Onset Of Denitrification Research Articles

Denitrification in Soil Aggregate Analogues-Effect of Aggregate Size and Oxygen Diffusion

Soil-borne nitrous oxide (N$_2$O) emissions have a high spatial and temporal variability which is commonly attributed to the occurrence of hotspots and hot moments for microbial activity in aggregated soil. Yet there is only limited information about the biophysical processes that regulate the production and consumption of N$_2$O on microscopic scales in undisturbed soil. In this study, we introduce an experimental framework relying on simplified porous media that circumvents some of the complexities occuring in natural soils while fully accounting for physical constraints believed to control microbial activity in general and denitrification in particular. We used this framework to explore the impact of aggregate size and external oxygen concentration on the kinetics of O$_2$ consumption, as well as CO$_2$ and N$_2$O production. Model aggregates of different sizes (3.5 vs. 7\,mm diameter) composed of porous, sintered glass were saturated with a defined growth medium containing roughly 10$^9$ cells ml$^{-1}$ of the facultative anaerobic, \textsl{nosZ}-deficient denitrifier \textsl{Agrobacterium tumefaciens} with N$_2$O as final denitrification product and incubated at five different oxygen levels (0-13\,vol-$\%$). We demonstrate that the onset of denitrification depends on the amount of external oxygen and the size of aggregates. Smaller aggregates were better supplied with oxygen due to a larger surface-to-volume ratio, which resulted in faster growth and an earlier onset of denitrification. In larger aggregates, the onset of denitrification was more gradual, but with comparably higher N$_2$O production rates once the anoxic aggregate centers were fully developed. The normalized electron flow from the reduced carbon substrate to N-oxyanions (e$^{-}_{\rm denit}$/e$^{-}_{\rm total}$ ratio) could be solely described as a function of initial oxygen concentration in the headspace with a simple, hyperbolic model, for which the two empirical parameters changed with aggregate size in a consistent way. These findings confirm the important role of soil structure on N$_2$O emissions from denitrification by shaping the spatial patterns of microbial activity and anoxia in aggregated soil. Our dataset may serve as a benchmark for constraining or validating spatially explicit, biophysical models of denitrification in aggregated soil.

Functional robustness and gene pools of a wastewater nitrification reactor: comparison of dispersed and intact biofilms when stressed by low oxygen and low pH

The functional robustness of biofilms in a wastewater nitrification reactor, and the gene pools therein, were investigated. Nitrosomonas and Nitrosospira spp. were present in similar amounts (cloning-sequencing of ammonia-oxidizing bacteria 16S rRNA gene), and their estimated abundance (1.1 x 10(9) cells g(-1) carrier material, based on amoA gene real-time PCR) was sufficient to explain the observed nitrification rates. The biofilm also had a diverse community of heterotrophic denitrifying bacteria (cloning-sequencing of nirK). Anammox 16S rRNA genes were detected, but not archaeal amoA. Dispersed biofilms (DB) and intact biofilms (IB) were incubated in gas-tight reactors at different pH levels (4.5 and 5.5 vs. 6.5) while monitoring O(2) depletion and concentrations of NO, N(2)O and N(2) in the headspace. Nitrification was severely reduced by suboptimal O(2) concentrations (10-100 microM) and low pH (IB was more acid tolerant than DB), but the N(2)O/NO(3)(-) product ratio of nitrification remained low (<10(-3)). The NO(2)(-) concentrations during nitrification were generally 10 times higher in DB than in IB. Transient NO and N(2)O accumulation at the onset of denitrification was 10-10(3) times higher in DB than in IB (depending on the pH). The contrasting performance of DB and IB suggests that the biofilm structure, with anoxic/micro-oxic zones, helps to stabilize functions during anoxic spells and low pH.

Testing our understanding of Arctic denitrification using MIPAS-E satellite measurements in winter 2002/2003

Abstract. Observations of gas-phase HNO3 and N2O in the polar stratosphere from the Michelson Interferometer for Passive Atmospheric Sounding aboard the ENVISAT satellite (MIPAS-E) were made during the cold Arctic winter of 2002/2003. Vortex temperatures were unusually low in early winter and remained favourable for polar stratospheric cloud formation and denitrification until mid-January. MIPAS-E observations provide the first dataset with sufficient coverage of the polar vortex in mid-winter which enables a reasonable estimate of the timing of onset and spatial distribution of denitrification of the Arctic lower stratosphere to be performed. We use the observations from MIPAS-E to test the evolution of denitrification in the DLAPSE (Denitrification by Lagrangian Particle Sedimentation) microphysical denitrification model coupled to the SLIMCAT chemical transport model. In addition, the predicted denitrification from a simple equilibrium nitric acid trihydrate-based scheme is also compared with MIPAS-E. Modelled denitrification is compared with in-vortex NOy and N2O observations from the balloon-borne MarkIV interferometer in mid-December. Denitrification was clearly observed by MIPAS-E in mid-December 2002 and reached 80% in the core of the vortex by early January 2003. The DLAPSE model is broadly able to capture both the timing of onset and the spatial distribution of the observed denitrification. A simple thermodynamic equilibrium scheme is able to reproduce the observed denitrification in the core of the vortex but overestimates denitrification closer to the vortex edge. This study also suggests that the onset of denitrification in simple thermodynamic schemes may be earlier than in the MIPAS-E observations.

Simulating the evolution of the chemical composition of the 1988/89 Winter vortex

During the 1988/89 Airborne Arctic Stratospheric Expedition (AASE) observations of the chemical composition and aerosol characteristics of the winter vortex were obtained from a NASA ER‐2 aircraft. In this paper we present interpretations of observations obtained on three ER‐2 flights using a Lagrangian coupled photochemical‐microphysical model. It is argued that observations obtained on January 16 and 19, and February 10, represent different stages of the chemical evolution of the vortex, from the early stages of chlorine release, the onset of denitrification and the intensively processed state.

Some factors influencing denitrification and nitrogen immobilization in a clay soil

Nitrate-N, enriched with 15N, was added to small cores of the 0–10 cm layer of a clay soil. The base of each core was sealed, then water, equivalent to 0, 10, 20 or 30mm of rain, was added to the soil surface. The cores were incubated for 1 week at 10, 20, or 30°C in the presence or absence of wheat straw. The recovery of 15N in the soil mineral-N and organic-N fractions was then measured. No significant losses of 15N were detected in the cores which received 0–10 mm of added water, and in which the soil water content was close to 0.56 g g −1 (−10 kPa). However, 15N losses, assumed due to denitrification, were rapid from cores receiving 20 or 30 mm of water and incubated at 20–30°C. The onset of denitrification was quite sudden as the amount of added water increased from 10 to 20 mm. In this range, a small increment of added water apparently sealed a relatively large volume of soil from atmospheric O 2 diffusion. This phenomenon was strongly temperature-dependent since no losses were detected from any cores at 10°C even though the 30mm addition of water produced a thin layer of free water across the soil surface. The addition of straw did not promote denitrification in soil at water contents close to 0.56 g g −1. At high soil water contents, adcling straw increased immobilization of labelled NO 3 − and so reduced denitrification losses. The response of immobilization to changing soil water and temperature conditions was very different from that of denitrification.