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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Soil Greenhouse Gas Fluxes 04/2020-06/2024

Both raw and processed data measured using a LI-COR 7810 Greenhouse Gas Analyzer in the TEMPEST experiment, part of COMPASS-FME (https://compass.pnnl.gov/FME/COMPASSFME), at Smithsonian Environmental Research Center. This ecosystem-scale experiment probes the effects of saltwater versus freshwater flooding in a coastal deciduous forest.The data consist of both concentrations and fluxes of carbon dioxide and methane measured using static chambers on the soil surface, approximately every two weeks from early 2020 to mid 2024. Some of the measurement points are controls, and some subject to root-exclusion techniques; all measurements are embedded in the TEMPEST control, freshwater, and saltwater plots (see Hopple et al. 2023). These data were generated to understand changing soil greenhouse gas (CO2 and CH4) production and consumption. File types are comma-separated value (.csv) for data, and markdown (.md) for supplementary information.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Experiment Tree Inventory

This is the tree inventory (diameter, species, and live/dead status) data from the Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental site. This manipulative, ecosystem-scale TEMPEST experiment is part of the COMPASS-FME (Coastal Observations, Mechanisms, and Predictions Across Systems and Scales: Field Measurements and Experiments; see https://compass.pnnl.gov/FME/COMPASSFME) project. It addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in eastern Maryland, USA. The experiment uses a large-unit (2000 m2), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments.This dataset includes:- An overall dataset README file.- The tree inventory data in both "wide" and "long" forms. These contain the same information but are structured differently, with the former more useful for human viewers and the latter more amenable for programmatic analyses.- A key to the species/genus codes used, which follow the U.S. Department of Agriculture's PLANTS schema (https://plants.usda.gov/).- A copy of the R code used to generate the wide- and long-form data files.All files are comma-separated value (CSV) and no special software is required to read them.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Experiment Level 1 Sensor Data v2-1

This is the version 2-1 Level 1 (L1) data release for COMPASS-FME environmental sensors located at our Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental site. This manipulative, ecosystem-scale TEMPEST experiment addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in MD, USA. The experiment uses a large-unit (2000 m2), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments. L1 data are close to raw, but are units-transformed and have out-of-instrument-bounds, out-of-service, and outlier flags added. Duplicates and missing data are removed but otherwise these data are not filtered, and have not been subject to any additional algorithmic or human QA/QC. Any scientific analyses of L1 data should be performed with care. **This dataset will be updated quarterly with new data for the duration of the project** This dataset includes: - An overall dataset README file that describes the current version, gives citation and contact information, etc. - Site- and year-specific folders, each holding variable-specific CSV (comma separated value) data files for each site and plot in that year. - Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, detailed flood times, as well as a general description of the site. - Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are normally logged every 15 minutes. Please see v2-1 TEMPEST L1 Sensor Package Quick Start.pdf for detailed information on data package structure, temporal coverage, and versioning. The TEMPEST flood events occurred on the following dates. They lasted for ~10 hours each day and delivered ~80,000 gallons to each plot; many data streams are available at 1 or 5 minute frequency during these periods. * Tests: Aug 25 (fresh plot) and Sep 9 (salt plot), 2021 * TEMPEST 1: June 22, 2022 * TEMPEST 2: June 6-7, 2023 * TEMPEST 3: June 11-13, 2024 This dataset was updated 2026-03-12: (i) data now go through 2025-12-31 (previous end was 2025-06-30) and (ii) dataset and file names updated to “…v2-1” (previously was “v2-0”).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces

These data are from Bandopadhyay et al., "Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces". This study aims to understand the soil microbial ecology along terrestrial-aquatic interfaces of a freshwater and estuarine region and how it relates to organic matter. We analyzed soil microbial (16S rRNA gene) and organic matter (Fourier-transform ion cyclotron resonance mass spectrometry, FTICR-MS) composition from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. This dataset includes 16S rRNA gene amplicon data (only processed file types included here) and organic matter composition from FTICR-MS data (raw and processed files included here) from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie and Chesapeake Bay regions. These sites are part of the COMPASS-FME project (https://compass.pnnl.gov/FME/COMPASSFME). File formats and software needed to access files: 16S rRNA gene amplicon data: These files follow the format reported here https://ess-dive.gitbook.io/amplicon-sequencing-reporting-format#updates-in-v1.0.1. As per this format, there are four file types reported: 1. Taxon tables (also called sequence-by-sample or OTU (operational taxonomic unit)/ESV (exact sequence variant) tables) : available in a .txt file format and accessible using TextEdit or MS Excel. 2. Representative sequences (also called consensus sequences) : available in a .fasta format and accessible using TextEdit. 3. Sequencing metadata : available in a MS Excel workbook file format and CSV file format 4. Bioinformatic metadata : available in a MS Excel workbook file format and CSV file format FTICR-MS data: 1. Raw data converted to a processed file with intensities of the peaks in the given samples : available in a MS Excel CSV file format 2. Processed file used in analyses and visualizations (appended as icr_long_) : available in a MS Excel CSV file format 3. Metadata file for ICR features (appended as icr_meta) : available in a MS Excel CSV file format

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Experiment Level 2 Sensor Data v2-1

This is the version v2-1 Level 2 (L2) data release for COMPASS-FME environmental sensors located at our Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental site. This manipulative, ecosystem-scale TEMPEST experiment addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in MD, USA. The experiment uses a large-unit (2000 m2), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments. Level 2 (L2) data consist of sensor observations from the COMPASS-FME synoptic sites, TEMPEST, and DELUGE. Compared to the L1 data, these are more consistent (always 15-minute timestamps for the entire year); better QA/QC’d (out of bounds, out of service, and extreme outlier values are removed); and more complete, with a gap-filled time series available alongside the main observations, and additional derived (calculated) variables. L2 data are intended to be rapidly and easily usable in analyses and simulations. However, algorithmic outlier identification always carries the risk of removing valid data, and Level 1 data may be more suitable for analyses that focus on variability or extreme events. This dataset includes: - An overall dataset README file that describes the current version, gives citation and contact information, etc. - Site- and year-specific folders, each holding variable-specific Parquet (a high performance, space efficient format; see https://parquet.apache.org) data files for each site and plot in that year. - Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, detailed flood times, as well as a general description of the site. - Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are reported every 15 minutes. Please see v2-1 TEMPEST L2 Sensor Package Quick Start.pdf for detailed information on data package structure, temporal coverage, and versioning. Data files are in Apache Parquet, a high performance, space efficient format for tabular data. These files can be read using R's `arrow` package (https://arrow.apache.org/docs/r/), with similar tools available in other languages. The TEMPEST flood events occurred on the following dates. They lasted for ~10 hours each day and delivered ~80,000 gallons to each plot; many data streams are available at 1 or 5 minute frequency during these periods. * Tests: Aug 25 (fresh plot) and Sep 9 (salt plot), 2021 * TEMPEST 1: June 22, 2022 * TEMPEST 2: June 6-7, 2023 * TEMPEST 3: June 11-13, 2024

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATU↗
DOE OSTI2026

AmeriFlux US-MCP Moro Cojo Slough, PG&E Treatment Wetland

This is the AmeriFlux version of the carbon flux data for the site US-MCP Moro Cojo Slough, PG&E Treatment Wetland. Site Description - Freshwater coastal wetland, restored in 2016, native grasses and sedges among freshwater ponds, surrounded 400m in each direction by agricultural plots, native plants remove excess agrcultural nitrogen from the soil

Paytan, Adina [University of California, Santa Cru↗
DOE OSTI2020

Supply Chain Sustainability Analysis of Renewable Hydrocarbon Fuels via Indirect Liquefaction, Ex Situ Catalytic Fast Pyrolysis, Hydrothermal Liquefaction, Combined Algal Processing, and Biochemical Conversion: Update of the 2019 State-of-Technology Cases

This technical report describes the supply chain sustainability analysis (SCSAs) for the production of renewable hydrocarbon transportation fuels via a range of conversion technologies: (1) renewable high octane gasoline (HOG) via indirect liquefaction (IDL) of woody lignocellulosic biomass (note that the IDL pathway in this SCSA represents the syngas conversion design in the 2019 SOT); (2) renewable gasoline (RG) and diesel (RD) blendstocks via ex situ catalytic fast pyrolysis of woody lignocellulosic biomass; (3) RD via hydrothermal liquefaction (HTL) of wet sludge from a wastewater treatment plant; (4) renewable hydrocarbon fuels via biochemical conversion of herbaceous lignocellulosic biomass; (5) renewable diesel via HTL of a blend of algae and woody biomass; and (6) renewable diesel via combined algae processing (CAP). This technical report focuses on the environmental performance of these six biofuel production pathways in their 2019 SOT cases. The results of these renewable hydrocarbon fuel pathways in these SCSA analyses update those for the respective 2018 SOT cases. They also provide an opportunity to examine the impact of technology improvements in both biomass feedstock production and biofuel production that have been achieved in 2019 SOTs on the sustainability performance of these renewable transportation fuels, and they reflect updates to Argonne National Laboratory’s Greenhouse gases, Regulated Emissions, and Energy use in Transportation (GREET®) model, which was released in October 2019. These GREET updates include the production of natural gas, electricity, and petroleum-based fuels that can influence biofuels’ supply chain greenhouse gas (GHG) (CO₂, CH₄, and N₂O) emissions, water consumption, and air pollutant emissions. GHG emissions, water consumption, and nitrogen oxides (NO x ) emissions are the main sustainability metrics assessed in this analysis. In this analysis, we define water consumption as the amount of water withdrawn from a freshwater source that is not returned (or returnable) to a freshwater source at the same level of quality. Life-cycle fossil energy consumption and net energy balance, which is the life-cycle fossil energy consumption deducted from the renewable biofuel energy produced, are also assessed.

09 BIOMASS FUELS↗
DOE OSTI2021

Supply Chain Sustainability Analysis of Renewable Hydrocarbon Fuels via Indirect Liquefaction, Ex Situ Catalytic Fast Pyrolysis, Hydrothermal Liquefaction, Combined Algal Processing, and Biochemical Conversion: Update of the 2020 State-of-Technology Cases

This technical report describes the SCSAs for the production of renewable hydrocarbon transportation fuels via a range of conversion technologies in the 2020 SOTs: (1) renewable high octane gasoline (HOG) via indirect liquefaction (IDL) of woody lignocellulosic biomass (note that the IDL pathway in this SCSA represents the syngas conversion design); (2) renewable gasoline (RG) and diesel (RD) blendstocks via ex situ catalytic fast pyrolysis of woody lignocellulosic biomass; (3) RD via hydrothermal liquefaction (HTL) of wet sludge from a wastewater treatment plant; (4) renewable hydrocarbon fuels via biochemical conversion of herbaceous lignocellulosic biomass; (5) renewable diesel via HTL of a blend of algae and woody biomass; and (6) renewable diesel via combined algae processing (CAP). This technical report focuses on the environmental performance of these six biofuel production pathways in their 2020 SOT cases. The results of these renewable hydrocarbon fuel pathways in these SCSA analyses update those for the respective 2019 SOT cases. They also provide an opportunity to examine the impact of technology improvements in both biomass feedstock production and biofuel production that have been achieved in 2020 SOTs on the sustainability performance of these renewable transportation fuels. The SCSA results also reflect updates to Argonne National Laboratory’s Greenhouse gases, Regulated Emissions, and Energy use in Technologies (GREET ® ) model, which was released in October 2020. These GREET updates include the production of natural gas, electricity, and petroleum-based fuels that can influence biofuels’ supply chain greenhouse gas (GHG) (CO 2 , CH 4 , and N 2 O) emissions, water consumption, and air pollutant emissions. GHG emissions, water consumption, and nitrogen oxides (NO x ) emissions are the main sustainability metrics assessed in this analysis. In this analysis, we define water consumption as the amount of water withdrawn from a freshwater source that is not returned (or returnable) to a freshwater source at the same level of quality. Life-cycle fossil energy consumption and net energy balance, which is the life-cycle fossil energy consumption deducted from the renewable biofuel energy produced, are also assessed.

09 BIOMASS FUELS↗
DOE OSTI2021

Supply Chain Sustainability Analysis of Renewable Hydrocarbon Fuels via Indirect Liquefaction, Ex Situ Catalytic Fast Pyrolysis, Hydrothermal Liquefaction, Combined Algal Processing, and Biochemical Conversion: Update of the 2020 State-of-Technology Cases

The Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) aims to develop and deploy technologies to transform renewable biomass resources into commercially viable, high-performance biofuels, bioproducts, and biopower through public and private partnerships (U.S. Department of Energy, 2016). BETO and its national laboratory teams conduct in-depth techno-economic assessments (TEA) of biomass feedstock supply and logistics and conversion technologies to produce biofuels. There are two general types of TEAs: A design case outlines a target case (future projection) for a particular biofuel pathway. It enables identification of data gaps and research and development needs and provides goals and benchmarks against which technology progress is assessed. A state of technology (SOT) analysis assesses progress within and across relevant technology areas based on actual results at current experimental scales relative to technical targets and cost goals from design cases, and includes technical, economic, and environmental criteria as available. In addition to developing a TEA for a pathway of interest, BETO also performs a supply chain sustainability analysis (SCSA). The SCSA takes the life-cycle analysis approach that BETO has been supporting for about 20 years. It enables BETO to identify energy consumption, environmental, and sustainability issues that may be associated with biofuel production. Approaches to mitigate these issues can then be developed. Additionally, the SCSA allows for comparison of energy and environmental impacts across biofuel pathways in BETO’s research and development portfolio. This technical report describes the SCSAs for the production of renewable hydrocarbon transportation fuels via a range of conversion technologies in the 2020 SOTs: (1) renewable high octane gasoline (HOG) via indirect liquefaction (IDL) of woody lignocellulosic biomass (note that the IDL pathway in this SCSA represents the syngas conversion design [Harris et al. 2021]); (2) renewable gasoline (RG) and diesel (RD) blendstocks via ex situ catalytic fast pyrolysis of woody lignocellulosic biomass [Abhijit et al. 2021]; (3) RD via hydrothermal liquefaction (HTL) of wet sludge from a wastewater treatment plant; (4) renewable hydrocarbon fuels via biochemical conversion of herbaceous lignocellulosic biomass (Davis et al. 2021; Lin et al. 2021); (5) renewable diesel via HTL of a blend of algae (Davis and Klein, 2021) and woody biomass (Hartley et al. 2020); and (6) renewable diesel via combined algae processing (CAP) (Wiatrowski and Davis, 2021). This technical report focuses on the environmental performance of these six biofuel production pathways in their 2020 SOT cases. The results of these renewable hydrocarbon fuel pathways in these SCSA analyses update those for the respective 2019 SOT cases (Cai et al. 2020). They also provide an opportunity to examine the impact of technology improvements in both biomass feedstock production and biofuel production that have been achieved in 2020 SOTs on the sustainability performance of these renewable transportation fuels. The SCSA results also reflect updates to Argonne National Laboratory’s Greenhouse gases, Regulated Emissions, and Energy use in Technologies (GREET®) model, which was released in October 2020 (Wang et al. 2020). These GREET updates include the production of natural gas, electricity, and petroleum-based fuels that can influence biofuels’ supply chain greenhouse gas (GHG) (CO 2 , CH 4 , and N 2 O) emissions, water consumption, and air pollutant emissions. GHG emissions, water consumption, and nitrogen oxides (NO x ) emissions are the main sustainability metrics assessed in this analysis. In this analysis, we define water consumption as the amount of water withdrawn from a freshwater source that is not returned (or returnable) to a freshwater source at the same level of quality. Life-cycle fossil energy consumption and net energy balance, which is the life-cycle fossil energy consumption deducted from the renewable biofuel energy produced, are also assessed.

09 BIOMASS FUELS↗
DOE OSTI2023

Water Recovery From Cooling Tower Plumes

According to studies by the UN and the US State Department, we are on the path to an extreme freshwater shortage by 2030. The US’s largest water withdrawal source is power plants, which account for 39% of total US freshwater withdrawals, mostly for cooling. Cooling towers are the most common cooling system. To solve these problems and enable efficient water- based cooling – Infinite Cooling’s novel technology uses electric fields to ionize the air, charge the escaping water leaving cooling towers and direct the water toward mesh collectors where it collects and gets recycled for use in the cooling system. This technology was developed at MIT and was reduced to practice on a lab-scale prototype, and a prototype at the MIT Cogeneration Power Plant. This DOE award funded taking this technology from a lab-scale prototype to TRL 5 on an operating cooling tower in the field at the MIT Nuclear Research Laboratory. The funding helped to design and optimize an electrostatic plume collection system and test it in high-fidelity lab setting and in actual field conditions on a cooling tower. Throughout the award, Infinite Cooling investigated the formation of plumes on cooling towers, used that information to optimize the design, material and electrical properties of the collection device and quantified the collection yield via flow rate and water quality.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2025

Integrated Hydro-terrestrial Modeling 2.0: Progress and Path Forward on Building a National Capability

It is the role of the U.S. federal government and its supporting agencies, including academia and future scientists, to ensure that its people have sustained and equitable freshwater services, as well as the critical knowledge necessary to make decisions about the future as it relates to freshwater services. Clear and consistent information and guidance from federal agencies is critical. Integrated Hydro-Terrestrial Modeling (IHTM), as a United States (U.S.) national capability, focuses on understanding, quantifying, and managing the replenishment of water supply through hydrologic cycle processes and their governing forces. To provide that information, we need enhanced IHTM capabilities that capitalize on the strengths of each U.S. governmental agency and its core mission. The first IHTM workshop was held in 2019, and its subsequent report was published in 2020. The U.S. Global Change Research Program (USGCRP) and member agencies held a second IHTM workshop (IHTM 2.0) from October 31 to November 2, 2023 in Reston, Virginia. The IHTM 2.0 workshop focused on the need to support a multiscale framework to accelerate research insights, better integrate operational and planning perspectives, and bridge national-to-regional capabilities to address major interdependent societal water challenges. The workshop was organized according to a “WHAT” and “HOW” framework, with the common underlying “WHY” being the integrated water resource challenges and the “WHO” defined through interagency and cooperating academic partners. The report provides a summary of plenary presentations and breakout discussions, and a road map that focuses on near-term activities.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Assessment of the bioconversion potential of minimally processed seaweed by halophilic yeasts

Building an advanced economy using biomanufacturing requires robust sources of carbon for converting into chemicals and products. Macroalgae hold significant potential due to their fast growth rates, lack of freshwater usage, and lack of land usage. To be used as a common feedstock, there are two primary challenges that need to be addressed: 1) unusual chemical composition and 2) high salinity. A solution to both issues is to use a resilient, salt-loving organism with a broad consumption profile for the conversion of macroalgae. Here we evaluate the ability of the oleaginous yeast Rhodosporidium toruloides to grow in wild macroalgae-derived feedstocks and identify a conversion process that is functional for two species of Sargassum collected from the Caribbean using R. toruloides that does not require washing of the input seaweed material. Together this demonstrates a future avenue of work that minimizes freshwater usage for incorporating macroalgae as a biomanufacturing carbon source.

09 BIOMASS FUELS↗
DOE OSTI2026

Interactions between molecular-scale biogeochemical processes and hyporheic exchange for understanding coupled Fe-S-C cycling in iron-rich riparian wetlands (Final Technical Report)

Riparian wetlands are dynamic interfaces that exert strong control over water quality, contaminant mobility, and greenhouse gas emissions. These systems are characterized by hyporheic exchange between oxic surface water and anoxic groundwater, which generates steep redox gradients and promotes spatially and temporally variable microbial activity. Despite growing recognition of tightly coupled iron (Fe), sulfur (S), and carbon (C) cycling in these environments, the mechanisms governing these interactions—particularly under low-sulfate freshwater conditions—remain poorly constrained. This project developed a mechanistic understanding of how hydrologic variability and microbial processes interact to control Fe–S–C cycling in iron-rich riparian wetlands. Using a multi-scale and multi-method approach integrating field observations, geochemical and spectroscopic analyses, metagenomics, and reactive transport modeling, we demonstrate that “cryptic” sulfur cycling—rapid sulfur transformations involving intermediate-valence species—plays a dominant and previously underrecognized role in freshwater wetlands. These processes persist despite low sulfate concentrations and significantly influence iron reduction, carbon mineralization, and methane dynamics. The results show that cryptic sulfur cycling enhances dissolved Fe 2+ production, regulates methane concentrations, and is strongly controlled by climate-driven hydrologic fluxes. By linking hydroclimate, subsurface flow, and biogeochemical reactions, this work provides a predictive framework for understanding how wetland systems respond to environmental change, with direct implications for water quality and carbon cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Feasibility of Multi-Use Ocean Thermal Energy Conversion (OTEC) Platforms

Tropical islands and coastal communities in the United States and internationally suffer from high energy costs, unreliable electrical supplies, poverty, and underemployment, which are all being exacerbated by climate change. Multi-use Ocean Thermal Energy Conversion (OTEC) systems could align with the goals and values of these underserved and remote communities as scalable platforms that can provide baseload power, freshwater, and food, as well as potentially support new industries. The cold, nutrient-rich deep seawater needed for OTEC’s power cycles has many promising byproduct applications such as seawater air conditioning (SWAC) for residential and industrial cooling, enhancing aquaculture farms (e.g., cooling and nutrients for seaweed, shellfish, finfish), producing freshwater through desalination, and generating efuels such as ammonia and hydrogen.

16 TIDAL AND WAVE POWER↗
DOE OSTI2022

Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss

Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, whereas others undergo anadromous migration. Because there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous ( n = 39) and resident ( n = 78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA, with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single-nucleotide polymorphisms that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. Although a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR, and PYD domain–containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.

Collins, Erin E.↗
DOE OSTI2023

Estuarine nutrient pollution impact reduction assessment through euphotic zone avoidance/bypass considerations

The feasibility of reducing nutrient pollution impact by redirecting the effluent to depths below the euphotic zone was investigated for the deep estuarine Puget Sound region of the Salish Sea in the Pacific Northwest of America. The hypothesis tested was that the thickness of the outflow layer in deep estuaries may be greater than the euphotic zone depth, allowing a fraction of nutrients to be exported out passively through the layers immediately below. The euphotic zone depth in Puget Sound varies from 8 to 25 m while the depth of the outflow layer can reach up to ≈ 60 m. Outfall relocation strategies were tested on 99% of the anthropogenic nutrient loads currently delivered to Puget Sound. The impact was quantified using the previously established biophysical Salish Sea Model, using gross primary production and exposure to low dissolved oxygen (DO) levels as the metric (< 2 mg/L for hypoxia and < 5 mg/L for impairment). Eliminating nutrient pollution (above natural) from rivers and wastewater reduced hypoxia exposure by 8.1% and 11.2%, respectively. Relocating the outfalls to deeper waters resulted in improvements, but only in the sill-less sub-basins such as Whidbey, where hypoxia and DO impairment exposure decreased (7.9% and 6.8%, respectively). The presence of multiple sills and circulation cells in Puget Sound resulted in increased exposure and rendered nutrient bypass goals unfeasible as originally envisioned. However, an alternate nutrient export pathway was identified through bottom exchange flow out of Puget Sound via Whidbey Basin and Deception Pass. An unexpected reduction in the exchange outflow magnitude (≈ 4%) due additional (22%) freshwater discharged to the estuary bottom was also noted. The potential loss in circulation strength due to rerouting of natural surface freshwater through submerged deep-water outfalls is identified as a new unforeseen anthropogenic impact.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Assessing shellfish water exposure to fecal bacteria pollution in Salish Sea: three-dimensional modeling and implications for monitoring

Fecal bacteria (FB) contamination poses significant risks to shellfish safety and management in coastal and estuarine waters. Despite extensive pollution identification and correction efforts, FB contamination in shellfish-growing areas persists in the Salish Sea, highlighting the need to identify overlooked sources and better understand FB transport from riverine and shoreline inputs to shellfish beds. To address this, a high-resolution three-dimensional hydrodynamic model coupled with FB kinetics was developed and applied to a case study site in Salish Sea—Portage Bay—to simulate freshwater plume circulation, flushing dynamics, and bacterial transport. Daily FB loading from the major freshwater inflow—Nooksack River was generated by both linear interpolation and integrating a machine learning approach (XGBoost), trained on historical hydrological and meteorological data. The model successfully reproduced both the magnitude and seasonal variation of FB concentrations in Portage Bay for the year of 2021, demonstrating that simplified FB kinetics with first-order decay due to mortality was effective in this dynamic coastal environment with short flushing time. Model results identified the Nooksack River as the dominant far-field FB source, while scenario simulations showed that near-field coastal stormwater outfalls elevated local FB levels following rainfall, particularly under low-flow conditions. The XGBoost prediction provided comparable or superior accuracy to linear interpolation, particularly during periods of missing observational data, by capturing short-term variability and event-driven loading more effectively. Integrating data-driven riverine FB inputs with mechanistic coastal numerical modeling provides a robust framework for operational forecasting of shellfish bed exposure risk and supports adaptive monitoring and management of shellfish growing areas in the Salish Sea and similar coastal systems.

Salish Sea↗
DOE OSTI2020

Impacts of Hurricane Disturbance on Water Quality across the Aquatic Continuum of a Blackwater River to Estuary Complex

Hurricanes cause landscape-scale disturbances that affect biogeochemical cycling and water quality in coastal ecosystems. During Hurricane Irma’s passage through northern Florida, water movements driven by wind velocities up to 105 km h-1 caused a salinity peak in an estuary/blackwater river complex. Water quality was monitored across the 15 km site to detect the magnitude and duration of disturbance. Saline water intruded 15 km inland into a freshwater portion of the river that peaked at a salinity of 2 psu. Due to the volume of precipitation from the hurricane, significant runoff of freshwater and dissolved organic matter (DOM) caused a decrease in salinity, dissolved oxygen (DO), and Chlorophyll-a concentrations while increasing turbidity and fluorescent dissolved organic matter (fDOM). The disturbance caused rapid changes observed by in-situ water quality monitors over a 3-week period, but some effects persisted for longer periods as shown by 3-month weekly water sampling. This disturbance caused shifts in DOM loading, altered salinity dynamics, and reshaped landscapes due to wind and wave surge both in upland marsh and downstream estuary. Hurricane disturbance temporarily and abruptly alters the aquatic continuum, and observations of system response can help us understand the mechanisms associated with ecosystem resilience and recovery.

54 ENVIRONMENTAL SCIENCES↗