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Kate Scow, a professor of soil science and soil microbial ecology at �鶹��ý, keeps plastic bags filled with soil on her desk.

We are meeting in her office in Plant and the Environmental Sciences Building on campus, not out at , where she’s the director of the university’s unique 300-acre research facility studying the long-term impacts of management practices and climate on agricultural sustainability. California is finally rainy again. “Our soils are sopping wet and it’s kind of hard to move around there right now,” says Scow.

One of the bags is filled with crumbly light-brown earth that holds together in small clumps. It’s from an organically-managed tomato field. Another bag holds an almost solid, gray block of dirt, like a brick of cement.

“It’s because it was tilled when it was wet. The structure has completely broken down.” She grabs the bag and holds it up. “But you might be surprised that even this boulder has some microorganisms in it. They are everywhere.”

Microbial ecology is one of Scow’s primary research areas. What she is trying to understand is how we can refocus agricultural practices “below-ground” and enhance the activity of beneficial microorganisms. Just a few of her recent research projects include looking at the sensitivity of bacteria and fungi to tillage and cover crops, and the  on managed and nonmanaged agricultural systems.

Even though microbes in soil are essential for life on earth, scientists readily admit they still know relatively little about them. What they do know is that they are very, very plentiful and very, very diverse.

“A gram of soil — about a quarter of a teaspoon — can easily contain a billion bacterial cells and several miles of fungal filaments,” says Scow.

And how many different types of organisms might be in the soil? “Soil is overwhelmingly diverse, with an estimated 10,000 to 50,000 different taxa in a teaspoon of soil. These numbers are difficult to guess and keep getting adjusted as we learn more about the soil microbiome through sequencing efforts,” says Scow, referencing genomic sequencing, which identifies organisms by their unique genetic traits.

A living ecosystem

Unlike Scow, when most of us drive by a freshly plowed agricultural field, we see dirt. We might picture the presence of a few bugs, maybe worms, but essentially, most of us see soil as an inanimate substrate into which plants grow.

But soil is actually a living entity, a diverse ecosystem that is one of the most complex on the planet. And it is one that is essential for human life through all the functions it provides — food production, water purification, greenhouse gas reduction, and pollution cleanup, to name a few.

“A lot of processes that are really important in soil, like the decomposition of organic material, goes into building up the soil structure — the aggregates — which are the structural units of soil,” says Scow. “These aggregates determine how well the water drains when it rains, how well it is retained when it gets dry. And the exchange of gases — like the ability to get oxygen to plant roots — is determined by the structure of the soil.”

What you see when you turn over a shovelful of healthy soil isn’t just happenstance. “Microbes are the architects that build that structure,” says Scow. And she points out that how we manage our farm soils can determine whether we help or hinder these microscopic structural engineers.

Healthy soils could help mitigate climate change

Gut microbes have received a lot of attention in recent years as researchers continue to unlock the complex relationship between human health and what is living in our intestines.

For humans there are helpful prebiotics and probiotics. It turns out that the Lactobacillus bulgaricus and Streptococcus thermophiles bacteria in yogurt are good for us. But are there similar “good bacteria” for plants and soils?

I ask Radomir Schmidt, a postdoctoral researcher in Kate Scow’s lab, that question. He laughs. “That’s the million-dollar question. We know there are a lot of soil microbes but we don’t know what a lot of them do. Not yet, anyway.”

He explains that there are helpful microbes in soil, but that researchers don’t yet know how interactions between soil microbes lead to different practical outcomes.

Microbes have incredibly diverse functions in the soil. There are nitrifying microbes that convert ammonium to nitrite, and then nitrate. There are microbes that can metabolize fertilizers and pesticides and even pollutants. But even though the properties of some soil microbes are known, there is a lot still to learn, such as how important teamwork among different organisms is in providing these services.

Carbon sequestration in soil

I had met Schmidt when he was attending a microbiome workshop on campus sponsored by the Office of Research to help �鶹��ý researchers network about possible interdisciplinary microbiome projects. He was there to brainstorm projects like carbon sequestration.

Soil has become a focus for looking at ways to mitigate climate change. Healthy soil is more resilient in a changing environment. It also nourishes plants, which allows the plants to remove carbon dioxide — a greenhouse gas — from the atmosphere.

And the soil itself is also a massive repository for carbon: It houses the carbon compounds of decaying plants and animals, as well as everything that lives within the soil — from microbes to worms to tree roots. And carbon is essential for soil microbes to be able to flourish.

Research has shown that changes to agricultural practices