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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Inoculated biocrust cover and functions diverged over a gradient of soil textures and water availability

Restoring biological crust (biocrust) in disturbed drylands is challenging due to the difficult environmental conditions, such as limited soil moisture, low soil nutrients, and extreme temperatures, that impede growth. Understanding how the key components of biocrust—mosses, lichens, and cyanobacteria—react to different environmental factors informs the optimal timing, locations, and species composition for biocrust reintroduction, thereby increasing the likelihood of establishment. Here, we inoculated soils with a diverse range of biocrust organisms, analogous to seeding an area with diverse vascular plant seeds, and varied environmental conditions to observe how these changes influenced the development and functions of reintroduced biocrust. We found that by manipulating soil texture and time spent wet, we can change the proportional cover of biocrust within a restoration‐like setting. Specifically, we found that 4 months after inoculation, finer textured soils that received more water become dominated by moss cover, while coarser textured soils with less water remained dominated by cyanobacteria cover, and the interactions between texture and time spent wet strongly influenced cover. We found biocrust morphological group cover had a small, but detectable, effect on ecosystem functions (soil stability and nitrogenase activity, a proxy for nitrogen fixation), but that environmental conditions had a stronger impact on the functions we measured. Manipulative experiments in controlled environments, like this one, can help elucidate the mechanisms underlying the establishment rate and patterns of biocrusts post‐inoculation, and inform implementation of inoculations in the field.

Environmental Sciences & Ecology↗
DOE OSTI2022

Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase

Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin – a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomic fingerprints of the world’s soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Using mid-infrared spectroscopy to estimate soil microbial properties at the continental scale

Understanding microbial community properties is critical to improving the predictions of biogeochemical processes for enhancing soil carbon sequestration. Here, in this observational study, mid-infrared (MIR) spectroscopy and partial least squares regression was used to predict soil microbial and chemical properties from diverse ecosystems across the continental USA. Random calibration and validation demonstrated the prediction potential for soil properties using MIR spectra, with the strongest predictions for microbial respiration, followed by microbial biomass carbon and nitrogen, ß-glucosidase activity, as well as soil chemical properties including organic carbon and total nitrogen. Microbial properties were mainly positively correlated to spectral regions associated with aliphatic C-H groups and C=O stretches of polysaccharides and negatively correlated to quartz and silicate-associated regions. We conclude that MIR spectroscopy can characterize soil microbial functions and be useful for the improvement of continental-scale soil carbon modeling and prediction programs.

59 BASIC BIOLOGICAL 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 OSTI2020

Dryland feedbacks to future climate change: how species mortality and replacement will affect coupled biogeochemical cycles and energy balance (Final Technical Report)

The overall goal of the dryland climate manipulation experiment is to improve our understanding and ability to forecast dryland responses to increasing temperatures and altered precipitation regimes. Drylands cover over 40% of Earth’s terrestrial surface and are predicted to increase in size 11-23% by 2100. Yet our understanding of this vast biome, which exchanges enormous amounts of CO 2 and energy with the atmosphere, is exceedingly poor. This project aims to transform and improve that understanding in order to reduce uncertainty and increase the confidence with which we can make global predictions of future climate. We focus on both above- and belowground processes, and explore temperature controls over critical aspects of carbon and nutrient cycling for dryland plants, soil, and microbes. We have 60 climate manipulation plots where plants (from above the canopy) and soils are warmed using infrared lamps and where precipitation has been altered using targeted watering regimes. We have measured myriad aspects of plant physiology, morphology, carbon exchange, energy exchange, and phenology, as well as analogous climate-induced changes to biological soil crusts and soil microbial communities. Our goals are to investigate temperature responses and acclimation potential of dryland plant and soil processes. Concurrent soil incubation experiments complement the in-situ soil warming component and enable more controlled mechanistic investigations of temperature response on microbial function. Automated soil CO 2 efflux chambers within the plots provide phenomenal opportunity to improve our understanding of dryland CO 2 exchange with the atmosphere and are coupled with plant CO 2 exchange measurements. The project has been exceptionally successful, with 35 peer-reviewed publications (and more in review), including in high-profile journals such as Nature Climate Change and PNAS. We have given over fifty presentations on the work and it has been featured in many high-profile media outlets, such as Discover Magazine and on NPR.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Functional succession of actively growing soil microorganisms during rewetting is shaped by precipitation history

Rewetting of seasonally dry soils induces a burst of microbial activity and carbon mineralization that changes nutrient availability and leads to succession. Yet the microbial functions that underpin this succession are not well described. Further, it’s unclear how previous precipitation frames microbial capacities after rewetting and how long these effects persist. We used isotopically-labeled water to rewet seasonally dry annual grassland soil that experienced either mean annual or reduced precipitation during the previous two years, and sampled at five subsequent time points. We used quantitative stable isotope probing (qSIP)-informed genome- resolved metagenomics to identify growing microorganisms, predict their capabilities, and analyze how these traits differed over time and between precipitation treatments. Organisms that grew after wetup were more abundant than non-growing organisms prior to the wet-up, suggesting that traits that initiate succession are pre-defined at the end of the prior plant growing season or via survival over the summer. Fast-growing organisms had fewer carbohydrate active enzyme (CAZy) genes per genome than slower-growing organisms, suggesting that although fast-growers were capable of degrading complex C, they may not specialize in this process. Differential abundance of CAZy genes in growing organisms throughout the succession implies that substrate availability varied with time. In contrast, the abundance of peptidases in growing organisms differed between precipitation treatments, but not over time following wet-up. Before wet-up, the soil organisms’ gene inventories were different between the two precipitation treatments. Surprisingly, this legacy effect waned after just one week. Thus, pre-wetup differences in microbial functional capacity converged shortly after rewetting.

Sieradzki, E T↗
DOE OSTI2024

Learning Constitutive Relations From Soil Moisture Data via Physically Constrained Neural Networks

Abstract The constitutive relations of the Richardson‐Richards equation encode the macroscopic properties of soil water retention and conductivity. These soil hydraulic functions are commonly represented by models with a handful of parameters. The limited degrees of freedom of such soil hydraulic models constrain our ability to extract soil hydraulic properties from soil moisture data via inverse modeling. We present a new free‐form approach to learning the constitutive relations using physically constrained neural networks. We implemented the inverse modeling framework in a differentiable modeling framework, JAX, to ensure scalability and extensibility. For efficient gradient computations, we implemented implicit differentiation through a nonlinear solver for the Richardson‐Richards equation. We tested the framework against synthetic noisy data and demonstrated its robustness against varying magnitudes of noise and degrees of freedom of the neural networks. We applied the framework to soil moisture data from an upward infiltration experiment and demonstrated that the neural network‐based approach was better fitted to the experimental data than a parametric model and that the framework can learn the constitutive relations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

​​Hydrogen Transportation and Distributed Energy Systems Seismic Risk Assessment for Cascadia Subduction Zone Airport Facilities​

Portland International Airport in Oregon is exploring operating a fleet of 28 fuel cell electric buses to support airport operations and possibly provide backup power during outages. In this report, we evaluate the risk of hydrogen deployment at an airport considering the potential for seismic activity. We present a seismic risk assessment for pressurized piping for a generic hydrogen refueling station at the airport. Only pressurized piping was considered in the risk analysis because of its vulnerability and availability of fragility information unlike the other components. Seismic capacity of other components should be included as more information becomes available. To characterize the seismic hazard, we considered the initiating event frequency of a Cascadia Subduction Zone earthquake event based on data from the literature. Seismic stressors that translate to the site from an earthquake event are expressed as peak ground acceleration. Site disturbance is characterized as a function of soil conditions, represented by different shear wave velocity values, which affect how seismic waves propagate and impact structures. Pipe fragility curves as a function of seismic capacity were used to correlate ground acceleration and failure probability. These fragility characteristics were combined with site-specific soil conditions to calculate the probability of pipe rupture during a seismic event. It should be noted that multiple simultaneous failures due to an earthquake event as a common cause are not considered. Some epistemic uncertainties such as self-exciting shocks, aftershocks, and the time variant nature of the ground motion are not considered either.

08 HYDROGEN↗
DOE OSTI2021

Decreased land use intensity improves surface soil quality on marginal lands

The Conservation Reserve Program (CRP) has been a major factor in land transitions out of intensive row-crop management on marginally productive lands in the central United States. While CRP can protect these more environmentally sensitive lands against erosion and potential nutrient loss, information on how CRP affects soil quality over time is limited. Using a chronosequence with 0–40 yr of CRP conversion history, we evaluated soil quality under different land use intensities (CRP, pasture, row crop) using the Soil Management Assessment Framework (SMAF). Effects of slope classes (higher [14–25%] and lower [2–14%]) and soil depth (0–120 cm) were also evaluated. Our results show that the soils were functioning at 84 and 78% of their theoretical capacity under CRP and row crop, respectively. Conversion to CRP enhanced overall soil quality by increasing soil biological, physical, and chemical attributes, but soil nutrient availability decreased due to the absence of fertilizer application. Increasing soil organic C (SOC) enhanced overall soil quality because of its impact on soil biological, physical, chemical, and nutrient conditions. Conversion to CRP will likely have greater benefits for more environmentally sensitive soils (i.e., higher slope) as demonstrated by structural equation modeling. Land use effects were also depth dependent, with more prominent effects within the 0-to-5-cm than the 5-to-15-cm depth increment. Overall, our methods focused on key soil quality indicators, confirmed ecological benefits of CRP conversion, and provided guidance for improved and simplified land management recommendations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

Abstract Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effects of Revegetation on Soil Physical and Chemical Properties in Solar Photovoltaic Infrastructure

Solar photovoltaic (PV) technology is being deployed at an unprecedented rate. However, utility-scale solar energy development is land intensive and its large-scale installation can have negative impacts on the environment. In particular, solar energy infrastructure can require extensive landscape modification that transforms soil ecological functions, thereby impacting hydrologic, vegetative, and carbon dynamics. However, reintroducing native vegetation to solar PV sites may be a means of restoring their soils. To this end, we investigated critical soil physical and chemical parameters at a revegetated photovoltaic array and an adjacent reference grassland in Colorado, United States. Seven years after revegetation, we found that carbon and nitrogen remained lower in the PV soil than in the reference soil and contained a greater fraction of coarse particles. We also found that the PV modules introduced heterogeneity in the soil moisture distribution, with precipitation accumulating along the lower edges of panels. The redistribution of soil moisture by panel arrays could potentially be used in concert with planting strategies to maximize plant growth or minimize soil erosion, and should be considered when evaluating the potential to co-locate vegetation with solar infrastructure.

14 SOLAR ENERGY↗
DOE OSTI2022

Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils

Microbial community structure and function regularly covary with soil pH, yet effects of these interactions on soil carbon are rarely tested experimentally within natural ecosystems. We investigated the enduring (25 year) impacts of liming on microbial community structure and decomposition at an acidic northern hardwood forest, where experimental liming increased pH one unit and surprisingly doubled the organic carbon stocks of the forest floor. Here we show that this increase in carbon storage corresponded with restructuring of the bacterial and fungal communities that drive decomposition. In the Oe horizon, liming reduced the activities of five extracellular enzymes that mediate decomposition, while the Oa horizon showed an especially large (64%) reduction in the activity of a sixth, peroxidase, which is an oxidative enzyme central to lignocellulose degradation. Decreased enzyme activities corresponded with loss of microbial taxa important for lignocellulose decay, including large reductions in the dominant ectomycorrhizal genera Russula and Cenococcum, saprotrophic and wood decaying fungi, and Actinobacteria (Thermomonosporaceae). These results demonstrate the importance of pH as a dominant regulator of microbial community structure and illustrate how changes to this structure can produce large, otherwise unexpected increases in carbon storage in forest soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mycorrhiza Better Predict Soil Fungal Community Composition and Function than Aboveground Traits in Temperate Forest Ecosystems

Forests in the northeastern US are experiencing shifts in community composition due to the northward migration of warm-adapted tree species and certain species’ declines (for example, white ash and eastern hemlock) due to invasive insects. Changes in belowground fungal communities and associated functions will inevitably follow. Therefore, we sought to investigate the relative importance of two important tree characteristics—mycorrhizal type [ectomycorrhizal (EcM) or arbuscular mycorrhizal (AM)] and leaf habit (deciduous or evergreen) on soil fungal community composition and organic matter cycling. We sampled soil in the organic and mineral horizons beneath two AM-associated (Fraxinus americana and Thuja occidentalis) and two ECM-associated tree species (Betula alleghaniensis and Tsuga canadensis), with an evergreen and deciduous species in each mycorrhizal group. To characterize fungal communities and organic matter decomposition beneath each tree species, we sequenced the ITS1 region of fungal DNA and measured the potential activity of carbon- and nitrogen-targeting extracellular enzymes. Each tree species harbored distinct fungal communities, supporting the need to consider both mycorrhizal type and leaf habit. However, between tree characteristics, mycorrhizal type better predicted fungal communities. Across fungal guilds, saprotrophic fungi were the most important group in shaping fungal community differences in soils beneath all tree species. The effect of leaf habit on carbon- and nitrogen-targeting hydrolytic enzymes depended on tree mycorrhizal association in the organic horizon, while oxidative enzyme activities were higher beneath EcM-associated trees across both soil horizons and leaf habits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Tendencies of Soil Microbial NO Emissions During HI‐SCALE as Predicted by a Nitrification/Denitrification Scheme

Many atmospheric chemical processes, including the formation of secondary organic aerosol (SOA), are strongly modulated by the reactions of NO and NO 2 (NO x ). Though NO x is controlled by anthropogenic emissions near urban areas, in rural areas soil microbes can be a significant contribution to NO emission globally. The relative rates of emissions of different nitrogen-containing species (e.g., NO, N 2 O, HONO, and N 2 ) are strong functions of soil properties such as temperature, moisture content, pH, and soil carbon and nitrogen pools. However, typical large-scale biogeochemical models either express these emissions simplistically, or not at all. Here we investigate the potential impact of soil NO emissions on atmospheric chemistry and SOA formation over regional and monthly time scales, specifically the 2016 spring and summer Intensive Observational Periods (IOPs) of the Holistic Interactions of Shallow Clouds, Aerosols and Land Ecosystems (HI-SCALE) field campaign. We implement the soil NO nitrification/denitrification parameterization of Rasool et al. (2019) into the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem), supplemented by a 1-km soil moisture analysis. We then simulate both IOPs over the U.S. Great Plains, evaluating against ground stations and flight data. We show that soil NO emissions can account for a large fraction of total NO x and locally increase O 3 concentrations by up to 25%, while alleviating negative biases of gases and aerosols toward observations. Soil moisture and temperature changes between IOP1 and IOP2 lead to overall differences in emissions, but with large regional variability due to heterogeneous surface characteristics.

Atmoshpheric Chemistry↗
DOE OSTI2020

Ectomycorrhizal fungal diversity interacts with soil nutrients to predict plant growth despite weak plant-soil feedbacks

Background and aims Plant-soil feedbacks are the result of multiple abiotic and biotic mechanisms. However, few studies have addressed how feedbacks vary based on abiotic context or attempted to identify microbiota responsible for feedbacks. In this work, we investigated whether plant-soil feedbacks of an ectomycorrhizal tree (Quercus macrocarpa) varied based on soil nutrient status and whether fungal community composition and diversity could explain feedback patterns. Furthermore, we inoculated Q. macrocarpa seedlings with field-sampled soils taken from five soil origins – including heterospecific and conspecific trees and an old field – which were profiled using fungal DNA metabarcoding.Results Despite finding that soils associated with different hosts harbored distinct fungal communities and that fungal communities were predictive of plant growth, we did not find any significant plant-soil feedbacks regardless of fertilization status. We did find that the growth promotive effect associated with ectomycorrhizal OTU diversity was weakened with fertilization, suggesting context-dependent relations between plant growth and a guild of fungal mutualists. Our results demonstrate that the host-specific accumulation of functionally important soil microbes is not always sufficient to drive observable plant-soil feedbacks. Our data provide support for a role for ECM fungal diversity in mediating plant growth responses, though it is unclear whether this effect is direct or indirect.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Comparative genomics of pyrophilous fungi reveals a link between fire events and developmental genes

Forest fires generate a large amount of carbon that remains resident on the site as dead and partially ‘pyrolysed’ (i.e. burnt) material that has long residency times and constitutes a significant pool in fire–prone ecosystems. In addition, fire–induced hydrophobic soil layers, caused by condensation of pyrolysed waxes and lipids, increase post–fire erosion and can lead to long–term productivity losses. A small set of pyrophilous fungi dominate post–fire soils and are likely to be involved with the degradation of all these compounds, yet almost nothing is currently known about what these fungi do or the metabolic processes they employ. In this study, we sequenced and analyzed genomes from fungi isolated after Rim fire near Yosemite National Park in 2013 and showed the enrichment/expansion of CAZymes and families known to be involved in fruiting body initiation when compared to other basidiomycete fungi. We found gene families potentially involved in the degradation of the hydrophobic layer and pyrolysed organic matter, such as hydrophobic surface binding proteins, laccases (AA1_1), xylanases (GH10, GH11), fatty acid desaturases and tannases. Furthermore, pyrophilous fungi are important actors to restate the soil's functional capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Revisiting the definition of field capacity as a functional parameter in a layered agronomic soil profile beneath irrigated maize

The soil water content at the condition of field capacity (θ FC ) is a key parameter in irrigation scheduling and has been suggested to be determined by running a synthetic drainage experiment until the flux rate (q) at the bottom of the soil profile achieves a predefined negligible value (q FC ). We question the impact of q FC on the assessment of field capacity. Moreover, calculating θ FC as the integral mean of the water content profile when q is equal to q FC is strictly valid only for uniform soil profiles. By contrast, this practice is ambiguous and biased for stratified soil profiles due to the soil water content discontinuity at the layer interfaces. In this study, the concept of field capacity was revisited and adapted to practical agronomic heuristics. By resorting to the assessment of root-zone water storage capacity (W), we envision field capacity as a functional hydraulic parameter derived from synthetic irrigation scheduling scenarios to minimize drought stress, drainage, and nitrate leachate below the root zone. A functional analysis was carried out on a 135-cm-thick layered soil profile beneath maize in eastern Nebraska. On-farm irrigation scheduling applications and agricultural practices were recorded for 20 years (2001–2020) at a daily time step. Hydrus-1D was calibrated and validated with direct measurements of the soil water retention curve and soil water content data, respectively, in each soil layer. A set of functional field capacity values was derived from 24 irrigation scheduling scenarios, and the optimal water storage capacity at field capacity (W FC ) was approximately 50 cm (corresponding to about 80% saturation in the soil profile). An average irrigation amount of 217.5 mm distributed over 21 events was obtained by using optimal irrigation scheduling, which was initiated when the matric pressure head took on a value of –700 cm and the irrigation rate was set at 1.0 cm d –1 . This irrigation practice ensured water storage at approximately the same level (ideally at W FC ) by sustaining only evapotranspiration fluxes in the uppermost portion of the root zone and by limiting excessive drainage. This protocol can be transferred to other agricultural fields.

54 ENVIRONMENTAL SCIENCES↗