A surge of research into the human microbiome in the last 20 years unveiled that there are as many microorganisms in and on the human body as there are cells. And now plant research is following in these footsteps. Scientists are creating ways to treat seeds with optimum microbials at high density to increase crop production, says Mekdem Tesfaye, a 5-year research associate at Indigo Ag.

The company hosted a webinar in November to teach no-tillers how microbes work, the on-farm benefits and demonstrated results of certain traits of microbes under real conditions, and recommendations on new biological offerings.

From Plants, For Plants

Indigo Ag's agriculturally beneficial microbial isolates come from inside the plants or the rhizosphere, the area of soil close to the roots. The company focuses on a subset of these microorganisms called endophytes, which are often a fungus or bacteria within the plant.

"These microbes make their homes inside the plant tissues, forming closed, long-term associations with their plant host. They have co-evolved with the plant," Tesfaye says. “Beneficial fungi often produce antibiotic molecules that inhibit the growth of pathogenic strains."

Microbial ecologists say there is likely a naturally occurring microbe to combat the environmental stresses a crop could encounter in the field, including fungal disease, insects, nutritional deficiencies and stress from draught. The key is identifying the right microbe and then introducing any missing microbes through seed treatments. 

"Our seed treatments are sort of a plant probiotic," Tesfaye says. "We try to understand what the microbial community in a healthy plant looks like. We travel to healthy agricultural fiends undergoing stress and identify the plants that seem resilient to that stress and those non-resilient to it. We sequence all of the microbial community present in these two subpopulations as the microbiome of the healthy plant."

For example, a field in Iowa seemed to be experiencing nitrogen (N) deficiency, which Indigo confirmed through analysis of plant tissue and soil nutrient analysis. An agronomist team collected plants that were showing resistance to the N deficiency stress and plants that were unhealthy and exhibiting N deficiency, and brought them back to the company's Boston labs. Researchers sequenced the fungal and bacterial microbial communities of both the healthy and unhealthy plants. 

The lab determined that there was a large variation in the microbials of the healthy plants in comparison to the unhealthy ones. They isolated two microbial groups that possessed N-fixing organisms present in the healthy plants. Indigo concluded that the microbes associated with the healthy plant are providing them and advantage in this stressful environment, says Tesfaye.

Indigo has collected over 8,000 plant tissue samples from across the U.S., across various crops and environmental conditions, and has more than 25,000 crop-associated microbes isolated and identified to date.

“We use this data to isolate, identify and sequence this genome of each of these unique microbes, allowing us to predict or nominate which candidate which might be best for our research and development pipeline, giving us a deep understanding of these microbiome communities," Tesfaye says.

Creating Commercial Product

The company utilizes a three-step process for identifying and isolating microbials: laboratory testing, greenhouse testing and field testing, says Kevin Calzia, senior director of formulations and quality assurance at Indigo.

“We have to make sure these microbes stay alive through the seed-treatment process," he says. "We do this is by keeping the microbes dormant, so they don't grow until put back in the soil with nutrients and water — the same way a seed grows once it has nutrients and moisture.

"The fermentation processes are akin to brewing beer or other sorts of industrial microbial growth. You don’t want a microbe coming out of fermentation that is on its way to being dead. We want one coming out young and healthy. We do this by adjusting the nutrients during fermentation."

Once out of fermentation, researchers determine if the microbe will perform best as a liquid or powder. Key factors include the market — where the product will be used and why it will be used. Additives might be included to make the microbials adhere to the seeds better. Dilution to the best concentration before treating the seed could also be part of this work, Calzia says. 

Seed Treatment Options 

Indigo's microbials are available in three formulations: water dispersion, a liquid state that can be dispersed using standard seed-treatment equipment; wettable powder that is dispersed in liquid and then applied using standard seed treatment equipment; and flowable powder applied directly to seeds. The stability of each microbe helps determine the formulation. The microbes dispersed in water are the most stable, followed by the wettable powder and the flowable powder, the least stable of the three. Calzia says the flowable powder does not do well around moisture, but it’s the best for on-farm treatments. 

Uniformity in seed coverage is critical. Indigo has been able to document that they are meeting these two criteria through laboratory work, specifically for treatment of corn seed. If instructions are followed, no-tillers can expect to have 10,000 microbes per seed of when applying a half-ounce of product to a 50-pound bag of seed.

"This means that you're going to have all the seeds covered at the same level of dose and the same level of response for each of the corn seeds that have been treated," Calzia says.

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