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Food System Primer

Crops and Ecology    


The preservation of fertility is the first duty of all that live by the land … there is only one rule of good husbandry – leave the land far better than you found it.

– George Henderson1

Agriculture is built upon fertile soil, a favorable climate, ample freshwater, a diversity of plant and animal species, and the skills and labor of farmers and farm workers. These are the ecological foundations of our food system. They are also endangered by depletion, disruption, or disease. Finding ways to better preserve the health of agricultural ecosystems is key to the long-term sustainability of our food supply.

Most of the challenges described here relate most directly to crop production, but because crops are grown in large part to feed livestock, the production of meat, milk, and eggs is also heavily implicated. In North America, for example, only 40 percent of cropland is used to feed people directly; most of the remainder is used to grow feed for animals.2


Will Allen

“Farming is all about the soil. … If you can grow good soil, you can grow good food.” – Will Allen

Will Allen (right) is the founder and CEO of the Milwaukee-based community food center known as Growing Power. Allen’s nonprofit grows enough food to feed 12,000 people each year, and it all starts with healthy soil. Each year Growing Power transforms 22 million pounds of food waste into fertile compost—with a lot of help from earthworms.

Photo credit: Michael I. Kienitz. All rights reserved.

Myco Fungi

Far from being lifeless dirt, fertile soil is teeming with organisms that have important roles in agriculture. Bacteria living inside the roots of plants in the legume family, such as beans and clover, extract nitrogen (a key nutrient for plants) from the atmosphere. Certain species of fungi that grow on the surfaces of roots (pictured) also help deliver nutrients to plants. Earthworms, meanwhile, help decompose decaying leaves, excrete nutrient-rich castings, and loosen soil by burrowing through it.5

Image source: Nilsson et al., 2005. BMC Bioinformatics, volume 178, issue 6. Creative Commons CC BY 2.0.

Dust Storm

Dust storm approaching Stratford, Texas.

The Dust Bowl of the mid-1930s demonstrated the devastating potential of soil erosion. Eager to cultivate the fertile land of the American Midwest, farmers plowed up prairie grasses with deep root systems that held soil in place. A prolonged drought was followed by high winds, which swept away hundreds of millions of tons of topsoil. Dust storms moved up to 100 miles an hour, choking people and killing livestock in their path.6

Photo credit: NOAA, 1935. Public domain.

Click images for captions

Land, then, is not merely soil; it is a fountain of energy flowing through a circuit of soils, plants, and animals.

– Aldo Leopold

Almost everything we eat can be traced back to soil. Far from being lifeless dirt, fertile soil is teeming with organisms, including worms, arthropods, bacteria, fungi, and plant life. The decaying (and fully decayed) remains of these and other organisms, and their excrement, make up the part of soil called organic matter. The remaining mineral fraction of soil is composed of sand, silt, and clay.

Organic matter and the organisms that inhabit it are a large part of what makes soil fertile. Organic matter soaks up water and nutrients like a sponge, helping plant roots to access them. Because soil organic matter helps capture and hold water, it is particularly important during droughts. Organic matter also helps aerate soil, providing roots with oxygen, and it stores carbon that would otherwise contribute to climate change.

Building and maintaining healthy soil require care on the part of farmers. Throughout history, farmers have mismanaged this essential resource, sometimes with catastrophic results. Plowing soil and compacting it (e.g., by driving over it with heavy machinery), for example, can make soil more prone to erosion—the removal of soil by wind, rain, and other forces. Erosion is particularly damaging because the top layer of soil (topsoil) is richest in organic matter. Erosion can also contribute to water pollution by transporting pesticides and excess nutrients into nearby streams and rivers. On much of the world’s agricultural land, fertile soil is still being eroded much faster than it can be restored by natural processes.3,4


Irrigation Circle

This satellite photo shows irrigated crop circles in Kansas. Each plot is between 800 and 1,600 meters (1 mile) in diameter. In these systems, water is pumped from a well in the center of the circle and distributed through a long sprinkler that pivots around a central point. This area draws water from the Ogallala Aquifer, an underground water body that lies beneath portions of eight U.S. states.

Photo credit: NASA. Public domain.

Globe Water Use

The large sphere over North America represents all the water on earth, including in oceans, rivers, the atmosphere, and living organisms.

Only 2.5 percent of Earth’s water is freshwater, of which 60 percent is frozen in ice caps, glaciers, and snow. The remaining liquid fraction is represented by the smaller sphere over Kentucky. Nearly all (99 percent) liquid freshwater is below ground. The remaining amount in lakes and rivers, represented by the tiny sphere over Georgia, is responsible for most human water needs.

Image credit: Jack Cook, Woods Hole Oceanographic Institution. Used with permission. Data source: Howard Perlman, USGS.7 Adapted from Shiklomanov, 1993.8

Mexico River

Left: Colorado River at the Mexican border. Right: Effects of freshwater depletion on Mexican farmland.

A once-thriving ecosystem at the Colorado River’s delta has given way to mudflats, and the region’s crop production has suffered without a reliable source of irrigation water. While there have been attempts to fairly allocate water use rights between the U.S. and Mexico, the Colorado remains among the most contested waters in the world.13

Photo credit: Charles O'Rear, 1972. U.S. National Archives and Records Administration.

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We know the value of water when the well runs dry. 

– Benjamin Franklin

Growing crops and raising animals for food depend on a reliable supply of freshwater. This resource is surprisingly scarce: of all the water on Earth, only 2.5 percent is freshwater; the rest is salty. The vast majority (99 percent) of freshwater is locked in glaciers, icecaps, or below ground, and is mostly unavailable. The remaining amount—a tiny fraction of all the water on Earth—is responsible for serving most of our water needs.7,8

Where rainfall is inadequate, farmers draw from rivers, lakes, reservoirs, wetlands, and groundwater to supply crop fields with freshwater. An estimated 17 percent of global agricultural lands are irrigated, and crop irrigation accounts for an estimated 90 percent of global freshwater consumption.9

In many parts of the world, freshwater supplies are being depleted much faster than natural processes can restore them. The High Plains Aquifer, for example, is an underground freshwater body that lies beneath portions of eight U.S. states. Parts of the aquifer have already been drained by as much as 30 percent, in large part for corn—a particularly thirsty crop, in high demand for cattle feed and biofuels.10 Many farmers in the area have already reported that their wells no longer supply water, or have become more costly to operate.11 The aquifer could take hundreds if not thousands of years to naturally recharge.


Potato Famine

By the mid-1800s, one-third of Ireland’s population had become dependent on a single potato variety for the bulk of their sustenance. When a plant disease wiped out this staple crop, the resulting famine—known as the Great Hunger—took an estimated 1 million lives.19 Since then, a lack of crop biodiversity has played a role in several other major crop failures across parts of North America and Asia.17

Image credit: Illustrated London News, December 22, 1849. Public domain.

Biodiverse Bean

Beans stored at a seed bank in Colombia.

Many useful crop varieties that were developed over centuries are now rarely used in agriculture. Seed banks act as a botanical “Noah’s Ark,” preserving crop varieties to help ensure the world has access to them in the future. Storing these genetic resources can protect them during catastrophic events, such as wars and natural disasters. 

Photo credit: Neil Palmer, CIAT, 2011. Creative Commons CC BY 2.0.

Biodiverse Bean

The Pavlovsk agricultural research station in St. Petersburg, Russia, is the world’s first seed bank. During the German siege of that city (then called Leningrad) in World War II, at least 12 Russian scientists working at the Pavlovsk station died of starvation rather than eat the edible seeds and tubers stored in the bank.  

Photo credit: Neil Palmer, CIAT, 2011. Creative Commons CC BY-SA 2.0.

Click images for captions

Agrobiodiversity is the variety within and among species involved in food and agriculture.

There are roughly 10,000 known edible plant species in the world. From this vast diversity of food sources, only three—rice, maize, and wheat—provide nearly 60 percent of the calories and protein that people derive from plants.14 In the U.S., roughly half of cropland is used for monocultures (large areas planted with a single genetically uniform crop) of corn and soybeans.15 Relying on such a narrow range of agrobiodiversity is like putting all our eggs in one basket—if one variety succumbs to a pest outbreak, or becomes unsuitable for a region’s climate, food supplies suffer a major loss.16

More than just the “spice of life,” diversity helps farmers adapt to changing conditions. Some crop varieties, for example, are better than others at tolerating droughts or resisting certain pests. These and other traits are particularly important in the face of a rapidly changing climate.

Each crop variety also offers unique flavors, textures, and nutritional properties. Many serve medicinal purposes, or have cultural significance to the people who grow and eat them. Over the past century, however, thousands of crop varieties  and animal breeds have become rare or extinct.17 Farmers can preserve agrobiodiversity by continuing to cultivate traditional foods.

The countless “wild” organisms that play supporting roles in food production are also an integral part of agrobiodiversity. One coffee plantation in Mexico, for example, is home to as many as 180 different species of birds that help control insect pests and disperse seeds.17 Globally, an estimated 35 percent of the food supply depends on a variety of bees, birds, butterflies, and other pollinators.18 Even among organisms in soil, greater diversity can enhance the beneficial services they offer.5

Pesticide use

Atrazine Frog Testes

Enlarged cross section of American leopard frog testes. What’s wrong with this picture?

The frogs in this study were exposed to atrazine, one of the most commonly used herbicides in the world. Atrazine has been shown to affect the sexual development of amphibians—the three large circular objects in this image are egg cells—not something one expects to find in male anatomy.

Image source: Tyrone Hayes, Kelly Haston, Mable Tsui, et al., 2002.35


Advertisement for Flit, an insecticide formulated with DDT. Dated between 1930 and 1940.

Theodore “Dr. Seuss” Geisel is best known for his children’s books, but earlier in his career, he illustrated advertisements for insecticides. His cartoons helped popularize the use of insecticides in American households before their health and ecological effects were widely understood. The Lorax, the Dr. Seuss tale about protecting the environment, may have been Geisel’s way of making amends.36

Image source: Dr. Seuss Collection, Special Collections & Archives, University of California, San Diego. Used with permission.


“If we are going to live so intimately with these [pesticides]—eating and drinking them, taking them into the very marrow of our bones—we had better know something about their nature and their power.”37

Rachel Louise Carson (1907–1964) was a marine biologist, author, and conservationist. Her book Silent Spring drew public attention to the impact of pesticides on health and ecosystems. Her work has been credited with advancing the global environmental movement.

Photo credit: USDA. Creative Commons CC BY 2.0.

Click images for captions

Pesticides are used with the intent of killing a target organism (pest), such as an insect, plant, or fungus that interferes with a food crop. Pesticides often have unintended effects on other, non-target organisms. Some pesticides are non-toxic to humans, while others are highly toxic. Some pesticides persist (do not break down) in the environment, remaining toxic to people and wildlife for many years.

People may be exposed to pesticides by breathing or touching them (e.g., while working on a farm where pesticides are sprayed), drinking contaminated water, or eating produce with pesticide residues. Depending on the pesticide, exposure may increase people’s risk for certain cancers and problems with their reproductive, immune, endocrine, and nervous systems.16

Pesticide use has also been implicated in sex reversals in amphibians;20 weakened immune systems in dolphins, seals, and whales;16 declining populations of beneficial organisms (e.g., pollinators and predators of pests);16,21,22 and other harms to wildlife. Many studies suggest insecticides are contributing to recent and dramatic declines in honey bee populations—a global phenomenon called colony collapse disorder (CCD).23–27 Recent surveys indicate that roughly 30 percent of U.S. honey bee colonies are lost each winter, in part due to CCD.28 Beekeepers can recover some of these losses, but they are still alarmingly high. In the words of one entomologist, “If we lost one in every three cows in the winter… the National Guard would be out.”29

Over time, pests may develop resistance to the chemicals used against them. When this happens, farmers may apply more (or different) pesticides to achieve the desired result,30,31 worsening the potential dangers posed by their use. 

Refer to Food Safety for more on pesticides in food.

Farm worker health

Migrant Worker

A migrant worker carries cucumbers in Blackwater, Virginia.

"Our very lives are dependent, for sustenance, on the sweat and sacrifice of the campesinos. Children of farm workers should be as proud of their parents' professions as other children are of theirs.” – Cesar Chavez, American farm worker, labor leader, and activist on behalf of migrant workers.

Photo credit: Laura Elizabeth Pohl/Bread for the World, 2011. Creative Commons CC BY-NC 2.0.


Preparing alachlor, the second most widely used herbicide in the U.S., to be sprayed on food crops.32

The biotech company Monsanto, a leading manufacturer of alachlor, was found guilty of chemical poisoning when a French farmer suffered memory loss, headaches, and other neurological symptoms after inhaling the chemical.33 Alachlor was banned from use in the European Union in 2006.34

Photo credit: USDA.

Click images for captions

It's ironic that those who till the soil, cultivate and harvest the fruits, vegetables, and other foods that fill your tables with abundance have nothing left for themselves.

– Cesar Chavez

U.S. agriculture depends on an estimated 2.5 million hired farm workers. Hired farm workers are distinct from farmers, who manage the farm and are usually self-employed.38 Farm workers are often hired for part of the season to help with labor-intensive tasks such as harvesting, washing, and processing fruits and vegetables.

Despite their crucial roles in the U.S. food supply chain, farm workers are often poorly compensated and subjected to occupational hazards.

Nearly two-thirds of seasonal farm workers involved in crop production live in poverty, half earn less than $7,500 a year, and fewer than one in five has health insurance. Most seasonal farm workers are from Mexico or Central America, and at least half who migrate to the U.S. are undocumented.38 Poverty, lack of insurance, and language barriers may deter them from seeking medical assistance, and fears of deportation may deter them from advocating for safer working conditions.38

U.S. farm workers face particularly high risks of toxic exposure to pesticides, particularly when pesticides drift (are blown by wind) away from where they are sprayed.39 Workers in crop production also suffer 80 percent more injuries compared to the national average for private industries.40 Only one in 10 seasonal farm workers claims the ability to read or speak English fluently, potentially increasing their risks of pesticide exposure and injury (e.g., if they are unable to read warning labels).

See also Industrial Food Animal Production.

Nutrient pollution

To provide crops with nutrients for growth, farmers often apply fertilizers such as synthetic nitrogen, minerals, animal manure, or human sewage. The use of human and animal excrement as fertilizer is an ancient method of recycling organic matter, transforming waste into food. But when more fertilizer or manure is applied than plants can use, the excess nutrients become “too much of a good thing,” seeping down into groundwater or being carried into nearby waterways by runoff (the flow of water, e.g., rain or irrigation water, over land).

Nutrient pollution in aquatic ecosystems can stimulate algal blooms—rapid accumulations of algae. After the algae die, bacteria feed on the decomposing remains, using up oxygen from the water. This process can create dead zones—underwater regions where oxygen levels are too low for most plants and animals to survive.41 Dead zones have become common in U.S. coastal regions, such as the Chesapeake Bay. Globally, the number of dead zones has roughly doubled every decade since the 1960s.42 A dead zone in the Gulf of Mexico, largely a result of fertilizer and manure runoff from corn and soy fields in the Midwestern United States,, reaches the size of the state of New Jersey at times of the year.42,43

Nutrient pollution can also impact health. Drinking groundwater contaminated with high levels of nitrate (a form of nitrogen, an important crop nutrient) has been linked to reproductive problems, diabetes, thyroid conditions, and blue baby syndrome—a potentially fatal condition among infants.44

In surface waters, nutrient pollution can stimulate the growth of toxin-producing microorganisms. People may be exposed to these toxins by fishing or swimming in contaminated waters, or eating contaminated seafood. Exposure may cause neurological impairments, liver damage, stomach illness, skin lesions, and other health problems.45

See also Industrial Food Animal Production.

Fossil resources


Guano mining operation, Chincha Islands.

The value of phosphorus as an agricultural fertilizer is illustrated by the extraordinary efforts made to obtain it. Deposits of phosphorus-rich bird guano, some up to 200 feet deep, were discovered blanketing islands off the coast of South America. Guano was such a hotly contested commodity that the islands became the epicenter of international conflicts.6

Image credit: Various, 1863. Public domain.

Click images for captions

Some resources, such as fertile soil and fresh water, have always been essential to agriculture. Fossil fuels, by contrast, have been widely used in agriculture only since the early 1900s, with the invention of mechanized tractors and synthetic nitrogen fertilizers (manufactured using natural gas). These resources are called “fossil” fuels because they are made from the decayed remains of prehistoric life.

Today, over half of the global energy use for commercial agriculture is attributable to manufacturing synthetic nitrogen fertilizers.46 Fossil fuels are also used in manufacturing pesticides, powering irrigation systems, and transporting goods to and from farms.47

Global oil reserves are estimated to be near or beyond peak oil—the point at which their rate of extraction begins to decline.48 As oil becomes scarce, prices will inevitably rise, leading to higher food prices and more widespread hunger—unless  agriculture and other industries swiftly transition to alternative energy sources.47

Phosphorus, a nutrient necessary for plant growth, is present in animal manure and other sources. Like oil, phosphorus can also be obtained from the buried remains of once-living organisms.

The value of phosphorus as an agricultural fertilizer is illustrated by the extraordinary efforts made to obtain it. By the 1800s, England had dug up the phosphorus-rich skeletal remains of countless soldiers from European battlefields, to be ground up and applied to farm fields.6 A German chemist once said of this practice, “Already in her eagerness for bones [England] has turned up the battle-fields of Leipsic, of Waterloo, and of the Crimea… Like a vampire, she hangs from the neck of Europe.”49 Today, commercial sources of phosphorus are obtained by mining phosphate rock—a nonrenewable resource estimated to be depleted in 50 to 100 years.50

Crop breeding and genetic engineering


Domesticated crops like broccoli, corn, and tomatoes often appear to have little in common with their wild ancestors. Teosinte (pictured), a wild grass, is thought to be the ancestor of modern maize (corn). Over centuries, farmers and plant breeders have transformed agricultural crops by making them more productive, safer to eat, or better adapted to certain growing conditions.

Photo credit: Matt Lavin, 2009. Creative Commons CC BY-SA 2.0.

Click images for captions

Over centuries, farmers and plant breeders have transformed agricultural crops by making them more productive, safer to eat, or better adapted to certain growing conditions. Traditionally, this has been achieved by selectively interbreeding plants to accentuate desirable traits, such as size or sweetness.

Genetic engineering (GE) is a radical departure from traditional breeding methods that use sexual or asexual reproduction. GE takes genetic material from one organism (e.g., a bacterium) and inserts it into another that may be entirely unrelated (e.g., a plant)—a process that does not occur in nature.51

Introduced in 1996, GE crops are now grown on more than 400 million acres—an area roughly the size of Alaska. Nearly two-thirds of GE acreage is in the U.S. and Brazil.52 Most GE crops are engineered either to resist the herbicide Roundup, allowing farmers to spray it without affecting their crops (Roundup is sold by the same company that markets “Roundup Ready” seeds); or to exude a chemical that is toxic to insects using a gene from the bacterium Bacillus thuringiensis (Bt).

After over 20 years of research, thousands of trials, and promises of “feeding the world,” GE’s potential to boost the food supply remains uncertain. Most GE crops have shown little or no increase in yields,53 while the widespread use of Roundup on “Roundup Ready” crops has led numerous weed species to develop a resistance to it.54 According to one survey, nearly half of U.S. farmers reported Roundup-resistant weeds on their farm in 2012.55

While genetically engineered organisms may hold promise, their pervasiveness in agriculture—and our food supply—raises unanswered questions about their potential effects on public health and ecosystems.56,57


The following list of suggested resources is intended as a starting point for further exploration, and is not in any way comprehensive. Some materials may not reflect the views of the Johns Hopkins Center for a Livable Future.

For teachers




Pesticide use

Farm worker health

Nutrient pollution

Fossil resources

Crop breeding and genetic engineering


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29. VanEngelsdorp D. A plea for bees. TED. 2008.
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31. Kirschenmann FL. Cultivating an Ecological Conscience: Essays from a Farmer Philosopher. Lexington, KY: The University Press of Kentucky; 2010.
32. U.S. Environmental Protection Agency. Technical Fact Sheet on Alachlor.
33. Douet M. Monsanto guilty of chemical poisoning in France. Reuters. February 2012.
34. Pesticide Action Network. What substances are banned and authorised in the EU market? 2003.
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40. Bureau of Labor Statistics. Injuries, Illnesses, and Fatalities. 2013.
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52. ISAAA. Global Status of Commercialized Biotech/GM Crops: 2013. 2014.
53. Gurian-Sherman D. Failure to Yield. Union of Concerned Scientists; 2009.
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55. Farm Industry News. Glyphosate-resistant weed problem extends to more species, more farms. 2013.
56. Dona A, Arvanitoyannis IS. Health risks of genetically modified foods. Crit Rev Food Sci Nutr. 2009;49(2):164-75.
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