobic bacteria in the soil usually indicate soil that needs better aeration and is possibly waterlogged or too compact.


These organisms are very nutritionally versatile and capable of degrading many natural and synthetic organic compounds. These are typically aerobic and contribute to the decomposition and nutrient release process by attacking a wide variety of organic substrates including humic acids and synthetic pesticides.

Particular pseudomonads have been linked to the biological control of plant pathogens.

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