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DOE OSTI2022

Fungal necromass presents a high potential for Mercury immobilization in soil

Past industrial activities have generated many contaminated lands from which Mercury (Hg) escapes, primarily by volatilization. Current phytomanagement techniques aim to limit Hg dispersion by increasing its stabilization in soil. Although soil fungi represent a source of Hg emission associated with biovolatilization mechanisms, there is limited knowledge about how dead fungal residues (i.e., fungal necromass) interact with soil Hg. This study determined the Hg biosorption potential of fungal necromass and the chemical drivers of passive Hg binding with dead mycelia. Fungal necromass was incubated under field conditions with contrasting chemical properties at a well-characterized Hg phytomanagement experimental site in France. After four months of incubation in soil, fungal residues passively accumulated substantial quantities of Hg in their recalcitrant fractions ranging from 400 to 4500 μg Hg/kg. In addition, infrared spectroscopy revealed that lipid compounds explained the amount of Hg biosorption to fungal necromass. In conclusion, based on these findings, we propose that fungal necromass is likely an important factor in Hg immobilization in soil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Partitioning sources of CO 2 emission after soil wetting using high-resolution observations and minimal models

Wetting dry soil triggers a pulse of microbial respiration. Respiration pulses after wetting can be complex, evolving through several stages before subsiding—possibly reflecting contributions from multiple carbon (C) sources. In this work we hypothesized that respiration after wetting combines C from cellular sources (notably trehalose, a cellular osmo-protectant) and soluble extracellular C made available by the physical effects of wetting, with cellular sources contributing early during the pulse and extracellular C dominating later. We tested this hypothesis by making measurements of soil respiration, microbial biomass, trehalose, and water extractable organic C after wetting dry soil in the laboratory. We then devised several alternative minimal models to evaluate the potential contributions of trehalose and extracellular C to the respiration pulse. We found that the chloroform-labile fraction of the microbial biomass was comprised of 50% trehalose in dry soil. Both trehalose and water extractable organic C pools declined rapidly after wetting; trehalose disappeared within 3 h of water addition. Chloroform-labile glucose increased 3 h after water addition and then declined, suggesting rapid hydrolysis of trehalose and consumption of the resulting glucose. Respiration dynamics after wetting could be best explained by models that included two C sources, combining rapid metabolism of trehalose with slower consumption of extracellular soluble C. These results suggest that pulses of respiration after wetting reflect both osmolyte consumption within the microbial biomass and enhanced extracellular C availability; hence, models of microbial drought response must account for both processes to fully resolve soil C dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Meeting report: International soil virus conference 2024

The research field of soil viral ecology continues to advance rapidly as the roles of viruses in the functioning of soil ecosystems are increasingly recognized. To address recent developments in the field, the second International Soil Virus Conference was held in Livermore, California, USA, from June 25 to 27th, 2024, providing soil viral ecologists the opportunity to share new findings and suggest guidelines for future research, while encouraging international scientific discussion and collaboration. The meeting was held in person with sessions simultaneously streamed online. Fifty researchers attended from ten different countries and spanned a wide range of subfields and career stages. A total of 21 oral presentations were presented, followed by discussions covering key themes in soil viral research. This report summarizes the main takeaways and recommendations from the talks and discussions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A data-driven global soil heterotrophic respiration dataset and the drivers of its inter-annual variability

Soil heterotrophic respiration (SHR), one of the primary carbon fluxes from terrestrial ecosystems to the atmosphere, is important for carbon-climate feedbacks because of its sensitivity to available litter and soil carbon, climatic conditions, and nutrient availability. However, until recently limited SHR data were available, and most published global SHR estimates have either a short time span, coarse spatial resolution, or reply on overly-simple model formulations. To better understand and quantify the global distribution of SHR and its sensitivity to climate variability, we produced a new global SHR dataset using Random Forest algorithms, up-scaling 455 point data from the Global Soil Respiration Database (SRDB 4.0) with gridded fields of climatic, edaphic and productivity as explanatory variables. We estimated a global total SHR of 46.8 Pg C yr-1 over 1985-2013 (95% confidence interval: 38.6-56.3 Pg C yr-1), with a significant increasing trend of 0.03 Pg C yr-2 during this period. We found that the choice of soil moisture datasets contributes more to the difference among these data-driven SHR members rather than that of productivity, temperature and precipitation data sources. We also analyzed the influence of climatic variables on the inter-annual variability (IAV) of our SHR product. Water availability was the dominant driver of IAV at global scales, although the inferred sensitivity depends on the choice of the soil moisture gridded dataset. At the ecosystem scale, temperature strongly controls the IAV of SHR in tropical forests, while water availability dominates in extra-tropical forest and semi-arid regions. Our machine-learning gridded SHR dataset and outputs from process-based land surface models (TRENDYv6) show agreement for a strong association between water variability and SHR IAV at the global scale, but the two approaches lead to different temporal trend globally and different controlling variables for IAV at the ecosystem scale. Our study provides evidence for the pervasive and important role of water availability in driving SHR, indicating both a direct effect limiting decomposition rates and an indirect effect through the amount of fresh organic matter made available to SHR from productivity. In consideration of potential limitations and uncertainties remaining in our data-driven SHR datasets, we call for a more scientifically designed observation network for SHR, more observation data compilation, and increased use of deep learning methods making maximum use of observation data in hand. This will benefit process-based models, and improve our understanding of SHR response to future anomalous environmental conditions.

Yao, Yitong↗
DOE OSTI2020

Carbon Dioxide Production in Bedrock Beneath Soils Substantially Contributes to Forest Carbon Cycling

Abstract Soils are widely considered the primary terrestrial organic matter pool mediating carbon transactions with the atmosphere and groundwater. Because soils are both a host and a product of rhizosphere activity, they are thought to mark the location where photosynthetic fixation of carbon dioxide (CO 2 ) is balanced by the oxidation of organic matter. However, in many terrestrial environments, the rhizosphere extends below soils and into fractured bedrock, and it is unknown if the resulting biological and hydrologic dynamics in bedrock have a significant impact on carbon cycling. Here we show substantial production of CO 2 in weathered bedrock at 4–8 m below the thin soils (<0.5 m thick) of a Northern California forest using innovative monitoring technology for sampling gases and water in fractured rock. The deep CO 2 production supports a persistent upward flux of CO 2(g) year‐round from bedrock to soil, constituting between 2% and 29% of the average daily CO 2 efflux from the land surface. When water is rapidly transported across the fractured bedrock vadose zone, nearly 50% of the CO 2 produced in the bedrock dissolves into water, promoting water‐rock interaction and export of dissolved inorganic carbon (DIC) from the unsaturated zone to groundwater, constituting as much as 80% of the DIC exiting the hillslope. Such CO 2 production in weathered bedrock is subject to unique moisture, temperature, biological, and mineralogical conditions which are currently missing from terrestrial carbon models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Near‐Surface Hydrology and Soil Properties Drive Heterogeneity in Permafrost Distribution, Vegetation Dynamics, and Carbon Cycling in a Sub‐Arctic Watershed

Abstract Discontinuous permafrost environments exhibit strong spatial heterogeneity at scales too small to be driven by weather forcing or captured by Earth System Models. Here we analyze effects of observed spatial heterogeneity in soil and vegetation properties, hydrology, and thermal dynamics on ecosystem carbon dynamics in a watershed on the Seward Peninsula in Alaska. We apply a Morris global sensitivity analysis to a process‐rich, successfully tested terrestrial ecosystem model (TEM), ecosys , varying soil properties, boundary conditions, and weather forcing. We show that landscape heterogeneity strongly impacts soil temperatures and vegetation composition. Snow depth, O‐horizon thickness, and near‐surface water content, which vary at scales of O(m), control the soil thermal regime more than an air temperature gradient corresponding to a 140 km north–south distance. High shrub productivity is simulated only in talik (perennially unfrozen) soils with high nitrogen availability. Through these effects on plant and permafrost dynamics, landscape heterogeneity impacts ecosystem productivity. Simulations with near‐surface taliks have higher microbial respiration (by 78.0 gC m −2 yr −1 ) and higher net primary productivity (by 104.9 gC m −2 yr −1 ) compared to runs with near‐surface permafrost, and simulations with high shrub productivity have outlying values of net carbon uptake. We explored the prediction uncertainty associated with ignoring observed landscape heterogeneity, and found that watershed net carbon uptake is 60% larger when heterogeneity is accounted for. Our results highlight the complexity inherent in discontinuous permafrost environments and demonstrate that missing representation of subgrid heterogeneity in TEMs could bias predictions of high‐latitude carbon budget.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The Changing Influence of Precipitation on Soil Moisture Drought With Warming in the Mediterranean and Western North America

Abstract Anthropogenic climate change has already affected drought severity and risk across many regions, and climate models project additional increases in drought risk with future warming. Historically, droughts are typically caused by periods of below‐normal precipitation and terminated by average or above‐normal precipitation. In many regions, however, soil moisture is projected to decrease primarily through warming‐driven increases in evaporative demand, potentially affecting the ability of negative precipitation anomalies to cause drought and positive precipitation anomalies to terminate drought. Here, we use climate model simulations from Phase Six of the Coupled Model Intercomparison Project (CMIP6) to investigate how different levels of warming (1, 2, and 3°C) affect the influence of precipitation on soil moisture drought in the Mediterranean and Western North America regions. We demonstrate that the same monthly precipitation deficits (25th percentile relative to a preindustrial baseline) at a global warming level of 2°C increase the probability of both surface and rootzone soil moisture drought by 29% in the Mediterranean and 32% and 6% in Western North America compared to the preindustrial baseline. Furthermore, the probability of a dry (25th percentile relative to a preindustrial baseline) surface soil moisture month given a high (75th percentile relative to a preindustrial baseline) precipitation month is 6 (Mediterranean) and 3 (Western North America) times more likely in a 2°C world compared to the preindustrial baseline. For these regions, warming will likely increase the risk of soil moisture drought during low precipitation periods while simultaneously reducing the efficacy of high precipitation periods to terminate droughts.

Environmental Sciences & Ecology↗
DOE OSTI2024

Upscaling Soil Organic Carbon Measurements at the Continental Scale Using Multivariate Clustering Analysis and Machine Learning

Abstract Estimates of soil organic carbon (SOC) stocks are essential for many environmental applications. However, significant inconsistencies exist in SOC stock estimates for the U.S. across current SOC maps. We propose a framework that combines unsupervised multivariate geographic clustering (MGC) and supervised Random Forests regression, improving SOC maps by capturing heterogeneous relationships with SOC drivers. We first used MGC to divide the U.S. into 20 SOC regions based on the similarity of covariates (soil biogeochemical, bioclimatic, biological, and physiographic variables). Subsequently, separate Random Forests models were trained for each SOC region, utilizing environmental covariates and SOC observations. Our estimated SOC stocks for the U.S. (52.6 ± 3.2 Pg for 0–30 cm and 108.3 ± 8.2 Pg for 0–100 cm depth) were within the range estimated by existing products like Harmonized World Soil Database, HWSD (46.7 Pg for 0–30 cm and 90.7 Pg for 0–100 cm depth) and SoilGrids 2.0 (45.7 Pg for 0–30 cm and 133.0 Pg for 0–100 cm depth). However, independent validation with soil profile data from the National Ecological Observatory Network showed that our approach ( R 2 = 0.51) outperformed the estimates obtained from Harmonized World Soil Database ( R 2 = 0.23) and SoilGrids 2.0 ( R 2 = 0.39) for the topsoil (0–30 cm). Uncertainty analysis (e.g., low representativeness and high coefficients of variation) identified regions requiring more measurements, such as Alaska and the deserts of the U.S. Southwest. Our approach effectively captures the heterogeneous relationships between widely available predictors and the current SOC baseline across regions, offering reliable SOC estimates at 1 km resolution for benchmarking Earth system models.

58 GEOSCIENCES↗
DOE OSTI2024

Modeling Interactive Effects of Manganese Bioavailability, Nitrogen Deposition, and Warming on Soil Carbon Storage

Manganese (Mn) is a redox–active micronutrient that has been shown to accelerate plant litter decomposition; however, the effect of Mn–promoted decomposition on soil C storage is unclear. We present a novel biogeochemical model simulating how Mn bioavailability influences soil organic C (SOC) stocks in a soil profile (<50 cm) within a temperate forest. In our model, foliar Mn increased in response to increasing soluble Mn released through Mn–oxide (birnessite) dissolution in mineral soil layers. The ensuing Mn enrichment in leaf litter redistributed Mn to the surface forest floor layer, promoted enzymatic oxidation of lignin, and decreased SOC stocks. Total SOC loss was partially mitigated by accumulation of lignin–oxidation products as mineral–associated organic C. We also explored how Mn–driven changes to C storage interacted with effects of N deposition and warming. Nitrogen enrichment inhibited Mn–dependent lignin degradation, increasing SOC stocks and weakening their dependence on Mn bioavailability. Warming stimulated decomposition and reduced C stocks but was less effective at low Mn bioavailability. Our model results suggest that SOC stocks are sensitive to Mn bioavailability because increased plant uptake redistributes Mn to surface soils where it can enhance litter decomposition. Finally, based on our simulations, we predict that Mn becomes limiting to litter decomposition where Mn is poorly soluble. Depletion of bioavailable Mn or other cofactors that are critical to decomposition could limit the response of organic C stocks to warming over time, but quantitative projections of the role of Mn bioavailability in regulating decomposition requires additional measurements to constrain model uncertainties.

58 GEOSCIENCES↗
DOE OSTI2025

Combined Meteorological and Hydrologic Uncertainties Shape Projections of Future Soil Moisture in the Eastern United States

Physical hazards pose risks to many critical systems. Designing adaptive measures to mitigate these risks is challenging due to large uncertainties in modeling future hazards and the associated sectoral responses. Here, we help address this challenge in a hydrologic context by examining the combined role of meteorological forcing and hydrologic parameter uncertainties in shaping projections of future soil moisture. By encoding a simple conceptual water balance model in a differentiable programming framework, we facilitate fast runtimes and an efficient calibration, enabling an improved uncertainty analysis. We characterize uncertainty in model parameters by calibrating against different target data sets and by using several loss functions. We then convolve the resulting parameter ensemble with a set of Earth system model projections to produce a large ensemble (2,340 members) of daily soil moisture simulations. Focusing on the eastern United States, we find that most ensemble members project a drying of soils across the region, although some simulate wetter conditions throughout this century. Our ensemble shows an increase in the frequency and intensity of dry extremes while there is less agreement for wet extremes. We conduct sensitivity analyses on several soil moisture signatures to measure the relative influence of meteorological and hydrologic uncertainties across space and time. Both meteorological and hydrologic factors contribute consistently to uncertainty surrounding long-term trends, while changes to both wet and dry soil extremes are typically more sensitive to hydrologic parameter uncertainty. Our results underscore the need to account for varied sources of uncertainty when developing long-term hydrometeorological projections.

Lafferty, David C. [University of Illinois Urbana‐↗
DOE OSTI2025

Geochemical Phosphorus Sequestration in Tundra Soils Impedes Delivery of Bioavailable Phosphorus to the Kuparuk River, Alaska, USA: Implications for the Broader Arctic Region

Long-term river monitoring of the Kuparuk River (North Slope, Alaska, USA) confirms significant increases in solutes that are indicative of active layer thickening due to thawing permafrost. However, there is no evidence of an increase in total dissolved phosphorus (TDP) or soluble reactive phosphorus (SRP), the nutrient that limits primary production in this and similar rivers in the region. Here, we show that Mehlich-3 extractable iron (Fe) and aluminum (Al) in active layer soils impart high P geochemical sorption capacities across a range of landscape features that we would expect to promote lateral movement of water and solutes to headwater streams in our study watershed. Reanalysis of a recently published pan-Arctic soils database that includes active layer and permafrost soil samples suggests that this high P sorption capacity could be common in other parts of the Arctic region. We conclude that soil minerals enhance P retention on hillslopes and propose pedogenic secondary Fe and Al minerals may continue to retain P in these soils and limit biological productivity in the adjacent river even as active layer thickening increases potential P mobility in the watershed. We suggest that similar interactions may occur in other areas of the Arctic where comparable geochemical conditions prevail.

Sutor, Frederick W. [Univ. of Vermont, Burlington,↗
DOE OSTI2026

Soil Moisture Buffers the Impact of Precipitation Variability on Ecosystem Productivity

Water availability governs ecosystem productivity, yet estimates of vegetation sensitivity to water can differ greatly depending on whether the sensitivity is examined spatially or temporally. In particular, the spatial sensitivity is often reported to be much stronger than temporal sensitivities, leading to highly uncertain projections of ecosystem responses to future climate change when using space-for-time substitution. The large difference between spatial and temporal sensitivities remains unexplained. Prior research, however, primarily relied on precipitation as the water availability proxy, whereas vegetation responds to soil moisture. Here, we combined satellite estimates of vegetation productivity with soil moisture data across water-limited ecosystems of the continental United States (CONUS) to identify a convergent sensitivity of productivity to water availability. Using precipitation, we show that temporal sensitivity is 66% lower than spatial sensitivity overall. Our analysis identified the cause of the difference to be primarily driven by the seasonal variability of water availability, rooting depth, and soil properties. When using soil moisture instead of precipitation, we observed widespread convergence in the spatial and temporal sensitivities—that is, the two sensitivities became much more similar in magnitude across all water-limited ecosystems within CONUS. These results show that overlooking soil hydrology can inflate perceived discrepancies between spatial and temporal vegetation sensitivities, leading to biased projections of ecosystem dynamics under future hydro-climatic change.

Wang, Huiqi [University of California, Berkeley, C↗
DOE OSTI2022

Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification

Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO 2 -derived 13 C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of 13 C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of 13 C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in 13 C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbial diversity drives carbon use efficiency in a model soil

Abstract Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Temporal changes in global soil respiration since 1987

As the second-largest terrestrial carbon (C) flux, soil respiration (R S ) has been stimulated by climate warming. However, the magnitude and dynamics of such stimulations of soil respiration are highly uncertain at the global scale, undermining our confidence in future climate projections. Here, we present an analysis of global R S observations from 1987–2016. R S increased (P < 0.001) at a rate of 27.66 g C m -2 yr -2 (equivalent to 0.161 Pg C yr -2 ) in 1987–1999 globally but became unchanged in 2000–2016, which were related to complex temporal variations of temperature anomalies and soil C stocks. However, global heterotrophic respiration (R h ) derived from microbial decomposition of soil C increased in 1987–2016 (P < 0.001), suggesting accumulated soil C losses. Given the warmest years on records after 2015, our modeling analysis shows a possible resuscitation of global R S rise. This study of naturally occurring shifts in R S over recent decades has provided invaluable insights for designing more effective policies addressing future climate challenges.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Hi-C metagenome sequencing reveals soil phage–host interactions

Abstract Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi–C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Composition and metabolism of microbial communities in soil pores

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13 C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition

Soil organic matter (SOM) decomposition by microorganisms is a major uncertainty in predicting terrestrial carbon–atmosphere feedbacks, partly because we lack understanding of the microbial diversity involved in depolymerizing different carbon pools across environmental gradients. We address this gap using a continental-scale dataset pairing shotgun metagenomes with high-resolution SOM chemistry, assembling 0.76 Tbp of prokaryotic MAGs (828 genomes) and identifying 66,727 SOM molecules from 47 standardized U.S. soil cores selected using respiration rates from 106 soils. Integrating these datasets reveals widespread microbial potential for depolymerizing chemically-recalcitrant SOM previously considered stable. We uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of complex SOM through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our results show that a substantial portion of ostensibly stable SOM remains vulnerable to microbial decomposition, a mechanism not captured in current Earth System Models.

Song, Young C. [Pacific Northwest National Laborat↗