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Common methods for measuring soil denitrification in situ include monitoring the accumulation of 15N-labelled N2 and N2O evolved from 15N-labelled soil nitrate pool in closed chambers that are placed on the soil surface. Gas diffusion is considered to be the main transport process in the soil. Because accumulation of gases within the chamber decreases concentration gradients between soil and the chamber over time, the surface efflux of gases decreases as well, and gas production rates are underestimated if calculated from chamber concentrations without consideration of this mechanism. Moreover, concentration gradients to the non-labelled subsoil exist, inevitably causing downward diffusion of 15N-labelled denitrification products. A numerical 3-D model for simulating gas diffusion in soil was used in order to determine the significance of this source of error. Results show that subsoil diffusion of 15N-labelled N2 and N2O – and thus potential underestimation of denitrification derived from chamber fluxes – increases with chamber deployment time as well as with increasing soil gas diffusivity. Simulations based on the range of typical soil gas diffusivities of unsaturated soils showed that the fraction of N2 and N2O evolved from 15N-labelled NO3- that is not emitted at the soil surface during 1 h chamber closing is always significant, with values up to >50 % of total production. This is due to accumulation in the pore space of the 15N-labelled soil and diffusive flux to the unlabelled subsoil. Empirical coefficients to calculate denitrification from surface fluxes were derived by modelling multiple scenarios with varying soil water content. Modelling several theoretical experimental set-ups showed that the fraction of produced gases that are retained in soil can be lowered by lowering the depth of 15N labelling and/or increasing the length of the confining cylinder. Field experiments with arable silt loam soil for measuring denitrification with the 15N gas flux method were conducted to obtain direct evidence for the incomplete surface emission of gaseous denitrification products. We compared surface fluxes of 15N2 and 15N2O from 15N-labelled micro-plots confined by cylinders using the closed-chamber method with cylinders open or closed at the bottom, finding 37 % higher surface fluxes with the bottom closed. Modelling fluxes of this experiment confirmed this effect, however with a higher increase in surface flux of 89 %. From our model and experimental results we conclude that field surface fluxes of 15N-labelled N2 and N2O severely underestimate denitrification rates if calculated from chamber accumulation only. The extent of this underestimation increases with closure time. Underestimation also occurs during laboratory incubations in closed systems due to pore space accumulation of 15N-labelled N2 and N2O. Due to this bias in past denitrification measurements, denitrification in soils might be more relevant than assumed to date. Corrected denitrification rates can be obtained by estimating subsurface flux and storage with our model. The observed deviation between experimental and modelled subsurface flux revealed the need for refined model evaluation, which must include assessment of the spatial variability in diffusivity and production and the spatial dimension of the chamber.

Biogeochemical models are useful for the prediction of nitrogen (N) cycling processes, but accurate description of the denitrification and decomposition sub-modules is critical. Current models were developed before suitable soil N2 flux data were available; new measurement techniques have enabled the collection of improved N2 data. We use measured data from two laboratory incubations to test the denitrification sub-modules of existing biogeochemical models. Two arable soils – a silt-loam and a sand – were incubated for 34 and 58 days, respectively. Fluxes of N2, N2O and CO2 were quantified using gas chromatography and isotope-ratio mass spectrometry (IRMS). For the loamy soil, seven moisture and three NO3− contents were included, with temperature changing during the incubation. The sandy soil was incubated with and without incorporation of litter (ryegrass), with temperature, water content and NO3− content changing during the incubation. Three common biogeochemical models (Coup, DNDC and DeNi) were tested using the data. No systematic calibration of the model parameters was conducted since our intention was to evaluate the general model structure or “default” model runs. As compared with measured fluxes, the average N2+N2O fluxes of the default runs for loamy soil were approximately 3 times higher for Deni, 105 times smaller for DNDC and 22 times smaller for Coup. For the sandy soils, default runs were 3 times higher for DeNi, 7 times smaller for DNDC and 12 times smaller for Coup. While measured fluxes were overestimated by DeNi and underestimated by DNDC and Coup, the temporal patterns of the measured and the modeled emissions were similar for the different treatments. None of the models was able to determine litter-induced decomposition correctly. The reason for the differences between the measured and modeled values can be traced back to model structure uncertainty and/or parameter uncertainty. Given the aim of our work – to assess existing model processes for further development and/or to identify missing processes within the models – these results provide valuable insights into avenues for future research. We conclude that the predicting power of the models could be improved through future experiments that collect data on denitrification activity with a concurrent focus on control parameter determination.

The approaches based on natural abundance N2O stable isotopes are often applied for the estimation of mixing proportions between various N2O producing pathways as well as for estimation of the extent of N2O reduction to N2. But such applications are associated with numerous uncertainties and hence their limited accuracy needs to be considered. Here we present the first systematic validation of these methods for laboratory and field studies applying the 15N gas-flux method as the reference approach. Besides applying dual isotope plots for interpretation of N2O isotopic data, for the first time we propose a three dimensional N2O isotopocule model based on Bayesian statistics to estimate the N2O mixing proportions and reduction extent based simultaneously on three N2O isotopic signatures (δ15N, δ15NSP and δ18O). Determination of mixing proportions of individual pathways with N2O isotopic approaches appears often imprecise, mainly due to imperfect isotopic separation of the particular pathways. Nevertheless, the estimation of N2O reduction is much more robust, when applying optimal calculation strategy, reaching typically accuracy of N2O residual fraction determination of about 0.1.

Chemical composition of root and shoot litter controls decomposition and, subsequently, C availability for biological nitrogen transformation processes in soils. While aboveground plant residues have been proven to increase N2O emissions, studies on root litter effects are scarce. This study aimed (1) to evaluate how fresh maize root litter affects N2O emissions compared to fresh maize shoot litter, (2) to assess whether N2O emissions are related to the interaction of C and N mineralization from soil and litter, and (3) to analyze changes in soil microbial community structures related to litter input and N2O emissions. To obtain root and shoot litter, maize plants (Zea mays L.) were cultivated with two N fertilizer levels in a greenhouse and harvested. A two-factorial 22 d laboratory incubation experiment was set up with soil from both N levels (N1, N2) and three litter addition treatments (control, root, root + shoot). We measured CO2 and N2O fluxes, analyzed soil mineral N and water-extractable organic C (WEOC) concentrations, and determined quality parameters of maize litter. Bacterial community structures were analyzed using 16S rRNA gene sequencing. Maize litter quality controlled NO3- and WEOC availability and decomposition-related CO2 emissions. Emissions induced by maize root litter remained low, while high bioavailability of maize shoot litter strongly increased CO2 and N2O emissions when both root and shoot litter were added. We identified a strong positive correlation between cumulative CO2 and N2O emissions, supporting our hypothesis that litter quality affects denitrification by creating plant-litter-associated anaerobic microsites. The interdependency of C and N availability was validated by analyses of regression. Moreover, there was a strong positive interaction between soil NO3- and WEOC concentration resulting in much higher N2O emissions, when both NO3- and WEOC were available. A significant correlation was observed between total CO2 and N2O emissions, the soil bacterial community composition, and the litter level, showing a clear separation of root + shoot samples of all remaining samples. Bacterial diversity decreased with higher N level and higher input of easily available C. Altogether, changes in bacterial community structure reflected degradability of maize litter with easily degradable C from maize shoot litter favoring fast-growing C-cycling and N-reducing bacteria of the phyla Actinobacteria, Chloroflexi, Firmicutes, and Proteobacteria. In conclusion, litter quality is a major driver of N2O and CO2 emissions from crop residues, especially when soil mineral N is limited.

The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO2-rich fluids. Anomalous concentrations of N2O and NO2 were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO2 and CH4 during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O-2, temperature, and GHG concentration. Both the N2O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N2O and NO2 emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH2OH, NO, and NO2- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla. (C) 2020 Elsevier B.V. All rights reserved.

Chemical composition of root and shoot litter controls decomposition and, subsequently, C availability for biological nitrogen transformation processes in soils. While aboveground plant residues have been proven to increase N2O emissions, studies on root litter effects are scarce. This study aimed (1) to evaluate how fresh maize root litter affects N2O emissions compared to fresh maize shoot litter, (2) to assess whether N2O emissions are related to the interaction of C and N mineralization from soil and litter, and (3) to analyze changes in soil microbial community structures related to litter input and N2O emissions. To obtain root and shoot litter, maize plants (Zea mays L.) were cultivated with two N fertilizer levels in a greenhouse and harvested. A two-factorial 22 d laboratory incubation experiment was set up with soil from both N levels (N1, N2) and three litter addition treatments (control, root, root + shoot). We measured CO2 and N2O fluxes, analyzed soil mineral N and water-extractable organic C (WEOC) concentrations, and determined quality parameters of maize litter. Bacterial community structures were analyzed using 16S rRNA gene sequencing. Maize litter quality controlled NO−3 and WEOC availability and decomposition-related CO2 emissions. Emissions induced by maize root litter remained low, while high bioavailability of maize shoot litter strongly increased CO2 and N2O emissions when both root and shoot litter were added. We identified a strong positive correlation between cumulative CO2 and N2O emissions, supporting our hypothesis that litter quality affects denitrification by creating plant-litter-associated anaerobic microsites. The interdependency of C and N availability was validated by analyses of regression. Moreover, there was a strong positive interaction between soil NO−3 and WEOC concentration resulting in much higher N2O emissions, when both NO−3 and WEOC were available. A significant correlation was observed between total CO2 and N2O emissions, the soil bacterial community composition, and the litter level, showing a clear separation of root + shoot samples of all remaining samples. Bacterial diversity decreased with higher N level and higher input of easily available C. Altogether, changes in bacterial community structure reflected degradability of maize litter with easily degradable C from maize shoot litter favoring fast-growing C-cycling and N-reducing bacteria of the phyla Actinobacteria, Chloroflexi, Firmicutes, and Proteobacteria. In conclusion, litter quality is a major driver of N2O and CO2 emissions from crop residues, especially when soil mineral N is limited. Open-Access-Publikationsfonds 2020 peerReviewed