Infectious microorganisms grab the news headlines. Meanwhile, the beneficial microorganisms we rely on remain mostly unappreciated. They keep our living world (and a good chunk of the nonliving one) up, running, and interconnected.
Most of the living things on Earth are microorganisms, or microbes. A teaspoonful of healthy soil contains more microbes than there are people on Earth. Microbes play starring roles in plant and animal survival, and in maintaining soils, biodiversity, water supplies, and climate stability.
Food production practices have killed or disrupted many of the microbes that help maintain the health of our planet and its inhabitants. If we restore the microbial life in agricultural soils, we can upgrade our food, health, environment, security, and prosperity.
The way we produce our agricultural products matters because food is the most basic way we fit into the web of life. Poor diet causes more human deaths globally than any other health risk. And our flawed food system — which includes growing, processing, storage, distribution, and waste management — generates widespread environmental impacts. It is the number one cause of biodiversity loss, climate change, soil depletion, and water depletion.
Microbes include bacteria, fungi, viruses, archaea, protozoa, algae, and other life forms. They have been found as far as ten miles below the Earth’s surface and in the stratosphere five miles above it. A single species — for example, the bacterial species Micrococcus luteus — may reside in soils, plants, and humans.
Plants and animals, including humans, evolved from microbes. And most plant and animal cells contain structures that likely evolved from engulfed microbes that once lived free. These include mitochondria, the “power grids” in plant and animal cells with their own sets of DNA, which are similar to bacterial DNA and about the same size. Like bacteria, mitochondria can create copies of themselves. Some regions of the human brain have as many as two million mitochondria per nerve cell (neuron). These structures also include chloroplasts in plant cells, which produce carbohydrates and oxygen from sunlight, carbon dioxide, and water.
Microbes Grow Us
Microbes cover the surfaces of the human body, inside and out — for example, in the skin, mouth, and gut. Bacterial cells alone outnumber human cells by 10 to 1, which means that more than 90 percent of the cells of our body are microbes. Because of their small size, microbes make up only about five pounds of our total body mass. More than 1,000 species of them colonize our intestinal tract in a complex ecosystem, or “microbiome.”
Each of us inherited our microbiome from our mother. It became established in the first few years of our life. We alter our microbiome by the food we eat, air we breathe, antibiotics we take, and our contact with objects in the world.
In exchange for room and board, microbes help break down our food. They control our immune system, brain function, metabolism, and weight. They keep pathogens in check and manufacture enzymes, vitamins, and other essentials. Microbes in our gut produce neurotransmitters, chemical messengers in the nervous system that influence mood, muscle movement, heart rate, and many other functions. For example, more than 90 percent of our serotonin — which is essential for the generation of emotions — is made in the gut.
Microbes Grow Our Food
Most of us have heard about the health benefits of microbes in fermented or cultured foods such as yogurt. Plants are also steeped in microbes, inside and out. A single spinach leaf teems with more than 800 species of bacteria.
Soil microbes make nutrients from organic matter and rock particles available to plants. They also detoxify harmful chemicals, suppress disease organisms and weeds, help plants withstand drought and other stresses, and produce hormones that spur plant growth.
Fungi that attach to plant roots create vast “internets” below the Earth’s surface. The largest organism on the planet may be a fungus in Oregon that occupies almost four square miles. In exchange for food, fungal networks bring nutrients and water to plants and facilitate complex chemical signaling among plants.
Rock particles contain plenty of the minerals that plants need, but not in an available form. Microbes convert these minerals into forms plants can take up and use. To capitalize on this process, plants actively cultivate bacteria and fungi in soil around their root tips by secreting food for them. As microbes thrive on this food, they accumulate nutrients, including minerals and nitrogen. The microbes enter the plant roots. The plant extracts nutrients from the microbes to use for its own growth. Then, the microbes exit the plant (via root hairs), go back into to the soil, and regrow, accumulating more nutrients. The cycle repeats. Experiments show significantly more plant growth and higher nutrient concentrations in plants grown with microbes than without. Higher nutrient concentrations in plants mean more nutritious food for animals.
Farm animals have microbiomes much like humans’. They take up microbes in the plants they eat and then return microbes to the soil via manure, along with organic matter, nutrients, and plant seeds.
Microbes Enrich Soil and Cool the Climate
Healthy soil contains rock particles and abundant organic matter, water, and air. Soil organic matter consists of plant and animal residues at various stages of decomposition, soil organisms, and substances synthesized by organisms. Soil organic matter is about 50 percent carbon by weight. Microbes convert soil organic matter into forms useful to the rest of the organisms in the soil ecosystem.
They also convert soil organic matter into forms that are relatively stable and are thus good for long-term carbon storage. These include humus (a deep brown, spongy material) and carbon combined with minerals. Fungal networks transport carbon downward, into the soil, for long-term storage. Storing carbon in soils helps stabilize our climate.
Microbes increase soil fertility and structure. They form clumps of soil called aggregates, creating pockets of air between these clumps that enable soil to function like a sponge, absorbing and retaining water. The pockets of air also promote air movement, and therefore oxygenation, of the soil.
Healthy soil contains astounding biodiversity that includes microbes, plants, and animals. Microbial biodiversity in soil is about ten times that of the human gut.
Tilling and Synthetic Chemicals Kill Microbes and the Environment
The diversity of microbes in humans and in soils has been plummeting, perhaps because we have not maintained healthy soils on our planet. Humans have significantly degraded about 75 percent of Earth’s land area.
The agricultural practice called tilling includes plowing, harrowing, and other actions that break up and mix the soil. Tilling disrupts fungal networks and exposes organic matter in the soil to more oxygen. Microbes use that oxygen to devour precious soil organic matter, and in so doing they release climate-damaging carbon dioxide into the air. Tilling leads to soil erosion and compaction, which reduces soil aeration and the amount of water able to soak into the ground. This diminishes groundwater supplies and increases runoff and evaporation, disrupting the water cycle.
Since the early 1990s, we have further damaged our agricultural lands through a cascade of shortsighted practices. Large-scale, petroleum-based farms typically utilize energy-intensive synthetic nitrogen fertilizers. Those fertilizers can kill and alter soil microbiology and release the greenhouse gas nitrous oxide. They also promote the growth of weeds.
Growing large areas of monoculture crops invites pest problems. Farmers have responded to weeds and pests by applying biocides (-cide is the Latin suffix for “killer”), lethal chemicals that include antibiotics, pesticides, insecticides, herbicides, and fungicides. Biocides tend to broadly injure or kill diverse living things in their paths. They kill microbes and harm the microbiomes of soil, plants, and animals ranging from insects to mammals.
With fewer microbes to provide them with usable organic and inorganic nutrients, plants become undernourished and more vulnerable to attack. Farmers apply more biocides. Unwanted species adapt to the biocides and proliferate. Farmers apply more biocides, and damages escalate.
Most farm animals eat foods that contain biocide residues, and many are given foods their digestive systems are not designed for, further disrupting their microbes. Administration of antibiotics to farm animals can cause further disruption. The microbiomes of corn-fed cattle raised on industrial-scale farms, for example, have reduced richness, diversity, and functionality.
Chemical Agriculture Harms Our Health
At the same time that chemical agriculture may have increased food production, it is also a major cause of significant declines in the nutrient content in foods since 1950. Examples include calcium, iron, riboflavin, and vitamin C. Much of our food now is calorie-dense but nutrient-poor. Two billion people globally are affected by micronutrient deficiencies.
Our gut microbes largely determine our health. Accordingly, diet is the chief cause of, and also the chief solution to, chronic diseases. Chronic diseases — such as cardiovascular disease, autoimmune diseases, diabetes, and dementia — remain chronic because conventional medicine is unable to completely and rapidly cure them. In the US, diet-related chronic diseases are leading killers, and 60 percent of us live with at least one chronic disease.
When we eat whole, real, fresh, biocide-free foods, we grow helpful microbes in our gut. And when we eat a diversity of these foods, we grow a diversity of gut microbes, which enhances our health as well as theirs.
“Junk foods” — such as highly processed chips and cakes — grow microbes that produce toxins and cause inflammation and other problems. Gut microbes can even steer our eating behaviors, increasing cravings for foods they like, such as sugar.
Biocides and other toxins can damage our microbiome. Microbiome damage contributes to diseases such as inflammatory bowel disease, obesity, diabetes, cardiovascular disease, liver disease, colorectal cancer, and neurological disorders. Because the health of our microbiome factors into inflammation levels and immune-system function, gut microbes may affect our risk for diseases as varied as depression, multiple sclerosis, asthma, autism, Alzheimer’s, Parkinson’s, and cancer.
Microbes Can Save Us
Regenerative agriculture refers to farming and ranching practices that can restore biodiversity, rebuild soil structure and organic matter, help the climate, and conserve water, all while sustainably producing nutritious food. Microbes are crucial players in regenerative agriculture.
Regenerative agriculture minimizes or eliminates tilling. It keeps the soil surface covered to prevent evaporation and erosion. It keeps living roots in the soil for as long in the year as possible (to keep soil microbes well fed and happy). It encourages biodiversity (therefore chemicals and monocultures are avoided), and it may incorporate raising livestock. Currently, only 1 percent of US cropland is organic, and far less is regenerative.
We Can Help
The crises in our world might seem so daunting that we don’t know how to begin to solve them. We might also be struggling with one or more chronic health conditions. Food provides a fantastic starting point on both counts because of its vast and far-reaching consequences. We can transform ourselves and our world by choosing regeneratively grown, or at least organically grown, food.
Microbes can do the heavy lifting for us. Working in partnership with plants and animals (including humans), they can help regenerate soil and biodiversity, conserve water, stabilize the climate, and sustainably produce healthy food.
Microorganisms might be our best hope for healing our health and our world.
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