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The Science Behind Microbial and Biological Products

Microbial products have the potential to help farmers better manage nutrients and slay pests. Improving product consistency, though, is key.

On the surface, a crop field seems as dull as, well, dirt. Underneath it, though, is an invisible war that’s constantly being waged. Soil microbes (like bacteria and fungi) continually slug it out for food and dominance. Some of these microbes are bad, but many are good since they aid in tasks like the transfer of crop nutrients or pest control. 

It’s into this fray that microbial and biological products enter. At best, microbes introduced to the soil as seed treatments or as liquid can play well with existing soil organisms and help crops better use nutrients or slay pests. Soybean farmers have long used inoculants to jump-start nitrogen-fixing rhizobia bacteria in the soil. 

At worst, these products suffer from a “bugs in a jug” stigma of the days when salesmen sold them with a shoe shine, a smile, no science, and no benefit. 

“If you look back over the last 15, 20, 25 years at the evolution of microbial products in agriculture, the road is littered with ones that have come and gone. It’s not because they never worked; it’s because they gave inconsistent results,” says Michael Miille, CEO of Joyn Bio, a joint venture formed earlier this year between Bayer and Ginkgo Bioworks to develop products to improve plant nitrogen efficiency. 

Ernie Sanders
“We want to get away from the image of the guy brewing something in a bathtub and selling it to his neighbor,” says Ernie Sanders, vice president of product development for Pivot Bio. “It’s not how the chemical industry grew, it’s not how the biotech industry grew, and it’s not how the biological industry will grow.”

step change 

Miille says the industry gained more credibility earlier this decade, when large agricultural seed and chemical companies bought small microbial firms. Bayer bought AgraQuest in 2012. Later that year, BASF acquired Becker Underwood and Syngenta bought Pasteuria Bioscience. Novozymes and Monsanto – since purchased by Bayer – closed on the BioAg Alliance in 2013. DuPont – now part of Corteva Agriscience – acquired Taxon Biosciences in 2015. 

“In Bayer’s case, I think it was concerned about the restrictions on and the (potential) loss of its chemical portfolio,” says Miille. “The company saw biologicals as an alternative solution that could either complement or, in some cases, help bolster its chemical portfolio. I think Monsanto got into it with the BioAg Alliance from a totally different viewpoint. It had this enormous DeKalb franchise that became dependent on seed treatments. It also started to see some success with some of these microbes.

“All of a sudden, you started moving from $3 to $5 million (annual) R&D (research and development) budgets to being part of $400 to $500 million R&D budgets,” says Miille. 

Farmers don’t have to use microbial and biological products to their fields to boost microbe numbers. Covering the ground year-round with cash and cover crops can spur microbial growth on its own, says Jodi DeJong-Hughes, University of Minnesota Extension soils specialist.

“Improve their food source and stabilize their environment, and the microbe numbers will grow automatically,” she says. 

Selectively optimizing microbes 

Industry officials, though, say they are aiming microbial and biological products for certain tasks. 

“The industry has evolved from just going out and collecting microbes and seeing how they work to now using technologies that actually engineer or selectively optimize microbes for specific purposes,” says Miille.

“As late as the 1970s, scientists would use microscopes to study the shapes of microbes to classify them,” adds Brooke Bissinger, director of entomology for AgBiome. Today, scientists can sequence microbe genomes at a low cost, just as they have sequenced human and corn genomes. (A genome is an organism’s complete set of DNA, including all of its genes. Sequencing DNA means determining the order of four chemical building blocks – also called bases – that include adenine, thymine, cytosine, and guanine.)

AgBiome has isolated and sequenced more than 50,000 microbes that it stores in its genome database, says Bissinger.

“From these microbes, we’ve identified more than 12 million genes, 4,300 of which have the potential to control insects, and that’s really just the beginning. We’ve screened these microbes against important crop pests and weeds, so we can go back and mine our database to find similar microbes that rapidly expand our pool of candidates,” Bissinger says.

“You can take genes from one microbe that has a specific activity and insert them into another microbe,” adds Miille. “This is being done in a specific and controlled way. It’s evolving even further with gene-editing tools like CRISPR-Cas9 and others. Much of this is now automated, driven by software and high through-put instrumentation.”

So far, the regulatory approval path is clear for microbes. “Some of it goes through the EPA (Environmental Protection Agency), depending on the claims made, and some of it goes through the states,” Miille says. “It’s a much less onerous and an easier path than the one used for transgenic crops.”

What’s on Tap

The microbial products that companies sell are multiplying faster than microbes. 

“We can take advantage of the fact that microbes are always battling it out over resources and for survival,” says Bissinger. “These microbes already know how to kill and attack pests in crops. By studying these microbes, we can figure out how they do it and then put it to good use for agriculture.” 

Microbes also have the potential to complement tools like chemicals, Bissinger adds. 

BASF’s Poncho/Votivo 2.0 combines chemical insect control in the Poncho component with Votivo’s biological control of nematodes and a bacterium that BASF officials say enhances soil microbial activity. 

Some aim at diseases. AgBiome has a federally approved biological fungicide that is effective against fungal diseases like Rhizoctonia. AgBiome is teaming with SePRO to distribute the product in the U.S. turf and ornamental market under the trade name of Zio. 

Others, like Pivot Bio, has a microbial product on tap for 2019 that pull nitrogen from the atmosphere for use by corn roots.  

“Our microbe adheres to the root of the corn plant, takes nitrogen from the air, and converts it into a form for plant uptake,” Sanders says. Nitrogen that goes directly to the roots reduces the potential that commercially applied N has to leach into groundwater or waterways, he adds.

Other products promise to boost nutrient uptake in plants, such as a class of agricultural biological products from NewLeaf Symbiotics called M-trophs, says Sherman Hollins, business development manager with NewLeaf Symbiotics. They can be applied in-furrow, on seed, or as a foliar spray.

the wild west

Microbial and biological products face several hurdles that include the following.

Limited safety and efficacy regulation. 

Fertilizers and pesticides all have state and federal regulations to help ensure safety and efficacy. 

Caley Gasch
Microbial products? Welcome to the Wild West of agricultural inputs. 

“There are no regulations,” says Caley Gasch, a North Dakota State University soil scientist. “With these products, it’s pretty much a free-for-all. There are no guarantees.”

Survivability under adverse weather. Since microbes are living organisms, weather impacts survivability. 

“Microbial activity diminishes as soil temperatures reach 80°F.,” says DeJong-Hughes. This can be accentuated in dry soils.”

Soil disturbance. “Tillage resets the clock on microbial succession and development,” says Kurt Steineke, Michigan State University Extension soil specialist. “A different community is present in no-till vs. tilled systems.”

Frosty welcome

Microbes entering the soil also face an uphill battle due to existing soil microbes.  

“The soil is a busy place and a difficult community to infiltrate,” says Gasch. 

She calculates that 1 square meter of soil 15 centimeters deep contains 105 trillion colony-forming units (CFUs). A CFU is a unit used to estimate the number of viable bacteria or fungal cells in a sample.

Meanwhile, 10 gallons for a bacterial product containing 250 million CFU per gallon adds up to 2.5 billion CFUs. 

“Adding 2.5 billion cells to a fiercely competitive community of 105 trillion cells would initially increase the cell count by 0.0024%,” she says. “These numbers don’t account for fungi, which can be just as prevalent in soils as bacteria or other soil organisms that prey on bacteria. We do not have the tools to measure and track the success of the microbes that might be added in a commercial product.”

Any yield bump that may occur could be due to the death of nutrient-packed microbial cells that act as fertilizer, she adds. 

Guerrilla warfare

Most agricultural microbial products aim at the soil surrounding plants, says Geoffrey von Maltzahn, co-founder and chief innovation officer with Indigo Ag. 

“You’re attempting to add a microbe into a guerrilla warfare situation, where the number of unfriendly microbes vastly outnumbers the relatively small amount of microbes that you’re providing to that community,” he says. 

That’s why Indigo Ag is targeting microbes living in the plant, points out von Maltzahn. 

“I still remember being stunned by a seemingly simple observation that perhaps every plant in the world has microbes that live not only around them in the soil but also inside their tissues,” says von Maltzahn. “You see situations where, under extreme drought, there are two plants among thousands that thrive. These are situations where the environment is uniform, and genetics wouldn’t be the reason for such dramatic differences. We simply ask what role the microbes inside them play in their survival.”

Indigo Ag started a “survivor plant” sampling system in fields where it collects and genetically sequences survivor plants. The company then cultures these microbes and transfers them to agricultural seeds in the form of seed treatments.

“We then see if those seeds derive a benefit relative to the seeds that don’t receive the microbe,” says von Maltzahn. “We have demonstrated causal relationships between these microbes and stress resilience in our labs, greenhouses, and field trials over thousands of commercial acres.”

Deciphering claims

Not surprisingly, claims of yield increases, pest control, and input savings accompany all of these products. So do they work?

Tim Couser
Tim Couser always keeps this quote by John McGillicuddy (an Iowa City, Iowa, agronomist) handy: “Everything will work once in agronomy, and nothing works all the time.” 

“The farmer’s problem is that we test a product on a small area one year and it works,” says the Nevada, Iowa, farmer. “Then we put it on every acre the next year, and it doesn’t work.” 

Couser has worked with several companies and says the products have potential. Since their cost often ranges between $10 to $15 per acre, though, they need to be on-farm tested to make sure they provide a sufficient return, he says. 

“The best way to tell if they work is with a split planter test, with the product used on one side of the planter and the check on the other,” he says. 

Gasch advises farmers considering microbial and biological products to first test them on a few acres of their farm. 

“Look for validation from unbiased sources, such as from a university or an independent agronomist,” she says. 

Time will tell

Developing consistent results takes time, says Miille. 

“We have some preliminary indications that we’re on the right track and that it’s achievable,” he says. “We know enough about the genes and have the tools to believe that one day, we can actually take a host microbe and reduce synthetic nitrogen applications by having the microbe deliver 30%, 40%, and 50% of a plant’s nitrogen needs and still maintain the same yield.”

Still, Miille estimates product commercialization is four to five years away.  

“Companies have been trying to crack this nut for 30 to 40 years,” he says. “It’s not going to happen in one or two years. You don’t get many chances to make a first impression. When you launch a product, it better work all the time.”

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