Soil Biology Basics: Part II

by Joe Magazzi, MS

Soil Biology Basics: Part I introduced readers to some basic information on soil biology regarding all of the benefits plants, trees, and turf receive from building and maintaining healthy soil “life” – including providing and cycling carbon, retention and delivery of nutrients and water, healthier and better growth, and natural disease protection and resistance. In Part II, I follow that up with more practical information on how you can build, apply, and maintain beneficial biology and use these practices to reduce other inputs while increasing the quality and health of plants, trees, and turf.

Building Healthy Soil to Maintain Soil Biology (Bio-Stimulation)

There are multiple ways and approaches to adding soil biology (bio-supplementation).I will get to that in a bit; however, I want to start with a more basic concept: how to maintain and build the biology that you already have in your soil (bio-stimulation). Regular use of practices that destroy existing soil biology makes the ongoing addition of exogenous inputs less beneficial, sustainable, and cost-effective. Here are some products and practices to avoid, or use with caution, to help create a healthy environment for soil biology to flourish:

Fungicides & anti-bacterials: Fungicides and anti-bacterial products kill fungi and/or bacteria in a non-specific manner. Therefore, when you apply these products when attempting to eliminate pathogens, you’re also very likely adversely affecting populations of the beneficial fungi and bacteria that are so important for healthy plant, tree and turf growth. Use these types of products only when needed; keep in mind that this holds true for organic pesticides also.

Insecticides: Since many of these compounds are also non-specific, they can cause death to beneficial insect populations that work naturally to keep pathogens at bay. Maintaining healthy biology in the soil will actually lead to healthier plants and reductions in diseases and subsequently the need for insecticides, fungicides, and anti-bacterials. (For more details on how this works please refer to Part I).

Excess Fertilization: At high concentrations, phosphate is toxic to beneficial organisms. Excess nutrients can also stimulate pathogen growth while having little or no benefit for the turf, trees or plants1. Using a thorough soil test to determine the correct types and amounts of nutrients to add is the best way to avoid over treatment. Following this strategy will also save you money and is better for the environment.

Disturbing Soil: Tilling destroys the complex organization of the rhizosphere (the soil right around the root zone) and the crucial top layer of soil. Thus tilling actually leads to more compaction and depletes the soil of organic matter and carbon.2 This is more relevant in agriculture, but it is worth a mention as any practices that landscapers use to disturb the soil will have similar detrimental effects on soil biology. When tilling (or any disturbance of the soil) is necessary, be sure to supplement biology to help re-build the soil food web.

Herbicides: Glyphosate, the active ingredient in Roundup® and other herbicides, can reduce beneficial organism populations3 while at the same time increasing pathogen growth4. This side-effect is less of a concern to landscapers using these products in moderation. (Bigger problems are seen on farms where crops are now genetically engineered for resistance to glyphosate, and glyphosate is being applied at higher concentrations and multiple times per growing season). However, this is not specific to just glyphosate as many other types of herbicides can adversely affect soil biology or change the characteristics of the microbes present in the rhizoshpere.5

By limiting many compounds that are toxic to beneficial microbes, you will provide the basis for a healthy environment for building soil biology. There are several other things that can be done to promote healthy microbial growth. One is maintaining organic matter and micronutrient levels. Traditionally, typical fertilizers contain only nitrogen (N), phosphorous (P), and potassium (K). The application of these types of synthetic fertilizers helps to supplement those specific macronutrients, but not the many additional micronutrients that are also necessary for healthy growth. Maintaining and supplementing micronutrients is not only important for healthy plants, trees, and turf, but also for healthy microbial growth. Organic matter provides the carbon necessary for microorganisms to grow. Organically-derived fertilizers such as seaweeds (kelp), compost, manures, fish, and even molasses can provide carbon matter as well as many micronutrients and will stimulate healthier plant and microbial growth.

Adding Soil Biology (Bio-Supplementation)

Even while implementing good soil-building practices, it is often necessary and always beneficial to supplement soil biology. This is especially true in the landscape industry due to several factors: poor topsoil is often used following the construction of new homes, homeowners have not maintained healthy soil, or homeowners have used compounds that are toxic to biological growth (such as those mentioned above). In these cases, the quickest way to address these deficiencies is by using products that add beneficial biology directly. There are several ways to go about this:

Compost: Bacteria and fungi break down organic matter, so during the process of composting, beneficial organisms are grown and concentrated. Adding compost to soil directly provides a great source of soil biology (in addition to providing the carbon and micronutrients that are necessary for maintaining microbial growth). The drawback of compost is that it is difficult, labor-intensive, and time-consuming to move around and apply, especially in larger areas. That is where compost teas come in.

Compost is a concentrated source of beneficial organisms.

Compost teas: Since liquid applications are often easier than physically applying several inches of solid compost, compost teas are an alternative that is often more practical, especially for landscapers. Compost is actually brewed like a tea (hence the name), and the nutrients are extracted from the solid part of the compost. These “teas” can then be applied using standard liquid application equipment. This provides some of the nutrients and microbiology that you get from compost in an easier-to-apply manner. The drawbacks of compost teas are that some of the nutrient value and organic matter you get from compost is lost, teas are fairly unstable (you need to apply within days to get the full biology value), and they are input dependent and therefore can be inconsistent – that is, depending on what you put in, and the experience of the “brewer” you will get out differing nutrient and biology values. That brings us to the last method (for the sake of this article).

Controlled Biological Inoculations: Controlled biological products have guaranteed strains and counts of microorganisms. These products are usually tested for pathogens, so you get more consistent results, and safety and efficacy is much less of a concern. Controlled biological inoculants can contain bacteria, fungi, or combinations of the two. In addition, they are often more concentrated and stable than compost teas. There are both liquid and dry products that are available on the market that can fit in with most application equipment that landscapers use. There is also no brewing involved. For many of these reasons, controlled inoculants may be more suitable for large-scale and commercial applications. The drawbacks with controlled biological products are that they may cost more and may be less sustainable (especially if you’re using your own waste to compost or brew compost teas), and, depending on the products you get, there is less diversity in the species of bacteria and fungi.

Measuring Soil Biology

Now that we know how to maintain and add beneficial soil biology, the question is how do we know when or what we need to supplement? Although new genetic techniques are helping scientists make advances in understanding the complexity of the soil food web, still only a small fraction of what is found in healthy soil has thus far been identified (estimates are that there are between 1 million and 100 million species of bacteria and only 0.5% to 0.005% are likely described in detail at this point). So although this is not a perfect or exact science yet, there are good general methods that are available to help growers and landscapers measure soil biology, estimate what bio-supplements may be needed, and monitor progress in building healthy soil:

Sight and Smell: This is the oldest, and least scientific method of measuring soil biology – but is also the cheapest and easiest way to get a very general soil assessment. Does your soil smell like soil, or does it have no smell? Healthy soil should have more of an “earthy” smell such as that of walking through woods with decomposing leaves rather than no smell at all or a bad smell. When you pull roots from a plant, are the roots covered in small white fiber meshes? If so, you have good growth of Mycorrhizal fungi and therefore good soil biology supporting that plant. Do you have lots of earthworms in your soil – that is a great sign of a healthier soil food web. Most importantly, you should see good, healthy growth of plants, trees, or turf.

By-Product Analysis: There are kits available to measure by-products of microbes such as gas production (carbon dioxide or CO2), sugars secreted, enzymes produced, etc. Although these methods do not directly measure the number and types of soil microbes present, they measure compounds produced by soil microbes and can be useful and performed quickly and easily, often by growers or landscapers themselves right in the field.

General Microbial Measurements: The most cost effective and thorough general measurement method is available through Soil Foodweb Inc.

Western US:

Eastern US:

These tests will give general measurements of total and active bacteria and fungi, nematodes, and protozoa, but the tests cannot identify individual organisms.

Specific Microbial Measurements: Advanced methods are available to identify individual strains of microbes, such as plate counting (bacteria are grown under specific media and identified with a microscope or genetics) or pyrosequencing (DNA is extracted from microbes and complete sequencing is performed to identify individual strains). However, these methods are expensive and generally not necessary for growers and landscapers. I think it is worth mentioning these measurements since these types of technologies will become more cost effective in the future. Also these are the methods that are being used for research purposes to help us better understand the complexity of the diverse organisms that form the soil food web.


This two part series on soil biology describes the many benefits of building and maintaining good soil biology, and how to do it. This is only an introductory article and is just the tip of the iceberg. If you have questions, or want more specific treatment ideas or information on methods to measure soil biology, please feel free to contact me at any time (







Suggested Reading:

The Soil Biology Primer. Elaine R. Ingham, Andrew R. Moldenke and Clive A. Edwards. Soil and Water Conservation Society, in cooperation with the USDA Natural Resources Conservation Service (2000).

Available on-line:

Teaming With Microbes: A Gardener’s Guide to the Soil Food Web. Jeff Lowenfels, Wayne Lewis. Portland: Timber Press (2006).

About the Author

Joe Magazzi, MS, is the president and co-founder of GreenEarth Agriculture, a company that provides eco-friendly products and consulting services to landcare professionals and farmers. He has been involved in the research and development of microbial-based products for use in turf care and agriculture for many years. Joe has a Master’s degree in genetics (with a microbiology focus) from the University of Connecticut-Storrs, and his research has been published in scientific journals such as The New England Journal of Medicine. Joe may be reached at