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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

eDNAjoint: An R package for interpreting paired or semi‐paired environmental DNA and traditional survey data in a Bayesian framework

Abstract Environmental DNA (eDNA) sampling is increasingly used in surveys of species distribution as a potentially sensitive and efficient monitoring method. Yet access to modelling tools designed specifically for interpreting this new data type lags behind its ubiquity. While occupancy modelling software has dominated the analytical landscape for eDNA data analysis of single species, this type of model may not always be the most appropriate. The rate of eDNA detection often corresponds to species density, rather than just occupancy, and researchers often have access to observations from non‐genetic sampling methods at the same sites. To provide users access to a modelling framework designed to maximize the use of all available data, we developed an R package, eDNAjoint . The package provides an easy‐to‐use interface for fitting a ‘joint’ model that integrates data from paired or semi‐paired eDNA and traditional surveys in a Bayesian framework. The model can be used to estimate parameters like the probability of a false positive eDNA detection and mean catch rate at a site, and the package allows access to multiple model variations and Bayesian prior customization. Additional functionality can be used for model selection, summarising posteriors and comparing the relative sensitivities of the two survey methods. We demonstrate the use of eDNAjoint by fitting a variation of the model with site‐level covariates that scale the sensitivity of eDNA sampling relative to traditional sampling. The example workflow uses binary eDNA and seine count data for the endangered tidewater goby ( Eucyclogobius newberryi ) from a study by Schmelzle and Kinziger (2016). This use case includes a prior sensitivity analysis and an evaluation of the relationship between detection rates and environmental variables. eDNAjoint has the potential to greatly increase the range of users who will be able to rigorously analyse eDNA and traditional survey data in a Bayesian framework, understand if and how eDNA can improve monitoring practices, and gain confidence in the interpretability of eDNA data.

Keller, Abigail G. [Department of Environment Scie↗
DOE OSTI2024

Processes Associated with Boundary Layer Cloud Ice Phase Precipitation in the High Southern Latitudes (Final Technical Report)

This is a final technical report for DOE Award No. DE-SC0018995. Using data collected during the MARCUS deployment of the 2nd ARM mobile facility, this project sought to address the following scientific questions: 1. What are the conditions that govern phase partitioning in supercooled boundary layer clouds over the high latitude Southern Oceans? 2. To what extent are supercooled mixed phase clouds responsible for the high cloud fractions over the Southern Ocean and do these mixed phase clouds contribute to the model biases in absorbed shortwave radiation? 3. Can the cloud properties and phase partitioning over the Southern Ocean be linked to the underlying aerosol environment? 4. How do the aerosol properties at the surface vary spatially and seasonally over the high latitude Southern Ocean and what processes control these features? 5. How well defined are the atmospheric compositional boundaries between Southern Ocean marine, Antarctic free tropospheric, and Antarctic surface airmasses, and how does this influence the chemistry and physics of the Southern Ocean atmosphere? In this project we published three peer review journal articles that address these questions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Magnetic Gears for a Marine Hydrokinetic Generator Component Model

The goal of this project is to design, fabricate, and test a hermetically sealed 50 kilowatt (kW) multistage magnetically geared generator (MGG). The Component Content Model provides data submitters with an easy and consistent means of uploading data and associated meta data about a component that is currently under development. The data fields include generic information about the component, technology classifications, current costs and performance, proposed target goals, and the environment that the component is operated in. These data are important to DOE and will be used to develop data products that provide quantitative information to guide and support programmatic decisions. Data will also be used by DOE in general assessments of MHK component readiness, performance, costs, and proposed plans. The ultimate goal is to use these data to perform research and tailor programs to best benefit the industry.

16 TIDAL AND WAVE POWER↗
DOE OSTI2023

MOSAiC Radar b1 Processing: Corrections, Calibrations, and Processing Report

The U.S. Department of Energy’s (DOE) Atmospheric Radiation Measurement (ARM) user facility deployed many instruments on board a German ice breaker, the Research Vessel (RV) Polarstern, for one year from October 2019 to October 2020. The purpose of the Multidisciplinary Drifting Observatory for the Study of Arctic Climate (MOSAiC) field campaign was to study the decline in the sea-ice pack around the North Pole, and what factors may be at play. After the campaign ended, efforts were undertaken to provide a calibrated radar data set for future studies. MOSAiC presented new challenges to this process, as existing methodologies often were not applicable for the frozen environment with little to no ground clutter, and concurrent engineering updates or calibrations could not be accomplished once the ship set off. Like the previous Cloud, Aerosol, and Complex Terrain Interactions (CACTI) and Cold-air Outbreaks in the Marine Boundary Layer Experiment (COMBLE) documentation (Hardin et al. 2020, Matthews et al. 2023), the data correction and calibration process is known in ARM as creating a “b1” datastream. This means that the radar datastreams have been well characterized to the best possible quality. This report will detail the status of the raw “a1” level data sets during the MOSAiC campaign, the corrections that were applied to create the “b1” data files, and the details of the applied methods.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A geospatial environmental and techno-economic framework for sustainable phosphorus management at livestock facilities

Nutrient pollution of waterbodies is a major worldwide water quality problem. Excessive use and discharge of nutrients can lead to eutrophication and algal blooms in fresh and marine waters, resulting in environmental problems associated with hypoxia, public health issues related to the release of toxins and freshwater scarcity. A promising option to address this problem is the recovery of nutrient releases prior to being discharged into the environment. Driven by the sustainable materials management concept, the COW2NUTRIENT (Cattle Organic Waste to NUTRIent and ENergy Technologies) framework is developed for the techno-economic evaluation and selection of nutrient recovery systems at livestock facilities. Furthermore, environmental vulnerability to nutrient pollution determined through a geographic information system (GIS)-based model and techno-economic information of different state-of-the-art nutrient management technologies are combined in a multi-criteria decision analysis (MCDA) model, resulting in the selection and economic analysis of the most suitable process for each studied livestock facility. This framework has been employed for studying the implementation of sustainable phosphorus management systems at 2,217 livestock facilities in the Great Lakes area, resulting in capital expenses of 2.5 billion USD if only phosphorus recovery technologies are installed, and up to 5.2 billion USD if nutrient management is combined with biogas and power production. However, considering potential economic incentives for the recovery of phosphorus, net revenues up to 230 million USD per year can be achieved. Therefore, the framework presented reveals the potential of implementing nutrient management systems at regional scale for the abatement of phosphorus releases from livestock facilities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A new Devonian euthycarcinoid reveals the use of different respiratory strategies during the marine-to-terrestrial transition in the myriapod lineage

Myriapods were, together with arachnids, the earliest animals to occupy terrestrial ecosystems, by at least the Silurian. The origin of myriapods and their land colonization have long remained puzzling until euthycarcinoids, an extinct group of aquatic arthropods considered amphibious, were shown to be stem-group myriapods, extending the lineage to the Cambrian and evidencing a marine-to-terrestrial transition. Although possible respiratory structures comparable to the air-breathing tracheal system of myriapods are visible in several euthycarcinoids, little is known about the mechanism by which they respired. Here, we describe a new euthycarcinoid from Upper Devonian alluvio-lagoonal deposits of Belgium. Synchrotron-based elemental X-ray analyses were used to extract all available information from the only known specimen. Sulfur X-ray fluorescence (XRF) mapping and spectroscopy unveil sulfate evaporation stains, spread over the entire slab, suggestive of a very shallow-water to the terrestrial environment prior to burial consistent with an amphibious lifestyle. Trace metal XRF mapping reveals a pair of ventral spherical cavities or chambers on the second post-abdominal segment that do not compare to any known feature in aquatic arthropods, but might well play a part in air-breathing. Our data provide additional support for amphibious lifestyle in euthycarcinoids and show that different respiratory strategies were used during the marine-to-terrestrial transition in the myriapod lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

PNNL Review of Federal and State Agency Regulatory Streamlining Practices

All major federal actions that have the potential to significantly affect the environment (e.g., land purchases and/or issuing grants, permits, leases, or licenses) are subject to multiple statutes including the following: • an environmental analysis under the National Environmental Policy Act (NEPA) • potential consultations with the U.S. Fish and Wildlife Service (USFWS) and/or National Marine Fisheries Service (NMFS) under the Endangered Species Act of 1973, as amended (ESA) • potential consultations with State Historical Preservation Officers (SHPOs) and/or tribal nations [often Tribal Historic Preservation Officers (THPOs)] under the National Historic Preservation Act of 1966 (NHPA). Given the size of the federal government and the corresponding variability and complexity in its missions, different branches within the federal government have a fairly wide range of approaches to fulfill their NEPA and consultation requitements. Many of these approaches are founded on the desire to streamline their NEPA and consultation processes while meeting the spirit and letter of the regulations. Some federal and state environmental/engineering agencies have developed web-based dashboards that provide a single web location for permit application submittals. They also use general permits in their various permitting processes. General permits can streamline the permitting process by establishing identical requirements for all eligible applicants. This reduces the time these agencies need to spend reviewing individual permits and setting specific requirements. In addition, general permits do not require a case-specific permit application. This paper presents a sampling of effective agency examples of streamlining the NEPA process and associated agency consultations. It also includes several examples of federal and state agency web portals, online application systems, and general permits that make application processes more efficient and accessible.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Evaluating the effectiveness of M-AMBI with other biotic indexes in a temperate estuary

Need for a scalable and widely applicable index has been increasingly important. This study evaluates the applicability of the M-AMBI, a potential comprehensive index, at small spatial scales. M-AMBI was compared to regional indices (EMAP-E and GOM B-IBI), assessing response to natural environmental gradients and low oxygen stress. Results indicate poor agreement between indices with M-AMBI and GOM B-IBI showing positive correlation but significant disagreement in habitat condition. EMAP-E had no agreement. Indices showed similar patterns of better habitat scores in higher salinities. M-AMBI also showed a negative relationship with sediment organic matter and total nitrogen. DO influenced all indices with M-AMBI the most sensitive. However, mismatches between DO and index score were observed further calibration may be needed before adoption into programs. Altogether, the M-AMBI demonstrates potential at smaller, local scales, but additional studies are needed to validate its performance in different coastal environments and under different conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Modular RivGen LCOE Content Model

The Modular RivGen LCOE Content Model contains estimates of levelized cost of energy (LCOE) for three array configurations operating in a theoretical river environment. The LCOE is distinguished by the CapEx, OpEx, and annual energy production and capture for each river environment.

16 TIDAL AND WAVE POWER↗
DOE OSTI2025

Dissolved Organic Carbon in Coastal Waters: Global Patterns, Stocks and Environmental Physical Controls

Abstract Dissolved organic carbon (DOC) in coastal waters is integral to biogeochemical cycling, but global and regional drivers of DOC are still uncertain. In this study we explored spatial and temporal differences in DOC concentrations and stocks across the global coastal ocean, and how these relate to temperature and salinity. We estimated a global median coastal DOC stock of 3.15 Pg C (interquartile range (IQR) = 0.85 Pg C), with median DOC concentrations being 2.2 times higher than in open ocean surface waters. Globally and seasonally, salinity was the main driver of DOC with concentrations correlated negatively with salinity, without a clear relationship to temperature. DOC concentrations and stocks varied with region and season and this pattern is likely driven by riverine inputs of DOC and nutrients that stimulate coastal phytoplankton production. Temporally, high DOC concentrations occurred mainly in months with high freshwater input, with some exceptions such as in Eastern Boundary Current margins where peaks are related to primary production stimulated by nutrients upwelled from the adjacent ocean. No spatial trend between DOC and temperature was apparent, but many regions (19 out of 25) had aligned peaks of seasonal temperature and DOC, related to increased phytoplankton production and vertical stratification at high temperatures. Links of coastal DOC with salinity and temperature highlight the potential for anthropogenic impacts to alter coastal DOC concentration and composition, and thereby ecosystem status.

Lønborg, Christian [Section for Marine Diversity a↗
DOE OSTI2026

Influence of Surface Aerosol Injection on Stratocumulus‐to‐Cumulus Transition: Cloud‐Surface Coupling and Background Aerosol Concentrations

The influence of surface aerosol injection on the stratocumulus‐to‐cumulus transition (SCT) is explored using large‐eddy simulations. We examine how cloud‐surface coupling (or the strength of the marine boundary layer (MBL) stratification that limits vertical turbulent mixing and convection) impacts the vertical transport of aerosols, and how injected aerosols influence cloud properties and associated cloud radiative effects during the SCT. By injecting aerosols at different stages of the SCT, noting that cloud is more decoupled from the surface over time due to entrainment warming, we find that cloud‐surface coupling significantly affects aerosol vertical transport. However, injection timing (before drizzle if any) does not notably affect the SCT and the efficiency of marine cloud brightening, because aerosol number concentrations due to injections at different times rapidly converge before the transition onset. By varying the background aerosol concentration, we find that injected aerosols can significantly extend the persistence of stratocumulus decks by suppressing precipitation in clean environments but have little impact on stratocumulus breakup with higher background aerosol concentrations due to saturated aerosol effects. In clean MBLs, the SCT‐delay‐induced increase in cloud fraction dominates the overall cooling effects in response to aerosols, followed by Twomey effects. These cooling effects are slightly offset by decreased liquid water path (LWP) due to entrainment drying. In polluted MBLs, the Twomey effect is more dominant, followed by cloud fraction adjustments, and these coolings are also partly offset by LWP adjustments. All the simulations are made in relatively small domains in which injected aerosols are homogenized over a short time scale.

Zhang, Haipeng [Univ. of Maryland, College Park, M↗
DOE OSTI2023

Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias

Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in “light stress.” The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Potential Activities and Long Lifetimes of Organic Carbon-Degrading Extracellular Enzymes in Deep Subsurface Sediments of the Baltic Sea

Heterotrophic microorganisms in marine sediments produce extracellular enzymes to hydrolyze organic macromolecules, so their products can be transported inside the cell and used for energy and growth. Therefore, extracellular enzymes may mediate the fate of organic carbon in sediments. The Baltic Sea Basin is a primarily depositional environment with high potential for organic matter preservation. The potential activities of multiple organic carbon-degrading enzymes were measured in samples obtained by the International Ocean Discovery Program Expedition 347 from the Little Belt Strait, Denmark, core M0059C. Potential maximum hydrolysis rates (V max ) were measured at depths down to 77.9mbsf for the following enzymes: alkaline phosphatase, β- d -xylosidase, β- d -cellobiohydrolase, N-acetyl-β- d -glucosaminidase, β-glucosidase, α-glucosidase, leucyl aminopeptidase, arginyl aminopeptidase, prolyl aminopeptidase, gingipain, and clostripain. Extracellular peptidase activities were detectable at depths shallower than 54.95mbsf, and alkaline phosphatase activity was detectable throughout the core, albeit against a relatively high activity in autoclaved sediments. β-glucosidase activities were detected above 30mbsf; however, activities of other glycosyl hydrolases (β-xylosidase, β-cellobiohydrolase, N-acetyl-β-glucosaminidase, and α-glucosidase) were generally indistinguishable from zero at all depths. These extracellular enzymes appear to be extremely stable: Among all enzymes, a median of 51.3% of enzyme activity was retained after autoclaving for an hour. We show that enzyme turnover times scale with the inverse of community metabolic rates, such that enzyme lifetimes in subsurface sediments, in which metabolic rates are very slow, are likely to be extraordinarily long. A back-of-the-envelope calculation suggests enzyme lifetimes are, at minimum, on the order of 230days, and may be substantially longer. These results lend empirical support to the hypothesis that a population of subsurface microbes persist by using extracellular enzymes to slowly metabolize old, highly degraded organic carbon.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Mechanisms of Low-Level Jet Formation in the U.S. Mid-Atlantic Offshore

Abstract Low-level jets (LLJs), in which the wind speed attains a local maximum at low altitudes, have been found to occur in the U.S. mid-Atlantic offshore, a region of active wind energy deployment as of 2023. In contrast to widely studied regions such as the U.S. southern Great Plains and the California coastline, the mechanisms that underlie LLJs in the U.S. mid-Atlantic are poorly understood. This work analyzes floating lidar data from buoys deployed in the New York Bight to understand the characteristics and causes of coastal LLJs in the region. Application of the Hilbert–Huang transform, a frequency analysis technique, to LLJ case studies reveals that mid-Atlantic jets frequently occur during times of adjustment in synoptic-scale motions, such as large-scale temperature and pressure gradients or frontal passages, and that they do not coincide with motions at the native inertial oscillation frequency. Subsequent analysis with theoretical models of inertial oscillation and thermal winds further reveals that these jets can form in the stationary geostrophic wind profile from horizontal temperature gradients alone—in contrast to canonical LLJs, which arise from low-level inertial motions. Here, inertial oscillation can further modulate the intensity and altitude of the wind speed maximum. Statistical evidence indicates that these oscillations arise from stable stratification and the associated frictional decoupling due to warmer air flowing over a cold sea surface during the springtime land–sea breeze. These results improve our conceptual understanding of mid-Atlantic jets and may be used to better predict low-level wind speed maxima. Significance Statement The purpose of this work is to identify and characterize the atmospheric mechanisms that result in an occasional low-level maximum in the wind speed off the U.S. mid-Atlantic coastline. Our findings show that these low-level jets form due to horizontal temperature gradients arising from fronts and synoptic systems, as well as from the land–sea breeze that forces warmer air over the cold ocean surface. This work aids predictability of such jets, improves our understanding of this coastal environment, and has implications for future deployment of offshore wind energy in this region.

17 WIND ENERGY↗
DOE OSTI2023

Natural marine cloud brightening in the Southern Ocean

Abstract. The number of cloud droplets per unit volume (Nd) is a fundamentally important property of marine boundary layer (MBL) liquid clouds that, at constant liquid water path, exerts considerable controls on albedo. Past work has shown that regional Nd has a direct correlation to marine primary productivity (PP) because of the role of seasonally varying, biogenically derived precursor gases in modulating secondary aerosol properties. These linkages are thought to be observable over the high-latitude oceans, where strong seasonal variability in aerosol and meteorology covary in mostly pristine environments. Here, we examine Nd variability derived from 5 years of MODIS Level 2-derived cloud properties in a broad region of the summer eastern Southern Ocean and adjacent marginal seas. We demonstrate latitudinal, longitudinal and temporal gradients in Nd that are strongly correlated with the passage of air masses over high-PP waters that are mostly concentrated along the Antarctic Shelf poleward of 60∘ S. We find that the albedo of MBL clouds in the latitudes south of 60∘ S is significantly higher than similar liquid water path (LWP) clouds north of this latitude.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Integrated path planning and control through proximal policy optimization for a marine current turbine

This paper presents an integrated path planning and tracking control framework for a marine current turbine (MCT), where the MCT is treated as an energy-harvesting autonomous underwater vehicle (AUV). Considering the ocean (space of action) is continuous, the proposed framework employs two modules to address path planning and path tracking enabled by the proximal policy optimization (PPO) algorithm, which is a policy gradient deep reinforcement learning (RL) method. Further, to enable fully autonomous operation in a stochastic oceanic environment, the proposed path planning seeks a primary objective of maximizing the harvested energy; then, the path tracking module is designed to minimize the tracking error and avoid collisions with static and dynamic obstacles. Using field-collected acoustic Doppler current profiler (ADCP) data, the performance of the proposed framework is evaluated. Comparative studies with baseline algorithms in three different scenarios of path planning, path tracking without an obstacle, and path tracking with collision avoidance verify the effectiveness of our proposed approach.

16 TIDAL AND WAVE POWER↗
DOE OSTI2022

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling.

54 ENVIRONMENTAL SCIENCES↗