Managing Soil Microbes Leads to More Sustainable Farming


The role of single cell, microscopic, organisms in soil is crucial in the natural recycling process of organic materials, soil building, and plant nutrition. These organisms also serve as the initial link in the food chain that stretches all the way to plants, animals, and humans. As a result, managing the microscopic world of soil used for food production is very important.

By far, the largest majority of microscopic organisms in soil belong to three kingdoms: bacteria, fungi, and protozoa. Bacteria are the most numerous and the most diverse, followed by fungi, and protozoa. They are also the most active and the most crucial resource to manage in productive soils.

The­ Good,­The ­Bad ­And ­The ­Ugly

When it comes to usefulness in agriculture, microscopic organisms, commonly referred to as “microbes,” can further be classified as “good” (beneficial), “bad” (pathogenic), and “ugly” (spoilagecausing). They are all considered beneficial when they degrade organic matter to simple plant nutrients. Without their ability to “digest” organic materials, the world would drown in organic waste and life would cease to exist as we know it. Even though plants have an ability to harness sun light and generate simple sugars from water and carbon dioxide, they have no ability to scavenge for other necessary nutrients such as nitrogen, phosphorous, or potassium. They depend on microbes to simplify or “mineralize” nutrients in soil and prepare them for their consumption. Some microbial groups are known to be more beneficial than others.

For example, mycorrhizal fungi establish a symbiotic relationship with plant roots helping the plants obtain water and nutrients from soil in exchange for food stuffs such as simple sugars. Nitrogen fixing bacteria such as Rhizobia convert the elemental nitrogen from the air into useful nitrogen forms (e.g. nitrates) that the plants can use. Some beneficial microbes can also be used to guard against pathogens by a process called Competitive Inhibition (CI). During CI, the beneficial microbes establish colonies in places where pathogens are undesirable or unacceptable, and thus prevent the onset of disease.

Controlling­ The ­Sneaky ­Bad­ Guys

Pathogenic microbes have an ability to invade plants, animals, and/or humans, and cause illness or death. Pathogens are ubiquitous in the environment, and as a result, a significant portion of today’s agricultural practices are devoted to controlling pathogens in our food supply.

We also must guard against food packaging and storage conditions that may preferentially select for the growth of pathogens between the point of food handling/processing and consumption; however, this hazard may not always be easily identified. For example, in a routine study of modified atmosphere packaging (MAP) systems, we found that even though the shelf life of fresh North American ginseng roots could be extened from two months to eight months under refrigerated MAP conditions, temperature abuse facilitated Clostridum botulinum toxin production after fourteen weeks at ten degrees Celcius, and well before the product was considered unfit for human consumption. (Reference: Macura, D. A. M. McCannel, M. Z.C. Li, 2001, Food Research International, 34, 123-125.)

By comparison, when the same product was stored at 21 degrees Celcius, under the same packaging and handling conditions, the product posed no danger to human health, as it spoiled and was unacceptable for consumption within six weeks, demonstrating that CI kept C. botulinum from establishing sufficient growth to produce its deadly toxin.

New packaging, processing, or storage conditions should always be checked by food science or microbiology specialists to verify that a dangerous situation does not develop unexpectedly.

Building The ­Good ­Guys

Organic fertilizers and soil amendments, together with crop rotation methods, help build organic content in soil. They also provide the environment for microbial habitat. Microbial proliferation facilitates nutrient conversion, nutrient retention, and subsequent improvement in plant nutrition, leading to plant growth and disease resistance. It is often said by experienced farmers that a good farmer will “feed the soil, not the plants.” In this context, the plant benefits from the consequence of “happy microbes in healthy soil.” Healthy soil is usually rich in organic matter and microbial activity.

By far the most abundant and usual form of organic amendment in California agriculture is compost. Compost carries a healthy inoculum of beneficial bacteria and fungi, a good source of macro and micro nutrients, organic carbon, humic acids, and moisture-absorbing particles that facilitate soil aeration, moisture retention, and a good habitat for soil microbes. In the soil food chain, bacteria serve as food for a succession of microbial groups, protozoa, beneficial nematodes, earthworms and other members of a healthy soil ecosystem.

Composting also accomplishes an important environmental stewardship goal of converting organic wastes to useful agricultural commodity. Over the years, and particularly in response to the recent demand for organic amendments by both conventional and organic farmers, there has been an upsurge of alternative organic fertilizers and soil amendments.

Most of them either replace or compliment traditional compost activities in agriculture by delivering functionalities that are normally obtained from compost. For example, some liquid products provide soil beneficial microbes, such as mycorrhizal fungi or nitrogen fixing bacteria, while others provide a variety of humic acids or organic carbon formulations designed to enhance the activity of indigenous soil micro flora and/or prevent nutrient leaching.

The­ Results ­Are ­Anything­ But ­Ugly

In a 2005 study of the effect of soil amendments on soil microbial communities by UC Davis researchers, it was found that organic carbon and soil fumigation, not microbial inoculums, had an effect on soil microbilogy. (Reference: Dernovsky, R. E., R.A. Duncan and K.M. Scow, 2005, California Agriculture, Vol. 59, No. 3, pp 176 to 181.) These results show that the feeding of indigenous microbes in soil affects soil fertility more than the external inoculation does.

Another group of new organic fertilizers and soil amendments gaining prominence with growers are the so called “high temperature liquid fertilizers” (HTLF). These are liquid fermented products made in large stainless steel digesters at high temperatures utilizing all the basic technologies of good composting practices, but are suitable for water-run applications due to their liquid form.

HTLF can be made with higher nutrient content, the process is easier to control than composting, and there is no additional cost of application. If combined with a good manufacturing practices designed to eliminate post- process cross contamination, HTLF’s can be delivered to the grower completely pathogen-free. Yet, they carry a relatively high content of water soluble macro- and micro-nutrients, organic carbon, and a very high content of beneficial microbes.

Very good results have been obtained with HTLF’s on both certified organic and conventional crops. Certified organic growers use HTLF’s as a major component of their fertility program, while conventional growers use HTLF’s to enhance soil microbial activity and to provide extra organic content to their soil that assists with the assimilation and release of nutrients already there. Conventional growers can reduce their use of chemical fertilizers such as UN32 or AN20 by fifteen to thirty-five percent, and often retain—or in some cases increase—yields.

Where’s The Proof

In one case, HTLF product was used on conventional tomatoes in Lockwood, CA, to replace 31.5 percent of UN32. Yield increased by seven tons per acre. Every commercial grade of tomato was increased substantially, the largest increase being for large grade from 7.4 percent of total crop for untreated, to 17.8 percent of total crop for HTLF treated.

In another case, by replacing 20 gallons of AN20 in the growers nutrient program with HTLF at a Gonzales, CA farm, the average yield of broccoli was increased by 32 extra cartons, amounting to a 5.3 percent increase in yield. This equated to  an increase in revenue of $290 per acre  to the grower.

HTLF products are usually made from food industry wastes that would otherwise end up in municipal landfills. They can be made from animal manures or any other organic waste that can be liquefied, creating organic fertilizers that have potential in organic- and sustainable agriculture, as they facilitate fast and effective conversion of organic waste to quality organic fertilizers and soil amendments.

HTLF products have potential to bridge the gap between increasing accumulation of organic waste caused by urbanization and accelerated depletion of organic matter from agricultural soils due to high intensity farming. Increased soil organic matter and microbial activity leads to reduction of chemical fertilizers and pesticides, resulting in a steady shift to sustainable methods of food production.

Organic and sustainable farming must lead the way in reducing pollution and producing healthier and safer food. Microbial communities in soil are the indispensible agents of change that will help us get there.