Residues from -cides and antibiotics can wreak havoc on your compost; testing it is vital
Sometimes two people use the same word but have very different pictures in their minds as to what that word actually means. This is more common than we realize — in farming, as in all of life, nuance matters, and the words we use sometimes need to be defined so we can clarify what we are saying or hearing.
One of these terms is “compost.” There are folks who think that if it’s compost, it’s good. There are others who feel like there’s good and bad compost. And then there are even a few who have noticed or learned that there are many different types of “good,” and it depends on our context — not just the methods employed or even the completeness of the soil food web in that compost.
Most thermophilic “hot” composts are high in pH (typically pH 8.0) and oxidized. This is just how the reaction works: as a flame generates heat as wood is oxidized, so the compost pile releases energy and heat when we get the carbon:nitrogen ratios right. Oxidation, after all, is the loss of energy, so we are adding in oxygen while we lose energy. That means we are going to turn the organic nitrogen in the pile into nitrates — NO3 (and we see this quite clearly when we test).
This means that your compost amendments can easily disrupt the C:N ratio, oxidize the soil, and imbalance the nitrate levels in our plants — causing four times the water requirements as they form watery, low-nutrient, thin-walled, large plant cells that are vulnerable to attack. But this is just scratching the surface — there’s so much more that I worry about!
Always test your pile’s pH, nitrogen, phosphate and potassium; you can predict the effects they will have. Then test for biological completeness or biology utility (predators, fungal, etc.) You can combine piles to make a complete soil food web or to balance the ppm or pH. In fact, that seems like a best practice given all the success Todd Harrington has had doing just that (and given the scale of some of his projects, there was no other way to do it — he had to source multiple composts and combine them synergistically).
What Really Worries Me
What really worries me in regard to compost, though, is the manure folks are using. More people today know to source clean straw or hay (spray-free and local), but most struggle to find enough manure that is “clean.” On a local level, folks typically work with local horse rescues, bunny operations and goat owners to gather enough manure if they don’t generate it themselves, but even then the animal feed and deworming regiments can ruin a compost or ruin a field. I’ve read and heard from students who have experienced this — certain sprayed feed can generate manure that passes through compost and can still ruin a garden for years unless actively remediated.
I worry about this for several reasons. First, antibiotics and dewormers can kill off the microbial life that powers the soil and our compost breakdown process; they can stall a hot compost and prevent it from getting hot enough. Sometimes you can talk with the owners or managers and figure out when the window is best for taking their manure and using it in your composting system, but this is impossible for many farmers.
I’ve had several farmers and ranchers in my courses share that they are making compost with feedlot manure, which has some serious risks associated with it. Any pesticide, herbicide, insecticide or fungicide residues, or constituent parts on the feedlot’s feed, can potentially be found in the manure.
In fact, operators are finding glyphosate in manure (I’m sure if other biocides were focused on, we’d find them more ubiquitously as well). Glyphosate selects for and promotes pathogens like fusarium species in plants and in soil — and even more concerning, fusarium is a pathogenic endophyte. That means it is beneficial to the plant when the plant is providing enough sugars, but when the late season arrives and the sunlight wanes, the plant becomes the food source for the pathogens (they switch roles from endophytic to pathogenic when the photosynthetic sugars slow down). We see this all the time with late-season blights that seem to come out of nowhere. It was already in the plant. This is why beneficial endophytes like L. Plantarum, S. Cerevasaie, and R. Palustris are so critical to get established within our plants — to prevent pathogens from taking over.
This is another reason why using glyphosate and other biocides is a terrible idea. It creates a compounding loop: the more glyphosate used on animal feed, the more fusarium and other pathogenic endophytes are selected for and are inside the feed, which will turn into more animals getting sick from the fusarium in the grain, and more manure seeded with fusarium spores will be sold to farmers. Those farmers are going to compost it, thinking that fixes it, but they’ll only be returning an inoculant of fusarium, and likely glyphosate residues, to their soils, further selecting for it to be dominant in that soil and in those plants.
Much of this information comes from extensive field research compiled in Dr. Don Huber and Charles Wilson in their book Synthetic Pesticide Use in Africa: Impact on People, Animals, and the Environment. Doctors treating people with high levels of mold in their bodies are finding links to mold exposure in soybean fields states away. It’s not just in the seed and in the manure — it’s also releasing spores on the wind as it decomposes the crop residues in the field, and if it’s hurting folks states away, it’s more than likely affecting the people farming that land. This is also why they get sold fungicides, and as fusarium adapts, they continue to innovate and increase dosages, preventing the natural biocontrol fungi from doing their work.
We have to get off the merry-go-round. The first step is simple: test your compost!
How Hard Is It to Identify Fusarium?

Under the microscope it looks like a segmented banana — it’s one of the most recognizable and easy-to-identify spores in the world. Once it’s visible to the eye as an infection on the surface, or in the flesh of the plant, it’s deeply embedded. We can displace these microbes, but not if we keep importing them into our systems. We can sometimes save plants, but often when we use sugars to boost the plant, we are just feeding the pathogens too and delaying the inevitable.
We can identify them, we can apply biocontrols, and we can interrupt this pattern. But if we don’t remove the glyphosate from our soils (and it can last over 20 years in some soils), we’ll just keep inhibiting the beneficial microbes and promoting pathogens.
Wait, not all endophytes are good? Exactly — some are plant pathogens, and some are human pathogens, and sometimes they are both, on top of being endophytes. We want probiotic, beneficial-to-human endophytes. Remember that when someone tries to sell you A.Fumigatus with it labeled as a biofertilizer. While it is true that it is an endophyte, and technically a biofertilizer because it releases nitrogen while it is in this role inside the plant, it does not mean that it is safe or good for you, your soil, your customers, or your community.
We have to make sure people truly understand our definitions for these words. There are human-friendly and beneficial endophytes that are not pathogenic, and then there are endophytes that are plant pathogens, and endophytes that are human pathogens. Nature fills roles and niches if we don’t.
















