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We describe the ocean general circulation model Icosahedral Nonhydrostatic Weather and Climate Model (ICON‐O) of the Max Planck Institute for Meteorology, which forms the ocean‐sea ice component of the Earth system model ICON‐ESM. ICON‐O relies on innovative structure‐preserving finite volume numerics. We demonstrate the fundamental ability of ICON‐O to simulate key features of global ocean dynamics at both uniform and non‐uniform resolution. Two experiments are analyzed and compared with observations, one with a nearly uniform and eddy‐rich resolution of ∼10 km and another with a telescoping configuration whose resolution varies smoothly from globally ∼80 to ∼10 km in a focal region in the North Atlantic. Our results show first, that ICON‐O on the nearly uniform grid simulates an ocean circulation that compares well with observations and second, that ICON‐O in its telescope configuration is capable of reproducing the dynamics in the focal region over decadal time scales at a fraction of the computational cost of the uniform‐grid simulation. The telescopic technique offers an alternative to the established regionalization approaches. It can be used either to resolve local circulation more accurately or to represent local scales that cannot be simulated globally while remaining within a global modeling framework., Plain Language Summary: Icosahedral Nonhydrostatic Weather and Climate Model (ICON‐O) is a global ocean general circulation model that works on unstructured grids. It rests on novel numerical techniques that belong to the class of structure‐preserving finite Volume methods. Unstructured grids allow on the one hand a uniform coverage of the sphere without resolution clustering, and on the other hand they provide the freedom to intentionally cluster grid points in some region of interest. In this work we run ICON‐O on an uniform grid of approximately 10 km resolution and on a grid with four times less degrees of freedom that is stretched such that in the resulting telescoping grid within the North Atlantic the two resolutions are similar, while outside the focal area the grid approaches smoothly ∼80 km resolution. By comparison with observations and reanalysis data we show first, that the simulation on the uniform 10 km grid provides a decent mesoscale eddy rich simulation and second, that the telescoping grid is able to reproduce the mesoscale rich circulation locally in the North Atlantic and on decadal time scales. This telescoping technique of unstructured grids opens new research directions., Key Points: We describe Icosahedral Nonhydrostatic Weather and Climate Model (ICON‐O) the ocean component of ICON‐ESM 1.0, based on the ICON modeling framework. ICON‐O is analyzed in a globally mesoscale‐rich simulation and in a telescoping configuration. In telescoping configuration ICON‐O reproduces locally the eddy dynamics with less computational costs than the uniform configuration., https://swiftbrowser.dkrz.de/public/dkrz_07387162e5cd4c81b1376bd7c648bb60/kornetal2021, https://mpimet.mpg.de/en/science/modeling-with-icon/code-availability

Background: The most likely genetic cause of X‐linked dystonia‐parkinsonism, a neurodegenerative movement disorder endemic to the Philippines, is a 2672‐bp‐long retrotransposon insertion in intron 32 of the TAF1 gene. The objectives of this study were to investigate whether (1) TAF1 expression is altered in induced pluripotent stem cells and differentiated neuronal models and (2) excision of the retrotransposon insertion restores normal TAF1 expression. Methods: Expression of TAF1 and its neuronal isoform were determined in induced pluripotent stem cells and in induced pluripotent stem cell‐derived cortical neurons and spiny projection neurons using quantitative PCR. Genome editing‐based excision of the retrotransposon insertion was performed on induced pluripotent stem cells from 3 X‐linked dystonia‐parkinsonism patients. Edited and unedited induced pluripotent stem cells from X‐linked dystonia‐parkinsonism patients and controls were differentiated into cortical neurons and spiny projection neurons, and TAF1 expression was compared across groups. Results: TAF1 was reduced in patient‐derived induced pluripotent stem cells (P ≺ 0.05) and spiny projection neurons (P ≺ 0.01). After genome editing, we observed higher TAF1 expression in edited compared with unedited induced pluripotent stem cells (P ≺ 0.0001). In edited spiny projection neurons, TAF1 expression was also increased, but did not reach statistical significance. No expression differences were observed in cortical neurons. Conclusions: (1) TAF1 reduction in X‐linked dystonia‐parkinsonism is likely due to the retrotransposon insertion and is recapitulated in induced pluripotent stem cells and differentiated spiny projection neurons. (2) TAF1 reduction is a tractable molecular phenotype of X‐linked dystonia‐parkinsonism that can be driven by excision of the retrotransposon insertion. (3) Successful rescue of the molecular phenotype in an endogenous, genome‐edited model serves as a proof of principle that may successfully be transferred to other inherited neurodegenerative diseases.

Forests in Europe are changing due to interactions between climate change, nitrogen (N) deposition and new forest management practices. The concurrent impact on the forest greenhouse gas (GHG) balance is at present difficult to predict due to a lack of knowledge on controlling factors of GHG fluxes and response to changes in these factors. To improve the mechanistic understanding of the ongoing changes, we studied the response of soil–atmosphere exchange of nitrous oxide (N2O) and methane (CH4) at twelve experimental or natural gradient forest sites, representing anticipated future forest change. The experimental manipulations, one or more per site, included N addition (4 sites), changes of climate (temperature, 1 site; precipitation, 2 sites), soil hydrology (3 sites), harvest intensity (1 site), wood ash fertilisation (1 site), pH gradient in organic soil (1 site) and afforestation of cropland (1 site). On average, N2O emissions increased by 0.06 ± 0.03 (range 0–0.3) g N2O-N m−2 yr−1 across all treatments on mineral soils, but the increase was up to 10 times higher in an acidic organic soil. Soil moisture together with mineral soil C / N ratio and pH were found to significantly influence N2O emissions across all treatments. Emissions were increased by elevated N deposition, especially in interaction with increased soil moisture. High pH reduced the formation of N2O, even under otherwise favourable soil conditions. Oxidation (uptake) of CH4 was on average reduced from 0.16 ± 0.02 to 0.04 ± 0.05 g CH4-C m−2 yr−1 by the investigated treatments. The CH4 exchange was significantly influenced by soil moisture and soil C / N ratio across all treatments, and CH4 emissions occurred only in wet or water-saturated conditions. For most of the investigated forest manipulations or natural gradients, the response of both N2O and CH4 fluxes was towards reducing the overall GHG forest sink. The most resilient forests were dry Mediterranean forests, as well as forests with high soil C / N ratio or high soil pH. Mitigation strategies may focus on (i) sustainable management of wet forest areas and forested peatlands, (ii) continuous forest cover management, (iii) reducing atmospheric N input and, thus, N availability, and (iv) improving neutralisation capacity of acid soils (e.g. wood ash application).

Current understanding of the variability in soil properties and their relationship to processes and spatial patterns in forested landscapes is limited due to the scarcity of datasets providing such information. Here we present a spatially highly resolved dataset (http://teodoor.icg.kfa-juelich.de/ibg3searchportal2/dispatch?metadata.detail.view.id=e3886301-7252-4142-b1a4-333dfe7f1ca4) that provides detailed information on the three-dimensional variability of biogeochemical properties in the Wustebach catchment (western Germany), a long-term environmental observation site of the TERENO (Terrestrial Environmental Observatories) project. High-resolution soil sampling was conducted, and physical and biogeochemical soil parameters were recorded per horizon. The dataset is helpful in the analysis of the spatial heterogeneity in biogeochemical properties within soil horizons and with depth through the soil profile. In addition, it shows links between hydrological and biogeochemical properties and processes within the system. Overall, the dataset provides a high-resolution view into (re) cycling, leaching, and storage of nutrients on the catchment scale in a forested headwater catchment.

The remarkable complexity of soil and its importance to a wide range of ecosystem services presents major challenges to the modeling of soil processes. Although major progress in soil models has occurred in the last decades, models of soil processes remain disjointed between disciplines or ecosystem services, with considerable uncertainty remaining in the quality of predictions and several challenges that remain yet to be addressed. First, there is a need to improve exchange of knowledge and experience among the different disciplines in soil science and to reach out to other Earth science communities. Second, the community needs to develop a new generation of soil models based on a systemic approach comprising relevant physical, chemical, and biological processes to address critical knowledge gaps in our understanding of soil processes and their interactions. Overcoming these challenges will facilitate exchanges between soil modeling and climate, plant, and social science modeling communities. It will allow us to contribute to preserve and improve our assessment of ecosystem services and advance our understanding of climate-change feedback mechanisms, among others, thereby facilitating and strengthening communication among scientific disciplines and society. We review the role of modeling soil processes in quantifying key soil processes that shape ecosystem services, with a focus on provisioning and regulating services. We then identify key challenges in modeling soil processes, including the systematic incorporation of heterogeneity and uncertainty, the integration of data and models, and strategies for effective integration of knowledge on physical, chemical, and biological soil processes. We discuss how the soil modeling community could best interface with modern modeling activities in other disciplines, such as climate, ecology, and plant research, and how to weave novel observation and measurement techniques into soil models. We propose the establishment of an international soil modeling consortium to coherently advance soil modeling activities and foster communication with other Earth science disciplines. Such a consortium should promote soil modeling platforms and data repository for model development, calibration and intercomparison essential for addressing contemporary challenges.

Forest soils are a significant source for the primary and secondary greenhouse gases N2O and NO. However, current estimates are still uncertain due to the still limited number of field measurements and the herein observed pronounced variability of N trace gas fluxes in space and time, which are due to the variation of environmental factors such as soil and vegetation properties or meteorological conditions. To overcome these problems we further developed a process-oriented model, the PnET-N-DNDC model, which simulates the N trace gas exchange on the basis of the processes involved in production, consumption and emission of N trace gases. This model was validated against field observations of N trace gas fluxes from 19 sites obtained within the EU project NOFRETETE, and shown to perform well for N2O (r2=0.68, slope=0.76) and NO (r2=0.78, slope=0.73). For the calculation of a European-wide emission inventory we linked the model to a detailed, regionally and temporally resolved database, comprising climatic properties (daily resolution), and soil parameters, and information on forest areas and types for the years 1990, 1995 and 2000. Our calculations show that N trace gas fluxes from forest soils may vary substantial from year to year and that distinct regional patterns can be observed. Our central estimate of NO emissions from forest soils in the EU amounts to 98.4, 84.9 and 99.2 kt N yr−1, using meteorology from 1990, 1995 and year 2000, respectively. This is x emissions. For N2O emissions the central estimates were 86.8, 77.6 and 81.6 kt N yr−1, respectively, which is approx.14.5% of the source strength coming from agricultural soils. An extensive sensitivity analysis was conducted which showed a range in emissions from 44.4 to 254.0 kt N yr−1 for NO and 50.7 to 96.9 kt N yr−1 for N2O, for year 2000 meteorology. The results show that process-oriented models coupled to a GIS are useful tools for the calculation of regional, national, or global inventories of biogenic N trace gas emissions from soils. This work represents the most comprehensive effort to date to simulate NO and N2O emissions from European forest soils.

Trace gas exchange of N2O, NO/NO2 and CH4 between soil and the atmosphere was measured in a typical Mediterranean pine (Pinus pinaster) forest during two intensive field campaigns in spring and autumn 2003. Furthermore, gross and net turnover rates of N mineralization and nitrification as well as soil profiles of N2O and CH4 concentrations were determined. For both seasons a weak but significant N2O uptake from the atmosphere into the soil was observed. During the unusually dry and hot spring mean N2O uptake was −4.32 µg N m-2 h-1, whereas during the wet and mild autumn mean N2O uptake was −7.85 µg N m-2 h-1. The observed N2O uptake into the soil was linked to the very low availability of inorganic nitrogen at the study site. Organic layer gross N mineralization decreased from 5.06 mg N kg-1 SDW d-1 in springtime to 2.68 mg N kg-1 SDW d-1 in autumn. Mean NO emission rates were significantly higher in springtime (9.94 µg N m-2 h-1) than in autumn (1.43 µg N m-2 h-1). A significant positive correlation between NO emission rates and gross N mineralization as well as nitrification rates was found. The negative correlation between NO emissions and soil moisture was explained with a stimulation of aerobic NO uptake under N limiting conditions. Since NO2 deposition was continuously higher than NO emission rates the examined forest soil functioned as a net NOx sink. Observed mean net CH4 uptake rates were in spring significantly higher (−73.34 µg C m-2 h-1) than in autumn (−59.67 µg C m-2 h-1). Changes in CH4 uptake rates were strongly negatively correlated with changes in soil moisture. The N2O and CH4 concentrations in different soil depths revealed the organic layer and the upper 0.1 m of mineral soil as the most important soil horizons for N2O and CH4 consumption.

Soil emissions of NO and N2O were measured continuously at high frequency for more than one year at 15 European forest sites as part of the EU-funded project NOFRETETE. The locations represent different forest types (coniferous/deciduous) and different nitrogen loads. Geographically they range from Finland in the north to Italy in the south and from Hungary in the east to Scotland in the west. The highest NO emissions were observed from coniferous forests, whereas the lowest NO emissions were observed from deciduous forests. The NO emissions from coniferous forests were highly correlated with N-deposition. The site with the highest average annual emission (82 μg NO-N m−2 h−1) was a spruce forest in South-Germany (Höglwald) receiving an annual N-deposition of 2.9 g m−2. NO emissions close to the detection limit were observed from a pine forest in Finland where the N-deposition was 0.2 g N m−2 a−1. No significant correlation between N2O emission and N-deposition was found. The highest average annual N2O emission (20 μg N2O-N m−2 h−1) was found in an oak forest in the Mátra mountains (Hungary) receiving an annual N-deposition of 1.6 g m−2. N2O emission was significantly negatively correlated with the C/N ratio. The difference in N-oxide emissions from soils of coniferous and deciduous forests may partly be explained by differences in N-deposition rates and partly by differences in characteristics of the litter layer and soil. NO was mainly derived from nitrification whereas N2O was mainly derived from denitrification. In general, soil moisture is lower at coniferous sites (at least during spring time) and the litter layer of coniferous forests is thick and well aerated favouring nitrification and thus release of NO. Conversely, the higher rates of denitrification in deciduous forests due to a compact and moist litter layer lead to N2O production and NO consumption in the soil. The two factors soil moisture and soil temperature are often explaining most of the temporal variation within a site. When comparing annual emissions on a regional scale, however, factors such as nitrogen deposition and forest and soil type become much more important.

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