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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Leaf gas exchange and fitted parameters, San Lorenzo, Panama, 2020

This data package contains photosynthetic CO2 response curves (ACi curves), light response curves (AQ curves), dark adapted dark respiration, conductance curves, and survey measurements for leaves measured at the San Lorenzo forest canopy crane site, Panama (PA-SLZ) from January to March 2020. Leaves were sampled from both the top of the canopy and multiple heights within the canopy from 10 vertical profiles and included around 50 species. In addition, six core species were also measured, from the top of the canopy. Fitted maximum carboxylation rate (Vcmax), maximum electron transport rate (Jmax), and triose phosphate utilization rate (TPU) were derived from measured data as well as the convexity, light use efficiency, apparent quantum yield, and Rdark. The measurements can also be used to derive the conductance parameters g0 and g1 of stomatal model. All the gas exchange data and metadata are presented in .csv files and complete instrument output are included in .zip folders. Data and metadata meet the ESS-DIVE leaf-level gas exchange reporting format requirements. The protocol details are provided as pdf documents. In addition to gas exchange data described here these samples were also used for measurement of leaf optical properties, carbon and nitrogen content, and leaf mass per unit leaf area (LMA) these data can be cross linked using the unique sample ID and are provided in separate related data packages. Sample information including canopy elevation and leaf area index (LAI) can be found in the related “Leaf and canopy traits” data package.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Leaf gas exchange and fitted parameters, two sites in Panama, 2022

Photosynthetic CO2 response curves (ACi curves), light response curves (AQ curves), dark adapted dark respiration, conductance curves, and survey measurements for leaves measured in the Parque Natural Metropolitano (PNM) and Gamboa, Panama, from January to April 2022 are presented. Measurements were made on leaves from 46 different tree, shrub and liana species, from sunlit canopy and understory locations. Leaf area index from 8 vertical profiles at PNM are also included. The aim of this measurement campaign was three-fold: (i) to improve our understanding of the vertical variation in leaf-level water use efficiency; (ii) to develop an understanding of the sensitivity of stomata to changes in environmental conditions, especially light, humidity, and temperature; (iii) to improve models which can predict leaf traits from leaf contact spectral measurements. All the gas exchange data and metadata are presented in .csv files and complete instrument output are included in .zip folders. Data and metadata meet the ESS-DIVE leaf-level gas exchange reporting format requirements. The protocol details are provided as pdf documents. In addition to gas exchange data reported here these samples were also used for measurement of leaf optical properties, carbon and nitrogen content, and leaf mass per unit leaf area (LMA). These data can be cross linked using the unique sample ID and are provided in separate data packages.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Plant Physiology, Alder and Willow Species, Seward Peninsula, Alaska, 2019

Photosynthetic parameters (Vcmax and Jmax), CO2 response (ACi) curves and dark respiration (Rdark) measurements of tundra shrub species. Data were collected at the NGEE-Arctic Kougarok and Teller study sites on the Seward Peninsula, AK, USA in July 2019. Four species were measured using LI-COR LI-6400 portable gas exchange systems: Alnus viridis ssp. fruticosa, Salix richardsonii and Salix pulchra. The data package files include data files, metadata files, dGPS locations and the complete instrument output for all gas exchange measurements in .csv format. See the related data packages for foliar trait data (leaf mass per area, leaf nitrogen concentration), and leaf spectral reflectance data collected simultaneously on the same shrubs (NGA210, NGA212).The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

ABSTRACT Denitrification is a form of anaerobic respiration wherein nitrate (NO 3 − ) is sequentially reduced via nitrite (NO 2 − ), nitric oxide, and nitrous oxide (N 2 O) to dinitrogen gas (N 2 ) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria,Rhodopseudomonas palustrisCGA0092 andRhodobacter capsulatusSB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO 2 − to N 2 , and SB1003 reduced N 2 O to N 2 . For each bacterium, N 2 O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N 2 O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO 3 − served as a stable, non-catalyzable molecule that was sufficient to activate N 2 O reduction. Using a β-galactosidase reporter, we found that NO 3 − acted, at least in part, by stimulating N 2 O reductase gene expression. In SB1003, NO 2 − but not NO 3 − activated N 2 O reduction, but NO 2 − was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use. IMPORTANCE Denitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.

Biotechnology & Applied Microbiology↗
DOE OSTI2025

Vertical canopy gradients of respiration drive plant carbon budgets and leaf area index

Despite its importance for determining global carbon fluxes, leaf respiration remains poorly constrained in land surface models (LSMs). We tested the sensitivity of the Energy Exascale Earth System Model Land Model – Functionally Assembled Terrestrial Ecosystem Simulator (ELM-FATES) to variation in the canopy gradients of leaf maintenance respiration (R dark ). We ran global and point simulations varying the canopy gradient of R dark to explore the impacts on forest structure, composition, and carbon cycling. In global simulations, steeper canopy gradients of R dark lead to increased understory survival and leaf biomass. Leaf area index (LAI) increased up to 77% in tropical regions compared with the default parameterization, improving alignment with remotely sensed benchmarks. Global vegetation carbon varied from 308 Pg C to 449 Pg C across the ensemble. In tropical forest simulations, steeper gradients of R dark had a large impact on successional dynamics. Results show the importance of canopy gradients in leaf traits and fluxes for determining plant carbon budgets and emergent ecosystem properties such as competitive dynamics, LAI, and vegetation carbon. The high-model sensitivity to canopy gradients in R dark highlights the need for more observations of how leaf traits and fluxes vary along light micro-environments to inform critical dynamics in LSMs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data from: "Snowmelt Timing Regulates Community Composition, Phenology, and Physiological Performance of Alpine Plants"

This archive contains data that were used to support conclusions drawn in “Snowmelt Timing Regulates Community Composition, Phenology, and Physiological Performance of Alpine Plants”, by Winkler et al., 2018. Data were collected throughout the 2009 growing season on Niwot Ridge, Colorado, before the site became part of the Alpine Treeline Warming Experiment (ATWE). Geospatial files are included in this archive to provide additional locational context. The files in this data package consist of five comma-separated-values (.csv) files, one keyhole markup language (.kml) file, and two ESRI shapefiles (.shp). The .csv files can be opened by Microsoft Excel, R, or any simple text-editor software, such as TextEdit (MacOS) or Notepad (Windows). The .kml files can be opened by Google Maps or Google Earth, and the .shp files are compatible with GIS softwares such as ESRI’s ArcGIS suite, and QGIS.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------We asked how plant community composition, phenology, plant water relations, and photosynthetic gas exchange of alpine-restricted and wide-ranging species differ in their responses to a ca. 40-day snowmelt gradient in the Colorado Rocky mountains (Lewisia pygmaea, Sibbaldia procumbens, and Hymenoxys grandiflora were alpine-restricted and Artemisia scopulorum, Carex rupestris, and Geum rossii were wide-ranging species). To do this, we measured percent cover and flowering initiation across 20 plots varying in snowmelt timing and measured net photosynthesis and stomatal conductance in multiple individuals of each target species in these plots in 2009.As hypothesized, species richness and foliar cover increased with earlier snowmelt, due to a greater abundance of wide-ranging species present in earlier melting plots. Flowering initiation occurred earlier with earlier snowmelt for 12 out of 19 species analyzed, while flowering duration was shortened with later snowmelt for six species (all but one were wide ranging species). We observed >50% declines in net photosynthesis from July to September as soil moisture and plant water potentials declined. Early-season stomatal conductance was higher in wide-ranging species, indicating a more competitive strategy for water acquisition when soil moisture is high. Even so, there were no associated differences in photosynthesis or transpiration, suggesting no strong differences between these groups in physiology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Data from: "Ecophysiological variation in two provenances of Pinus flexilis seedlings across an elevation gradient from forest to alpine"

This archive contains data used to support conclusions drawn in “Ecophysiological variation in two provenances of Pinus flexilis seedlings across an elevation gradient from forest to alpine”, by Reinhardt et al., 2011. Data were collected over one summer season in plots within the Alpine Treeline Warming Experiment (ATWE), before climate manipulations began. The experiment was located on Niwot Ridge, in the Front Range of the Colorado Rocky Mountains. This data package includes five comma-separated-values (.csv) files, five Microsoft Excel (.xlsx) files, one .pdf file, and two types of geospatial files: keyhole markup language (.kml), and ESRI shapefiles (.shp). .csv files can be opened using any simple text-editing software (such as Notepad and TextEdit), R, and Microsoft Excel. .xlsx files can only be opened using Microsoft Excel. The .pdf file can be opened using Adobe Acrobat Reader or any other compatible file viewing software. The .kml file can be opened using Google Earth and Google Maps, and shapefiles can be opened using any software compatible with the file type, such as ESRI’s ArcGIS suite and QGIS.Data archived contain gas exchange and plant physiology measurements, non-structural carbohydrate data, among others. Geospatial files are also provided for additional locational context. The files and their contents in this data package are summarized under "Data Summary" in the included Data User's Guide. All files (excluding geospatial) are available in both Microsoft Excel and in .csv format, and are indicated in the Data Summary list as well.-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Climate change is predicted to cause upward shifts in forest tree distributions, which will require seedling recruitment beyond current forest boundaries. However, predicting the likelihood of successful plant establishment beyond current species’ ranges under changing climate is complicated by the interaction of genetic and environmental controls on seedling establishment. To determine how genetics and climate may interact to affect seedling establishment, we transplanted recently germinated seedlings from high- and low-elevation provenances (HI and LO, respectively) of Pinus flexilis in common gardens arrayed along an elevation and canopy gradient from subalpine forest into the alpine zone and examined differences in physiology and morphology between provenances and among sites. Plant dry mass, projected leaf area and shoot:root ratios were 12–40% greater in LO compared with HI seedlings at each elevation. There were no significant changes in these variables among sites except for decreased dry mass of LO seedlings in the alpine site. Photosynthesis, carbon balance (photosynthesis/respiration) and conductance increased >2× with elevation for both provenances, and were 35–77% greater in LO seedlings compared with HI seedlings. There were no differences in dark-adapted chlorophyll fluorescence (Fv/Fm) among sites or between provenances. Our results suggest that for P. flexilis seedlings, provenances selected for above-ground growth may outperform those selected for stress resistance in the absence of harsh climatic conditions, even well above the species’ range limits in the alpine zone. This indicates that forest genetics may be important to understanding and managing species’ range adjustments due to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Data from: "Moisture rivals temperature in limiting photosynthesis by trees establishing beyond their cold-edge range limit under ambient and warmed conditions"

This archive contains data files that were used to draw conclusions in “Moisture rivals temperature in limiting photosynthesis by trees establishing beyond their cold-edge range limit under ambient and warmed conditions”, by Moyes et al., 2015. All field research was completed in common garden plots set up as part of the Alpine Treeline Warming Experiment (ATWE) on Niwot Ridge, Colorado, USA.There are two main data file formats in this archive: comma-separated values (.csv), and Microsoft Excel (.xls and .xlsx). .xlsx files can be read using Microsoft Excel and Google Sheets, and .csv files can be read using any simple text editor program, such as TextEdit (Mac) and Notepad (Windows). This .pdf data user’s guide can be read using Adobe Acrobat Reader, or any other compatible software. Seedling photographs and their corresponding leaf area-processed images are available in .jpg/.JPG image format, and can be opened using Preview (Mac) and Photos (Windows). To provide additional spatial context, two types of geospatial files are also published in this data package: ESRI shapefiles (.shp) and .kml files. Shapefiles are compatible with any GIS software able to read the file type (such as QGIS or ESRI’s ArcGIS suite), and .kml files can be opened with Google Earth or Google Maps. Figures 3 and 4 in the publication contain data from Moyes et al. 2013. This publication is cited in the References section in this archive, and data files can be accessed via the Alpine Treeline Warming Experiment project portal on ESS-DIVE. ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Climate change is altering plant species distributions globally, and warming is expected to promote uphill shifts in mountain trees. However, at many cold-edge range limits, such as alpine treelines in the western United States, tree establishment may be colimited by low temperature and low moisture, making recruitment patterns with warming difficult to predict.- We measured response functions linking carbon (C) assimilation and temperature- and moisture-related microclimatic factors for limber pine (Pinus flexilis) seedlings growing in a heating × watering experiment within and above the alpine treeline. We then extrapolated these response functions using observed microclimate conditions to estimate the net effects of warming and associated soil drying on C assimilation across an entire growing season.- Moisture and temperature limitations were each estimated to reduce potential growing season C gain from a theoretical upper limit by 15–30% (c. 50% combined). Warming above current treeline conditions provided relatively little benefit to modeled net assimilation, whereas assimilation was sensitive to either wetter or drier conditions.- Summer precipitation may be at least as important as temperature in constraining C gain by establishing subalpine trees at and above current alpine treelines as seasonally dry subalpine and alpine ecosystems continue to warm.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Leaf gas exchange, leaf water potential and spectral reflectance, BIONTE, Brazil, 2023

Leaf traits measured at the top of the canopy on 30 tree species in the BIONTE experimental forest, near Manaus, Brazil, at three time points during August to November, 2023. The aim of this study was to test the relationship between leaf water use efficiency and wood density. Leaf gas exchange was measured on top-of-canopy leaves accessed by an articulated boom lift. Response curves (A-Ci and A-Q), and dark adapted respiration were measured on cut branches. Survey gas exchange measurements were performed on attached leaves at various times during the day. Following gas exchange, leaves were harvested, and measured for leaf water potential and spectral reflectance. Data in this data package is presented in csv files, with metadata in csv and descriptive experimental protocols as pdf. Gas exchange data and metadata meets the requirements of the ESS-DIVE reporting format for leaf-level gas exchange data and metadata.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Vegetation Warming Experiment: Plant Physiology, Utqiagvik (Barrow), Alaska, 2021

Leaf gas exchange measurements on Carex aquatilis Wahlenb. following a single season warming treatment. Data were collected in 2021 from 5 treatment warming chambers and paired control plots located on the Barrow Environmental Observatory (BEO), Utqiagvik, Alaska. Data include CO2 response (ACi) curves, light response (AQ) curves, and dark-adapted respiration (Rdark) logged data measured at controlled leaf temperatures from 5–25 °C. The data package includes 4 data files in .csv format, 10 metadata files and the complete instrument output for all measurements. These data were collected as part of an experiment using Zero Power Warming (ZPW) chambers that delivered a single season warming treatment of ~4 °C above ambient air temperature. Four different plant species were targeted over four experimental years from 2017–2021. See related data packages for processed gas exchange data, leaf trait data (leaf mass per area, leaf nitrogen concentration), ambient and chamber environmental conditions, phenocamera images, thaw depth and GPS locations of chambers. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Vegetation Warming Experiment: Plant Physiology, Utqiagvik (Barrow), Alaska, 2017

Leaf gas exchange measurements on Petasites frigidus (L.) Fr. following a single season warming treatment. Data were collected in 2017 from 5 treatment warming chambers and paired control plots located on the Barrow Environmental Observatory (BEO), Utqiagvik, Alaska. Data include CO2 response (ACi) curves, light response (AQ) curves, and dark-adapted respiration (Rdark) logged data measured at controlled leaf temperatures from 5-25 °C. The data package includes 4 data files in .csv format, 10 metadata files and the complete instrument output for all measurements. These data were collected as part of an experiment using Zero Power Warming (ZPW) chambers that delivered a single season warming treatment of ~4 °C above ambient air temperature. Four different plant species were targeted over four experimental years from 2017-2021. See related data packages for processed gas exchange data, leaf trait data (leaf mass per area, leaf nitrogen concentration), ambient and chamber environmental conditions, phenocamera images, thaw depth and GPS locations of chambers. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Vegetation Warming Experiment: Plant Physiology, Utqiagvik (Barrow), Alaska, 2018

Leaf gas exchange measurements on Arctagrostis latifolia (R. Br.) Griseb. following a single season warming treatment. Data were collected in 2018 from 5 treatment warming chambers and paired control plots located on the Barrow Environmental Observatory (BEO), Utqiagvik, Alaska. Data include CO2 response (ACi) curves, light response (AQ) curves, and dark-adapted respiration (Rdark) logged data measured at controlled leaf temperatures from 5–25 °C. The data package includes 4 data files in .csv format, 10 metadata files and the complete instrument output for all measurements. These data were collected as part of an experiment using Zero Power Warming (ZPW) chambers that delivered a single season warming treatment of ~4 °C above ambient air temperature. Four different plant species were targeted over four experimental years from 2017–2021. See related data packages for processed gas exchange data, leaf trait data (leaf mass per area, leaf nitrogen concentration), ambient and chamber environmental conditions, phenocamera images, thaw depth and GPS locations of chambers. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Vegetation Warming Experiment: Plant Physiology, Utqiagvik (Barrow), Alaska, 2019

Leaf gas exchange measurements on Eriophorum angustifolium Honck. following a single season warming treatment. Data were collected in 2019 from 5 treatment warming chambers and paired control plots located on the Barrow Environmental Observatory (BEO), Utqiagvik, Alaska. Data include CO2 response (ACi) curves, light response (AQ) curves, and dark-adapted respiration (Rdark) logged data measured at controlled leaf temperatures from 5–25 °C. The data package includes 4 data files in .csv format,, and include 4 data files, 10 metadata files and the complete instrument output for all measurements. These data were collected as part of an experiment using Zero Power Warming (ZPW) chambers that delivered a single season warming treatment of ~4 °C above ambient air temperature. Four different plant species were targeted over four experimental years from 2017–2021. See related data packages for processed gas exchange data, leaf trait data (leaf mass per area, leaf nitrogen concentration), ambient and chamber environmental conditions, phenocamera images, thaw depth and GPS locations of chambers. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Canopy position influences the degree of light suppression of leaf respiration in abundant tree genera in the Amazon Forest

Leaf respiration in the dark (R dark ) and light (R day ) is poorly characterized in diverse tropical ecosystems, and little to no information exists on the degree of light suppression in common tree species within the Amazon basin, and their dependences upon plant functional traits and position within the canopy. We quantified R dark and apparent R day using the Kok method and measured key leaf traits in 26 tree individuals of different species distributed in three different canopy positions: canopy, lower canopy, and understory. To explore the relationships between the leaf traits we used the standardized major axis (SMA). We found that canopy trees had significantly higher rates of R dark and R day than trees in the understory. The difference between R dark and R day (the light suppression of respiration) was greatest in the understory (68 ± 9%, 95% CI) and lower canopy (49 ± 9%, 95% CI) when compared to the canopy (37 ± 10%, 95% CI). We also found that R day was significantly and strongly correlated with R dark (p < 0.001) for all the canopy positions. Also, leaf mass per area (LMA) and leaf Phosphorus concentration (P) had a significant relationship with R dark (p < 0.001; p = 0.003), respectively. In addition, a significant relationship was found for LMA in the canopy and lower canopy positions (p = 0.009; p = 0.048) while P was only significant in the canopy (p = 0.044). Finally, no significant relationship was found between R dark and nitrogen, sugars, and starch. Our results highlight the importance of including representation of the light suppression of leaf respiration in terrestrial biosphere models and also of accounting for vertical gradients within forest canopies and connections with functional traits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The end game(s) of photosynthetic carbon metabolism

Abstract The year 2024 marks 70 years since the general outline of the carbon pathway in photosynthesis was published. Although several alternative pathways are now known, it is remarkable how many organisms use the reaction sequence described 70 yrs ago, which is now known as the Calvin–Benson cycle or variants such as the Calvin–Benson–Bassham cycle or Benson–Calvin cycle. However, once the carbon has entered the Calvin–Benson cycle and is converted to a 3-carbon sugar, it has many potential fates. This review will examine the last stages of photosynthetic metabolism in leaves. In land plants, this process mostly involves the production of sucrose provided by an endosymbiont (the chloroplast) to its host for use and transport to the rest of the plant. Photosynthetic metabolism also usually involves the synthesis of starch, which helps maintain respiration in the dark and enables the symbiont to supply sugars during both the day and night. Other end products made in the chloroplast are closely tied to photosynthetic CO2 assimilation. These include serine from photorespiration and various amino acids, fatty acids, isoprenoids, and shikimate pathway products. I also describe 2 pathways that can short circuit parts of the Calvin–Benson cycle. These final processes of photosynthetic metabolism play many important roles in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A dynamic thermal algal growth model for pilot-scale open-channel raceways

Here this study describes the makeup of and results from a simulation consisting of a lumped thermal model integrated with a dynamic algae growth model to simulate the microalgae productivity of an open-channel raceway cultivation system. The thermal model considers the dynamic effects of weather, light absorption, convective heat transfer, radiation heat transfer, conductive heat transfer, thermal capacitance, and water control strategies. The dynamic algae growth model solves a set of ordinary differential equations consisting of growth functions dependent on incident radiation, temperature, nutrient availability, basal metabolism, and losses due to dark- and photo-respiration. Relative errors in the predicted ash-free dry weight of Nannochloropsis oceanica are 12.5%, -6.1%, and 4.4% for three separate replicates of cultivation cycles (~4.2 m 2 ) performed at AzCATI during the ATP 3 Unified Field Studies in Fall, Spring, and Summer. This research demonstrates that thermal modeling is an essential contributor to the validation of microalgae growth models.

09 BIOMASS FUELS↗
DOE OSTI2023

Light-independent regulation of algal photoprotection by CO 2 availability

Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO 2 conditions. When light energy exceeds CO 2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO 2 Concentrating Mechanism (CCM). How light and CO 2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO 2 concentrations and that depletion of CO 2 drives these responses, even in total darkness. High CO 2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO 2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO 2 levels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.

60 APPLIED LIFE SCIENCES↗