An Examination of Factors Controlling the Activity of Ammonia- and Nitrite-oxidizers in Diverse Soils

Graduation date: 2017Nitrification is a critical step in the global nitrogen cycle involving the biological oxidation of ammonia (NH₃) to nitrite (NO₂⁻ ) and then to nitrate (NO₃⁻). The first step in nitrification is carried out by NH₃-oxidizing bacteria (AOB) and archaea (AOA), and the second by NO₂⁻-oxidizing bacteria (NOB). In addition to NO₂⁻ and NO₃⁻ being products of nitrification, nitrous oxide (N₂O) can also be a by-product of NH₃ oxidation. Despite the importance of nitrification in agriculture, wastewater treatment, and greenhouse gas accumulation, much remains unknown about the factors controlling nitrification activity, particularly in soils. In the studies presented here, I examined factors controlling the relative contributions of AOA and AOB to nitrification activity. A survey of cropped and non-cropped soils from diverse regions of Oregon showed that AOB activity was more responsive to NH₄⁺ additions in cropped soils than was AOA activity, whereas the opposite situation occurred in non-cropped soils. A larger addition of NH₄⁺ was required to stimulate nitrification in cropped soils than in non-cropped soils (67 and 16 mg N kg soil respectively), and summer sampled soils had greater nitrifying activity than winter sampled soils. Upon further examination of the nitrifying response of non-cropped soils to NH₄⁺ addition, both AOA and AOB-driven activities gave rise to NO₂⁻ accumulation and was accompanied by N₂O formation. Nitrite additions to these soils stimulated acetylene-sensitive N₂O production, and a positive, non-linear relationship was revealed between the concentration of accumulated NO₂⁻ and N₂O production rates. Additions of the NO₂⁻ oxidizing bacterium, Nitrobacter vulgaris, to either prevent NO₂⁻ accumulation, or to remove accumulated NO₂⁻, effectively eliminated N₂O formation in two of three soils. Additional investigation showed that the dynamic nature of NO₂⁻ accumulation was driven by shifts in the kinetic properties of soil NO₂⁻ oxidizing activity. Although no significant changes were detected in population size of NOB during the 48 h experiments, an increase in the maximum rate of NO₂⁻ oxidizing capacity (apparent V[subscript max]) was detected in the three soils and proven to be protein synthesis dependent in two of the three soil. When protein synthesis and V[subscript max] increase was prevented by addition of antibiotics, the rate of NO₃- production also increased in response to the increase in the NO₂⁻ concentrations; suggesting that both protein synthesis dependent and independent mechanisms can be used to attempt to recouple the rate of NH₃ oxidation to NO₂⁻ oxidation. Recoupling occurred in all three soils, and was attributed to protein synthesis in two of the three soils, while protein synthesis independent recoupling occurred in one soil. Significant statistical interactions were detected among the soils, indicating that unknown soil properties and environmental factors, as well as metabolic properties of AOA, AOB, and NOB, are interlinked in these phenomena