Physical constraints for respiration in microbial hotspots in soil and their importance for denitrification

Abstract

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.

Effect of legume intercropping on N<sub>2</sub>O emissions and CH<sub>4</sub> uptake during maize production in the Great Rift Valley, Ethiopia

“…Inorganic and organic N added to soil provide ammonium (NH + 4 ) and nitrate (NO − 3 ) for nitrification and denitrification, respectively, which are the two main processes of microbial N 2 O production in soil (Khalil et al, 2004). The rate of N 2 O formation depends greatly on the extent and distribution of anoxic microsites in soils, which is controlled by moisture, texture and the distribution of decomposable organic matter and NH + 4 fueling heterotrophic and autotrophic respiration, respectively (Schlüter et al, 2019;Wrage-Mönnig et al, 2018). The magnitude of soil N 2 O emissions depends on O 2 availability as controlled by soil moisture and respiration, the availability of mineral N and readily decomposable C (Harrison-Kirk et al, 2013), and soil pH (Russenes et al, 2016), all of which are affected by management practices.…”

“…Mulching and the incorporation of crop residues lead to increased N mineralization and respiratory O 2 consumption, thus potentially enhancing N 2 O emissions both from nitrification and denitrification (Drury et al, 1991) if soil moisture is sufficient to support microbial activity and restrict O 2 diffusion into the soil. Accordingly, N 2 O emissions are variable in time, often following rainfall events (Schwenke et al, 2016).…”

Pore‐scale modeling of microbial activity: What we have and what we need

“…Nevertheless, exciting yet old research has touched indirectly on the interplay of different elements mentioned before by showing that even after flushing out most of the microorganisms from soil (∼90%) with CHCl 3 , the mineralization of soil OM carries on at the same rate (Jenkinson, 1966). Schlüter, Zawallich, Vogel, and Dörsch (2019) investigated the effect of hot spots on the transition from aerobic to anaerobic respiration and showed the significance of these hot spots for the denitrification process. However, many obtained their results using controlled yet simplified experimental setups (e.g., batch reactor systems), while in contrast, the soil is an open system with spatiotemporal variation of water content and microorganism distributions (Rein et al, 2016).…”

Automated Laboratory and Field Techniques to Determine Greenhouse Gas Emissions

“…Typically, incubations are initiated under oxic or anoxic conditions by flushing the headspace of the incubation bottles with various gas mixtures. The transition from oxic to anoxic metabolism can be studied by letting the sample consume a finite amount of O 2 while monitoring the evolution of gaseous intermediates (NO, N 2 O, H 2 ), and final products (N 2 , CH 4 , H 2 S) involved in anoxic metabolism (Schlüter et al 2019). Notably, replacing the bottle atmosphere with He or a mixture of He and O 2 allows for quantifying N 2 , the final product of denitrification which cannot be detected at ambient N 2 background levels (but see section on Raman spectroscopy Chap.…”