What is the soil microbiome?

The soil microbiome is the community of bacteria, fungi, and other tiny organisms living in soil. It is enormous. A review in Nature Reviews Microbiology describes soil as holding the most diverse and complex microbiome on Earth, and Colorado State University researchers note that a single handful can contain tens of thousands of different species.

Why it matters for plants and food

These microbes do quiet, constant work. They break down dead material and cycle nutrients like nitrogen into forms plants can use, a role the USDA Natural Resources Conservation Service describes as central to a working soil. Many live around plant roots, helping them draw up nutrients, fend off disease, and cope with stress. A research review by Banerjee and van der Heijden describes these root-zone microbes as shaping how well plants grow. Our food grows out of this web, so soil health and food health are closely tied.

The thread to the gut

There may be a thread running from the soil to us. Microbes that live on fruit and vegetables can travel into the human gut, and some research suggests they may add to its diversity. A 2025 paper in Nature Communications sets out a soil-plant-human gut axis, the idea that the microbes we have lived alongside for a long time helped shape our gut and immune systems. This is an active area of study rather than a settled story.

Worth being curious about

Soil isn't just dirt. It may be one of the busiest living systems we walk past every day. Next time you're handling soil, or rinsing a bunch of vegetables, you could notice the chain that runs from the ground to your plate to you. That small act of noticing is a quiet way in.