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In the majority of agricultural soils, ammonium (NH +) is rapidly converted to nitrate (NO 3-) in the biological ammonia and nitrite oxidation processes known as nitrification. The often rate-limiting step of ammonia oxidation to nitrite is mediated by ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA). The response of AOA and AOB communities to organic and conventional nitrogen (N) fertilizers, and their relative contributions to the nitrification process were examined for an agricultural silage corn system using a randomized block design with 4 N treatments: control (no additional N), ammonium sulfate (AS) fertilizer at 100 and 200 kg N ha-1 , and steer-waste compost (200 kg total N ha-1) over four seasons. DNA was extracted from the soil, and real-time PCR and 454-pyrosequencing were used to evaluate the quantity and diversity of the amoA gene which encodes subunit A of ammonia monooxygenase. Soil pH, nitrate pools, and nitrification potentials were influenced by ammonium and organic fertilizers after the first fertilization, while changes in AOB abundance and community structure were not apparent until after the second fertilization or later. The abundance of AOA was always greater than AOB but was unaffected by N treatments. In contrast, AOB abundance and community structure were changed significantly by ammonium fertilizers. Specific inhibitors of nitrification were used to evaluate the relative contribution of AOA and AOB to nitrification. We found that AOB dominantly contributed to potential nitrification activity determined at 1 mM ammonium in soil slurries and nitrification potential activity was higher in soils treated with ammonium fertilizers relative to control soils. However, AOA dominated gross nitrification activity in moist soils. Our result suggests that AOB activity and community are more responsive to ammonium fertilizers than AOA but that in situ nitrification rate is controlled by ammonium availability in this agricultural soil. Understanding this response of AOA and AOB to N fertilizers may contribute to improving strategies for the management of nitrate production in agricultural soils.

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Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.

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