New Tests of Soil Quality:
Evaluating the Health of Your Soil's Microbial Community

Copyright 1997, Don Lotter

Farmer to Farmer Magazine, January-February 1997

Under a lone streetlight in a dark city neighborhood, a scientist is on his hands and knees, searching for something on the ground. "What are you looking for?" inquires a passerby. "My keys," answers the scientist. "I lost them down by the railroad tracks." "Why are you looking here, if you lost them two blocks away?" asks the passerby. "There's no light over there," he replies.

This picture of science is particularly apt in regard to soil ecology, whose dynamics have until recently remained literally in the dark. Most soil organisms are just plain difficult to analyze and describe. One teaspoon of soil may contain up to 10,000 species of micro-organisms and billions of individuals. Although some of these can cause plant diseases, many can be beneficial and even necessary for crop health.

Numerous research groups are studying soil microbial dynamics, and they have developed a number of methods for characterizing and quantifying the nature of the soil microbial community. However, only a few commercial soil microbial analysis laboratories exist, and the results they generate may be difficult to translate into management alternatives.

The Soil Ecological Community. The major soil biota groups are often categorized by size: microflora (bacteria, fungi, and algae) and microfauna (protozoa and nematodes), and mesofauna and macrofauna (earthworms and arthropods such as insects, spiders, and mites).

Microfauna are critically important in nutrient cycling and retention, and in the breakdown of organic matter. They also immobilize and release nitrogen, phosphorus, sulfur, and other nutrients, creating a kind of slow release system which prevents nutrients from leaching and preserves them for plant use.

Bacteria and fungi play critical roles in the formation of soil aggregates in good soil structure and the biological control of root diseases. They promote the detoxification of soil contaminants and the production of plant growth promoters and organic chelating agents.

Vesicular-arbuscular mycorrhiza (VAM), a symbiotic fungus that infects the plant root, obtains carbohydrates from the plant while at the same time bringing in nutrients and water. VAM becomes a powerful extension of the plant's root system and also has been shown to play a role in protecting the roots from disease. These and other types of fungi, such as Trichoderma and Gliocladium, are commercially available for biological control of plant pathogens.

Populations of soil bacteria and fungi are sensitive to soil management practices. Cultivation and disturbance create an environment favorable to bacteria. Soils subject to conservation practices, such as minimum tillage and cover crop use, tend to have greater populations of fungi, typical of forest soils. Ratios of fungal to bacterial biomass may range from less than 1:1 in cultivated soils, to 3:1 in minimum tillage situations, to more than 100:1 in forest soils.

Other microfauna are central to the cycling of nutrients. These are primarily the nematodes (microscopic, worm-like organisms which feed on bacteria and fungi) and protozoans (amoebae, ciliates, and žagellae, which primarily feed on bacteria). Nematodes and protozoans can account for as much as 80% of the nitrogen cycling through the system. While there are many species of pathogenic nematodes, several are beneficial, such as the insect-consuming Steinernema and Heterohabditis species.

Mesofauna and macrofauna break down organic residues and regulate microbial populations. Earthworms transport and mix organic, mineral, and microbial soil components to deeper soil horizons. They create pathways in soil for plant roots to explore, increasing the water and oxygen infiltration capacity of the soil. In addition, earthworms can regulate soil pH, and have been reported to excrete plant growth-stimulating hormones.

Soil arthropods, while taking part in the breakdown of organic matter and the regulation of microbial populations, are especially important in agricultural systems because they can be voracious predators of the ground-dwelling stages of crop pests, many of which must descend from the above-ground parts of the plant in order to pupate in the soil. Especially important in attacking this weak link in the life cycle of many pests are carabid and staphylinid beetles. These predaceous fauna require permanently untilled areas of soil in order to nest and overwinter, and should be considered when making decisions about tillage regimes and the management of hedgerows, riparian areas, inter-row strips, and other "waste" areas near crop fields.

Measures of Microbial Biomass and Activity. All of the physical and chemical parameters used in assessing soil quality-texture, bulk density, infiltration capacity, organic matter, pH, electrical conductivity, and fertility-can be measured by most commercial soil laboratories. (See resources). The biological parameters-microbial biomass, potentially mineralizable nitrogen, and respiration-are newer indicators, and therefore more problematic. Root diseases are generally not diagnosed in microbial biomass laboratories. These problems are usually sent to agricultural extension services or private consultants.

There are three basic ways to assess the soil microbial community: counting them with a microscope, measuring an indicator of activity like CO2, or measuring microbe parts, such as membranes. Generally, these methods are broad indicators of microbial biomass or activity. However, one method, called the phospholipid-fatty acid or PLFA, quantifies microbial biomass, community diversity and species composition. For this reason PLFA may be the "soil test of the future."

Microbial Biomass Counts. Two count methods-plate counts and direct counts-are being used at two of the three commercial soil microbial analysis laboratories we've been able to and in the US. (See Resources.) There is some controversy among soil microbiologists about the accuracy of the count methods for quantifying microbial biomass, especially in soils with recent additions of organic matter. Another problem with counts is that the number of samples needed for accuracy raises the cost into the high hundreds or even thousands of dollars to compare two or more treatments or fields.

Despite the costs and limitations of the count methods, there may be situations in which soil microbial biomass counts would be useful, especially where soils are being reclaimed from a history of toxic inputs or severe degradation. Biomass counts can be a tool for comparing management regimes such as organic versus conventional methods, different soil amendments, or pesticides versus no pesticides.

Dr. Elaine Ingham of the Soil Microbial Biomass Service (SMBS) at Oregon State University in Corvallis, is perhaps the best known researcher of soil microbial dynamics. SMBS analyzes soil samples for soil microbial community structure by the direct count method, which means they dilute soil samples in water, add a stain, and count individuals. Each of the soil biota components can be quantified at a cost of $8 (active fungi, active bacteria) to $45 (nematodes) per component per sample. A minimum of three, and preferably five, soil samples is recommended for each field or treatment. SMBS can give you a report on the following: fungal/bacterial biomass ratio, total fungi biomass, active fungi biomass, total bacteria count, active bacteria count, protozoa count, nematode count and community structure, VAM spore numbers, or percent of VAM colonization.

BBC Laboratories in Tempe, Arizona uses the plate count method for quantifying soil microbial populations, which involves culturing different "functional groups" of organisms-in this case aerobes, anaerobes, pseudomonads, actinomycetes, fungi, and nitrogen fixing bacteria-on agar plates and then counting populations. Because only 1-5% of microbes are culturable, omitting the majority of the community from the count, the plate count method is only partially effective. BBC also does pathogen inhibition assays, a method of assessing whether soils or composts are disease-suppressive, by "challenging" the sample soil with pathogens such as Fusarium, Phytophthora, Pythium, Sclerotium, and Verticillium.

On-Farm Microbial Activity Test. In Methods of Assessing Soil Quality (see Resources) a technique is outlined for on-farm evaluation of soil quality, including soil respiration, a measure of microbial activity. The method uses an inexpensive kit which can be put together quite easily from hardware store materials, made up of a 5-inch-long piece of 6-inch-wide irrigation pipe, a thermometer, a syringe, and a gas detection device. Using this kit and additional inexpensive equipment, measurements can be made of soil pH, respiration, electrical conductivity, bulk density, infiltration rate, water holding capacity, & soil nitrate.

Soil respiration rate, which is related to soil microbial biomass, has been and continues to be one of the most common methods of measuring soil microbial activity and can be a useful tool for comparing the effects of management methods on the soil. It is important that respiration measurements be done at a standard temperature and soil water content, and not immediately after the incorporation of fresh residues.

PMN Test. Potentially mineralizable nitrogen (PMN), a method which correlates well with soil microbial biomass, may be a better way to assess microbial biomass than the counting methods. Currently, few commercial labs do PMN, which involves a simple one week anaerobic incubation of soil, although the ones I talked with said they could start doing it if there is demand. A disadvantage of PMN is that it is a single gross number, expressed as micrograms of NH4-N per gram of soil and does not distinguish between fungi, bacteria, actinomycetes, nematodes, VAM etc. as do counts. However, until accuracy increases and costs decrease for the count methods, gross estimates such as PMN or soil respiration, may be the best way to go because of their cost effectiveness. A method for assessing PMN is described on my World Wide Web page (see Resources).

PLFA: The Future Is Almost Here. As yet there is no soil test that will list each species of organism and its population density, but if any technique has the potential to do this, it is the phospholipid-fatty acid (PLFA) method. In PLFA, the sample is processed so that lipids-part of the membranes of all microorganisms-are extracted, separated, and quantified using gas chromatography. Each species of microbe has its own "signature" pattern of lipids, and even gives a unique pattern when under stress. For characterizing and quantifying the soil microbial community structure, PLFA provides more information than any other commonly used method. According to Professor Kate Scow, soil microbiologist at UC Davis, whose research focuses on PLFA, "Molecular approaches using DNA have even greater promise for characterization of the entire community but still need more development for application to soils. Much work still needs to be done before the PLFA method's applications are fully realized." I know of only one commercial laboratory that does PLFA analysis of soils: Microbial Insights of Knoxville, Tennessee. For $250 per sample you get a highly technical 10-page printout with an analysis of the community structure of the soil sample.

Earthworms: The Best Soil Testers. Earthworms are excellent indicators of soil health, and no professional services or kits are needed to enumerate them. Earthworms live by consuming organic matter, and an abundance of earthworms indicates ample soil organic matter and good decomposition dynamics.

Dr. Matthew Werner, a soil ecologist in the agroecology program at UC Santa Cruz, believes that if a soil has plenty of earth-worms, it is safe to assume that it has a healthy microbial community. Other experts agree with this, including Dr. David White of the Center for Environmental Biotechnology at the University of Tennessee at Knoxville- a major player in the development of the phospholipid-fatty acid (PLFA) method of soil microbial community analysis-and Dr. Kate Scow, soil microbiologist at UC Davis. Scow cautions, however, that soils can be healthy and productive without earthworms, as when intensive tillage inhibits earthworms.

Werner, otherwise known as "the earth-worm guy," has an easy method for assessing earthworm numbers in soil. "Dig down 8-10 inches with a shovel, turn over the soil, and count the earthworms. Do this in half a dozen or more spots. An average of 5-10 worms per shovel indicates a healthy earthworm community." Earthworm populations may take years to build up in a soil and are sensitive to many insecticides and fungicides. (See Werner's article on worms in Farmer to Farmer Number 6, October 1994). -

Soil Sampling for Analysis. Sampling technique is important for all soil microbial analysis. Brush aside any litter at the surface and take at least three samples from each field. Each sample should be made up of 3-10 soil cores 1 inch in diameter and 2-3 inches deep.

Conclusion. Soil microbial analysis clearly has potential as a tool for growers to assess their management methods and their soils. Currently, it may not be cost effective to use commercial testing unless you have a strong curiosity about what is in your soil. Gross measures such as soil respiration, which can be done on the farm quite inexpensively, may be the way to go for now, as long as attention is given to the method's limitations. In the next few years we should see rapid progress in the development of cost effective methods of characterizing and quantifying the soil microbial community. n


Information Required for Evaluation of Soil Quality


  • Texture
  • Depth of soil, topsoil, and rooting
  • Bulk density and infiltration capacity
  • Chemical
  • Organic matter
  • pH
  • Electrical conductivity
  • Fertility (extractable N, P, K)
  • Biological
  • Microbial biomass C & N
  • Potentially mineralizable N (PMN)
  • Soil respiration
  • "Minimum data set for assessing soil quality." from Methods for Assessing Soil Quality.

    The Soul of Soil: A Guide to Ecological Soil Management.
    1995. Grace Gershuny and Joseph Smillie. agAccess, Davis, CA. Layperson's guide to soil ecology, with the organic gardener/farmer in mind.

    Fundamentals of Soil Ecology. 1996. David C. Coleman and D.A. Crossley, Jr. Academic Press. A small book by very well respected soil ecologists.

    Methods of Assessing Soil Quality. January, 1997. John W. Doran and Alice Jones (Eds.) Soil Science Society of America, Madison, WI. (608) 273-8090. Brand new, and should be very useful for those interested in soil ecology.

    Methods of Soil Analysis, Part 2: Microbiological and Biochemical Properties. 1994. R.W. Weaver (Ed.) Soil Science Society of America, Madison, WI. The technical Bible of soil microbial analysis.