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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Climate Forcing of Bioenergy Feedstocks: Insights From Carbon and Energy Flux Measurements

Bioenergy from biofuels has the potential to slow growing atmospheric carbon dioxide concentrations by reducing fossil fuel use. However, growing bioenergy feedstocks is a land-intensive process. In the United States, the recent expansion of maize bioethanol has presented some environmental costs, prompting the development of several alternative bioenergy feedstocks. These feedstocks, selected in part for traits associated with ecosystem services, may provide opportunities for environmental benefits beyond fossil fuel displacement. We hypothesized that these bioenergy ecosystems will provide direct climatic cooling through their influence on carbon and radiative energy fluxes (i.e., through albedo). To test this hypothesis, we investigated the potential cooling effect of five current or potential bioenergy feedstocks using multi-year records from eddy covariance towers. Perennial feedstocks were carbon sinks, with an annual mean net ecosystem carbon balance (NECB) of –2.7 ± 2.1 Mg C ha –1 for miscanthus, –0.8 ± 1.1 Mg C ha –1 for switchgrass, and –1.4 ± 0.7 Mg C ha –1 for prairie. In contrast, annual rotations were generally carbon sources, with an annual mean NECB of 2.6 ± 2.4 Mg C ha –1 for maize-soy and 3.2 ± 2.1 Mg C ha –1 for sorghum-soy. Using maize-soy as a baseline, conversion to alternative feedstocks increased albedo, inducing further cooling. This effect was strongest for miscanthus, with –3.5 ± 2.0 W m –2 of radiative forcing, and weakest for sorghum, with –1.4 ± 1.4 W m –2 . When feedstock effects on carbon and albedo were compared using carbon equivalents, carbon fluxes were the stronger ecosystem effect, underscoring the role of perennial species as effective carbon sinks. This work highlights the impact of feedstock choice on ecosystem processes as an element of bioenergy land conversion strategies.

09 BIOMASS FUELS↗
DOE OSTI2026

Contrasting Carbon–Water–Energy Dynamics in Perennial and Annual Bioenergy Agroecosystems Using Eddy Covariance and Interpretable Machine Learning

Understanding how agroecosystems respond to environmental variability is fundamental to predicting productivity and sustainability under a changing climate. We analyzed 55 site-years of high-frequency eddy covariance observations from five agroecosystems—two perennial grasses (miscanthus and switchgrass), two annual rotation systems (maize–soybean and sorghum–soybean), and a restored native prairie—to examine ecosystem-scale carbon, water, and energy fluxes. Using an interpretable machine-learning framework with regression tree ensembles, Shapley Additive Explanations, and Accumulated Local Effects, we quantified how environmental and temporal factors regulate gross primary productivity (GPP), evapotranspiration (ET), water-use efficiency, and the Bowen ratio. Perennials exhibited stronger physiological buffering and maintained fluxes across a broader range of temperature and moisture conditions, reflecting deeper rooting and persistent canopy cover. Annuals, in contrast, showed greater short-term variability and stronger coupling to atmospheric demand, with GPP and ET declining rapidly under low humidity or soil moisture. Differences in temperature sensitivity of Bowen ratio further revealed that perennials sustained proportionally greater sensible heat flux under cool conditions, whereas annuals exhibited constrained energy exchange when evaporative demand was low. Together, these results demonstrate that crop life cycle and canopy structure are fundamental determinants of ecosystem-scale carbon–water–energy coupling. By integrating long-term flux observations with interpretable machine learning, this study identifies the environmental drivers that shape agroecosystem function and highlights how conversion from annual to perennial feedstocks can enhance climatic resilience and alter land–atmosphere energy feedbacks. These findings provide a data-driven basis for improving crop and Earth-system models and for guiding bioenergy landscape design under future climate scenarios.

Accumulated Local Effects↗
DOE OSTI2024

Divide and conquer: using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods

Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. Sometimes, the amount of roots in a sample is too much to fit into a single scanned image, so the sample is divided among several scans, and there is no standard method to aggregate the data. Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image. These concatenated images and the original images were processed with RhizoVision Explorer, a free and open-source software. An R script was developed, which identifies rows of data belonging to the same sample and applies correct statistical methods to return a single data row for each sample. These two methods were compared using example images from switchgrass, poplar, and various tree and ericaceous shrub species from a northern peatland and the Arctic. Most root measurements were nearly identical between the two methods except median diameter, which cannot be accurately computed by statistical aggregation. We believe the availability of these methods will be useful to the root biology community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bioenergy sorghum maintains photosynthetic capacity in elevated ozone concentrations

Abstract Elevated tropospheric ozone concentration (O 3 ) significantly reduces photosynthesis and productivity in several C 4 crops including maize, switchgrass and sugarcane. However, it is unknown how O 3 affects plant growth, development and productivity in sorghum ( Sorghum bicolor L.), an emerging C 4 bioenergy crop. Here, we investigated the effects of elevated O 3 on photosynthesis, biomass and nutrient composition of a number of sorghum genotypes over two seasons in the field using free‐air concentration enrichment (FACE), and in growth chambers. We also tested if elevated O 3 altered the relationship between stomatal conductance and environmental conditions using two common stomatal conductance models. Sorghum genotypes showed significant variability in plant functional traits, including photosynthetic capacity, leaf N content and specific leaf area, but responded similarly to O 3 . At the FACE experiment, elevated O 3 did not alter net CO 2 assimilation ( A ), stomatal conductance ( g s ), stomatal sensitivity to the environment, chlorophyll fluorescence and plant biomass, but led to reductions in the maximum carboxylation capacity of phosphoenolpyruvate and increased stomatal limitation to A in both years. These findings suggest that bioenergy sorghum is tolerant to O 3 and could be used to enhance biomass productivity in O 3 polluted regions.

09 BIOMASS FUELS↗
DOE OSTI2022

Identification of xylan arabinosyl 2- O -xylosyltransferases catalyzing the addition of 2- O -xylosyl residue onto arabinosyl side chains of xylan in grass species

Grass xylan, the major hemicellulose in both primary and secondary cell walls, is heavily decorated with α-1,3-linked arabinofuranosyl (Araf) residues that may be further substituted at O-2 with xylosyl (Xyl) or Araf residues. Although xylan 3-O-arabinosyltransferases (XATs) catalyzing 3-O-Araf addition onto xylan have been characterized, glycosyltransferases responsible for the transfer of 2-O-Xyl or 2-O-Araf onto 3-O-Araf residues of xylan to produce the Xyl-Araf and Araf-Araf disaccharide side chains remain to be identified. In this report, we showed that a rice GT61 member, named OsXAXT1 (xylan arabinosyl 2-O-xylosyltransferase 1) herein, was able to mediate the addition of Xyl-Araf disaccharide side chains onto xylan when heterologously co-expressed with OsXAT2 in the Arabidopsis gux1/2/3 (glucuronic acid substitution of xylan 1/2/3) triple mutant that lacks any glycosyl substitutions. Recombinant OsXAXT1 protein expressed in human embryonic kidney 293 cells exhibited a xylosyltransferase activity catalyzing the addition of Xyl from UDP-Xyl onto arabinosylated xylooligomers. Further, consistent with its function as a xylan arabinosyl 2-O-xylosyltransferase, CRISPR-Cas9-mediated mutations of the OsXAXT1 gene in transgenic rice plants resulted in a reduction in the level of Xyl-Araf disaccharide side chains in xylan. Furthermore, we revealed that XAXT1 close homologs from several other grass species, including switchgrass, maize, and Brachypodium, possessed the same functions as OsXAXT1, indicating functional conservation of XAXTs in grass species. Together, our findings establish that grass XAXTs are xylosyltransferases catalyzing Xyl transfer onto O-2 of Araf residues of xylan to form the Xyl-Araf disaccharide side chains, which furthers our understanding of genes involved in xylan biosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Co-expression of a β-d-xylosidase from Thermotoga maritima and a Family 10 xylanase from A. cellulolyticus significantly improves the xylan degrading activity of the Caldicellulosiruptor bescii exoproteome

Caldicellulosiruptor species are hyperthermophilic, Gram-positive, anaerobes and the most thermophilic cellulolytic bacteria so far described. They have been engineered to convert switchgrass to ethanol without pretreatment and represent a promising platform for the production of fuels, chemicals and materials from plant biomass. Xylooligomers such as xylobiose and xylotriose that result from the breakdown of plant biomass more strongly inhibit cellulase activity than do glucose or cellobiose. High concentrations of xylobiose and xylotriose, are present in C. bescii fermentations after 90 h incubation and removal or breakdown of these types of xylooligomers is crucial to achieve high conversion of plant biomass to product. In previous studies the addition of exogenous β-d-xylosidase substantially improved the performance of glucanases and xylanases in vitro. β-d-Xylosidases are, in fact, essential enzymes in commercial preparations for efficient deconstruction of plant biomass. In addition, the combination of xylanase and β-d-xylosidase is known to exhibit synergistic action on xylan degradation. In spite of its ability to grow efficiently on xylan substrates, no extracellular β-d-xylosidase was identified in the C. bescii genome. Here we report that the co-expression of a thermal stable β-d-xylosidase from Thermotoga maritima and a xylanase from Acidothermus cellulolyticus in a C. bescii strain containing the A. cellulolyticus E1 endoglucanase significantly increased the activity of the exoproteome as well as growth on xylan substrates. The combination of these enzymes also resulted in increased growth on crystalline cellulose in the presence of exogeneous xylan.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

OxyR regulates the oxidative stress response in Zymomonas mobilis during oxic growth and anoxic biofuel fermentation

The bacterium Zymomonas mobilis is widely studied for its potential as an industrial biofuel producer. Anoxic fermentation by Z. mobilis in lignocellulosic hydrolysate can generate bioethanol from renewable plant biomass. In this study, we deleted a gene from the Z. mobilis genome encoding a homolog of OxyR, a transcription factor that activates an oxidative stress response in bacteria to reduce reactive oxygen species (ROS). Deletion of this transcription factor inhibited growth of Z. mobilis in oxic, but not anoxic, conditions in laboratory media. A ROS probe revealed that the oxyR response is required to reduce intracellular ROS during oxic growth. Importantly for biofuel production, the absence of oxyR inhibited growth and delayed ethanol production during anoxic hydrolysate fermentation. To determine the source of oxidative stress in hydrolysates, we grew ΔoxyR in a synthetic hydrolysate containing known inhibitors found in hydrolysates. There was no growth defect in ΔoxyR in the synthetic hydrolysate, indicating that known inhibitory compounds are not the source of anoxic oxidative stress. We determined that ammonia-fiber expansion switchgrass hydrolysate contains significant peroxide concentrations. Addition of catalase to hydrolysate improves growth of both ΔoxyR and wild-type Z. mobilis in hydrolysate. This study uncovers an important source of stress to Z. mobilis during biofuel fermentation.

OxyR↗
DOE OSTI2019

Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins ($ T\overline{a}pirins\ $) from Extremely Thermophilic Caldicellulosiruptor Species

Genomes of extremely thermophilic Caldicellulosiruptor species encode novel cellulose binding proteins, called $ t\overline{a}pirins\ $, located proximate to the type IV pilus locus. The C-terminal domain of Caldicellulosiruptor kronotskyensis $ t\overline{a}pirin\ $ 0844 (Calkro_0844) is structurally unique and has a cellulose binding affinity akin to that seen with family 3 carbohydrate binding modules (CBM3s). Here, full-length and C-terminal versions of $ t\overline{a}pirins\ $ from Caldicellulosiruptor bescii (Athe_1870), Caldicellulosiruptor hydrothermalis (Calhy_0908), Caldicellulosiruptor kristjanssonii (Calkr_0826), and Caldicellulosiruptor naganoensis (NA10_0869) were produced recombinantly in Escherichia coli and compared to Calkro_0844. All five $ t\overline{a}pirins\ $ bound to microcrystalline cellulose, switchgrass, poplar, and filter paper but not to xylan. Densitometry analysis of bound protein fractions visualized by SDS-PAGE revealed that Calhy_0908 and Calkr_0826 (from weakly cellulolytic species) associated with the cellulose substrates to a greater extent than Athe_1870, Calkro_0844, and NA10_0869 (from strongly cellulolytic species). Perhaps this relates to their specific needs to capture glucans released from lignocellulose by cellulases produced in Caldicellulosiruptor communities. Calkro_0844 and NA10_0869 share a higher degree of amino acid sequence identity (>80% identity) with each other than either does with Athe_1870 (~50%). The levels of amino acid sequence identity of Calhy_0908 and Calkr_0826 to Calkro_0844 were only 16% and 36%, respectively, although the three-dimensional structures of their C-terminal binding regions were closely related. Unlike the parent strain, C. bescii mutants lacking the $ t\overline{a}pirin\ $ genes did not bind to cellulose following short-term incubation, suggesting a role in cell association with plant biomass. Given the scarcity of carbohydrates in neutral terrestrial hot springs, $ t\overline{a}pirins\ $ likely help scavenge carbohydrates from lignocellulose to support growth and survival of Caldicellulosiruptor species.The mechanisms by which microorganisms attach to and degrade lignocellulose are important to understand if effective approaches for conversion of plant biomass into fuels and chemicals are to be developed. Caldicellulosiruptor species grow on carbohydrates from lignocellulose at elevated temperatures and have biotechnological significance for that reason. Novel cellulose binding proteins, called $ t\overline{a}pirins\ $, are involved in the way that Caldicellulosiruptor species interact with microcrystalline cellulose, and additional information about the diversity of these proteins across the genus, including binding affinity and three-dimensional structural comparisons, is provided here.

09 BIOMASS FUELS↗
DOE OSTI2017

Expression of a Cellobiose Phosphorylase from Thermotoga maritima in Caldicellulosiruptor bescii Improves the Phosphorolytic Pathway and Results in a Dramatic Increase in Cellulolytic Activity

Members of the genus Caldicellulosiruptor have the ability to deconstruct and grow on lignocellulosic biomass without conventional pretreatment. A genetically tractable species, Caldicellulosiruptor bescii , was recently engineered to produce ethanol directly from switchgrass. C. bescii contains more than 50 glycosyl hydrolases and a suite of extracellular enzymes for biomass deconstruction, most prominently CelA, a multidomain cellulase that uses a novel mechanism to deconstruct plant biomass. Accumulation of cellobiose, a product of CelA during growth on biomass, inhibits cellulase activity. Here, we show that heterologous expression of a cellobiose phosphorylase from Thermotoga maritima improves the phosphorolytic pathway in C. bescii and results in synergistic activity with endogenous enzymes, including CelA, to increase cellulolytic activity and growth on crystalline cellulose. CelA is the only known cellulase to function well on highly crystalline cellulose and it uses a mechanism distinct from those of other cellulases, including fungal cellulases. Also unlike fungal cellulases, it functions at high temperature and, in fact, outperforms commercial cellulase cocktails. Factors that inhibit CelA during biomass deconstruction are significantly different than those that impact the performance of fungal cellulases and commercial mixtures. Here, this work contributes to understanding of cellulase inhibition and enzyme function and will suggest a rational approach to engineering optimal activity.

09 BIOMASS FUELS↗
DOE OSTI2016

LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313

Organisms regulate gene expression in response to the environment to coordinate metabolic reactions. Clostridium thermocellum expresses enzymes for both lignocellulose solubilization and its fermentation to produce ethanol. In one LacI regulator termed GlyR3 in C. thermocellum ATCC 27405 we identified a repressor of neighboring genes with repression relieved by laminaribiose (a β-1,3 disaccharide). To better understand the three C. thermocellum LacI regulons, deletion mutants were constructed using the genetically tractable DSM1313 strain. DSM1313 lacI genes Clo1313_2023, Clo1313_0089, and Clo1313_0396 encode homologs of GlyR1, GlyR2, and GlyR3 from strain ATCC 27405, respectively. Furthermore, growth on cellobiose or pretreated switchgrass was unaffected by any of the gene deletions under controlled-pH fermentations. Global gene expression patterns from time course analyses identified glycoside hydrolase genes encoding hemicellulases, including cellulosomal enzymes, that were highly upregulated (5- to 100-fold) in the absence of each LacI regulator, suggesting that these were repressed under wild-type conditions and that relatively few genes were controlled by each regulator under the conditions tested. Clo1313_2022, encoding lichenase enzyme LicB, was derepressed in a Δ glyR1 strain. Higher expression of Clo1313_1398, which encodes the Man5A mannanase, was observed in a Δ glyR2 strain, and α-mannobiose was identified as a probable inducer for GlyR2-regulated genes. For the Δ glyR3 strain, upregulation of the two genes adjacent to glyR3 in the celC-glyR3-licA operon was consistent with earlier studies. Electrophoretic mobility shift assays have confirmed LacI transcription factor binding to specific regions of gene promoters. IMPORTANCE Understanding C. thermocellum gene regulation is of importance for improved fundamental knowledge of this industrially relevant bacterium. Most LacI transcription factors regulate local genomic regions; however, a small number of those genes encode global regulatory proteins with extensive regulons. This study indicates that there are small specific C. thermocellum LacI regulons. Finally, the identification of LacI repressor activity for hemicellulase gene expression is a key result of this work and will add to the small body of existing literature on the area of gene regulation in C. thermocellum .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates

Screening the genetic diversity of 45 Yarrowia lipolytica strains identified five candidates with unique metabolic capability and robustness in undetoxified switchgrass hydrolysates, including superior lipid production and efficient pentose sugar utilization. Here, we report the genome sequences of these strains to study their robustness and potential to produce fuels and chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Physiological and metabolic responses of Zymomonas mobilis to lignocellulosic hydrolysate

Zymomonas mobilis is a promising biocatalyst for the sustainable conversion of lignocellulosic sugars into biofuels and bioproducts, yet its response to lignocellulosic hydrolysates remains poorly understood. Here, we investigate the physiological response of Z. mobilis to ammonia fiber expansion (AFEX)-pretreated switchgrass hydrolysate using a systems-level approach integrating LC–MS/MS-based lipidomics and shotgun proteomics. Growth on hydrolysate induced substantial shifts in fatty acid and membrane phospholipid composition, alongside broad proteomic remodeling. Notably, Z. mobilis exhibited a stress response characterized by the upregulation of heat shock proteins and efflux transporters and the downregulation of cell motility proteins. Unexpectedly, hydrolysate exposure also led to a robust upregulation of the Entner–Doudoroff pathway, the ethanol fermentation pathway, and other central carbon metabolism enzymes, indicating a substantial cellular investment potentially driven by additional nutrient availability in hydrolysate. These findings provide new insights into the metabolic adaptations of Z. mobilis to lignocellulosic hydrolysates, informing strategies to enhance its biofuel production capabilities.

Zymomonas mobilis↗
DOE OSTI2023

Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress

In this work we identify changes in high-resolution zones across the globe linked by environmental similarity that have implications for agriculture, bioenergy, and zoonosis. We refine exhaustive vector comparison methods with improved similarity metrics as well as provide multiple methods of amalgamation across 744 months of climatic data. The results of the vector comparison are captured as networks which are analyzed using static and longitudinal comparison methods to reveal locations around the globe experiencing dramatic changes in abiotic stress. Specifically we (i) incorporate updated similarity scores and provide a comparison between similarity metrics, (ii) implement a new feature for resource optimization, (iii) compare an agglomerative view to a longitudinal view, (iv) compare across 2-way and 3-way vector comparisons, (v) implement a new form of analysis, and (vi) demonstrate biological applications and discuss implications across a diverse set of species distributions by detecting changes that affect their habitats. Species of interest are related to agriculture (e.g., coffee, wine, chocolate), bioenergy (e.g., poplar, switchgrass, pennycress), as well as those living in zones of concern for zoonotic spillover that may lead to pandemics (e.g., eucalyptus, flying foxes).

Cashman, Mikaela↗
DOE OSTI2021

GENESPACE R Package (GENESPACE) v1.0

In short, the GENESPACE pipeline conducts analysis of orthology networks, constrained within syntenic regions. Since analyses are limited to local tests conducted within syntenic blocks, GENESPACE is agnostic to ploidy, duplicated regions, inversions or other whole-genome chromosomal complexities that are common across many evolutionary lineages. This advantage allows for evolutionary tests in polyploids (e.g. switchgrass, manuscript in review), species with ancient, but retained whole-genome duplications (e.g. pecan, manuscript in prep), high levels of tandem array proliferation (e.g. eukalypts, manuscript in review) and many other factors that can confound comparative genomic analyses. The major advances of GENESPACE are three-fold: First, this is the first R package to integrate visualization and analysis of large-scale comparative genomics. R, which offers a high-level environment for graphical and statistical exploration of data, is often speed- and memory-limited and not used for computationally intensive tasks such as comparative genomics. The highly efficient C++ scripts used in GENESPACE (via data.table) permit a much faster and computationally lightweight implementation of comparative genomics than is currently available. Second, the pipeline itself is novel. To the best of our knowledge, no other program accomplishes synteny-constrained and ploidy-agnostic comparative genomics. Since nearly all plants and many animals have a history of whole-genome duplications, this is a major and necessary advance to the field. Third, GENESPACE offers high-level and intuitive multi-genome graphical outputs. The dotplots and 'riparian' plots produced herein, which are produced entirely through original R code, are publication-ready and easily customizable.

Schmutz, Jeremy↗
DOE OSTI2015

jacobteter/CropWatR

Biofuels policies induce land use changes (LUC), including cropland expansion and crop switching, and this in turn alters water and soil management practices. Policies differ in the extent and type of land use changes they induce and therefore in their impact on water resources. We quantify and compare the spatially varying water impacts of biofuel crops stemming from LUC induced by two different biofuels policies by coupling a biophysical model with an economic model to simulate the economically viable mix of crops, land uses, and crop management choices under alternative policy scenarios. We assess the outputs of an economic model with a high-resolution crop-water model for major agricultural crops and potential cellulosic feedstocks in the US to analyze the impacts of three alternative policy scenarios on water balances: a counterfactual ‘no-biofuels policy’ (BAU) scenario, a volumetric mandate (Mandate) scenario, and a clean fuel-intensity standard (CFS) scenario incentivizing fuels based on their carbon intensities. While both biofuel policies incentivize more biofuels than in the counterfactual, they differ in the mix of corn ethanol and advanced biofuels from miscanthus and switchgrass (more corn ethanol in Mandate and more cellulosic biofuels in CFS). The two policies differ in their impact on irrigated acreage, irrigation demand, groundwater use and runoff. Net irrigation requirements increase 0.7% in Mandate and decrease 3.8% in CFS, but in both scenarios increases are concentrated in regions of Kansas and Nebraska that rely upon the Ogallala aquifer for irrigation water. Our study illustrates the importance of accounting for the overall LUC and shifts in agricultural production and management practices in response to policies when assessing the water impacts of biofuels.

Teter, Jacob↗
DOE OSTI2022

Energy Exascale Earth System Model v2.0.2

Second patch release of v2.0.0 Changes since v2.0.1 [Important change] Add and update SSP370 and SSP585 cases, add tests, fix use-case files, Change ocean and sea-ice IC for ARRM60to10. [EAM] allow thetaxx as a CAM_TARGET, enable northamericax4v1pg2_WC14to60E2r3 for AMIP, fix ndrop initialization, allow up to 15 history files. [EAMxx] allow use of readnl [EAM-MMF] allow transient SST case for C++ MMF, remove specific task/thread count for ESMT test, modify the variance transport diagnostic, reorg tests, [HOMME] Allow optional sponge layer. [ELM] add 2 land-atm compsets, update FATES to API 17.0.0, allow FATES sp mode, allow ELM harvest to drive FATES harvest, fix memleaks, reduce test build times, modified parameters for miscanthus and switchgrass based on calibration [MPAS-Ocean] turn on ocean BGC in BGC cases, fix interface locations for 60L PHC grid, add mode spec to conservation check streams, allow oRRS18to6v3 grid to run with JRA, update ocean and sea ice ICs for ARRM60to10 (needed for v2), GPU port of thickness tendency, add CMPASO-JRA1p4, [MPAS framework] Add new reproducible global sum module for MPAS components, Add mostRecentAccessTime attribute to streams [MPAS-landice] Update MALI version and Greenland mesh [MPAS-seaice] add single-cell test case, fix BGC restart, Adds omp critical directives for ice warnings seen on cori. [CIME] Fix component namelist creation bugs when NINST>1, add OpenACC, OpenMP and CXX GPU tests, fix nonBFB tests, stop using config_compilers, reduce ELM test build times with shared executable, update OpenMPI on Chrysalis. fix baseline handling, provenance handling with update to cime6.0.33, also use component-specific config_pes files and add the ones from master [Machine updates] cori modules after maint, Chrysalis to OpenMPI-4.1.3 [run_e3sm] replace default case name and group. [Externals] update SCORPIO to 1.3.2

ECP↗