Ozone Pollution and Organic Fertilizers Reshape the Hidden Nitrogen Engine Beneath Wheat

Deep beneath every wheat field lies a microscopic engine that decides how much of the world’s fertilizer actually feeds crops and how much escapes into rivers and the atmosphere. A new two-year field experiment conducted under real-world conditions shows that two of the most powerful levers in modern agriculture, rising ground-level ozone and the shift toward blended organic-inorganic fertilization, both rev up this engine, but at different times and through different mechanisms. The findings, published in the journal Plant and Soil, offer one of the clearest pictures yet of how air pollution and soil management interact in the rhizosphere, the narrow zone of soil wrapped around living roots where most of the action in the nitrogen cycle takes place.

The study, led by Bo Shang, Ziyi Guo and colleagues working with corresponding author Zhaozhong Feng at Nanjing University of Information Science and Technology, together with Chao Xiong of the University of Western Australia, used a Free-Air Ozone Concentration Enrichment platform, known as O3-FACE, to fumigate a growing wheat crop with elevated ozone without enclosing the plants in chambers. This technology releases ozone into open-air plots through a network of pipes, allowing researchers to study pollution effects under authentic field conditions of wind, rain, temperature and soil biology. On top of the ozone treatment, the team applied two fertilization regimes: conventional inorganic fertilizer and a combined organic-inorganic treatment, abbreviated COM, in which part of the synthetic nitrogen is replaced with organic manure.

The central measurement was the soil potential nitrification rate, or PNR, a laboratory assay that quantifies how fast soil microbes can convert ammonium into nitrate. Nitrification is a double-edged process in agriculture. On one hand, it supplies nitrate, the form of nitrogen many crops preferentially absorb. On the other hand, nitrate is highly mobile in soil water, leaching into groundwater, and can be transformed by denitrifying microbes into nitrous oxide, a greenhouse gas roughly 300 times more potent than carbon dioxide. Faster nitrification therefore means both quicker nutrient supply and greater risk of nitrogen loss, which is why understanding what controls it matters enormously for sustainable farming.

The researchers also probed the organisms responsible. Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by two very different groups of microorganisms: ammonia-oxidizing archaea, or AOA, and ammonia-oxidizing bacteria, or AOB. Using quantitative PCR of the amoA gene, the molecular marker for ammonia monooxygenase, the team tracked the abundance of both groups, while amplicon sequencing of the 16S ribosomal RNA gene, analyzed with standard pipelines such as QIIME and UNOISE-based error correction, revealed shifts in AOB community diversity. Alongside the biological data, they measured a suite of soil physicochemical properties, including pH, ammonium, dissolved organic carbon and dissolved organic nitrogen.

The ozone results carried a striking temporal signature. Elevated ozone significantly stimulated potential nitrification only in the first year of the experiment, which happened to be the year with higher ambient ozone concentrations. This stimulation was linked to an increase in AOA amoA gene abundance, greater AOB diversity, and measurable shifts in soil pH and ammonium availability. The mechanism is indirect but logical: ozone does not touch the soil directly, since it is highly reactive and largely consumed in the air and on plant surfaces. Instead, it stresses the wheat canopy, altering photosynthesis, root exudation and the flow of carbon and nitrogen from plant to soil, and those altered rhizosphere conditions cascade down to the ammonia oxidizers. Previous work by some of the same community, including five-year fumigation studies on wheat, had hinted that chronic ozone can raise nitrifying enzyme activities, but the new experiment adds a crucial caveat: the effect is not guaranteed every year.

The fertilization results were equally revealing, and equally dependent on time. In the first year, combined organic-inorganic fertilization did not change potential nitrification at all. In the second year, however, COM enhanced PNR across all measured growth stages. The authors attribute this delayed response to the cumulative nature of organic matter inputs: manure does not transform soil chemistry overnight. By the second season, the accumulated organic amendments had improved dissolved organic carbon levels and shifted soil pH, creating conditions more favorable for nitrification. Notably, this stimulation occurred without any change in the abundance or diversity of AOA or AOB, suggesting that the existing microbial community simply became more active as its chemical environment improved, rather than the community composition itself being restructured.

Perhaps the most intriguing result is what the team did not find. Despite both treatments stimulating nitrification, no statistically significant ozone-by-fertilization interaction emerged for PNR. The authors propose that this apparent independence is not biological at all but temporal: ozone dominated the first year while the fertilizer effect took over in the second, so the two drivers never overlapped strongly enough to interact. The design of the experiment, in other words, separated in time what might interact in principle. Supporting this interpretation, the study did detect an interaction at a finer scale: under combined fertilization, ozone-induced changes in dissolved organic nitrogen and ammonium were amplified at the grain-filling stage in the first year, showing that the treatments could indeed modulate each other’s effects on specific soil pools even when the headline nitrification rate did not show it.

The broader context makes these findings urgent. Ground-level ozone is one of the most damaging air pollutants for agriculture, with East Asian studies estimating substantial yield losses for staple crops including wheat and rice, and ozone is known to reduce fertilizer efficiency, meaning more applied nitrogen ends up wasted. At the same time, governments and agronomists are actively promoting partial substitution of synthetic fertilizer with organic manure to rebuild soil organic matter, improve soil structure and reduce reactive nitrogen losses. Both pressures are converging on the same square meters of soil, yet until now their combined influence on the microbial nitrogen engine remained essentially unmapped. This experiment demonstrates that evaluating either factor in isolation, or in a single season, risks badly misleading conclusions.

The practical implications cut in several directions. First, interannual variability in ambient ozone matters: a one-year study conducted in a low-ozone year could have concluded that ozone has no effect on rhizosphere nitrification, while a study in a high-ozone year might overstate its consistency. Second, the benefits of organic amendments on nitrogen cycling are cumulative, so short-term trials may underestimate their long-term influence on nitrification, nitrate leaching and nitrous oxide emissions. Third, because COM stimulated nitrification without changing the ammonia-oxidizer community, management strategies aimed at slowing nitrification, such as nitrification inhibitors, may need to target microbial activity rather than community structure in soils receiving organic inputs. Farmers and modelers alike will need to account for both the year-to-year swings in air quality and the slow-burn chemistry of organic matter when predicting nitrogen behavior in wheat systems.

For a warming, polluted world in which roughly half of humanity depends on wheat as a staple, the invisible choreography between root, microbe and atmosphere is no longer a niche curiosity. This O3-FACE experiment shows that the air above a wheat field and the manure spread on it are not independent stories but chapters of the same nitrogen narrative, unfolding on different timescales. Understanding that choreography, the authors argue, is essential if agriculture is to keep feeding people while keeping reactive nitrogen out of the atmosphere and the water supply. The full study is available in Plant and Soil under DOI 10.1007/s11104-026-09085-3.

Subject of Research: Effects of elevated ozone and combined organic-inorganic fertilization on soil nitrification and ammonia-oxidizing microbes in the wheat rhizosphere

Article Title: Effects of ozone and combined organic-inorganic fertilization on soil nitrification in wheat rhizosphere: insights from an O3‑FACE experiment

Article References: Shang, B., Guo, Z., Deng, T., Xiong, C., Ding, X., Xu, Y., Zhang, B., & Feng, Z. (2026). Effects of ozone and combined organic-inorganic fertilization on soil nitrification in wheat rhizosphere: insights from an O3‑FACE experiment. Plant and Soil. https://doi.org/10.1007/s11104-026-09085-3

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09085-3

Keywords: ozone, soil nitrification, wheat, rhizosphere, organic fertilizer, ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrogen cycle, O3-FACE, soil microbiology, sustainable agriculture, Plant and Soil