Soil Microbiology 101 - October 13, 2010
Jeff Schalau, Associate Agent, Agriculture & Natural Resources
University of Arizona Cooperative Extension, Yavapai County


Productive garden soils should contain a multitude of living organisms. Many are visible to the naked eye: earthworms, beetles, mites, springtails, and others. However, the majority of soil-borne organisms are microscopic. Of these, many are beneficial and help convert decaying organic matter into nutrients and humus. A teaspoonful of soil of amended garden soil contains hundreds of millions to billions of individual microbes. Its difficult to imagine, but soil microbial biomass can range from several hundred to thousands of pounds per acre.

By far, the most numerous microbes in soil are bacteria: free-living, single-celled organisms. Also abundant are fungi, which produce long, slender strings of cells called hyphae. Fungi also include yeasts and molds. The actinomycetes are in-between these two organisms and are advanced bacteria that can form branches like fungi. Its the actinomycetes that give soil its characteristic earthy smell. Fungi and actinomycetes are good at starting the decomposition of organic residues, breaking down materials that are more resistant to decomposition. Bacteria finish the job by eating the more digestible ingredients.

Many other microbes can be found in smaller numbers in soil, including algae, cyanobacteria (often called blue-green algae), and protozoa (one-celled organisms that decompose organic materials and also consume bacteria). Nematodes are microscopic roundworms; some of these are beneficial and a few are plant parasites.

The soil zone located immediately around active roots is called the rhizosphere. This is an area of high microbial activity. Roots are not tightly sealed structures they leak releasing sugars and proteins (called exudates). This creates a food-rich environment for the growth of microorganisms. Rhizosphere microorganisms often form symbiotic relationships with plants which help plants access essential nutrients by dissolving soil minerals and decomposing organic matter.

Some microbes have a specialized role in the rhizosphere. Rhizobia bacteria associate with the roots of legumes to form nodules. This symbiotic relationship provides the bacteria with a source of carbon (sugars) in exchange for making nitrogen available to the plant. Many gardeners are familiar with this process and encourage it by inoculating legume seeds with a commercial preparation of the Rhizobium species that is suited to the crop species they are planting. This practice increases soil nitrogen reserves and organic matter content.

A special group of fungi are called mycorrhizae and form symbiotic relationships with plant roots. By colonizing large areas of roots and reaching out into the soil, mycorrhizae aid in transfer of soil nutrients and water into the plant. The plant provides a source of carbon to the mycorrhizae. This is especially important in our native ecosystems where nutrient and moisture availability are limited.

Microbes promote good soil structure, which increases water infiltration and drainage, soil aeration, and vigorous root growth. Gummy substances produced by soil microbes (complex sugars and mucilages) also help soil particles adhere to each other, which contributes to soil structure. This also makes aggregates less likely to crumble when exposed to wind and water. Fungal hyphae further stabilize soil structure as their threadlike structures spread through the soil, surrounding particles and aggregates like a hairnet.

Some soil microbes can cause plant diseases. In vegetable gardens, this often occurs when a certain type of crop is grown in the same space year after year. Crop rotation decreases the probability of soil-borne disease by varying the host plant species present in an area of soil. Disease causing organisms are also marginalized when beneficial microbes are occupying available niches in the rhizosphere.

In order to encourage microbial activity in your garden, soil has to be managed to create a favorable environment for both crops and microbes. This can be done by timely and appropriate tillage that avoids soil compaction; irrigation practices that keep the soil moist but not water-logged, and frequent additions of organic residues to provide energy for the microbes. In general, the abundance of microbes in soil is proportional to the organic matter content. Soils that have large amounts of organic residues regularly added to them tend to support a larger microbial population. This column was adapted from: Soil Microbiology: A Primer by Vern Grubinger, University of Vermont Extension Specialist

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Arizona Cooperative Extension
Yavapai County
840 Rodeo Dr. #C
Prescott, AZ 86305
(928) 445-6590
Last Updated: October 6, 2010
Content Questions/Comments: jschalau@ag.arizona.edu

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