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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.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Evaluation of Howard A. Hanson Dam Juvenile Fish Passage and Survival Study: Downstream Passage and Survival (Acoustic Telemetry) (Task Final Report)

The Downstream Passage and Survival (Acoustic Telemetry) task was one of several tasks for the Evaluation of Howard A. Hanson Dam (HAHD) Juvenile Fish Passage and Survival study. For this task, a juvenile fish passage and survival study was conducted at HAHD from March 10, 2024 through June 27, 2024 for arrays in the HAHD Reservoir and Green River, and through July 9, 2024 for the arrays in the Duwamish River. Fish releases occurred over four times from March through May. Active tag (acoustic telemetry) technology was used to provide biological baseline information for the passage and survival of juvenile Puget Sound (PS) Chinook salmon (Oncorhynchus tshawytscha). Results will be used by biologists, engineers, resource managers, and regional decision-makers to inform the engineering design of the new fish passage facility (FPF) at HAHD. However, hatchery sub-yearling PS Chinook salmon of the appropriate size for tag implantation during the study period (> 95 mm in fork length, Geist et al. 2018) were unavailable. Therefore, yearling Coho salmon (O. kisutch) were used as a surrogate species for this acoustic telemetry study.

13 HYDRO ENERGY↗
DOE OSTI2024

Endogeneity of pedestrian survival time and emergency medical service response time: Variations across disadvantaged and non-disadvantaged communities

The Vision Zero-Safe Systems Approach prioritizes fast access to Emergency Medical Services (EMS) to improve the survivability of road users in transportation crashes, especially concerning the recent increase in pedestrian-involved crashes. Pedestrian crashes resulting in immediate or early death are considerably more severe than those taking longer. The time gap between injury and fatality is known as survival time, and it heavily relies on EMS response time. The characteristics of the crash location may be associated with EMS response and survival time. A US Department of Transportation initiative identifies communities often facing challenges. Six disadvantaged community (DAC) indicators, including economy, environment, equity, health, resilience, and transportation access, enable an analysis of how survival and EMS response times vary across DACs and non-DACs. To this end, this study created a unique and comprehensive database by linking DACs data with 2017–2021 pedestrian-involved fatal crashes. This study utilizes two-stage residual inclusion models with segmentation for DACs and non-DACs accounting for the endogenous relationship between EMS response and pedestrian survival time. The results indicate that EMS response time is higher and pedestrian survival time is lower in DACs than in non-DACs. A delayed EMS response time is associated with a greater reduction in survival time in DACs compared to non-DACs. Factors, e.g., nighttime and interstate crashes, contribute to higher EMS response time, while pedestrian drugs, driver speeding, and hit-and-run behaviors are associated with a greater reduction in survival time in DACs than non-DACs. Finally, the implications of the findings are discussed in the paper.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Enhancing the Survivability of Power Systems With Grid-Edge DERs Against DoS Attacks

Power system survivability, defined as the ability of a system to maintain steady-state functionality under varying operational conditions, reflects its resilience against disturbances. While existing research primarily focuses on physical-layer disturbances, the increasing prevalence of grid-edge DERs, which are primarily used for integrating renewable energy, has significantly expanded the cyber attack surface. As a result, operational disruptions caused by cyber threats are posing significant challenges to system survivability and cannot be overlooked. To fill this gap, we redefine system survivability to incorporate the cyber layer’s status and propose a Distributionally Robust Optimization (DRO) approach to enhance power system survivability against potential cyber-physical threats. In this paper, we first analyze the operational guidelines of systems with a high penetration of DERs under various cyber network conditions and redefine survivability in this context. Next, we focus on the most common cyber threat, Denial-of-Service (DoS) attacks, and develop a corresponding attack model. This model allows for the creation of a kernel-based ambiguity set that captures attack uncertainties using historical data. Finally, we transform the proposed DRO model as a tractable optimization problem, with its solution providing an optimal cyber redundancy plan to enhance system survivability in DoS attack scenarios. Simulation results on the IEEE 13-node and 123-node test feeders demonstrate the effectiveness of our proposed model in improving system survivability. This model can also be expanded to include other types of common attacks and serve as a comprehensive planning tool to improve overall cyber physical survival of the system.

cybersecurity↗
DOE OSTI2024

Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater

Many factors contribute to the ability of a microbial species to persist when encountering complexly contaminated environments, including time of exposure, the nature and concentration of contaminants, availability of nutritional resources, and possession of a combination of appropriate molecular mechanisms needed for survival. Herein we sought to identify genes that are most important for survival of Gram-negative Enterobacteriaceae in contaminated groundwater environments containing high concentrations of nitrate and metals using the metal-tolerant Oak Ridge Reservation isolate, Pantoea sp. MT58 (MT58). Survival fitness experiments in which a randomly barcoded transposon insertion (RB-TnSeq) library of MT58 was exposed directly to contaminated Oak Ridge Reservation groundwater samples from across a nitrate and mixed metal contamination plume were used to identify genes important for survival with increasing exposure times and concentrations of contaminants, and availability of a carbon source. Genes involved in controlling and using carbon, encoding transcriptional regulators, and related to Gram-negative outer membrane processes were among those found to be important for survival in contaminated Oak Ridge Reservation groundwater. A comparative genomics analysis of 75 Pantoea genus strains allowed us to further separate the survival determinants into core and non-core genes in the Pantoea pangenome, revealing insights into the survival of subsurface microorganisms during contaminant plume intrusion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Lethality is Local, but Survival is Systemic: Temporal and Multi-Organ Responses to Chlorine Gas Exposure in a Murine Model

Chlorine gas (Cl2) is a highly toxic chemical associated with both localized lung injury and systemic health effects. While pulmonary damage has been well characterized, the systemic inflammatory and metabolic responses remain poorly understood. We aimed to define the temporal and multi-organ responses to Cl2 exposure in a murine model, with a focus on identifying spatiotemporal inflammation and its impact on survival and lethality. SKH1 mice were exposed for 10 min to varying concentrations of Cl2 (94.4–810 ppm, representative of non-lethal, LD10, and LD50 doses) and monitored for respiratory function, perfusion, and acidosis using organ-specific imaging. At multiple time points (40 min, 6 h, 24 h, and 7 d), we measured phosphoproteins, cytokines, chemokines, growth factors, and metabolic hormones in the lungs, heart, cortex, and plasma. Statistical modeling and logistic regression were used to identify biomarkers associated with lethality and survival. We found that lung injury was the primary cause of potential lethality, particularly via early phosphoprotein signaling disruptions. However, survival correlated with early systemic coordination of inflammatory and metabolic signals across organs. Perfusion and acidosis imaging were strongly associated with chemokine and hormone responses. Key survival-associated plasma biomarkers included decreased insulin, increased ghrelin, and decreased eotaxin. While potential lethality from Cl2 exposure is locally driven by pulmonary injury, survival depends on systemic, multi-organ responses that occur rapidly post-exposure. Within this model, our findings identify a potential therapeutic window to enhance survival and suggest candidate biomarkers that may be explored translationally for both triage and treatment of chlorine-related incidents.

chlorine gas↗
DOE OSTI2026

Comparison of juvenile white sturgeon blade strike survival through a conventional and a novel hydropower turbine

Hydropower is a globally important renewable energy source with profound impacts on aquatic organisms, including direct injury and mortality to fish that move through hydropower facilities. While it is expected that the characteristics of turbine design and operation influence the type, frequency, and magnitude of injuries suffered by entrained fish, few direct comparisons exist to illustrate differences in fish survival outcomes for conventional and novel turbine designs. This study evaluated blade strike-associated injury and mortality rates for juvenile white sturgeon (Acipenser transmontanus) passed through a model-scale turbine equipped with a runner having conventional blade profiles (thin, straight leading edges) and the same turbine equipped with a runner designed for improved fish survival (thick, slanted leading edges). In both trials, head and turbine runner rotational speeds were matched to produce five blade peripheral speeds between 15.0 and 27.6 m/s. High-speed video was captured for all turbine passage events. Fish were assessed for injuries following passage, and mortalities were assessed immediately after passage and after 48 h. Conventional runner passage resulted in 42% to 78% survival after 48 h, with approximately one-third of all tested fish killed by severing. Under the same test conditions, immediate and 48 h survival rates through the novel runner were 100% except at the highest speed condition (95.6% survival at 48 h). These results clearly indicate that turbine design has a profound effect on fish survival, and suggest that thoughtful redesign of hydropower equipment could significantly ameliorate the risks of blade strike mortality.

13 HYDRO ENERGY↗
DOE OSTI2025

Effects of sampling techniques on short-term survival and genotyping success of salmonid fry

ABSTRACT Objective Genetics tools have become an integral part of managing and understanding fish populations. Generally, a small tissue sample, such as a fin clip, is taken and then genotyped, with little effect on survival of the fish. However, tissue sampling may have a larger effect on juvenile fish survival compared to their adult counterparts. We evaluated survival and genotyping success of various genetic sampling techniques for Chinook Salmon Oncorhynchus tshawytscha and Rainbow Trout Oncorhynchus mykiss fry. Methods Three sampling treatments were evaluated including control (anesthetized and handled), fin clipping (partial caudal fin clip), and swabbing (OmniSwab was used to collect external mucus). Survival was monitored for 12 d posttreatment, and genotyping success was evaluated. Results Survival was high in all treatment groups (i.e., 0.93–1.00) but, on average, was lower in the swab treatment group. Genotyping was successful in 100% of the fin clip samples and 11–50% of the swab samples. Conclusions Results of this study suggest that sampling caudal-fin tissue does not negatively affect fry short-term survival and the small tissue samples yield highly successful genotyping results. Swabbing did not produce successful genotyping results, and fish sampled with swabs experienced higher mortality than those that received fin clips. Results indicate that fin clips should be used for collection of genetic samples from fry.

McCarrick, Darcy K.↗
DOE OSTI2026

Structural Aspects of Neutron Survival Probabilities

The neutron survival probability (and related quantities including probabilities of extinction and initiation) is a central element of the broader stochastic theory of neutron populations and finds application in fields including reactor start-up, analysis of reactor power bursts and criticality accidents, and safeguards. In a full neutron transport formulation, the equation governing the single-neutron survival probability is a backward or adjoint-like integro-partial differential equation with the added complexity of being highly nonlinear. Analogous formulations of this equation exist in the context of many approximate theories of neutron transport, with the point kinetics formulation having received significant theoretical attention since the 1940s. This work continues this tradition by providing a novel analysis of the single-neutron survival probability equation using the tools of boundary layer theory. The analysis reveals that the “fully dynamic” solution of the single-neutron survival probability equation—and some key probability distributions derived from it—may be cast as a singular perturbation around the underlying quasi-static single-neutron probability of initiation. In this perturbation solution, the expansion parameter is the ratio of the neutron generation time to a macroscopic time scale characterizing the overall system evolution; this interpretation illuminates some of the fundamental structural aspects of neutron survival phenomena.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Pan‐Cancer Survival Impact of Immune Checkpoint Inhibitors in a National Healthcare System

ABSTRACT Background The cumulative, health system‐wide survival benefit of immune checkpoint inhibitors (ICIs) is unclear, particularly among real‐world patients with limited life expectancies and among subgroups poorly represented on clinical trials. We sought to determine the health system‐wide survival impact of ICIs. Methods We identified all patients receiving PD‐1/PD‐L1 or CTLA‐4 inhibitors from 2010 to 2023 in the national Veterans Health Administration (VHA) system (ICI cohort) and all patients who received non‐ICI systemic therapy in the years before ICI approval (historical control). ICI and historical control cohorts were matched on multiple cancer‐related prognostic factors, comorbidities, and demographics. The effect of ICI on overall survival was quantified with Cox regression incorporating matching weights. Cumulative life‐years gained system‐wide were calculated from the difference in adjusted 5‐year restricted mean survival times. Results There were 27,322 patients in the ICI cohort and 69,801 patients in the historical control cohort. Among ICI patients, the most common cancer types were NSCLC (46%) and melanoma (10%). ICI demonstrated a large OS benefit in most cancer types with heterogeneity across cancer types (NSCLC: adjusted HR [aHR] 0.56, 95% confidence interval [CI] 0.54–0.58,p < 0.001; urothelial: aHR 0.91, 95% CI 0.83–1.01,p = 0.066). The relative benefit of ICI was stable across patient age, comorbidity, and self‐reported race subgroups. Across VHA, 15,859 life‐years gained were attributable to ICI within 5‐years of treatment, with NSCLC contributing the most life‐years gained. Conclusion We demonstrated substantial increase in survival due to ICIs across a national health system, including in patient subgroups poorly represented on clinical trials.

Oncology↗
DOE OSTI2025

Emigration and Survival of Hatchery‐Reared Coho Salmon Released as Parr and Smolts in a Reintroduction Program

ABSTRACT Releasing fish at varied life stages is an underutilized hatchery‐rearing practice. Columbia River Treaty tribes have been working to reintroduce extirpated Coho Salmon to historical habitats in upper watersheds. This effort has included the release of hatchery‐origin fish at both the parr and smolt life stages in the Yakima River Basin (Washington State USA), a tributary to the Columbia River. We evaluated releases of parr and smolts tagged with passive integrated transponders over 11 brood years. We assessed emigration timing, fish survival, and age‐at‐return for the two release groups. Emigrating juveniles released as smolts had higher survival and arrived downstream earlier than fish released as parr. Survival from release locations to adult return did not significantly differ for the two release groups. However, we observed a difference in apparent marine survival as fish released as parr had mean juvenile‐to‐adult return rates greater than fish released as smolts. Parr releases also tended to return at older age than smolt releases. Our results indicate that implementing practices to reduce homogenization of hatchery releases may produce survival and diversity benefits as fish mature to later life stages. Given the rapid ecosystem changes Pacific Salmon are experiencing throughout their life cycles, practices such as this may have increasing utility and import.

Bosch, William J. [Yakama Nation Fisheries Toppeni↗
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 OSTI2025

Feed status and skin injury modulate immunopathology, global gene expression, and survival in channel catfish during virulent Aeromonas hydrophila infection

Introduction VirulentAeromonas hydrophilais a major pathogen in channel catfish (Ictalurus punctatus), that causes motileAeromonassepticemia and significant economic losses. We investigated the effect of feeding status and skin integrity on the host immune response, disease survival, and gastrointestinal pathology following a vAh challenge. Methods Using a bath immersion model, channel catfish were divided into four treatment groups: fin clipped and fed (FCF), fin clipped but not fed (FCN), not fin clipped but fed (NCF), and not fin clipped nor fed (NCN) alongside non-challenged control groups The FCF and NCF groups were fed 2 h prior to the challenge, but the FCN and NCN groups were not. Survival analysis, histopathological assessment, and RNA sequencing were conducted across groups at different time intervals throughout the vAh challenge. Results Survival rates were lowest in the FCF and FCN groups (30% and 23% survival, respectively), suggesting that both feeding and skin damage contributed to disease severity. Histopathological analyses revealed more severe intestinal and gastric lesions in fed groups, characterized by epithelial necrosis, hemorrhage, and edema. Transcriptomic analysis among the groups identified significant differentially expressed genes associated with inflammation, apoptosis, and metabolic stress, with notable upregulation of interleukin 1-beta (il-1β), and complement C3 (c3). Gene ontology enrichment highlighted distinct immune activation patterns between fed and unfed groups, with enhanced pathogen recognition and pro-inflammatory responses in unfed fish. Discussion These findings suggest feeding prior to infection may exacerbate disease pathology, potentially by creating a physiological state conducive to facilitate pathogen proliferation and dampened early immune responses, whereas short-term fasting appears to promote early immune activation. This study provides novel insights into the complex interplay between feed status, physical injury, and immune response to vAh infection.

Immunology↗
DOE OSTI2025

Impact of developmental methylmercury exposure on avian embryonic development, hatchling growth, and survival

Abstract Methylmercury (MeHg) is a globally ubiquitous and persistent environmental toxicant that negatively affects animal behavior, health, and reproduction. In birds, MeHg is transferred from female to egg, contaminating embryos during sensitive stages of early embryonic development and growth. This toxic exposure in the prenatal environment not only induces mortality but also possible lasting impacts on physiology, health, and survival, even once hatched. The purpose of our study was to further elucidate the negative effects of MeHg exposure during avian embryonic development and explore how such exposure can impact offspring development, growth, and survival, both in ovo and posthatch. To assess this, we experimentally dosed fertile mallard and wood duck eggs with MeHg II chloride and reared developing embryos and ducklings to various endpoints. We found that embryos not only readily accumulated MeHg throughout incubation, but they also displayed varying dose-dependent disparities in body mass and morphometrics, with control individuals being larger during early and late embryonic stages of development (p < 0.05). Furthermore, hatched offspring exposed to MeHg exhibited increasingly slower growth rates between 7 to 10 and 10 to 15 days posthatch (p < 0.05), and were found to have lower survival probabilities both under controlled laboratory conditions (p < 0.005), and in the natural environment (p < 0.05). Our findings on the detrimental effects of MeHg on avian embryos and hatchlings emphasize the need for more proactive means of environmental protection and remediation to protect vulnerable avian populations and the ecosystems they inhabit.

Leaphart, James C.↗
DOE OSTI2025

Housing-Performance Atlas of Baltimore Row Homes: Archetype-Based Multi-Hazard Baseline of Energy, Heat, Survivability, and Durability

Baltimore’s historic row-home neighborhoods face escalating risks to energy, heat, and durability under intensifying climate stress. This study develops a Housing-Performance Atlas that quantifies multi-hazard performance for eight representative archetypes using DesignBuilder/EnergyPlus Version 7.3.1.003, under Baltimore TMY3 boundary conditions. Performance is evaluated across the following four adaptation domains: energy use intensity, passive survivability during 72 h outage events, roof overheating exposure (>150 °F exceedance hours), and material service life derived from ISO 15686 and synthesized into Lean and Full Deficit Indices for comparative resilience ranking. Results show that EUI ranged from 46.7 to 67.6 kBtu ft −2 ·yr −1 , survivability from 0 to 23 h, and roof temperatures exceeded 150 °F for 150–210 h, shortening roof service life by up to 10 years. Composite Lean and Full Deficit Indices ranged 7.8–92.4, ranking Model 5 (end-unit, flat roof, two-story with basement) as the most resilient configuration and Model 8 (end-unit, pitched roof, three-story above-grade) as the least resilient due to compounded overheating and energy losses. Heat-related domains accounted for nearly 70% of overall resilience deficits, confirming thermal safety and roof reflectivity as retrofit priorities. The Housing-Performance Atlas establishes a reproducible diagnostic framework linking simulation, service life, and resilience metrics to guide cost-effective, climate-responsive retrofits in Baltimore’s aging urban housing stock.

Housing-Performance atlas↗
DOE OSTI2025

Supercooling of Alaskan Beetle Larvae as a Winter Survival Strategy

Insects are able to survive subfreezing temperatures by either limiting ice crystal formation in their bodies or through freeze avoidance. Beetle larvae are able to avoid freezing in winter by dehydrating in the fall months and replacing their body water content with high concentrations of glycerol. This enables the body fluid of the insect to supercool, and even vitrify, recovering unharmed when the temperature warms in the spring. Using nondestructive, high‐energy X‐ray synchrotron diffraction experiments, direct insight into how cryopreservation occurs at the atomic level within the beetle larvae has been obtained. The results shed light on the molecular‐level interactions associated with the mechanism responsible for surviving freezing temperatures. The molecular models of severely dehydrated Alaskan beetle larvae, based on glycerol‐water mixtures, yield a total of 4.2 ± 1.2 intermolecular hydrogen bonds per glycerol molecule at 275 K, in good agreement with existing molecular dynamics simulations. Most importantly, they show that if just over half the body fluid content is water, the water clusters are too small to form ice crystals that cause cellular damage.

Benmore, Chris J. [X‐Ray Science Division Advanced↗
DOE OSTI2025

An elastin-like polymer targeting vascular endothelial growth factor receptor-1 reduces survival in serum-starved endothelial cells

Peptides often exhibit biological activity that depends on the context in which they are displayed and delivered. Understanding and controlling these contextual effects on peptide function is critical for designing targeted and responsive peptide-based biomaterials and therapeutics. Genetically engineered protein polymers such as elastin-like polypeptides (ELPs) can incorporate bioactive peptide motifs and are attractive candidates for biomaterials used in tissue engineering and targeted drug delivery. They also present an opportunity for investigating and modulating cell signaling pathways by presenting a peptide ligand in various defined chemical and physical environments. Vascular endothelial growth factor receptor-1 (VEGFR1) signaling plays important and complex roles in cell survival and angiogenesis, but polymeric materials that interact with this signaling axis are scarce. In this study, a novel genetically engineered elastin-like polymer that targets VEGFR1 is characterized. This polymer, termed R1B-ELP, binds to human endothelial cells in a manner dependent on its VEGFR1-targeting motif and, based on cell proliferation and cytotoxicity assays, demonstrates activity consistent with disrupting pro-survival signaling necessary for endothelial cell function under conditions of environmental stress. Notably, these findings indicate that ELP fusion alters the functional behavior of the targeting peptide. Modulators of VEGFR1 signaling have potential applications in basic studies of angiogenesis as well as in therapeutic applications targeting vascular or inflammatory diseases.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Dust Survival in Galactic Winds

This repository contains three-dimensional volumetric data from an Eulerian hydrodynamical simulation (conducted on a uniform Cartesian grid) generated by the Cholla hydrodynamics code. The datasets contain snapshots (full-grid, projections, and slices) in the HDF5 format of a multi-phase medium in which a hot, diffuse, dust-free background wind accelerates a cool, dense cloud of gas and dust. This scenario is intended to represent a supernova-driven galactic outflow, in which hot supernova winds are thought to accelerate cool interstellar medium material out of the galactic disk into the surrounding circumgalactic medium. There are three separate datasets for simulations corresponding to three cloud evolutionary scenarios: long-term cloud survival (surv), marginal cloud survival (disr), and cloud destruction (dest). Projection and slice images of the simulations are also included in this repository.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

EvoNet: A phylogenomic and systems biology approach to identify genes underlying plant survival in marginal, low‐N soils

The DOE‐BER “EvoNet” project investigates the genetic and molecular basis of plant resilience in extreme environments. We do this by identifying key genes that enable “extreme survivor” species to thrive in the nitrogen-poor soils of Chile’s hyper-arid Atacama Desert. Our collections focus on 32 Atacama extremophile species, including seven grass species with potential biofuel applications. To identify genes-of-importance to survival we compared genomic and transcriptomic profiles of extremophile species that thrive in the Atacama to those of closely related “sister” species from nitrogen-rich arid and mesic regions of California. Deep RNA sequencing and de novo transcriptome assembly across these triplet species sets supported a phylogenomic framework for identifying positively selected genes associated with adaptive divergence. Our integrative analysis combined ecological and environmental data, metagenomics, evolutionary and systems biology, and metabolomics. This enabled us to create an unprecedented framework for systematically understanding how non-model plants have adapted to survive in extreme conditions. Our resulting database of positively selected ortholog groups in the extremophile plants offers promising targets for engineering crop and biofuel species with enhanced resilience to drought and extreme weather. Additionally, our newest dataset explores and exploits a complementary metabolomic approach. This new aspect provides innovative strategies to manipulate plant cell metabolism, further supporting efforts to improve agricultural productivity in the face of extreme climates. Importantly, our combined evolutionary- and metabolomic-based strategies focused on convergent patterns of adaptation, providing a genetic and metabolomic toolkit for improving crop and biofuel resilience across diverse plant species. Finally, our novel exploration of ecological and evolutionary dynamics delivered to the community a phylogenomic computational pipeline called “PhyloGeneious.” Our continued adaptations of this pipeline are publicly available to expedite evolutionary genomic research for future scientific discoveries. In total, our DOE-BER has provided genomic, metabolomic, and computational strategies to understand how extremophile plants provide evolutionary and physiological targets for improving agricultural and biofuel production.

59 BASIC BIOLOGICAL SCIENCES↗