Soil Science and The Secret Life of Plants

Regenerative Cultivation Secrets
8 min readMay 17, 2021

Dr. Elaine Ingham has become somewhat of a celebrity scientist in recent years. If you’ve read or heard anything about growing with living soil, it’s likely that you’ve heard Elaine Ingham’s name mentioned. As one of the first scientists in the United States to discover the importance of soil microlife for plant growth, she was tapped to write a good portion of the USDA’s “Soil Biology Primer” in 1999. This was one of the first times that a US government body acknowledged the importance of soil biology in plant growth. But her rise to stardom began with a lot of obstacles, not the least of which was being a woman in the world of agricultural science, a field highly dominated by men.

A young Dr. Elaine Ingham

After getting her undergraduate degree from St. Olaf’s College in Minnesota, and her masters from Texas A&M, Ingham landed at Colorado State University in the late 1970s to get her PhD on developing methods to assess the activity of fungal hyphae in the soil. The technique she used is called Fluorescein diacetate (FDA) hydrolysis, and today it’s a commonly used method to detect enzymatic activity of microbes. The technique causes the areas of the organism where enzymes are the most active to light up with fluorescent light. While her project was initially narrowly focused on fungi, Ingham was surprised one day when some of the Fluorescein diacetate accidentally made it onto a microarthropod crawling through her soil sample. The creature was lit up with fluorescent light, demonstrating that the technique could be used for much more than just fungal hyphae. That got Ingham curious, and she started wondering if the technique could also be used on the nematodes that her husband was studying for his PhD, or on bacteria and protozoa.

When she proposed this idea to her PhD supervisor, he suggested she go around to all the Professors who were studying microbial life and ask them if such a project was a good project, with the emphasis being on whether or not such a project could land her a job after graduation. So she made the rounds and told several professors — who were all male at the time — about her idea to study the various soil microorganisms. “They all responded with the same condescending, horrified look,” Ingham recalls. “They all basically said ‘these organisms don’t do anything.’ But my thought was, these organisms have been on this planet doing their jobs for the last 3.5 billion years. And you’re telling me mother nature has no purpose for them? That was when I saw what I was up against.”

So with some trepidation, she started working on this project. After she finished writing her dissertation, she started giving talks about it around the country. “But the university folk were still not fully convinced that these organisms have a function.” But perhaps underneath this skepticism was something more sinister. This kind of thinking could really mess up the whole agricultural system and the multi-billion dollar chemical industry, if it were true that something besides fertilizers could cause plants to grow big. To Dr. Ingham, this was just common sense. How could mother nature not have a system for cycling nutrients? Moreover, every inorganic fertilizer is technically speaking, a salt. That means that they take water out of an organism’s body. Too much salt will kill them. She began to see that our modern agricultural system had ensured that nutrients in the soil cannot be cycled naturally, and fertilizers would continue to be required.

Over time, attitudes began to change, but it was a long, slow process. Even when she later became the chief scientist at Rodale in 2001, and gave a talk at an NRCS meeting about what she had by then come to call the Soil Food Web, she recalls “all the guys from the agricultural school at Rutgers lined up against the back wall and stood there, with nasty looking faces,” she recalls. “It seemed like they were thinking, ‘we’re determined to find holes in what you’re talking about.’” Today, attitudes at Rutgers have changed. Dr. James White is among the younger, rising stars at Rutgers, and his work revolves around studying endophyte species — microbes that live inside and have benefits for plants.

Since starting this work over four decades ago, Dr. Ingham has devoted her life to spreading the word about what she calls The Soil Food Web, and how farmers and growers can harness it to grow high yielding, healthy plants with no synthetic inputs.

Dr. Ingham was one of the first scientists to fully see the picture that was unfolding at the end of the 20th century as microbiologists, aided by more powerful microscopes, began to examine soil microbial life more and more closely. What they found is causing the greatest shift in agriculture since the invention of synthetic nitrogen fertilizers over 100 years ago. Remember how Liebig discovered that plants were consuming Nitrogen, Phosphorus and Potassium (N-P-K), not humus, as scientists had previously thought? This led them to believe that humus — otherwise known as soil organic matter — was not as important to the growing process as previously thought. However, what we now know is that soil humus, although composed mostly of carbon, hydrogen and oxygen, is in fact a reservoir of N, P, K and all the micronutrients plants need. Not only that, but perhaps more importantly, it creates a habitat where microbes like bacteria, fungi, protozoa and nematodes can live, and these microscopic creatures are what make these nutrients available to plants.

Elemental nutrients like Nitrogen, Phosphorus, Potassium, Calcium, Magnesium, Sulphur, and others, all exist readily in nature. In fact, some speculate that most soils contain these elements in enough abundance — either within the organic matter or in the mineral component of the soil — to provide plants with as much as they need. The reason why plants can still experience deficiencies even when grown in soil is that those nutrients may not be in a form that the plant can readily consume. It’s just like digestion for humans. We need our stomachs and intestines, which are full of microbes, to break down the food we swallow, and turn it into a form that our bodies can absorb and benefit from. Plants require the same thing. So feeding plants synthetic nutrients is like a person getting fed intravenously. Sure, that person is getting the nutrients they need, in a form they can consume without digestion, but are they going to make them happy, healthy and fit if they continue to receive nutrients that way in the long run? Probably not. An IV is typically an emergency measure, when a person’s health has already deteriorated.

So it’s microbes that find the nutrients plants need in the soil, and deliver it to the plant, in just the right amounts, at just the right time. But why would the microbes do this? What’s in it for them? And how do they know better than us what the plant needs? It turns out that plants and microbes, through millions of years of evolution, have developed a form of communication. And through this communication, they have even set up a sort of nutrient marketplace that David Montgomery likes to call the “Biological Bazar.” What this means is that plants can tell microbes exactly what they need, and the microbes can bring it to them. Now, while I know some growers will talk to their plants, I don’t know of any growers that can claim to have had their plants talk back to them, and understand what those plants want (at least not sober, and not with a straight face).

How do the plants communicate? Through the process of photosynthesis, they produce sugary substances that are not found in the soil, and excrete them through their roots to feed microbes. These excretions are called Exudates. Soil microbes are attracted to these exudates, and flock to the plant’s roots to consume them. But they don’t come to the market empty handed. With them they bring nutrients to feed the plants. There is a wide variety of microbial life in the soil, and different groups of microbes specialize in bringing different nutrients to the plant. Therefore, not all exudates are alike. In fact, the plant will tailor the composition of the exudate to attract specific types of microbes. If the plant is experiencing a deficiency in Calcium for example, it will excrete an exudate formula specifically designed to attract microbes that will bring available Calcium to the roots. Not only that, but the proliferation of these microbes will also temporarily adjust the pH of the soil so that Calcium uptake can be optimized.

Compare this to the difficulty ensuring your plant is getting just the right amount of Calcium with the synthetic approach. When a plant is fed a product like CalMag, the plant stops producing the exudates to feed the microbes responsible for bringing them Calcium, and those microbes die off. Now the plant is dependent on the grower to feed them just the right amount, and to make sure the soil pH is just right for Calcium absorption. The ratio of Calcium to Magnesium also has to be just right, otherwise one of these nutrients could lock out the other, thus a product like CalMag is commonly used. But what if the plant is experiencing an excess of Nitrogen and a deficiency of Iron at the same time? Excess Nitrogen can be easily washed out of the soil because it’s highly mobile. But Magnesium is also highly mobile, and will be washed out just as easily. After the washing, calcium and magnesium are present in the wrong ratios, and we’re back to having a potential Calcium deficiency. The Iron deficiency can be fixed by lowering the pH of the soil, but now the pH is too low for calcium and nitrogen uptake, and suddenly the grower has gone from an excess of nitrogen to a deficiency. Another element that is easy to be deficient without living soil is Phosphorus, which is key to improving and energizing the rooting and flowering process. Phosphorus can get locked up in synthetic systems that lack soil microbes quite easily, thus leading to plant deficiencies.

All this complexity can be solved by dropping the synthetics and letting the Soil Food Web take care of everything. Compared to chemical fertilizers, organic matter is slower releasing, which means there is less of a chance for overfeeding or nutrient burns. This makes organic matter, in a sense, much safer to use. The plants will tell the microbes what it needs through producing the right exudates, and the microbes in turn will make sure the soil pH is adjusted to the right level to allow those nutrients to be consumed by the plant. As long as the soil has an abundance of organic matter and a diversity of microbes, the system will take care of itself. After all, this is what microbes and plants evolved to do over hundreds of millions of years. To think that we humans can replace and do better than this extremely complex soil ecosystem with just a few decades of experience is nothing short of hubris. To be clear, we don’t blame the individual grower or farmer for thinking they can outsmart mother nature with modern chemicals. The military-agro-industrial complex has done such a good job ingraining this belief into our society that they’ve got just about everyone fooled. It’s time to start taking advantage of the science that has now verified why some ancient farming practices have kept soil fertilize for thousands of years.



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