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Supported by the U.S. Department of Energy (DOE), the Energy Exascale Earth System Model (E3SM) project aims to optimize the use of DOE resources to address the grand challenge of actionable predictions of Earth system variability and change. This requires sustained advancement to (1) integrate model development with leading‐edge computational advances toward ultra‐high‐resolution modeling; (2) represent the coupled human‐Earth system to address energy sector vulnerability to variability and change; and (3) address uncertainty in model simulations and projections. Scientific development of the E3SM modeling system is driven by the simulation requirements in three overarching science areas centering on understanding the Earth's water cycle, biogeochemistry, and cryosphere systems and their future changes. This paper serves as an introduction to the E3SM special collection, which includes 50 papers published in several AGU journals. It provides an overview of the E3SM project, including its goals and science drivers. It also provides a brief history of the development of E3SM version 1 and highlights some key findings from papers included in the special collection. Plain Language Summary Earth system models are important tools for predicting future changes in the Earth system. Supported by the U.S. Department of Energy (DOE), the Energy Exascale Earth System Model (E3SM) project aims to improve predictions of Earth system variability and change. The latter has a particular focus on predicting changes in the water cycle that influences precipitation and storms, biogeochemistry that influences greenhouse gases and future warming, and cryosphere systems that influence sea‐level rise that threatens coastal communities. This paper serves as an introduction to the E3SM special collection, which includes 50 papers published in several AGU journals. It provides an overview of the E3SM project, including its goals and science drivers. It also provides a brief history of the development of E3SM version 1 and highlights some key findings from papers included in the special collection. Key Points The Energy Exascale Earth System Model (E3SM) project aims to improve actionable predictions of Earth system variability and change Water cycle, biogeochemistry, and cryosphere systems are the three key science drivers of model development and numerical experiments This paper provides an overview of the E3SM project and introduces the E3SM special collection of papers published in AGU journals

The design of accurate, conservative, consistent, and monotone operators for remapping scalar fields between computational grids on the sphere has been a persistent issue for global modeling groups. This problem is especially pronounced when mapping between distinct discretizations (such as finite volumes or finite elements). To this end, this paper provides a novel unified mathematical framework for the development of linear remapping operators. This framework is then applied in the development of high-order conservative, consistent, and monotone linear remapping operators from a finite-element discretization to a finite-volume discretization. The resulting scheme is evaluated in the context of both idealized and operational simulations and shown to perform well for a variety of problems.

Potato production is often constrained by abiotic stresses such as drought and high temperatures which are often present in combination. In the present work, we aimed to identify key mechanisms and processes underlying single and combined abiotic stress tolerance by comparative analysis of tolerant and susceptible cultivars. Physiological data indicated that the cultivars Desiree and Unica were stress tolerant while Agria and Russett Burbank were stress susceptible. Abiotic stress caused a greater reduction of photosynthetic carbon assimilation in the susceptible cultivars which was associated with a lower leaf transpiration rate. Oxidative stress, as estimated by the accumulation of malondialdehyde was not induced by stress treatments in any of the genotypes with the exception of drought stress in Russett Burbank. Stress treatment resulted in increases in ascorbate peroxidase activity in all cultivars except Agria which increased catalase activity in response to stress. Transcript profiling highlighted a decrease in the abundance of transcripts encoding proteins associated with PSII light harvesting complex in stress tolerant cultivars. Furthermore, stress tolerant cultivars accumulated fewer transcripts encoding a type-1 metacaspase implicated in programmed cell death. Stress tolerant cultivars exhibited stronger expression of genes associated with plant growth and development, hormone metabolism and primary and secondary metabolism than stress susceptible cultivars. Metabolite profiling revealed accumulation of proline in all genotypes following drought stress that was partially suppressed in combined heat and drought. On the contrary, the sugar alcohols inositol and mannitol were strongly accumulated under heat and combined heat and drought stress while galactinol was most strongly accumulated under drought. Combined heat and drought also resulted in the accumulation of Valine, isoleucine, and lysine in all genotypes. These data indicate that single and multiple abiotic stress tolerance in potato is associated with a maintenance of CO assimilation and protection of PSII by a reduction of light harvesting capacity. The data further suggests that stress tolerant cultivars suppress cell death and maintain growth and development fine tuning of hormone signaling, and primary and secondary metabolism. This study highlights potential targets for the development of stress tolerant potato cultivars.

We derive a formulation of the nonhydrostatic equations in spherical geometry with a Lorenz staggered vertical discretization. The combination conserves a discrete energy in exact time integration when coupled with a mimetic horizontal discretization. The formulation is a version of Dubos and Tort (2014, https://doi.org/10.1175/MWR-D-14-00069.1) rewritten in terms of primitive variables. It is valid for terrain following mass or height coordinates and for both Eulerian or vertically Lagrangian discretizations. The discretization relies on an extension to Simmons and Burridge (1981, https://doi.org/10.1175/1520-0493(1981)109<0758:AEAAMC>2.0.CO;2) vertical differencing, which we show obeys a discrete derivative product rule. This product rule allows us to simplify the treatment of the vertical transport terms. Energy conservation is obtained via a term‐by‐term balance in the kinetic, internal, and potential energy budgets, ensuring an energy‐consistent discretization up to time truncation error with no spurious sources of energy. We demonstrate convergence with respect to time truncation error in a spectral element code with a horizontal explicit vertically implicit implicit‐explicit time stepping algorithm. Plain Language Summary Energy consistent discretizations have proven useful in guiding the development of numerical methods for simulating fluid dynamics. They ensure that the discrete method does not have any spurious sources of energy, which can lead to unstable and unrealistic simulations. Here we provide an energy consistent discretization of the equations used by global models of the Earth's atmosphere. The discretization is written in terms of standard variables in spherical coordinates and supports a wide variety of terrain following vertical coordinates. It can be used with any horizontal discretization that has a discrete version of the integration‐by‐parts identity. Key Points We give a discrete Hamiltonian formulation of the nonhydrostatic equations in primitive variables The formulation supports mass or height terrain following coordinates The Lorenz staggered vertical discretization obeys a derivative product rule

Potato, , is one of the most important global crops, but has high levels of waste due to tuber greening under light, which is associated with the accumulation of neurotoxic glycoalkaloids. However, unlike the situation in de-etiolating seedlings, the mechanisms underlying tuber greening are not well understood. Here, we have investigated the effect of monochromatic blue, red, and far-red light on the regulation of chlorophyll and glycoalkaloid accumulation in potato tubers. Blue and red wavelengths were effective for induction and accumulation of chlorophyll, carotenoids and the two major potato glycoalkaloids, α-solanine and α-chaconine, whereas none of these accumulated in darkness or under far-red light. Key genes in chlorophyll biosynthesis ( , encoding the rate-limiting enzyme glutamyl-tRNA reductase, , and and six genes ( , , , , and ) required for glycoalkaloid synthesis were also induced under white, blue, and red light but not in darkness or under far-red light. These data suggest a role for both cryptochrome and phytochrome photoreceptors in chlorophyll and glycoalkaloid accumulation. The contribution of phytochrome was further supported by the observation that far-red light could inhibit white light-induced chlorophyll and glycoalkaloid accumulation and associated gene expression. Transcriptomic analysis of tubers exposed to white, blue, and red light showed that light induction of photosynthesis and tetrapyrrole-related genes grouped into three distinct groups with one group showing a generally progressive induction by light at both 6 h and 24 h, a second group showing induction at 6 h in all light treatments, but induction only by red and white light at 24 h and a third showing just a very moderate light induction at 6 h which was reduced to the dark control level at 24 h. All glycoalkaloid synthesis genes showed a group one profile consistent with what was seen for the most light regulated chlorophyll synthesis genes. Our data provide a molecular framework for developing new approaches to reducing waste due to potato greening.

Summary For many commercial potato cultivars, tuber yield is optimal at average daytime temperatures in the range of 14–22 °C. Further rises in ambient temperature can reduce or completely inhibit potato tuber production, with damaging consequences for both producer and consumer. The aim of this study was to use a genetic screen based on a model tuberization assay to identify quantitative trait loci (QTL) associated with enhanced tuber yield. A candidate gene encoding HSc70 was identified within one of the three QTL intervals associated with elevated yield in a Phureja–Tuberosum hybrid diploid potato population (06H1). A particular HSc70 allelic variant was linked to elevated yield in the 06H1 progeny. Expression of this allelic variant was much higher than other alleles, particularly on exposure to moderately elevated temperature. Transient expression of this allele in Nicotiana benthamiana resulted in significantly enhanced tolerance to elevated temperature. An TA repeat element was present in the promoter of this allele, but not in other HSc70 alleles identified in the population. Expression of the HSc70 allelic variant under its native promoter in the potato cultivar Desiree resulted in enhanced HSc70 expression at elevated temperature. This was reflected in greater tolerance to heat stress as determined by improved yield under moderately elevated temperature in a model nodal cutting tuberization system and in plants grown from stem cuttings. Our results identify HSc70 expression level as a significant factor influencing yield stability under moderately elevated temperature and identify specific allelic variants of HSc70 for the induction of thermotolerance via conventional introgression or molecular breeding approaches.

A variable-resolution option has been added within the spectral element (SE) dynamical core of the U.S. Department of Energy (DOE)–NCAR Community Atmosphere Model (CAM). CAM-SE allows for static refinement via conforming quadrilateral meshes on the cubed sphere. This paper investigates the effect of mesh refinement in a climate model by running variable-resolution (var-res) simulations on an aquaplanet. The variable-resolution grid is a 2° (∼222 km) grid with a refined patch of 0.25° (∼28 km) resolution centered at the equator. Climatology statistics from these simulations are compared to globally uniform runs of 2° and 0.25°. A significant resolution dependence exists when using the CAM version 4 (CAM4) subgrid physical parameterization package across scales. Global cloud fraction decreases and equatorial precipitation increases with finer horizontal resolution, resulting in drastically different climates between the uniform grid runs and a physics-induced grid imprinting in the var-res simulation. Using CAM version 5 (CAM5) physics significantly improves cloud scaling at different grid resolutions. Additional precipitation at the equator in the high-resolution mesh results in collocated zonally anomalous divergence in both var-res simulations, although this feature is much weaker in CAM5 than CAM4. The equilibrium solution at each grid spacing within the var-res simulations captures the majority of the resolution signal of the corresponding globally uniform grids. The var-res simulation exhibits good performance with respect to wave propagation, including equatorial regions where waves pass through grid transitions. In addition, the increased frequency of high-precipitation events in the refined 0.25° area within the var-res simulations matches that observed in the global 0.25° simulations.

We investigate mechanisms governing moist energy exchanges at the atmosphere-ocean interface in global Earth system models. The goal of this work is to overcome deficiencies like energy fixers and unphysical thermodynamic formulations and designs that are commonly used in modern models. For example, while the ocean surface evaporation is one of the most significant climatological drivers, its representation in numerical models may not be physically accurate. In particular, existing schemes give an incorrect atmospheric air temperature tendency during evaporation events. To remedy this, starting from first principles, we develop a new mechanism for the ocean-atmosphere moist energy transfers. It utilizes consistent thermodynamics of water species, distributes latent heat of evaporation in a physically plausible way, and avoids reliance on artificial energy fixers. The temperature and water mass tendencies are used to formulate a set of ordinary differential equations (ODEs) representing a simple box model of ocean-air exchange. We investigate the properties of the ODEs representing the proposed mechanism and compare them against those derived from the current designs of the Energy Exascale Earth System Model (E3SM). The proposed simplified box model highlights the advantages of our approach in capturing physically appropriate atmospheric temperature changes during evaporation while conserving energy.

It is the purpose of this paper to provide a comprehensive documentation of the new NCAR (National Center for Atmospheric Research) version of the spectral element (SE) dynamical core as part of the Community Earth System Model (CESM2.0) release. This version differs from previous releases of the SE dynamical core in several ways. Most notably the hybrid sigma vertical coordinate is based on dry air mass, the condensates are dynamically active in the thermodynamic and momentum equations (also referred to as condensate loading), and the continuous equations of motion conserve a more comprehensive total energy that includes condensates. Not related to the vertical coordinate change, the hyperviscosity operators and the vertical remapping algorithms have been modified. The code base has been significantly reduced, sped up, and cleaned up as part of integrating SE as a dynamical core in the CAM (Community Atmosphere Model) repository rather than importing the SE dynamical core from High‐Order Methods Modeling environment as an external code. Key Points The CESM2.0 release of the spectral element dynamical core (CAM‐SE) is documented Model has comprehensive treatment of condensates and energy The CAM‐SE model has been sped up significantly compared to its predecessor CAM‐HOMME

Carotenoids are one of the most diverse classes of natural compounds. Plant carotenoids are composed of a C40 isoprenoid skeleton with or without epoxy, hydroxy and keto groups. They have fundamental roles in human nutrition as antioxidants and vitamin A precursors and their consumption is increasingly associated with protection from a range of diseases. They are also used commercially as safe food, feed and cosmetic colorants and they protect plants from photooxidative stress. In the past six years many metabolic engineering efforts have been undertaken in plants aiming to improve the nutritional value of staple crops, to enable the use of plants as ‘cell factories’ for producing specialty carotenoids and to improve plant resistance to abiotic stress.