Nitrogen fertilizer has long carried a scientific paradox beneath its promise of higher yields. The same nutrient that fuels crop growth can also trigger soil acidification, while the microbial process that converts ammonium into nitrate—nitrification—is often treated as the main biological engine behind that decline in pH. A new study by Wu, Huang, Huang and colleagues, published in Nature Communications, tackles this apparent contradiction, asking how nitrogen fertilization can influence nitrification without producing a simple, universal pattern of soil acidification.
The question matters because nitrogen fertilizer is used on a vast scale across modern agriculture. Ammonium-based products, including ammonium sulfate and urea, supply plants with nitrogen that is eventually transformed into ammonium and nitrate. During nitrification, specialized microorganisms oxidize ammonium first to nitrite and then to nitrate. These reactions generate acidity, consuming soil’s buffering capacity over time. In simplified terms, more nitrification can mean more hydrogen ions released into the soil solution, potentially lowering pH and altering the chemical environment around plant roots.
Yet soils do not respond to fertilizer as if they were identical laboratory vessels. Their response depends on mineral composition, organic matter, rainfall, crop uptake, microbial communities and the quantity and chemical form of nitrogen applied. Some soils contain carbonate minerals that neutralize acidity, while others have limited buffering capacity and can become acidic more quickly. Plants may also absorb nitrate before it moves through the soil profile, reducing losses, whereas excessive applications can promote nitrate leaching and carry accompanying positively charged ions away from the root zone.
The study’s central contribution is to reconcile these interacting processes rather than treating nitrification and acidification as interchangeable measurements. Nitrification describes a transformation of nitrogen, while acidification describes a shift in the balance of protons and bases within the soil system. The two processes are linked, but the strength of that link can vary substantially. A burst of microbial nitrification may not immediately produce a measurable fall in pH if the soil has strong buffering capacity. Conversely, modest nitrogen transformations may contribute to serious long-term acidification in vulnerable soils exposed to repeated fertilization.
This distinction could help explain why previous studies have sometimes produced apparently conflicting conclusions. Nitrogen inputs can stimulate nitrifying microorganisms, but the resulting chemical effects may be concealed temporarily by calcium and magnesium released from soil minerals, by organic matter reactions or by the uptake of nitrate by crops. Over years or decades, however, repeated fertilizer applications can gradually exhaust those protective reserves. The result may be a delayed transition in which soil pH declines more rapidly after the system’s buffering capacity has been weakened.
The chemistry also changes with fertilizer type. When plants absorb nitrate, they tend to release hydroxide or bicarbonate ions, which can partially offset acidity. When they absorb ammonium, they release hydrogen ions, potentially intensifying acidification. Urea adds another layer of complexity: it is hydrolyzed to ammonium, followed by nitrification, but the initial reactions can temporarily raise pH near fertilizer granules before later processes generate acidity. These short-term fluctuations can obscure the cumulative effects of nitrogen management when soil is sampled only once or at a single depth.
The consequences extend beyond a number on a soil-pH test. Acidification can alter the solubility of nutrients and toxic metals, reduce the availability of phosphorus, and affect the activity and composition of soil microorganisms. In strongly acidic conditions, aluminum and manganese may become more soluble and potentially harmful to roots. Changes in microbial communities can also influence carbon decomposition, greenhouse-gas emissions and the persistence of nitrogen in soil. At the same time, nitrate that escapes crop uptake can enter groundwater or surface waters, contributing to eutrophication and creating a second pathway through which fertilizer affects ecosystems.
By placing nitrification within the broader chemical balance of soils, the research points toward more precise nitrogen management rather than a simple call to eliminate fertilizer. Matching applications to crop demand, choosing suitable nitrogen forms, dividing fertilizer into multiple doses and maintaining adequate organic matter could reduce unnecessary nitrogen transformations and losses. Liming may restore neutralizing capacity in acidified soils, although it does not replace the need to prevent excessive nitrogen inputs. The study’s message is especially relevant as agriculture faces the difficult task of sustaining food production while reducing environmental damage.
The work arrives at a moment when the global nitrogen cycle is under intense scrutiny. Fertilizer has helped transform agricultural productivity, but inefficient nitrogen use has connected farms to air pollution, climate change, groundwater contamination and declining soil health. Understanding when nitrification translates into acidification—and when soil properties interrupt or delay that pathway—could improve models of agricultural change and make fertilizer recommendations more locally specific. The researchers’ attempt to reconcile these processes offers a more realistic picture of soil chemistry: nitrogen fertilization does not produce one predictable outcome, but a chain of biological and chemical reactions whose consequences depend on time, place and management.
Subject of Research: Soil nitrification, nitrogen fertilization, and agricultural soil acidification
Article Title: Reconciling nitrogen fertilization effects on soil nitrification with acidification
Article References: Wu, L., Huang, Y., Huang, Y. et al. “Reconciling nitrogen fertilization effects on soil nitrification with acidification.” Nature Communications (2026). https://doi.org/10.1038/s41467-026-76609-x
Image Credits: AI Generated
DOI: 10.1038/s41467-026-76609-x
Keywords: nitrogen fertilization, soil nitrification, soil acidification, ammonium, nitrate, soil microorganisms, agricultural sustainability, nitrogen cycle, soil health
