CO-Horts Blog

Tuesday, May 13, 2014

Soil Microbes: Your Silent Partner in the Garden

Eric Hammond- Adams County Extension

When most people think of bacteria, fungi and amebas they think of ear infections, sniffley noses, antibiotics and brain-eating single celled organisms contracted from improper use of a “neti pot” (maybe that last one is just me).  However, the soil in your yard in garden is full of these microscopic organisms as well as many others like nematodes, algae and actinomycetes (a word which I have not once pronounced correctly in my entire public life).  As the soil warms this spring they are starting to become more active and for the most part they are doing great things for your lawn and garden. 


Nutrient Cycling (Mineralization)-

Soil microbes feed on organic material decomposing it.  As they do this nutrients are taken from complex forms which plants can’t adsorb (or at least do not commonly absorb) to simpler forms that they can.  For example, in plant material nitrogen is incorporated into the molecules making up the plant’s DNA, cell walls and other structures.  As soil microbes digest this material some of this nitrogen is released into the soil solution as ammonium or nitrate, the two forms of nitrogen commonly absorbed by plants.  Without soil microbes plant nutrients in organic matter would remain tied up in unavailable forms.

Mineralization nitrogen from organic forms to nitrate- diagram by Ray Daugherty


Soil Structure-

Both soil microbes and larger soil fauna help build structure in soils.  There are several mechanisms through which this happens.   Some soil life such as earthworms create large continuous pores through the soil allowing for increased and deeper infiltration of air and water into soil.  Soil microbes affect soil structure by producing compounds that act as binding agents.  These compounds help the various elements of the soil (groups of clay platelets, chunks of organic matter, granules of sand and etc) aggregate, forming structures with a good mix of smaller pores that the can hold water against gravity and larger pores which drain rapidly and are commonly filled with air.
Desirable soil structure has a variety of pore sizes

Plant Symbiotic Microbes-

Some microbes have symbiotic relationships with plants.  Generally these relationships involve the exchange of carbohydrates from the plants in return for nutrients or water from the soil microbes.  The two most common examples of these types of soil microorganisms are Mycorrhizal fungi and Rhizobia.   Mycorrhizae are a group of symbiotic fungi that grow in association with plant roots.  They receive carbohydrates from the plant and in return supply the plant with water and nutrients- most commonly micronutrients and phosphorus.  The fungi are better able to extract tightly held soil water and less soluble forms of some of these nutrients than the plant.  It should also be noted that these relationships are species specific.  A given species of Mycorrhizae form symbiotic relationships with specific groups of plants.  Rhizobia are a group of bacteria which colonize the roots of the legume family.  They are capable of fixing gaseous atmospheric nitrogen into a form that the host plant can use.  In return the plant supplies them with carbohydrates.
The white hairs are Mycorrhizal fungi

Encouraging Beneficial Soil Life

There are a few simple things that we can do as gardeners to encourage these beneficial soil organisms.  Happily, many of them are things we already do to encourage good health in our plants (what a coincidence). 

1) Provide a good habitat-

Soil microbes need both food (organic material) and oxygen to complete their life cycles.  In natural systems, organic matter is added each year through natural cycles (think of leaves dropping in the fall in a forest).  In some portions of urban landscapes we can adopt practices that mimic this.  For example, we can leave grass clippings on the lawn or mulch leaves into the turf in the fall instead of raking them up.  In other areas, like a vegetable garden, organic matter must be added to replace that consumed by soil microbes.  Generally 2”-3” of plant based compost or 1” of manure tilled in at least 8” deep is the recommended application rate for vegetable gardens or annual flower beds (more information here). 

Potential soil organic matter is often removed from landscapes

Soil microbes need oxygen to perform respiration (the process which turns carbohydrates into energy).  So taking steps to alleviate and\or avoid soil compaction (which reduces the amount and size of large air-holding pores) such as regular aeration of lawns, raised bed gardening and using wood mulch around perennial beds, trees and shrubs may also encourage beneficial microbes.

Basic formula for respiration
2) Avoid excessive tilling or other disturbances when possible especially if the soil is very wet-

Such practices can have a number of negative effects on soil microbial populations.  They can destroy aggregates, degrading the soil’s structure, which in turn can create issues with aeration and drainage.  This is especially true if a more aggressive form of tilling such as rototilling is used at a time when soil aggregates are already fragile, such as when they are very wet.  Such practices also increase the rate of decomposition of soil organic matter by exposing it to the oxygen in the atmosphere.   Excessive tilling can also harm soil microbes by physically damaging them.  Fungi and actinomycetes are particularly at risk because of their larger thread-like bodies.

This is the great paradox of organic amendments and soil life.   There are situations where we need to add them to the soil regularly to replenish soil organic matter.  However, in doing so we are disturbing soil life and degrading its habitat.  We can minimize the damage by using less destructive methods to amend.  For example, instead of using a rototiller to mix in annual amendments, consider an old fashioned shovel or a broadfork (there are several informative videos about the use of broadforks that can he found here -no endorsement or criticism of these specific products is implied).

There is a lot of discussion about whether or not inoculating your soil with microbes is helpful.  I won’t rehash it here, but you can find a bunch of discussion about it on the garden professors blog.  Here is my attempt to sum up the topic in few sentences:  If the soil has conditions favorable to beneficial soil life (well aerated, moist and has adequate organic matter) you probably already have a healthy population of soil microbes or will develop one over time.  If a soil is low in organic matter and\or is poorly aerated any soil microbes which you add are unlikely to thrive anyway.    

There are some proven benefits to specific inoculations.  For example in a first time garden inoculating the soil with Rhizobia maybe beneficial if you are growing beans peas or other legumes.  Likewise specific species of Mycorrhizae may be used to aid in the production of specific plants, however, research on their wider use is mixed.

More information on soil life can be found in Colorado Master Gardener Garden Note #212 


  1. Great blog, Eric! Soil really is amazing. And by the way, I am now going to throw my Neti-pot in the trash.

  2. Just boil the water first. Then you can continue to flush your nasal cavities with confidence! Also I fixed a couple types….Opps

    1. err typos... I may have an issue