Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “root productivity”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Characterization of switchgrass ( Panicum virgatum L.) PvKSL1 as a levopimaradiene/abietadiene‐type diterpene synthase

Abstract The diverse class of plant diterpenoid metabolites serves important functions in mediating growth, chemical defence, and ecological adaptation. In major monocot crops, such as maize (Zea mays), rice (Oryza sativa), and barley (Hordeum vulgare), diterpenoids function as core components of biotic and abiotic stress resilience. Switchgrass (Panicum virgatum) is a perennial grass valued as a stress‐resilient biofuel model crop. Previously we identified an unusually large diterpene synthase family that produces both common and species‐specific diterpenoids, several of which accumulate in response to abiotic stress. Here, we report discovery and functional characterization of a previously unrecognized monofunctional class I diterpene synthase (PvKSL1) viain vivoco‐expression assays with different copalyl pyrophosphate (CPP) isomers, structural and mutagenesis studies, as well as genomic and transcriptomic analyses. In particular, PvKSL1 convertsent‐CPP intoent‐abietadiene,ent‐palustradiene,ent‐levopimaradiene, andent‐neoabietadiene via a 13‐hydroxy‐8(14)‐ent‐abietene intermediate. Notably, although featuring a distinctent‐stereochemistry, this product profile is near‐identical to bifunctional (+)‐levopimaradiene/abietadiene synthases occurring in conifer trees. PvKSL1 has three of four active site residues previously shown to control (+)‐levopimaradiene/abietadiene synthase catalytic specificity. However, mutagenesis studies suggest a distinct catalytic mechanism in PvKSL1. Genome localization ofPvKSL1distant from other diterpene synthases, and its phylogenetic distinctiveness from known abietane‐forming diterpene synthases, support an independent evolution of PvKSL1 activity. Albeit at low levels,PvKSL1gene expression predominantly in roots suggests a role of diterpenoid formation in belowground tissue. Together, these findings expand the known chemical and functional space of diterpenoid metabolism in monocot crops.

Plant Sciences↗
DOE OSTI2025

Time‐series multi‐omics analysis of micronutrient stress in Sorghum bicolor reveals iron and zinc crosstalk and regulatory network conservation

Micronutrient stress impacts growth, biomass production, and grain yield in crops. Multi-omics studies are valuable resources in identifying genes for functional studies and trait improvement, such as accumulation of Fe or Zn under deficient or excess conditions for bioenergy or grain agriculture. We conducted transcriptomics and ionomics analyses on Sorghum bicolor BTx623, grown under Fe and Zn limited and excess conditions over a 21-day period. To identify early and late transcriptional response in roots and leaves, 180 RNAseq libraries were sequenced for differential expression and co-expression network analyses. Fe and Zn accumulation was measured using ICP-MS at each time point, and a fluorometer was used to estimate chlorophyll content in leaves. Among the four treatments, Fe limitation and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves. Several of the reduction (Strategy I) and chelation (Strategy II) strategy genes that improve bioavailability of Fe and Zn in plant roots often used by non-grass and grass species, respectively, were differentially expressed. Gene regulatory network (GRN) analysis of roots revealed enrichment of genes from Fe limiting and Zn excess which strongly connect to homologues of SbFIT, SbPYE, and SbBTS as hub genes. The GRN for leaf responses showed homologues of SbPYE and SbBTS as hubs connecting genes for chloroplast biosynthesis, Fe-S cluster assembly, photosynthesis, and ROS scavenging. Expression analyses suggest sorghum uses Strategy II genes for Fe and Zn uptake, as expected, but can also utilize Strategy I genes, which may be advantageous in variable moisture environments. We found strong overlap between Fe and Zn responsive GRNs, indicative of micronutrient crosstalk. We also found conservation of root and leaf GRNs, and known homologous genes suggest strong constraints on homeostasis networks in plants. These data will provide a resource for functional genetics to enhance micronutrient transport in sorghum, and opportunities to conduct further comparative GRN analysis across diverse crops species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor‐like kinase

Summary Soil‐borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole‐genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor‐like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor‐root colonization by the ectomycorrhizal fungus Laccaria bicolor . By introducing PtLecRLK1 into a perennial grass known to be a non‐host of L. bicolor , switchgrass ( Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro‐PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non‐host to a host of L. bicolor . Furthermore, transcriptomic and proteomic analyses on inoculated‐transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defence pathway, consistent with the view that pathogenic defence response is down‐regulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N‐containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non‐host to enhance plant productivity and fitness on marginal lands.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A fresh perspective on the role of band bending, and related contributors, in light-driven production of electricity and chemicals

It is widely known that semiconductor-based solar energy conversion could power our planet. This is in part because high-quality semiconductor structures are unrivalled in their ability to separate photogenerated electrons and holes. One effective approach to achieving this photoinduced charge separation relies on a phenomenon known as “band bending”. But details to justify why band bending results in photoinduced charge separation are more complex than often appreciated. This underappreciation is an impediment to the rational, hypothesis-driven design of next-generation approaches to solar energy conversion. Herein we show, by means of derivations rooted in physical chemistry, that several phenomena – not just band bending – can facilitate photoinduced charge separation, and that each is influenced by nonequilibrium species concentration and a parameter, such as diffusion coefficient or rate coefficient, that introduces dynamics. To help visualize the impact of each phenomenon, we introduce plots that depict their contributions as free energy, force, flux, force constant, and rate. We reveal that spatial dopant distributions that define band bending are predictors of initial photogenerated species transport rates. But charge separation alone does not guarantee high-efficiency operation. A photogenerated change in energy that is freely available to do useful work is also essential, and is strongly dependent on semiconductor optical properties and reaction kinetics. Notably, this information reveals that specificity of interfacial chemical reactions – even when they are not preceded by charge separation elsewhere – can result in efficient solar energy conversion. We expect that this tutorial will guide researchers in their pursuit to uncover new mechanisms for light to perform useful work.

14 SOLAR ENERGY↗
DOE OSTI2022

Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass ( Panicum virgatum )

Summary Switchgrass ( Panicum virgatum ) is a bioenergy model crop valued for its energy efficiency and drought tolerance. The related monocot species rice ( Oryza sativa ) and maize ( Zea mays ) deploy species‐specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown. To investigate specialized metabolic drought responses in switchgrass, we integrated tissue‐specific transcriptome and metabolite analyses of the genotypes Alamo and Cave‐in‐Rock that feature different drought tolerance. The more drought‐susceptible Cave‐in‐Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid‐biosynthetic genes showed drought‐inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype‐specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought‐induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis verified select drought‐responsive diterpenoids as oxygenated furanoditerpenoids. Drought‐dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass drought responses. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance.

transcriptomics↗
DOE OSTI2025

Comprehensive Life Cycle Analysis of Methanol Production and Methanol-to-Diesel Conversion

Methanol is a strategic chemical and intermediate in the manufacture of synthetic diesel, due to its versatility, diesel’s compatibility with existing infrastructure, and their role in industrial and transport applications. Conventional production methods for methanol, primarily steam methane reforming (SMR), rely on natural gas and are subject to the price variability due to market conditions and geopolitical events. They are also associated with greenhouse gas (GHG) emissions. Methanol and synthetic diesel production could be integrated with nuclear energy to stabilize fuel prices and insulate pricing from outside geopolitical events due to the relative stability of nuclear fuel as compared to natural gas. This could lead to increased transportation fuel security, reliability and resilience. An added benefit is the abatement of emissions when substituting nuclear energy for conventional energy from natural gas. This report presents a comprehensive life cycle analysis(LCA) framework which was developed to evaluate the GHG emissions reduction potential associated with nuclear integrated methanol production, methanol-to-diesel upgrading, and end-use combustion. Gate-to-gate methanol production and cradle-to-grave emissions were evaluated in, starting with a business-as-usual (BAU) SMR-based methanol plant, and then considering stepwise nuclear integration. Methanol-to-diesel (MTD) conversion was evaluated accounting for nuclear energy integration and hydrogen production via high-temperature steam electrolysis (HTSE) using electricity either from the grid or from a dedicated nuclear power system. This multi-step process diverts stable and reliable nuclear energy into the transportation sector by upgrading low energy dense natural gas into liquid fuels fully compatible with existing infrastructure.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production

Abstract Oilcane is a metabolically engineered sugarcane ( Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI 1 transgene. The WRI 1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.

09 BIOMASS FUELS↗
DOE OSTI2025

Rhizosphere Microbiome Diversity Potentially Supports Robust Nature of Field Pennycress ( Thlaspi arvense L.) in Dryland Cropping Systems of Eastern Washington

ABSTRACT Field pennycress ( Thlaspi arvense L.) is an annual in the Brassicaceae family and is currently being developed as an oilseed intermediate crop suitable for renewable biodiesel and jet fuel. It displays many desirable characteristics for this role including cold tolerance, a rapid life cycle, and a seed fatty acid profile conducive to bioenergy generation. These traits make field pennycress favorable for winter oilseed cultivation in the inland Pacific Northwest (iPNW). Simultaneously, intermediate crops are an increasingly recognized component of both agronomic sustainability and soil health management. Intermediate crops enhance soil microbial diversity, which benefits both soil and plant health. To understand the impact of field pennycress on soil microbial diversity, two natural accessions and seven experimental accessions were grown at three sites in Eastern Washington. Aboveground biomass and rhizosphere soil were then collected. Soil genomic DNA was extracted from rhizosphere samples and used to generate an amplicon library for bacterial (16S) and fungal (ITS) rRNA sequences. The resulting libraries were analyzed in QIIME2, which revealed that not only did the fad2 deficient line from the Spring32‐10 background have significantly increased aboveground biomass production compared to other pennycress genotypes, but also displayed significantly higher β‐diversity in the rhizosphere community specifically at the site experiencing the driest conditions. ANCOM analysis showed that multiple sequences similar to beneficial plant and soil health enhancing organisms such as Trichoderma spirale , Pseudomonas spp., and Methylobacterium goesingense were found to be enriched in the microbiome of the fad2 Spring32‐10 background also at that site. To add additional context to rhizosphere community data, root exudates from two pennycress genotypes were captured in magenta boxes and analyzed using HPLC. Future work will expand our understanding of the mechanisms by which field pennycress creates diversity in the rhizosphere, thus expanding our ability to cultivate this crop in the iPNW.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Economic Impact of Pacific Northwest National Laboratory (PNNL) on the State of Washington in Fiscal Year 2020

The FY 2020 Economic Impact Report details several of PNNL’s economic indicators, including PNNL’s total economic output, annual spending, jobs, number of employees, purchased goods and services, companies with roots in PNNL, STEM support and corporate charitable contributions. It also explains the economic impact of PNNL operations on the state of Washington—all within the context of PNNL’s response to the COVID pandemic and the effect of COVID-19 on PNNL’s economic impact within the state and local community during FY 2020. The results are impressive. Our response to COVID allowed for the majority of our staff to transition to telework, stay productive, avoid furloughs, and even hire new staff. COVID had minimal impact on our ability to positively effect economic impact in the state and community. Additionally, we directly and indirectly supported more than $1.59B through PNNL payroll and domestic purchased goods and services, and we generated 7,580 jobs in Washington State. PNNL’s annual spending was more than $1.1B. Battelle and PNNL contributions to philanthropic and civic organizations totaled $1.08M, many of which are outlined within the report. This information is intended to answer questions we often get from stakeholders who believe in the power of science and technology institutions to help sustain vibrant, educated communities in our state.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

Maximizing energy efficiency in wastewater treatment plants: A data-driven approach for waste heat recovery and an economic analysis using Organic Rankine Cycle and thermal energy storage

Maximizing energy efficiency through waste heat recovery (WHR) processes is crucial for sustainable and ecofriendly operations across multiple industries, notably in wastewater treatment plants (WWTPs). This work proposes a comprehensive approach for assessing the WHR feasibility in WWTPs, structured in two main objectives. Firstly, an Artificial Neural Network (ANN) model is developed to accurately predict WHR based on operational data, including biogas temperature, biogas pressure, daily production in kWh, and WHR values in kWh th . The second objective focuses on economically evaluating the WHR feasibility based on the estimated WHR values obtained by the ANN model, and then realistically assessing the economic feasibility of integrating the Organic Rankine Cycle (ORC) and Seasonal Thermal Energy Storage (STES) systems. With an application to the As-Samra WWTP located in Jordan, the developed ANN model demonstrates promising results in the validation phase, with a root mean square error (RMSE) of 2206 kWh/day, a mean absolute error (MAE) of 1674 kWh/day, and an R-squared (R 2 ) value of 68%. On the other hand, the economic analysis reveals that an optimal ORC system of 412.14 kW e capacity yields a Net Present Value (NPV) of 2.09 million US dollars, a Levelized Cost of Energy (LCOE) of 0.0749 USD/kWh, a Payback Period (PBP) of 4.8 years, and annual revenues of 428 kUSD. This work also investigates the techno-economic feasibility of integrating ORC-STES. Results indicate that the LCOE and PBP are highly affected by the ORC's capital cost, and integrating STES increases the LCOE to 0.0824 USD/kWh, rendering its integration with ORC infeasible. In conclusion, this study aims to advance the understanding and application of WHR in WWTPs, paving the way for more efficient and sustainable practices in the field.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Spatio–Temporal Coarse–Graining Decomposition of the Global Ocean Geostrophic Kinetic Energy

We expand on a recent determination of the first global energy spectrum of the ocean’s surface geostrophic circulation using a coarse-graining (CG) method. We compare spectra from CG to those from spherical harmonics by treating land in a manner consistent with the boundary conditions. While the two methods yield qualitatively consistent domain-averaged results, spherical harmonics spectra are too noisy at gyre-scales (> 1000 km). More importantly, spherical harmonics are inherently global and cannot provide local information connecting scales with currents geographically. CG shows that the extra-tropics mesoscales (100–500 km) have a root-mean-square (rms) velocity of ~15 cm/s, which increases to ~30–40 cm/s locally in the Gulf Stream and Kuroshio and to ~16–28 cm/s in the ACC. There is notable hemispheric asymmetry in mesoscale energy-per-area, which is higher in the north due to continental boundaries. We estimate that ≈25–50% of total geostrophic energy is at scales smaller than 100 km, and is un(der)-resolved by pre-SWOT satellite products. Spectra of the time-mean circulation show that most of its energy (up to 70%) resides in stationary eddies with characteristic scales smaller than (< 500 km). This highlights the preponderance of ‘standing’ small-scale structures in the global ocean due to the temporally coherent forcing by boundaries. By coarse-graining in space and time, we compute the first spatio-temporal global spectrum of geostrophic circulation from AVISO and NEMO. These spectra show that every length-scale evolves over a wide range of time-scales with a consistent peak at ≈200 km and ≈2–3 weeks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency

Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. Phosphorus deficiency is especially challenging for the production of bioenergy feedstock plantation species, such as poplars (Populus spp.), where fertilization may not be practically or economically feasible. While the phenotypic effects of P deficiency are well known, the molecular mechanisms underlying whole-plant and tissue-specific responses to P deficiency, and in particular the responses of commercially valuable hardwoods, are less studied. We used a multi-tissue and multi-omics approach using transcriptomic, proteomic, and metabolomic analyses of the leaves and roots of black cottonwood (Populus trichocarpa) seedlings grown under P-deficient (5 µM P) and replete (100 µM P) conditions to assess this knowledge gap and to identify potential gene targets for selection for P efficiency. In comparison to seedlings grown at 100 µM P, P-deficient seedlings exhibited reduced dry biomass, altered chlorophyll fluorescence, and reduced tissue P concentrations. In line with these observations, growth, C metabolism, and photosynthesis pathways were downregulated in the transcriptome of the P-deficient plants. Additionally, we found evidence of strong lipid remodeling in the leaves. Metabolomic data showed that the roots of P-deficient plants had a greater relative abundance of phosphate ion, which may reflect extensive degradation of P-rich metabolites in plants exposed to long-term P-deficiency. With the notable exception of the KEGG pathway for Starch and Sucrose Metabolism (map00500), the responses of the transcriptome and the metabolome to P deficiency were consistent with one another. No significant changes in the proteome were detected in response to P deficiency. Collectively, our multi-omic and multi-tissue approach enabled the identification of important metabolic and regulatory pathways regulated across tissues at the molecular level that will be important avenues to further evaluate for P efficiency. These included stress-mediating systems associated with reactive oxygen species maintenance, lipid remodeling within tissues, and systems involved in P scavenging from the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

3P Program: Phenotyping X Prediction = Productivity (Final Scientific/Technical Report)

The goal of the 3P Program was to establish integrated, real-time phenotyping and to analyze above- and below-ground plant architecture and total carbon partitioning and allocation to predict heterosis and develop superior crop hybrids by fully leveraging the Sorghum gene pool. There were two overarching themes: 1) the development of a new crop improvement approach utilizing advances in high-throughput phenotyping (HTP), computing, and genomics for public dissemination and 2) leveraging this platform for sorghum crop improvement and commercialization. The Clemson team worked on creating genomic resources and using both statistical learning and high-throughput phenotyping in genomics-assisted breeding. Research was broadly interested in the genetics of carbon partitioning, with the aim of improving crop performance and achieving sustainability. The technology and resources created can be readily found in the public domain and serve to advance scientific understanding of crop genomics and breeding. Genomic prediction was able to identify top crosses to be made, and a hybrid prediction pipeline is in place to drive year-over-year genetic gain. Roots have long been ignored by plant breeders and agronomists, not because they are unimportant but because they are hard to measure. This is an untapped white space of potential insight and innovation. To address this, Hi Fidelity Genetics developed the RootTracker to measure roots in the field on a continuous basis. A database system called RootTracker Tracker was developed to handle data coming from the RootTrackers. In using this device, valuable data was observed for plant breeding, hydrochemical development, and other agricultural biology applications. Carnegie Mellon’s goal was developing new techniques to generate high-resolution 3D models of plants from data collected in the field. The idea was that more useful and more informative phenotypes could be extracted by resolving small features, such as seeds and flowers, and that by modeling in 3D, the spatial structure of plants could be examined. To achieve this, multiple images collected by a new small format structured light stereo imager were fused together. A sorghum panicle modeling pipeline was developed to allow the collection and processing of data. Carolina Seed Systems is an agricultural technology company focused on decarbonizing the agricultural system. Their technology pipeline serves to drive fundamental progress towards creation and distribution of carbon negative crops. The genomic and the engineering technology developed through the 3P Program was leveraged to deliver both value and sustainability from the grower to the consumer. Promising sorghum hybrids were scaled up and commercialized. The overall goal of our research was to integrate, create, and deploy genetic and engineering concepts and technologies to enhance crop productivity in a sustainable fashion. The combination of public and private partners allowed the basic research and hypothesis testing to be quickly accelerated for commercial application by the companies yet maintained that the core framework and academic insights remain in the public domain for continued market disruption, competition, and innovation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Fermentation‐mediated growth, signaling, and defense in plants

Summary While traditionally considered important mainly in hypoxic roots during flooding, upregulation of fermentation pathways in plants has recently been described as an evolutionarily conserved drought survival strategy, with acetate signaling mediating reprograming of transcription and cellular carbon and energy metabolism from roots to leaves. The amount of acetate produced directly correlates with survival through potential mechanisms including defense gene activation, biosynthesis of primary and secondary metabolites, and aerobic respiration. Here, we review root ethanolic fermentation responses to hypoxia during saturated soil conditions and summarize studies highlighting acetate fermentation under aerobic conditions coupled with respiration during growth and drought responses. Recent work is discussed demonstrating long‐distance transport of acetate via the transpiration stream as a respiratory substrate. While maintenance and growth respiration are often modeled separately in terrestrial models, here we propose the concept of ‘Defense Respiration’ fueled by acetate fermentation in which upregulation of acetate fermentation contributes acetate substrate for alternative energy production via aerobic respiration, biosynthesis of primary and secondary metabolites, and the acetylation of proteins involved in defense gene regulation. Finally, we highlight new frontiers in leaf‐atmosphere emission measurements as a potential way to study acetate fermentation responses of individual leaves, branches, ecosystems, and regions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Aboveground woody biomass estimation of young bioenergy plantations of Populus and its hybrids using mobile (backpack) LiDAR remote sensing

Woody aboveground biomass (AGB) including short-rotation Populus is used as a feedstock for renewable and carbon-neutral bioenergy. While woody AGB can be estimated with allometric equations requiring labor-intensive field data, remote sensing technologies like mobile terrestrial light detection and ranging (LiDAR) can estimate woody AGB quickly and accurately. Therefore, the goals of this study were to develop a model to predict woody AGB of 2-year-old Populus spp. from three taxa (P. deltoides, P. deltoides × P. maximowiczii and P. deltoides × P. trichocarpa) using allometric (height and diameter at breast height (DBH)) or LiDAR-derived metrics from a mobile terrestrial (backpack) system. Likewise, we sought to compare LiDAR-estimated tree height and DBH with field-measured values. We found that a taxa-specific model containing LiDAR-measured tree height, crown volume, and taxa interactions with the height of the 10 th percentile, and the density of the lowest interval (density metric 0) explained 84 % of the variation in woody AGB with a root mean square error (RMSE) of 28.7 % and performed slightly better than the allometric model. The best model excluding taxa had a slightly higher RMSE but lower bias than the allometric model. LiDAR-derived tree heights were highly correlated with field-measured heights, but DBH could not be estimated accurately. Therefore, terrestrial mobile LiDAR systems can accurately estimate woody AGB and tree height of Populus in short rotation systems to aid in the fast and efficient quantification of woody bioenergy production and renewable energy resources.

AGB↗
DOE OSTI2024

Revealing the hidden structure of disordered materials by parameterizing their local structural manifold

Abstract Durable interest in developing a framework for the detailed structure of glassy materials has produced numerous structural descriptors that trade off between general applicability and interpretability. However, none approach the combination of simplicity and wide-ranging predictive power of the lattice-grain-defect framework for crystalline materials. Working from the hypothesis that the local atomic environments of a glassy material are constrained by enthalpy minimization to a low-dimensional manifold in atomic coordinate space, we develop a generalized distance function, the Gaussian Integral Inner Product (GIIP) distance, in connection with agglomerative clustering and diffusion maps, to parameterize that manifold. Applying this approach to a two-dimensional model crystal and a three-dimensional binary model metallic glass results in parameters interpretable as coordination number, composition, volumetric strain, and local symmetry. In particular, we show that a more slowly quenched glass has a higher degree of local tetrahedral symmetry at the expense of cyclic symmetry. While these descriptors require post-hoc interpretation, they minimize bias rooted in crystalline materials science and illuminate a range of structural trends that might otherwise be missed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome

Abstract Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac -like and iad -like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad -like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad -like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Estimating Soil Thermal Inertia Profiles From the Passive Equilibration of a Temperature Probe

Knowledge of the distribution of soil thermal properties is important for understanding subsurface hydrological and biogeochemical processes. This study describes and evaluates quick thermal profiling (QTP), a new measurement technique aimed at providing rapid, depth-resolved measurements of soil thermal inertia at numerous locations across the landscape. A cylindrical probe with temperature sensors at multiple depths is quickly inserted into the ground, and soil thermal inertia is estimated from how quickly the probe temperature equilibrates with the soil. To this end, a finite volume heat transfer model is used to generate temperature equilibration time series across combinations of controlling factors, and a gridded search inversion approach is applied to infer soil thermal inertia. Field tests in the Arctic indicate that QTP measurements have a minimum uncertainty of 0.14 J m −2 K −1 s −1/2 and covary with dual-probe heat pulse thermal analyzer measurements (concordance correlation coefficient = 0.56) with a root-mean-square error of 0.40 J m −2 K −1 s −1/2 . Besides demonstrating the value of QTP for estimating thermal inertia, this study identifies various sources of measurement uncertainty, particularly probe-soil contact resistance and frictional heating. Further, analysis of soil samples indicates that thermal inertia can be used to estimate thermal conductivity and dry bulk density in the studied area, although such inferences are highly site-specific. Overall, the QTP method holds promise to generate thermal inertia data products and to complement other characterization approaches for advancing understanding of soil properties across far more locations than is currently possible.

Lamb, J. R. [Lawrence Berkeley National Laboratory↗