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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Taxonomic patterns in the nitrogen assimilation of soil prokaryotes

Summary Nitrogen (N) is frequently a limiting nutrient in soil; its availability can govern ecosystem functions such as primary production and decomposition. Assimilation of N by microorganisms impacts the availability of N in soil. Despite its established ecological significance, the contributions of microbial taxa to N assimilation are unknown. Here we measure N uptake and use by microbial phylotypes and taxonomic groups within a diverse assemblage of soil microbes through quantitative stable isotope probing (qSIP) with 15 N. Following incubation with 15 , distinct patterns of 15 N assimilation among taxonomic groups were observed. For instance, glucose addition stimulated 15 N assimilation in most members of Actinobacteria and Proteobacteria but generally decreased 15 N use by Firmicutes and Bacteriodetes. While is considered a preferred and universal source of N to prokaryotes, the majority (> 80%) of N assimilation in our soils could be attributed to a handful of active orders. Characterizing N assimilation of taxonomic groups with 15 N qSIP may provide a basis for understanding how microbial community composition influences N availability in the environment.

Morrissey, Ember M.↗
DOE OSTI2019

Delineating Facies Spatial Distribution by Integrating Ensemble Data Assimilation and Indicator Geostatistics with Level-Set Transformation

The facies-based approach has been widely adopted to delineate an aquifer into distinct geological units with unique distributions of hydraulic, physical, and/or chemical properties. The recent development in ensemble-based data assimilation methods allows both the direct and indirect data to be used to improve facies delineation. A major difficulty in those applications is to honor the spatial continuity and avoid overfitting after data assimilation. We introduce a new facies delineation framework to integrate ensemble data assimilation with traditional transition probability-based geostatistics. A level-set concept is used to parametrize discrete facies indicators and for updating facies shape. During the iterative data assimilation process, we impose spatial continuity by conditioning facies field generation on points selected adaptively based on their sensitivity to observation data. This reconditioning step is a key step to maintain spatial continuity and overcome over-fitting problems in inversion. We selected two examples to evaluate the performance of the new framework in estimating facies-based permeability field. The first example is a two-dimensional synthetic system with transient head data induced by pumping tests used for delineating two facies. The second example is a three-dimensional case with three facies, conceptualized from a field tracer experiment within the Columbia River corridor in Washington State, USA. Both examples demonstrate that the new method can adequately capture the spatial pattern of hydrofacies with reconditioning, which leads to the improved prediction of system behaviors.

Song, Xuehang↗
DOE OSTI2018

A global coupled ensemble data assimilation system using the Community Earth System Model and the Data Assimilation Research Testbed

In this paper, we present a description of the CESM/DART ensemble coupled data assimilation (DA) system based on the Community Earth System Model (CESM) and the Data Assimilation Research Testbed (DART) assimilation software. The CESM/DART should be viewed as a flexible system to support the DA needs of the CESM research community and not as a static reanalysis product. In this implementation of the CESM/DART, conventional insitu observations of the ocean and atmosphere are assimilated into the respective component models of the CESM using a 30-member ensemble adjustment Kalman filter (EAKF). CESM/DART is run in a “weakly coupled” configuration wherein observations native to each climate system component only directly impact the state vector for that component. Information is passed between components indirectly through the short-term coupled model forecasts that provide the EAKF background ensemble. This system leverages previous ensemble DA development for the Community Atmosphere Model and Parallel Ocean Program models using the DART EAKF. The CESM/DART project is a step towards providing increasingly useful DA capabilities for the CESM research community. Results are presented for our prototype 12-year reanalysis, run from 1970 to mid 1982. Multiple lines of evidence demonstrate that the system is capable of constraining the CESM coupled model to simulate the historical variability of the climate system in the well-observed Northern Hemisphere. A collection of monthly average variables, climate mode indices, observation diagnostics and snapshots of synoptic weather in the ocean and atmosphere are compared to established datasets, showing especially good agreement in the Northern Hemisphere. A discussion of the CESM/DART as a modular, community facility and the benefits and challenges associated with this vision is also included.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Soil thermal dynamics, snow cover, and frozen depth under five temperature treatments in an ombrotrophic bog: Constrained forecast with data assimilation: Forecast With Data Assimilation

We report that accurate simulation of soil thermal dynamics is essential for realistic prediction of soil biogeochemical responses to climate change. To facilitate ecological forecasting at the Spruce and Peatland Responses Under Climatic and Environmental change site, we incorporated a soil temperature module into a Terrestrial ECOsystem (TECO) model by accounting for surface energy budget, snow dynamics, and heat transfer among soil layers and during freeze-thaw events. We conditioned TECO with detailed soil temperature and snow depth observations through data assimilation before the model was used for forecasting. The constrained model reproduced variations in observed temperature from different soil layers, the magnitude of snow depth, the timing of snowfall and snowmelt, and the range of frozen depth. The conditioned TECO forecasted probabilistic distributions of soil temperature dynamics in six soil layers, snow, and frozen depths under temperature treatments of +0.0, +2.25, +4.5, +6.75, and +9.0°C. Air warming caused stronger elevation in soil temperature during summer than winter due to winter snow and ice. And soil temperature increased more in shallow soil layers in summer in response to air warming. Whole ecosystem warming (peat + air warmings) generally reduced snow and frozen depths. The accuracy of forecasted snow and frozen depths relied on the precision of weather forcing. Uncertainty is smaller for forecasting soil temperature but large for snow and frozen depths. Lastly, timely and effective soil thermal forecast, constrained through data assimilation that combines process-based understanding and detailed observations, provides boundary conditions for better predictions of future biogeochemical cycles.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Temperature sensitivity of soil organic carbon decomposition increased with mean carbon residence time: Field incubation and data assimilation

Abstract Temperature sensitivity of soil organic carbon ( SOC ) decomposition is one of the major uncertainties in predicting climate‐carbon (C) cycle feedback. Results from previous studies are highly contradictory with old soil C decomposition being more, similarly, or less sensitive to temperature than decomposition of young fractions. The contradictory results are partly from difficulties in distinguishing old from young SOC and their changes over time in the experiments with or without isotopic techniques. In this study, we have conducted a long‐term field incubation experiment with deep soil collars (0–70 cm in depth, 10 cm in diameter of PVC tubes) for excluding root C input to examine apparent temperature sensitivity of SOC decomposition under ambient and warming treatments from 2002 to 2008. The data from the experiment were infused into a multi‐pool soil C model to estimate intrinsic temperature sensitivity of SOC decomposition and C residence times of three SOC fractions (i.e., active, slow, and passive) using a data assimilation ( DA ) technique. As active SOC with the short C residence time was progressively depleted in the deep soil collars under both ambient and warming treatments, the residences times of the whole SOC became longer over time. Concomitantly, the estimated apparent and intrinsic temperature sensitivity of SOC decomposition also became gradually higher over time as more than 50% of active SOC was depleted. Thus, the temperature sensitivity of soil C decomposition in deep soil collars was positively correlated with the mean C residence times. However, the regression slope of the temperature sensitivity against the residence time was lower under the warming treatment than under ambient temperature, indicating that other processes also regulated temperature sensitivity of SOC decomposition. These results indicate that old SOC decomposition is more sensitive to temperature than young components, making the old C more vulnerable to future warmer climate.

Zhou, Xuhui↗
DOE OSTI2021

Assimilation of X-band Phased-Array Radar Data with EnKF for the Analysis and Warning Forecast of a Tornadic storm

The impact of assimilating China's operational X-band Phased-Array radar's (X-PAR) data on the analysis and warning forecast of the vortex structure and intensity of the June 8, 2018 Foshan, Guangdong province, tornadic storm was investigated for the first time using an Ensemble Kalman Filter (EnKF) data assimilation system. Both radar radial velocity (Vr) and reflectivity (Z) from two S-band operational radars and one X-PAR were assimilated. Deterministic forecasts were launched every 6 min from 05:42 UTC (20 min before the tornado touched down) to 06:00 UTC from the EnKF mean analysis field. Five experiments were conducted to examine the added capability of Z assimilation of the EnKF system, and to investigate the impact of assimilating X-PAR data on the analysis and prediction of the tornadic storm. Compared to the experiment without Z assimilation, the assimilation of Z reduced the analysis error and greatly reduced the forecast error of Z. Furthermore, the assimilation of X-PAR data greatly improved the vortex structure of the tornadic storm at low levels, and improved the intensity of the rear inflow of the tornadic storm, especially with a higher assimilation frequency. Compared to the experiments without X-PAR data assimilation, assimilating X-PAR data improved the predictability of tornadic storm.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Estimating surface carbon fluxes based on a local ensemble transform Kalman filter with a short assimilation window and a long observation window: an observing system simulation experiment test in GEOS-Chem 10.1

We developed a carbon data assimilation system to estimate surface carbon fluxes using the local ensemble transform Kalman filter (LETKF) and atmospheric transport model GEOS-Chem driven by the MERRA-1 reanalysis of the meteorological field based on the Goddard Earth Observing System model,version 5 (GEOS-5). This assimilation system is inspired by the method of Kang et al. (2011, 2012), who estimated the surface carbon fluxes in an observing system simulation experiment (OSSE) as evolving parameters in the assimilation of the atmospheric CO 2 , using a short assimilation window of 6 h. They included the assimilation of the standard meteorological variables, so that the ensemble provided a measure of the uncertainty in the CO 2 transport. After proposing new techniques such as “variablelocalization”, and increased observation weights near the surface, they obtained accurate surface carbon fluxes at grid-point resolution. We developed a new version of the local ensemble transform Kalman filter related to the “running-in-place”(RIP) method used to accelerate the spin-up of ensemble Kalman filter (EnKF) data assimilation(Kalnay and Yang, 2010; Wang et al., 2013; Yang et al., 2012). Like RIP, the new assimilation system uses the “no cost smoothing” algorithm for the LETKF (Kalnay et al., 2007b), which allows shifting the Kalman filter solution forward or backward within an assimilation window at no cost. In the new scheme a long “observation window” (e.g., 7 d or longer) is used to design a LETKF ensemble at 7 d. Then, the RIP smoother is used to obtain an accurate final analysis at 1 d. This new approach has the advantage of being based on a short assimilation window, which makes it more accurate,and of having been exposed to the future 7 d observations, which improves the analysis and accelerates the spin-up. The assimilation and observation windows are then shifted forward by 1 d, and the process is repeated.This reduces significantly the analysis error, suggesting that the newly developed assimilation method can be used with other Earth system models,especially in order to make greater use of observations in conjunction with models.

58 GEOSCIENCES↗
DOE OSTI2020

Linking the Dynamic Response of the Carbon Dioxide-Concentrating Mechanism to Carbon Assimilation Behavior in Fremyella diplosiphon

ABSTRACT Cyanobacteria use a carbon dioxide (CO 2 )-concentrating mechanism (CCM) that enhances their carbon fixation efficiency and is regulated by many environmental factors that impact photosynthesis, including carbon availability, light levels, and nutrient access. Efforts to connect the regulation of the CCM by these factors to functional effects on carbon assimilation rates have been complicated by the aqueous nature of cyanobacteria. Here, we describe the use of cyanobacteria in a semiwet state on glass fiber filtration discs—cyanobacterial discs—to establish dynamic carbon assimilation behavior using gas exchange analysis. In combination with quantitative PCR (qPCR) and transmission electron microscopy (TEM) analyses, we linked the regulation of CCM components to corresponding carbon assimilation behavior in the freshwater, filamentous cyanobacterium Fremyella diplosiphon . Inorganic carbon (C i ) levels, light quantity, and light quality have all been shown to influence carbon assimilation behavior in F. diplosiphon . Our results suggest a biphasic model of cyanobacterial carbon fixation. While behavior at low levels of CO 2 is driven mainly by the C i uptake ability of the cyanobacterium, at higher CO 2 levels, carbon assimilation behavior is multifaceted and depends on C i availability, carboxysome morphology, linear electron flow, and cell shape. Carbon response curves (CRCs) generated via gas exchange analysis enable rapid examination of CO 2 assimilation behavior in cyanobacteria and can be used for cells grown under distinct conditions to provide insight into how CO 2 assimilation correlates with the regulation of critical cellular functions, such as the environmental control of the CCM and downstream photosynthetic capacity. IMPORTANCE Environmental regulation of photosynthesis in cyanobacteria enhances organismal fitness, light capture, and associated carbon fixation under dynamic conditions. Concentration of carbon dioxide (CO 2 ) near the carbon-fixing enzyme RubisCO occurs via the CO 2 -concentrating mechanism (CCM). The CCM is also tuned in response to carbon availability, light quality or levels, or nutrient access—cues that also impact photosynthesis. We adapted dynamic gas exchange methods generally used with plants to investigate environmental regulation of the CCM and carbon fixation capacity using glass fiber-filtered cells of the cyanobacterium Fremyella diplosiphon . We describe a breakthrough in measuring real-time carbon uptake and associated assimilation capacity for cells grown in distinct conditions (i.e., light quality, light quantity, or carbon status). These measurements demonstrate that the CCM modulates carbon uptake and assimilation under low-C i conditions and that light-dependent regulation of pigmentation, cell shape, and downstream stages of carbon fixation are critical for tuning carbon uptake and assimilation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Comparing field and lab quantitative stable isotope probing for nitrogen assimilation in soil microbes

ABSTRACT Soil microbial communities play crucial roles in nutrient cycling and can help retain nitrogen in agricultural soils. Quantitative stable isotope probing (qSIP) is a useful method for investigating taxon-specific microbial growth and utilization of specific nutrients, such as nitrogen (N). Typically, qSIP is performed in a highly controlled lab setting, so the field relevance of lab qSIP studies remains unknown. We conducted and compared tandem lab and field qSIP to quantify the assimilation of 15 N by maize-associated soil prokaryotic communities at two agricultural sites. Here, we show that field qSIP with 15 N can be used to measure taxon-specific microbial N assimilation. Relative 15 N assimilation rates were generally lower in the field, and the magnitude of this difference varied by site. Rates differed by method (lab vs field) for 19% of the top N assimilating genera. The field and lab measures were more comparable when relative assimilation rates were weighted by relative abundance to estimate the proportion of N assimilated by each genus with only ~10% of taxa differing by method. Of those that differed, the taxa consistently higher in the lab were inclined to have opportunistic lifestyle strategies, whereas those higher in the field had niches reliant on plant roots or in-tact soil structure (biofilms, mycelia). This study demonstrates that 15 N-qSIP can be successfully performed using field-incubated soils to identify microbial allies in N retention and highlights the strengths and limitations of field and lab qSIP approaches. IMPORTANCE Soil microbes are responsible for critical biogeochemical processes in natural and agricultural ecosystems. Despite their importance, the functional traits of most soil organisms remain woefully under-characterized, limiting our ability to understand how microbial populations influence the transformation of elements such as nitrogen (N) in soil. Quantitative stable isotope probing (qSIP) is a powerful tool to measure the traits of individual taxa. This method has rarely been applied in the field or with 15 N to measure nitrogen assimilation. In this study, we measured genus-specific microbial nitrogen assimilation in two agricultural soils and compared field and lab 15 N qSIP methods. Our results identify taxa important for nitrogen assimilation in agricultural soils, shed light on the field relevance of lab qSIP studies, and provide guidance for the future application of qSIP to measure microbial traits in the field.

Reed, Kinsey (ORCID:0000000155178664)↗
DOE OSTI2022

The intermediate in a nitrate-responsive ω-amidase pathway in plants may signal ammonium assimilation status

Abstract A metabolite of ammonium assimilation was previously theorized to be involved in the coordination of the overall nitrate response in plants. Here we show that 2-hydroxy-5-oxoproline, made by transamination of glutamine, the first product of ammonium assimilation, may be involved in signaling a plant’s ammonium assimilation status. In leaves, 2-hydroxy-5-oxoproline met four foundational requirements to be such a signal. First, when it was applied to foliage, enzyme activities of nitrate reduction and ammonium assimilation increased; the activities of key tricarboxylic acid cycle-associated enzymes that help to supply carbon skeletons for amino acid synthesis also increased. Second, its leaf pools increased as nitrate availability increased. Third, the pool size of its precursor, Gln, reflected ammonium assimilation rather than photorespiration. Fourth, it was widely conserved among monocots, dicots, legumes, and nonlegumes and in plants with C3 or C4 metabolism. Made directly from the first product of ammonium assimilation, 2-hydroxy-5-oxoproline acted as a nitrate uptake stimulant. When 2-hydroxy-5-oxoproline was provided to roots, the plant’s nitrate uptake rate approximately doubled. Plants exogenously provided with 2-hydroxy-5-oxoproline to either roots or leaves accumulated greater biomass. A model was constructed that included the proposed roles of 2-hydroxy-5-oxoproline as a signal molecule of ammonium assimilation status in leaves, as a stimulator of nitrate uptake by roots and nitrate downloading from the xylem. In summary, a glutamine metabolite made in the ω-amidase pathway stimulated nitrate uptake by roots and was likely to be a signal of ammonium assimilation status in leaves. A chemical synthesis method for 2-hydroxy-5-oxoproline was also developed.

59 BASIC BIOLOGICAL SCIENCES↗
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↗
DOE OSTI2024

The 4DEnVar-based weakly coupled land data assimilation system for E3SM version 2

Abstract. A new weakly coupled land data assimilation (WCLDA) system based on the four-dimensional ensemble variational (4DEnVar) method is developed and applied to the fully coupled Energy Exascale Earth System Model version 2 (E3SMv2). The dimension-reduced projection four-dimensional variational (DRP-4DVar) method is employed to implement 4DVar using the ensemble technique instead of the adjoint technique. With an interest in providing initial conditions for decadal climate predictions, monthly mean anomalies of soil moisture and temperature from the Global Land Data Assimilation System (GLDAS) reanalysis from 1980 to 2016 are assimilated into the land component of E3SMv2 within the coupled modeling framework with a 1-month assimilation window. The coupled assimilation experiment is evaluated using multiple metrics, including the cost function, assimilation efficiency index, correlation, root-mean-square error (RMSE), and bias, and compared with a control simulation without land data assimilation. The WCLDA system yields improved simulation of soil moisture and temperature compared with the control simulation, with improvements found throughout the soil layers and in many regions of the global land. In terms of both soil moisture and temperature, the assimilation experiment outperforms the control simulation with reduced RMSE and higher temporal correlation in many regions, especially in South America, central Africa, Australia, and large parts of Eurasia. Furthermore, significant improvements are also found in reproducing the time evolution of the 2012 US Midwest drought, highlighting the crucial role of land surface in drought lifecycle. The WCLDA system is intended to be a foundational resource for research to investigate land-derived climate predictability.

58 GEOSCIENCES↗
DOE OSTI2023

Improving Tropical Cyclogenesis Forecasts of Hurricane Irma (2017) through the Assimilation of All-Sky Infrared Brightness Temperatures

The assimilation of satellite all-sky infrared (IR) brightness temperatures (BTs) has been shown in previous studies to improve intensity forecasts of tropical cyclones. Here, in this study, we examine whether assimilating all-sky IR BTs can also potentially improve tropical cyclogenesis forecasts by improving the pregenesis cloud and moisture fields. By using an ensemble-based data assimilation system, we show that the assimilation of upper-tropospheric water vapor channel BTs observed by the Meteosat-10 SEVIRI instrument two days before the formation of a tropical depression improves the genesis forecast of Hurricane Irma (2017), a classic Cape Verde storm, by up to 24 h while also capturing its later rapid intensification in deterministic forecasts. In an experiment that withholds the assimilation of all-sky IR BTs, the assimilation of conventional observations from the Global Telecommunications System (GTS) leads to the premature genesis of Hurricane Irma by at least 24 h. This premature genesis is shown to result from an overestimation of the spatial coverage of deep convection within the African easterly wave (AEW) from which Irma eventually forms. The gross overestimation of deep convection without all-sky IR BTs is accompanied by higher column saturation fraction, stronger low-level convergence, and the earlier spinup of a low-level meso- β -scale vortex within the AEW that ultimately becomes Hurricane Irma. Through its adjustment to the initial moisture and cloud conditions, the assimilation of all-sky IR BTs leads to a more realistic convective evolution in forecasts and ultimately a more realistic timing of genesis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Potential Impacts of Assimilating All-sky Satellite Infrared Radiances on Convection-Permitting Analysis and Prediction of Tropical Convection

Geostationary infrared satellite observations are spatially dense [< 1/(20 km)2] and temporally frequent (< 1/hour). These suggest the possibility of using these observations to constrain sub-synoptic features over data sparse regions, such as tropical oceans. In this study, the potential impacts of assimilating water vapor channel brightness temperature (WV-BT) observations from the geostationary Meteorological Satellite 7 (Meteosat-7) on tropical convection analysis and prediction were systematically examined through a series of ensemble data assimilation experiments. WV-BT observations were assimilated hourly into convection-permitting ensembles using Penn State’s ensemble square root filter (EnSRF). Comparisons against independently observed Meteosat-7 window channel brightness temperature (Window-BT) show that the assimilation of WV-BT generally improved the intensities and locations of large-scale cloud patterns at spatial scales larger than 100 km. However, comparisons against independent soundings indicate that the EnSRF analysis produced a much stronger dry bias than the no data assimilation experiment. This strong dry bias is associated with the use of the simulated WV-BT from the prior mean during the EnSRF analysis step. A stochastic variant of the ensemble Kalman filter (NoMeanSF) is proposed. The NoMeanSF algorithm was able to assimilate the WV-BT without causing such a strong dry bias and the quality of the analyses’ horizontal cloud pattern is similar to EnSRF’s analyses. Finally, deterministic forecasts initiated from the NoMeanSF analyses possess better horizontal cloud patterns above 500 km than those of the EnSRF. These results suggest that it might be better to assimilate all-sky WV-BT through the NoMeanSF algorithm than EnSRF algorithm.

Chan, Man-Yau↗