Crop Tillage, Microbes, and Their Impact on Human Health

Dr. Kris Nichols

Dr. Kris Nichols, previously at Rodale, is principal of KRIS (Knowledge for Regeneration and Innovation in Soil) Systems, an education and consulting company focused on regenerating soil as a foundation to an agrosystems approach toward resilience. It is devoted to healthy crops, food, animals, and a vital planet.

Everyone has heard the Hippocrates quote: ‘Let food be thy medicine and medicine be thy food.’ Most people nod sagely at such advice, as if it reflects some inner wisdom. Did we not, after all, evolve eating simple foods from nature and did we not have adequate eons to adapt our metabolisms to natural food — incorporating the means of creating key nutrients that were not available to us in our food (humans synthesize 11 of the 20 standard amino acids and get the rest in our foods), and losing the capability of creating others because they were so prevalent in our foods (our human ancestors lost the ability to synthesize Vitamin C, as can dogs and cats, because — so theorizes Linus Pauling –we outlived the need to do so by spending tens of thousands of years eating Vitamin C-rich fruits in trees, before being driven by drought to make a new living on the now treeless African veldt.)


Yet the more scientists research food-borne nutrients, the clearer it becomes that while plants and animals are their bearers, such organisms are not their creators. The B vitamins, for which your mother told you to eat certain foods, are a case in point. For vitamin B12, for instance, we are told to eat meat, milk, eggs and fish. Yet the only organisms to produce vitamin B12 are certain bacteria, and archaea (single celled organisms without even a nucleus). Some of these are found in the soil around the grasses and other plants that animals eat; they are taken into the animal, proliferate, form part of their gut flora, and continue to produce vitamin B12. Just a little more than ten years ago the final pathways of this synthesis were found by researchers at the Massachusetts Institute of Technology. Still unclear are the reasons B12 is made. Soil microorganisms don’t require B12 to survive, and the plants they attach themselves to don’t need it either. More than 30 genes are involved in vitamin B12 synthesis, and “that’s a lot [for bacteria, and archaea] to carry around if you don’t need to make it,” said Graham Walker, MIT professor of biology and senior author of the 2007 research paper exploring the B12 pathway. The same for vitamin B6. It is a potent anti-oxidant involved in more bodily functions than any other nutrient. Animals have lost the ability to make it, yet it is synthesized by many soil bacteria, such as Rhizobium leguminosarum, and fungi, such as Saccharomyces cerevisiae and Candida utilis.

Another interesting vitamin is Ergothioneine, a uniquely powerful and versatile antioxidant. The fact that humans have a transporter for it (a membrane protein involved in moving it across a biological membrane) in the key cells and tissues that are highly sensitive to the forces of aging — principally inflammation and free radical damage — indicates that ergothioneine protection in those cells is important to their survival. Over sixty years ago Cornell researcher Donald Melville found that ergothioneine was synthesized by fungi and transferred to oats grown in soil associated with those fungi.

Dr. Emmanuel Omondi

Dr. Emmanuel Omondi trims oat plants serving as control weeds in Shade Avoidance study at Rodale Institute greenhouse in summer 2016.

Now researchers Kris Nichols and Emmanuel Omondi, when they were working at Rodale Institute, have found that the level of ergothioneine in crops is dependent on the farming practices, particularly tillage, used to grow them. Excerpts from their 2017 Farming Systems Trial (FST) Project Report tell the story:

For the last 38 years, Rodale Institute has been conducting a side-by-side analysis of organically versus conventionally grown grains in their FST. Data on soil health parameters, yields, profit, energy input, and carbon sequestration have revealed organic agriculture to have a higher profit, lower energy input, better soil health, and less carbon emissions overall when compared to conventional farming methods.

During the 2016 growing season, research on the Farming Systems Trial (FST) was expanded beyond annual crop production to identify new techniques for managing weed pests, include an in-depth analysis of nutrient density in oats grown in 2014 and examine the links between soil health and human health.

In 2016, a new objective, to evaluate the impacts of management practices on the nutritive quality of food, was pursued. This was made possible by a decision in 2014 to plant all 72 plots of the FST to oats in order to reset the trial and update upcoming rotations to reflect current agricultural trends to address pest, disease and fertility issues. This provided an excellent opportunity to compare nutrient quality between the organic and conventional grain cropping systems in the same crop without confounding variables from different rotational crops. The project examined nutrient density measured as antioxidant content, vitamins, proteins, and minerals and linked this to farm management practices and their influence on the health of the soil.

Studies have shown that nutrient density of crop produce has been declining at rates between 10 and 50% over the last several decades. The decline has been attributed to modern agricultural technologies that have tended to focus on productivity in terms of crop yield at the expense of nutrient quality. The decline has also been attributed to degradation of soil from which crops are grown, mostly due to agro-chemical based conventional farming methods that are associated with decline in soil quality, decrease in water infiltration, increase in nitrogen leaching and ground water contamination, and depletion of soil nutrients. Reduction in nutrient availability in food crops calls for increased consumption of plant produce to obtain adequate nutrition, often leading to nutritional disorders.

Rodale’s research work on evaluating food nutrient density differences between different agricultural practices led to the establishment of a partnership be-tween research scientists at Rodale Institute with those from Penn State University Medical School and Penn State College of Agricultural Sciences. Penn State scientists have been undertaking extensive research on the naturally occurring amino acid ergothioneine (ERGO), a strong antioxidant capable of mitigating oxidative stress and chronic inflammatory diseases. ERGO is acquired exclusively through the diet and has been shown to accumulate in various cells and tis-sues of the human body such as red blood cells, bone marrow, liver, kidney, seminal fluid and the lens and cornea of eyes. Although ERGO has not yet been classified as an essential dietary component, its role as a strong antioxidant and potential for decelerating the aging process and mitigating advanced age-related ailments has recently gained great interest in medical science. According to Penn State medical scientists, ERGO protects developing red blood cells against auto-catalytic oxidation, suggesting that absence of ERGO in the diet may precipitate the genesis of chronic inflammatory diseases, or ERGO sup-plementation may mitigate the disease.

Recent research has revealed that ERGO is exclusively biosynthesized by fungi and mycobacteria and captured by plants through their roots. Based on previous studies showing that agricultural practices such as reduced tillage can increase microbial biomass, diversity, and activities, oat samples collected from the FST in 2014 were analyzed for ERGO concentration to test the potential role of different grain cropping systems and tillage practices on ERGO concentration. (Six systems were compared: conventional till and no-till, organic till and no-till using manure, and organic till and no-till using legumes). Results from this analysis found that tillage had a significant effect on ERGO concentration.

ERGO concentration was higher in conventional no-till and organic manure no-till systems compared to the other systems. No-till treatment in each cropping system (conventional, organic manure, and organic legume) led to consistently higher ERGO concentration than corresponding tilled treatments.

Results from this study also found very similar results with Vitamin B6 and Beta Glucans (Beta-glucans are naturally occurring polysaccharides that are constituents of the cell wall of certain pathogenic bacteria and fungi. They increase host immune defense and enhance macrophages and natural killer cell function.)

There were no statistical differences between organic and conventional systems for most of the vitamins measured. However, Vitamin B6 concentration was higher in the conventional no-till and organic manure no-till systems in a similar manner to ERGO concentration discussed above. While oat ERGO and Vitamin B6 concentration in the no-till conventional system were not statistically different from the no-till organic manure system or tilled conventional system, and while there were no statistical differences in Beta Glucans between treatments, these results indicate a trend showing reduction in these three important nutrients with tillage.

Use of herbicides to control weeds ensured that conventional no-till plots remained untilled since reduced tillage practices were introduced in FST research design in 2008. Rotational organic “no-till” on the other hand were tilled at least once every two years beginning 2008. In spite of this, however, ERGO, Vitamin B6, and Beta glucan concentration in conventional no-till plots were comparable to (not statistically different than) organic manure rotational no-till plots. This suggests that, had there been less tillage in organic no-till plots, the results may have been a lot more different.

This project has also inspired the establishment of a preliminary study to explore the potential for enriching crop produce with ERGO through fungal-crop cultures and interactions. The goal of this project is to determine mechanisms for ERGO enrichment in the soil and crops and to develop strategies to increase ERGO levels in crops to improve soil and human health outcomes. Recognizing that mushrooms are the leading sources of ERGO, tomato seedlings were transplanted into plots inoculated with mushroom spawn to test the hypothesis that mushroom culture would enrich tomato fruits with ERGO. A separate control treatment was maintained in which tomatoes were grown in non-inoculated plots. Tomatoes are being periodically harvested to determine both yield data and ERGO concentration. This project aims to determine the association between soil microbiology and soil and crop concentrations of ERGO, investigate the role of soil microbiology on ERGO production and plant uptake, and evaluate cultural methods that promote healthy soil microbiology.

Although I was convinced by the project that no-till practices, which allow fungal soil populations to thrive, can result in crops with higher levels of the beneficial antioxidant ergothioneine, I was confused about one point. I asked Dr. Nichols:

The report suggests that compounds with value in human nutrition are synthesized by soil microbes like fungi. Yet nowhere have I seen any discussion of what value those compounds bring to the microbes. Do you have any information about why the microbes might be doing this? Might the compounds work at a level so basic that any life can benefit from them, even microbial creatures? Or is there perhaps some symbiotic role they play as part of the fungal mycorrhizal relationship with plants? Or something else?

She replied:

Microbes make compounds, like ergothioneine, hydrophobins, biofilms, and glomalin, to protect themselves — particularly because they are often growing in environments in which there are many changing conditions including pressure, temperature and moisture conditions. In the soil, in the small, microsite environments where these organisms grow, there are frequent changes in water and gas concentrations. Fungi, in particular, make these different compounds because they have to grow through these differing environments simultaneously. For example, mushroom-producing fungi frequently grow in an aquatic environment below ground, but then grow into an aerial environment aboveground. Just like ergothioneine acts in animals, in fungi ergothioneine helps to protect against stressors, particularly oxidative stress, and provide cell wall integrity. It is important to note that although organisms differ in shapes, sizes and activities, their biochemical reactions and patterns are surprisingly similar.

I asked her for other examples of soil microbes performing complex chemical activities. She replied with this fascinating example of different soil organisms cooperating in a five-part arrangement to benefit them all:

Like with my answer above, research that I have conducted and studies that I have read about that others have performed have highlighted such elegantly complex, but simply repeated patterns of chemical and energy flow. One of my favorite examples of chemical wizardry and complexity involves five types of organisms: two plants – legume and non-legume, two bacteria – nitrogen-fixing rhizobium and phosphate-solubilizing bacteria; and arbuscular mycorrhizal (AM) fungi. The AM fungi connect the roots of both plants and allow for mineral nutrients, water and defense responses to flow between them. The rhizobium bacteria fix nitrogen for the legume plant and some of this nitrogen can also be transferred through the AM fungi to the non-legume plant. The AM fungi will trade this nitrogen for carbon (i.e. food). This process requires the rhizobium to fix more nitrogen because it now needs to satisfy the needs of two plants.

But this process of nitrogen fixation is very energy-intensive and requires the rhizobium bacteria to run the TCA (tricarboxylic acid) Cycle thirty-two times to ‘fix’ or convert one molecule of nitrogen (N2) gas into a form usable by plants. (The TCA Cycle is a cycle where a molecule called ATP (adenosine triphosphate) is converted to ADP (adenosine diphosphate) by breaking the bond between one of the phosphate groups and carbon in adenosine, which releases electrons. These electrons then provide the energy needed for nitrogen fixation.)

To keep this cycle going, new phosphate groups need to be ‘fed’ into it. Therefore, to meet the increased nitrogen demand, the rhizobium has an increased phosphate demand that it passes on to the legume. The legume then increases the phosphate demanded from the AM fungi. To help address this demand, as well as the normal demand for phosphorus, the phosphate-solubilizing bacteria colonizing or living on the hyphae of the AM fungi produce enzymes to make normally unavailable phosphate (from nearby rocks or mineral deposits) available just outside of the AM hyphal wall, where it may be easily absorbed by the fungi and rapidly transported to the plant roots.

Frankly impressed with such a level of communication and cooperation, enabling all five types of organisms to get their mutual needs met, I asked Dr. Nichols:

In reviewing some examples of other microbially-created human nutrients, like vitamins, I’ve see how commonly these products are synthesized in labs and introduced into foods to ‘enrich’ or ‘fortify’ them. Do you think such man-made nutrients are identical with the biologically created ones?

She replied:

Once the chemical structure of any molecule is known, scientists typically can find a way to chemically (or in some cases biochemically) synthesize these molecules. However, some of the things researchers are learning are how the gut microbiome processes these molecules. This research is indicating that there may be other co-factors or biomolecules that are provided in our food (when this food is naturally ‘fortified’ by being grown in regenerated soil with an active, diverse microbial community) to assist the gut microbiome in making these nutrients bioavailable to the human body. In the case of commercially synthesized human nutrients, however, these co-factors or other biomolecules may not be present, making it more difficult for the gut microbiome to provide these nutrients to the human body.