Soil microbes, human health and what we don't know

Soil microbes, human health and what we don't know

Scientists have identified only about 1% of the microbes that live in the soil; curiosity about other 99% grows

More than a billion different bacteria, fungi, archaea and protists live in a single teaspoon of soil. While it might be difficult to imagine miles and miles of these microscopic organisms, called microbes, in that tiny teaspoon, perhaps even more interesting is scientists only know about 1 percent of them.

“It’s fascinating, at least for microbiologists, because some would argue soil has the most diverse ecosystem. The most unknown living organisms are in the soil,” said Chuck Rice, a soil microbiologist and distinguished professor of agronomy at Kansas State University.

SOIL AND HEALTH: Scientists say they know about only 1% of the microbes that live in the soil. Now, there are new efforts to learn more about the other 99% and unlock the human health benefits they might provide.

Many people understand that soils are necessary for growing plants, Rice said, and they help clean water. But, what most people don’t understand is the value of soil microbes directly for human health. As an example, about 90 percent of antibiotics we use currently come from these microbes. Other drugs, including anti-cancer and immunosuppressant drugs, have been discovered in soil as well.

“If you realize that we only know 1 percent of those microbes in the soil,” Rice said, “what are the other 99 percent doing for us or have the potential to do for us?” 

In addition to supplying humans with micronutrients in foods for growth and development, and drugs to ward off diseases, soil microbes are the key components for health in all features of the planet—such as water, air and other aspects of the environment. “Soils Support Health” is the August theme for the 2015 International Year of Soils.

 History of efforts in medicine

Rice said perhaps the two most famous instances of using soils to create disease-fighting drugs are Alexander Fleming’s discovery of penicillin and Selman Waksman’s discovery of several antibiotics, including streptomycin—the first effective antibiotic to treat tuberculosis. These drugs, discovered in 1928 and 1943 respectively, were discovered using cultures of soil microbes.

Traditionally, these drugs have been discovered on agar plates. The scientists examined these plates to find where disease cultures were growing and where they were not. The microbes fought culture growth in the bare areas; therefore, they could be isolated, replicated and used in medicines.

“We have concerns about the over-use of antibiotics and antibiotic resistance,” Rice said. “By digging down into the soil, we can now find new antibiotics that will help overcome the resistance that has occurred naturally from use in humans and animals.”

Most of those unknown soil organisms—that 99 percent—don’t grow on agar plates, he said. Recently, scientists have been using a modern technique called metagenomics that allows them to extract the DNA of microbes directly from the soil. In fact, a new class of antibiotics was discovered earlier this year using this new method.

 Extracting the DNA from the soil is a lot like how forensic scientists extract DNA from a crime scene, he said. Finding new DNA means understanding the genetic makeup of those unknown microbes and appreciating their diversity. Eventually, scientists will need to find ways to grow them and make more useful drugs for the health industry.

 “It’s not well appreciated that the microbes that live in soil live in a harsh environment,” Rice explained. “They’re used to that, but when we try to put them in a perfect environment, they don’t grow easily.”

Continued need for soil health

Soil is an extremely valuable resource, Rice said, and if we lose the healthiness of the soil, we lose potential organisms that could help us directly through disease management and through the foods we consume.

Nutrients, particularly micronutrients like zinc, are critical for human physical and mental development, he said. Microbes live on plant roots and supply the plant such nutrients. So, low zinc levels in depleted soils can affect zinc levels in plants and the development of children who consume them.

Likewise, soil health helps protect the environment. Microbes in soil help sequester carbon, Rice said. They take carbon out of the atmosphere through plants and help store it in the soil, which helps moderate and protect the climate.

Scientists at K-State and beyond are studying how toxicity in the soil that comes from lead and arsenic, as examples, can be combated with microbes that bind to those elements and prevent water contamination. Rice said soils are commonly used to in septic tanks and help purify wastewater.

“We count on the microbes to clean up that water, so as it leeches through to groundwater or runs off the surface, that water is drinkable,” he said. “With water shortage, we’re looking at ways to use recycled water for other uses, and it’s the microbes that help clean it up.”

To watch a video interview about “Soils Support Health” that features Rice, log on to the K-State Research and Extension YouTube page

The Soil Science Society of America has resources for the public, teachers and children about soil and each monthly theme for the International Year of Soils at

Source: Kansas State University News Service

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