Emissions of nitrogen-containing trace gases from agricultural systems may be a significant local to regional flux of reactive nitrogen. In China, the combined emissions of ammonia (NH₃) and nitric oxide (NO) rival the emissions of NO_x from industrial sources. But perhaps more importantly from a management stand point, emissions of the nitrogen oxides and ammonia from agricultural systems can be reduced though agricultural techniques while emissions from energy use may be less amenable to reductions. For this reason it is important to understand the processes responsible for trace gas production in soils and the effects of management activities and land use change on these processes and fluxes. There are numerous techniques available for process level studies of trace gas emissions, and the effects of management techniques on these fluxes and use of these techniques can provide the information necessary for attempts to reduce nitrogen oxide emissions from soils.

In order to control emissions of N-containing trace gases from soils, it is important to understand the mechanisms responsible for their production in soils. Emissions of NO, N₂O and NH₃ all occur as byproducts of the cycling nitrogen in soils. The cycling of nitrogen through soils occurs in three distinct conceptual stages. These stages include the conversion of organic nitrogen to ammonium (NH ₄), known as mineralization, followed by the conversion of NH₄ to nitrate (NO₃), known as nitrification, and finally by the reduction of NO₃ to NO, N₂O or N₂, a process called denitrification.

The production of NO and N₂O can occur during either nitrification or denitrification and in some cases, NO may be produced during the chemodenitrification (chemical denitrification) of nitrite (NO₂). Both nitrification and denitrification can be affected by a number of factors including oxygen availability (nitrification requires oxygen and denitrification requires near-absence to absence of oxygen), substrate availability (NH₄ for nitrification and carbon and NO₃ for denitrification). These factors can then be affected by a wide range of additional soil characteristics many of which can be significantly affected by agricultural activities. There are two steps to understanding trace gas production in soils. The first step requires the identification of the process or processes responsible for the production of a trace gas, and the second requires understanding the factors that control these processes.

To determine the effects of biomass clearing and burning on soil NO emissions and the processes responsible for the production of NO, Neff et al. conducted a series of experiments at sites in the Atlantic Lowlands of Costa Rica. These experiments provided a case study of the techniques available for determining process controls on NO production in soils. Clearing and burning of secondary tropical rain forest significantly increased soil NO emissions. Soil NO fluxes averaged 0.5 ng NO-N cm^-2 hr^-1 prior to clearing and increased to 4.1 ng NO-N cm^-2 hr^-1 following clearing and to 12.0 ng NO-N cm -2 hr^-1 following burning. In order to determine the probable mechanism responsible for elevated NO emissions, substrates were added to simulate microbial nitrification (ammonium), denitrification (nitrate) and chemical denitrification (nitrite) to autoclaved (killed) and non-autoclaved (live) soil cores.

Compared to water or nitrate additions, ammonium caused a significant increase in NO emissions from live cores. Nitrite additions resulted in highly significant increases in NO emissions from both killed and live soil cores. In a second experiment, soil cores were treated with acetylene (1 Kpa C₂H₂) to selectively inhibit nitrification, and oxygen to inhibit denitrification. The oxygen treatment had no effect on NO production while acetylene significantly reduced NO production. The results from the substrate addition and inhibition experiments demonstrate that microbial denitrification is not a major pathway for NO production in these soils. In contrast, microbial nitrification appears to be a critical process responsible for NO emissions throughout the clearing and burning period. Techniques such as these can be used in both agricultural and natural ecosystems in order to determine process level controls on soil trace gas production.

To examine the effects of fertilization on NO and N₂O emissions from a palm plantation in Costa Rica, Michael Keller of the U.S. Forest Service conducted a study in which fluxes of these gases were monitored following fertilization additions. When fertilizer was added, both NO and N₂O fluxes increased dramatically, and in the case of N₂O, these emissions remained high for at least 30 days. Integrated losses of added fertilizer nitrogen through trace gas emissions averaged approximately 15% via N₂O and 2% via NO. These losses were strongly seasonal with the bulk of the N₂O lost during Winter months when soil moisture was high and with NO loss occur ring primarily in the Spring dry season. These results highlight the effect of oxygen availability on nitrification and denitrification. Nitrification rates are reduced when the soils are wet probably due to oxygen limitations. Conversely, denitrification rates are highest when soil oxygen is limited. Again it appears that NO is primarily produced during nitrification while denitrification is probably responsible for N₂O production and so losses of these gases from soils are closely tied to both fertilization and seasonal changes in the soil moisture content and thus oxygen availability.

Once the processes responsible for trace gas losses are known, it is possible to structure management techniques in such a way as to reduce these losses. For example there are commercially available nitrification inhibitors which could potentially reduce both NO and N₂O loss. The use of these inhibitors will, of course, have multiple impacts on the soil-plant system and a complete understanding of these effects should precede any decisions to use these chemicals. A more simple approach to trace gas emission control can be taken though the use of fertilizers. In general, increases in fertilizer use cause increases in trace gas emissions. In addition, the type, timing and manner of fertilizer application can dramatically alter trace gas losses from agricultural systems. It is possible to significantly reduce trace gas losses simply through an understanding of the soil nitrogen cycle and plant phenological demands for nitrogen. As fertilizer use rates increase into the future, management of the emissions of nitrogen-containing trace gases will become increasingly important.