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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Land‐based climate solutions for the United States

Abstract Meeting end‐of‐century global warming targets requires aggressive action on multiple fronts. Recent reports note the futility of addressing mitigation goals without fully engaging the agricultural sector, yet no available assessments combine both nature‐based solutions (reforestation, grassland and wetland protection, and agricultural practice change) and cellulosic bioenergy for a single geographic region. Collectively, these solutions might offer a suite of climate, biodiversity, and other benefits greater than either alone. Nature‐based solutions are largely constrained by the duration of carbon accrual in soils and forest biomass; each of these carbon pools will eventually saturate. Bioenergy solutions can last indefinitely but carry significant environmental risk if carelessly deployed. We detail a simplified scenario for the United States that illustrates the benefits of combining approaches. We assign a portion of non‐forested former cropland to bioenergy sufficient to meet projected mid‐century transportation needs, with the remainder assigned to nature‐based solutions such as reforestation. Bottom‐up mitigation potentials for the aggregate contributions of crop, grazing, forest, and bioenergy lands are assessed by including in a Monte Carlo model conservative ranges for cost‐effective local mitigation capacities, together with ranges for (a) areal extents that avoid double counting and include realistic adoption rates and (b) the projected duration of different carbon sinks. The projected duration illustrates the net effect of eventually saturating soil carbon pools in the case of most strategies, and additionally saturating biomass carbon pools in the case of forest management. Results show a conservative end‐of‐century mitigation capacity of 110 (57–178) Gt CO 2 e for the U.S., ~50% higher than existing estimates that prioritize nature‐based or bioenergy solutions separately. Further research is needed to shrink uncertainties, but there is sufficient confidence in the general magnitude and direction of a combined approach to plan for deployment now.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

High impact of bacterial predation on cyanobacteria in soil biocrusts

Diverse bacteria lead a life as pathogens or predators of other bacteria in many environments. However, their impact on emerging ecological processes in natural settings remains to be assessed. Here we describe a novel type of obligate, intracellular predatory bacterium of widespread distribution that preys on soil cyanobacteria in biocrusts. The predator, Candidatus Cyanoraptor togatus, causes localized, cm-sized epidemics that are visible to the naked eye, obliterates cyanobacterial net primary productivity, and severely impacts crucial biocrust properties like nitrogen cycling, dust trapping and moisture retention. The combined effects of high localized morbidity and areal incidence result in decreases approaching 10% of biocrust productivity at the ecosystem scale. Our findings show that bacterial predation can be an important loss factor shaping not only the structure but also the function of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Data from: Land-based climate solutions for the United States

Meeting end-of-century global warming targets requires aggressive action on multiple fronts. Recent reports note the futility of addressing mitigation goals without fully engaging the agricultural sector, yet no available assessments combine both nature-based solutions (reforestation, grassland and wetland protection, and agricultural practice change) and cellulosic bioenergy for a single geographic region. Collectively, these solutions might offer a suite of climate, biodiversity, and other benefits greater than either alone. Nature-based solutions are largely constrained by the duration of carbon accrual in soils and forest biomass; each of these carbon pools will eventually saturate. Bioenergy solutions can last indefinitely but carry significant environmental risk if carelessly deployed. We detail a simplified scenario for the U.S. that illustrates the benefits of combining approaches. We assign a portion of non-forested former cropland to bioenergy sufficient to meet projected mid-century transportation needs, with the remainder assigned to nature-based solutions such as reforestation. Bottom-up mitigation potentials for the aggregate contributions of crop, grazing, forest, and bioenergy lands are assessed by including in a Monte Carlo model conservative ranges for cost-effective local mitigation capacities, together with ranges for (a) areal extents that avoid double counting and include realistic adoption rates and (b) the projected duration of different carbon sinks. The projected duration illustrates the net effect of eventually saturating soil carbon pools in the case of most strategies, and additionally saturating biomass carbon pools in the case of reforestation. Results show a conservative end-of-century mitigation capacity of 110 (57 – 178) Gt CO2e for the U.S., ~50% higher than existing estimates that prioritize nature-based or bioenergy solutions separately. Further research is needed to shrink uncertainties but there is sufficient confidence in the general magnitude and direction of a combined approach to plan for deployment now.

09 BIOMASS FUELS↗
DOE OSTI2020

Predicting Plant-Soil Feedback in the Field: Meta-Analysis Reveals That Competition and Environmental Stress Differentially Influence PSF

Past research on plant-soil feedbacks (PSF), largely undertaken in highly controlled greenhouse conditions, has established that plant species differentially alter abiotic and biotic soil conditions that in turn affect growth of other conspecific and heterospecific individuals in that soil. Yet, whether feedbacks under controlled greenhouse conditions reflect feedbacks in natural environments where plants are exposed to a range of abiotic and biotic pressures is still unresolved. To address how environmental context affects PSF, we conducted a meta-analysis of previously published studies that examined plant growth responses to multiple forms of competition, stress, and disturbance across various PSF methodology. We asked the following questions: (1) Can competition, stress, and disturbance alter the direction and/or strength of PSF? (2) Do particular types of competition, stress, or disturbance affect the direction and/or strength of PSF more than others? and (3) Do methods of conducting PSF research (i.e., greenhouse vs. field experiments and whether the source of soil inoculum conditioning is from the field vs. greenhouse) affect plant growth responses to PSF or competition, stress, and disturbance, or their interactions? We discovered four patterns that may be predictive of what future PSF studies conducted under more realistic conditions might reveal. First, relatively little is known about how PSF responds to environmental stress and disturbance compared to plant-plant competition. Second, specific types of competition enhanced negative effects of soil microbes on plant growth, and specific environmental stressors enhanced positive effects of soil microbes on plant growth. Third, whether PSF experiments are conducted in the field or greenhouse can change plant growth responses. And, fourth, how the soil conditioning phase is conducted can change plant growth responses. With more detail than previously shown, these results confirm that environmental context writ large can change plant growth responses in PSF experiments. These data should aid theory and predictions for conservation and restoration applications by showing the relative importance of competition, stress, and disturbance in PSF studies over time. Lastly, these data demonstrate how variation in experimental methods can alter interpretation and conclusions of PSF studies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Design and demonstration of a low‐field magnetic resonance imaging rhizotron for in‐field imaging of energy sorghum roots

Abstract Root phenotyping provides critical information to plant breeders for developing varieties with improved drought tolerance, greater root biomass, and greater nutrient use efficiency. Phenotyping roots in the natural environment is important for understanding the effect of the soil environment on root genotypic expressions. The goal of this work was to design and test a field‐scale mobile low‐field magnetic resonance imaging (LF‐MRI) Rhizotron that produces actionable root phenotyping data. We demonstrated this novel technology for root visualization and quantification using a LF‐MRI Rhizotron operating at 47 mT with two soil types. The LF‐MRI Rhizotron weights 453 kg, with a height of 90 cm, a diameter of 28 cm and an imaging field of view of 28 cm × 28 cm. The unit was operated in a Belk clay (Entic Hapluderts) and Weswood silt loam (Udifluventic Halustepts) generating 2‐D and 3‐D image data sets. The 2‐D image data had a collection time of 16.5 min per image at an image resolution of 2.2 mm per pixel. The 3‐D data had a collection time of 13 h per image with a 2.2 × 2.2 × 2.2 mm voxel resolution. Low‐field magnetic resonance imaging worked well for visualizing roots in moderate to high clay soils, demonstrating the potential for this technology; however, the broad application of this platform is hampered due to the prohibitively long scanning time to obtain 3‐D images. By increasing the field strength, and therefore the signal‐to‐noise ratio, faster scan times can enable a more useful system for root phenotyping.

Bagnall, G. Cody↗
DOE OSTI2023

Draft Genome Sequence of Pedococcus sp. Strain 5OH_020, Isolated from California Grassland Soil

The draft genome sequence of the soil bacterium Pedococcus sp. strain 5OH_020, isolated on a natural cobalamin analog, comprises 4.4 Mbp, with 4,108 protein-coding genes. Its genome encodes cobalamin-dependent enzymes, including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests that it is a novel species within the genus Pedococcus .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Development of Laboratory Testbeds Simulating Real-World Greenhouse Gas Emissions [Slides]

In this presentation, I discussed the development of laboratory test beds that simulate field greenhouse gas emissions. Field experiments are used to test new landscape management practices that could reduce greenhouse gas emissions. However, field experiments are very expensive and time consuming. Laboratory experiments are generally more cost efficient and timesaving. There are methods that can be used to make these laboratory tests more closely replicate natural systems for the improvement of agricultural lands used in biofuel and food production. The goal of this project is to develop a laboratory testbed that will mimic field greenhouse gas emissions. To achieve this goal, we used soil cores taken from agricultural and marginal lands, then attached fiberglass wicks to improve the drainage system in the core to simulate a more natural hydraulic system. The combination of using native soils and fiberglass wicks should demonstrate similar greenhouse gas emissions between the lab and the field. Our preliminary results suggest that the carbon dioxide and nitrous oxide flux from the agricultural land site were comparable to the greenhouse soil cores equipped with the drainage wicks. The data suggests that laboratory testbeds can be used to mimic field greenhouse gas emissions if parameters, such as soil water content are in a set range.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Disturbance legacies regulate coastal forest soil stability to changing salinity and inundation: A soil transplant experiment

Coastal forests worldwide are vulnerable to a dramatic transition from upland to wetland as sea-level rise accelerates and regimes of precipitation and storms change. However, the biogeochemical impacts of shifting salinity and inundation disturbance that foreshadow forest to wetland state transitions are largely unknown. This experiment used a natural salinity gradient in a tidal creek in eastern Maryland, U.S.A., to examine how soil respiration and chemistry may change under novel salinity and inundation disturbance regimes. Soil monoliths were transplanted in a reciprocal design among plots varying in seawater exposure and elevation above the creek. We monitored the monoliths’ carbon dioxide (CO 2 ) flux for two years and performed soil chemical analyses at the end of the experiment. Soil CO 2 flux was affected by changing disturbance regimes and responses were dependent upon the salinity and inundation legacies associated with each study location. Lowland soil CO 2 flux was resistant to changing salinity and inundation disturbance, with transplanted soil monolith chemistry composition in between that of its origin and destination. Conversely, upland soil CO 2 flux was sensitive to changing salinity and inundation disturbance and remained suppressed throughout the 2-year study when exposed to wetter, saline conditions. Additionally, transplanted upland soil chemistry composition was like that of its destination, rather than origin, with upland soils displaying higher pH, base saturation, and nutrient availability relative to lowland soils. Here, we hypothesize that reductions in soil respiration rates were driven by loss of soil nutrients and osmotic and redox stress on microbial communities following exposure to seawater. Together, our results suggest that disturbance legacies shape coastal forest soil responses to changing salinity and inundation disturbance regimes. However, fully understanding the dependence of system responses on disturbance legacies requires future study across a variety of systems and spatial and temporal scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. Here, we created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.

58 GEOSCIENCES↗
DOE OSTI2022

Effects of Microbial-Mineral Interactions on Organic Carbon Stabilization in a Ponderosa Pine Root Zone: A Micro-Scale Approach

Soil microbial communities affect the formation of micro-scale mineral-associated organic matter (MAOM) where complex processes, including adhesion, aggregate formation, microbial mineral weathering and soil organic matter stabilization occur in a narrow zone of large biogeochemical gradients. Here we designed a field study to examine carbon stabilization mechanisms by using in-growth mesh bags containing biotite that were placed in a ponderosa pine root zone for 6 months and compared to the surrounding bulk soil. We sought to determine the composition of the microbial community in the mesh bags compared to the surrounding soils, analyze the direct interactions between microbes and biotite, and finally identify the nature of the newly formed MAOM within the mesh-bags. Our results revealed that minerals in the mesh bags were colonized by a microbial community that produced organic matter in situ. The 16S rRNA gene sequencing and ITS2 region characterization showed phylogenetic similarity between the mesh bag and bulk soil archaea/bacteria and fungi microbiomes, with significant differences in alpha- and beta-diversity and species abundances. Organic matter pools in the mesh bags, analyzed by Fourier transform ion cyclotron resonance mass spectrometry, contained protein- (peptides) and lipid-like compounds while the bulk soil OM was comprised of lignin-like and carboxyl-rich alicyclic molecules. These results support that the newly formed biotite associated organic compounds have a microbial signature in the mesh bags. High-resolution electron microscopy documented strongly adhered organic compounds to biotite surfaces, formation of microaggregates, elemental uptake at the microbe (organic matter)-mineral interface, and distortion of biotite layers. Overall, this study shows the direct and indirect involvement of soil microbial communities from the root zone of ponderosa pine in the formation of MAOM, soil organic carbon stabilization, microaggregation, and mineral weathering at micro- and nano-scales.

58 GEOSCIENCES↗
DOE OSTI2021

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Abstract Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Modeling methane dynamics in three wetlands in Northeastern China by using the CLM-Microbe model

Wetlands account for up to 70% of the natural source of methane (CH 4 ) in terrestrial ecosystems on a global scale. Soil microbes are the ultimate producers and biological consumers of CH 4 in wetlands. Therefore, simulating microbial mechanisms of CH 4 production and consumptionwould improve the predictability of CH 4 flux in wetland ecosystems. In this study, we applied a microbial-explicit model, the CLM-Microbe, to simulate CH 4 flux in three major natural wetlands in northeastern China. The CLM-Microbe model was able to capture the seasonal variation of gross primary productivity (GPP), dissolved organic carbon (DOC), and CH 4 flux. The CLM-Microbe model explained more than 40% of the variation in GPP and CH 4 flux across sites. Marsh wetlands had higher CH 4 flux than mountain peatlands. Ebullition dominated the CH 4 transport pathway in all three wetlands. The methanogenesis dominates while methanotroph makes a minor contribution to the CH 4 flux, making all wetlands a CH 4 source. Sensitivity analysis indicated that microbial growth and death rates are the key factors governing CH 4 emission and vegetation physiological properties (flnr) and maintenance respiration predominate GPP variation. Explicitly simulating microbial processes allows genomic information to be incorporated, laying a foundation for better predicting CH 4 dynamics under the changing environment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Balancing Trade-Offs Imposed by Growth Media and Mass Spectrometry for Bacterial Exometabolomics

The bacterial exometabolome consists of a vast array of specialized metabolites, many of which are only produced in response to specific environmental stimuli. For this reason, it is desirable to control the extracellular environment with a defined growth medium composed of pure ingredients. However, complex (undefined) media are expected to support the robust growth of a greater variety of microorganisms than defined media. Here, we investigate the trade-offs inherent to a range of complex and defined solid media for the growth of soil microorganisms, production of specialized metabolites, and detection of these compounds using direct infusion mass spectrometry. We find that complex media support growth of more soil microorganisms, as well as allowing for the detection of more previously discovered natural products as a fraction of total m/z features detected in each sample. However, the use of complex media often caused mass spectrometer injection failures and poor-quality mass spectra, which in some cases resulted in over a quarter of samples being removed from analysis. Defined media, while more limiting in growth, generated higher quality spectra and yielded more m/z features after background subtraction. These results inform future exometabolomic experiments requiring a medium that supports the robust growth of many soil microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Nitrogen addition alters soil fungal communities, but root fungal communities are resistant to change

Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. Understanding and harnessing these interactions will be useful in both managed and natural ecosystems faced with global change, but it is still unclear how variation in environmental conditions and soils influence the trajectory of these interactions. In this study, we examine how nitrogen addition alters plant-fungal interactions within two species of Populus - Populus deltoides and P. trichocarpa. In this experiment, we manipulated plant host, starting soil (native vs. away for each tree species), and nitrogen addition in a fully factorial replicated design. After ~10 weeks of growth, we destructively harvested the plants and characterized plant growth factors and the soil and root endosphere fungal communities using targeted amplicon sequencing of the ITS2 gene region. Overall, we found nitrogen addition altered plant growth factors, e.g., plant height, chlorophyll density, and plant N content. Interestingly, nitrogen addition resulted in a lower fungal alpha diversity in soils but not plant roots. Further, there was an interactive effect of tree species, soil origin, and nitrogen addition on soil fungal community composition. Starting soils collected from Oregon and West Virginia were dominated by the ectomycorrhizal fungi Inocybe (55.8% relative abundance), but interestingly when P. deltoides was grown in its native West Virginia soil, the roots selected for a high abundance of the arbuscular mycorrhizal fungi, Rhizophagus. These results highlight the importance of soil origin and plant species on establishing plant-fungal interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Cryo-EM visualization of viruses from partially irrigated soils

Viruses are numerically the most abundant forms on Earth, and most are present in soil. Even though viruses are highly abundant in soil and critical to rhizosphere function, visualizing the diverse morphotypes within soil has been challenging. The difficulty is primarily due to the heterogenous nature of isolated suspensions that typically contain nanometer to micron scale debris which renders protein crystallography for structural studies unfeasible and hinders cryo-electron microscopy due to ice thickness and contrast issues. Here we employed and compared a simple spin filtration method to cleanup solutions of extracted viruses for direct observation with cryo-electron microscopy. The method employs common physical biochemical separation steps to remove large and small debris which dramatically improves image quality and preservation of structural features to permit visualizing morphotypes not typically seen with conventional negative stain approaches. In addition to tailed and non-tailed polyhedral phages, several under reported or novel morphotypes of soil viruses are directly visualized as a particle library with both 2D and 3D information.

cryo-EM↗
DOE OSTI2025

Root architectural plasticity optimizes nutrient acquisition in switchgrass under variable phosphorus forms

Aims Understanding the influence of different forms of phosphorus (P) over the different root traits and how those traits are related to increasing the efficiency of nutrient acquisition strategies. Methods Investigation of switchgrass (Panicum virgatum L.) root morphology responses to inorganic P (Pi) soluble (Potassium-P), insoluble (Aluminum-P), and organic P (Po) (Inositol Hexa-Phosphate, IHex-P) in rhizoboxes. Roots were traced over the root box and scanned using WinRhizoTM. The CRootbox model was employed to simulate root growth. Results Significant plasticity observed under IHex-P treatment, with a 46% increase in root branching, leading to a 74% rise in total root length and a 65% increase in root surface area compared to inorganic P forms. IHex-P resulted in a 73% higher root biomass than Aluminum-P and a 26% increase compared to Potassium-P. Most of the differences were attributed to the elongation of root branches. Conclusions Here, the study emphasizes the dynamic nature of switchgrass root architecture and morphology in response to varying P forms in the soil. The absence of Pi in the soil triggered increased plasticity in root traits, facilitating root access to Po and uptake of P. These findings offer valuable insights into the adaptive mechanisms of perennial plants, with significant implications for optimizing nutrient acquisition strategies in both agricultural and natural ecosystems.

Organic phosphorus↗
DOE OSTI2023

Methylmercury Degradation by Trivalent Manganese

Methylmercury (MeHg) is a potent neurotoxin and has great adverse health impacts on humans. Organisms and sunlight-mediated demethylation are well-known detoxification pathways of MeHg, yet whether abiotic environmental components contribute to MeHg degradation remains poorly known. Here, in this paper, we report that MeHg can be degraded by trivalent manganese (Mn(III)), a naturally occurring and widespread oxidant. We found that 28 ± 4% MeHg could be degraded by Mn(III) located on synthesized Mn dioxide (MnO 2–x ) surfaces during the reaction of 0.91 μg·L –1 MeHg and 5 g·L –1 mineral at an initial pH of 6.0 for 12 h in 10 mM NaNO 3 at 25 °C. The presence of low-molecular-weight organic acids (e.g., oxalate and citrate) substantially enhances MeHg degradation by MnO 2–x via the formation of soluble Mn(III)-ligand complexes, leading to the cleavage of the carbon–Hg bond. MeHg can also be degraded by reactions with Mn(III)-pyrophosphate complexes, with apparent degradation rate constants comparable to those by biotic and photolytic degradation. Thiol ligands (cysteine and glutathione) show negligible effects on MeHg demethylation by Mn(III). This research demonstrates potential roles of Mn(III) in degrading MeHg in natural environments, which may be further explored for remediating heavily polluted soils and engineered systems containing MeHg.

54 ENVIRONMENTAL SCIENCES↗