Fertilizers, Pesticides and Plastic Resides: How Farm Chemicals Quietly Steer Greenhouse Gas Emissions

Every sack of synthetic fertilizer and every spray of pesticide that reaches a farm field does more than feed or protect a crop. It also perturbs an invisible, teeming underworld of soil microbes whose metabolic handiwork determines how much nitrous oxide, carbon dioxide and methane drifts from the soil into the atmosphere. A new review published in the journal Plant and Soil argues that the scientific community has been studying this problem in fragments, one contaminant class at a time, and that a more unified mechanistic framework is urgently needed if agriculture is to rein in its greenhouse gas footprint without undermining global food security.

The review, led by Waqas Mohy-Ud-Din of Tianjin University together with colleagues at institutions across China, synthesizes evidence on synthetic fertilizers and pesticides alongside the contaminants that travel with them: heavy metals, microplastics and a growing suite of emerging pollutants such as antibiotic residues. Rather than treating each chemical group as a separate story, the authors organize the evidence around five shared control points that govern greenhouse gas production in soil: the supply of reactive substrates such as nitrogen and carbon, soil aeration and redox status, pH and toxicity stress, the composition of microbial functional guilds, and the effects of co-exposure when multiple contaminants arrive together.

The logic behind this framework is deceptively simple but technically consequential. Soil microbes produce nitrous oxide primarily through nitrification and denitrification, two linked arms of the nitrogen cycle whose rates depend on how much ammonium and nitrate are available, how much oxygen diffuses through soil pores, and how acidic the soil has become. Carbon dioxide fluxes track the decomposition of organic matter by heterotrophic microbes, while methane emissions in flooded paddies are set by the balance between methane-producing archaea and methane-oxidizing bacteria. Any agrochemical that shifts substrate availability, oxygen diffusion, pH or the abundance of key functional genes will, in principle, bend these fluxes.

Among all the contaminant classes examined, synthetic nitrogen fertilizers emerge as the most consistent and best understood driver, particularly of nitrous oxide. Adding reactive nitrogen directly fuels nitrifier and denitrifier communities, and decades of field and laboratory work compiled in the review show that nitrous oxide emissions rise predictably with nitrogen input, especially when over-application leaves surplus nitrate in the soil. Fertilization also acidifies soils over time, and lower pH is known to suppress the final step of denitrification, the reduction of nitrous oxide to harmless dinitrogen gas, causing incomplete denitrifiers to leak more of the potent greenhouse gas into the air. Meta-analyses cited by the authors confirm that optimizing nitrogen rates, using enhanced-efficiency fertilizers and harmonizing chemical fertilizer with manure can meaningfully cut emissions while maintaining yields.

Pesticides tell a messier story. Fungicides such as mancozeb and chlorothalonil, herbicides like bensulfuron methyl and pretilachlor, and insecticides including sulfoxaflor and thiamethoxam have all been shown to alter carbon dioxide, nitrous oxide or methane fluxes, but the direction and magnitude of the response depend on dose, soil type, water regime and the sensitivity of the resident microbial community. In flooded rice systems, some herbicides suppress methane oxidation and thereby increase methane emissions, while in aerobic soils certain fungicides inhibit denitrifiers and shift the balance of nitrogen gases. A recent study highlighted in the review also found that increasing the diversity of pesticides applied to a soil can impair broader microbial functions, raising concerns about the cumulative effects of modern multi-chemical crop protection regimes.

Heavy metals, which enter farmland through contaminated irrigation water, phosphate fertilizers that carry cadmium impurities, industrial deposition and animal manures, add another layer of complexity. Metal toxicity can inhibit specific steps of the nitrogen cycle, and studies of metal-polluted paddy soils show altered abundance and composition of ammonia-oxidizer and denitrifier communities. Intriguingly, the review notes that water regime modulates these effects: cadmium, for example, appears to disrupt nitrogen transformation processes more strongly under non-flooded than flooded conditions, and water management changes the microbial mechanisms by which nitrous oxide is produced in metal-contaminated paddies. Some work even suggests that bacterivorous protists can suppress nitrification and nitrous oxide emissions in cadmium-polluted soils through negative feedback loops, hinting at unexpected biological levers within contaminated systems.

Microplastics, perhaps the most visually striking of the associated contaminants, have accumulated in agricultural soils through decades of plastic film mulching, with some fields now hosting substantial macro- and microplastic loads after more than thirty years of continuous mulch use. The evidence on their climatic consequences is heterogeneous. Polyethylene microplastics have been reported to increase nitrous oxide emissions from paddy soils and to alter microbial functional gene abundances, while biodegradable plastics such as PBAT and polylactic acid can stimulate carbon dioxide emissions by enhancing organic matter decomposition, or in some cases induce negative priming that improves carbon sequestration. Effects also depend on interactions with other amendments: co-existence with biochar or hydrochar can stimulate methane emissions while suppressing nitrous oxide, and combinations with earthworms or antibiotics produce outcomes that no single-contaminant experiment would predict.

Emerging contaminants, particularly veterinary and human antibiotics that reach fields through manure and wastewater irrigation, round out the picture. Tetracyclines, sulfonamides and quinolones have all been shown to perturb nitrogen cycling in soil. Tetracycline and sulfamethazine can alter dissimilatory nitrate reduction pathways and increase nitrous oxide release from rice fields, while ciprofloxacin contamination appears to selectively favor antibiotic-resistant denitrifiers that drive nitrous oxide production. Yet the dose-response relationships are not straightforward: some studies find that environmentally relevant, even ultralow, antibiotic exposures shift nitrate and nitrous oxide fluxes, whereas chronic low-level exposure in sediments can alter bacterial communities without changing denitrification rates. Plants, too, can mitigate nitrous oxide emissions from antibiotic-contaminated soils, underscoring how many interacting variables govern the final flux.

The central insight of the review is that these seemingly disparate contaminant stories become coherent when read through the five shared control points. Fertilizers act overwhelmingly through substrate supply, acidification and nitrogen-cycling microbes, which is why their effects are consistent across studies. Pesticides, heavy metals, microplastics and emerging contaminants act more diffusely through toxicity, changes to soil structure and hydrology, dose-dependent stress and co-exposure, which is why their effects scatter across the literature. This reframing matters for mitigation: interventions that target the shared control points, such as optimized nitrogen management, alternate wetting and drying in rice paddies, reduced tillage, diversified crop rotations and integrated nutrient management, can cut emissions regardless of which contaminant cocktail a particular field carries, while contaminant-specific strategies remain necessary for hotspots of metal or plastic pollution.

The authors are candid about what remains unknown. Multi-contaminant interactions, in which heavy metals, microplastics, pesticides and antibiotics co-occur as they do in real fields, are grossly under-studied compared with single-stressor experiments. Long-term field observations are scarce, leaving open questions about whether laboratory responses persist under real farming conditions and how climate change itself feeds back on contaminant behavior and microbial emissions. Closing these gaps, the review concludes, will require mechanistic experiments designed around the shared control points, sustained long-term monitoring networks, and mitigation frameworks that treat agrochemicals and their associated contaminants as an integrated system rather than a list of separate pollutants. For a sector responsible for a substantial share of global greenhouse gas emissions, the message is clear: the chemistry we put in our fields, and everything that chemistry drags along with it, is quietly shaping the climate math of agriculture.

Subject of Research: Mechanisms linking agrochemicals and associated soil contaminants to greenhouse gas emissions in agricultural ecosystems

Article Title: Linking agrochemicals and associated contaminants to greenhouse gas emissions in agricultural ecosystems

Article References: Mohy-Ud-Din, W., Yan, Z., Ge, Z., Zhang, W., Yan, S., Qi, Y., & Liu, Y.-R. (2026). Linking agrochemicals and associated contaminants to greenhouse gas emissions in agricultural ecosystems. Plant and Soil. https://doi.org/10.1007/s11104-026-09153-8

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09153-8

Keywords: agrochemicals, greenhouse gases, nitrous oxide, soil microbiology, fertilizers, pesticides, heavy metals, microplastics, antibiotics, nitrogen cycle, agriculture, climate change