Glyphosate, Roundup, GMOs and the microbiome part 1: crowdsourcing literature

For many reasons I have been interested for the last few years in how agricultural practices affect microbiomes.  For example in regard to crops, how do farming practices affect the microbiomes of the plants, the microbiomes of the soil and area around the plants, and the microbiomes of organisms (including humans) who make use of the plants?

I won’t go into all the detail right now for why I am interested in this topic but for some examples of my work in this area see The microbes we eat abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types and Structure, variation, and assembly of the root-associated microbiomes of rice.

Anyway, the reason I am writing this now is that tomorrow I am “testifying” to a NRC Committee about this topic and some related topics.  The presentation will be shown live online (register here).  And I thought, in the interest of openness, I would post some of what I am thinking about here before hand.

One of the key topics for tomorrow is something I have been snooping around at for a few years – how does glyphosate (the key ingredient of RoundUp and a widely used herbicide) affect microbiomes?  I am interested in this from both a scientific point of view (I think it is an interesting topic) and also from a “public policy / education” point of view.  I think this is a really good topic to have a public discussion of “microbiomes” and both the importance of microbial communities and the challenges with studying them.  So a few years ago I started thinking about working on this and developing a “Citizen Science” project around it.  And, well, I am still working on that idea and probably will be trying to launch something in the near future.  As a first start I thought it would be good to start to engage the community (researchers, teachers, the public, etc) in a discussion of this topic.  So .. this is the beginning of that I guess.

Some questions I think are interesting:

  • Does glyphosate affect plant microbiomes?
  • Does glyphosate affect soil microbiomes?
  • Does consumption of plants treated with glyphosate affect the microbiomes of the consumer? 
    • Directly (e.g., by glyphosate itself being in the food and directly affecting microbomes”
    • Indirectly (by glyphosate affecting the microbiome of the food which in turn affects the microbiome of the consumer)
  • If glyphosate affects any of these microbiomes above, are these significant affects (e.g., in terms of health)?
Now I am not the only person who is interested in this topic.  In fact, there have been many people looking into these and related topics for years.  Some of the things I have seen on this topic in the popular press and the scientific literature are, well, not good science.  And some of the things I have seen are fascinating and well done. 
So as a first step in looking into this, I scoured the literature for papers of interest.  And that is really why I am writing this.  I created an open collection of the papers I have found with the Zotero reference collection system.  See this link for the collection.  And if you know of any other papers truly related to this topic, please add them to the collection (learn more about Zotero here).  I do not profess to know everything about this topic.  But I think it is interesting and possibly important.  
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About Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

9 thoughts on “Glyphosate, Roundup, GMOs and the microbiome part 1: crowdsourcing literature

  1. Jonathan, I'm glad you are doing this for the NRC. In all of the work that is done in this area there is one key point that is never made… how much glyphosate is on transgenic-crop based food products? Before we can consider the effect on a microbiome, we need to know what is the actual input.

    Application is about 80 mg/ square meter, weeks before there are flowers, let alone food, on the plants. Most of it ends up on weeds and soil some on the resistant plants.

    Even if all of it were magically sequestered into the, say soybeans, if we do the math and then overlay it on the known biological fate of glyphosate, there is not much there to actually cause any issues. I suppose I could work it out to number of glyphosate molecules in the intestine per bacterium, but I think the number would be far less than 1.

    When we look at USDA assessments the limit is 40 ppm, and that is seldom seen. Detection is awfully good, and I've seen 1-3 ppm here and there, but there just is not input-side product to cause an effect in the microbial communities.

    I have always been interested in which microbes are affected by glyphosate and which aren't. Doesn't seem like it can be too many, or this stuff would have been offered up as an antibiotic in many applications. I don't think the Big MON would have passed on an opportunity to sell a blockbuster new drug.

    Thanks for the link collection. I'll look at this too to see if there's anything I've missed. Have fun!



  2. A few comments

    1. I agree that to determine the possible DIRECT effects of glyphosate on microbiomes of organisms that consume treated plants, we need to know how much makes it into the consumer.

    2.I am personally more interested right now in possible indirect affects – for example if glyphosate affects plant microbiomes which in turn then impact consumers.

    3. Since you bring it up – there is actully a lot of online discussion about Monsanto patents related to antimicrobial properties of glyphosate. Monsanto has responded to some of these discussions multiple times with some of their own take on the story. More on this later.


  3. Last semester I had a group of students interested in this topic and wanted to do their mini-project on glyphosate impacts. With our limited resources the best approach we came up with was to do some plating experiments looking for glyphosate tolerant bacteria in different soils. Time and technical issues led to no results but I am convinced we could incorporate this kind of project into future labs and if we had the resources I would love to do some true microbiome analysis in lab class.


  4. I think that those farmers following the Roundup Harvest Management Practices (see the last comment for the document link) and apply within 1 week of harvest (for “Harvest Management”) will see higher levels than mentioned in Kevin Folta's comments of 4/05/15. I keep seeing people assuming that it's only applied early in the season, but Monsanto is really pushing application within 1 week of harvest.


  5. Here are two papers to add as well:

    Effects of Roundup® and Glyphosate on Three Food Microorganisms: Geotrichum candidum, Lactococcus lactis subsp. cremoris and Lactobacillus delbrueckii subsp. bulgaricus
    Emilie Clair – Current Microbiology 2012
    doi: 10.1007/s00284-012-0098-3

    Survey of Aspergillus section Flavi presence in agricultural soils and effect of glyphosate on nontoxigenic A. flavus growth on soil-based medium.
    Carranza CS – J Appl Microbiol 2014
    DOI: 10.1111/jam.12437


  6. Normally a plant will translocate glyphosate to the apical areas (the parts of the plant that are actively growing – shoots and tips). In a glyphosate resistant plant like soy or corn this means that eventually the plant moves the glyphosate into the corn kernels and soybeans (note also that some glyphosate is also metabolized to AMPA by the plant so there will always be less glyphosate in the final product than is applied to the surface).

    With pre-harvest application in wheat the crop is done producing the grains. It would be a mistake for the farmer to apply to an immature wheat crop (there is no Roundup Ready wheat, so it will diminish yield). Since the plant is no longer actively growing at the seed head there will be little translocation of glyphosate to that area, if any.

    You can see photos of what mature wheat looks like and a further discussion of the topic here:


  7. Added one paper you missed:
    Isolation and characterization of endophytic bacteria from soybean (Glycine max) grown in soil treated with glyphosate herbicide

    This paper shows that glyphosate DOES affect the endophytic species balance of plants.


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