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DOE OSTI2020

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range-restricted butterflyfishes across the Red Sea and Arabian Sea using genome-wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Using transparent fish to observe barotrauma associated with downstream passage through hydropower turbines

During downstream passage of hydroelectric facilities, fish can be injured by rapid decompression; this is especially noted during hydroturbine passage. The rapid decrease in pressure can cause barotrauma as undissolved gas expands according to Boyle’s law. However, it is difficult to see barotrauma occurring within the body of the fish in real time. In order to determine if transparent fish could provide greater insight into barotrauma, five species of transparent tropical fish were exposed to rapid decompressions so internal injuries could be viewed noninvasively. Before and after photos were taken to review the injuries and high speed video allowed observations of barotrauma pathways in vivo. High speed video recordings show the expansion of the swim bladder and subsequent release of gas through the mouth and gills, and into the body cavity when the swim bladder ruptured. Post-decompression photographs show that many internal injuries were visible and included hemorrhaging and the presence of emphysema within the body cavity and tissues. These observations provide new opportunities to understand the pathways and effects of barotrauma.

13 HYDRO ENERGY↗

DOE OSTI2021

Characterizing the movements and habitat use of two fish species of concern in a regulated ecosystem

In freshwater ecosystems in the northwest United States, the distribution and movements of fish between their essential habitats are particularly impacted by the presence of hydroelectric dams. Bull Trout Salvelinus confluentus and Westslope Cutthroat Trout Oncorhynchus clarkii var. lewisi are two fish species of concern inhabiting the Pend Oreille River between Idaho and Washington states. The purpose of this study was to identify the behavior and habitat use of Bull Trout and Westslope Cutthroat Trout in the restricted area of the Pend Oreille River, downstream of Albeni Falls Dam (AFD), using a long-term radiotelemetry dataset. Between 2015 and 2018, 24 Bull Trout and 24 Westslope Cutthroat Trout were captured, tagged, and released downstream AFD. Among the fish tagged, 79% (n = 19 of 24) of Bull Trout and 67% (n = 16 of 24) of Westslope Cutthroat Trout were detected during the study period. Our results revealed movements of fish towards tributary confluences mostly in May, June, and July for both species with Bull Trout traveling longer distances than Westslope Cutthroat Trout. Although the sample size was limited, Bull Trout individual movements towards the dam suggested attempts to re-ascend the river, indicating the importance of restoring upstream connectivity.

Garavelli, Lysel↗

DOE OSTI2023

Digital holography for real-time non-invasive monitoring of larval fish at power plant intakes

Effective evaluation of technological and operational approaches to reduce entrainment of marine organisms at cooling water intake structures (CWIS) requires accurate organism-sensing systems. Current detection methods lead to large temporal data gaps, require tedious manual analysis, and are fatal to organisms. In this report we describe integrating deep learning with a non-lethal, non-intrusive imaging method—digital holography—to rapidly detect fish larvae. Laboratory experiments demonstrated that the instrument could successfully image fish larvae at flow rates exceeding ranges seen in CWIS. Holograms of two fish larvae species, in the presence of bubbles and detritus, were collected to build a large database for training a lightweight convolutional neural network. The model achieves 97% extraction accuracy in quantifying larvae, and distinguishing them from other particles, including detritus and bubbles, when applied to a dataset of manually classified images, exceeding previous metrics for non-lethal, accurate, and real-time detection. These results demonstrate the potential of in situ holographic imaging for monitoring endangered larval fish species at power plant intake structures, and for high-fidelity, real-time applications in monitoring aquatic ichthyoplankton.

endangered species↗

DOE OSTI2021

Autonomous Acoustic Receiver System for 3D Tracking and Monitoring Real-Time Fish Survival (CRADA 448)

Develop technologies that reduce the delay between changing hydropower operations and the acquisition of knowledge regarding fish behavior and survival and to reduce the cost and effort to obtain behavioral information of fish that is both accurate and detailed. The technologies being proposed would allow hydropower operators to quickly understand the impact of operational changes on fish and allow fisheries researchers to study fish behavior in high resolution at locations that previously would have been unfeasible.

13 HYDRO ENERGY↗

DOE OSTI2021

Biological Response Models: Predicting Injury and Mortality of Fish During Downstream Passage through Hydropower Facilities

This report describes the U.S. Department of Energy’s HydroPASSAGE project efforts to develop and collect biological response models for integration into the Biological Performance Assessment (BioPA) toolset and the Hydropower Biological Evaluation Toolset (HBET). These models help understand how fish are likely to respond during dam passage when exposed to hydraulic and physical stressors associated with turbines and other hydropower structures. When fish pass through hydropower facilities, they may encounter several stressors, of which the three most common are collision, rapid decompression, and fluid shear. Specialized equipment has been used to develop 99 biological response models for exposure to blade strike, rapid decompression, or fluid shear. The models were gathered from the literature or developed as part of this effort and include models for 31 different species of fish that have various predicted endpoints (i.e., injury or mortality). Among these models, considerable variation in susceptibility to the stressors has been observed from one species to another, and a species’ susceptibility to one stressor does not necessarily indicate similar susceptibility to another. Although several species have been examined, it is still unclear how many other species, which may have different morphological traits, may respond to these stressors, so further examination of the different species is needed. These models can and have been applied in several different cases, often using the BioPA toolset and HBET, to better understand the potential for injury and mortality that may occur during fish passage at hydropower facilities, including specific applications, such as turbine replacement, the installation of new turbines, or changing operations of currently installed turbines. As hydropower is continually developed to meet the electricity needs of society, tools such as HBET and BioPA, used with the integrated biological response models, will aid in the development of technologies and strategies that avoid, minimize, mitigate, or manage environmental effects.

13 HYDRO ENERGY↗

DOE OSTI2024

Definition and Execution of Regulatory requirements for acceptance of the Whooshh Fish Transport System (Abstract)

The purpose of this project is to assist in the definition, summarization, and execution of the regulatory requirements that validate the Whooshh Fish Transport System (WFTS) as an accepted method of fish passage transport for Endangered Species Act- (ESA) listed species; moving these fish past in-stream barriers, such as hydropower facilities. Validation of this technology, through testing by PNNL, means that regulatory agencies will have documented evidence from which to support an approval decision enabling Whooshh to quickly commercialize their product for use in waterways with ESA listed species and provide the hydropower relicense/development marketplace a viable solution to the fish passage problem that threatens the hydropower industry. Given the definition of “take” in the ESA, without validation, commercialization in this space in the U.S. will not happen because the regulatory agencies will not have the determinative study results they require to authorize the use of this new technology that interact with ESA-listed species.

13 HYDRO ENERGY↗

DOE OSTI2025

Evaluating User Errors and Temporal Trends in Marine Fish Communities Using 360-Degree Underwater Photography

The use of environmental DNA (eDNA) sampling has been proposed as a complementary method to monitor fish species in marine environments, offering a non-invasive and potentially more efficient approach to marine species observations. eDNA monitoring could be especially useful in and around sites targeted for marine energy generation as these regions need regular monitoring that would be impractical with traditional techniques. Before we can fully rely upon eDNA, we must first verify its accuracy against other proven methods, such as the use of underwater photography. In this study, I deployed a 360-degree camera in the tidal channel of Sequim Bay once a month during several hours overlapping slack tide. I investigated how having multiple people identify and count fish on underwater images could affect the overall results. Using chi square tests in R, I compared my fish identifications and counts to those made by another intern on the same images recorded in August. I found significant differences in the number of species identified and the total individual counts between the two different datasets. I also tested the statistical differences in both Shannon diversity and Pielou evenness indices between the August, September, and November camera deployments using a Hutcheson t-test. Only one significant difference was found in the Shannon index comparisons, and none were found between the Pielou evenness comparisons. These findings show that if multiple identifiers are used to process underwater images, quality control checks must be made to reduce the potential for error. This also points toward the possibility to leverage more advanced image analysis processes, such as automated image analysis software. The findings from this study also show that the dynamics of marine fish communities can vary over a few months; however, further analysis is needed to determine the extent of the seasonal changes in Sequim Bay.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

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

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

13 HYDRO ENERGY↗

DOE OSTI2023

A symbiotic bacterium of Antarctic fish reveals environmental adaptability mechanisms and biosynthetic potential towards antibacterial and cytotoxic activities

Antarctic microbes are important agents for evolutionary adaptation and natural resource of bioactive compounds, harboring the particular metabolic pathways to biosynthesize natural products. However, not much is known on symbiotic microbiomes of fish in the Antarctic zone. In the present study, the culture method and whole-genome sequencing were performed. Natural product analyses were carried out to determine the biosynthetic potential. We report the isolation and identification of a symbiotic bacterium Serratia myotis L7-1, that is highly adaptive and resides within Antarctic fish, Trematomus bernacchii . As revealed by genomic analyses, Antarctic strain S. myotis L7-1 possesses carbohydrate-active enzymes (CAZymes), biosynthetic gene clusters (BGCs), stress response genes, antibiotic resistant genes (ARGs), and a complete type IV secretion system which could facilitate competition and colonization in the extreme Antarctic environment. The identification of microbiome gene clusters indicates the biosynthetic potential of bioactive compounds. Based on bioactivity-guided fractionation, serranticin was purified and identified as the bioactive compound, showing significant antibacterial and antitumor activity. The serranticin gene cluster was identified and located on the chrome. Furthermore, the multidrug resistance and strong bacterial antagonism contribute competitive advantages in ecological niches. Our results highlight the existence of a symbiotic bacterium in Antarctic fish largely represented by bioactive natural products and the adaptability to survive in the fish living in Antarctic oceans.

Xiao, Yu↗

NASA NTRS1978

Locomotor behavior of fish hatched from embryos exposed to flight conditions

Embryos of Fundulus heteroclitus in various stages of development were exposed to space flight conditions aboard Apollo spacecraft and Cosmos satellites. The objective of the study was to ascertain whether fish hatched from these embryos displayed locomotor behavior different from that of control fish of the same age. An electronic monitoring technique was used to record behavior. Results indicate no change in locomotor behavior in fish on Apollo Spacecraft, but inexplicable significant changes were noted in fish aboard Cosmos Satellites.

Kleerekoper, H.↗

NASA NTRS1978

Effect of prehatching weightlessness on adult fish behavior in dynamic environments

At 16-17 months of age, three groups of fish from the embryonated eggs in the ASTP killifish experiment were subjected to postflight tests consisting of rapidly changing environments. It was found that the group of fish with the least amount of development at orbital insertion (A-32) had a decreased rheotropism for both the moving background and the rotating water current tests when compared to ground control fish. Exposure to parabolic aircraft flight conditions revealed that the A-32 fish were less disoriented during zero gravity periods and were hypersensitive to high-gravity periods. These results suggested a modified vestibular competency due to a 9-d prehatching weightlessness exposure.

Hoffman, R. B.↗

NASA NTRS1995

Sensory Cells of the Fish Ear: A Hairy Enigma

Analysis of the structure of the ears in teleost fishes has led to the tentative suggestion that otolithic endorgans may function differently, in different species. Recently, evidence has demonstrated different 'types' of sensory hair cells can be found in the ears of teleost fishes, and individual hair cell types are found in discrete regions of individual sensory, epithelia. The presence of multiple hair cell types in fishes provides strong support to the hypothesis of regional differences in the responses of individual otolithic sensory epithelia. The finding of hair cell types in fishes that closely resemble those found in amniote vestibular endorgans also suggests that hair cell heterogeneity arose earlier in the evolution of the vertebrate ear than previously thought.

Popper, A. N.↗

DOE OSTI2024

Fish Friendly Water Rules' Impact On the Power Grid with High VRE Levels

Columbia River basin multipurpose reservoirs are operated for hydropower production and many other purposes considering the aquatic habitat of the river basin. Specifically, the river basin fish population is a vital element for the tribal community of the river basin. When conventional thermal power plants are retired, hydropower flexibility balances the wind and solar variability of the power grid and provides grid services to maximize the high renewable power absorption. On the other hand, over-reliance on hydropower could harm the river basin fish habitat. For example, water release pulses during peak electricity demand hours and shorter-term water release variation could harm the fish population. Power grid planners, environmentalists, Columbia Basin tribes, hydro regulators, and water resource planners work together to understand the impacts of Columbia River basin operation in a fish-friendly way in the current power grid and power grid with higher renewable power share. We examine different levels of renewable share in the Western Interconnection to understand the multiple weather years and future climate projection and operating scenario impact on the power grid and water system. We measure power grid impacts for various water resources planning scenarios in terms of total system operating cost, system reliability indicators, changes in wind and solar generation and curtailments, local marginal prices, and revenue for hydropower producers. The study results inform reservoir operating rules decisions from hydropower power producers, system operators, other water users, tribes, environmentalists, and other stakeholders.

environmental↗

DOE OSTI2023

Towards assessing the impact of anthropogenic sound on fishes: Gaps, perspectives, and a case study of a large floating bridge

Underwater anthropogenic sound can cause physical, physiological, and behavioral impacts on fishes. With the development of marine energy facilities, the impact of man-made underwater sound on fishes has become a growing regulatory concern. Large gaps remain in how to perform an underwater sound assessment. Such gaps mainly reside in scientific evidence, regulatory criteria, sound characterization metrics, sound field modeling, and instrumentation for field measurement. Here, this paper reviewed existing work on underwater sound assessment for fishes to identify critical gaps and provide perspectives on how to deal with these gaps, demonstrated with a case study on the impact of the Hood Canal Bridge traffic sound on migrating steelhead smolts in Washington State, U.S. We also provide perspectives on future research directions to bridge the identified gaps for aquatic ecological assessment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Analysis of the linear and nonlinear stability of Alfven eigenmodes and fish-bones in JET DT discharges: mode identification and shear flows generation

The plasma in future nuclear fusion reactors will be heated by neutral beam injectors (NBIs) and high frequency electromagnetic waves as well as fusion born alpha particles. Energetic particles (EPs), with energies up to two orders of magnitude larger than the thermal plasma, can trigger EP driven modes and induce harmful EP losses, reducing the plasma heating efficiency and the economical viability of the reactor. The present study is dedicated to analyze the Alfven Eigenmode (AE) activity in JET D–T discharges, the closest experiment to reactor-like operation performed until now. There, EP driven modes are induced by the combined effect of tangential NBIs and ion cyclotron resonance heating (ICRH) driven EP. Linear and nonlinear simulations are performed with the gyro-fluid FAR3d code to analyze the AE activity observed in the discharge 99896. The linear simulations reproduce the unstable n = 3 to 5 toroidal AEs (TAE) at the inner plasma region observed in the experiment, triggered by highly energetic passing deuterium populations injected by the tangential NBIs, further accelerated by the effect of the ICRH up to 1 MeV. In addition, fish-bones triggered by energetic trapped hydrogen induced by the ICRH are also reproduced. On the other hand, the alpha particles density is too small to destabilize AEs in the experiment. Nonetheless, increasing artificially the alpha density by one order of magnitude, an n = 1 beta induced AE can be destabilized in the inner plasma region. Nonlinear simulations indicate the generation of zonal structures during the AE/fish-bone saturation phase. TAE and fish-bones causes a rather weak increase of the passing D and trapped H EP (around 2%), respectively. Shear flows and zonal currents are generated during the saturation of TAE and fish-bones. Nonlinear simulations performed for D–T and pure deuterium thermal plasma indicate AE/fish-bone activity is weaker and shear flows are less intense in the pure deuterium case, trends consistent with the experimental observations that also indicates a deterioration of the thermal plasma confinement. Therefore, both numerical studies and experimental evidence indicate the generation of shear flows by AE/fish-bones could be connected with an improvement of the thermal plasma confinement.

AE↗

DOE OSTI2023

Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides

Marine herbivorous fish that feed primarily on macroalgae, such as those from the genus Kyphosus, are essential for maintaining coral health and abundance on tropical reefs. Here, deep metagenomic sequencing and assembly of gut compartment-specific samples from three sympatric, macroalgivorous Hawaiian kyphosid species have been used to connect host gut microbial taxa with predicted protein functional capacities likely to contribute to efficient macroalgal digestion. Bacterial community compositions, algal dietary sources, and predicted enzyme functionalities were analyzed in parallel for 16 metagenomes spanning the mid- and hindgut digestive regions of wild-caught fishes. Gene colocalization patterns of expanded carbohydrate (CAZy) and sulfatase (SulfAtlas) digestive enzyme families on assembled contigs were used to identify likely polysaccharide utilization locus associations and to visualize potential cooperative networks of extracellularly exported proteins targeting complex sulfated polysaccharides. These insights into the gut microbiota of herbivorous marine fish and their functional capabilities improve our understanding of the enzymes and microorganisms involved in digesting complex macroalgal sulfated polysaccharides.

09 BIOMASS FUELS↗

DOE OSTI2024

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

ABSTRACT Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea ) and Verrucomicrobiota (order Kiritimatiellales ) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors. IMPORTANCE Seaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.

59 BASIC BIOLOGICAL SCIENCES↗