Coming Next in Smart Farming Agronomy —Digitizing the Microbiome

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AI-driven tools are digitizing the soil microbiome and will eventually become another layer of data to drive precision farming

Have you heard of 23andme? It’s a DNA sequencing tool for regular folks. Just take a cotton swab sample, mail it off and presto — a report on your personal genetic ancestry, your susceptibility to different health problems and whether you carry any genetic diseases. Pretty clever. Now imagine the same thing for your farm.

A DNA, genetic “fingerprint” of your soil. A record of all the microscopic critters, bacteria and fungi and an analysis of the complex interactions that happen below ground and support plant growth. Think of it as a “soil test” of your farm’s microbiome.

It might sound far-fetched, but DNA sequencing of soil is a significant area of soil health research. Understanding the genetic fingerprint of a farm’s specific microbiome will help farmers wondering which agricultural biologics (a market worth $7.42 billion in 2018) will work for them.

Instead of taking a chance and plunking down some hard-earned dollars for the latest “Foo-Foo Juice” sold at the co-op, farmers that know their soil’s DNA sequence will be able to choose the right “juice” for their farm, with the correct bacteria (or biopesticide, biostimulant or biofertilizer) needed to address their soil issues. 

It doesn’t matter if a particular biologic achieved astounding results in published field trials if the bacteria or stimulants they add are ones your farm already has naturally.

Unlocking the DNA of a farm’s unique microbiome “fingerprint” makes agricultural biologics a much more palatable and effective purchase. It isn’t just any biologic that will do the trick, but the one that is right for your specific farm’s soil DNA.

Soil DNA Sequencing is Becoming Widely Available

If it feels like everybody (and everything) is getting their DNA sequenced these days, that’s because they are!

Advances in genomics have made whole genome sequencing much easier, cheaper and faster (hence the popularity of human DNA-sequencing services, like 23andme). This has created many new applications like the FDA’s genomic sequence to track foodborne illness outbreaks. Or mapping the entire genome of sheep (from the University of Roslin, the same folks that brought us Dolly, the first cloned mammal), useful for isolating genes that affect sheep’s physical and physiological characteristics.

But nothing is ever that simple when it comes to soil. Our cropland isn’t made up of just one DNA-sequence — like humans or sheep —but is its very own ecosystem. It’s the genomes of all those microscopic critters — bacterias, fungi, algae, nematodes and protozoa — and their more visible brethren — springtails, mites, earthworms, ants, beetles and other underground insects — plus how they work together that we care about. Scientists call this ‘metagenomics‘— the study of a collection of genetic material from a community of organisms.

It’s a lot of information to take in but technology is an amazing thing. Companies like Trace Genomics and BiomeMakers are building out services using machine-learning and cost-effective data analysis to sequence and index unique soil samples. Then, they are taking that analysis and making recommendations.

Sequencing still isn’t cheap at around $150 a sample, which can be high for a commodity crop farmer. But when farmers consider the amount of information they get and the much deeper level of insight into soil health DNA sequencing provides, it could quickly become a game changer.

We All Have That “One” Field (Or Section)

On Gunzenhauser Farms, we farmed land neighboring our own for two generations.

Eventually, my dad purchased the piece and about a decade ago, we took out the fence. Now we farm the whole section north to south. To this day, I can always tell when I have crossed the line between our original farm and the newer piece. The soil feels different and the weed population is unique.

Every farmer has a similar story. That one field that just never performs quite the same. Or even that poorly-yielding section of an otherwise solid piece of land. If that soil could tell a story, it probably would – which is what it does with microbiome sequencing.

With precision farming techniques, we have already been working to address those problem areas — heavier fertilization applications or adjusting our variable seeders to fit specific conditions. Now, imagine we have also digitized the microbiome of those problem areas.

Suddenly we can understand the unique challenges of that specific area’s underground soil ecosystem on a molecular level. Once we know that, we can identify which biologics are a match to address our problems. Combine that with precision planting techniques and we now have a new piece of the puzzle toward optimizing soil productivity on a granular level.

Soil DNA sequencing, once it’s widely adopted, will take working with your trusted farm adviser and getting your annual crop prescription to the next level. Maybe we’ll call it a “hyper-prescription.”  

Combining Soil Microbiome Sequencing with Whole Farm Digitization

Now the race is on. Who will put microbiome sequencing together with fertility analysis and develop recommendations that are differentiated and proven to be of value? I expect we’ll start to see this in the next five years or so.

The ultimate goal is digital, farm-specific tools giving certified service agents and farmer’s agronomic advisers the ability to combine fertility analysis, market predictions, yield projections, weather, satellite-directed crop scouting, farm practices and financials supercharged with a new understanding of each farms’ individual microbiome.

We will be able to model whether the cost of the biologic outweighs the projected financial gains of an expected yield increase. And how that biologic application might pay off toward better soil health for years down the road. With time, the year-over-year information farmers gather and record digitally about their microbiome will inform us about what helped and what didn’t, revealing even more insights.

Give us just a few more years and we will be talking not just about precision farming but precision soil health. For better & more profitable farming of course.

About the Author

Bob Gunzenhauser is the Agronomy Science Manager for Granular, part of Corteva. Bob has been involved in the development of Decision Agriculture over the last 25 years, from its early days of yield monitors to today’s predictive analytics and crop modeling. He has developed a well-rounded background that spans technology, agronomy, farm management, and software development, with the ability to put new ideas and concepts to work to help feed the world more efficiently. Bob has led development of software and practices that enable growers to fully take advantage of the insights their operations generate, and supported those developments with his personal experience as a fifth generation farmer in Iowa. Bob holds Bachelors of Science degrees in Ag Systems Technology and Ag Education and a Masters degree in Business Administration, all from Iowa State University.

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