November 1, 2016

SOIL ANALYSIS Trace Genomics Brings Cutting Edge Technology to Testing

Using high-tech genome sequencing, a San Francisco start-up company is beginning to offer growers a much more detailed, and quickly achieved, look at their soil profile before planting.

Trace Genomics, which won an innovation award at the July Forbes AgTech conference in July, is currently offering growers a pathogen panel test for $199, which delivers a snapshot of soil-borne diseases.  Results from the soil test are available within three weeks, which allows a grower the opportunity to make important cultural decisions before the plants are in the ground.

This panel approach takes a look at 10 different microbes, including Verticillium, Fusarium, Macrophomia, and Phytophthora.  The company is also developing other products, based on the same concept, which will be unveiled over the next several months.

Western Growers Senior Vice President of Science, Technology & Strategic Planning Hank Giclas believes the company has a bright future in the ag space.  “Trace Genomics is a great example of young, brilliant minds who want to connect with the agricultural industry to solve problems,” he said.  “Their current services will test for disease pathogens.  Their technology, to quickly and cheaply examine the microbial diversity in the soil, will be helpful in mitigating crop loss to key pests and disease.”

The company was founded by two Stanford PhDs, who met while working on genomic sequencing during their doctoral programs.  Co-founders Poornima Parameswaran and Diane Wu were initially studying how infectious diseases can be transmitted across populations through touchpoints, such as a door knob or soil.  Genomic sequencing, they found, could be used to quickly identify the disease profile of difficult environments.  Fast forward a few years as the pair joined forces to try to market the technology in a meaningful, and profitable way, through the participation in an “accelerator” program, designed for just that purpose.  Parameswaran said the commercial application of discovering soil-borne diseases in agriculture is much more apparent than in the human infectious disease world.  She explained that in agriculture there are many tools available to fight these diseases once they are identified.  That is not the case with human infectious disease.  Consequently, initially they are viewing agriculture as a clearer path to viability.

Wu said the proprietary genomic sequencing process and data interpretation that the firm has developed is “sector agnostic.”  Over time, the firm does plan to use the process in other areas of diagnostics, including human infectious diseases.

But for the time being, testing soil is their niche.  “Early detection of diseases is the crucial first step for disease prevention and management,” says the firm’s website.  “At Trace Genomics, our vision is to make it easy for growers to understand the disease pressures in their land before putting plants into the ground.”

Wu called these pathogens “silent killers” with the control of them being the difference between profit and loss.  Parameswaran said it is currently an information problem.  Many growers currently use a chemical-based test on their soil.  That does not present a full picture and it takes much longer to get the results…typically three months.  Senior Scientist Scott Hickey explained that the chemistry test looks at the chemistry of the soil while the Trace Genomics tests looks at the biology of the soil.  Neither test makes the other obsolete, but rather they can be used in conjunction with each other.  The chemical tests, which many PCAs and growers utilize, test the make-up of the soil determining, for example, whether it is nitrogen deficient.  Wu said chemical tests can look for pathogens on a one by one basis.  Parameswaran likened the chemical test approach to using a flashlight to shine a light on a specific pathogen that you are searching for, with each test costing $75 to $150.  She said the Trace Genomoics pathogen panel screening approach is like turning the lights on and seeing everything that is there (or at least 10 different pathogens) for one relatively inexpensive price.

Growers or PCAs (pest control advisors) can go onto the Trace Genomics website and order the pathogen panel test.  Initially the tests have been designed for strawberry and lettuce fields as those two crops have immediate need for soil-borne disease knowledge because of the elimination of methyl bromide as a grower tool.

The company’s website spells out the technology behind the effort.  “Our proprietary molecular assay for soil-borne pathogens enables affordable detection of hundreds of pathogens and beneficial organisms simultaneously.  Our assay is based on genetic sequencing technology, enabling strain-specific identification and quantitation.”

Ordering the pathogen panel test from Trace Genomics is a very simple process, also spelled out on the company’s website (  Growers order the kit, follow the instructions for gathering a soil sample and send it to the firm.  Within three weeks, a report will be generated illuminating the disease profile of that sample.


Trace Genomics Launches Healthy Soils Program


In an effort to increase the body of knowledge related to healthy soils, Trace Genomics is asking growers to participate, free of charge, in an effort to identify the makeup of productive soil.

The San Francisco-based firm, which provides a genome sequencing-based, pathogen screening test for unhealthy soils, is partnering with growers and academics to launch a “Microbial Soil Health Initiative,” championing a community-wide-effort to work together and advance the science and knowledge about soil biology. This initiative is structured to meet an urgent need for identifying what makes a soil productive from the perspective of the millions of microbes in the soil that are responsible for soil and crop productivity. The long-term goal for this program is to develop and open-source a set of tools and strategies to help us increase the health of our soils individually and as a community.

Company Co-founder Diane Wu said each samples that is analyzed will add to that knowledge.  The more samples the company receives and analyzes, the greater the knowledge will be.

She said there is no charge to participate and the researchers will disseminate the information in some form—possibly a white paper—as trends develop and information is accumulated.

“Through this joint endeavor, we will work closely with growers and academics to build a representative collection of productive soils. This collection will allow us to surface community insights on the microbial composition of our healthy soils in California,” said Wu, adding that insights from this project will be aggregated and anonymized to protect individual sample identities, and made available for access by all participants in the initiative.

She added: “We are actively collecting samples, and welcome growers to send in samples from their healthy, productive fields. For more information about how to get involved, please email us at [email protected].”