Microorganisms: Making miracles in the soil

In the 1958 textbook Introduction to Soils, there is one modest chapter about life in the soil, and that’s about all the “Ag” students got. It includes the macrofauna (visible life forms; now called macroorganisms): mammals, earthworms, mites, millipedes, insects, and slugs. Then a few pages cover all they knew about microscopic organisms: protozoa, nematodes, bacteria, actinomycetes, fungi, and algae. They called them microflora; now we say “microorganisms.” I pity the students who had to memorize those texts. It was dry going. There was no excitement in the writing, no wonder at the processes they couldn’t explain. Yet the chapter was describing miracles. 

What we do and do not know

I am not a soil scientist, but for several decades I have studied and taught organic gardening, and headed hundreds of soil science classes. And wow, has it all changed. What those 1950s scientists focused on was the mechanical or physiological aspect of soil composition and soil building—how the organisms affected soil structure. But they only guessed at the rest of the story: “Symbiotic fungi live on the roots of certain plants, and both fungus and plant are mutually benefited … It is presumed that mycorrhizae aid the host plant in the absorption of certain nutrients.”

And those statements summarize what soil scientists have been working on ever since, with mind-blowing breakthroughs. Now it’s all about the biological process of soil building—how living organisms turn organic material into forms that plants can use, and how mycorrhizae enable nutrient absorption. The field is so dynamic and so vast that one university scientist told me, “We know more today about outer space—the universe—than we know about the life beneath the soil!” What an opportunity for young scientists, if we can only engage them.

Applying what we know

For practical purposes, three conceptual breakthroughs have changed the way many of us treat our soil and the life in it. 

1. Soil is full of living organisms that help our plants, and those organisms have needs.

Once we know that, it’s almost impossible for a gardener to see soil being wasted or damaged without wincing. There are life forms in there that require air spaces, moisture, and organic matter to live, so how can we drive trucks on it or walk over that soil? And it’s obvious we should keep putting organic matter into the soil. These ideas are no longer news for most of us. It’s basic knowledge, but it drives the choices organic farmers and gardeners make—about garden layout, tilling (or not), composting, cover-cropping, and soil amendments. We know there is precious life in the soil, so we work to protect and feed the organisms. 

2. Synthetic fertilizers and pesticides alter or damage soil life.

As a beginning organic gardener it was clear to me why I wouldn’t use pesticides, but I didn’t see the harm in using some 5-10-5 or 10-10-10 fertilizer to boost my crops. Then I read reports from Rodale Institute and some land-grant colleges revealing that earthworm counts were radically lower on plots fertilized with the synthetics, compared to manure or no fertilizers at all. That was reason enough to stop using synthetics.

It was also enlightening to read Eliot Coleman’s wonderful book, The New Organic Grower (Chelsea Green, 1989), that is often considered a textbook for contemporary organic farming. He took this position on the farming question about using purchased products such as fungicides, fertilizers, etc.: “… I simply do not know enough to tamper with the natural system … the intricate cyclical systems of the natural world, and I prefer to study them in order to make less work for myself, not more. … I would rather let it be done for me by the real experts. The real experts in this case are all the processes that take place in a fertile soil—the interrelated activities of bacteria, fungi, dilute soil acids, chemical reactions, rhizosphere effects, and countless others we are unaware of.”

He concludes, and I agree, that the natural world with its soil-making machinery is an amazingly efficient system. Our job is to give it the raw materials to work with, and not mess it up.

Fifteen years later, in Teaming with Microbes (Timber Press, 2006), author Jeff Lowenfels presented weighty evidence that synthetic fertilizers also damage the microorganisms that plants need. Simply, we should provide the organic matter and back off. 

3. Plants require particular communities of organisms to absorb the nutrients in the soil, so it does matter what kind of mulch and compost we use.

Lowenfels’s book presented this case clearly, and it was a game-changer for many gardeners. We’d known for some time why rhododendrons required acidic soil in order to thrive: The mycorrhizae that live on rhododendron plant roots, that transfer the nutrients from the soil to the plant, can only live in an acid soil. Alkaline soil supports the wrong kinds of mycorrhizae for rhododendrons, so the plants will be starved, literally, of nutrients that are right there in the soil.

But it goes far beyond the acid/alkaline story. Every natural plant community has an optimum soil, containing a specific composition of soil organisms. When we put down any old compost and any old mulch around our plants, we may be radically disturbing the microorganism community (even if we’re doing the other good things that mulch and composts do). For instance (the simple version), most woody plants have mycorrhizae hanging around their roots that require a fungal-based organic matter. So we use chopped leaves, leaf mold, shredded pine bark, and woody chips, around those shrubs. But vegetable plants and many flowers (or actually, their related mycorrhizae) are better helped by mulches such as straw, grass clippings, plant scraps, and nearly finished compost. Those have predominantly bacterial populations that are basically better munchies for microorganisms. Who knew?

Now we have whole books on the soil food web, starring microorganisms, and I’m drastically simplifying the information. But ultimately, it boils down to a complicated process that works very well in nature. We garden, so we’re messing with things; we’re doing the unnatural. So the least we can do is to learn what serves the systems already in place. Don’t kill the soil organisms. Add organic matter to feed them, thereby building the soil. Then figure out what kind of compost and mulches work best for the invisible workers that serve the plants you’re growing. So much is going on down there—miracle after miracle. The more we know, the more we wonder.          



Sally Cunningham is the author of Great Garden Companions (Rodale Books, 1998), and contributor to many gardening books including The Encyclopedia of Organic Gardening (Rodale, 2009). She is also a garden consultant, lecturer, and TV gardening advisor. She composts, and gardens organically.  


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