Editor’s Note (9/3/2019): This is a substantially revised version of an earlier post, published on August 20, that contained claims and sourcing that did not meet Scientific American’s editorial standards. It is our normal policy to append a note explaining, point by point, what the original said and how it has been corrected. In this case, the revisions are substantial enough that we are simply posting the new version. For the sake of transparency and comparison, the original post can be found here.

Food writer Mark Bittman has argued that because food is defined as “a substance that provides nutrition and promotes growth” and poison is a substance “that promotes illness,” then “much of what is produced by industrial agriculture is, quite literally, not food but poison.” While that may be an extreme statement, our food system is arguably at risk for several reasons, including the increasing use of herbicides and pesticides; the rise of genetically modified organisms (GMOs); and climate change.

Since 1892, the U.S. Department of Agriculture has been collecting data on the nutritional composition of our foods. Over the decades since, there has been enough variability in how samples have been harvested, stored, prepared and analyzed to make it hard to tease out exact trends or causes of them. There is some evidence that vitamin and mineral content of foods such as broccoli has declined and some to the contrary. Given how fundamental nutrition is to our health, it’s surprising there is so little robust research on how agricultural practices affect the nutrient content of crops.

But that is changing. Recent studies have shown, for example, that the increase in atmospheric carbon dioxide is accelerating photosynthesis. That may sound like a good thing, but it means that while plants are growing faster, they also contain more carbohydrates but fewer nutrients, which could ultimately lead to worldwide nutrient deficiencies.

In addition, many crops are getting sprayed more and more heavily with pesticides and weed killers. To protect them from the latter, biotechnologists have genetically modified plants to be herbicide-resistant. About 90 percent of the corn grown in the U.S. (our number-one crop) has been altered adding protective genes from other species. These modifications allow corn to be sprayed repeatedly with herbicides including glyphosate (the active ingredient in Monsanto’s Roundup, the most used herbicide in the country and likely globally as well), 2,4-D and dicamba. Nature doesn’t take this affront lying down, and weeds quickly evolve herbicide resistance, leading to a chemical arms race.

All three of these herbicides are water-soluble, meaning they can dissolve and can go anywhere water goes. They’re also systemic (they can get inside plants, so they can’t be washed off before eating). Glyphosate, in particular, is ubiquitous. It’s an active ingredient in hundreds of products sold in the U.S. and has been found in air, rainwater, drinking water, rivers, and wetlands and in the groundwater used for crop irrigation. And the synergistic effects of these and other pesticides are inadequately tested.

Corn is also engineered with genes that can enable it to produce multiple insecticidal proteins in every cell, which the Environmental Protection Agency euphemistically terms “plant-incorporated protectants.” Plus, corn seeds are often coated with neonicotinoids (insecticides that can harm bees, including types associated with colony collapse) and fungicide. This means they don’t need to be sprayed with as much pesticide—but whether this is a net benefit for human and animal health is poorly known.

But because corn is an ingredient in so many foods (corn syrups and oils; corn-fed farm animals), we are often ingesting these pesticides and insecticidal proteins in every bite. Modified soy, the number-one genetically modified crop globally, has glyphosate residues and perhaps a less healthy nutritional profile compared with organic soy. More broadly, there is some evidence that exposure to glyphosate can lead to cancer, endocrine issues and other health problems. A group of medical and environmental scientists recently published its strong, collective concerns about the risks and urged more research.

If ever there was a scenario in which to apply the precautionary principle, this is it. As applied to environmental science, wrote David Kriebel of the University of Massachusetts, Lowell, and his colleagues in a 2001 paper, this entails four components: “taking preventive action in the face of uncertainty; shifting the burden of proof to the proponents of an activity; exploring a wide range of alternatives to possibly harmful actions; and increasing public participation in decision making.”

In the mid-20th century, the green revolution introduced the wide use of chemical fertilizers and pesticides around the world. And over the past two decades, we’ve undergone a “gene revolution” in industrial agriculture. Proponents of these two advances claim that the chemical and technological transformation of our food system is necessary to feed the world—but there is reason to be skeptical, especially when two thirds of America’s corn crop goes to animal feed or ethanol production. As the United Nations’ Human Rights Council put it, “The assertion promoted by the agrochemical industry that pesticides are necessary to achieve food security is not only inaccurate, but dangerously misleading.”

And as if the potential health risks from these two revolutions weren’t enough, both have relied on the intensive use of fossil fuels for synthesizing agricultural chemicals; running tractors, combines and other farm equipment; processing and precooking food; manufacturing plastic packaging; and powering refrigeration and long-distance transport. As a result, modern agriculture and land use changes are one of the leading causes of climate change.

Do these factors mean a doomsday scenario? Well, maybe. Or they could signal that it’s time for a third revolution.

Climate Victory Garden at Skyhill Farm in July, nearing peak summer verdancy, thanks to a well-nurtured soil microbiome. Credit: Louise Maher-Johnson.

The Microbiome Renaissance

A microbiome is simply a community (or biome) of microorganisms—bacteria, fungi, archaea and protozoa. The microbiome renaissance we envision will include respecting both our internal and external ecosystems, at a microscopic scale but with macro implications.

In soil, microorganisms by the trillions are essential for the growth, nutrition and health of plants. They do everything from fixing nitrogen to delivering minerals and trace elements, to decomposing organic matter and defending against plant diseases. In short, soil microorganisms drive plant productivity—and greater plant diversity results in both more microbial activity and carbon storage.

To reap all these benefits of healthy soil, we must nurture the soil microbiome and plants’ own microbiomes. There is a whole highly-connected microbial food web within the soil that intensive industrial agriculture disrupts. Glyphosate has been shown to hinder the beneficial colonization of mycorrhizal fungi on roots, as has GM corn. Conversely, organic practices support a more diverse and robust microbial community and soils with higher microbial biomass, activity and diversity—as well as up to three times more earthworms. As a February 2015 editorial in Science put it, we should “give soils their due.”

In humans, our 30 trillion or so cells are matched by a similar number of microorganisms, our “inner soil,” that function throughout our body in exchange for food and shelter. Our microbiome performs a wide range of critical functions, such as bolstering our immune system, manufacturing vitamins and supporting digestion. (Have you thanked your microbiome today?)

This is why the overuse of antibiotics (more than 800 prescriptions are written each year for every 1,000 people in the U.S.) is a cause for concern: our internal microorganisms, in balance, help keep us healthy, whereas growing antibiotic resistance, fueled in part by overprescription and in part by the indiscriminate use of these drugs in animal feed, is a serious health problem.

The key to this microbiome renaissance will be nurturing rather than killing or disrupting the balance of our friendly and essential microbiota. Achieving this will require humanity to make organic regenerative farming and gardening the status quo. Regenerative farming means working with, not warring against, nature: planting and saving diverse varieties of heritage seeds; protecting pollinators; growing biodiverse crops; using natural fertilizers such as legumes and nitrogen from the atmosphere; recycling organic matter (mulches and composts); utilizing multispecies cover cropping and crop rotations to build soil; and grazing (not confining) farm animals.

Not only is transforming agriculture to regenerative practices a likely win for our health—and for nature more broadly—it can also be a key climate solution. As we’ve written previously, humanity can sequester carbon and improve nutrition through the regenerative farming of land and sea. This approach can be applied at all scales, including Climate Victory Gardens in yards, local parks, terraces and rooftops.

This is also a food justice issue, because organics are often more expensive and less available in poor communities and communities of color. Hence the importance of efforts to make organic foods available to everyone and of ending huge “farm bill” subsidies to corn and other big commodity crops—and instead subsidizing the transition to regenerative practices.

A 2018 report by the InterAcademy partnership, a global network of more than 100 national and regional science and medicine academies concluded, “living within planetary boundaries (including those for nutrients, water and climate) and having healthy populations requires new approaches to food systems.”

It is pure hubris to think we can manipulate nature into agricultural perfection with synthetic fertilizers and pesticides. Instead, to adapt to and mitigate the intertwined ecological, human-health and climate crises, we must respect the elegant complexity of nature. We must overhaul our food system. And it can all start by ensuring that microbiomes flourish.