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The permafrost zone is expected to be a substantial carbon source to the atmosphere, yet large-scale models currently only simulate gradual changes in seasonally thawed soil. Abrupt thaw will probably occur in <20% of the permafrost zone but could affect half of permafrost carbon through collapsing ground, rapid erosion and landslides. Here, we synthesize the best available information and develop inventory models to simulate abrupt thaw impacts on permafrost carbon balance. Emissions across 2.5 million km2 of abrupt thaw could provide a similar climate feedback as gradual thaw emissions from the entire 18 million km2 permafrost region under the warming projection of Representative Concentration Pathway 8.5. While models forecast that gradual thaw may lead to net ecosystem carbon uptake under projections of Representative Concentration Pathway 4.5, abrupt thaw emissions are likely to offset this potential carbon sink. Active hillslope erosional features will occupy 3% of abrupt thaw terrain by 2300 but emit one-third of abrupt thaw carbon losses. Thaw lakes and wetlands are methane hot spots but their carbon release is partially offset by slowly regrowing vegetation. After considering abrupt thaw stabilization, lake drainage and soil carbon uptake by vegetation regrowth, we conclude that models considering only gradual permafrost thaw are substantially underestimating carbon emissions from thawing permafrost.Analyses of inventory models under two climate change projection scenarios suggest that carbon emissions from abrupt thaw of permafrost through ground collapse, erosion and landslides could contribute significantly to the overall permafrost carbon balance.

Abstract In climate and weather models, the quantitative description of aerosol and cloud processes relies on simplified assumptions. This contributes major uncertainties to the prediction of global and regional climate change. Therefore, models need good parameterizations for heterogeneous ice nucleation by atmospheric aerosols. Here the authors present a new parameterization of immersion freezing on desert dust particles derived from a large number of experiments carried out at the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) cloud chamber facility. The parameterization is valid in the temperature range between −12° and −36°C at or above water saturation and can be used in atmospheric models that include information about the dust surface area. The new parameterization was applied to calculate distribution maps of ice nuclei during a Saharan dust event based on model results from the regional-scale model Consortium for Small-Scale Modelling–Aerosols and Reactive Trace Gases (COSMO-ART). The results were then compared to measurements at the Taunus Observatory on Mount Kleiner Feldberg, Germany, and to three other parameterizations applied to the dust outbreak. The aerosol number concentration and surface area from the COSMO-ART model simulation were taken as input to different parameterizations. Although the surface area from the model agreed well with aerosol measurements during the dust event at Kleiner Feldberg, the ice nuclei (IN) number concentration calculated from the new surface-area-based parameterization was about a factor of 13 less than IN measurements during the same event. Systematic differences of more than a factor of 10 in the IN number concentration were also found among the different parameterizations. Uncertainties in the modeled and measured parameters probably both contribute to this discrepancy and should be addressed in future studies.

The mandate of the Task Force Hemispheric Transport of Air Pollution (TF HTAP) under the Convention on Long-Range Transboundary Air Pollution (CLRTAP) is to improve the scientific understanding of the intercontinental air pollution transport, to quantify impacts on human health, vegetation and climate, to identify emission mitigation options across the regions of the Northern Hemisphere, and to guide future policies on these aspects. The harmonization and improvement of regional emission inventories is imperative to obtain consolidated estimates on the formation of global-scale air pollution. An emissions data set has been constructed using regional emission grid maps (annual and monthly) for SO2, NOx, CO, NMVOC, NH3, PM10, PM2.5, BC and OC for the years 2008 and 2010, with the purpose of providing consistent information to global and regional scale modelling efforts. This compilation of different regional gridded inventories - including that of the Environmental Protection Agency (EPA) for USA, the EPA and Environment Canada (for Canada), the European Monitoring and Evaluation Programme (EMEP) and Netherlands Organisation for Applied Scientific Research (TNO) for Europe, and the Model Inter-comparison Study for Asia (MICS-Asia III) for China, India and other Asian countries - was gap-filled with the emission grid maps of the Emissions Database for Global Atmospheric Research (EDGARv4.3) for the rest of the world (mainly South America, Africa, Russia and Oceania). Emissions from seven main categories of human activities (power, industry, residential, agriculture, ground transport, aviation and shipping) were estimated and spatially distributed on a common grid of 0.1 degree 0.1 degree longitude-latitude, to yield monthly, global, sector-specific grid maps for each substance and year. The HTAP_v2.2 air pollutant grid maps are considered to combine latest available regional information within a complete global data set. The disaggregation by sectors, high spatial and temporal resolution and detailed information on the data sources and references used will provide the user the required transparency. Because HTAP_v2.2 contains primarily official and/or widely used regional emission grid maps, it can be recommended as a global baseline emission inventory, which is regionally accepted as a reference and from which different scenarios assessing emission reduction policies at a global scale could start. An analysis of country-specific implied emission factors shows a large difference between industrialised countries and developing countries for acidifying gaseous air pollutant emissions (SO2 and NOx) from the energy and industry sectors. This is not observed for the particulate matter emissions (PM10, PM2.5), which show large differences between countries in the residential sector instead. The per capita emissions of all world countries, classified from low to high income, reveal an increase in level and in variation for gaseous acidifying pollutants, but not for aerosols. For aerosols, an opposite trend is apparent with higher per capita emissions of particulate matter for low income countries.

After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models (GEMs). However, it is not known whether the predicted pathway usage in FBA solutions is consistent with gene and protein expression in the wild‐type and evolved strains. Here, we report that >98% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data. Moreover, when E. coli adapts to growth rate selective pressure, the evolved strains upregulate genes within the optimal growth predictions, and downregulate genes outside of the optimal growth solutions. In addition, bottlenecks from dosage limitations of computationally predicted essential genes are overcome in the evolved strains. We also identify regulatory processes that may contribute to the development of the optimal growth phenotype in the evolved strains, such as the downregulation of known regulons and stringent response suppression. Thus, differential gene and protein expression from wild‐type and adaptively evolved strains supports observed growth phenotype changes, and is consistent with GEM‐computed optimal growth states. Synopsis When prokaryotes are maintained at early‐ to mid‐log phase growth through serial passaging for hundreds of generations, the strains improve fitness and evolve a higher growth rate (Lenski and Travisano, 1994; Ibarra et al, 2002). This increased growth rate is the result of the appearance of a few causal mutations (Herring et al, 2006; Conrad et al, 2009). In Escherichia coli, these altered growth phenotypes are consistent with predictions from genome‐scale models of metabolism (GEMs) (Ibarra et al, 2002; Fong and Palsson, 2004). However, it is still not known (1) whether absolute gene and protein expression levels and expression changes are consistent with optimal growth predictions from in silico GEMs or (2) whether measured expression changes can be linked to physiological changes that are based on known mechanisms or pathways. In this study, we begin to address these questions using constraint‐based modeling of E. coli K‐12 metabolism (Feist and Palsson, 2008) to analyze omic data that document the expression changes in E. coli under adaptive evolution in three different growth conditions. Mapping high‐throughput data to a network can be useful for interpretation. However, it does not account for upstream and downstream effects of gene and protein expression changes. The analysis of data in the context of GEMs can suggest if predicted activity is consistent with the data. For this work, we used a variant of flux balance analysis (FBA), called Parsimonious enzyme usage FBA (pFBA) (Figure 1), to classify all genes according to whether they are used in the optimal growth solutions. Results from these models were compared with the data to assess whether the data were consistent with genes and proteins within the predicted optimal solutions, and whether the expression changes were consistent with measured physiology. Through this analysis, we find that the data provide a high coverage of genes that contribute to the optimal growth solutions (Figure 1B). In fact, the union of the proteomic and transcriptomic data for non‐essential genes provides support for 97.7% of all non‐essential gene‐associated reactions within the optimal growth predictions. Thus, the spectrum of expressed genes and proteins is consistent with the pathway utilization that is predicted for these optimal growth phenotypes. Laboratory‐evolved strains attain a higher growth rate. This higher growth rate is usually associated with an increased substrate uptake rate (Ibarra et al, 2002; Fong et al, 2005) and in some cases more efficient metabolism (Ibarra et al, 2002). Both of these properties are also witnessed in the strains studied here. It has been reported that in most cases, evolved strain growth phenotype is consistent with GEM predictions (Ibarra et al, 2002; Teusink et al, 2009). Here, we evaluate whether the laboratory‐evolved strains adjust the gene and protein expression levels in accordance with pathway usage in the optimal growth predictions. Essential and non‐essential genes and proteins within the optimal growth solutions are significantly upregulated (Figure 1B). This suggests that these proteins may be acting as bottlenecks that are relieved through the adaptive process, thereby allowing for a higher substrate uptake rate and growth rate. However, genes and proteins associated with reactions that cannot carry a flux in the given growth conditions are downregulated in the evolved strains (Figure 1B). Furthermore, there is downregulation of genes associated with less efficient pathways (Figure 5C). Thus, the omic data support the emergence of the predicted optimal growth states, consistent with the increased substrate uptake upstream and the increased biomass production downstream of these internal pathways. Regulatory mechanisms, both known and unknown, are responsible for the changes seen here. Across all data sets, several metabolic regulons are significantly downregulated. However, no known regulons were enriched among upregulated genes or proteins for all but one data set. Aside from just regulating the metabolic pathways directly, these mechanisms lead to additional physiological changes. For example, in the minimal media growth conditions used here, the stringent response normally represses growth while upregulating amino‐acid biosynthetic processes. However, evolved strain gene expression shows a suppression of the stringent response, as evolved strain gene expression shows either no expression change or changes opposite to the normal stringent response. The implications of this work are as follows: (1) genome‐scale gene and protein expression data are consistent with FBA computed optimal growth states, and evolved strains reinforce these optimal states; (2) genome‐scale models will have an important function bridging the gap between genotype and phenotype; and (3) the development of additional genome‐scale models of other growth‐related processes such as transcription and translation (Thiele et al, 2009) will have an important function in elucidating the mechanisms that contribute the most to altered phenotypes (Lewis et al, 2009a). In addition, reconstruction of the transcriptional regulation network will aid in identifying the control of expression changes seen in the other systems. Proteomic and transcriptomic data from wild‐type and laboratory‐evolved strains of Escherichia coli are consistent with predicted pathway usage from optimal growth rate solutions. In laboratory‐evolved strains, there is an upregulation of the pathways in the computed optimal growth states, and downregulation of non‐functional pathways. Known regulatory mechanisms are only partially responsible for altered metabolic pathway activity.

Climate change can reduce surface-water supply by enhancing evapotranspiration in forested mountains, especially during heatwaves. We investigate this ‘drought paradox’ for the European Alps using a 1,212-station database and hyper-resolution ecohydrological simulations to quantify blue (runoff) and green (evapotranspiration) water fluxes. During the 2003 heatwave, evapotranspiration in large areas over the Alps was above average despite low precipitation, amplifying the runoff deficit by 32% in the most runoff-productive areas (1,300–3,000 m above sea level). A 3 °C air temperature increase could enhance annual evapotranspiration by up to 100 mm (45 mm on average), which would reduce annual runoff at a rate similar to a 3% precipitation decrease. This suggests that green-water feedbacks—which are often poorly represented in large-scale model simulations—pose an additional threat to water resources, especially in dry summers. Despite uncertainty in the validation of the hyper-resolution ecohydrological modelling with observations, this approach permits more realistic predictions of mountain region water availability. Mountain forest drought can paradoxically increase evapotranspiration (green water), helping vegetation at the expense of runoff (blue water). This is quantified for the 2003 event in the European Alps, highlighting underappreciated vulnerability of blue-water resources to future warmer summers.

Continental- to global-scale hydrologic and land surface models increasingly include representations of the groundwater system. Such large-scale models are essential for examining, communicating, and understanding the dynamic interactions between the Earth system above and below the land surface as well as the opportunities and limits of groundwater resources. We argue that both large-scale and regional-scale groundwater models have utility, strengths, and limitations, so continued modeling at both scales is essential and mutually beneficial. A crucial quest is how to evaluate the realism, capabilities, and performance of large-scale groundwater models given their modeling purpose of addressing large-scale science or sustainability questions as well as limitations in data availability and commensurability. Evaluation should identify if, when, or where large-scale models achieve their purpose or where opportunities for improvements exist so that such models better achieve their purpose. We suggest that reproducing the spatiotemporal details of regional-scale models and matching local data are not relevant goals. Instead, it is important to decide on reasonable model expectations regarding when a large-scale model is performing “well enough” in the context of its specific purpose. The decision of reasonable expectations is necessarily subjective even if the evaluation criteria are quantitative. Our objective is to provide recommendations for improving the evaluation of groundwater representation in continental- to global-scale models. We describe current modeling strategies and evaluation practices, and we subsequently discuss the value of three evaluation strategies: (1) comparing model outputs with available observations of groundwater levels or other state or flux variables (observation-based evaluation), (2) comparing several models with each other with or without reference to actual observations (model-based evaluation), and (3) comparing model behavior with expert expectations of hydrologic behaviors in particular regions or at particular times (expert-based evaluation). Based on evolving practices in model evaluation as well as innovations in observations, machine learning, and expert elicitation, we argue that combining observation-, model-, and expert-based model evaluation approaches, while accounting for commensurability issues, may significantly improve the realism of groundwater representation in large-scale models, thus advancing our ability for quantification, understanding, and prediction of crucial Earth science and sustainability problems. We encourage greater community-level communication and cooperation on this quest, including among global hydrology and land surface modelers, local to regional hydrogeologists, and hydrologists focused on model development and evaluation.

Mesoplasma florum, a fast‐growing near‐minimal organism, is a compelling model to explore rational genome designs. Using sequence and structural homology, the set of metabolic functions its genome encodes was identified, allowing the reconstruction of a metabolic network representing ˜ 30% of its protein‐coding genes. Growth medium simplification enabled substrate uptake and product secretion rate quantification which, along with experimental biomass composition, were integrated as species‐specific constraints to produce the functional iJL208 genome‐scale model (GEM) of metabolism. Genome‐wide expression and essentiality datasets as well as growth data on various carbohydrates were used to validate and refine iJL208. Discrepancies between model predictions and observations were mechanistically explained using protein structures and network analysis. iJL208 was also used to propose an in silico reduced genome. Comparing this prediction to the minimal cell JCVI‐syn3.0 and its parent JCVI‐syn1.0 revealed key features of a minimal gene set. iJL208 is a stepping‐stone toward model‐driven whole‐genome engineering. SYNOPSIS The first genome‐scale metabolic model for the near‐minimal bacterium Mesoplasma florum is reported. Comparing the model‐driven prediction of a M. florum genome reduction scenario to a closely related minimal cell reveals key features of a minimal gene set. iJL208, the first genome‐scale metabolic model for the near‐minimal organism Mesoplasma florum, comprises 370 reactions and accounts for ˜ 30% of the total gene count in the genome. Model‐driven predictions are validated through the integration of extensive experimental data, including gene expression datasets and growth phenotypes on various sugars. A robust M. florum genome reduction scenario is predicted using gene essentiality data and transcription units, resulting in a minimal genome containing 535 protein‐coding genes. A detailed comparison of this prediction to the phylogenetically related minimal cell JCVI‐syn3.0 reveals key features of a minimal gene set. The first genome‐scale metabolic model for the near‐minimal bacterium Mesoplasma florum is reported. Comparing the model‐driven prediction of a M. florum genome reduction scenario to a closely related minimal cell reveals key features of a minimal gene set.

Although the African Great Lakes are important regulators for the East African climate, their influence on atmospheric dynamics and the regional hydrological cycle remains poorly understood. This study aims to assess this impact by comparing a regional climate model simulation that resolves individual lakes and explicitly computes lake temperatures to a simulation without lakes. The Consortium for Small-Scale Modelling model in climate mode (COSMO-CLM) coupled to the Freshwater Lake model (FLake) and Community Land Model (CLM) is used to dynamically downscale a simulation from the African Coordinated Regional Downscaling Experiment (CORDEX-Africa) to 7-km grid spacing for the period of 1999–2008. Evaluation of the model reveals good performance compared to both in situ and satellite observations, especially for spatiotemporal variability of lake surface temperatures (0.68-K bias), and precipitation (−116 mm yr−1or 8% bias). Model integrations indicate that the four major African Great Lakes almost double the annual precipitation amounts over their surface but hardly exert any influence on precipitation beyond their shores. Except for Lake Kivu, the largest lakes also cool the annual near-surface air by −0.6 to −0.9 K on average, this time with pronounced downwind influence. The lake-induced cooling happens during daytime, when the lakes absorb incoming solar radiation and inhibit upward turbulent heat transport. At night, when this heat is released, the lakes warm the near-surface air. Furthermore, Lake Victoria has a profound influence on atmospheric dynamics and stability, as it induces circular airflow with over-lake convective inhibition during daytime and the reversed pattern at night. Overall, this study shows the added value of resolving individual lakes and realistically representing lake surface temperatures for climate studies in this region.

Recent advancements in catchment hydrology (such as understanding catchment similarity, accessing new data sources, and refining methods for parameter constraints) make it possible to apply catchment models for ungauged basins over large domains. Here we present a cutting-edge case study applying catchment-modelling techniques with evaluation against river flow at the global scale for the first time. The modelling procedure was challenging but doable, and even the first model version showed better performance than traditional gridded global models of river flow. We used the open-source code of the HYPE model and applied it for >130 000 catchments (with an average resolution of 1000 km2), delineated to cover the Earth's landmass (except Antarctica). The catchments were characterized using 20 open databases on physiographical variables, to account for spatial and temporal variability of the global freshwater resources, based on exchange with the atmosphere (e.g. precipitation and evapotranspiration) and related budgets in all compartments of the land (e.g. soil, rivers, lakes, glaciers, and floodplains), including water stocks, residence times, and the pathways between various compartments. Global parameter values were estimated using a stepwise approach for groups of parameters regulating specific processes and catchment characteristics in representative gauged catchments. Daily and monthly time series (>10 years) from 5338 gauges of river flow across the globe were used for model evaluation (half for calibration and half for independent validation), resulting in a median monthly KGE of 0.4. However, the World-Wide HYPE (WWH) model shows large variation in model performance, both between geographical domains and between various flow signatures. The model performs best (KGE >0.6) in the eastern USA, Europe, South-East Asia, and Japan, as well as in parts of Russia, Canada, and South America. The model shows overall good potential to capture flow signatures of monthly high flows, spatial variability of high flows, duration of low flows, and constancy of daily flow. Nevertheless, there remains large potential for model improvements, and we suggest both redoing the parameter estimation and reconsidering parts of the model structure for the next WWH version. This first model version clearly indicates challenges in large-scale modelling, usefulness of open data, and current gaps in process understanding. However, we also found that catchment modelling techniques can contribute to advance global hydrological predictions. Setting up a global catchment model has to be a long-term commitment as it demands many iterations; this paper shows a first version, which will be subjected to continuous model refinements in the future. WWH is currently shared with regional/local modellers to appreciate local knowledge.

This study analyzes simulated regional-scale ozone burdens both near the surface and aloft, estimates process contributions to these burdens, and calculates the sensitivity of the simulated regional-scale ozone burden to several key model inputs with a particular emphasis on boundary conditions derived from hemispheric or global-scale models. The Community Multiscale Air Quality (CMAQ) model simulations supporting this analysis were performed over the continental US for the year 2010 within the context of the Air Quality Model Evaluation International Initiative (AQMEII) and Task Force on Hemispheric Transport of Air Pollution (TF-HTAP) activities. CMAQ process analysis (PA) results highlight the dominant role of horizontal and vertical advection on the ozone burden in the mid-to-upper troposphere and lower stratosphere. Vertical mixing, including mixing by convective clouds, couples fluctuations in free-tropospheric ozone to ozone in lower layers. Hypothetical bounding scenarios were performed to quantify the effects of emissions, boundary conditions, and ozone dry deposition on the simulated ozone burden. Analysis of these simulations confirms that the characterization of ozone outside the regional-scale modeling domain can have a profound impact on simulated regional-scale ozone. This was further investigated by using data from four hemispheric or global modeling systems (Chemistry - Integrated Forecasting Model (C-IFS), CMAQ extended for hemispheric applications (H-CMAQ), the Goddard Earth Observing System model coupled to chemistry (GEOS-Chem), and AM3) to derive alternate boundary conditions for the regional-scale CMAQ simulations. The regional-scale CMAQ simulations using these four different boundary conditions showed that the largest ozone abundance in the upper layers was simulated when using boundary conditions from GEOS-Chem, followed by the simulations using C-IFS, AM3, and H-CMAQ boundary conditions, consistent with the analysis of the ozone fields from the global models along the CMAQ boundaries. Using boundary conditions from AM3 yielded higher springtime ozone columns burdens in the middle and lower troposphere compared to boundary conditions from the other models. For surface ozone, the differences between the AM3-driven CMAQ simulations and the CMAQ simulations driven by other large-scale models are especially pronounced during spring and winter where they can reach more than 10 ppb for seasonal mean ozone mixing ratios and as much as 15 ppb for domain-averaged daily maximum 8 h average ozone on individual days. In contrast, the differences between the C-IFS-, GEOS-Chem-, and H-CMAQ-driven regional-scale CMAQ simulations are typically smaller. Comparing simulated sur face ozone mixing ratios to observations and computing seasonal and regional model performance statistics revealed that boundary conditions can have a substantial impact on model performance. Further analysis showed that boundary conditions can affect model performance across the entire range of the observed distribution, although the impacts tend to be lower during summer and for the very highest observed percentiles. The results are discussed in the context of future model development and analysis opportunities.