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Center for Regenerative Agriculture and Resilient Systems

There is no Planet B

Microbiologist Dr. David Johnson is a premiere, paradigm-shifting scientist with regard to soil biology. He studies biological diversity as it relates to healthy soil, with particular interest in the species composition required for maximal carbon sequestration and optimal system photosynthetic capacity. During a talk he recently gave at a soil health workshop, he addressed the degeneration of our food supply, and how we can fix it by changing our production practices in a way that supports living soil. 

We’re all connected

In nature, no creature is a standalone. Everything and everyone is connected. Interactions take place all throughout nature. This is clearly seen upon study of the Large Blue Butterfly in England. Ecologists fenced off a critical breeding habitat to prevent any interference from other species. Unbeknownst to the ecologists, in its caterpillar stage, the Large Blue Butterfly intentionally falls to the ground, allowing itself to be carried by ants into the ground. There, the ants feed it in exchange for a sugary exudate that is secreted by the caterpillar. Symbiosis at its finest. Unfortunately, when the area was fenced off, grazers could no longer make their way in. The grasses became overgrown, resulting in a temperature decrease of the soil, making it uninhabitable for ants. In trying to protect the butterfly from other species, these ecologist inadvertently set the stage for their extinction. Nature functions as whole systems. No species works independently of all others. 

“One little change can make a big difference in survival,” Johnson said. “This is a dynamic system. We are linear thinkers. To this point, we’ve been reductionist in our science. We just study one thing. But as John Muir said, ‘Tug on one thing, and you will find it attached to the rest of the world.’ We've been addressing symptoms instead of causes. This needs to change. If we want to survive on this planet we need to find our place within this system. In addressing the symptoms, we have unexpected consequences.”

A life history lesson

Water came about 4.2 billion years ago. Bacteria 4 billion years ago. Cyanobacteria anoxygenic photosynthesis 3.8 billion years ago. Nitrogen fixation 3.2 billion years ago. Oxygenic photosynthesis, oxygen rich atmosphere 2.4 billion years ago. Fungi 2.2 billion years ago. Ozone layer multicellular life 1.6 billion years ago. Mitochondria 1.45 billion years ago. First single cell animals 750 million years ago. Land plants 700 million years ago. Glomeromycota 400 to 500 million years ago. Then came us. We are a compilation of every novel adaptation on this planet that these organisms have developed. 

CO2 levels used to be at around 7 thousand parts per million. They are now at 400 parts per million. “Life has changed this planet completely,” Johnson said. The Cambrian Explosion and evolution of plants drastically altered earth’s atmospheric CO2 levels. Over time, organisms have adapted the ability to utilize energy from the sun and pull CO2 down in their growth process. Shelled sea critters alone pull massive amounts of CO2 out of the atmosphere, putting it into the ocean. Mammals and grassland work together to produce soil healthy enough to sequester carbon. Everything we enjoy in our society is because of the adaptations these organisms created⁠—to capture, store and utilize energy from the sun. Because of them, we have abundant energy resources (coal, oil and gas) to produce electricity for fueling industries and economies. Microbially mediated deposition of metals also allows us access to rich ores (iron, copper, and aluminum) that we can use to produce tools, machinery, etc. Many of these novel adaptations have been associated with the reduction of atmospheric CO2 levels.

“We also have to look and see that diversity is the key to survival on this planet,” Johnson said. 250 million years ago, when the continents were connected, a meteor struck the Yucatan Peninsula, completely disrupting the land mass and causing the extinction of 90-96% of earth's species. This event likely started the tectonic plates motion, causing the continents to separate. That single strike profoundly influenced the diversification of the planet. “That particular hit is why we are here if you look at this from an evolutionary perspective. Mammals developed right after this hit,” Johnson said.


10,000,000,000,000,000,000,000 biochemical reactions occur every second in the human body. “We’re talking regeneration here. You’re never the same. Your body, pretty much all of it, is replaced every four months. Everything but cells in you brain, female reproductive cells and body fatcells,” Johnson said. “We need to understand that microbes are the backbone of every organism and ecosystem on this planet. There is not a multicellular living creature on this planet that does not depend on this biology.” Humans have 10 trillion human cells and 90 trillion microbe cells. Humans have 20 thousand human genes and 2-20 million microbial genes.

Things these genes do for you...
  • Digest food
  • Generate nutrients
  • Comprise 80 percent of the immune system
  • Control appetite and cravings
  • Control vitamin synthesis
  • Detoxify carcinogens
  • Prevent allergies
  • Prevent skin diseases
  • Prevent asthma
  • Renew cells
  • Control the genes that regulate brain development, anxiety, depression, autism, arthritis, and emotional behavior
What happens when these genes are disrupted? What do they affect?
  • Cancer 
  • Inflammatory bowel disease
  • irritable bowel disease
  • Diverticulosis
  • Surgical infections
  • Liver disease
  • Metabolic syndrome
  • Cardiovascular disease
  • Diabetes
  • Obesity
  • Acne
  • Atopic dermatitis
  • Psoriasis
  • Auto-immune diseases
  • Sarcoidosis
  • Asthma
  • Seasonal allergies
  • Hormonal imbalance
  • Dry eyes
  • Response to vaccines
  • Food-pet allergies
  • Antibiotic recovery, C
  • Difficile colitis
  • MRSA colitis
  • Sinusitis
  • Influenza
  • Depression
  • Anorexia
  • PTSD
  • Anxiety
  • Autism
  • Alzheimer's dental caries
  • Body odor
  • Parkinson’s
  • Dementia
  • Hyperphagia
  • Exercise
  • Smoking
  • Alcohol
  • Breast milk vs. formula
  • Household pets
  • Artificial sweeteners
  • Prematurity
  • Cesarean vs. vaginal birth
  • Polycystic ovaries
  • Sickle cell disease
  • Amenia
  • Renal disease
  • Chronic pulmonary disease
  • Type 1 and 2 diabetes
  • Encephalopathy
  • Incontinence
  • Diarrhea
  • Rheumatoid arthritis
  • Cardiovascular disease
  • Etc…

Since the 50’s, there has been a 400 percent increase in Crohn’s disease and multiple sclerosis, and a 300 percent increase in asthma and type 1 diabetes. In 1975, 1 in 5,000 Americans had autism. Now, 1 in 59 Americans have autism. Much of this has to do with the application of glyphosate. “We need to be careful with the chemicals we’re using. We need to get away from them as fast as we can, because they’re building up in our ecosystems,” Johnson said. Chemicals that we added to the world of agriculture in the 40’s and 50’s have not gone away. They are still prevalent in the foods we eat today.

Generation after generation, we are losing diversity in stomach microbiota. We have destroyed the communities in these systems. Can we bring back a healthy community just through inoculation? Since microbiota transfers work in the human gut microbiome, can a simple inoculation of beneficial microbes restore microbiome structure and function in agricultural soils?


First, we need to understand how the system works on this planet. Changing from a bacterial dominance to a fungal dominance makes a difference. Organic matter with fungal mass results in healthy soil. Weeds are always looked upon negatively, yet they are critical in the effort to bring efficient systems back. We need to grow the right crops to balance the system.

Agriculture is controlled disturbance. Nature’s controlled disturbance was the bison on the Great Plains. Before the advent of conventional agriculture, bison would graze a certain area, deposit their dung, urine and saliva, then move on. By doing so, they inoculated a whole system. Their dung was rolled up in small balls by dung beetles, placed underground and composted in place. Since not everyone can have bison or cattle on their land, a practical alternative is compost. This prompted Johnson, with his wife Hui-Chun Su, to create a bioreactor. This invention leads to a fungal dominant and biologically diverse compost. It is like clay in its appearance and texture. Just as wine matures with age, so does compost.

Over the course of a year, you see a change in the community structure in the bacteria on the phyla level. This process is aerobic, undisturbed, with a 70 percent moisture content. This invention is meant to change a bacterial dominant system to a fungal dominant system. When applied in agricultural systems, they observed that, in ten weeks, the soils developed the ability to create as much biomass as a tropical forest does in a year. They tracked carbon and nitrogen going into the plant root, shoot and fruit, carbon going into respiration, and nitrogen going into soils. Through doing so, they observed concentration-dependent regulation by interactions between the plants and their microbial complement, finding that it’s an intelligent system. 

The food we eat today is depleted of the micronutrients we need for our health. The microbiota from bioreactors can renew, rejuvenate and regenerate the degraded system we’ve fallen into. During their first 20 months of applying BEAM (biologically enhanced agricultural management) compost, they saw a 1,100 percent increase in the availability of manganese and iron, with significant increases in magnesium, calcium, zinc, copper nitrogen, phosphorous, potassium, plus an increase in soil water storage capacity. See more research and learn how to construct a bioreactor.(opens in new window) “You’ve got nothing to lose by doing this,” Johnson said.

We can meet the challenges ahead. We can rebuild earth’s soil supply. We can increase nutrient density in our food and forage. We can use less water to grow crops by increasing both plant water use efficiency and soil water storage. We can reduce energy use in agriculture by letting nature extract these elements out of the atmosphere. We can reduce both agrichemical pollution and atmospheric CO2. We can improve productivity and profitability at the same time. Why should we do all of this? “Because there is no planet B.”