Renewable Farming

Soil health needs an abundance of microbes, especially “good fungi” that build humus

Renewable Farming team member Blake Carlson returned from the Bionutrient Food Association’s “7th Annual Soil & Nutrition Conference” in Southbridge, Massachusetts, loaded with ideas on improving soil health and human nutrition. 

Dec. 8, 2017   By Jerry Carlson — One of the most significant conference themes was how the blend of microbial communities impacts total nutrient uptake into grains and other crops. Linked with this is the growing realization that pesticides, anhydrous and salt-laced fertilizers distort the populations of soil bacteria and fungi. 

After returning home, Blake copied me on an e-mail exchange he had with a friend, an Iowa organic grower. Blake gave permission to publish his comments and his friend’s, as their comments carry much of the conference message. Here’s an excerpt from that message:

Dr. Elaine Ingham

Blake: At the Bionutrient conference, keynote speaker Dr. Elaine Ingham stressed that it’s very important to have a diversity of plants in your soil throughout the growing season. Each kind of plant puts out certain exudates through its roots. These exudates encourage specific organisms. That’s basically what I heard at an ACRES conference last year from Dr. Bob Kremer, USDA microbial scientist. He estimates that each species of cover crop stimulates colonization of ten microbial species — bacteria and fungi.

Ingham said that when you look at a root under a microscope, you want the roots to have what looks like dreadlocks around the root hairs: colonies of organisms living in that rhizosphere. Those colonies include both bacteria and fungi. 

Minimizing disturbance using no-till seems to be more important the more I learn, especially for the long tendrils of fungi, such as mycorrhiza and actinomycetes.

Friend’s response: The growing plans that I make this winter are going to be much more diverse, with vegetables, cover crops, flowers interspersed.

Here’s a great quote about that from Mycorrhizal Planet: “The real impetus behind gardening with mulches, digging with broadforks, shallow cultivation, forest-edge orcharding, no-till farming, low-impact forestry, and everything permaculture is to disturb the soil as little as possible. This in turn allows the fungal dynamic to thrive. Virtue lies in doing less so as not to screw things up, a tenet that I suspect most of us can handle.”  

Blake: I’ve learned here on our farm that when you use inorganic nitrogen fertilizers which contain certain salts and acids, these compounds greatly reduce beneficial organisms which would otherwise be making nutrients available to the plant. Christine Jones confirmed that. Her research can be found on

Inorganic nutrients make the plant more dependent on mineral fertilizers, which at first give you lush growth but a cruddy root system — because the plant doesn’t need to create a healthy root network. 

When a plant grows in undisturbed soils and relies more on natural nutrients, a wider variety of fungal and bacterial microbes colonize the roots. They thrive on the root exudates including the sugars, amino acids and a blend of other energy sources. 

It’s a symbiotic relationship. In turn, the fungi and bacteria convert soil minerals to plant-available nutrients. This happens with complex microbial and mineral interactions. Beneficial fungi produce compounds to unlock minerals. Dead microbes are eaten by larger organisms; then the larger organisms release excess food for the plant to take up in soluble forms. The crop root absorbs whatever the plant needs, just when it needs it. 

God designed this system so when you’re doing it right, there is almost no nutrient runoff. At the Bionutrient Conference, Elaine Ingham emphasized the composting of a huge diversity of carbon-containing materials. Each type of organic material favors its own types of organisms colonizing around it. So when many different materials are composted, there is a diversity of aerobic organisms. The “good fungi” are especially important as they’re the main builders of active humus and glomalin, which hang onto plant-available soil nutrient elements.

Key words here are “diversity” and “aerobic.” Elaine Ingham said to inoculate your growing area, too, with known sources of beneficial microbes. She recommends checking those populations with a microscope. I personally think I can do this just by “composting” on site. 

With a huge diversity of different plants on the mulch and compost, they will all bring a variety of microbial life. “Inoculating” on site this way means less work. And in theory it means more gained: Whenever it rains, water filtering through the decomposing mix of mulch goes to the roots and soil. 

Friend’s response:That’s the way I plan to do it, also.  

Blake Carlson

Blake:  I recommend using the Haney soil tests to check the level of biological life along with nutrient availability. Microbial respiration, measured by the Haney procedure, is an indicator of how well soil organisms will be mobilizing mineral nutrition. 

If you go to a healthy forest and sample an average soil, a standard soil analysis with strong extract solutions will probably indicate it’s low in several NPK and mineral elements.

But in reality, life in the soil is eating, living and making nutrient/mineral transfers every minute. So there aren’t massive amounts of plant-available nutrients just sitting there waiting to be washed away. 

So through photosynthesis the plant creates a cocktail of certain exudates such as sugars, starches, protein synthesis and lipid formation and other compounds according to what it needs. All this complexity takes time to build, but gradually it allows the grower to trim back on purchased fertilizers and create wider profit margins. And meanwhile it can also strengthen the crop’s ability to fend off disease attacks.  There’s a wealth of detail on Dr. Elaine Ingham’s website at

Friend’s response: Well-nourished plants can resist pests and diseases if their metabolism can complete four steps.

  1. It starts with photosynthesis that creates sugars.
  2. Then protein synthesis.
  3. Lipid formation.
  4. Finally metabolites formed for the plant’s immune system. 

Each one of these steps needs trace minerals provided by fungi that search them out and deliver them to the plants, so the environment needs to have minerals available and an environment suitable for fungi. When those things are not there, then the sugars, proteins, and lipids manufactured stop at the simple level (glucose for the sugars, amino acids for the proteins) instead of the complex structures that are built when minerals/fungi are available.

Since pests and diseases cannot digest the complex sugars, proteins and lipids —  they are drawn to sources of glucose and amino acids which are the building blocks for them, so the weak plants are the ones that they attack (the ones without minerals and fungi).  

Blake accompanied leading Iowa crop consultant Bob Streit to the Bionutrient Conference. They attended a pre-conference unveiling of a new, portable “nutrition testing” instrument which promises the ability to instantly indicate elemental composition of foods. We mentioned this event in a Nov. 17 report.

Basically, a wide-spectrum beam is focused on the food, and a sensor reads the spectrum of reflections. Variations in measured wavelengths indicate the product’s minerals and other components.  The catch: It’s going to take a lot of database building to correlate the readings with the quantities of each element. 

That’s the “body of knowledge” which has to be the foundation for any new measuring tool, such as sap testing. The developers intend to make this database building an “open source” project.  The meter will be foundational to the Association’s “Real Food Campaign” — background facts at this link.

Update Dec. 9, 2017 — Upon reading the article above, Hal Brown of Mulberry, Indiana sent a new photo of his cover crops plus observations on soil health in organic versus cover-cropped land. The cover crop photo shot Dec. 7 is an update of one Hal took on Oct. 13. The field was drilled with a Horsch Pronto Air Drill on Sept. following soybeans. The mix was oats, tillage radish, turnips and flax. Hal notes that “Oats and flax are very mycorrhizal,” backing what Dr. Ingham and Dr. Kremer have observed: Each species favors certain microbes. The grasses — flax and oats — favor the beneficial mycorrhiza which are the primary builders of stable humus.

The first photo is the one that Hal shot Oct. 13. The second was shot Dec. 7.

Above: Cover crop as of mid-October


Above: Same field on Dec. 7, 2017


Hal observes that “No way tillage can do what these covers do.” He added these perspectives: 

“I sampled soil from the organic farm we rented last year, and sent it to Ward Labs to get Haney tests.  The rented organic farm is our lowest-testing farm for soil biology … very low.  After 10 tillage trips per year, no wonder. Where we no-till, use cover crops and manure, the biology is quite high and fields yield more. But we are scorned by our neighboring tillage farmers. No-till by itself is not in the same league as it is with cover crops. There are hardly any cover crops besides ours in this area of the state. Are we perfect with our practices? No. Always room for improvement.

“I have heard Elaine Ingham many times — the compost tea expert. I don’t have a phD; just a B.S. in agronomy from Purdue (which Michael Horsch calls the ‘Harvard of all ag schools.’ What I know today wasn’t learned at Purdue. That all started with me reading your LandOwner newsletter; that’s what got me initiated. I always look forward to your next article on the Renewable Farming website. Thanks again. For my journey, I also thank Dr. Skow and Wendell Owen of International Ag Labs. And Dave Larson, founder of AgriEnergy Resources. The cover crops were basically self-taught.”