Healthy microbiome delivers yield, manages nutrients

CHAMPAIGN, Ill. — Even though a microscope is needed to see them, they’re mighty in size for their role in maintaining soil health, supporting plant growth and ensuring a functioning ecosystem.

Soil microbiome are microscopic organisms that help drive below-ground nutrient cycling, contribute to soil carbon formation and improve the uptake of nitrogen, phosphorus, potassium and other nutrients.

They also have the ability to support soil structure, contributing to water filtration and access.

Lizzie French, Waypoint Analytical soil biology manager, and Mick Goedeken, Waypoint Analytical regional agronomist, discussed the role of microbiome in nutrient management in a recent Illinois Nutrient Loss Reduction podcast with host Todd Gleason and producers Rachel Curry, Nicole Haverback and Luke Zwilling.

Waypoint Analytical uses DNA analysis through soil testing to identify specific microbial functions, including nitrogen fixation and phosphorous solubilization.

Gleason: Why is the soil microbiome so important?

French: The soil microbiome is everything, all the living organisms you can’t see in your soil. You have bacteria, you have fungi, you have viruses, protists, nematodes. There are thousands of different species of organisms.

If you pick up just a spoonful of soil, there’s going to be billions and billions of these tiny microscopic organisms living in your soil, making up that soil ecosystem and doing a lot of really important jobs that we don’t always think about just because we can’t see these organisms.

They’re really important for nutrient cycling, mineralization of nutrients, breaking down residues, building up soil structure — all really important things that need to happen in our soils from both from a production standpoint and a conservation standpoint.

Gleason: Can you put it in terms that I can understand as a farmer who just wants to know what nitrogen, phosphorous and potassium might look like on my soils?

Goedeken: For years, as producers or agronomists, we’ve focused on the chemistry aspect of the soil, getting the soil chemistry correct. Then we started looking at the physical properties and saying, now this biome portion is bringing everything.

We have the biological, the physical and the chemical all included in it so that we can see exactly what that soil can do for us and make us more efficient.

Some of the things that the biome test allows us to see is how many microbes are out there that can help facilitate keeping nitrogen in an available form.

Nitrogen is a very complex cycle and is biologically driven. If we have the wrong microbes in there, we’re going to cause a lot of denitrification. We don’t want denitrification to happen.

If we know more about our soil, we can know more how to treat that soil and how to apply our nitrogen more efficiently.

Gleason: This is about the biology, the mechanics of the soil, really the ecology of the soil itself and how it works together. What do you think creates a healthy soil across the Corn Belt?

French: It’s those three components together. You need to have the soil structure that allows you to have good air infiltration, good water infiltration. The soil biology plays a role in that where you’ve got microbes producing these sticky glues that help kind of build that soil structure. You need the chemistry.

You have to be able to grow a crop. That’s what soil health is in production agriculture. You have got to be able to grow a crop and you want your grandkids to be able to grow a crop, too. So, you need to have the chemistry there to be able to grow that crop.

“Whether you’ve realized it or not, you’ve been farming your microbes this whole time.”

—  Lizzie French, soil biology manager, Waypoint Analytical

The biology piece interacts with all of that. You need to have a healthy, thriving community of microbes that are able to cycle those nutrients into available forms that are helping to build that soil structure, and all of those things affect each other.

So, when you’re talking about the Midwest, having sufficient levels of the nutrients that you need to build those crops, having solid soil structure and then having high, high levels of soil biology that are able to then make those nutrients available, keep that soil structure where it needs to be.

Gleason: How is it that you measure a microbiome, and are there good things and bad things about it?

French: There are lots of ways to measure. The thing most people are probably familiar with is something like the Haney test where you’re getting a respiration metric. That is really kind of a 40,000-foot view of how much overall microbial activity do I have, and are they living and breathing?

That is a great high-level metric. It doesn’t tell you specifically what those microbes are doing and what they’re capable of doing in your soil.

With our test we’re looking at the DNA of the microbes in the soil. When you do a nutrient extraction, you have a specific process where you’re separating out those nutrients, and then you’re able to analyze them on an instrument.

We’re doing the same thing, but we are finding the microbes in the soil, taking their DNA, and then we’re able to specifically look at that DNA and say, how many of you are nitrogen fixers? How many of these microbes in the soil can solubilize phosphorus?

How many of you are mycorrhizal fungi that are going to help essentially extend the root system and help those that crop acquire more nutrients?

Gleason: Mick, you’re an agronomist, you’re also a farmer. When you talk to producers after they’ve taken a look at what their soil biome is like with Waypoint Analytical, how do you tell them about deploying that biome and what practices will help them to do so?

Goedeken: The best way I can describe it is we take the information that is in that biome test and we can manage our individual fields more successfully. If I know a field has a lot of phosphorus-mineralizing bacteria in it that’s going to make phosphorus more available, then I can be assured that I can manage that phosphorus more efficiently in that field.

If I don’t have that, then how do I get to there? I’m a true believer that a lot of the bacteria that we need in our soil is there. We just haven’t fed it the right way to get it to where we need to get it, and so then maybe it’s a practice where we change what we’re doing so that we can build the bacteria there.

Gleason: It’s important to understand how the soil biology interacts with the fertilizer management. Can you improve the biology to manage that fertilizer? How do you do it and what are the biggest opportunities?

French: From a big-picture perspective, any practices you can implement. This part maybe gets re-branded every 10 years or so, but it’s still the same principles of you can boil it down to your microbes need food and they need housing.

If you think of that from a soil health perspective, that’s protecting your soil structure — minimizing tillage as much as possible. That’s going to prevent you from breaking up all of those nice fungal networks that spread out throughout the soil and help your crop get to nutrients, and it’s going to help protect the soil structure, protect the housing for those bacteria, as well.

Then you need to feed them. Whether that is through organic inputs, like manures, composts, all of those things provide carbon to the soil for those microbes to live. Cover crops keep a living root in the soil for a longer period of the year, where you’re able to then feed that soil biology longer.

All of those practices are going to build up those populations of microbes overall and help you do more with the fertilizer that you’re adding, because you’re able to then soak up that fertility into that microbial biomass that you’re feeding.

You’ve got populations of solubilizing organisms and mineralizing organisms that are going to help if, say, phosphorus is getting tied up in your soil, you have that microbial activity that can help kind of bring it back into solution versus if you if you have lower levels of biological activity, you’ll need to apply more fertility to get the same result in your crop.

Gleason: What kinds of things should farmers understand about the soil biome, the test that you provided at Waypoint? How they might deploy it?

French: Whether you’ve realized it or not, you’ve been farming your microbes this whole time. They’re they’ve always been a part of the agricultural system whether we recognized what they were doing or, or we didn’t. They’re a huge component and it’s a big blind spot if you don’t know where you’re at as a system in terms of your levels of soil biology.

I would encourage folks to just to take a look, try just one or two samples across across a field that’s got maybe some variability in yields where you can maybe try to understand, “Hey, is this low-yielding area on my field that maybe is normally on a high-yielding field, is that a biological limitation or is there something else going on there that you might be able to identify with this type of testing?”

Just being able to think through better how to use the fertilizer you’re applying most efficiently when you have all of the information available about your field.

Gleason: Are there things farmers should consider before getting a soil biome test?

Goedeken: Consider learning from what you’ve done and don’t be afraid to change, because when you do this biome test, you’re going to learn some things.

Not every field’s the same. A blanket treatment of your entire farm doesn’t work. If we start managing field by field, I think we can improve efficiency a lot.