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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Soil resistance and recovery during neotropical forest succession

The recovery of soil conditions is crucial for successful ecosystem restoration and, hence, for achieving the goals of the UN Decade on Ecosystem Restoration. Here, we assess how soils resist forest conversion and agricultural land use, and how soils recover during subsequent tropical forest succession on abandoned agricultural fields. Our overarching question is how soil resistance and recovery depend on local conditions such as climate, soil type and land-use history. For 300 plots in 21 sites across the Neotropics, we used a chronosequence approach in which we sampled soils from two depths in old-growth forests, agricultural fields (i.e. crop fields and pastures), and secondary forests that differ in age (1–95 years) since abandonment. We measured six soil properties using a standardized sampling design and laboratory analyses. Soil resistance strongly depended on local conditions. Croplands and sites on high-activity clay (i.e. high fertility) show strong increases in bulk density and decreases in pH, carbon (C) and nitrogen (N) during deforestation and subsequent agricultural use. Resistance is lower in such sites probably because of a sharp decline in fine root biomass in croplands in the upper soil layers, and a decline in litter input from formerly productive old-growth forest (on high-activity clays). Soil recovery also strongly depended on local conditions. During forest succession, high-activity clays and croplands decreased most strongly in bulk density and increased in C and N, possibly because of strongly compacted soils with low C and N after cropland abandonment, and because of rapid vegetation recovery in high-activity clays leading to greater fine root growth and litter input. Furthermore, sites at low precipitation decreased in pH, whereas sites at high precipitation increased in N and decreased in C : N ratio. Extractable phosphorus (P) did not recover during succession, suggesting increased P limitation as forests age. These results indicate that no single solution exists for effective soil restoration and that local site conditions should determine the restoration strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Effects of fine-root senescence upon soil communities and nutrient flux into soil pools (Final Report)

Fine roots represent an important flux of carbon into terrestrial soils. Much of this flux occurs through the exudation of polysaccharides and other carbon compounds during the lifetime of fine-roots, but little is known about their contributions to flux as roots senesce, die and decompose. This project was designed 1) to test approaches for inducing senescence in fine roots and 2) assess the effects of the treatments on fine roots and the associated rhizosphere community. We implemented two fine-root treatments, a steam girdling approach and full severing of fine root modules from the tree, and we contrasted them with a control where roots were handled but not girdled. Fine roots and their associated community subjected to each of these three treatments were subsequently analyzed for changes in physical structure, nutrient content, community structure and gene function. Both girdling manipulations resulted in tissue disruption in fine roots and changes in the soil community relative to controls. In particular, microbial diversity for most taxa declined in girdled treatments whereas fungal diversity increased. We also observed changes in overall plant and fungal gene expression associated with treatment with plant gene expression declining over time in girdled roots with a simultaneous increase in fungal gene expression in these same treatments. Finally, in girdled fine root modules, we observed changes in gene function associated with senescence and plant stress in pine-associated genes while at the same time observing upregulation of genes associated with growth and proliferation in fungi. In conclusion, we were able to successfully girdle fine-roots in a field setting and resolve plant-level and community level changes in response to these girdling treatments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data from a throughfall exclusion experiment: Fine root dynamics, morphology, chemistry, and AMF colonization across four lowland Panamanian forests

Fine roots regulate forest nutrient, carbon, and water cycling, yet their variation within and among tropical forests remains under-characterized. We quantified root productivity, disappearance, and stocks to 1 m using minirhizotron imaging, and we measured morphology, elemental composition [root carbon (C), root nitrogen (N), root phosphorus (P)], and arbuscular mycorrhizal fungi (AMF) colonization to 20 cm using ingrowth cores and sequential coring. Sampling took place in four distinct lowland Panamanian forests (32 plots; 8 per forest) from 2018 through 2022 under control and throughfall-exclusion (drought) treatments in the Panama Rainforest Changes with Experimental Drying (PARCHED) experiment.The dataset is presented as an Excel workbook with six tabs. The first tab is the data dictionary. Tab S1 contains ingrowth-core production and mortality, morphology and soil moisture. Tab S2 contains sequential-coring standing stocks with associated morphology and soil moisture. Tab S3 contains minirhizotron row data records to 1 m depth, including per-frame root length and diameter, normalized length metrics, and session timing. Tab S4 contains AMF colonization. Tab S5 contains fine-root chemistry at 0–10 cm, reporting %P, %C, %N, and C:N for samples collected via ingrowth cores and sequential-coring standing stocks. CSV mirrors for each tab are provided, and a KML file supplies coordinates for all 32 plots.Key variables span live and dead fine-root biomass (and coarse fractions where applicable), specific root length (SRL) and area (SRA), diameter, root tissue density (RTD), soil moisture, AMF colonization, root %N, %C, %P, and C:N, along with minirhizotron root length and diameter. Depth, season, treatment, and plot/site identifiers are included to support cross-tab integration and analysis from 0–100 cm (minirhizotron) and 0–20 cm (cores).Units are reported in-column and missing values are coded as NA. No special software is required to open or use the files (Excel, CSV, and KML compatible).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Temporal patterns of fine‐root dynamics have little influence on seasonal soil CO 2 efflux in a mixed, mesic forest

Among the contributors to soil CO 2 efflux, there remains uncertainty about the contribution of root activity to the overall soil efflux. Soil water and temperature frequently have been used to predict a large portion of the variation in soil CO 2 efflux. We hypothesized that fine-root dynamics explain most of the remaining variability in soil CO 2 efflux that cannot be explained by soil temperature and water content. We anticipated that seasonal increases in root production, mortality via decomposition, and standing crop would result in corresponding increases in soil CO 2 efflux. We tested our hypotheses by collecting and analyzing two years of minirhizotron and soil chamber CO 2 flux data from plots distributed throughout the Shale Hills Catchment of the Susquehanna-Shale Hills Critical Zone Observatory in Central Pennsylvania, USA. Here we showed that: (1) seasonal fluctuations in fine-root dynamics yielded only a very small increase in the predictability of soil CO 2 efflux; (2) fine-root mortality effects on soil CO 2 efflux were strongly tied to soil temperature; (3) fluctuations in fine-root presence or standing mass independent of temperature and moisture had little effect on soil CO 2 efflux; and (4) new fine-root length and root length mortality had limited impacts on soil CO 2 efflux rates. We conclude that, at least in temperate forests on rocky soils, characterizing fine-root dynamics may provide only limited improvement in the estimation of soil CO 2 efflux.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2020

Synergistic Use of SMAP and OCO-2 Data in Assessing the Responses of Ecosystem Productivity to the 2018 U.S. Drought

Soil moisture and gross primary productivity (GPP) estimates from the Soil Moisture Active Passive (SMAP) and solar-induced chlorophyll fluorescence (SIF) from the Orbiting Carbon Observatory-2 (OCO-2) provide new opportunities for understanding the relationship between soil moisture and terrestrial photosynthesis over large regions. Here we explored the potential of the synergistic use of SMAP and OCO-2 based data for monitoring the responses of ecosystem productivity to drought. We used complementary observational information on root-zone soil moisture and GPP (9 km) from SMAP and fine-resolution SIF (0.05°; GOSIF) derived from OCO-2 SIF soundings. We compared the spatial pattern and temporal evolution of anomalies of these variables over the conterminous U.S. during the 2018 drought, and examined to what extent they could characterize the drought-induced variations of flux tower GPP and crop yield data. Our results showed that SMAP GPP and GOSIF could well capture the spatial extent and dynamics of drought indicated by the U.S. Drought Monitor maps and the SMAP root-zone soil moisture deficit. Over the U.S. Southwest, monthly anomalies of soil moisture showed significant positive correlations with those of SMAP GPP (R2=0.44, p<0.001) and GOSIF (R2=0.76, p<0.001), demonstrating strong water availability constraints on plant productivity across dryland ecosystems. We further found that SMAP GPP and GOSIF captured the impact of drought on tower GPP and crop yield. Our results suggest that synergistic use of SMAP and OCO-2 data products can reveal the drought evolution and its impact on ecosystem productivity and carbon uptake at multiple spatial and temporal scales, and demonstrate the value of SMAP and OCO-2 for studying ecosystem function, carbon cycling, and climate change.

Soil Moisture Active Passive↗
NASA NTRS2021

Extensive Characterization of Aerosol Optical Properties and Chemical Component Concentrations: Application of the GRASP/Component Approach to Long-term AERONET Measurements

A recently developed GRASP/Component approach (GRASP: Generalized Retrieval of Atmosphere and Surface Properties) was applied to AERONET (Aeronet Robotic Network) sun photometer measurements in this study. Unlike traditional aerosol component retrieval, this approach allows the inference of some information about aerosol composition directly from measured radiance, rather than indirectly through the inversion of optical parameters, and has been integrated into the GRASP algorithm. The newly developed GRASP/Component approach was applied to 13 AERONET sites for different aerosol types under the assumption of aerosol internal mixing rules to analyze the characteristics of aerosol components and their distribution patterns. The results indicate that the retrievals can characterize well the spatial and temporal variability of the component concentration for different aerosol types. A reasonable agreement between GRASP BC retrievals and MERRA-2 BC products is found for all different aerosol types. In addition, the relationships between aerosol component content and aerosol optical parameters such as aerosol optical depth (AOD), fine-mode fraction (FMF), absorption Ångström exponent (AAE), scattering Ångström exponent (SAE), and single scattering albedo (SSA) are also analyzed for indirect verifying the reliability of the component retrieval. It was demonstrated the GRASP/Component optical retrievals are in good agreement with AERONET standard products [e.g., correlation coefficient (R) of 0.93–1.0 for AOD, fine-mode AOD (AODF), coarse-mode AOD (AODC) and Ångström exponent (AE); R = ~ 0.8 for absorption AOD (AAOD) and SSA; RMSE (root mean square error) < 0.03 for AOD, AODF, AODC, AAOD and SSA]. Thus, it is demonstrated the GRASP/Component approach can provide aerosol optical products with comparable accuracy as the AERONET standard products from the ground-based sun photometer measurements as well as some additional important inside on aerosol composition.

Xindan Zhang↗
DOE OSTI2021

Influence of shrub willow buffers strategically integrated in an Illinois corn-soybean field on soil health and microbial community composition

We report soil serves many important ecological functions and is an integral part of our existence as a society. However, concerns for soil health are growing globally, in part due to the negative impacts of agricultural management on soil resources. The production of perennial bioenergy crops on marginal land in row-crop production systems is one solution that could improve land-use efficiency and address the sustainability of cropland management. Because the relationship between crop management and the environment is complex, more research is needed to evaluate the potential benefits perennial bioenergy crop production has on soil health, as well as other ecosystem services. In this study, shrub willow buffers were strategically integrated into a corn-soybean cropping system with the main objective of reducing nitrate-N leaching from grain crop production while producing biomass for bioenergy. Two buffer systems (defined by landscape positions) were included for comparison, one on marginal land with exposure to nitrate-N leaching from upslope grain (southern plots) and one on fertile soils with less nitrate-N leaching potential (northern plots). Evaluation of soil (chemistry, bulk density, microbial community) and shrub willow vegetation properties ( fine roots, leaf litter decomposition, and nutrient uptake dynamics), showed that landscape position plays an important role in (1) the dynamics of soil chemical properties, (2) shrub willow's influence and productivity, and (3) the provision of additional ecosystem services such as reductions in nitrous oxide emissions and nitrate-N leaching. In addition, the combination of crop type and landscape position (N-grain, N-willow, S-grain, and S-willow) influenced the species composition of the soil microbial community, resulting in unique and identifiable communities. These results highlight the potential application of shrub willow buffers for ecosystem service provision and support of ecosystem processes; however, understanding the relationship between the microbial community, crop type, and landscape is important for understanding the sustainability of the design.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

ACORN Review: NPK fertilizer use in loblolly pine plantations: Who are we really feeding?

Optimizing loblolly pine (Pinus taeda L.) productivity using fertilizers and various site management practices has been a goal of foresters for decades. Nitrogen (N), phosphorus (P), and potassium (K) are the three most operationally applied fertilizers to loblolly pine silviculture and are of primary importance to their total productivity. Fertilizer recommendations for N, P, and K in loblolly pine are primarily made on abiotic factors such as site and soil characteristics, while the biological factors controlling nutrient uptake are typically overlooked in the production and optimization of these stands. Arguably the most important of these biological factors are the diverse ectomycorrhizal fungal (ECM) communities that colonize the fine roots of almost all loblolly pine trees. The mantle formed by ECM fungi on short-root tips presents a barrier for direct apoplastic uptake of N, P, and K from soil solution by pine roots. In well-colonized roots, the tree is dependent on symplastic fungal transport of N, P, and K foraged from the soil by the extraradical hyphal network. This raises the question: Who are we really feeding if the ECM fungi are the ones assimilating most of the tree's total nutritional requirements? Considering multiple species of ECM fungi can inhabit a single root system, many questions remain regarding the drivers of colonization, why some species are more efficient at taking up and exchanging nutrients with their hosts than others, and why certain fertilizers directly affect the morphology of ECM growth. The purposes of this review here are (1) to explore how the most commonly commercially applied macronutrients, N, P, and K, affect the relationship between loblolly pine and ECM communities, and (2) to propose future directions to investigate, preserve, and manipulate these interactions in pine plantations to optimize productivity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Shifts in belowground processes along a temperate forest edge

Abstract Context Forests are increasingly fragmented, and as a result most forests in the United States are within one km of an edge. Edges change environmental conditions of the forest—especially radiation, roughness, temperature, and moisture—that can have consequences for plant productivity and ecosystem functions. However, edge effects on aboveground characteristics of plants and the environment are better understood relative to plant roots and soil in the belowground environment. Objectives Our main objectives were to determine if soil C pools and fluxes are higher at the edge relative to other landscape positions, and to understand how specific belowground processes contribute to bulk differences in pools and fluxes. Methods We measured environmental conditions, live and dead fine root traits, soil chemistry, and soil respiration along a 75 m transect from interior forest to meadow in Gaithersburg, MD. Results We observed differences in the soil chemical, biological and hydrological environment between the forest interior, edge and adjacent meadow. In some cases, the forest edge represented a mid-point in environmental or belowground characteristics between the forest interior and meadow ( e.g. , pH, C-to-N ratio [C:N], live fine root biomass, heterotrophic respiration), likely reflecting the change in litter type and quality associated with the transition from grass to woody species. In other cases, neighboring landscape positions were different from the forest edge, which was drier and had higher dead fine root biomass. Although soil C contents were not significantly different across landscape positions, there was a tendency towards higher average soil C content at the edge relative to other landscape positions, suggesting that increased C loss related to root decay and greater soil respiration at the edge relative to the forest interior may have been offset by increased C gain from high plant productivity and subsequent inputs to soil. Conclusions This research provides insight into how forest edge environments may differ from the interior and how concurrent processes above- and belowground may contribute to those differences.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Overlooked branch turnover creates a widespread bias in forest carbon accounting

Most measurements and models of forest carbon cycling neglect the carbon flux associated with the turnover of branch biomass, a physiological process quantified for other organs (fine roots, leaves, and stems). Synthesizing data from boreal, temperate, and tropical forests (184,815 trees), we found that including branch turnover increased empirical estimates of aboveground wood production by 16% (equivalent to 1.9 Pg Cy −1 globally), of similar magnitude to the observed global forest carbon sinks. In addition, reallocating carbon to branch turnover in model simulations reduced stem wood biomass, a long-lasting carbon storage, by 7 to 17%. This prevailing neglect of branch turnover suggests widespread biases in carbon flux estimates across global datasets and model simulations. Branch litterfall, sometimes used as a proxy for branch turnover, ignores carbon lost from attached dead branches, underestimating branch C turnover by 38% in a pine forest. Modifications to field measurement protocols and existing models are needed to allow a more realistic partitioning of wood production and forest carbon storage.

Lim, Hyungwoo↗
NASA NTRS1994

Effect of land use change on the carbon cycle in Amazon soils

The overall goal of this study was to provide a quantitative understanding of the cycling of carbon in the soils associated with deep-rooting Amazon forests. In particular, we wished to apply the understanding gained by answering two questions: (1) what changes will accompany the major land use change in this region, the conversion of forest to pasture? and (2) what is the role of carbon stored deeper than one meter in depth in these soils? To construct carbon budgets for pasture and forest soils we combined the following: measurements of carbon stocks in above-ground vegetation, root biomass, detritus, and soil organic matter; rates of carbon inputs to soil and detrital layers using litterfall collection and sequential coring to estimate fine root turnover; C-14 analyses of fractionated SOM and soil CO2 to estimate residence times; C-13 analyses to estimate C inputs to pasture soils from C-4 grasses; soil pCO2, volumetric water content, and radon gradients to estimate CO2 production as a function of soil depth; soil respiration to estimate total C outputs; and a model of soil C dynamics that defines SOM fractions cycling on annual, decadal, and millennial time scales.

Trumbore, Susan E.↗
DOE OSTI2020

Modeling the Effects of Global Change on Ecosystem Processes in a Tropical Rainforest

Ongoing land-use change and climate change in wet tropical forests can potentially drive shifts in tree species composition, representing a change in individual species within a functional group, tropical evergreen trees. The impacts on the global carbon cycle are potentially large, but unclear. We explored the differential effects of species within this functional group, in comparison with the effects of climate change, using the Century model as a research tool. Simulating effects of individual tree species on biome-level biogeochemical cycles constituted a novel application for Century. Background and Objectives: A unique, long-term, replicated field experiment containing five evergreen tree species in monodominant stands under similar environmental conditions in a Costa Rican wet forest provided data for model evaluation. Our objectives were to gain insights about this forest’s biogeochemical cycles and effects of tree species within this functional group, in comparison with climate change. Materials and Methods: We calibrated Century, using long-term meteorological, soil, and plant data from the field-based experiment. In modeling experiments, we evaluated effects on forest biogeochemistry of eight plant traits that were both observed and modeled. Climate-change simulation experiments represented two climate-change aspects observed in this region. Results: Model calibration revealed that unmodeled soil processes would be required to sustain observed P budgets. In species-traits experiments, three separate plant traits (leaf death rate, leaf C:N, and allocation to fine roots) resulted in modeled biomass C stock changes of >50%, compared with a maximum 21% change in the climate-change experiments. Conclusions: Modeled ecosystem properties and processes in Century were sensitive to changes in plant traits and nutrient limitations to productivity. Realistic model output was attainable for some species, but unusual plant traits thwarted predictions for one species. Including more plant traits and soil processes could increase realism, but less-complex models provide an accessible means for exploring plant-soil-atmosphere interactions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Estimating Fine-Resolution Shortwave Broadband Albedo of Croplands from Harmonized Landsat and Sentinel-2 Data

Altered surface albedo due to land-cover conversions and management is a significant driver of global climate change. Albedo can be directly measured at ground stations, and remote sensing data can be used to scale-up albedo values to regional and global levels. Some previous studies have retrieved fine-resolution (10–30 m) instantaneous albedo and coarse-resolution (500–1000 m) daily mean albedo from remote sensing data, but they all required the input of Moderate Resolution Imaging Spectroradiometer (MODIS) albedo information at 500-m resolution, and none have assembled both instantaneous and daily albedo based exclusively on fine-resolution satellite data. Here, to address this issue, we compiled 387 instantaneous and 346 daily albedo records using field net radiometer measurements from the bioenergy croplands at the W. K. Kellogg Biological Station in southwest Michigan. We then connected these albedo records with a suite of variables derived from harmonized Landsat and Sentinel-2 data through two machine learning algorithms (random forest regression and extreme gradient boosting) to retrieve clear-sky instantaneous and daily shortwave broadband albedo. The performance statistics indicate reasonable accuracy of model results [root-mean-square error (RMSE)] around or below 0.03 except for snow-covered surfaces), suggesting that the retrieval of both instantaneous and daily albedo based exclusively on fine-resolution satellite data is promising. To facilitate the use of fine-resolution albedo products at the global level, future efforts need to include more albedo records of diverse surface cover types, as well as to accurately model daily albedo for cloudy days to address the “clear-sky bias.”

Harmonized Landsat and Sentinel-2↗
DOE OSTI2025

SPRUCE Root Production Assessed with Manual Minirhizotrons Resolved to Plant Functional Type, 2015-2021

This dataset contains raw root length and diameter for individual roots and estimated root population production measurements from the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental site within the Marcell Experimental Forest in northern Minnesota, USA. Measurements started at the beginning of whole ecosystem warming manipulations in 2015 through 2021 (2015-05-26 to 2021-09-01). Root morphology and estimated production were quantified throughout the peat profile with manual minirhizotrons deployed within SPRUCE plots. Images were processed using commercial software to quantify the length and diameter of individual roots. Roots were visually assigned to a plant functional type (PFT) of either (ericaceous) shrub, herb (sedges and Maianthemum trifolium), or tree (Larix laricina, Picea mariana) based on expert opinion. The biomass of individual roots was estimated using PFT-specific allometric equations (Iversen et al., 2018). Production per day was estimated as the length of new roots produced between imaging sessions, divided by the number of days between imaging sessions. These values were placed on a m2 aboveground area basis and scaled to a standard depth of 1m (roots are not evenly distributed with depth, do not interpret value as being on a m3 basis). Maximum and average (weighted by production length) depth of each PFT were also estimated within each minirhizotron tube. Annual production was interpolated as the average of four methods to scale these data (see Weber et al, 2026). Standing crop of roots was estimated for each tube as the maximum visible amount (both length and mass) of roots of that PFT for that year. These data expand the ability of researchers to accurately estimate the belowground dynamics of peatland vegetation, as well as the role that fine roots may play in impacting the fluxes of carbon within peatlands. This dataset contains three data files in comma-separate values (*.csv) format. This dataset contains one data file in comma-separate values (.csv) format. Additional metadata are provided: three data dictionaries and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2001

Implementing a Nitrogen-Based Model for Autotrophic Respiration Using Satellite and Field Observations

The rate of carbon accumulation by terrestrial plant communities in a process-level, mechanistic modeling is the difference of the rate of gross photosynthesis by a canopy (A(sub g)) and autotrophic respiration (R) of the stand. Observations for different biomes often show that R to be a large and variable fraction of A(sub g), ca. 35% to 75%, although other studies suggest the ratio of R and A(sub g) to be less variable. Here, R has been calculated according to the two compartment model as being the sum of maintenance and growth components. The maintenance respiration of foliage and living fine roots for different biomes has been determined objectively from observed nitrogen content of these organs. The sapwood maintenance respiration is based on pipe theory, and checked against an independently derived equation considering sapwood biomass and its maintenance coefficient. The growth respiration has been calculated from the difference of A(sub g) and maintenance respiration. The A(sub g) is obtained as the product of biome-specific radiation use efficiency for gross photosynthesis under unstressed conditions and intercepted photosynthetically active radiation, and adjusted for stress. Calculations have been done using satellite and ground observations for 36 consecutive months (1987-1989) over large contiguous areas (ca. 10(exp 5) sq km) of boreal forests, crop land, temperate deciduous forest, temperate grassland, tropical deciduous forest, tropical evergreen forest, tropical savanna, and tundra. The ratio of annual respiration and gross photosynthesis, (R/A(sub g)), is found to be 0.5-0.6 for temperate and cold adopted biome areas, but somewhat higher for tropical biome areas (0.6-0.7). Interannual variation of the fluxes is found to be generally less than 15%. Calculated fluxes are compared with observations and several previous estimates. Results of sensitivity analysis are presented for uncertainties in parameterization and input data. It is found that uncertainty in determining maintenance respiration for tropical biomes is such that R/A(sub g) for these biomes could be similar to that for temperate biomes.

Choudhury, Bhaskar J.↗
DOE OSTI2022

N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon

Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25–30 plants h -1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH 4 NO 3 the benefit appears through N fixation, while at 0.5 mM NH 4 NO 3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An ML-based terrestrial data fusion and augmentation framework to enable advanced understanding of the terrestrial carbon and water interactions

Soil moisture is essential to the terrestrial carbon and water cycles and land–atmosphere interactions. There are various types of soil moisture data, and each type has the distinct spatiotemporal strengths and limitations, depending on the diverse applications and retrieval methodologies of different data types (Li et al., in review; The PNNL-82151 FY23 Report). However, the limitations of different soil moisture data in terms of accuracy and spatiotemporal coverage hinder our ability to further understand the soil moisture dynamics across scales. To have a gap free soil moisture data product with a fine spatiotemporal coverage and vertical profiles, we train extreme gradient boosting (XGBoost) models by using (1) in-situ soil moisture measurements from the International Soil Moisture Network (ISMN), (2) soil moisture from the ECMWF reanalysis (ERA) at the 9 km and sub-daily spatiotemporal resolution, (3) the Daymet meteorological fields, and (4) data products that characterize surface conditions, including soil texture, organic content, topography, vegetation type, and rooting depth. We use the trained XGBoost models that have consistent performance across seven soil layers, i.e., 0–5 cm, 5–10 cm, 10–20 cm, 20–40 cm, 40–60 cm, 60–100 cm, and 100–200 cm, and the gridded model predictors to generate a soil moisture data at the 1 km and daily spatiotemporal resolution for the Continental United States (CONUS) from 2001–2020. This dataset can be broadly used for Earth system model benchmark, monitoring extreme weathers, making informed decisions regarding agriculture, water resource management, climate change mitigation, and ecosystem preservation.

58 GEOSCIENCES↗
DOE OSTI2021

SYMBIOSYS: A Methodology for Performance Analysis of Composable HPC Data Services

Microservices are a powerful new way of building, customizing, and deploying distributed services owing to their flexibility and maintainability. Several large-scale distributed platforms have emerged to serve the growing needs of data-centric workloads and services in commercial computing. Concurrently, high-performance computing (HPC) systems and software are rapidly evolving to meet the demands of diversified applications and heterogeneity. The interplay of hardware factors, software configuration parameters, and the flexibility offered with a microservice architecture makes it nontrivial to estimate the optimal service instantiation for a given application workload. Further, this problem is exacerbated when considering that these services operate in a dynamic and heterogeneous HPC environment. An optimally integrated service can be vastly more performant than a haphazardly integrated one. Existing performance tools for HPC either fail to understand the request-response model of communication inherent to microservices or they operate within a narrow scope, limiting the insight that can be gleaned from employing them in isolation. We propose a methodology for integrated performance analysis of HPC microservices frameworks and applications called SYMBIOSYS. We describe its design and implementation within the context of the Mochi framework. This integration is achieved by combining distributed callpath profiling and tracing with a performance data exchange strategy that collects fine-grained, low-level metrics from the RPC communication library and network layers. The result is a portable, low-overhead performance analysis setup that provides a holistic profile of the dependencies among microservices and how they interact with the Mochi RPC software stack. Using HEPnOS, a production-quality Mochi data service, we demonstrate the low-overhead operation of SYMBIOSYS at scale and use it to identify the root causes of poorly performing service configurations.

microservices↗