Cindy Shapton writes, speaks, blogs and ponders life beneath her garden clogs with her canine helper, Rosie. Get a copy of her book The Cracked Pot Herb Book at

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by Cindy Shapton    

When you are digging in the garden do you ever wonder about the world down under? I’m not talking about Australia but the microscopic life that lives just under our feet. An unseen communal of bacteria, fungi, nematodes and protozoa – microorganisms that may be micro-small but are macro-mighty when it comes to building healthy soil.

Resist working up soil before planting so as not to tear up long strands of fungi networks.

In case you can’t recall from biology class or maybe never really understood the whole microorganism business, here is a simple breakdown as to why these tiny guys (and gals?) are so important.

An island in your yard for trees and hardy perennials mulched with wood chips will help create the right environment for fungi to thrive and lessen any compaction problems.

Microorganisms down under work 24/7 to:

•  Decompose organic matter

•  Replenish soil nutrients

•  Make humus

•  Help roots grow

•  Get nutrients up to the plant

•  Break down herbicides and pesticides

•  Destroy “bad guys”

•  Help control diseases

And you thought soil was boring, right? Turns out there is an underground community of microbial workers that combine their natural talents to form a balanced soil food network that helps make your soil happy, healthy and productive so you can grow the best possible plants.

So, we can all agree that bacteria, fungi and nematodes are vital to healthy garden soil, but without a powerful microscope how can we be sure we have a good supply of microbes?

With some old-fashioned common sense and a few questions, I feel confident you can deduce your garden’s microbial condition by asking yourself a few questions:

1. Do you use chemical fertilizers? In plant and soil science classes I was taught that plants see no difference in organic or inorganic (Chemical) fertilizer. Well, they may not see the difference but the results are definitely different and once you start applying chemical fertilizers you have to continue because, you guessed it, created addicts.

Vegetables and annual flowers do best when the soil has a higher ratio of bacteria to fungi.

Straw mulch in the kitchen garden provides more food for the bacteria that help veggies grow.

This may sound harsh, but the truth is, when you apply chemical fertilizer you kill off mass amounts of microbes so the plants become dependent on the inorganic fertilizer and can’t do without it.

2. Is rototilling or turning soil part of your spring and fall garden ritual? This may seem like a good idea, spread some fertilizer or compost, and then work it into the soil. In reality, rototilling and hand digging or turning actually breaks up long strands of fungi and makes the soil particles so fine that there are no longer any air pockets, devastating soil structure along with microbe diversity, two very important factors of healthy soil. Along comes rain or overhead watering and the soil starts to compact, plus you have brought weed seeds into the light that now are happy to germinate.

3. After a good rain, does your garden puddle? This is one sign that your soil is compacted and doesn’t allow drainage. Compacted soil changes in structure and chokes out microbial diversity. Nematodes and protozoa become small in number or disappear, while many fragile root fungi (mycorrhizal) drown which causes an imbalance – making your plants at risk for nutrient deficiencies, disease, root rot and perhaps eventual death.

If you answered yes to any of the above questions, you probably already surmised your underground friends are struggling, died an ugly death or simply vacated the premises. But no worries, you can fortify or rebuild a microbial network with a little know-how and some muscle in as little as six months.

Step one: Add organic matter and some homemade microbes in the form of compost. Compost and compost tea (use an aquarium pump to bubble tea) are teaming with microscopic life to add to or create a community of microbes doing their jobs to boost your soil’s ability and fertility to grow healthy flora by working together.

Compost will also help the soil structure by adding space for air and allowing water to drain properly. Aerating compacted soil and spreading a ½-1 inch of compost will go a long way to get the healing process started.

Raised beds are a creative fix for areas that have been compacted or where the amount of soil is impeded by rocky terrain or heavy soil that doesn’t naturally drain well.

Step two: As gardeners we know that mulch helps to keep moisture in and weeds out of our soil but it also helps to keep soil from compaction. It is also vital to our hard working microbes since they like many of us really love to eat. Applying green mulches like grass clippings, straw, alfalfa meal and comfrey around annuals and vegetables will ramp up needed food sources for bacterial microbes which are necessary for good growth and development.

Trees need mycorrhizal fungi to grow strong roots help resist diseases.
Raised beds help microorganisms thrive and are a quick fix for rocky terrain or areas that don’t drain well.

Most trees, shrubs and perennials need a soil with more fungi activity (think forest floor) so spreading a layer of brown, carbon mulch like woodchips, pine straw, and brown leaves can help create the right environment for fungi to thrive. Up to 2 inches of mulch should be plenty.

Mulch spread on top of compost works like a microbial sandwich inoculating both the soil and the mulch to amp up bacteria and fungi production. But, according to Jeff Lowenfels and Wayne Lewis, authors of Teaming with Microbes, to have an even bigger effect on plants, a nutrient cycler needs to be added on top of the mulch in the form of what they term as a “protozoa soup.” This soup is easy to make yourself by soaking fresh grass clippings, alfalfa, hay or straw in de-chlorinated water for three to four days. They recommend an aquarium air pump and air stone to keep the soup aerobic. Simply pour soup on top of mulch and get ready for some great results.

With the right environment and a little help from millions of unsung microbial heroes, you can have soil that is alive and kicking, which in turn grows strong, healthy plants, which makes you look good and just might create a little garden envy in your neck of the woods.


A version of this article appeared in a May 2015 print edition of State-by-State Gardening.
Photography courtesy of Cindy Shapton.


Posted: 05/01/17   RSS | Print


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