Image credit: Trace Genomics

How Trace Genomics is bringing soil analysis out of the dark with hi-definition genome sequencing

February 23, 2023

A new class of biological inputs and precision farming tools promises to unlock economic benefits for farmers and ag companies with minimal impact on the planet.

But, according to Poornima Parameswaran, CEO, president and co-founder of Trace Genomics, a provider of comprehensive, precise soil analytics, much of the work in alternative crop health protection today is “being done in the dark” because of the limitations of current soil analysis tools.

Put another way, we simply don’t know enough about what’s going on in the soil to effectively match various problems in the ground with their appropriate agtech solutions. The result is often less-than-maximum yields and wasted resources.

As a newly released report from the company outlines, Trace Genomics addresses the soil analysis problem with its hi-definition genomics technology that can decode and catalog the complete soil environment.

Limitations of current soil analysis

The soil ecosystem is made up of billions of microorganisms that perform vital functions, from decomposing plant matter to ensuring plants are able to take in nutrients like nitrogen and phosphorus. Every field must have an optimal mix of these microorganisms in order to grow the most robust crop.

Typically, though, even just knowing what that optimal mix is eludes farmers and agronomists. As Parameswaran notes, most still use the soil analysis methods and technologies from the mid-20th century.

And yet, today’s farmer or agronomist is inundated with new ag technologies, including biologicals, precision agriculture software and hardware, and data analytics platforms.

“Optimizing how we manage soil can help set the stage for better utilization of the products and technologies that we already have today, as well as new technologies that will help us with food security and making it economically viable to do farming right,” says Parameswaran.

Image credit: Trace Genomics

A “systems approach” 

Trace Genomics’ report explains how the company’s “systems approach” is a more effective means of analyzing soil.

Other technologies — the DNA sequencing method 16S, for example — can name and describe what microorganisms might be in the soil. But when it comes to connecting the microorganism to their function, the line is dotted at best. Because of this, turning data into actionable information – for example, knowing what biologicals to use, and when and where to use it – is murky in the context of methods such as 16S.

As the report notes, “…just because you know someone’s name doesn’t mean you know their personality.”

Trace Genomics instead uses a type of DNA sequencing called whole-genome sequencing that can directly quantify the abundance and the functions of microorganisms.

“Measuring and modeling the abundance of microbes in the soil (for example, those that cause disease) is important for seed selection, and use of seed treatments and crop protection to improve productivity,” Parameswaran notes. “Scientifically validated interpretation of soil function is required for optimal application of fertilizers, biologicals and other soil amendments to manage nutrient cycling, soil health, carbon and crop health. And both are important when it comes to choosing the right management practices.”

“With whole-genome sequencing, you get information on both who’s there in soil as well as what they do,” she adds. “It’s a far more powerful technology for turning microbiome data into action you can trust, and Trace Genomics is doing it at cost, speed, scale accuracy.”

The geography of microorganisms

Another point highlighted in the report is Trace Genomics’ ability to map the geographic patterns (including abundance) of where pathogens live. This enables a farmer or agronomist to compare data from their fields to abundance benchmarks for their geography and crop of interest.

Farmers and agronomists can use this information to determine how to treat fields.

For example, if Trace Genomics shows a farmer is in the 60th percentile in a defined geographic area for sudden soybean death syndrome, they might think about planting a different bean variety or using the proper crop protection products.

Conversely, if they are in the 10th percentile, they might not use a different variety because doing so could have a yield-drag effect, says Parameswaran.

Beyond agriculture

As the report notes, this type of data aggregation and analysis isn’t just for agriculture, but also for human health, and is particularly relevant for tracking emerging diseases to determine how quickly are they spreading and to which areas. This is no different than current genomic surveillance efforts to track Covid in sewage systems, but as applied to tracking emerging human pathogens in soil.

For example, Trace Genomics has been tracking the pathogen Coccidioides immitis and where it can be found in high concentrations in the soil. This pathogen does not affect crops, but it can cause a fungal infection in humans called Valley Fever.

“One of the main reasons we started Trace Genomics is that we really believe the data from the soil is impactful not just for agriculture – but for systems decisions at the nexus of plant, animal, human and planetary health,” says Parameswaran.

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