Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “ECOLOGY”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

Summary Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.

Plant Sciences↗
DOE OSTI2024

The role of emerging scientists in restoration ecology: insights from a SER2023 conference workshop

Emerging professionals are crucial in advancing ecological restoration by connecting newcomers with established leaders and blending new ideas with traditional practices. This paper highlights the vital role emerging scientists play in restoration ecology and the Society for Ecological Restoration (SER). A survey conducted during the SER2023 conference workshop, organized by the Students and Emerging Professionals committee, showed that emerging professionals contribute significantly to every stage of scientific work, from planning to publication. However, participants emphasized the scarcity of funding opportunities for non‐senior scientists, which limits academic growth. The workshop underscored the importance of nurturing emerging professionals to develop future leaders for SER and ensure continuity. Fostering non‐hierarchical and inclusive networking is key to engaging and empowering these professionals, ultimately contributing to the long‐term success of ecological restoration efforts.

Weidlich, Emanuela W. A.↗
DOE OSTI2018

Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages

Background: As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown. Results: Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeota may impact methanogenesis in inland ecosystems. Conclusions: The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Screening Level Ecological Exposure Assessment Work Plan

This work plan is part of an effort to complete an updated evaluation of the potential for adverse effects from miscellaneous treatment unit emissions to potential ecological receptors within and surrounding Site 200. It will address potential pathways between air emissions from the Lawrence Livermore National Laboratory’s (LLNL) Decontamination and Waste Treatment Facility (DWTF), single emission stack, and ecological receptors (i.e., plants and wildlife) present onsite and within a one-mile radius from the DWTF stack. This work plan outlines the procedures by which data collected as part of the previous investigations will be evaluated to assess risks to ecological receptors. It presents the problem formulation, initial conceptual site models, methods for characterizing exposure, toxicity, and risks that will be used if a more detailed “baseline” ecological risk assessment (BERA) is required.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

2023 Central Hanford Ecological Integrity Assessments Monitoring Report

The Hanford Site is comprised of an expanse of shrub-steppe habitats that provides exceptional ecological value to plants and animals located on the site and in the surrounding greater Columbia Basin. The U.S. Department of Energy (DOE)-managed portion of the Hanford Site, referred to from here on as Central Hanford, has been the focus of various ecological monitoring efforts, including vegetation monitoring. The scope and goals of vegetation surveys have varied greatly since the Hanford Site was established, but previous studies have documented a rapidly changing landscape, making it clear that continued vegetation monitoring is integral to preserving the ecological value of Central Hanford. A new vegetation monitoring effort was initiated in 2023 using methods based on ecological integrity assessments (EIA) (Natural Heritage Report [NHR] 2020-05) developed by the Washington Natural Heritage Program (WNHP), a division of the Washington State Department of Natural Resources (DNR) and NatureServe®. The methods were modified and supplemented to meet monitoring goals at the Hanford Site. The 2023 EIA monitoring effort consisted of field surveys to evaluate vegetation and soil condition across Central Hanford. Surveys were focused on upland habitats, and areas under consideration for upcoming projects were prioritized. Vegetation cover estimates were used to score a variety of metrics for vegetation conditions in each area. In 2023, approximately half of the site was surveyed. Monitoring methods and results for the 2023 field season are summarized in this report, and management recommendations are also provided.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Finally, once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.

(meta) transcriptomics↗
DOE OSTI2020

Data from: Comparing traditional and Bayesian approaches to ecological meta-analysis

Despite the wide application of meta-analysis in ecology, some of the traditional methods used for meta-analysis may not perform well given the type of data characteristic of ecological meta-analyses. We reviewed published meta-analyses on the ecological impacts of global climate change, evaluating the number of replicates used in the primary studies (ni) and the number of studies or records (k) that were aggregated to calculate a mean effect size. We used the results of the review in a simulation experiment to assess the performance of conventional frequentist and Bayesian meta-analysis methods for estimating a mean effect size and its uncertainty interval. Our literature review showed that ni and k were highly variable, distributions were right-skewed, and were generally small (median ni =5, median k=44). Our simulations show that the choice of method for calculating uncertainty intervals was critical for obtaining appropriate coverage (close to the nominal value of 0.95). When k was low (<40), 95% coverage was achieved by a confidence interval based on the t-distribution that uses an adjusted standard error (the Hartung-Knapp-Sidik-Jonkman, HKSJ), or by a Bayesian credible interval, whereas bootstrap or z-distribution confidence intervals had lower coverage. Despite the importance of the method to calculate the uncertainty interval, 39% of the meta-analyses reviewed did not report the method used, and of the 61% that did, 94% used a potentially problematic method, which may be a consequence of software defaults. In general, for a simple random-effects meta-analysis, the performance of the best frequentist and Bayesian methods were similar for the same combinations of factors (k and mean replication), though the Bayesian approaches had higher than nominal (>95%) coverage for the mean effect when k was very low (k<15). Our literature review suggests that many meta-analyses that used z-distribution or bootstrapping confidence intervals may have over-estimated the statistical significance of their results when the number of studies was low; more appropriate methods need to be adopted in ecological meta-analyses.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1983

An integrated remote sensing approach for identifying ecological range sites

A model approach for identifying ecological range sites was applied to high elevation sagebrush-dominated rangelands on Parker Mountain, in south-central Utah. The approach utilizes map information derived from both high altitude color infrared photography and LANDSAT digital data, integrated with soils, geological, and precipitation maps. Identification of the ecological range site for a given area requires an evaluation of all relevant environmental factors which combine to give that site the potential to produce characteristic types and amounts of vegetation. A table is presented which allows the user to determine ecological range site based upon an integrated use of the maps which were prepared. The advantages of identifying ecological range sites through an integrated photo interpretation/LANDSAT analysis are discussed.

Jaynes, R. A.↗
NASA NTRS2022

Automatic variable selection in ecological niche modeling: A case study using Cassin’s Sparrow (Peucaea cassinii)

MERRA/Max provides a feature selection approach to dimensionality reduction that enables direct use of global climate model outputs in ecological niche modeling. The system accomplishes this reduction through a Monte Carlo optimization in which many independent MaxEnt runs, operating on a species occurrence file and a small set of randomly selected variables in a large collection of variables, converge on an estimate of the top contributing predictors in the larger collection. These top predictors can be viewed as potential candidates in the variable selection step of the ecological niche modeling process. MERRA/Max’s Monte Carlo algorithm operates on files stored in the underlying filesystem, making it scalable to large data sets. Its software components can run as parallel processes in a high-performance cloud computing environment to yield near real-time performance. In tests using Cassin’s Sparrow (Peucaea cassinii) as the target species, MERRA/Max selected a set of predictors from Worldclim’s Bioclim collection of 19 environmental variables that have been shown to be important determinants of the species’ bioclimatic niche. It also selected biologically and ecologically plausible predictors from a more diverse set of 86 environmental variables derived from NASA’s Modern-Era Retrospective Analysis for Research and Applications Version 2 (MERRA-2) reanalysis, an output product of the Goddard Earth Observing System Version 5 (GEOS-5) modeling system. We believe these results point to a technological approach that could expand the use global climate model outputs in ecological niche modeling, foster exploratory experimentation with otherwise difficult-to-use climate data sets, streamline the modeling process, and, eventually, enable automated bioclimatic modeling as a practical, readily accessible, low-cost, commercial cloud service.

John L. Schnase↗
NASA NTRS2023

A Community Convention for Ecological Forecasting: Output Files and Metadata Version 1.0

This paper summarizes the open community conventions developed by the Ecological Forecasting Initiative (EFI) for the common formatting and archiving of ecological forecasts and the metadata associated with these forecasts. Such open standards are intended to promote interoperability and facilitate forecast communication, distribution, validation, and synthesis. For output files, we first describe the convention conceptually in terms of global attributes, forecast dimensions, forecasted variables, and ancillary indicator variables. We then illustrate the application of this convention to the two file formats that are currently preferred by the EFI, netCDF (network common data form), and comma-separated values (CSV), but note that the convention is extensible to future formats. For metadata, EFI's convention identifies a subset of conventional metadata variables that are required (e.g., temporal resolution and output variables) but focuses on developing a framework for storing information about forecast uncertainty propagation, data assimilation, and model complexity, which aims to facilitate cross-forecast synthesis. The initial application of this convention expands upon the Ecological Metadata Language (EML), a commonly used metadata standard in ecology. To facilitate community adoption, we also provide a Github repository containing a metadata validator tool and several vignettes in R and Python on how to both write and read in the EFI standard. Lastly, we provide guidance on forecast archiving, making an important distinction between short-term dissemination and long-term forecast archiving, while also touching on the archiving of code and workflows. Overall, the EFI convention is a living document that can continue to evolve over time through an open community process.

Michael C. Dietze↗
DOE OSTI2016

Applications of Ecological Engineering Remedies for Uranium Processing Sites, USA

The U.S. Department of Energy (USDOE) is responsible for remediation of environmental contamination and long-term stewardship of sites associated with the legacy of nuclear weapons production during the Cold War in the United States. Protection of human health and the environment will be required for hundreds or even thousands of years at many legacy sites. USDOE continually evaluates and applies advances in science and technology to improve the effectiveness and sustainability of surface and groundwater remedies (USDOE 2011). This paper is a synopsis of ecological engineering applications that USDOE is evaluating to assess the effectiveness of remedies at former uranium processing sites in the southwestern United States. Ecological engineering remedies are predicated on the concept that natural ecological processes at legacy sites, once understood, can be beneficially enhanced or manipulated. Advances in tools for characterizing key processes and for monitoring remedy performance are demonstrating potential. We present test cases for four ecological engineering remedies that may be candidates for international applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Ecological risk assessment software for radioactive waste management facilities - 15464

Environmental Risk Assessment (ERA) is a systematic process which can be used to identify, quantify and characterize the risk posed by contaminants and physical stressors in the environment on biological receptors, including human and non-human biota. Human receptors can be addressed through a Human Health Risk Assessment and non-human biota can be addressed through an Ecological Risk Assessment (EcoRA). In 2012 the Canadian Standards Association (CSA) issued a CSA standard N288.6 Environmental Risk Assessment at Class I Nuclear Facilities and Uranium Mines and Mills. The standard applies to radioactive waste management facilities, as well as nuclear power plants. The ERA can also be used retrospectively, to estimate the effect that a contaminant or stressor has already had on the environment; and can be used to assist in determining possible remedial or risk management options to return the quality of the affected environment to a predetermined state. While industry-standard tools for estimating radiological doses to humans are readily available, there is a need for a tool to implement the CSA N288.6 standard for Ecological Risk Assessment. To address this need, AMEC developed a computer code called -Assessment of Impact of Contaminants on Ecological Receptors (AICER)-. The code was developed to be consistent with the CSA standard N288.6, by assessing the impact of radiological contamination on non-human biota for normal operations. The code can also be used to screen for the potential effects of conventional contamination on the environment. In addition, the code is also applicable for abnormal events and accidents with the appropriate modification of some parameters used in the code. The AICER code was qualified in accordance with the requirements of the Canadian quality standard CSA N286.7 -Quality Assurance of Analytical, Scientific, and Design Computer Programs for Nuclear Power Plants-. The functionality of the code is illustrated with screen shots in the paper, following the introduction of the theoretical model for the dose calculation. An inter-comparison with RESRAD-BIOTA and ERICA Assessment tool at the conceptual level was conducted. In addition, the practical application of the code for the assessment of the impacts related to an existing radioactive waste management facility is provided. In particular, analysis was conducted to evaluate radiological doses to non-human biota resulting from a fire accident scenario involving an existing waste storage and processing facility. Analysis included all feasible waterborne and airborne exposure pathways. Doses were evaluated for a range of species representing valued ecological components at various trophic levels and compared with benchmark values for indicator species. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Social-ecological network analysis for sustainability sciences: a systematic review and innovative research agenda for the future

Social-ecological network (SEN) concepts and tools are increasingly used in human-environment and sustainability sciences. We take stock of this budding research area to further show the strength of SEN analysis for complex human-environment settings, identify future synergies between SEN and wider human-environment research, and provide guidance about when to use different kinds of SEN approaches and models. We characterize SEN research along a spectrum specifying the degree of explicit network representation of system components and dynamics. We then systematically review one end of this spectrum, what we term ‘fully articulated SEN’ studies, which specifically model unique social and ecological units and relationships. Results show a larger number of papers focus on methodological advancement and applied ends. While there has been some development and testing of theories, this remains an area for future work and would help develop SENs as a unique field of research, not just a method. Authors have studied diverse systems, while mainly focusing on the problem of social-ecological fit alongside a scattering of other topics. There is strong potential, however, to engage other issues central to human-environment studies. Analyzing the simultaneous effects of multiple social, environmental, and coupled processes, change over time, and linking network structures to outcomes are also areas for future advancement. This review provides a comprehensive assessment of (fully articulated) SEN research, a necessary step that can help scholars develop comparable cases and fill research gaps.

environmental governance↗
DOE OSTI2026

Custom surface reflectance, shade mask, and equivalent water thickness maps for the Colorado Headwaters Ecological Spectroscopy Study (2025)

This dataset contains land surface reflectance estimates and additional derived products generated from NEON Imaging Spectrometer (NIS) data collected in the Upper Gunnison river basin during June and July of 2025. Data was collected over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). These products were derived from radiance and LiDAR data collected by the NEON Airborne Observation Platform (AOP) campaign funded by the Colorado Headwaters Ecological Spectroscopy Study (CHESS) (doi:10.15485/3017965). Products include per-pixel surface reflectance (rfl) and reflectance uncertainty (rfl_unc), observational data (obs), canopy equivalent water thickness (ewt), and shade masks. Atmospheric correction was performed per flightline using the ISOFIT (Imaging Spectrometer Optimal FITting) optimal estimation framework to estimate surface reflectance and the associated per-band reflectance uncertainty. Reflectance retrievals achieved a mean absolute error of 1.5% across diverse validation surfaces (see validation report.pdf). Equivalent water thickness was calculated from surface reflectance using the Beer–Lambert absorption of liquid water. Shade masks were generated based on the geometry between the sun angle, ground surface, and sensor at the time of flight. Data products are provided per-flightline and as mosaics for each domain. Flightline data products are provided as ENVI-formatted binary files (rfl, rfl_unc, ewt) and GeoTIFFs (shade). Reflectance and uncertainty mosaics are provided as tiled NetCDFs, while all other mosaicked products are provided as cloud-optimized GeoTIFFs. These formats are supported by common geospatial software (e.g., QGIS, ArcGIS, ENVI) and programmatic libraries in Python (e.g., rasterio, xarray, spectral, netCDF4) and R (e.g., terra, ncdf4). Processing workflows were designed to be equivalent to those used to generate the 2018 CHESS campaign airborne imaging spectroscopy data products (doi:10.15485/3013527). All outputs were co-registered to a common spatial grid to support time series analyses. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: Data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). Computational research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004) and was funded by EMIT Extended Mission Phase E Science.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2014

Approaches to advancescientific understanding of macrosystems ecology

Macrosystem ecological studies inherently investigate processes that interact across multiple spatial and temporal scales, requiring intensive sampling and massive amounts of data from diverse sources to incorporate complex cross-scale and hierarchical interactions. Inherent challenges associated with these characteristics include high computational demands, data standardization and assimilation, identification of important processes and scales without prior knowledge, and the need for large, cross-disciplinary research teams that conduct long-term studies. Therefore, macrosystem ecology studies must utilize a unique set of approaches that are capable of encompassing these methodological characteristics and associated challenges. Several case studies demonstrate innovative methods used in current macrosystem ecology studies.

data management↗
DOE OSTI2019

Ecological Risk Assessment of Neodymium and Yttrium on Rare Earth Element Mine Sites in Ganzhou, China

Nowadays rare earth elements (REEs) are widely applied in high-technology and clean energy products, but their environmental risks are still largely unknown. To estimate the ecological risk of REEs, soil samples were collected from REE mine tailings with and without phytoremediation. The results showed that the tailings had rather low organic matter and high total REE concentrations, up to 808.5 mg/kg. The 10% effective concentration (EC10) of neodymium (Nd) and yttrium (Y) were calculated based on the toxicity tests of seed germination and root growth. For both wheat and mung bean, the EC10 of Nd and Y in soils were in the range of 1053.1–1300.1 mg/kg. The average hazard quotient of mine tailing soil without phytoremediation was higher than that with phytoremediation. All the hazard quotient of Nd and Y were less than 1, indicating that Nd or Y alone was unlikely to cause adverse ecological effects. Given to the coexistence of REEs on mine sites, the ecological risk of REE mixture could be potentially high towards local soil environments, even for soils with phytoremdiation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Complexity of bioindicator selection for ecological, human, and cultural health: Chinook salmon and red knot as case studies

There is considerable interest in developing bioindicators of ecological health that are also useful indicators for human health. Yet, human health assessment usually encompasses physical/chemical exposures and not cultural well-being. In this paper, we propose that bioindicators can be selected for all three purposes. We use Chinook or king salmon (Oncorhynchus tshawytscha) and red knot (Calidris canutus rufa, a sandpiper) as examples of indicators that can be used to assess human, ecological, and cultural health. Even so, selecting endpoints or metrics for each indicator species is complex and is explored in this paper. Here, we suggest that there are several endpoint types to examine for a given species, including physical environment, environmental stressors, habitat, life history, demography, population counts, and cultural/societal aspects. Usually cultural endpoints are economic indicators (e.g., number of days fished, number of hunting licenses), rather than the importance of a fishing culture. Development of cultural/societal endpoints must include the perceptions of local communities, cultural groups, and tribal nations, as well as governmental and regulatory communities (although not usually so defined, the latter have cultures as well). Endpoint selection in this category is difficult because the underlying issues need to be identified and used to develop endpoints that tribes and stakeholders themselves see as reasonable surrogates of the qualities they value. We describe several endpoints for salmon and knots that can be used for ecological, human, and cultural/societal health.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Beneath the surface: Unsolved questions in soil virus ecology

Soil virus ecology is an exciting but still nascent field of research in soil microbiology. While there has been a recent surge in soil virus research studies, many fundamental questions remain unanswered, and a range of technical and bioinformatic challenges need to be overcome. In this perspective article, we present a series of key questions that highlight fruitful research areas for ongoing and future efforts. These include describing the challenges involved in understanding soil viral abundance and activity, spatiotemporal dynamics, life strategy prevalence, virus-mediated biogeochemical impacts, viral protein function, host prediction, and soil RNA virus discovery. In the near term, combining approaches (e.g., cultivation-based, meta-omics, biogeochemical, experimental, and bioinformatic) will be key to assessing the ecological and biogeochemical impacts of soil viruses from the microscopic to the field and global scales. Still, we stress that results must be tempered by current methodological limitations and highlight knowledge gaps that are most pressing to fill via new methods or measurements, such as the prevalence of different viral replication strategies across soils, the fate of microbial necromass carbon after viral lysis, the frequency of virus-host encounters that do not lead to successful infections yet could be bioinformatically mistaken as infections, and the diversity and ecological impacts of RNA viruses in soil.

59 BASIC BIOLOGICAL SCIENCES↗