Multipesticide exposure: the impact on soil microbes
When we think about pesticides and their potential effects, the first idea that comes to our mind is probably related to our health. If you haven’t noticed yet, we humans tend to prioritise ourselves under the guise of protecting the world. Yet beyond us, there’s a hidden world of organisms just as affected by pollutants as we are—organisms we often overlook. In this article, we’ll step away from the human-centred spotlight and focus on our tiniest friends: the microorganisms.
Over the years, concerns about the extensive use of pesticides in agriculture have grown. From biodiversity loss to water pollution, many questions remain unanswered as we strive to find a sustainable yet productive way to manage pests. But what do microorganisms have to do with this topic? And why does it matter? Let’s dive in!
Pesticides: more than meets the eye
First of all, what are pesticides? Pesticides are substances or mixtures of chemical or biological ingredients designed to repel, destroy, or control pests—or even regulate plant growth. Though we often picture pests as insects feeding on the precious leaves of our plants, they can also include unwanted plants or microorganisms. In fact, in the EU, fungicides and bactericides are the most sold group of pesticides, accounting for 43% of total sales in 2022¹. This means many pesticides are specifically designed to target microbial processes, impacting the communities inhabiting plants and soil.
Take prothioconazole, for example: it inhibits the synthesis of a crucial component in the fungal cell membrane, thus being a broad-spectrum fungicide (i.e., it can affect many different types of fungi). Similarly, some pesticides—or their degradation byproducts—can be metabolised by microbial communities, altering their composition. These changes can have effects on soil and plant health.
How do pesticides reach the soil?
Many pesticides are applied directly to leaves, but some are sprayed onto the ground. Even when applied to plants, pesticide residues often find their way into the soil. In fact, recent estimations point out that 30% to 50% of the applied substances do not reach the target, instead accumulating in the soil². Half of agricultural topsoil is now estimated to contain residues from more than five different pesticides!
Why should we care about microbes?
Microbial communities, though unseen, are essential for maintaining healthy soils and plants. They are key players in nutrient cycling, realising nutrients used by the plant or fixating carbon. Many microbes promote plant growth and even contribute to soil structure. For instance, mycorrhizal fungi and nitrogen-fixing bacteria are estimated to provide 5–20% of the nitrogen used by plants annually in grasslands and savannas and up to 80% in temperate and boreal forests. These same microbes also supply up to 75% of the phosphorus absorbed by plants each year³.
Despite their importance, few studies have assessed the effect of multiple pesticide applications on soil microbial communities in depth. Common agricultural practices often involve the use of several pesticides, and each can affect microbes differently. When combined, their impact on the complex networks of microbial interactions could be significant.
A Closer Look: The Role of Multi-pesticide Application
A recent study published in Proceedings of the National Academy of Sciences (PNAS) by Xiao and colleagues sought to fill this knowledge gap. They conducted an experiment where plots were treated with every possible combination of five pesticides, creating scenarios with none, one, two, three, four, or all five pesticides applied simultaneously. To explore the potential influence of nutrient levels, they replicated this experiment with soils both supplemented and unsupplemented with nitrogen fertiliser.
To assess the effects on microorganisms, the researchers applied a range of different techniques. They used genomic sequencing, allowing them to read the sequence of the genes found in the community. Through computational processes, they reconstructed the microbial genomes. This allowed them to understand what “tools” (i.e., metabolic pathways) microbes have and how they serve them for growing, survival, and management of resources. This is what scientists call the “life strategy”” a very useful concept for understanding how the community responds to environmental stresses.
According to their findings, as pesticide diversity increased, the proportion of microorganisms capable of feeding on a wide range of substrates—called generalists—decreased. In their place, specialists that feed on specific chemicals, including pesticides, became more abundant.
Specialist microbes often depend on other organisms for survival, reducing their genome content and metabolic capabilities. With more specialists and fewer generalists, there’s less redundancy in critical metabolic functions. This could make the ecosystem less resilient to stress, such as extreme weather events linked to climate change.
Additionally, the authors observed a reduction in soil nutrients like carbon, nitrogen, and phosphorus as pesticide diversity increased. In line with these results, increased pesticide diversity enriched genes linked to denitrification—a process that releases nitrous oxide (N₂O), a potent greenhouse gas. These results highlight the importance of studying the soil microbial community as it can produce serious changes in soil fertility profile and contribute to climate change.
Can fertilisers offset these impacts?
If pesticides influence how microbes utilise soil nutrients, could adding nutrients alter this dynamic? The researchers tested this by supplementing the soil with a nitrogen-based fertiliser. Interestingly, they found that higher nitrogen levels mitigated the effects of pesticide diversity on microbial communities, reversing the shift toward specialisation. However, soil nutrient decline still occurred, though to a lesser extent.
Why is this significant?
Understanding how pesticide use affects microbial communities is essential for shaping policies that promote sustainable agricultural practices. Since microbial communities play a key role in soil nutrient cycling, it’s critical to understand how stressors like pesticides influence them and, in turn, affect soil nutrient levels. The authors observed decreases in both carbon and nitrogen content along with variations in metabolic pathways—changes that can lead to atmospheric emissions and negatively impact plant health. By studying the relationship between pesticide diversity, nutrient cycling, and soil health, we can better support sustainable farming practices. The secrets to healthier soils and a greener future may lie in the tiny but mighty world of microorganisms. Let’s continue uncovering their role in shaping our environment!
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References
1. European Commission. (2024). Agri-environmental indicator - consumption of pesticides. Eurostat. Retrieved January 17, 2025, from https://ec.europa.eu/eurostat/statistics-explained/index.php?title=Agri-environmental_indicator_-_consumption_of_pesticides.
2. Ni, B., Xiao, L., Lin, D., Zhang, T. L., Zhang, Q., Liu, Y., ... & Zhu, Y. G. (2025). Increasing pesticide diversity impairs soil microbial functions. Proceedings of the National Academy of Sciences, 122(2), e2419917122.
3. Van Der Heijden, M. G., Bardgett, R. D., & Van Straalen, N. M. (2008). The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology letters, 11(3), 296-310.
