We’ve heard that the microbiome in our gut is of unprecedented importance—we have overlooked a hidden (and massive) world of organisms crucial to our health. The result has been an influx of foods and supplements tailored to the human microbiome, as well as initiatives to map the genome of the microbes in our stomachs and ultimately apply those insights to the medical industry. We have found ourselves the residence for quite a host of microscopic species integral to human health.

It’s not a surprise that the most fervor in discussing the microbiome has to do with the most personal application, our bodies themselves. But there is another microbiome to which we urgently need to pay attention—the one beneath us, in our soil. Soil health will determine whether or not we can feed a growing population, and how well we will adapt to climate change as it affects agricultural systems around the world. Our soil is crucial to human health, especially when we consider how large of a role it plays in the quality, quantity, and resilience of our crops. When it comes to the future of our food system, there may not be anything as pressing as the health of the “dirt” in our fields and farms.

Topsoil is crucial to agriculture for its role in retaining water, as well as providing nutrients, minerals, plant-derived organic matter, and gases (carbon in particular, to mention one of special note). It is the vehicle through which minerals from earth’s rocky crust make it into biological matter, i.e. plants. The soil itself plays host to a huge amount of biological matter—up to 90 percent of all organisms that live on land can be found in the ground. There can be anywhere from 100 million to 1 billion bacteria in just a teaspoon of soil. This is the key to how we have to start thinking about soil—it should be treated as a living biome. Researchers in the past two decades have explicitly sought a definition of soil “quality” that takes into consideration “the living and dynamic nature of soil” and that “the soil resource must be recognized as a dynamic living system.”


Of course, high-quality soil is of utmost concern to producing food. Not only can productive and healthy soil directly affect crop yields and, some argue, the quality of the crops themselves, but it can help mitigate the effects of climate change on farms. According to Anne Bilkè, author of The Hidden Half of Nature: The microbial roots of life and death, healthy soil is key to a crop’s ability to deal with drought, pathogens, pests, and viruses. Organic soil matter helps to retain water, improve soil structure (which prevents agricultural waste runoff), reduce erosion, and, importantly, “results in greater productivity of plants,” according to a recent study in the journal Nature. Healthy soil may also be able to sequester carbon in the long run, helping mitigate climate change. Ultimately, these benefits safeguard our potential food security.

The catch? We have to consider the inverse of a regenerative farming system—i.e. the impact of current industrial agricultural practices. Modern farming has stripped topsoil over the past century, resulting from unforeseen (and occasionally reckless) farming methods.

In the 19th century, German scientists discovered how to fix nitrogen—literally pulling it from the air into a usable form for plants. Prior to this discovery, plants’ only means of obtaining nitrogen (as fertilizer) came from the natural process of microbial nitrogen fixation, and crops were limited by its bioavailability. In 1909, nitrogen fixation was applied, for the first time, to manufacture a synthetic fertilizer usable to plants, ushering in the “green revolution”. However, with a reliance on synthetic nitrogen, farmers did not have to concern themselves with the quality of their soil and its ability to be regenerated and productive on it’s own. As farms got bigger and bigger, the issue was only exacerbated by monocropping.

With the directive from Earl Butz—former Secretary of Agriculture—in the 1970s for farmers to “get big or get out,” huge farms became the norm, and monocropping became the primary form of agriculture in the US. Monocropping has reduced the diversity of the soil microbiome, according to Anne Bilké, by suppressing the variety of naturally-occurring inputs that plants send into the soil. One crop planted season after season cannot recruit and maintain a diverse microbiome on it’s own. Furthermore, these large farms’ reliance on synthetic inputs and chemicals “scrambles” the communication between plants and organisms they evolved to coexist with in the soil.

Thus we are left with a dying topsoil that is not only unable to bestow its benefits to plants and the environment, but is releasing greenhouse gasses further increasing agriculture's destructive toll on our environment. (Our agricultural practices contribute a staggering one-third of all greenhouse gas emissions.)


With our soil depleted in up to one-third of global agricultural system, we are not only compromising the quality of the food grown (the composition of what you eat is necessarily a result of the soil it was grown in), but we face a real threat in our ability to feed a growing population. If soil degradation continues, some researchers estimate that we will have exhausted the soil’s potential in the next 50-60 years. The effectiveness of chemicals and fertilizers declines on dead soil and without real change we should expect decreasing yields.

What can be done to restore our soil's health? Organic farming is the most obvious starting point. Organic farming systems have more robust microbial systems than traditional agriculture. Unfortunately, they currently make up only 0.7% of farms in the domestic food system. Farmers are also looking at specific ways to increase microbial health such as applying cover crops in place of bare fields (which tend to increase soil erosion and the leaching of soil nutrients); adding organic matter and compost to fields; planting trees and other forms of biodiversity on or near farms; evaluating inputs; reducing soil compaction; and practicing longer crop rotations with more diversity. Recent agtech innovations may also play a large role. Soil monitoring allows farmers to know exactly what is going on in their fields. The HydraProbe is one of the most highly developed soil sensors—it utilizes technology developed by the physics department at Dartmouth College and measures soil moisture, salinity and temperature. An increasing number of startups are adding to the available technology and tools for farmers: CoolPlanet has developed a porous soil additive which helps to retain crucial nutrients and water, while Trace Genomics is working on a soil microbiome testing kit which can be used to determine the health of soil before farmers start planting.

The aims of these initiatives in soil health are not purely altruistic—there is a business case for placing a value on the soil microbiome. Trace Genomics claims a substantial 30 percent increase in yields thanks to proper soil management—a statistic that is backed up by USDA case studies. Companies have begun investigating the development of commercial mycorrhizal fungi products to be added to soil, potentially re-introducing diversity to the microbiome. Despite some current challenges, including “appropriate, cheap, highly reproducible and effective methods for … testing and quality control,” early research points to increased yields and stimulated plant growth from such inputs.

The soil microbiome has, in fact, been a hidden and undervalued component to global food security, but demands our attention for both human health and the health of our planet. If we continue to degrade the earth’s arable land at our current pace, then the challenge of feeding 10 billion people by 2050 may become insurmountable. In supporting the soil microbiome, we can sustain long-term farming yields and thereby incomes, reduce greenhouse gas emissions (and potentially sequester additional CO2), and reduce farm runoff into rivers and lakes.