Why Looking at Your Garden Soil under a Microscope can Change Everything

by Kendra Shillington April 10, 2019

Why Looking at Your Garden Soil under a Microscope can Change Everything

by Meredith Leigh (www.mereleighfood.com)

Gardening in tune with nature very easily brings us back to soil. Regardless of whether land stewards seek to produce carrots or cattle, the soil is the key to the productivity and nutrient density of human and animal foods. While the good food movement has done well to recognize that “feeding the soil, not the crop” is the mantra for a more lasting and restorative agriculture, the means by which we “feed the soil” are still largely borrowed from an agriculture that isn’t working and as such, an incomplete understanding of the soil’s true needs.

We tend to focus on nutrients. And most importantly, macronutrients, which is to say, major plant food groups. But there are micronutrients and trace minerals which have received less focus. A decent comparison might be raising a baby and focusing on feeding her bread, milk, and bananas simply because she got fatter when she ate that stuff. And then being surprised when our overgrown baby encountered health problems because well, we neglected to give her fat, or seed, or roughage.

Oh, and one more thing. It turns out, the macro and micro food nutrients and the trace minerals aren’t always accessible, useful, or digestible without microbes. So if we purge microbes in the soil, through the use of harmful chemicals (no, not just the conventional but the other ones too) or mechanical disturbance (tiller, plow, etc), yet keep dumping in the nutrients, things are going to get out of balance. As in, baby ate too many bananas and the colon ran out of digestive oomph. Uh oh.

As with all things, there is a balance, informed by nature, which growers at the small scale and on the fringe are beginning to understand how to turn into action. To paraphrase the author Charles Massey, it’s up to us to take the best of the systems built for what we oppose, and apply them to the revolution toward what we value. The sciences of soil ecology and agronomy and mycology and microbiology have within them champions for natural balance. If we endeavor to learn from them, our gardens and our soils will prosper.

How shall we start? By looking into the soil to see what life is in it. Elaine Ingham has been doing this work for years, and large and small fractions of the growing community have listened (or not), and connected (or not) that work to the larger bodies of knowledge we have about how nature works. I’m a newbie, relatively speaking, to soil microscopy, having studied Dr. Ingham’s methods for the last five years. What I am not new to is growing food in a lot of wrong ways and a few right ways, always trying to figure out nature’s strange, starry will.

The first time I looked into a microscope at a soil sample, it changed everything about my management of food production. This is not to say that I completely abandoned protocol and forged an unexplored path, but rather that a giant and very cluttered toolbox of sustainable techniques, which I had been gathering and making heavier for two decades, suddenly organized itself into my brain and my muscles. I can now make decisions about mulching, tilling, cover cropping, amending, or otherwise managing my soil with better focus. What I’m after is a diversity of life below ground. That’s the big kahuna. If I know what drives healthy soil life, I know which tool to pick up and with what force it should be wielded. For anyone building a new paradigm, this is a gift of serious importance.

So, what is in the soil, in terms of microscopic life? And why does it matter from a management perspective? Broadly, what should be in healthy soil is an entire food web of organisms that are consuming oxygen, as well as each other, excreting and dying and otherwise creating byproducts and biomass. A few examples of the byproducts and plant benefits I speak of are carbon, special “glues” that allow soil to aggregate and hold water, new forms of plant nutrients (plant food groups like nitrogen or phosphorus), or pathways for disease resistance. This is but a fraction of the functions and benefits of a healthy soil food web. More specifically, when one peers through a microscope at soil, one hopes to find the following members of a dynamic community:

Bacteria: There are many different types. ‘Good bacteria’ will:

  • Suppress disease
  • Inhibit toxins
  • Build soil structure
  • Maintain soil pH balance
  • Hold nutrients and water

Groups of bacteria that aren’t beneficial to garden/farm soils will cause disease, release toxins, and mess up soil pH.

Protozoa: Again, many different types. ‘Good’ protozoa will:

  • Make stored nutrients in bacteria available to plants (by eating said bacteria)
  • Build soil structure

Undesirable protozoa can indicate a lack of oxygen (as can the presence of

unwanted forms of bacteria and fungi)

Fungi: Beneficial fungi will:

  • Suppress disease
  • Build carbon and larger soil aggregates
  • Decompose toxins
  • Retain water and nutrients

Undesirable fungi are in many cases plant pathogens (molds, mildews, and wilts) or will otherwise reduce optimum soil conditions

Nematodes: Nematodes are round worms. Livestock people, don’t go bonkers. The nematodes that infect your animals are roundworms, too, but there are beneficial roundworms too. Let’s discuss. ‘Good’ nematodes will:

  • Stimulate other food web groups like the protozoa and bacteria (by eating them)
  • Build soil structure
  • Further make nutrients available to plants (by eating lower level life)
  • Inhibit the ‘bad’ nematodes like intestinal parasites and root-feeding roundworms

We can quickly see that the are many, many little allies and obstacles down in the soil that by the sheer fact of their existence can make or break plant (and subsequently, animal) health. And that not only their existence but that their interaction is paramount. They have to eat each other to provide benefit. Yes, they have to eat and metabolize their food and die in order to make the system work.

So, how do you know whether the life you’re looking at through the scope is ‘beneficial’ or not? Simply by the structure, or “morphology” of the organisms. So, people like me have learned (and are still learning, mind you) to recognize physical characteristics of good soil critters and bad ones, and to notice the presence or absence of markers of their interaction. By doing this, even without counting all the different organisms in a scientific assay, or conducting gene sequencing, I can tell you quite a few things about your soil’s health and condition.

For example, many and most soils from gardens and farms that I look at have an overabundance of bacteria. They might be ‘good’ bacteria indeed, and there might be a wonderful diversity of shapes and sizes. This is a functioning system, usually, that produces food for sure, but the other thing it does is make management quite intense. Why? Because in this extreme sense of bacterial domination you encounter 1) the tying up of nutrients in the bodies of the bacteria, so that regardless of how your soil is amended, the nutrients may not be available to plants. 2) the persistence of weeds that don’t need complex nutrient availability to germinate and thrive 3) the persistence of diseases that don’t have competition from natural predators and 4) an overall “monoculture” in the soil, which is less resilient to instances of compaction, disturbance, or cataclysm.

Sound familiar? If the aforementioned soil is managed to encourage the presence of “higher trophic levels” in the soil community, like protozoa, fungi and nematodes, then the system sees a diversity that serves it well. 1) higher level organisms eating bacteria will “release” nutrients tied up in their bodies and also subsequently convert those nutrients to different forms, making them plant available 2) suppress weeds by fostering a more nutritive environment for more mature plant life 3) suppress disease by actually eating or decomposing the disease organisms that might be present and 4) overall produce a system that is less fragile.

The methods by which we encourage a diversity of life in soils are myriad, and many of them are for other posts. To name a few:

  • the use of mulches and the selection of certain kinds of mulch
  • reduction or eradication of soil tillage
  • reduction of soil compaction
  • cover cropping, and the selection and combination of specific cover crop species
  • compost making and compost application
  • compost tea making and application
  • soil amendment budgeting and application

While many of these practices may not sound new to you, the method by which they are practiced and the reason for doing them a certain way is utterly transformed by a knowledge of what life is in your soil. For example, in the example of the typical, heavily bacterial soil, would adding any old compost (perhaps a heavily bacterial compost) make sense? Not at all. This soil needs to be managed in such a way that more mature microbes can thrive. That means fungally dominant composts and mulches, less tillage, and more carbon-rich cover crops— to name just a few approaches.

The most accessible soil assessments for most growers come by way of land grant universities, and while these services are a free and easy way to assess your soil on a very general level, the method of assessment and the recommendations do not test for soil biology (the microbes that are so essential), and the recommendations provided are often in the vein of macronutrient-obsessed, more conventional management.

And so, I'm teaming up with Villagers, with the help of Living Web Farms, to provide qualitative biological assessment of soils for any type of grower. I've got the microscope. All you have to do is take samples according to the instructions provided, label them, and complete a short form, and you'll get a look at your soil that might just change everything.

Assessments are $55 per sample, and come back via email complete with pictures of the life in your soil, with explanations of what has been observed and notes for management approaches that will increase diversity and overall resilience. You may drop your samples at Villagers, and I'll come and get them from there. Services start just after Mother’s Day, when the soil is warm and the critters are alive with spring.

Order your Soil Microscope Analysis

Order your Questions? Contact me at mereleighfood@gmail.com or contact Villagers.

Kendra Shillington
Kendra Shillington


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