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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A model-independent data assimilation (MIDA) module and its applications in ecology

Abstract. Models are an important tool to predict Earth system dynamics. An accurate prediction of future states of ecosystems depends on not only model structures but also parameterizations. Model parameters can be constrained by data assimilation. However, applications of data assimilation to ecology are restricted by highly technical requirements such as model-dependent coding. To alleviate this technical burden, we developed a model-independent data assimilation (MIDA) module. MIDA works in three steps including data preparation, execution of data assimilation, and visualization. The first step prepares prior ranges of parameter values, a defined number of iterations, and directory paths to access files of observations and models. The execution step calibrates parameter values to best fit the observations and estimates the parameter posterior distributions. The final step automatically visualizes the calibration performance and posterior distributions. MIDA is model independent, and modelers can use MIDA for an accurate and efficient data assimilation in a simple and interactive way without modification of their original models. We applied MIDA to four types of ecological models: the data assimilation linked ecosystem carbon (DALEC) model, a surrogate-based energy exascale earth system model: the land component (ELM), nine phenological models and a stand-alone biome ecological strategy simulator (BiomeE). The applications indicate that MIDA can effectively solve data assimilation problems for different ecological models. Additionally, the easy implementation and model-independent feature of MIDA breaks the technical barrier of applications of data–model fusion in ecology. MIDA facilitates the assimilation of various observations into models for uncertainty reduction in ecological modeling and forecasting.

58 GEOSCIENCES↗
NASA NTRS2021

A model-independent data assimilation (MIDA) module and its applications in ecology

Models are an important tool to predict Earth system dynamics. An accurate prediction of future states of ecosystems depends on not only model structures but also parameterizations. Model parameters can be constrained by data assimilation. However, applications of data assimilation to ecology are restricted by highly technical requirements such as model-dependent coding. To alleviate this technical burden, we developed a model-independent data assimilation (MIDA) module. MIDA works in three steps including data preparation, execution of data assimilation, and visualization. The first step prepares prior ranges of parameter values, a defined number of iterations, and directory paths to access files of observations and models. The execution step calibrates parameter values to best fit the observations and estimates the parameter posterior distributions. The final step automatically visualizes the calibration performance and posterior distributions. MIDA is model independent, and modelers can use MIDA for an accurate and efficient data assimilation in a simple and interactive way without modification of their original models. We applied MIDA to four types of ecological models: the data assimilation linked ecosystem carbon (DALEC) model, a surrogate-based energy exascale earth system model: the land component (ELM), nine phenological models and a stand-alone biome ecological strategy simulator (BiomeE). The applications indicate that MIDA can effectively solve data assimilation problems for different ecological models. Additionally, the easy implementation and model-independent feature of MIDA breaks the technical barrier of applications of data–model fusion in ecology. MIDA facilitates the assimilation of various observations into models for uncertainty reduction in ecological modeling and forecasting.

Earth system dynamics↗
DOE OSTI2025

Combining Observations and Models: A Review of the CARDAMOM Framework for Data‐Constrained Terrestrial Ecosystem Modeling

The rapid increase in the volume and variety of terrestrial biosphere observations (i.e., remote sensing data and in situ measurements) offers a unique opportunity to derive ecological insights, refine process‐based models, and improve forecasting for decision support. However, despite their potential, ecological observations have primarily been used to benchmark process‐based models, as many past and current models lack the capability to directly integrate observations and their associated uncertainties for parameterization. In contrast, data assimilation frameworks such as the CARbon DAta MOdel fraMework (CARDAMOM) and its suite of process‐based models, known as the Data Assimilation Linked Ecosystem Carbon Model (DALEC), are specifically designed for model‐data fusion. This review, motivated by a recent CARDAMOM community workshop, examines the development and applications of CARDAMOM, with an emphasis on its role in advancing ecosystem process understanding. CARDAMOM employs a Bayesian approach, using a Markov Chain Monte Carlo algorithm to enable data‐driven calibration of DALEC parameters and initial states (i.e., carbon pool sizes) through observation operators. CARDAMOM's unique ability to retrieve localized model process parameters from diverse datasets—ranging from in situ measurements to global satellite observations—makes it a highly flexible tool for analyzing spatially variable ecosystem responses to environmental change. However, assimilating these data also presents challenges, including data quality issues that propagate into model skill, as well as trade‐offs between model complexity, parameter equifinality, and predictive performance. We discuss potential solutions to these challenges, such as reducing parameter equifinality by incorporating new observations. This review also offers community recommendations for incorporating emerging datasets, integrating machine learning techniques, strengthening collaboration with remote sensing, field, and modeling communities, and expanding CARDAMOM's relevance for localized ecosystem monitoring and decision‐making. CARDAMOM enables a deep, mechanistic understanding of terrestrial ecosystem dynamics that cannot be achieved through empirical analyses of observational datasets or weakly constrained models alone.

Bayesian inference↗
NASA NTRS2019

Global Ocean Primary Production Trends in the Modern Ocean Color Satellite Record (1998-2015)

Ocean primary production (PP), representing the uptake of inorganic carbon through photosynthesis, supports marine life and affects carbon exchange with the atmosphere. It is difficult to ascertain its magnitude, variability, and trends due to our inability to measure it directly at large scales. Yet it is paramount for understanding changes in marine health, fisheries, and the global carbon cycle. Using assimilation of ocean color satellite data into an ocean biogeochemical model, we estimate that global net ocean PP has experienced a small but significant decline −0.8 PgC/y (−2.1%) per decade (P < 0.05) in the 18-year satellite record from 1998 to 2015. This decline is associated with shallowing surface mixed layer depth (−2.4% per decade) and decreasing nitrate concentrations (−3.2% per decade). Relative contributions to PP by various types of ocean phytoplankton have changed, with decreases in production by intermediate-sized phytoplankton represented by chlorophytes (−14.3% per decade). This is partially compensated by increases from the unique, more nutrient-efficient, coccolithophores (8.4% per decade). Geographically, the North and Equatorial Indian Oceans are responsible for much of the decline in PP, falling 0.16 and 0.69 PgC/y per decade, respectively. Reduced production by large, fast-growing diatoms along with chlorophytes characterizes the decline here. In contrast, increases in PP are found in the North and North Central Pacific. The increases here are led by chlorophytes in the North Pacific and the small cyanobacteria in the North Central Pacific. These results suggest that the multi-decadal satellite observational record, coupled with an underlying representation of marine biodiversity in a model, can monitor the uptake of carbon by phytoplankton and that changes, although small, are occurring in the global oceans.

Watson W Gregg↗
DOE OSTI2022

Critical Enzyme Reactions in Aromatic Catabolism for Microbial Lignin Conversion

The application of microbes to valorize aromatic compounds derived from the abundant plant biopolymer lignin is a rapidly developing area of research that may ultimately enable viable conversion of this recalcitrant and heterogeneous resource to valuable bio-based chemical products. Starting from the three canonical lignin building blocks, which differ in the extent of aromatic ring methoxylation, several common classes of enzymatic reaction occur in the upper pathways of aromatic catabolism to prepare aromatic compounds for assimilation into central carbon metabolism, including aromatic O-demethylation, hydroxylation and decarboxylation. These critical enzymatic steps can often be rate-limiting for efficient biological funnelling of aromatic compounds. Here we review the known enzymatic mechanisms for these reactions that are relevant for aerobic aromatic catabolism of lignin-related monomers, highlighting opportunities at the intersection of biochemistry, enzyme engineering and metabolic engineering for applications in the expanding field of microbial lignin valorization.

aromatic catabolism↗
DOE OSTI2020

SnRK1-ZmRFWD3-Opaque2: A Nexus of Seed Nutrient Accumulation and Diurnal Cycles

Plant seeds store nutrients in the form of protein, starch, and oil to support seed germination and seedling establishment. The seed nutrient reserves are supplied with carbon and nitrogen assimilated in vegetative tissues, where primary metabolism oscillates in a circadian manner (Farré and Weise, 2012). However, whether the nutrient accumulation in developing seeds is also tuned during the diurnal cycle remained unclear until now. In a recent study, Li et al. (2020) identified a signaling module at the nexus between nutrient accumulation in maize (Zea mays) seed and the diurnal cycle.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Ammonium and nitrate uptake by soybean during recovery from nitrogen deprivation

Soybean [Glycine max (L.) Merrill] plants that had been subjected to 15 d of nitrogen deprivation were resupplied for 10 d with 1.0 mol m-3 nitrogen provided as NO3-, NH4+, or NH4(+) + NO3- in flowing hydroponic culture. Plants in a fourth hydroponic system received 1.0 mol m-3 NO3- during both stress and resupply periods. Concentrations of soluble carbohydrates and organic acids in roots increased 210 and 370%, respectively, during stress. For the first day of resupply, however, specific uptake rates of nitrogen, determined by ion chromatography as depletion from solution, were lower for stressed than for non-stressed plants by 43% for NO3- resupply, by 32% for NH4(+) + NO3- resupply, and 86% for NH4+ resupply. When specific uptake of nitrogen for stressed plants recovered to rates for non-stressed plants at 6 to 8 d after nitrogen resupply, carbohydrates and organic acids in their roots had declined to concentrations lower than those of non-stressed plants. Recovery of nitrogen uptake capacity of roots thus does not appear to be regulated simply by the content of soluble carbon compounds within roots. Solution concentrations of NH4+ and NO3- were monitored at 62.5 min intervals during the first 3 d of resupply. Intermittent 'hourly' intervals of net influx and net efflux occurred. Rates of uptake during influx intervals were greater for the NH4(+)-resupplied than for the NO3(-)-resupplied plants. For NH4(+)-resupplied plants, however, the hourly intervals of efflux were more numerous than for NO3(-)-resupplied plants. It thus is possible that, instead of repressing NH4+ influx, increased accumulation of amino acids and NH4+ in NH4(+)-resupplied plants inhibited net uptake by stimulation of efflux on NH4+ absorbed in excess of availability of carbon skeletons for assimilation. Entry of NH4+ into root cytoplasm appeared to be less restricted than translocation of amino acids from the cytoplasm into the xylem.

NASA Discipline Number 61-10↗
NASA NTRS2023

Approaching a Thermal Tipping Point in the Eurasian Boreal Forest at its Southern Margin

Climate change is increasing the intensity and frequency of extreme heat events. Ecological responses to extreme heat will depend on vegetation physiology and thermal tolerance. Here we report that Larix sibirica, a foundation species across boreal Eurasia, is vulnerable to extreme heat at its southern range margin due to its low thermal tolerance (T crit of photosynthesis: ~ 37–48 °C). Projections from CMIP6 Earth System Models (ESMs) suggest that leaf temperatures might exceed the 25 th percentile of Larix sibirica’s T crit by two to three days per year within the next two to three decades (by 2050) under high emission scenarios (SSP3-7.0 and SSP5-8.5). This degree of warming will threaten the biome’s continued ability to assimilate and sequester carbon. This work highlights that under high emission trajectories we may approach an abrupt ecological tipping point in southern boreal Eurasian forests substantially sooner than ESM estimates that do not consider plant thermal tolerance traits.

Boreal ecology↗
NASA NTRS2008

NASA's Modern Era Retrospective-Analysis for Research and Applications (MERRA): Early Results and Future Directions

This talk will review the status and progress of the NASA/Global Modeling and Assimilation Office (GMAO) atmospheric global reanalysis project called the Modern Era Retrospective-Analysis for Research and Applications (MERRA). An overview of NASA's emerging capabilities for assimilating a variety of other Earth Science observations of the land, ocean, and atmospheric constituents will also be presented. MERRA supports NASA Earth science by synthesizing the current suite of research satellite observations in a climate data context (covering the period 1979-present), and by providing the science and applications communities with of a broad range of weather and climate data with an emphasis on improved estimates of the hydrological cycle. MERRA is based on a major new version of the Goddard Earth Observing System Data Assimilation System (GEOS-5), that includes the Earth System Modeling Framework (ESMF)-based GEOS-5 atmospheric general circulation model and the new NOAA National Centers for Environmental Prediction (NCEP) unified grid-point statistical interpolation (GST) analysis scheme developed as a collaborative effort between NCEP and the GMAO. In addition to MERRA, the GMAO is developing new capabilities in aerosol and constituent assimilation, ocean, ocean biology, and land surface assimilation. This includes the development of an assimilation capability for tropospheric air quality monitoring and prediction, the development of a carbon-cycle modeling and assimilation system, and an ocean data assimilation system for use in coupled short-term climate forecasting.

Schubert, Siegfried↗
NASA NTRSDate not supplied

FluxSat: Long-term Earth Science Data Record (ESDR) for Terrestrial Gross Primary Production (GPP) based on satellite data calibrated with eddy covariance data

Gross primary production (GPP), the amount of carbon dioxide (CO 2 ) assimilated by plants through photosynthesis, is one of the most variable and uncertain components of the global carbon cycle. Global GPP has been estimated with a number of process-based models, data-driven, and hybrid approaches. Dynamic global vegetation models (DGVMs), driven by observed environmental changes, are used for global carbon budget assessments and long-term (climate) prediction. Benchmarking these and other models globally with data-driven GPP estimates is critical for understanding the land sink and ensuring accurate forecasts of the carbon cycle. In addition, global data-driven GPP estimates are crucial for studies of interannual variability, including trends that are linked to mechanisms with large uncertainties, such as the indirect CO 2 fertilization effect related to greening. In response to a community need for a GPP data set that well captures spatio-temporal variability, we developed FluxSat, a data-driven approach that optimizes the use of satellite reflectance data from the NASA MODerate-resolution Imaging Spectroradiometer (MODIS) on the Terra and Aqua satellites, calibrated using ground-based eddy covariance (EC) data. We are enhancing (spatially, higher resolution) and extending FluxSat (in time, with additional sensors) to create a high quality long term GPP Earth System Data Record (ESDR) for use in model benchmarking, carbon cycle modeling, and studies of trends and interannual variability. Our team’s objectives are to: 1. Update and document the current MODIS FluxSat GPP (daily, 0.05o and 0.5o resolutions) products with latest available MODIS and EC data sets; 2. Extend FluxSat GPP record forward in time with the Visible Infrared Imaging Radiometer Suite (VIIRS) on operational weather satellites going forward; 3. Extend FluxSat GPP record backward in time using the Advanced Very High Resolution Radiometer (AVHRR) on weather satellites dating back to 1981; 4. Provide higher spatial resolution MODIS and VIIRS GPP (0.0083o). 5. Thoroughly evaluate all FluxSat products with independent data; and 6. Create a homogenized long-term GPP record spanning 40+ years. We will discuss plans for this long-term data set that is supported through the NASA Making Earth System Data Records for Use in Research Environments (MEaSUREs) program.

gross Primary Production↗
DOE OSTI2025

CO2 Plume Imaging with Accelerated Deep Learning-based Data Assimilation Considering Multiple Realizations: Application to the Illinois Basin-Decatur Carbon Sequestration Project

We propose a fast and efficient deep learning workflow for near real-time data assimilation, forecasting and visualization of CO2 plume evolution in saline aquifer and demonstrate its application at a field site. Unlike the previous work, this study incorporates the impact of spatial heterogeneity using multiple realizations. In the proposed workflow, a neural network model utilizes available monitoring data such as downhole pressure measurements as input and predicts the propagating pressure ‘front’ using the diffusive time of flight (DTOF) map which is considered as representative reservoir image of the flow field. The DTOF is the arrival time of pressure front propagation, which can be computed by the Fast Marching Method rapidly without flow simulations. Reservoir model calibration can be implemented by selecting the training data samples that describe the predicted DTOF map based on observed data. The power and efficacy of our workflow is demonstrated by application to the Illinois Basin-Decatur Project.

CO2 plume imaging↗
NASA NTRS2020

Assimilation of Vegetation Optical Depth Retrievals from Passive Microwave Radiometry

Vegetation optical depth (VOD) retrievals from passive microwave sensors provide analog estimates of above-ground canopy biomass. This study presents the development and analysis of assimilating VOD retrievals from X-, C-, and L-band passive microwave instruments within the Noah-MP land surface model over the Continental U.S. The results from this study demonstrate that the assimilation of VOD retrievals have a significant beneficial impact on the simulation of evapotranspiration and GPP, particularly over the agricultural areas of the U.S. The improvements in the water and carbon fluxes from the assimilation of VOD from X- and C-band sensors are found to be comparable to those obtained from the assimilation of vegetation indices from optical sensors.The study also quantifies the relative and joint impact of assimilating surface soil moisture and VOD from the Soil Moisture Active Passive (SMAP) mission. The utility of soil moisture assimilation for improving ET is more significant over water-limited regions, whereas VOD DA is more impactful over areas where soil moisture is not the primary controlling factor on ET. The results also indicate that the information on moisture and vegetation states from SMAP can be simultaneously exploited through the joint assimilation of surface soil moisture and VOD. Since passive microwave-based VOD retrievals are available in nearly all weather conditions, their use within data assimilation systems offers the ability to extend and improve the utility obtained from the use of optical/infrared based vegetation retrievals

Sujay V Kumar↗
NASA NTRS2021

Bias-Correcting Carbon Fluxes Derived From Land-Surface Satellite Data for Retrospective and Near Real-Time Assimilation Systems

The ability to monitor and understand natural and anthropogenic variability in atmospheric carbon dioxide(CO2) is a growing need of many stakeholders across the world. Systems that assimilate satellite observations, given their short latency and dense spatial coverage, into high resolution global models are valuable, if not essential, tools for addressing this need. A notable drawback of modern assimilation systems is the long latency of many vital in-put datasets, e.g., inventories, in situ measurements, and re-processed remote-sensing data can trail the current date by months to years. This paper describes techniques for bias-correcting surface fluxes derived from satellite observations of the Earth’s surface to be consistent with constraints from inventories and in situ CO2 datasets. The techniques are applicable in both short-term forecasts and retrospective simulations, thus taking advantage of the coverage and short latency of satellite data while reproducing the major features of long-term inventory and in situ records. Our approach begins with a standard collection of diagnostic fluxes which incorporate a variety of remote-sensing driver data, viz. vegetation indices, fire radiative power, and nighttime lights. We then apply an empirical sink so that global budgets of the diagnostic fluxes match given atmospheric and oceanic growth rates for each year. This step removes coherent, systematic flux errors that produce biases inCO2which mask the signals an assimilation system hopes to capture. Depending on the simulation mode, the empirical sink uses different choices of atmospheric growth rates: estimates based on observations in retrospective mode and projections based on seasonal fore-casts of sea surface temperature in forecasting mode. The retrospective fluxes, when used in simulations with NASA’s Goddard Earth Observing System (GEOS), reproduce marine boundary layer measurements with comparable skill to those using fluxes from a modern inversion system. The forecasted fluxes show promising accuracy in their application to the analysis of changes in the carbon cycle as they occur.

CO2↗
NASA NTRSDate not supplied

Detectability of anthropogenic impacts on terrestrial carbon storage through space-based greenhouse gas observations

While changes in human activity and their impact on the terrestrial biosphere may be apparent in inventory and land-surface satellite data, reliably matching these changes to signals in atmospheric greenhouse gases remains challenging. The dominant signals in atmospheric carbon dioxide (CO2) are those of the seasonal and diurnal variability of the terrestrial biosphere. As a result, the historically large short-term change in anthropogenic fossil fuel emissions due to COVID-19 produced an atmospheric CO2 signal near the threshold of detectability of the current space-based observing system. Impacts of anthropogenic activity on terrestrial carbon storage are likewise expected to be difficult, if not impossible, to detect and validate with atmospheric observations. For example, many forest management projects involve reduction of wood removals that would otherwise be taken off site and decompose years later and are thus not reflected in immediate onsite carbon fluxes. Nevertheless, changes implemented over a jurisdictional scale, as opposed to individual projects, may be detectable. This presentation will analyze to what extent NASA’s Goddard Earth Observing System (GEOS)/Orbiting Carbon Observatory 2 (OCO-2) assimilated column CO2 (XCO2) product is able to detect anthropogenic changes to terrestrial carbon storage and the results of several simulation experiments meant to represent potential forest management scenarios. As examples, we consider past and future changes due to conversion in the Tropics to agricultural land use from slash-and-burn, e.g., from Reducing emissions from deforestation and forest degradation in developing countries (REDD+) efforts. This has the potential to inform what practices may be observable with current and future technology, e.g., Europe’s upcoming CO2 monitoring mission (CO2M), and where improvement is needed.

Brad Weir↗
DOE OSTI2025

Glyceraldehyde-3-phosphate dehydrogenase homologs as bifunctional gatekeepers of metabolic segregation in Pseudomonas putida

Metabolically versatile Pseudomonas species can assimilate various glycolytic and gluconeogenic substrates. Simultaneous assimilation is known to segregate carbons from each substrate type into different metabolic pathways. However, the mechanisms of this metabolic segregation remain unresolved. Here, we investigate Pseudomonas putida KT2440 during processing of the sugar glucose through glycolysis versus the phenolic acid ferulate through gluconeogenesis. Metabolome profiling reveals up to twofold less tricarboxylic acid cycle metabolites but up to 10-fold higher metabolites of upper glycolysis, pentose-phosphate, and Entner–Doudoroff pathways in glucose-grown cells compared to ferulate-grown cells. After 13C-substrate switching, kinetic isotopic profiling captures rapid assimilation of new substrate carbons into initial catabolic pathways, but incorporation into downstream pathways is absent or incomplete. Proteomics identifies a 22-fold higher abundance of one homolog of glyceraldehyde-3-phosphate dehydrogenase (GAPDH, GapA) in cells fed on glucose relative to ferulate, while abundance of another homolog (GapB) remains unchanged. Growth phenotypes and quantitative metabolomics for single and double knockout mutants of these GAPDH homologs indicate only GapA involvement in glycolytic flux, which can be compensated by the Entner–Doudoroff pathway, and distinct preference of GapB with minimal role of GapA for gluconeogenic flux. Accordingly, growth of triple knockout mutant with deletion of gapA, gapB, and edd is possible only when glycolytic and gluconeogenic substrates are provided together to meet metabolic demands in a segregated fashion, but metabolic tradeoffs lead to slow growth. A mathematical, experimentally constrained, model of the GAPDH node shows that tuning of GapA and GapB concentrations enables transition between flux regimes for nutritional adaptability.

Zhou, Nanqing [Northwestern University, Evanston]↗
NASA NTRS2008

Chemical OSSEs in Global Modeling and Assimilation Office (GMAO)

This presentation will summarize ongoing 'chemical observing system simulation experiment (OSSE)' work in the Global Modeling and Assimilation Office (GMAO). Weather OSSEs are being studied in detail, with a 'nature run' based on the European Centre for Medium-Range Weather Forecasts (ECMWF) model that can be sampled by a synthesized suite of satellites that reproduces present-day observations. Chemical OSSEs are based largely on the carbon-cycle project and aim to study (1) how well we can reproduce the observed carbon distribution with the Atmospheric Infrared Sounder (AIRS) and Orbiting Carbon Observatory (OCO) sensors and (2) with what accuracy can we deduce surface sources and sinks of carbon species in an assimilation system.

Pawson, Steven↗
DOE OSTI2025

Unraveling metabolism underpinning biomass composition shift in Scenedesmus obliquus under simulated outdoor conditions using 13 C-fluxomics

To render the resulting biomass more attractive and amenable for utilization as the basis for low-carbon intensity bioproducts, single-celled algae need to be biochemically and metabolically poised to assimilate and store the delivered carbon in the fastest and most efficient manner. Accelerating biochemical carbon storage, as primarily carbohydrates or lipids, is critical to achieve the high carbon capture potential that is assigned to algae. To guide strain optimization and engineering for maximizing carbon capture and storage, it is essential to elucidate the link between carbon metabolism and biomass composition. Most published metabolomics work in algae remains largely restricted to ideal and simplified environmental conditions in model organisms, thereby limiting their translation to outdoor implementation. In this work, we utilize 13 C isotopic labeling to characterize distinct intracellular metabolic fluxes before, during, and after nitrogen depletion-induced compositional shifts in Scenedesmus obliquus UTEX 393. The results indicate that a transition to carbohydrates is characterized by diverting flux to starch instead of replenishing the Calvin cycle for CO 2 fixation whereas the subsequent transition to lipids is fueled by NADPH produced by upregulating the phosphoenolpyruvate carboxylase (PEPC)–malic enzyme (ME) cycle flux. Our work highlights bottlenecks to carbohydrate- and lipid-rich biomass and can guide implementable strategies to control the fate of fixed carbon in S. obliquus.

09 BIOMASS FUELS↗