What are Herbicide Effects on Soil Biology?
When we spray herbicide, we're not only affecting plants; we're changing the soil too. Glyphosate, for example, is patented as a "biocide" which means that it has some effect on soil bacteria and fungi, in addition to plants. Most herbicides will have a broader, biocidal impact on the soil ecosystem. This makes studying them important to understand our goals for habitat restoration, healthy ecosystem development, and carbon sequestration over time.
Let's continue with Glyphosate, which is the most commonly used herbicide for habitat restoration efforts. The glyphosate molecule is an enzyme inhibitor that disrupts a plants ability to produce amino acids (to build proteins), which weakens and eventually starves plants. Specifically, glyphosate targets and blocks a particular enzyme called EPSP synthase (5-enolpyruvylshikimate-3-phosphate synthase).
That enzyme is not only crucial for plants, it's also vital for many soil micro-organisms like bacteria and fungi. This means that soil microbes aren't able to build the proteins necessary for growth, reproduction, enzyme function, structural components, and virtually every other life process. Essentially, blocking this enzyme starves them of these vital building blocks, leading to their inability to thrive or survive.
In order to study this effect, Phoenix Regen conducted a small experiment in Summer 2025, spraying a biologically active and diverse compost soil with two mixes: (1) a 2% glyphosate solution and (2) a 0.15% humic acid solution. These concentrations were chosen because each product is commonly used at that concentration in habitat restoration projects.
When looking at soil biology through a microscope after 20 days, we observed that glyphosate applications reduced all biology compared to humic acid applications. Live protozoa and fungi decreased by 55% and 28%, respectively. Dormant forms, such as protozoa cysts and fungal spores, also decreased by 42% and 24%. This needs to be studied more extensively, but initial data shows a potentially severe effect from glyphosate on microbial populations.
It's important to understand that glyphosate applications may not always lead to a total decrease on fungi or bacteria. Instead, they may also alter the type of fungi and bacteria that are allowed to proliferate in a system. Here is more information from a recent journal article, "Indirect Effects of the Herbicide Glyphosate..."
Plant growth promoting rhizobacteria and beneficial intestinal bacteria often are negatively affected, while pathogenic bacteria and fungi are enhanced. Such shifts in microbial community composition have been implicated in enhanced susceptibility of plants to Fusarium and Rhizoctonia, of birds and mammals to toxic Clostridium and Salmonella species, and of bees to Serratia and Deformed Wing Virus. In animals and humans, glyphosate exposure and concentrations in urine have been associated with intestinal diseases and neurological as well as endocrine problems, but cause-effect relationships need to be determined in more detail.
This shows how species may shift towards disease-causing or pathogenic bacteria and fungi after herbicide application. It's also possible that bacteria lose genetic diversity according to the article, "Pesticide Diversity Impairs Soil Microbial Functions."
Pesticide diversity led bacteria to streamline their genomes while enhancing metabolic activity.
Accordingly, applications of multiple herbicide products may do more than reduce microbial genetic diversity. They may also lead to increased resource consumption of soil carbon and nitrogen reserves.
The implications of these studies result in a much more stressed environment for plant growth with:
- Increased soil pathogens and diseases
- Reduced microbial species diversity
- Reduced diversity of genetic expression within bacteria species
- Increased bacterial metabolism rates and consumption of soil nitrogen and carbon reserves
- Reduced soil carbon (organic matter), increased carbon off gassing, and reduced soil carbon sequestration
With this in mind, we know that herbicide is an important and vital tool for vegetation management. But we at Phoenix Regen believe that using herbicide responsibly requires learning about its impact in natural environments. Much more study is needed, as well as innovation to mitigate potential degrading effects on soil quality. In doing so, we may authentically achieve our goals for healthy soils that provide fundamental ecosystem services we need.
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