Abstract. Biogeochemical models are essential for the prediction and management of nitrogen (N) cycling in agroecosystems, but the accuracy of the denitrification and decomposition sub-modules is critical. Current models were developed before suitable soil N2 flux data were available, which may have led to inaccuracies in how denitrification was described. New measurement techniques, using gas chromatography and isotope-ratio mass spectrometry (IRMS), have enabled the collection of more robust N2, N2O and CO2 data. We incubated two arable soils – a silt-loam and a sand soil – for 34 and 58 d, respectively, with small field-relevant changes made to control factors during this period. For the silt-loam soil, seven treatments varying in moisture, bulk density and 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. The denitrification and decomposition sub-modules of DeNi, Coup and DNDC 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. Measured fluxes generally responded as expected to control factors. We assessed the direction of modeled responses to control factors using three categories: no response, a response in the same direction as measurements or a response in the opposite direction to measurements. DNDC responses were 14 %, 52 % and 34 %, respectively. Coup responses were 47 %, 19 % and 34 %, respectively. DeNi responses were 0 %, 67 % and 33 %, respectively. The magnitudes of the modeled fluxes were underestimated by Coup and DNDC and overestimated by DeNi for the sandy soil, while there was no general trend for the silt-loam soil. None of the models was able to determine litter-induced decomposition correctly. To conclude, the currently used sub-modules are not able to consistently simulate the denitrification and decomposition processes. For better model evaluation and development, we need to design better experiments, take more frequent measurements, use new or updated measurement techniques, address model complexity, add missing processes to the models, calibrate denitrifier microbial dynamics, and evaluate the anaerobic soil volume concept.

A photographic and computed tomography (CT) scanning study was carried out on the premolar teeth of 18 adult male Babyrousa babyrussa skulls, 10 skulls of Babyrousa celebensis, including 6 adult males, 1 adult female, 1 subadult male, 1 subadult female, and 1 juvenile male. The occlusal morphology of the permanent maxillary premolar teeth of B. babyrussa was very similar to that of B. celebensis. Almost all the maxillary third premolar teeth (107/207) had 2 roots, whereas maxillary fourth premolar teeth (108/208) had 3 or 4 roots. All of the mesial tooth roots of 107/207 and 108/208 were tapering rod-like structures; each contained a single pulp canal. Almost all distal roots of 107/207 were “C” shaped and contained 2 pulp canals. The 108/208 palatal roots were “C” shaped and contained 2 pulp canals. The mesial and distal roots of the mandibular third premolar teeth (307/407) teeth were uniformly rod-like, as were the mesial roots of the mandibular fourth premolar teeth (308/408) teeth. The distal roots of the 308/408 teeth were “C” shaped. All B. babyrussa 307/407 teeth have a single pulp canal located in each of the mesial and distal roots. The 308/408 mesial tooth root contained 1 pulp canal. In all but 3 of the 36 distal 308/408 roots of B. babyrussa teeth and in 7 of the 14 distal roots of B. celebensis teeth there was a single pulp canal; in the other 7 teeth there were 2 pulp canals. Each of the 3 medial roots contained 1 pulp canal.

Abstract. 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.

<p>Quantifying soil nitrogen processes – especially denitrification – are critical for the adequate prediction of the produced and emitted N<sub>2</sub>O and N<sub>2</sub> gasses and the production and consumption of NO<sub>3</sub><sup>-</sup> and NH<sub>3</sub>. Biogeochemical models are useful tools for the description of these N processes, but recent research progress is not considered on the denitrification sub-modules of these models. Denitrification typically occurs in hot-spots of the soils but the models describe the soils as a homogenized system. Another critical problem is the calibration of the decomposition sub-modules. Suitable soil N<sub>2</sub> flux data were not available during the development of the extensively used models but new measurement techniques provide appropriate N<sub>2</sub> gas flux data.</p><p>In this study we investigate the N<sub>2</sub> and N<sub>2</sub>O fluxes from mesocosm experiments of different complexity and use the measured data and experimental settings for testing the denitrification sub-module of existing biogeochemical models.</p><p>Two arable soils – a silty loam and a sandy soil – were used for the experiments and varied with N fertilization and organic matter amendment. The soils were incubated in laboratory incubation systems over 42 and 58 days, respectively. N<sub>2</sub>, N<sub>2</sub>O and CO<sub>2</sub> fluxes were quantified by gas chromatography and isotope-ratio mass spectrometry. Seven moisture and three NO<sub>3</sub><sup>-</sup> contents were set up to the loamy soil and only the temperature was manipulated during the experiment, while other factors were kept constant. In the experiment with the sandy soil, incubations were conducted with or without incorporation of organic litter (ryegrass) and initial water content was adjusted equivalent to 80% water-filled pore space. Temperature, water content and NO<sub>3</sub><sup>-</sup> content were manipulated during that experiment.</p><p>Three commonly used biogeochemical models – namely CoupModel, DNDC and DeNi (a self programmed early stage version of the nitrification and denitrification sub-model of the DailyDayCent) – were tested on the experimental data.</p><p>The average N<sub>2</sub>+N<sub>2</sub>O fluxes of the loamy soil as given by measurements, DNDC, DeNi and CoupModel calculations was 287.5±202.3, 1.8±0.5, 779.1±282.2, 67.9±8.4 gN ha<sup>-1</sup> day<sup>-1</sup>, respectively. For the sandy soil, these fluxes were 166.6±377.7, 23.7±34.7, 491.2±819.9 and 13.3±7.8 gN ha<sup>-1</sup> day<sup>-1</sup>, respectively. The results show that the models did not calculate the same magnitude of the measured values. The DeNi model overestimated and the DNDC and CoupModel underestimated the measured fluxes. However, in some cases the temporal patterns of the measured and the modeled emission were similar. Most cases of over- or underestimations by the models could be explained by certain deficiencies of the models or of the experimental data.</p>

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