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DOE OSTI2025

Community‐Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach

ABSTRACT The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long‐term established pastures in the Amazon. Machine learning‐derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein‐coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein‐coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long‐term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long‐term established pastures with implications for the C and N cycles.

carbon and nitrogen cycles↗

NASA NTRS2012

Soil Carbon and Nutrient Changes Associated with Deforestation for Pasture in Southern Costa Rica

We assessed the effects of deforestation on soil carbon (C) and nutrient stocks in the premontane landscape near Las Cruces Biological Station in southern Costa Rica, where forests were cleared for pasture in the mid-1960s. We excavated six soil pits to a depth of 1 m in both pasture and primary forest, and found that C stocks were ~20 kg C per square meters in both settings. Nevertheless, soil delta C-13 suggests ~50 percent of the forest-derived soil C above 40 cm depth has turned over since deforestation. Soil nitrogen (N) and phosphorus (P) stocks derived from the soil pits were not significantly different between land uses (P = 0.43 and 0.61, respectively). At a larger spatial scale, however, the ubiquity of ruts produced by cattle-induced erosion indicates that there are substantial soil effects of grazing in this steep landscape. Ruts averaged 13 cm deep and covered ~45 percent of the landscape, and thus are evidence of the removal of 0.7 Mg C/ ha/yr, and 70, 9 and 40 kg/ha/yr of N, P and potassium (K), respectively. Subsoils in this region are ~10 times less C- and N-rich, and ~2 times less P- and K-rich than the topsoil. Thus, rapid topsoil loss may lead to a decline in pasture productivity in the coming decades. These data also suggest that the soil C footprint of deforestation in this landscape may be determined by the fate of soil C as it is transported downstream, rather than C turnover in situ.

soil carbon↗

DOE OSTI2023

Evapotranspiration Partitioning of Eucalyptus benthamii and Pinus taeda During Early Stand Development

Increasing demand for bioenergy from intensively managed woody crops raises concerns of increased evapotranspiration and potential decreases in water yield. Pinus taeda (loblolly pine) is currently the most cultivated species in the southeastern USA, the country’s wood basket. However, Eucalyptus species could achieve greater productivity but with unknown ramifications for water budgets. To address the knowledge gap, we determined annual water budgets of loblolly pine and Eucalyptus benthamii (eucalypt) from growing years 3 through 5 in a replicated (n = 3) two-factor design comparing species and groundwater depth. Paired plots were established across a depth-to-groundwater gradient from shallow (~ 2 m) to deep (~ 8 m). Hydrologic budgets were constructed by measuring precipitation, interception, soil evaporation, and transpiration. Eucalypt evapotranspiration and above-ground biomass production for growing years 3 through 5 were on average 25 and 14% greater than pine, respectively; however, evapotranspiration did not differ across groundwater depths. At the end of growing year 5, eucalypt had higher transpiration and evapotranspiration per unit area than pine. Soil evaporation was substantial in young plantations (nearly 500 mm) in growing year 3 but declined as the canopy closed. Partitioning of evapotranspiration components in developing bioenergy plantations was dynamic due to canopy development driven decreases in soil evaporation and increases in transpiration and interception; total evapotranspiration was less variable from year to year. Water use efficiency (WUE, kg biomass/m 3 H 2 O) per unit evapotranspiration was similar between species, but WUE per unit transpiration was higher in pine. As a result, considering total evapotranspiration in young plantations can affect WUE interpretations.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

Regional Application of an Ecosystem Production Model for Studies of Biogeochemistry in the...

The degree to which primary production, soil carbon, and trace gas fluxes in tropical forests of the Amazon are limited by moisture availability and other environmental factors was examined using an ecosystem modeling application for the country of Brazil. A regional geographic information system (GIS) serves as the data source of climate drivers, satellite images, land cover, and soil properties for input to the NASA Ames-CASA (Carnegie-Ames-Stanford Approach) model over a 8-km grid resolution. Simulation results supports the hypothesis that net primary production (NPP) is limited by cloud interception of solar radiation over the humid northwestern portion of the region. Peak annual rates for NPP of nearly 1.4 kg C m-2yr -1are localized in the seasonally dry eastern Amazon in areas that we assume are primarily deep-rooted evergreen forest cover. Regional effects of forest conversion on NPP and soil carbon content are indicated in the model results, especially in seasonally dry areas. Comparison of model flux predictions along selected eco-climatic transects reveal moisture, soil, and land use controls on gradients of ecosystem production and soil trace gas emissions (CO2, N2O, and NO). These results are used to formulate a series of research hypotheses for testing in the next phase of regional modeling, which includes recalibration of the light-use efficiency term in CASA using field measurements of NPP, and refinements of vegetation index and soil property (texture and potential rooting depth) maps for the region.

Potter, C. S.↗

DOE OSTI2021

Plant ecological genomics at the limits of life in the Atacama Desert

The Atacama Desert in Chile—hyperarid and with high–ultraviolet irradiance levels—is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre–Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil–microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. Further, we deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growth-promoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codon-based methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a “genetic goldmine” to engineer crop resilience to face climate change.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2021

Microwave Radiometer RFI Detection Using Deep Learning

Radio frequency interference (RFI) is a risk for microwave radiometers due to their requirement of very high sensitivity. The Soil Moisture Active Passive (SMAP) mission has an aggressive approach to RFI detection and filtering using dedicated spaceflight hardware and ground processing software. As more sensors push to observe at larger bandwidths in unprotected or shared spectrum, RFI detection continues to be essential. This article presents a deep learning approach to RFI detection using SMAP spectrogram data as input images. The study utilizes the benefits of transfer learning to evaluate the viability of this method for RFI detection in microwave radiometers. The well-known pretrained convolutional neural networks, AlexNet, GoogleNet, and ResNet-101 were investigated. ResNet-101 provided the highest accuracy with respect to validation data (99%), while AlexNet exhibited the highest agreement with SMAP detection (92%).

Microwave radiometry↗

DOE OSTI2022

Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nitrogen Use Efficiency, Water Use Efficiency and Interactions with the Soil Microbiome (Final Report for DE-SC0014395)

The specific project objectives were to: 1) Conduct deep census surveys of root microbiomes concurrent with phenotypic characterizations of a diverse panel of sorghum genotypes across multiple years to define the microbes associated with the most productive lines under drought and low nitrogen conditions. 2) Associate systems-level genotypic, microbial, and environmental factors with improved sorghum performance using robust statistical approaches. 3) Develop culture collections of sorghum root/leaf associated microbes that recapitulate root-enriched sequences defined in the census. 4) Perform controlled environment experiments for in-depth characterization and hypothesis testing of G sorghum x G microbe x E interactions . Validate physiological mechanisms, map genetic loci for stress tolerance, and determine the persistence of optimal microbial strains under greenhouse and field conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Experimental Soil Warming Impacts Soil Moisture and Plant Water Stress and Thereby Ecosystem Carbon Dynamics

Experimental soil heating experiments have found a consistent increase in soil-surface CO 2 emissions ( F s ), but inconsistent soil organic carbon (SOC) responses. Interpretation of heating effects is complicated by spatial heterogeneity and soil moisture, nitrogen availability, and microbial and plant responses. Here we applied a mechanistic ecosystem model to interpret heating impacts on a California forest subjected to 1 m deep, 4°C heating. The model accurately simulated control-plot CO 2 fluxes, SOC stocks, fine root biomass, soil moisture, and soil temperature, and the observed increases in F s and decreases in fine root biomass. We show that a complex suite of interactions can lead to a consistent increase in F s (~17%) over the 5-year study period, with very small changes in SOC stocks (<1%). Modeled increases in leaf water stress from soil drying reduced GPP and NPP. The resulting reduction in leaf and fine root allocation increased fine root litter inputs to the soil and reduced root exudation. Soil heating led to about a 50% larger increase in root autotrophic respiration than in heterotrophic respiration, with the heating effect on both these fluxes decreasing over the simulation period. Increased heterotrophic respiration led to increased soil N availability and plant N uptake. These heating responses are mechanistically linked, of magnitudes that can affect ecosystem dynamics, and long-term observations of them are rarely made. Therefore, we conclude that a coupled observational and mechanistic modeling framework is needed to interpret manipulation experiments, and to improve projections of climate change impacts on terrestrial ecosystem carbon dynamics.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Effects of Slope Aspect and Rainfall on Belowground Deep Fine Root Traits and Aboveground Tree Height

The vertical root distribution and rooting depth are the main belowground plant functional traits used to indicate drought resistance in arid and semiarid regions. The effects of the slope aspect on the aboveground traits are visible but not the belowground deep root traits. We aimed to investigate the fine root traits of the locust tree ( Robinia pseudoacacia L.) planted on southerly and northerly aspects, and the variations in the rooting depth in regions with different rainfall, as well as assessing how deep rooting, might affect the response to drought in a loess region. We selected three study sites with different rainfall amounts, with six sampling plots at each site (three each with southerly and northerly aspects). Soil core samples were collected down to the depth where no roots were present. The locust trees tended to develop deeper fine roots rather than greater heights. The tree height and diameter were greater for locust trees on northerly aspects, whereas trees on southerly aspects had significantly deeper rooting depths. Fine root traits (root length, root area, and root dry weight density) were higher in the southerly aspect for both Changwu and Ansai, but lower in Suide. The ratio of the root front depth tree height ranged from 1.04 to 3.17, which was higher on southerly than northerly aspects, and it increased as the rainfall decreased. Locust tree growth traits (belowground fine root and aboveground tree height) were positively correlated with the mean annual rainfall. The soil moisture content of the topsoil decreased as the rainfall decreased, but the pattern varied in the deep layer. Our results suggest that the variations in the belowground rooting depth under different slope aspects may be related to plant survival strategies. The vertical extension of the rooting depth and tree height may be key functional traits that determine plant growth in drought-prone regions.

Lihui, Ma↗

DOE OSTI2023

Benzene polycarboxylic acids, lignin and hydrolysable lipids data from the whole-soil warming experiment at Blodgett Forest, CA, 2018, from: "Rapid loss of complex polymers and pyrogenic carbon in subsoils under whole soil warming"

This data package contains benzene polycarboxylic acids, lignin and hydrolysable lipids data used for the paper: “Rapid loss of subsoil plant-derived polymers and pyrogenic carbon with whole-soil warming”.On April 2018 (after 4.5 years of warming), we collected soil cores down to 90 cm depth from the whole soil profile warming experiment at the University of California Blodgett Forest Research Station, in the Sierra Nevada foothills near Georgetown, CA at 1370 m above sea level. Cores were collected from 6 experimental plots (three replicated blocks); samples were collected in 10 cm increments from 0 to 90 cm depth. This data package includes a file in .csv format and a file in .xlsx format, which can be accessed and processed using MS Excel or R. Benzene polycarboxylic acid, lignin and hydrolysable lipid concentrations are provided as processed data files.The aim of the measurements was to assess how +4°C of whole-soil warming for 4.5 years will affect structurally complex polymeric compounds at different soil depths. The research was supported by Swiss National Science Foundation (SNF) project 172744 (DEEP C) and U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under contract number DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2020

Joint retrieval of soil moisture and permafrost active layer thickness using L-band InSAR and P-band PolSAR

Seasonal subsidence measured by repeat-pass interferometric synthetic aperture radar (InSAR) can be used to infer the active layer thickness (ALT) in permafrost regions. The differential volume of soil water undergoing the phase change over the thaw season is one of the factors impacting the seasonal subsidence and is a function of both soil moisture profile and thaw depth. Without the information about soil moisture, this InSAR approach can have large biases in the ALT estimates when soil moisture profile is below saturation. Soil moisture and ALT can also be estimated from polarimetric synthetic aperture radar (PolSAR) backscatter observations but the sensing depth of the PolSAR approach is limited when deep ALT is present. In this paper, we integrated these two approaches and applied a joint retrieval method to estimate the soil moisture profiles and ALT from the L-band InSAR and P-band PolSAR data acquired over the Arctic-boreal region during the 2017 Arctic-Boreal Vulnerability Experiment (ABoVE) airborne campaign.

Schaefer, Kevin M.↗

DOE OSTI2025

Coupled THM modeling of bentonite heating and hydration in tank tests with a new temperature-dependent water retention model

This study presents a coupled thermo-hydro-mechanical (THM) model for simulating the heating and hydration behavior of bentonite, a buffer material in deep geological repositories (DGRs). The model incorporates a new temperature-dependent soil water retention curve which captures the thermal-induced shift in water retention behavior. It also distinguishes between liquid and gas permeability, modeling intrinsic gas permeability as a function of accessible porosity to improve vapor transport and desaturation predictions. The model was validated against two large-scale tank tests, demonstrating good agreement with measured temperature, relative humidity, and water inflow data. It revealed a complex porosity evolution driven by thermal expansion, vapor movement, vapor condensation, and hydration-induced swelling during heating and hydration processes. The simulation results also suggest that the permeability of the hydration layer plays a critical role in controlling water intake. Clogging of this layer can significantly reduce the volume of water inflow during the hydration phase. Furthermore, while the model effectively captures key THM behavior, further development of the mechanical constitutive law is required to account for possible thermo-elasto-plastic volume changes and microstructural effects. Overall, the model provides a robust tool for evaluating the evolution of bentonite-based barrier material in DGRs.

Guo, Guanlong [Lawrence Berkeley National Laborato↗

NASA NTRS1973

Conjectures about the evolution of the moon.

The principal questions about the derivation of the lunar surface have not yet been settled: is it the surface left over from the process of accumulation of the moon, or is it a surface generated by magmatic processes on the moon and subsequently altered by further infall from outside. The evidence derived from many sources now favors the former. Seismic data suggest an absence of bedrock down to a depth of several kilometers, and instead a compacted powder only. The 'mascon' evidence can be understood as a consequence of major impacts in a deep porous layer. The great abundance of cosmic ray tracks in most soil samples demands a much greater cosmic ray dosage than present rates would cause in the age of the moon, unless the dust represented infallen material previously irradiated.

Gold, T.↗

NASA NTRS1974

Transportation of detrital materials on the lunar surface - Evidence from Apollo 15

The thickness frequency distribution of stratigraphic layers intersected by the Apollo 15 deep core suggests that the majority of impact events reworking the lunar soil are small and produce ejecta blankets with an average thickness of less than 1.5 cm. The energy frequency distribution of the meteorites producing the layers may be bimodal. The impacting meteorites produce both normal and reverse graded beds which appear to be the end products of two depositional mechanisms. First, the normally graded beds appear to be produced in base surges as escaping gases fluidize the flowing debris and larger particles move downward in response to Stokes Law. Second, if the gas loss from the base surge is excessive, the fluidization may cease and inertial grain flow dominates. In this situation, the beds are reverse graded as larger particles move under dispersive pressure to the region of minimum shear stress at the upper boundary of the base surge.

Lindsay, J. F.↗

NASA NTRS1975

Surface exposure history of individual crystals in the lunar regolith

The paper reports measurements of solar-flare tracks, microcraters, and glass accretionary particles in crystals from several mature soil samples and from different levels of the Apollo 15 and 16 deep drill stems. Although almost every crystal appears to have been at (or very near) the surface of the moon, the crater data indicate that typical grains are exposed to free space for only 1000-10,000 years. Neither total track densities nor track gradients are correlated with the presence of or absence of crater surfaces. Also considered is the use of cratered crystals in assessing the nature of surface changes produced by various treatments employed to study 'surface' effects.

Poupeau, G.↗

NASA NTRS1979

Space construction engineering - A new career field

Opportunities for engineers in the design and construction of future large space structures are outlined. Possible space structures for the 1980's include a large mirror to reflect sunlight to earth for night lighting, an antenna for a personal communications system, a deep space communications relay system and a large passive radiometer to measure soil moisture. Considerations in the design of such structures include the lack of gravity, allowing structures to be built with much less supporting weight, the cost of transportation to orbit, leading to the use of aluminum or composite materials stored on reels and attached to a beam builder, and the required surface accuracy in the presence of thermal stresses. Construction factors to consider include the use of astronauts and remote manipulators in assembly, both of which have been demonstrated to be feasible.

Hagler, T.↗

NASA NTRS2003

Ultrasonic/Sonic Mechanisms for Drilling and Coring

Two apparatuses now under development are intended to perform a variety of deep-drilling, coring, and sensing functions for subsurface exploration of rock and soil. These are modified versions of the apparatuses described in Ultrasonic/Sonic Drill/Corers With Integrated Sensors (NPO-20856), NASA Tech Briefs, Vol. 25, No. 1 (January 2001), page 38. In comparison with the drilling equipment traditionally used in such exploration, these apparatuses weigh less and consume less power. Moreover, unlike traditional drills and corers, these apparatuses function without need for large externally applied axial forces.

Bar-Cohen, Yoseph↗

DOE OSTI2023

A hydrogeophysical framework to assess infiltration during a simulated ecosystem-scale flooding experiment

This study presents a framework to quantify changes in soil saturation in response to flooding caused by extreme hydrologic perturbation on coastal ecosystems at the interfaces and transition between terrestrial and aquatic systems. Subsurface heterogeneity limits the use of in situ measurements to quantify subsurface flow during flooding due to the spatial discontinuity in the measured data. While geophysical methods, including time-lapse electrical resistivity imaging (ERI), are increasingly used to monitor soil hydrological processes, their abilities to parameterize flow models have been underutilized. This study combines background ERI, ground penetrating radar (GPR), time-lapse ERI, soil characterization, and a numerical flow model developed using an Advanced Terrestrial Simulator (ATS) code to quantify the infiltration pathway and describe the hydrological dynamics during a simulated flooding experiment. We assessed the use of two conceptual models developed using [1] ERI and GPR data that described the stratigraphic distribution, and time-lapse ERI that mapped permeability contrast, and [2] information from a national soil database for capturing changes in saturation. Combining the ERI and GPR results with soil core data revealed the stratigraphic heterogeneity at the site with a silty clay layer from 1 to 2 m between an overlying loamy topsoil and an underlying saturated silty sand. This silty clay layer could restrict deep infiltration. The time-lapse ERI showed up to a 35% decrease in resistivity, which correlated with soil moisture data (R 2 value > 0.53) and revealed preferential infiltration zones used to inform the flow model. Numerical simulation results from both the geophysics- and soil database-informed models quantified changes in soil saturation with calculated soil moistures that agreed with field data. The geophysics-informed model captured more of the system’s variability, reflective of shallow subsurface heterogeneities. The framework presented will serve as a precursor for a robust ecohydrological model that can describe the impacts of extreme events induced by climate change on coastal ecosystems.

54 ENVIRONMENTAL SCIENCES↗