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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis

Abstract Background Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions. Results To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13 C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13 C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts. Conclusions Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Intraspecific Variation for Leaf Physiological and Root Morphological Adaptation to Drought Stress in Alfalfa ( Medicago sativa L.)

Drought stress reduces crop biomass yield and the profitability of rainfed agricultural systems. Evaluation of populations or accessions adapted to diverse geographical and agro-climatic environments sheds light on beneficial plant responses to enhance and optimize yield in resource-limited environments. This study used the morphological and physiological characteristics of leaves and roots from two different alfalfa subspecies during progressive drought stress imposed on controlled and field conditions. Two different soils (Experiments 1 and 2) imposed water stress at different stress intensities and crop stages in the controlled environment. Algorithm-based image analysis of leaves and root systems revealed key morphological and physiological traits associated with biomass yield under stress. The Medicago sativa subspecies (ssp.) sativa population, PI478573, had smaller leaves and maintained higher chlorophyll content (CC), leaf water potential, and osmotic potential under water stress. In contrast, M. sativa ssp. varia, PI502521, had larger leaves, a robust root system, and more biomass yield. In the field study, an unmanned aerial vehicle survey revealed PI502521 to have a higher normalized difference vegetation index (vegetation cover and plant health characteristics) throughout the cropping season, whereas PI478573 values were low during the hot summer and yielded low biomass in both irrigated and rainfed treatments. RhizoVision Explorer image analysis of excavated roots revealed a smaller diameter and a narrow root angle as target traits to increase alfalfa biomass yield irrespective of water availability. Root architectural traits such as network area, solidity, volume, surface area, and maximum radius exhibited significant variation at the genotype level only under limited water availability. Different drought-adaptive strategies identified across subspecies populations will benefit the plant under varying levels of water limitation and facilitate the development of alfalfa cultivars suitable across a broad range of growing conditions. The alleles from both subspecies will enable the development of drought-tolerant alfalfa with enhanced productivity under limited water availability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Increased leaf area index and efficiency drive enhanced production under elevated atmospheric [ CO 2 ] in a pine‐dominated stand showing no progressive nitrogen limitation

Abstract Enhancement of net primary production (NPP) in forests as atmospheric [CO 2 ] increases is likely limited by the availability of other growth resources. The Duke Free Air CO 2 Enrichment (FACE) experiment was located on a moderate‐fertility site in the southeastern US, in a loblolly pine ( Pinus taeda L.) plantation with broadleaved species growing mostly in mid‐canopy and understory. Duke FACE ran from 1994 to 2010 and combined elevated [CO 2 ] (eCO 2 ) with nitrogen (N) additions. We assessed the spatial and temporal variation of NPP response using a dataset that includes previously unpublished data from 6 years of the replicated CO 2 × N experiment and extends to 2 years beyond the termination of enrichment. Averaged over time (1997–2010), NPP of pine and broadleaved species were 38% and 52% higher under eCO 2 compared to ambient conditions. Furthermore, there was no evidence of a decline in enhancement over time in any plot regardless of its native site quality. The relation between spatial variation in the response and native site quality was suggested but inconclusive. Nitrogen amendments under eCO 2 , in turn, resulted in an additional 11% increase in pine NPP. For pine, the eCO 2 ‐induced increase in NPP was similar above‐ and belowground and was driven by both increased leaf area index ( L ) and production efficiency (PE = NPP/ L ). For broadleaved species, coarse‐root biomass production was more than 200% higher under eCO 2 and accounted for the entire production response, driven by increased PE. Notably, the fraction of annual NPP retained in total living biomass was higher under eCO 2 , reflecting a slight shift in allocation fraction to woody mass and a lower mortality rate. Our findings also imply that tree growth may not have been only N‐limited, but perhaps constrained by the availability of other nutrients. The observed sustained NPP enhancement, even without N‐additions, demonstrates no progressive N limitation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Implications from Monitoring Gopher Tortoises at Two Spatial Scales

A problem that conservation biologists face is how to monitor species, given both resource limitations and the inherent challenges of assessing long-term demographic processes. We assessed gopher tortoise (Gopherus polyphemus) abundance at a landscape scale and at the scale of 3 local populations within the Conecuh National Forest (CNF).USA between 1991 and 2017. Landscape-level data were collected 26 from line transect distance sampling arranged uniformly across the CNF and collected during a single season (2011); data for local populations were generated from long-term mark-recapture of individuals at three sites selected based on prior knowledge of high density at each. At a landscape scale, we estimated 5,242 (95% CI = 3,538-7,768) tortoises occurred across the approximately 34,000-ha forest, yielding a density of 0.14-0.32 tortoises/ ha. These low densities across the landscape suggest that, on average, management activities across the property have not allowed tortoise populations to retain social structure needed for long-term persistence. The three local populations, however, contained 25-60 individuals and densities of 1.9–6.9 tortoises/ha. Over the study period, populations at two sites were stable and the third experienced significant population growth. Mean annual survival of individuals was 0.89 and invariant across size classes. Altogether, line transect distance sampling is important for assessing landscape-scale abundance of tortoises but may fail to detect local clusters of high-density sites important for population persistence. Our mark-recapture efforts at the local scale revealed that small populations on these high-density sites can exhibit long-term stability or growth even though they do not meet current established criteria for viability. Improved models that incorporate immigration and emigration and better reflect dynamics of peripheral populations would assist in determining how such populations best contribute to species recovery and regional conservation targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Novel use of Direct Simulation Monte-Carlo to Model Dynamics of COVID-19 Pandemic Spread

In this report, we evaluate a novel method for modeling the spread of COVID-19 pandemic. In this new approach we leverage methods and algorithms developed for fully-kinetic plasma physics simulations using Particle-In-Cell (PIC) Direct Simulation Monte-Carlo (DSMC) models. This approach then leverages Sandia-unique simulation capabilities, and High-Performance Computer (HPC) resources and expertise in particle-particle interactions using stochastic processes. Our hypothesis is that this approach would provide a more efficient platform with assumptions based on physical data that would then enable the user to assess the impact of mitigation strategies and forecast different phases of infection. This work addresses key scientific questions related to the assumptions this new approach must make to model the interactions of people using algorithms typically used for modeling particle interactions in physics codes (kinetic plasma, gas dynamics). The model developed uses rational/physical inputs while also providing critical insight; the results could serve as inputs to, or alternatives for, existing models. The model work presented was developed over a four-week time frame, thus far showing promising results and many ways in which this model/approach could be improved. This work is aimed at providing a proof-of-concept for this new pandemic modeling approach, which could have an immediate impact on the COVID-19 pandemic modeling, while laying a basis to model future pandemic scenarios in a manner that is timely and efficient. Additionally, this new approach provides new visualization tools to help epidemiologists comprehend and articulate the spread of this and other pandemics as well as a more general tool to determine key parameters needed in order to better predict pandemic modeling in the future. In the report we describe our model for pandemic modeling, apply this model to COVID-19 data for New York City (NYC), assess model sensitivities to different inputs and parameters and , finally, propagate the model forward under different conditions to assess the effects of mitigation and associated timing. Finally, our approach will help understand the role of asymptomatic cases, and could be extended to elucidate the role of recovered individuals in the second round of the infection, which is currently being ignored.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Root and Leaf Traits of Alfalfa Exhibit Distinct Responses to Soil Microbial Communities and Environmental Stresses

Ongoing climate change is negatively impacting crop productivity globally. Past research has highlighted that a diverse soil microbial community and variation in plant traits for resource acquisition can mitigate the negative impacts of climate change factors on crop productivity. This study investigates the effects of two major environmental stressors—drought and salinity stress, on plant productivity, biomass allocation, and root and leaf trait responses under distinct soil microbial diversities. Our results showed that salinity stress had stronger negative impacts on plant productivity than drought stress. Shoot biomass decreased by 30% and 32.5% under drought and salinity stress, respectively, whereas the root biomass decreased by 32% only under salinity stress. Soil microbial diversity did not affect plant productivity. Next, root traits were mainly impacted by drought and salinity stress, whereas leaf traits were impacted by both environmental stresses and soil microbial diversity. Specific root length and specific root area decreased under drought, and root tissue density was minimal under salinity stress. Root traits were not affected by soil microbial communities. In contrast, the leaf nitrogen content increased, whereas pheophytin content (a breakdown product of chlorophyll) decreased when plants were grown in diverse microbial communities under environmental stresses, especially drought. These results highlight the importance of soil microbial diversity in impacting plant traits in response to environmental stresses. We showed that the soil microbial diversity influences both aboveground and belowground plant traits, indicating the need for better management practices to conserve and promote soil microbial diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data for Physiological Controls on Carbon Fluxes and Biomass Production in Miscanthus: Insights From a Process- Based Agroecosystem Model

Biomass crops serve as essential feedstocks for renewable energy and bioproducts and play a critical role in achieving lower emissions in the transportation sector. However, dedicated perennial biomass crops such as Miscanthus × giganteus (Miscanthus) remain underrepresented in process- based agroecosystem models, limiting robust evaluation of their economic and environmental performance. In this study, we developed a data- constrained representation of the sterile triploid Miscanthus (IL clone) within the process- based model ecosys, integrating global sensitivity analysis, ensemble simulation, and parameter calibration. Planting, harvesting, and fertilization practices consistent with field management were incorporated, and phenology was constrained using PhenoCam- derived Green Chromatic Coordinate (GCC) data. Using the Morris global sensitivity analysis method, we identified 11 key physiological parameters governing plant carbon, water, and nutrient relations, particularly processes associated with CO2 assimilation. We then conducted ensemble simulations by perturbing these parameters and calibrated the model against eddy covariance fluxes and field- measured biomass. Building on the calibrated operating state, parameter- response analyses show that different photosynthetic processes influence productivity in different ways. Protein allocation determines whether productivity increases toward a higher level, whereas electron transport capacity controls additional gains once protein allocation approaches saturation. These findings demonstrate that parameter importance depends on physiological context and on which photosynthetic processes remain limiting. Calibration and validation against observations show that ecosys can reliably reproduce carbon and water fluxes, as well as both above- and belowground biomass, with post- calibration GPP R2 improving from 0.67 to 0.95 during the calibration period and remaining high during validation (R2 = 0.95). These results provide a mechanistic foundation for regional simulations and sustainable bioenergy assessments.

Carbon↗
DOE OSTI2022

Root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism

Root angle in crops represents a key trait for efficient capture of soil resources. Root angle is determined by competing gravitropic versus antigravitropic offset (AGO) mechanisms. Here we report a root angle regulatory gene termed ENHANCED GRAVITROPISM1 ( EGT1 ) that encodes a putative AGO component, whose loss-of-function enhances root gravitropism. Mutations in barley and wheat EGT1 genes confer a striking root phenotype, where every root class adopts a steeper growth angle. EGT1 encodes an F-box and Tubby domain-containing protein that is highly conserved across plant species. Haplotype analysis found that natural allelic variation at the barley EGT1 locus impacts root angle. Gravitropic assays indicated that Hvegt1 roots bend more rapidly than wild-type. Transcript profiling revealed Hvegt1 roots deregulate reactive oxygen species (ROS) homeostasis and cell wall-loosening enzymes and cofactors. ROS imaging shows that Hvegt1 root basal meristem and elongation zone tissues have reduced levels. Atomic force microscopy measurements detected elongating Hvegt1 root cortical cell walls are significantly less stiff than wild-type. In situ analysis identified HvEGT1 is expressed in elongating cortical and stele tissues, which are distinct from known root gravitropic perception and response tissues in the columella and epidermis, respectively. We propose that EGT1 controls root angle by regulating cell wall stiffness in elongating root cortical tissue, counteracting the gravitropic machinery’s known ability to bend the root via its outermost tissues. We conclude that root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms

The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry.

16S RNA↗
DOE OSTI2020

Evaluation of residue management practices on barley residue decomposition

Optimizing barley (hordeum vulgare L.) production in Idaho and other parts of the Pacific Northwest (PNW) should focus on farm resource management. The effect of post-harvest residue management on barley residue decomposition has not been adequately studied. Thus, the objective of this study was to determine the effect of residue placement (surface vs. incorporated), residue size (chopped vs. ground-sieved) and soil type (sand and sandy loam) on barley residue decomposition. A 50-day(d) laboratory incubation experiment was conducted at a temperature of 25°C at the Aberdeen Research and Extension Center, Aberdeen, Idaho, USA. Following the study, a Markov-Chain Monte Carlo (MCMC) modeling approach was applied to investigate the first-order decay kinetics of barley residue. An accelerated initial flush of residue carbon(C)-mineralization was measured for the sieved (Day 1) compared to chopped (Day 3 to 5) residues for both surface incorporated applications. The highest evolution of carbon dioxide (CO 2 )-C of 8.3 g kg -1 dry residue was observed on Day 1 from the incorporated-sieved application for both soils. The highest and lowest amount of cumulative CO 2 -C released and percentage residue decomposed over 50-d was observed for surface-chopped (107 g kg -1 dry residue and 27%, respectively) and incorporated-sieved (69 g kg -1 dry residue and 18%, respectively) residues, respectively. There were no significant differences in C-mineralization from barley residue based on soil type or its interactions with residue placement and size (p >0.05). The largest decay constant k of 0.0083 d -1 was calculated for surface-chopped residue where the predicted half-life was 80 d, which did not differ from surface sieved or incorporated chopped. In contrast, incorporated-sieved treatments only resulted in a k of 0.0054 d -1 and would need an additional 48 d to decompose 50% of the residue. Future residue decomposition studies under field conditions are warranted to verify the residue C-mineralization and its impact on residue management.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Potential applications of microbial genomics in nuclear non-proliferation

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as “characteristic communities of microorganisms” found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project

Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. Here we describe a “follow the tissue” pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Evaluation of Howard A. Hanson Dam Juvenile Fish Passage and Survival Study Live Fish Injury Assessment, Sensor Fish, and BioPA Modeling Tasks

The live fish injury assessment, Sensor Fish, and BioPA modeling study tasks were conducted by researchers from Pacific Northwest National Laboratory (PNNL). The four tasks were part of the larger Evaluation of Howard A. Hanson Dam (HAHD) Juvenile Fish Passage and Survival study, which had six total tasks. To achieve study objectives for each of the four tasks, field work occurred at Green Peter Dam (GPR) to evaluate the highest elevation steep slope bypass pipe, at HAHD to evaluate baseline conditions of the horseshoe tunnel, and at PNNL’s Aquatic Research Laboratory (ARL) to evaluate simulated dam passage conditions (i.e., shear forces and collision). Each of these evaluations utilized live fish injury assessment, Sensor Fish, and BioPA modeling. Live fish injury assessment and survival (tagged with and without balloon or passive integrated transponder [PIT] tags) was correlated with Sensor Fish to determine thresholds. The CFD analyses were then performed, and the computed values were compared to the corresponding measured values of Sensor Fish data. The results of the overall injury and survival of fish was also used in the validation of the CFD modeling method. Collectively, the results will aid in future modeling of fish passage at HAHD. Results from these tasks can be used by biologists, engineers, resource managers, and regional decision-makers to inform baseline conditions under current operations and the engineering design of the new FPF at HAHD. This draft report contains initial data and results from the four tasks. Table 8 1, Table 8 2, and Table 8 3, and Figure 8 1, Figure 8 2, and Figure 8 3 depict the CFD modeling findings for the GPR steep slope bypass, HAHD horseshoe tunnel, and laboratory testing. Table 8 4, Table 8 5, and Table 8 6 depict the Sensor Fish findings for the GPR steep slope bypass and HAHD horseshoe tunnel testing. The Mv values observed in the HAHD were significantly lower compared to the laboratory experiments conducted at PNNL. Currently, investigations are underway to understand the reasons for this disparity and to establish an appropriate threshold value for Mv. Survival predictions presented in the tables below should be considered preliminary and should not be used until further analyses and adjustments are completed. The next steps for modeling will include the flow regime, (i.e., density of flow regimes due to water and air mixing ) to continue to improve on the threshold value for Mv.

13 HYDRO ENERGY↗
DOE OSTI2024

Land cover and space use influence coyote carnivory: evidence from stable-isotope analysis

For many species, the relationship between space use and diet composition is complex, with individuals adopting varying space use strategies such as territoriality to facilitate resource acquisition. Coyotes ( Canis latrans ) exhibit two disparate types of space use; defending mutually exclusive territories (residents) or moving nomadically across landscapes (transients). Resident coyotes have increased access to familiar food resources, thus improved foraging opportunities to compensate for the energetic costs of defending territories. Conversely, transients do not defend territories and are able to redirect energetic costs of territorial defense towards extensive movements in search of mates and breeding opportunities. These differences in space use attributed to different behavioral strategies likely influence foraging and ultimately diet composition, but these relationships have not been well studied. We investigated diet composition of resident and transient coyotes in the southeastern United States by pairing individual space use patterns with analysis of stable carbon (δ 13 C) and nitrogen (δ 15 N) isotope values to assess diet. During 2016–2017, we monitored 41 coyotes (26 residents, 15 transients) with GPS radio-collars along the Savannah River area in the southeastern United States. We observed a canopy effect on δ 13 C values and little anthropogenic food in coyote diets, suggesting 13 C enrichment is likely more influenced by reduced canopy cover than consumption of human foods. We also observed other land cover effects, such as agricultural cover and road density, on δ 15 N values as well as reduced space used by coyotes, suggesting that cover types and localized, resident-like space use can influence the degree of carnivory in coyotes. Finally, diets and niche space did not differ between resident and transient coyotes despite differences observed in the proportional contribution of potential food sources to their diets. Although our stable isotope mixing models detected differences between the diets of resident and transient coyotes, both relied mostly on mammalian prey (52.8%, SD = 15.9 for residents, 42.0%, SD = 15.6 for transients). Resident coyotes consumed more game birds (21.3%, SD = 11.6 vs 13.7%, SD = 8.8) and less fruit (10.5%, SD = 6.9 vs 21.3%, SD = 10.7) and insects (7.2%, SD = 4.7 vs 14.3%, SD = 8.5) than did transients. Our findings indicate that coyote populations fall on a feeding continuum of omnivory to carnivory in which variability in feeding strategies is influenced by land cover characteristics and space use behaviors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Using Novosphingobium aromaticivorans for Concurrent Production of Intracellular and Extracellular Products from Aromatics Extracted from Poplar Biomass

Achieving high biochemical production in biotransformations of renewable resources requires using concentrated cultures that not only generate the product of interest but also produce abundant microbial cell waste. We explored the concept of gaining value from microbial cells by producing intracellular products in tandem with a desired extracellular product. Specifically, we engineered a strain ofNovosphingobium aromaticivorans to extracellularly produce 2-pyrone-4,6-dicarboxylic acid (PDC) from aromatic substrates and to intracellularly accumulate astaxanthin along with coenzyme Q 10 , all of which are products of industrial interest. Achieving the goal of concurrent production of intracellular and extracellular products required the creative application of bioreactor engineering principles. Although a continuously fed membrane bioreactor (MBR) maximized extracellular product biosynthesis, it had a negative effect on intracellular product accumulation. However, operating the MBR as a sequencing batch reactor (MBR-SBR) with a step-feed resulted in stable concurrent production of both extracellular and intracellular products. With aromatics extracted from poplar biomass, we achieved productivities of 1.14 g of PDC/L-h for the extracellular product and 0.04 mg of astaxanthin/L-h and 0.64 mg of CoQ 10 /L-h for intracellular products, respectively. Our findings demonstrate that the mode of operation of a bioreactor impacts the simultaneous production of intracellular and extracellular products byN. aromaticivorans.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. In conclusion, STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Installation and imaging of thousands of minirhizotrons to phenotype root systems of field-grown plants

Roots are vital to plant performance because they acquire resources from the soil and provide anchorage. However, it remains difficult to assess root system size and distribution because roots are inaccessible in the soil. Existing methods to phenotype entire root systems range from slow, often destructive, methods applied to relatively small numbers of plants in the field to rapid methods that can be applied to large numbers of plants in controlled environment conditions. Much has been learned recently by extensive sampling of the root crown portion of field-grown plants. But, information on large-scale genetic and environmental variation in the size and distribution of root systems in the field remains a key knowledge gap. Minirhizotrons are the only established, non-destructive technology that can address this need in a standard field trial. Prior experiments have used only modest numbers of minirhizotrons, which has limited testing to small numbers of genotypes or environmental conditions. This study addressed the need for methods to install and collect images from thousands of minirhizotrons and thereby help break the phenotyping bottleneck in the field. Over three growing seasons, methods were developed and refined to install and collect images from up to 3038 minirhizotrons per experiment. Modifications were made to four tractors and hydraulic soil corers mounted to them. High quality installation was achieved at an average rate of up to 84.4 minirhizotron tubes per tractor per day. A set of four commercially available minirhizotron camera systems were each transported by wheelbarrow to allow collection of images of mature maize root systems at an average rate of up to 65.3 tubes per day per camera. This resulted in over 300,000 images being collected in as little as 11 days for a single experiment. The scale of minirhizotron installation was increased by two orders of magnitude by simultaneously using four tractor-mounted, hydraulic soil corers with modifications to ensure high quality, rapid operation. Image collection can be achieved at the corresponding scale using commercially available minirhizotron camera systems. Along with recent advances in image analysis, these advances will allow use of minirhizotrons at unprecedented scale to address key knowledge gaps regarding genetic and environmental effects on root system size and distribution in the field.

54 ENVIRONMENTAL SCIENCES↗