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Abstract. Soil denitrification is the most important terrestrial process returning reactive nitrogen to the atmosphere, but remains poorly understood. In upland soils, denitrification occurs in hotspots of enhanced microbial activity, even under well-aerated conditions, and causes harmful emissions of nitric (NO) and nitrous oxide (N2O). The timing and magnitude of such emissions are difficult to predict due to the delicate balance of oxygen (O2) consumption and diffusion in soil. To study how spatial distribution of hotspots affects O2 exchange and denitrification, we embedded microbial hotspots composed of porous glass beads saturated with growing cultures of either Agrobacterium tumefaciens (a denitrifier lacking N2O reductase) or Paracoccus denitrificans (a “complete” denitrifier) in different architectures (random vs. layered) in sterile sand that was adjusted to different water saturations (30 %, 60 %, 90 %). Gas kinetics (O2, CO2, NO, N2O and N2) were measured at high temporal resolution in batch mode. Air connectivity, air distance and air tortuosity were determined by X-ray tomography after the experiment. The hotspot architecture exerted strong control on microbial growth and timing of denitrification at low and intermediate saturations, because the separation distance between the microbial hotspots governed local oxygen supply. Electron flow diverted to denitrification in anoxic hotspot centers was low (2 %–7 %) but increased markedly (17 %–27 %) at high water saturation. X-ray analysis revealed that the air phase around most of the hotspots remained connected to the headspace even at 90 % saturation, suggesting that the threshold response of denitrification to soil moisture could be ascribed to increasing tortuosity of air-filled pores and the distance from the saturated hotspots to these air-filled pores. Our findings suggest that denitrification and its gaseous product stoichiometry depend not only on the amount of microbial hotspots in aerated soil, but also on their spatial distribution. We demonstrate that combining measurements of microbial activity with quantitative analysis of diffusion lengths using X-ray tomography provides unprecedented insights into physical constraints regulating soil microbial respiration in general and denitrification in particular. This paves the way to using observable soil structural attributes to predict denitrification and to parameterize models. Further experiments with natural soil structure, carbon substrates and microbial communities are required to devise and parametrize denitrification models explicit for microbial hotspots.

<p><strong>Abstract.</strong> Soil denitrification is the most important terrestrial process returning reactive nitrogen to the atmosphere, but remains poorly understood. In upland soils, denitrification occurs in hotspots of enhanced microbial activity, even under well-aerated conditions, and causes harmful emissions of nitric (NO) and nitrous oxide (N<sub>2</sub>O). Timing and magnitude of such emissions are difficult to predict due to the delicate balance of oxygen (O<sub>2</sub>) consumption and diffusion in soil. To study how spatial distribution of hotspots affects O<sub>2</sub> exchange and denitrification, we embedded porous glass beads inoculated with either <i>Agrobacterium tumefaciens</i> (a denitrifier lacking N<sub>2</sub>O reductase) or <i>Paracoccus denitrificans</i> (a <q>complete</q> denitrifier) in different architectures (random vs. layered) in sterile sand adjusted to different water saturations (30 %, 60 %, 90 %) and measured gas kinetics (O<sub>2</sub>, CO<sub>2</sub>, NO, N<sub>2</sub>O and N<sub>2</sub>) at high temporal resolution. Air connectivity, air distance and air tortuosity were determined by X-ray tomography after the experiment. The hotspot architecture exerted strong control on microbial growth and timing of denitrification at low and intermediate saturations, because the separation distance between the microbial hotspots governed local oxygen supply. Electron flow diverted to denitrification in anoxic hotspot centers was low (2–7 %) but increased markedly (17–27 %) at high water saturation. X-ray analysis revealed that the air phase around most of the hotspots remained connected to the headspace even at 90 % saturation, suggesting that the threshold response of denitrification to soil moisture could be ascribed solely to increasing tortuosity of air-filled pores. Our findings suggest that denitrification and its gaseous product stoichiometry do not only depend on the amount of microbial hotspots in aerated soil, but also on their spatial distribution. We demonstrate that combining measurements of microbial activity with quantitative analysis of diffusion lengths using X-ray tomography provides unprecedented insights into physical constraints regulating soil microbial respiration in general and denitrification in particular. This opens new avenues to use observable soil structural attributes to predict denitrification and to parameterize models. Further experiments with natural soil structure, carbon substrates and microbial communities are required to demonstrate this under realistic conditions.</p>

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<p>Denitrification is an important microbial process and potential source for nitrous oxide (N<sub>2</sub>O), an important greenhouse gas and destructor of stratospheric ozone. Quantitative predictions of denitrification in soils are difficult as denitrification, an anaerobic respiration process,  appears to occur even in well-areated soils. It is assumed that denitrification is active in dense aggregates over short time periods - so called hot spots and hot moments. While soil microbial metabolism occurs at the pore scale, the interest in denitrification is mostly at the field and landscape scale. Simulating both scales simultaneously is not feasible. Therefore, denitrification has to be upscaled from the pore to the aggregate scale without losing essential properties of the aggregates. An important key to effectively upscale is the anaerobic aggregate volume fraction.</p><p>In order to compare different upscaling techniques we conducted pure culture experiments with varying spatial structures. To avoid confounding effects associated with the transition of bacteria switching from oxic respiration to denitrification, we used bacteria only capable of the former. The investigated upscaling techniques include simplifying the microbial reaction as well as creating an effective one-dimensional diffusion model. We compare computation intensity and approximation quality of experimental results.</p>

A novel approach combining microfluidics with 2-D modeling validates the proposed microbial growth model for underground hydrogen storage and concludes space-limited growth and microbial gradients on the pore scale.

<p>Denitrification in unsaturated soils is widely assumed to be a result a result of the formation of so-called hot spots. However, this is a hypothesis, which is hard to test experimentally. Furthermore a better understanding of the microscale dynamics might be very helpful to derive better models at the macroscale.</p><p>Experiments have been conducted, where artificial aggregates from sintered glas have been inocculated with microorganisms and been placed in environments with different oxygen availabilities. Very high-resolution simulations are conducted to reproduce the dynamic of the generation of nitric and nitrous oxide based on a model of microbial growth parametrised with experimental data from batch experiments. The simulations allow a detailed analysis of the local and temporal dynamics of denitrification inside the aggregates.</p>

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