The research, led by Viney P. Aneja and Srijan Sengupta of North Carolina State University, together with Swarnali Sanyal of the University of Illinois Urbana-Champaign and William H. Schlesinger of the Cary Institute of Ecosystem Studies, examined ammonia emissions from swine operations that had retrofitted their waste management systems with anaerobic digestion. The team combined direct field measurements with outputs from a semiempirical mass-transfer model, a computational tool that estimates how quickly gaseous ammonia escapes from liquid manure surfaces based on chemical and physical conditions. Their central finding is striking: ammonia flux from so-called biogas secondary lagoons — open lagoons that receive digestate, the liquid residue left after anaerobic digestion — was statistically significantly higher than ammonia flux from conventional open-air lagoons used in traditional manure management, with the difference holding even after the analysis controlled for temperature, the single most important driver of volatilization.

To understand why this happens, it helps to follow the chemistry of nitrogen through a digester system. In a conventional lagoon, raw manure sits in open basins where organic nitrogen compounds are gradually mineralized to ammonium, and some of that ammonium escapes to the air as ammonia gas. In an anaerobic digester, by contrast, microbes decompose the organic matter in an oxygen-free environment, breaking down proteins and urea far more completely and rapidly. This process converts a large share of the organic nitrogen into total ammoniacal nitrogen, the pool of dissolved ammonia and ammonium ions from which gaseous ammonia can volatilize. At the same time, digestion consumes volatile acids and raises the pH of the digestate. Because the equilibrium between ammonium ions and free ammonia gas shifts strongly toward the gas phase as pH rises, digestate emerging from a digester is essentially primed for ammonia loss the moment it is exposed to air.

That exposure comes quickly. After digestion, the liquid effluent is typically transferred to a secondary storage lagoon before being pumped onto cropland as fertilizer. The study’s model simulations confirm that both during secondary storage and during subsequent land application under typical management practices, the elevated total ammoniacal nitrogen concentration and higher pH of digestate dramatically enhance the potential for volatilization. In effect, the digester concentrates the nitrogen problem: it converts slow, diffuse organic nitrogen into a chemically reactive, easily airborne form, then hands that material to an open lagoon where wind and warm temperatures can strip it into the atmosphere. The regression analysis, which statistically isolated the effect of the management system from confounding variables, found the difference between biogas secondary lagoons and conventional lagoons to be highly significant, with a p-value below 0.001 — a level of statistical confidence rarely achieved in environmental field studies.

The consequences extend well beyond the fence lines of the farms themselves. Ammonia is classified as a reactive nitrogen compound, and once released, it does not stay ammonia for long. In the atmosphere it reacts with acidic species such as nitric and sulfuric acids to form fine particulate matter, microscopic particles known as PM2.5 that penetrate deep into human lungs and are linked to asthma, cardiovascular disease, and premature death. Deposited back onto land and water, ammonia and its reaction products acidify soils, over-fertilize sensitive natural ecosystems in a process called eutrophication, and contribute to biodiversity loss in nitrogen-limited habitats. Some of the deposited nitrogen ultimately converts to nitrate, which can leach into groundwater and contaminate drinking water supplies — a cascade of impacts the study’s authors explicitly flag as a risk of degraded air quality and water quality relative to manure managed in systems open to the atmosphere.

The timing of this research matters. Across the United States, the livestock industry is actively retrofitting existing animal waste management systems at CAFOs to collect biogas, driven by a combination of renewable energy incentives, carbon credit markets, and corporate climate pledges. In states such as North Carolina and Iowa, major utility partnerships have funneled hundreds of millions of dollars into covering swine lagoons with anaerobic digesters. The shift from using animal waste solely as crop fertilizer toward producing biofuels is routinely advocated as an environmentally friendly strategy because of its potential to reduce greenhouse gas emissions, particularly methane, which traps far more heat per molecule than carbon dioxide over a twenty-year time horizon. The new findings do not dispute the climate accounting for methane. Instead, they reveal a blind spot in how the environmental performance of digesters is evaluated — one focused almost exclusively on carbon while ignoring the reactive nitrogen consequences of the same technology.

The study’s synopsis is blunt: anaerobic digesters used for biogas production from animal manure processing carry negative consequences for society and the environment and may not represent the cleaner energy future they are advertised to be. The authors caution that retrofitting digesters without integrated nitrogen management may simply shift environmental impacts from methane to reactive nitrogen, exchanging a visible, well-regulated climate problem for a diffuse air and water pollution problem that is harder to measure and easier to overlook. This kind of pollution shifting is a familiar trap in environmental engineering; solutions that solve one problem in isolation frequently create or amplify others when the full system is examined. The digester-ammonia connection is a textbook example, hidden in plain sight because the emissions occur at secondary lagoons and applied fields rather than at the digester itself.

Importantly, the researchers do not argue that biogas should be abandoned. Their conclusion is conditional but constructive: the environmental risk can be substantially reduced if digester systems are paired with mitigation technologies for animal waste management. Such technologies exist. Solid-liquid separation and acidification of digestate can lower pH and suppress the ammonia equilibrium shift. Covering secondary lagoons, capturing or scrubbing emitted ammonia, and applying digestate with injection or rapid incorporation into soils rather than surface spraying can all cut volatilization losses substantially. The key insight is that these controls must be designed into the retrofit from the beginning, not bolted on after air quality problems emerge. A digester project that captures methane but leaves hot, high-pH digestate evaporating in an open lagoon has, by the study’s measurements, made local air quality worse, not better.

For policymakers, the study lands at a sensitive moment. Regulatory frameworks in the United States reward digesters primarily for their methane capture, and renewable natural gas credits are priced on carbon metrics alone. If ammonia penalties were factored into the environmental accounting — as they increasingly are in European assessments of biogas systems — the calculus of which waste management strategies deserve public support could shift. The authors’ field-based evidence, strengthened by independent model confirmation, gives regulators a quantitative basis for requiring nitrogen management plans as a condition of digester incentives. It also gives communities near CAFOs, many of which are already overburdened by odor and particulate pollution, a new line of evidence in ongoing debates about the true cost of industrial livestock production.

Ultimately, the research is a reminder that environmental virtue in one dimension does not guarantee virtue in all. Capturing methane from manure is genuinely valuable for the climate, and the study does not challenge that. But the biogas story told to the public has been incomplete. The full lifecycle of digested manure — from the microbial transformations inside the digester to the moment the resulting liquid drifts off a secondary lagoon on a summer afternoon — determines the real environmental footprint of this technology. As the United States accelerates its retrofit of livestock operations in the name of renewable energy, the message from Biogeochemistry is clear: measure the nitrogen, manage the digestate, and do not assume that a covered lagoon means a cleaner farm. Without that vigilance, the cleaner energy future may arrive with an invisible plume of ammonia attached.

Subject of Research: Ammonia emissions from anaerobic digesters used for biogas production at swine concentrated animal feeding operations.

Article Title: Biogeochemical reactions in anaerobic digesters for biogas production yield enhanced ammonia emissions

Article References: Biogeochemical reactions in anaerobic digesters for biogas production yield enhanced ammonia emissions. (n.d.). https://doi.org/10.1007/s10533-026-01372-6

Image Credits: AI Generated

DOI: 10.1007/s10533-026-01372-6

Keywords: anaerobic digestion, biogas, ammonia emissions, reactive nitrogen, CAFOs, swine manure, digestate, methane capture, air quality, water quality, volatilization, renewable energy