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Soil Biology Basics, Part I

by Joe Magazzi

It is always difficult to understand concepts that we can’t see. Most landscapers understand the importance of healthy visible landscape ecology in terms of plants, trees and turf; the bees that pollinate them; etc. Many professionals employ practices that help this ecology naturally thrive, and this leads to a healthier landscape with less disease and fewer pests. What is often ignored, however, are the practices that increase and support the other ecology – that is the soil microorganisms below ground that are invisible to the naked eye but are as (or even more) vital for the healthy growth that we can see above ground.

We are just beginning to have a more complete understanding and characterization of this very complex ecosystem. It is estimated that one gram of soil contains one million fungi, and one billion bacteria. Of those one billion bacteria, estimates are that a mere 0.5% of soil bacteria have even been discovered or identified to date – a measure of the complexity of the soil food web that we have yet to discover. New genetic methods that allow much quicker and more thorough identification of new species are now emerging and they reveal a much more complex ecosystem than previously thought. This research is helping us “see” how invisible soil microorganisms provide vitally important support to plant, tree, and turf growth and health. Most importantly for landcare professionals, our increased understanding of how to exploit and use these natural relationships is leading to new best practices that are more sustainable, environmentally sound, cheaper, and easier without the sacrifice of health and quality.

The Soil Ecosystem

Much of our understanding of the soil ecosystem has been described through the research and the teachings of Dr. Elaine Ingham and the concept of the “soil food web” that she has made famous. Dr. Ingham breaks soil biology down to what she terms “trophic levels”. The first trophic level is made up of the primary producers, that is the photosynthetic sources that turn the energy from sunlight and carbon dioxide into sugars or energy for the plants and the entire soil food web (usually a plant or tree, but photosynthetic bacteria and algae may also be included in this group). The second trophic level consists of the decomposers and mutualists: non-photosynthetic bacteria and fungi. The third trophic level is made up of the shredders, predators, and grazers (nematodes, protozoa and some arthropods), and the fourth and fifth levels are made up of higher-level predators.

All elements of this system, including plants, trees, and turf, work together through very complex interactions. Organisms in one trophic level are dependent on organisms in both lower and higher trophic levels. This article focuses only on the interactions of the bacteria and fungi that comprise the first two trophic levels. Understanding, and then building and maintaining, these two levels helps the entire soil food web and results in better and healthier turf, plants and trees – and does so in a much more sustainable manner than conventional land care methods. First, let’s explore the relationships between organisms in the first two tropic levels.

The Roles of Bacteria and Fungi

The benefits that soil microbes provide to the plants and trees are numerous. In a very basic sense, the bacteria and fungi provide nutrients to plants and in return, a plant will provide sugars through their root exudates for consumption by soil microorganisms. In fact, the function of the soil biology is so important to the plant that it will give up almost half of its photosynthetically produced energy to the soil life. This relationship, however, is much more complex than just a sugar for nutrients bartering system. Here are some of the major benefits that bacteria and fungi provide for plants and trees:

1) Providing and cycling carbon and nutrients. Bacteria and fungi are the primary decomposers in the soil. If they weren’t present, we would be standing on a giant pile of dead plant and animal matter that never breaks down. The carbon and nutrients that make up all living matter is constantly recycled through the actions of the soil biology. Also, the microbes in the soil are responsible not only for the detoxification of harmful compounds such as many herbicides that are used in conventional horticulture, turf care, or agriculture, but also for naturally produced toxins that would otherwise accumulate and inhibit growth.

2) Retaining and delivering nutrients and water. The bacteria and fungi, along with the organic matter that is produced as a function of the actions of soil biology, are the retention and delivery system of the soil – that is they act like the soil’s plumbing system, or as the stomach for a plant. Microbe populations grow to the capacity of their environments. As nutrients are added (through fertilization, composting, mulching etc.), microbes will reproduce and the carbon, nutrients, and water will be locked up in their cell bodies. As the nutrient and water supplies start to decrease, microbes begin to die and re-release these components, acting in a sense like a living buffering system. Bacteria and fungi also live on and in the root system and inside the plant or tree itself. Fungi have complex, branching systems of hyphae that act like a plumbing system to transport nutrients and water that would otherwise not be accessible to roots. In addition, the movement of the organisms in the soil (including higher level organisms such as nematodes and worms) acts like a transportation system moving vital compounds into the reach of the root system. When nutrients run low, trees and plants will actually exude compounds through their roots to “recruit” fungi and bacteria that are able to provide for them in a mutualistic manner.

3) Promoting plant and tree growth. In an indirect manner, plants that are “fed” through the above actions of soil microbes are healthier, grow better, and produce more flowers and are therefore more fertile and attractive. However, soil microbes also contribute to plant and tree health in a much more direct manner. Bacteria and fungi actually produce plant hormones that stimulate plant growth, including all the major groups of plant hormones: gibbrellic acids, cytokinins and auxins. Maintaining or adding healthy soil biology is a great way to speed up germination and natural, healthier growth without the side-effects seen with synthetic hormones.

4) Encouraging natural disease protection and resistance. Since a tree or plant is considered the home for soil microorganisms and since these microbes rely on the sugars produced by the plant for their survival, bacteria and fungi have evolved mechanisms to protect their “home” at all costs. First, beneficial bacteria and fungi can actually produce compounds that directly kill pathogens. In fact, many anti-fungal or anti-bacterial compounds that we use for human health, including penicillin, came from bacteria or fungi. In nature, these compounds are used by beneficials to kill plant pathogens. Second, maintaining soil biology with numerous beneficial organisms will out-compete pathogens as both compete for many of the same resources. A diverse and healthy population of beneficial microorganisms makes it more difficult for pathogens to become established. In simple terms, it’s a numbers game. Lastly, pests such as insects evolved to eat dead or decaying plant manner. Pests starve on healthy plants – this is the basis of the concept of trophobiosis. Plants, trees, or turf that are healthier and more nutrient dense will be better fit to naturally fight off disease and predators, and pathogenic insects simply can’t digest healthily tissue. Plants are similar to humans in this way. People that eat well and are healthy get sick less often. Through the actions of soil biology directly increasing a plant, tree, or turf’s health through better nutrition, plants are better able and more fit to fight off pressures from disease and pests.

Sustainability through Biology

Maintaining healthy soil biology is much more sustainable than traditional practices that rely on high levels of synthetic fertilizers and pesticides such as fungicides, insecticides, etc. Most importantly for landscapers and growers, practices that build and maintain a healthy soil food web have been proven to be less expensive in the long-term. These systems also require less maintenance and labor-sustained microbial communities do the work for you. Soil Biology Basics: Part II covers the actual practices that can be employed to stimulate (bio-stimulation) or supplement (bio-supplementation) soil biology for improved care at home and by professional landscapers.

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