Underground Allies: How Soil Microbes Feed the World and Fight Climate Change

Place a spoonful of soil under a microscope and you’ll bear witness to a gripping microdrama: Bacteria, fungi, and protists competing for nutrients, breaking down organic matter, and funneling resources to nearby plants. 

There are more microorganisms within this teaspoon than there are people on Earth—all contributing to soil’s color, smell, structure, and ability to support plant life.¹ The modern agricultural system relies on healthy communities of soil microbes, but we’re losing them at alarming rates. 

Let’s explore how these invisible farmers feed the world—and why they need our help to keep doing so.

Digging Into the Soil Biome 

Every grocery store, farmer’s market, and restaurant you’ve ever visited exists because of microorganisms. 

Soils, plants, and their microbial ecosystems underpin 98.8% of the calories humans consume through a cycle of symbiotic (mutually beneficial) interactions.² Let’s dig into a few: 

• Food production begins when the microorganisms in soil break down organic matter (dead roots and leaves, animal manure, etc.) into nutrients that plants can use to grow, like nitrogen, phosphorus, sulfur, and potassium. Without microbial recycling, these nutrients would stay locked in dead material and be unusable to plants.
• Soil microbes gather in the rhizosphere, the region around a plant’s roots, to shuttle these nutrients where they’re needed most.³ You can think of this transport area as the “gut microbiome” of a plant—essential for digestion, nutrient absorption, and defense against pathogens.^4,5  
• At the same time, microbes also help give soil its structure. They hold sand, silt, and clay particles together, helping form stable clumps (aggregates) that can stay strong against forces like wind and rain. They also create tiny pockets that absorb moisture and store it for plants, forming a sponge-like environment that’s resistant to drought.⁶

Soil and its microorganisms also help support plants’ ability to pull carbon dioxide out of the atmosphere and utilize it for photosynthesis. And when plants die, microbes break them down into their constituent elements (mostly carbon) that can then be stored away underground. This process, called carbon sequestration, helps reduce CO₂ in the atmosphere and combat climate change.^6,7 

All told, soils store 3.1 times more carbon than the atmosphere itself—a key carbon sink that keeps our environment habitable.⁷ It’s a beautiful reminder of the “One Health” philosophy that healthy humans rely on a healthy planet. 

“Belowground diversity is foundational to nearly all life aboveground,” Erin Miller, a Senior Manager at SeedLabs, summarizes. “Yet it’s often overlooked in discussions about climate, food systems, and human health.” 

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We’re Treating Soil Microbes Like Dirt

When soil is rich in diverse, beneficial microbes, it’s a breeding ground for fast-growing, nutrient-dense plants. Soil that lacks microbial diversity, on the other hand, tends to be dry, rough, and ill-suited to grow crops without chemical inputs (i.e., fertilizers and pesticides). 

Unfortunately, many of the tools and techniques we currently use to grow food at scale reduce the number and variety of helpful microbes underground.⁸ 

Beneficial soil bacteria rely on a steady supply of organic matter to survive and thrive. This material is conspicuously absent on many of today’s monoculture farms, which only plant one type of crop year-round (draining the soil of certain nutrients), don’t use cover crops to feed soil or hold it in place, and don’t replenish soil with nutrient-rich amendments like compost. 

Many farms also use tilling machines to prepare large swaths of land for planting. While these machines effectively loosen and aerate soil, they also disturb beneficial microbes and make way for fast-growing microbial competitors.⁹ 

Applying synthetic fertilizers and pesticides further disrupts microbial communities underground, reducing their ability to protect plants from predators and kicking off a cycle in which farmers need to apply more and more chemicals to their land.¹⁰

Our reliance on plastic further threatens soil health. Microplastic and even smaller nanoplastic (which measure in at less than one micron, or one-millionth of a meter) particles can carry toxic chemicals and metals on their surface and block essential inputs like sunlight and rain from soils. They are also covered in microbial communities of their own (nicknamed the “plastisphere”), some of which may be harmful to plants.¹¹

We are just beginning to understand how plastic debris impacts our food system, but it seems to be able to reduce bacterial populations and hinder plant growth.¹² According to one estimate published last month, microplastic exposure could already be destroying up to 13% of terrestrial crops worldwide each year.¹³ 

Nearly every industry relies on plastics, and agriculture is no different. Plastic mulch films, plastic seed coatings, and plastic irrigation tubes are just a few farming mainstays that can shed microparticles into the ground beneath us.¹⁴

Clearly, current industrial farming practices are incompatible with healthy soils. But they don’t need to be. It’s more than possible to grow food in ways that support not just crops, but the microbes that feed them.

Visions of a Flourishing Future

What would agriculture look like if it were designed to maximize soil microbe health instead of crop yield? 

Farmers would load up on compost to replenish organic matter but minimize chemical fertilizers to avoid disrupting natural microbial nutrient cycles. Natural pest control methods, such as beneficial insects and microbial biocontrols, would protect crops without harming beneficial underground communities. Fields would likely be planted with a rotating variety of crop types to promote an abundance of microbial diversity, and underground communities would flourish without disruptions like machine tilling.¹⁵ 

To help make this future a reality, we can buy from farmers who are already instituting these more regenerative farming practices, and support policies that provide funding for others to follow suit.

On a smaller scale, we can build the world we want to see in our own backyards. If you have a garden or green space, you can conduct your own soil revitalization by spreading organic matter like compost (bonus if you make your own!) onto your yard; allowing leaves, trimmings, and branches to decompose and feed soil bacteria; and minimizing the use of plastic coverings and chemical pesticides and fertilizers. 

The Key Insight

The ground beneath our feet is alive with microbes that combat some of today’s biggest challenges—from climate change to food insecurity and human well-being. The microorganisms in soil break down organic matter into nutrients for plants, help retain soil structure and moisture, and keep carbon out of the atmosphere. Industrial agriculture practices, climate change impacts,  and microplastic pollution are degrading this vast underground network, but we can all play a role in restoring it.