Center for Regenerative Agriculture and Resilient Systems

Microbes: Friend or Foe?

When It Comes to Our Health and the Health of the Planet, Microbes In Our Soil May Hold the Key

by Sheryl Karas, RAI staff

farmer and child in a crop field

Could Microbes be Our Friends? 

Well, not always. There’s a reason most of us have been taught to avoid microbes like the plague—for example, the Plague! The Black Death(opens in new window), caused by the Yersinia pestis bacterium killed 25 million people(opens in new window) in Europe alone in just four years in the middle of the 14th century. The most common form kills 50% of all people infected; two other forms are almost 100% fatal and cause a painful death in just 3-4 days. It took 200 years for the world’s population to recover and created religious, social and economic upheavals that changed the course of history. 

Certainly, the development of antibiotics, almost 600 years later, was one of the biggest advances in medical history and was so celebrated and successfully utilized that we’ve actually gone too far with it. Antibiotic resistance(opens in new window) is becoming a serious health threat and, even though most of the time they still work well, antibiotics can throw off the healthy balance of microbiology in our bodies if adequate precautions are not taken. Did you know that we could not survive without those microbes? Sometimes antibiotics are necessary but the key is balance and managing the factors that keep a healthy balance in place. 

We are also learning that a healthy balance of microbes in our soil is essential to the health of the planet. In fact, microbes actually help create the fertile soil necessary to grow healthy food which, of course, has enormous implications for our survival as a species. One of the most important features of Regenerative Agriculture is working with soil microbiology to reclaim soil fertility where it has been degraded (70% worldwide(opens in new window)), to grow the healthiest, most nutritious food possible, and—believe it or not—fight climate change! The microbes play a role in that, too.

How is that possible? 

Well, let’s start by exploring the important role microbes play on the planet.

In a seminar talk(opens in new window) at CSU Chico in 2016, molecular biologist Dr. David Johnson said, “Our planet is what it is today because of what microbes have done.” He went on to describe how bacteria have been integral to shaping the Earth for the last 4 billion years.

Bacteria first appeared on the planet about 4 billion years ago. Then Cyanobacteria, aquatic bacteria that float on the surface of the ocean (also popularly known as blue-green algae), came along 3.5 billion years ago. This bacteria developed the ability to photosynthesize energy from the sun to grow on carbon dioxide and water and gave off oxygen as waste. They eventually oxygenated the atmosphere, creating what is considered to be the first global climate change catastrophe as oxygen was toxic to most of the Earth’s inhabitants which were anaerobic at the time. It led to an enormous mass extinction and, also, to one of the world’s worst Ice Ages after the oxygen removed much of the methane from the atmosphere by converting it to carbon dioxide. Oxygen has been part of our atmosphere ever since and is what made it breathable, but not before first destroying most of life on Earth.

Other species eventually evolved to live in this atmosphere. For example, fungi started to grow about 2.2 billion years ago. The ozone built up and the first single cell animals appeared 750 million years ago. The first land plants arrived about 300 million years after that.

And the plants came with an already built in relationship with Cyanobacteria and also with fungi. The chloroplast, green plant cells filled with chlorophyll where photosynthesis takes place in a plant, is actually a cyanobacterium(opens in new window) living within the plant's cells. The cyanobacteria are the source of the chlorophyl and the cells require this in order to make their food. They are also responsible for converting inert atmospheric nitrogen into an organic “fixed” form, such as the nitrates farmers depend on as fertilizer in the soil.  

Mycorrhizal fungi have a similarly symbiotic relationship with plants. They colonize and frequently interpenetrate the roots, allowing the plants to access more nutrients and water from the soil in exchange for some of the sugars the plants provide via photosynthesis. Fossil records show that the earliest land plants may not have had significant roots, depending entirely on the fungi to serve that function.

According to Dr. Johnson, all life forms on the planet have evolved as similar “super-organisms,” including human beings. Microbes are found in our stomachs, lungs, in our mouths, and provide important functions we depend on. “We are not individuals, we are ecosystems!” Dr. Johnson says. “For every cell in your body, you have 10 microbes . . . You have a gene count of about 30,000. They have a gene count of 8 million.” 

In exchange for the nutrients and housing we provide, they help us digest our food, synthesize vitamins that we can’t get from the food we eat any other way, break down xenobiotics (foreign substances our bodies don’t recognize), detoxify carcinogens, promote cell renewal, activate and support our immune system, control our appetites and cravings, alter immune system development(opens in new window) and turn on and off genes in our bodies that regulate brain development, anxiety and depression and emotional behavior.(opens in new window) Having the right population of gut bacteria alone is critical for human health.

But global comparison studies show that there has been a significant decrease in gut microbiota diversity in modern times, possibly because of Western diets, an increase in the use of caesarian section, antibiotics and formula-feeding of infants, and over-sanitation of the living environment. At the same time there has been an alarming rise in chronic inflammatory diseases(opens in new window) such as inflammatory bowel disease, diabetes, obesity, allergies and asthma in Western societies, all of which are linked with imbalances in the gut microbiome. Research into the effect of the environment on the diversity of gut bacteria is scanty so far, but we do know that children who grow up in rural communities(opens in new window) and on traditional farms worldwide are less likely to develop these diseases than those who grow up in cities. We also know that due to the use of conventional farming techniques like tillage, herbicide and pesticide use that the microbial diversity of our soils in modern conventional Western-style farming has become quite depleted. More research needs to be done but concern is being raised about whether the loss of microbial diversity in the soil may actually be a public health threat(opens in new window).

That’s a good enough reason to be investigating soil biology in agriculture alone but according to Dr. Johnson, the microbes also play a role in sequestering carbon. Plants and trees pull the global warming greenhouse gas carbon dioxide out of the atmosphere and put it into the ground where—if the process is not disrupted— the soil biology breaks it down and stores it in the soil. Getting the balance of that soil biology correct can have enormous pay-offs. The implications could be a game changer when it comes to reversing or at least mitigating the effects of climate change.

Agriculture, Climate Change, and Carbon Sequestration

According to a report by the Food and Agriculture Organization of the United Nations(opens in new window), conventional agriculture as it is practiced today—including clearing forests for crop production, tillage, herbicides, pesticides, and chemical fertilizers, typical animal grazing practices, and the emissions caused by farm machinery—is one of the largest contributors to global warming. And, as mentioned before, many of these techniques disrupt the soil biology. That makes it almost impossible to grow crops without the external inputs (fertilizers, pesticides, herbicides) this approach requires. Leaving the soil bare after harvest, as is most common, is also a significant contributor to soil erosion and worsened soil fertility. Finding more sustainable ways to grow our food is essential for stopping the worst impacts of climate change from coming to fruition as well as providing for food security. 

Luckily, innovative Regenerative farmers have been discovering that by using practices that nurture and support the soil biology, they can restore the soil and, step by step, not only let go of many of the practices contributing to climate change, they can often grow just as much food, if not more. And, when they get to the point of being able to let go of the inputs they were using before, they can usually do so at a greater profit.

A variety of techniques are employed. The most important are to keep the soil covered at all times and keep living roots in the soil as much as possible by the use of cover crops and minimal tillage of the soil. That gives the regeneration of soil biology a healthy start. Crop rotation is used so the nutrients put into the ground by one crop can nurture another without overly depleting it. By integrating managed grazing techniques, where the animals are able to move across the property to feed and help manage weeds while distributing their manure without compacting the soil, the results are even better. And some farmers even plant trees and shrubs with their crops and grazing land to improve the soil and increase the land’s biodiversity even more.

Dr. David Johnson standing outside with his cotton cropAccording to Dr. David Johnson, getting the bacteria to fungal ratio of the soil to 1:1 is important for the best results. When there is not enough fungi in the soil, the conditions are perfect for growing grasses and weeds but not good enough for growing most vegetable and tree food crops without application of fertilizers and other external inputs. Adding normal bacteria-dominant compost (a common organic farming technique) does nothing for that, it can even make the balance worse. But by using fully matured fungal dominant compost in addition to Regenerative farming techniques the results can be impressive.

In an agricultural field study lasting 4.5 years, Dr. Johnson found that by using the fungal dominant compost he made for this research combined with no-till and cover crop techniques, he saw a 25-times increase in active soil fungal biomass. That means the fungal content of the soil regenerated itself after getting started with the compost. When the soil was tested, they found that Johnson’s fields were capturing and storing approximately 38,000 pounds of CO2 from the atmosphere per acre per year. That’s climate change-fighting carbon sequestration 20-50 times the soil carbon increase in the 40 equivalent no-till soils tested. Given that conventionally tilled soil puts CO2 into the atmosphere instead of keeping it stored in the ground, this is an extremely important finding(opens in new window) by itself.

But Dr. Johnson’s crop yields were also dramatically improved.He reported that the cotton he used in his testing grew 6 feet high and produced over five bales of cotton per acre without fertilizers, herbicides or insecticides. The average in his area is about half that. Australian farmers using similar methods have seen similar results.

Some of this research is in its infancy stages. Full instructions(opens in new window) for creating Dr. Johnson’s compost and adding to the research needed to see if this approach will work across different climate, soil types and growing conditions are available on the website for the Center for Regenerative Agriculture at Chico State(opens in new window). But there are many researcher-farmers around the world getting wonderful results with a variety of Regenerative Agriculture approaches already. You can find a wealth of information gleaned from these Mentor Farmers(opens in new window) and international researchers(opens in new window) on the Center’s website as well.