The science of glyphosate

There are dozens of conspiracy theories about glyphosate.

One of those theories goes something like this: glyphosate, the active ingredient in Roundup, is an antibiotic and it kills all of the beneficial bacteria and fungi in soils.

“It makes the soil sterile in some cases leading to less nutrient rich soil and in turn (produces food) that is devoid of vital substance,” says a commentator on the website of the Rodale Institute, an organic farming research centre in Pennsylvania.

Online commenters and Twitter trolls aren’t the only people saying that glyphosate kills soil life. Journalists at major publications, like the New York Times and The Guardian, have written articles claiming the herbicide is hazardous to soil health.

“Why are nutrients in our food declining?” asked Scientific American in 2019. “Well, for one, we are killing the soil it grows in. Prodigious use of biocides … kill or disrupt soil micro-organisms that allow plants to absorb nutrients.”

Tim Paulitz, a plant pathologist with the United States Department of Agriculture in Pullman, Washington, heard similar concerns in the early 2000s from farmers in Washington and other parts of the Pacific Northwest.

Does glyphosate stimulate plant pathogens?

He was collaborating with minimal-till growers who relied on glyphosate to control weeds. A percentage of those producers wondered if glyphosate was harming beneficial microbes in the soil.

“I would go to these direct seed conferences and they would ask me these questions,” he said during a telephone interview from his office in Pullman. “I would say: I really don’t think we can answer that question with the technology we had at the time.”

Back then, adequate technology or not, many scientists wanted to know if Roundup was harmful to soil bacteria.

But soil micro-organisms are challenging to study. As noted on biology/, there can be 6,000 to 50,000 species of bacteria in one gram of soil. Plus, the microbiology of soil is often described as a “black box” because scientists only understand the function of a few species.

With the DNA technology of the 1990s and early 2000s, it was only possible to study a tiny fraction of the population of micro-organisms in a sample of soil.

“All we could do at the time is isolate things (certain bacteria or fungi) and look at effects,” said Paulitz, who was an associate professor in plant science at McGill University from 1989 to 2000. “You really couldn’t answer the question (about glyphosate) because you’re really only looking at .01 percent of (the microbes).”

In the early 2010s, scientists began using new and much improved technology for DNA sequencing. Next Generation Sequencing (NGS), with names like Illumina, allowed researchers to study a huge amount of genetic material in a short time.

“With Sanger sequencing (the old technology) we saw a limited DNA snapshot…. NGS and its massively parallel sequencing enable us to look at tens to hundreds of thousands of reads per sample,” says a scientist on

After the technology hit the market, Paulitz realized he could finally answer the glyphosate question because he could accurately study the majority of soil microbes.

He requested and received funding from the U.S. Department of Agriculture to study how glyphosate affected bacteria and fungi in soils associated with wheat crops.

Paulitz and his colleagues collected soil samples from four growers in the Pacific Northwest who had been following no-till practices for more than 20 years. They also collected samples from Conservation Reserve Program land (cropland set aside for habitat preservation), which was adjacent to the four farms.

The soil samples were taken to a greenhouse, where they grew wheat in the soil.

Half of the plants were sprayed with glyphosate. The other half were “terminated” by clipping the wheat.

Paulitz and his team did this over four or five cycles for two years. The result?

Glyphosate had a minimal impact on soil micro-biology.

“We described the bacterial communities in the soil and rhizosphere of wheat grown in Pacific Northwest soils across multiple years, different locations, and soils with different histories of glyphosate use,” Paulitz and his colleagues wrote in a 2017 paper, published in Applied Environmental Microbiology. “The effects of glyphosate were subtle and much less than those of drivers such as location and cropping systems…. Less than one percent of all taxa (microbes) were impacted by glyphosate.”

While Paulitz was studying glyphosate and wheat, a team of USDA researchers in Maryland conducted a similar experiment on soil with corn and soybeans.

They reached the same conclusion. Glyphosate doesn’t harm the community of soil microbes.

“We were able to determine that year-to-year weather variation, soil type and farming system history (crop rotation legacy) had more impact than the GM transgene or application of glypho­sate,” they said on a USDA website. “These results will give farmers and land managers confidence that continued use of glyphosate/glyphosate resistant system will not result in shifting the soil microbial community towards a community with more pathogenic potential.”

The theory that glyphosate kills soil microbes is based upon the shikimate pathway, a group of enzymes found in plants, bacteria and fungi. Glyphosate kills weeds because it shuts down those enzymes.

The herbicide isn’t a threat to humans because mammals don’t have the shikimate pathway.

However, glyphosate can harm soil microbes with the specific pathway.

“(But) not all of the bacteria and fungi have a form of that enzyme that’s sensitive to glyphosate,” Paulitz said. “That’s where the original Roundup Ready gene came from — a bacteria that was not sensitive to this enzyme.”

The other important factor is dose. A percentage of bacteria and fungi may be sensitive to glyphosate, but if levels of the herbicide are low the microbes should be safe.

“The real question is, do they ever see a (soil) concentration that’s going to be toxic?” Paulitz said. “A lot of the other research … they were using astronomical amounts you would never see in the field.”

As for the other research, it’s easy to find scientific papers saying that glyphosate is a threat to certain species of soil microbes.

However, the overall risk to soil micro-organisms is minimal, said Kari Dunfield, University of Guelph professor in the School of Environmental Sciences and Canada Research Chair in environmental microbiology of agro-ecosystems.

“(Glyphosate is) shifting the communities (of microbes) but just in a small amount in comparison to things like leaving a soil fallow or having a (poor) crop rotation,” she said. “The community will just kind of adapt.”

In other words, practices like no-till, cover crops and complex crop rotations are much more meaningful for soil microbes and soil functioning.

“You’re just impacting much more soil (with those practices),” said Dunfield, who earned her PhD at the University of Saskatchewan. Her doctorate thesis was on genetically modified crops and the potential impact on soil microbes.

“The glyphosate… because it’s breaking down quickly, it’s not there in high enough concentrations for a really long time to have a major shift…. (There isn’t) major changes in the soil function, for the most part.”

If glyphosate was damaging the microbiology of farmland, it should show up in crop yields because microbes play a significant role in soil functions like nutrient cycling. There’s no evidence of yield declines, even though glyphosate use has skyrocketed since 2000, when it came off patent.

“When you look at the yields of the three major glyphosate-resistant crops — corn, soybeans and cotton — there’s generally been a trend upwards that hasn’t changed since they were adopted,” Stephen Duke, USDA scientist in Mississippi, told the New York Times.

“If there was a significant problem, I don’t think you’d see that (yield increases).”

Crop yields may be rising but spraying the same piece of land with glyphosate, over and over again, likely has an impact.

Using the herbicide every year and multiple times per growing season will slightly alter the community of soil microbes, Dunfield said.

“You’re really driving your microbial community to be one thing,” she said. “It’s probably not a great practice…. If you happen to get a pathogen that likes to live (off) glyphosate that’s where you’ll see some (risk).”

In a report called The impact of glyphosate on soil health, scientists with the Soil Association of the United Kingdom reviewed the scientific literature on the topic.

They agreed with Dunfield: glyphosate can alter the composition of soil microbes because species sensitive to glyphosate will die off.

“There is evidence now to suggest that repeated glyphosate applications can impact on soil microbial communities as they adapt to repeated glyphosate applications.”

Dunfield said the risk may be higher in sandy soils. In heavier soils, the herbicide binds to clay particles

“It’s not bio-available, doesn’t have a chance to impact the micro-organisms,” she said. “In a sandy soil it tends to stay bio-available for longer.”

It’s possible that glyphosate could cause a small shift in the population of soil microbes, where specific bacteria and fungi would flourish and others would die.

But it’s difficult to know if that shift is a good thing or a bad thing, Paulitz said.

Glyphosate could select for beneficial microbes or encourage the growth of detrimental bacteria, he said.

Regardless, Paulitz stands behind the USDA research on wheat, corn and soybeans.

Using modern DNA sequencing and looking at tens of thousands of species, they found that glyphosate impacted only a tiny percentage of microbes in the soil.

As for glyphosate’s impact on soil health, that’s a trickier question, Paulitz said.

That’s because he can’t define soil health.

“I don’t think I could tell you what a healthy soil is.”

He is certain, however, that reduced tillage has a massive impact on the health of agricultural soils.

“I think the huge advance has been the reduction in tillage in the last 30 to 40 years…. That’s increasing your soil health because you’re not losing (the soil).”

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