How Soil Microbes Can Heal the World (If We Get Out of the Way)

The Soil Microbiome and the Fertility of Health

There are about 100 billion microorganisms in a teaspoon of productive top soil! And soils are the best reservoir of microbial diversity on land. There are, at minimum, 6 million species of bacteria in the soil. Soils are essential to the process that converts death into new life. The process starts with earthworms and other invertebrates, who shred dead plants and animals into progressively smaller pieces. Bacteria and fungi use enzymes to pull the nutrients they need out. This completes the decomposition process and ensures that the elements essential to life are in continuous circulation. “Collectively, a loss of soil diversity (microbes, fungi, protozoa, and animals) has been associated with lower plant diversity and crop yields, leading to reduced food security, erosion that reduces air and water quality, and increased soil-borne pathogen and pest load, which all can have indirect and direct human health impacts,” the authors wrote in a report regarding soil health and human health from the National Academies of Sciences.

Until recently, agricultural experts thought that soil was simply an inert material to hold plants and minerals. Recent advances in studying microbes have allowed scientists to find that these microbes:

• Prevent erosion

• Conserve water

• Break down pollutants

• Capture and store atmospheric carbon

• Communicate directly with our cells

• Increase the nutrient content of our food

Historically, people ate a lot more dirt, both accidentally and intentionally, so this cooperative relationship makes sense. This type of exposure to the dirt has a profound impact on our microbiomes. In a study on baboons, researchers found the effect of the geologic history and salt content of the soil was 15 times stronger than host ancestry in predicting which microbes were present in a baboon’s gut. However, we don’t yet understand the impact of healthy versus depleted soils. Unfortunately, our soils are not in the same condition as they were for our ancestors, it has been contaminated with:

• Heavy metals, which impact function of the nervous system, GI tract, immune system, liver and kidneys. They also impact the soil. Heavy metal contaminated soils have lower plant biomass and change the composition of the microbial communities.

• Polyaromatic hydrocarbons, which increase the frequency of mutations, the risk of cancer, and disrupt the endocrine system

• Microplastics, which increase the risk of heart attack, stroke, blood clots, and inflammation of the GI tract, change the microbiome, in addition to respiratory, immune, endocrine, and reproductive problems

• Antibiotic residues, which increase the risk of antibiotic resistance and decrease the amount of “good” bacteria in the soil

• Pathogens and other contaminants

We don’t yet know whether exposure to these contaminated soils is worse for human health than no soil exposure at all, but scientists have found that decreasing biodiversity in soils leads to increased likelihood of inflammatory diseases.

Understanding soil is a complicated endeavor. Microbial communities change in size and shape over time and space in response to a wide variety of factors. Compared to the human gut, the soil has 10 times greater species diversity. However, in soil, about 80% of the bacteria is dormant, while in the human gut only 20% of the bacteria are. In the research that has been done, when they study diversity, they are usually referring to the number of different species, but biodiversity isn’t only the number of different organisms or the different types of species, but also the complex interactions between species. Few species in the soil act alone. Most are interconnected in complex networks of predation, parasitism, cooperation, symbiosis, and competition. These interactions impact how nutrients cycle, how healthy plants are, and the ecosystem functioning as a whole.

Living plants also nourish soil microbes. They secrete exudate from their roots which feeds the soil microbes and attracts them into relationship with the plant’s root system. Soil microbes are 100 times more densely packed near root systems than other parts of the soil. When plants secrete exudates, the microbes near them are able to:

• Acquire nutrients and give them to plants in a form the plant can use

• Make compounds plants need to grow and to protect themselves against stressors like heat and drought

• Add organic matter to the soil, to make the soil healthier

• Serve as a critical barrier to keep out pathogens (disease-causing organisms)

It is especially important for plants to be able to access nitrogen, phosphorus, and potassium. Symbiotic relationships between soil microbes and plants are vital for obtaining this access. Bacteria convert nitrogen in the air into forms plants can use. For example, nitrogen fixing bacteria in the roots of field peas convert 155-175 pounds of nitrogen per acre per year. I’m no farmer, so correct me if I’m wrong, but some light googling revealed that this is remarkably similar to the amount of nitrogen that farmers add in ammonia fertilizers (about 140-160 pounds per acre according to this source). In addition, some plants also have these nitrogen-fixing bacteria in their roots and stems. Scientists used to think these bacteria did not produce much nitrogen, but recent research suggests they produce enough nitrogen to support the growth of rice, wheat, sugar cane, western red cedar, and lodgepole pine.

Mycorrhizal fungi are the kind of fungi people are talking about when they talk about the “wood wide web” or how plants and fungi partner together to communicate between plants. Mycorrhizal fungi place one end of their body inside a root or on the root’s surface. They allow plants to take up 80% more phosphorus, 25% more nitrogen, 10% more potassium, 5% more zinc, and 60% more copper (from the same soil).

Soil microbes are also essential to protecting crops, much like the human microbiome is vital to the function of the human immune system. They protect crops in very similar ways too, including:

• Competing with harmful bacteria to keep them from finding habitat and nutrients

• Activating plant immune responses

• Acting as parasites to harmful bacteria and fungi

• Producing compounds that prevent the growth and development of harmful bacteria and fungi

• Finding nutrients and making compounds that plants use to resist disease and infection and maintain metabolism

Young Herdsmen with Cows by Aelbert Culp from The Met Open Access

Soils containing chemical fertilizers contain 50% less “good” bacteria. This is because when plants receive nitrogen and phosphorus from other sources, they don’t make the exudates that are needed to attract microbes. Bacteria that convert the most nitrogen are most likely to be affected and those that are the least reliant on exudate are, unsurprisingly, least likely. Fertilizer also led to less diversity of nitrogen fixing bacteria as well. In addition, fertilizers also interfere with the timing of decomposition, so that it doesn’t match the natural timing. Fertilizers, especially nitrogen, cause bacterial populations to increase. This leads to nutrient release occurring before plants need the nutrients most.

Pesticides also interfere substantially with the soil microbiome. Fungicides are particularly problematic, because they not only kill fungi that cause diseases, but also the mycorrhizal fungi by interfering with their ability to form networks, and kill nitrogen fixing bacteria as well. In one species of bacteria, fungicide decreased the amount of nitrogen it was able to provide by 90%. In addition, glyphosate (Round-Up) tolerant crops secrete glyphosate in their exudates. This leads to a decrease in beneficial bacteria in and around plant roots, which interferes with several important processes like:

• The delivery of manganese to the plant

• The production of chemicals that protect the plant from disease

• Competition with a fungus that causes root disease

That leads to a decrease in the health of crops, and therefore a decrease in the health and stability of our food supply. Combinations of herbicides lead to even larger decreases in microbial diversity. Especially concerning, in one study, they found that soil bacteria exposed to several types of herbicides increased the abundance of antibiotic resistance genes in a given population and also the genes that facilitate the movement of those resistance genes between bacteria. It seems reasonable to conclude that this phenomena could increase antibiotic resistance in human disease as well.

How we use the land greatly impacts how much the land can adapt. From the 1780s to the 1980s, people converted 50% of United States wetlands for other uses, mainly agricultural. This decreases an ecosystem’s ability to clean the water. Conversion of land from natural to agricultural also significantly depletes the carbon in the soil, a major indicator used to measure the health of soil. In temperate regions, they lose about 60% of the carbon and in tropical regions they lose about 75% of the carbon.

The Weeders by Jules Breton from The Met Open Access

Tilling also has a major impact on the health of microbial communities. Tilling is loosening up the earth, usually using machinery, to remove weeds and old crops and prepare the ground for planting. Robert Beelman was a nutrition researcher who started wondering whether our agricultural practices were leading to decreased nutrition in our food. He focused on antioxidant, l-ergothionene. Research suggests l-ergothionene deficiency leads to increased inflammation and premature aging. Oats grown in fields that were not tilled had 25% more l-ergothionene than oats grown in fields that were tilled. Cover crops, diversifying the crops planted over time and space, and leaving fields to fallow all improve soil health as well.

We often forget how much we humans rely on soil. 95% of food is produced on/in soil. Many past increases in food production have come at the cost of the health of the soil. Enzymes from soil microbes are used in industrial applications and medical products. Healthy soils also protect us from air, soil, and water pollution, pull carbon from the atmosphere, reduce the impact of flooding, and prevent erosion, which is vital for the future of our food supply. Ultimately, health is about connection. All of the things we do that disturb relationships in the soil compromise the health of the soil and compromise our own health. As soil scientist Bill Robinson said, “Soil health is public health.”

Tad Hargrave

discussed competing views of health, one about sterility–the absence of life, antibiotics, sterile operating rooms, isolation. There are times when this view of health is necessary, but it is not the system for which our bodies are designed. The other view is about fertility–the abundance of life. The recent scientific advances in genomics allow us to see what many communities have long known, that more of health is about fertility than sterility. Our health is not simply a grocery list of the “right” chemicals, or even the “right” bacteria, that we can pop as a supplement. Our health depends upon how all of these chemicals, organisms, and our own cells interact in ways that are so complex that many of the interactions are beyond our comprehension. Some might say they are magical.

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