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The Science Behind It: Soil Microbiome 101

“The Science Behind It” is an educational video series by Dr. Tuesday Simmons, science writer at Trace Genomics. It was created to illuminate the scientific foundations of soil microbiology that form the basis of Trace technology.  This video is about the significance of soil and its microbiome, including the diversity and impact of microorganisms on soil health, and how understanding the soil microbiome can help farmers cultivate healthy soils for successful crop growth.

Video Script:

Soil. It is oftentimes underappreciated, but arguably the most important consideration for farmers when they sit down and plan out how they’re going to raise a successful crop. Soil is made up of minerals and rocks, organic matter, and (my favorite) microorganisms (also known as microbes).

In general, all the microbes that live in a specific environment are referred to as a microbiome. I got a PhD in microbiome sciences, and what is really exciting to me is that everything has a microbiome! Humans, our dogs, the lake you’re going to this summer, hot springs at Yellowstone, the crops we grow, and (you guessed it) soil. All of these microbiomes are very different and distinct, and as a microbiome scientist, the soil feels a bit like the final frontier. There is a lot still waiting to be discovered.

A lot of other, non-soil microbiomes consist of very simple communities, and by that I mean that there are way fewer species. In 1 teaspoon of soil, there can easily be 1 billion microbes. That’s billion with a “B”. That’s double the number of humans in the European Union. Not only are there a billion microbes in a teaspoon of soil, but those can represent anywhere from 10,000 to 50,000 species. For comparison, the number of microbial species in your gut microbiome is more on the order of 1,000. Trying to understand a community of 1,000 species can be a lot easier than 50x that amount. Of all the different species on Earth, 25% live in the soil.

When I say “microbe”, a lot of people will think “bacteria”, but there are other types of critters in the soil microbiome. There are microscopic animals like water bears (yes, those are a real thing), fungi, protists, and viruses (which may or may not be considered living, but that’s a debate for another video). Overall, most of these are either beneficial or neutral to humans and plants; pathogens are a small minority. And having a high diversity of microbes can actually help protect plants from pathogens because this makes the microbiome resistant to any invaders.

Much like how an upset in our gut microbiome can cause health problems for us, an unhealthy soil microbiome can be a cause or consequence of an unhealthy environment. What does it mean for a soil microbiome to be healthy or unhealthy and how do we measure that? That’s still a big debate among scientists, but in general, the things that make a soil healthy are:

  1. Being physically stable (not prone to erosion) – this is like having a house with a strong foundation to build on
  2. Good water holding capacity and regulation – we want the water to percolate down through the soil and into plant roots where it should
  3. Full (but not too full) of nutrients – carbon, nitrogen, phosphorus, and potassium plus many other essential micronutrients are stored and cycled in a healthy soil
  4. Breaking down or immobilizing harmful chemicals
  5. Healthy soil is able to sustain a diverse, productive ecosystem above ground

Of these points that make a healthy soil, which ones are impacted by the soil microbiome? Well, all of them. Microbes impact the structure of the soil to make it physically stable and able to hold water. They transform nutrients and help plants uptake those nutrients. They’re capable of bioremediation of harmful chemicals, or even essential heavy metals that might be present in too high of a concentration. And we know they can help protect plants from pathogens, and help plants grow during stressful weather like drought and high temperatures.

At Trace Genomics, we want to help farmers cultivate healthy soils through knowledge of their soil microbiome. By providing easy to understand, action-driven reports, that is what we do.

About the author: Dr. Tuesday Simmons is the Science Writer at Trace Genomics. She earned her Ph.D. in Microbiology from the University of California, Berkeley, studying the root microbiome of cereal crops.