Neonicotinoid Seed Treatments Quietly Reshape Soil Fungal Communities Over Time

Neonicotinoid insecticides have long been scrutinized for their effects on bees, butterflies, and other pollinators, but a new study suggests that another, far less visible set of victims may be sitting quietly in the dirt beneath treated crops. Soil fungi, the microscopic architects of healthy farmland, appear to shift in diversity and composition after exposure to three of the most widely used neonicotinoid seed treatments, according to research published in the journal Microbial Ecology. The findings, led by Sharmin Akter of the Fenner School of Environment and Society at the Australian National University, add a subterranean dimension to the ongoing debate over these controversial chemicals.

Neonicotinoids are systemic insecticides applied as coatings on crop seeds before planting. As the seed germinates and grows, the chemical is taken up into plant tissues, protecting the young seedling from chewing and sucking insects. But only a fraction of the active ingredient ends up inside the plant. The rest can persist in the soil, where it encounters an enormous community of microorganisms that drive nutrient cycling, decompose organic matter, and form partnerships with plant roots. While the impacts of neonicotinoids on insects and aquatic invertebrates have been studied extensively, their effects on soil fungal communities have remained surprisingly underexplored, a gap the new research set out to fill.

The team designed a controlled microcosm experiment in which soil was treated with three commonly applied neonicotinoids: imidacloprid, thiamethoxam, and clothianidin. These compounds represent the backbone of modern seed-treatment agriculture, coating millions of tonnes of seed annually across the world’s major cropping systems. By working in microcosms, the researchers could isolate the effect of each compound on the fungal community without the confounding noise of weather, cropping history, or management variation that complicates field studies. Soil samples were then collected at multiple time points after exposure, allowing the team to track not just whether the fungi responded, but when.

To profile the fungal communities, the researchers turned to amplicon sequencing of the internal transcribed spacer, or ITS, region of fungal DNA. The ITS region is the standard molecular barcode for fungi, allowing scientists to identify which fungal taxa are present in a soil sample even when those organisms cannot be cultured in the laboratory. This technique revealed hundreds of fungal taxa across the samples, spanning dominant phyla such as Ascomycota and Basidiomycota as well as rarer, more enigmatic lineages. Sequencing-based approaches like this have transformed microbial ecology in recent years, making it possible to detect subtle community shifts that would be invisible under a microscope.

One of the study’s most striking findings concerns timing. Overall diversity indices remained largely stable across the treatments when averaged over the whole experiment, which might initially suggest the fungicide exposure had little effect. But post-hoc comparisons told a different story: on day 10, fungal diversity dropped significantly under both imidacloprid and thiamethoxam exposure. This kind of delayed, transient response is exactly the sort of signal that single end-point sampling would miss. The lesson, the authors suggest, is that the ecological footprint of a pesticide cannot be judged from a single snapshot in time.

Beta diversity analysis, which measures how community composition differs between samples, reinforced this temporal picture. The researchers found significant effects of sampling day and, critically, a treatment-by-time interaction, meaning the fungal communities under different insecticide treatments did not simply follow the same trajectory. Instead, each compound appeared to push the community along its own path as the experiment unfolded. Such temporally variable responses complicate risk assessment, because a pesticide that looks benign in one week of a field season may produce measurable disruption in another.

Not all fungi responded equally. The dominant phyla, Ascomycota and Basidiomycota, which include many decomposers and plant-associated species, remained relatively stable throughout the experiment. But several less abundant phyla declined over time, including Mortierellomycota, Rozellomycota, and Olpidiomycota. These obscure-sounding groups are far from ecologically trivial. Mortierellomycota species are important decomposers and plant growth promoters, Rozellomycota comprises widespread intracellular parasites of other microorganisms, and Olpidiomycota includes fungi that can vector plant viruses. A decline in these rarer lineages may signal subtle erosion of functions that only become apparent when soil health degrades.

Perhaps the most consequential result came from functional guild analysis, which classifies fungi by their ecological roles rather than their taxonomy. Here the researchers found that clothianidin exposure drove an increase in saprotroph abundance, the fungi that break down dead organic matter, alongside a decrease in symbiotroph abundance, the fungi that live in mutually beneficial partnerships with plants. The most important symbiotrophs in agricultural soil are the arbuscular mycorrhizal fungi, which colonize crop roots and exchange soil nutrients for plant sugars. A shift away from symbiotrophs and toward saprotrophs could alter how nutrients flow through the soil food web, potentially affecting crop nutrition in ways that standard pesticide evaluations never measure.

Differential abundance analysis, a statistical technique for identifying which taxa increase or decrease under specific conditions, revealed that each compound left its own fingerprint on the community. Imidacloprid was associated exclusively with suppressed fungal biomarkers, meaning every taxon linked to this compound was depleted rather than enriched. Thiamethoxam induced both enriched and depleted taxa, suggesting a more mixed restructuring of the community. Clothianidin stood out as the most disruptive of the three, associated with the greatest number of discriminatory fungal biomarkers and accompanied by the increase in saprotrophs and reduction in symbiotrophs. The compound-specific nature of these responses suggests that treating all neonicotinoids as a single ecological hazard may obscure important differences among them.

The study, which was funded by the Australian National University and conducted with colleagues Julia F. Jasonsmith, Nilantha R. Hulugalle, and Craig L. Strong, carries implications well beyond the laboratory. As regulators and farmers weigh the costs and benefits of neonicotinoid seed treatments, fungal communities have rarely featured in the calculus, even though these organisms underpin soil fertility, carbon storage, and crop resilience. The authors argue that fungal community responses deserve a place in evaluations of the broader ecological effects of neonicotinoids, and they call for long-term, functionally oriented studies in real agroecosystem contexts. A ten-day microcosm can reveal the shape of a disturbance, but only sustained field research can determine whether these shifts persist, compound across seasons, or ultimately translate into measurable consequences for the crops that depend on the hidden life below ground.

Subject of Research: Effects of neonicotinoid seed treatments on soil fungal community diversity, composition, and function over time

Article Title: Fungal Responses to Neonicotinoid Seed Treatments in Soil: Temporal Shifts in Community Diversity and Composition

Article References: Akter, S., Jasonsmith, J. F., Hulugalle, N. R., & Strong, C. L. (2026). Fungal Responses to Neonicotinoid Seed Treatments in Soil: Temporal Shifts in Community Diversity and Composition. Microbial Ecology. https://doi.org/10.1007/s00248-026-02892-2

Image Credits: AI Generated

DOI: 10.1007/s00248-026-02892-2

Keywords: neonicotinoids, soil fungi, fungal diversity, imidacloprid, thiamethoxam, clothianidin, ITS amplicon sequencing, soil microbiome, temporal dynamics, saprotrophs, symbiotrophs, agroecosystems