Injecting Manure Cuts Ammonia but Sends More Nitrate Into Groundwater

Every spring, dairy farms across the United States spread millions of gallons of liquid manure onto cornfields, delivering a potent blend of nitrogen, phosphorus, and organic matter to hungry crops. But that same nitrogen has a habit of vanishing into the air or seeping into groundwater, and a new two-year field experiment from the University of Wisconsin-Madison shows that the most popular fix for one problem may quietly worsen the other. The study, published in the Journal of Agriculture and Food Research, tracked ammonia emissions, nitrous oxide fluxes, and nitrate leaching from a silt loam soil under six different manure management strategies, and its results upend the simple assumption that injecting manure below the surface is an unambiguous environmental win.

The stakes are larger than one Wisconsin cornfield. Agriculture is responsible for more than 81 percent of global ammonia emissions, and livestock production alone accounts for roughly 60 percent of those emissions in the United States. Once in the atmosphere, ammonia reacts with sulfur and nitrogen oxides to form fine particulate matter, or PM2.5, the microscopic pollution that penetrates deep into the lungs and contributes to respiratory disease, cardiovascular illness, and premature death. A portion of the gas also rains back down onto natural ecosystems, driving soil acidification and nutrient imbalances. Meanwhile, nitrate that escapes below the root zone contaminates aquifers and fuels algal blooms in lakes and coastal waters. Nitrous oxide, though a smaller share of the nitrogen budget, is a greenhouse gas roughly 273 times more potent than carbon dioxide over a century.

Researchers Juma Bukomba, Matthew D. Ruark, and Rebecca A. Larson set out to quantify the full nitrogen ledger under realistic field conditions. At the Arlington Agricultural Research Station on Plano silt loam, they compared surface broadcasting of liquid dairy manure, broadcasting followed by incorporation within one hour, subsurface injection at 15 centimeters, and versions of each treated with the urease inhibitor NBPT, alongside an unfertilized control. Plots stretched nine meters wide and 76 meters long, and the team buried ion exchange resin samplers at 90 centimeters to catch nitrate draining past the corn rooting zone. Ammonia and nitrous oxide were measured with a Fourier transform infrared gas analyzer mounted on a mobile cart, using chamber-based flux measurements that followed the USDA-ARS GRACEnet protocol. Sampling was deliberately concentrated in the first days after application, when ammonia losses peak.

The ammonia results were striking. Surface broadcasting lost the most nitrogen to the air, averaging 7 kilograms of nitrogen per hectare in 2024 and 18.2 kilograms per hectare in 2025 over the first 96 hours. Injection and injection with the inhibitor were statistically indistinguishable from the unfertilized control, meaning essentially no measurable ammonia escaped from the injected plots. Incorporation fell in between. The pattern held in both years, though emissions ran hotter in 2025, when the manure carried more total ammoniacal nitrogen, 87 versus 70 kilograms per hectare, and air temperatures in the critical first four days were about 4 degrees Celsius higher. Warmth accelerates the conversion of ammonium to ammonia gas and speeds its escape, a well-documented but vividly demonstrated effect here.

The urease inhibitor, NBPT, was the study’s most instructive disappointment. Added to manure at the manufacturer’s recommended rate, it failed to significantly reduce ammonia emissions whether manure was broadcast or injected. The reason lies in dairy manure chemistry. NBPT works by blocking the urease enzyme that converts urea into ammonium, but by the time manure leaves storage, most of the urea excreted in urine has already been hydrolyzed. In this study, total ammoniacal nitrogen made up 57 to 61 percent of the total nitrogen applied, suggesting little residual urea remained for the inhibitor to protect. The finding suggests that if inhibitors are to work for liquid dairy manure, they may need to be applied earlier in the management chain, in the barn or storage lagoon, rather than in the tanker on the way to the field.

Then came the trade-off. Nitrate leaching, measured over entire growing seasons, was highest in 2024, a year when rainfall from April through October totaled 836 millimeters, nearly double the 32-year average. That year, incorporation produced the greatest cumulative nitrate loss at 108.4 kilograms of nitrogen per hectare, 37 percent more than surface broadcasting and 89 percent more than the unfertilized control. Injection and injection with the inhibitor also leached substantially more nitrate than surface application. In 2025, a drier year, injection-based treatments again showed elevated leaching relative to broadcasting. The mechanism is intuitive: keeping nitrogen in the soil rather than the air means more of it is available for nitrification and downward transport when heavy rains arrive.

The crop data added another layer of nuance. In 2025, when residual soil nitrogen was low and the field responded to added fertilizer, injection produced the highest corn silage yield at 18.2 megagrams per hectare, with nitrogen uptake of 165.2 kilograms per hectare, significantly exceeding surface broadcasting and the control. Surface-applied manure, having lost so much nitrogen to volatilization, yielded barely more than unfertilized plots in that year. A companion nitrogen rate experiment showed that injected manure reduced the agronomic optimum nitrogen rate to 103 kilograms per hectare, compared with 177 for surface broadcasting and 181 for the unfertilized control, a clear signal that subsurface placement preserved more plant-available nitrogen. Silage quality metrics, including crude protein, fiber fractions, and digestible nutrients, were unaffected by treatment in both years.

Perhaps the most sobering finding concerned the nitrogen already in the ground. The unfertilized control plots leached 57.3 kilograms of nitrate-nitrogen per hectare in 2024, roughly four times the 2025 figure, and the researchers estimated that pre-existing soil nitrogen pools accounted for about half of the total nitrate leached that year. Fields with a history of heavy manure and fertilizer use carry a legacy nitrogen burden that no application method can undo. Managing that reservoir, through cover crops, adjusted application rates, or fallow-season strategies, may matter as much as refining how manure is placed.

Taken together, the study reframes the manure management debate. Injection and rapid incorporation genuinely deliver on their promise of slashing ammonia emissions, and in nitrogen-limited years they translate that conserved nitrogen into higher yields and lower fertilizer requirements. But the conserved nitrogen does not simply disappear into the crop; in wet years and leaky soils, a substantial fraction migrates downward instead. Nitrate leaching, not ammonia volatilization, was the dominant environmental loss pathway in every treatment and both years, sometimes exceeding 60 percent of applied manure nitrogen when measured against the control. The authors argue that ammonia-reduction practices must be paired with complementary leaching controls, such as cover crops or timing applications to avoid saturated conditions, to be truly sustainable.

For farmers and policymakers alike, the message is that there is no single best way to apply manure, only context-dependent trade-offs. Subsurface placement offers real benefits for air quality, human health, and fertilizer value, and it reduces nutrient losses in surface runoff. But on silt loam soils prone to drainage, it shifts the pollution problem from the atmosphere to the aquifer. The next generation of best management practices will need to think in whole-system terms, balancing the air, the soil, the water, and the crop in a single accounting, because this study shows that nitrogen saved from the sky has a way of finding its way into the ground.

Subject of Research: Effects of liquid dairy manure application methods on ammonia emissions, nitrous oxide fluxes, nitrate leaching, and corn silage nitrogen use in silt loam soil

Article Title: Effects of Manure Land Application Practices on Ammonia Emissions and Nitrate Leaching in a Silt Loam Soil

Article References: Bukomba, J., Ruark, M. D., & Larson, R. A. (2026). Effects of Manure Land Application Practices on Ammonia Emissions and Nitrate Leaching in a Silt Loam Soil. Journal of Agriculture and Food Research, Article 103364. https://doi.org/10.1016/j.jafr.2026.103364

Image Credits: AI Generated

DOI: 10.1016/j.jafr.2026.103364

Keywords: dairy manure, ammonia emissions, nitrate leaching, manure injection, urease inhibitor, NBPT, nitrous oxide, corn silage, nitrogen use efficiency, silt loam soil, groundwater contamination, Wisconsin agriculture