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At least 379 records · Page 21

Differential DNA methylation and metabolite profiling of Atlantic killifish (Fundulus heteroclitus) from the New Bedford Harbor Superfund site

Atlantic killifish (Fundulus heteroclitus) is a valuable model in evolutionary toxicology to study how the interactions between genetic and environmental factors serve the adaptive ability of organisms to resist chemical pollution. Killifish populations inhabiting environmental toxicant-contaminated New Bedford Harbor (NBH) show phenotypes tolerant to polychlorinated biphenyls (PCBs) and differences at the transcriptional and genomic levels. However, limited research has explored epigenetic alterations and metabolic effects in NBH killifish. To identify the involvement of epigenetic and metabolic regulation in the adaptive response of killifish, we investigated tissue- and sex-specific differences in global DNA methylation and metabolomic profiles of NBH killifish populations, compared to sensitive populations from a non-polluted site, Scorton Creek (SC). The results revealed that liver-specific global DNA hypomethylation and differential metabolites were evident in fish from NBH compared with those from SC. The sex-specific differences were not greater than the tissue-specific differences. We demonstrated liver-specific enriched metabolic pathways (e.g., amino acid metabolic pathways converged into the urea cycle and glutathione metabolism), suggesting possible crosstalk between differential metabolites and DNA hypomethylation in the livers of NBH killifish. Additional investigation of methylated gene regions is necessary to understand the functional role of DNA hypomethylation in the regulation of enzyme-encoding genes associated with metabolic processes and physiological changes in NBH populations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design and scale-up of 3D printed bat houses with biomass-derived polymer composites

Biomass (e.g., pine sawdust, especially high–ash content pine sawdust) is commonly disposed of as waste. Combining biomass with polymers to make composite feedstocks for 3D printing has been explored as a method to reduce or repurpose the biomass waste. Although not all biocomposite properties are known, the wood-based polylactic acid (PLA) composite has promising qualities for applications in ecological settings. In this work, pine wood–PLA composite feedstock was used to 3D print supplemental roost structures for endangered tree-roosting bats, which often face a paucity of suitable naturally occurring roosts. This material combination was selected because it is estimated to degrade faster than the synthetic material systems that are used widely in supplemental bat roosting structures to aid in the conservation of tree roosting bats. The layered, rough surface created by the 3D printing process serves as a surface that bats can grip while roosting. Computer-aided design (CAD) models were generated based on natural roost structures, and a full-size bat house was successfully additively manufactured using a pellet-fed large-scale 3D printing system. The 3D printed hexagon exhibited a tensile strength of 22–23 MPa and a Young’s modulus of 3202–3218 MPa in the x-direction. It has been demonstrated that the 3D printed bat house can be installed on a tree in a stable fashion. This successful demonstration of a bat roost manufactured using a bioderived composite should promote its use in other fish and wildlife structures and broader industrial applications such as construction and automobiles.

3D printing↗

Estimating the economic value of hydropeaking externalities in regulated rivers

Hydropower is a flexible form of electricity generation providing both baseload and balancing power to accommodate intermittent renewables in the energy mix. However, hydropower also generates various externalities. This study investigates individuals' preferences for policies aiming to reduce short-term regulations (i.e., hydropeaking in regulated rivers) while accounting for associated externalities with a discrete choice experiment. This is the first valuation study focusing on hydropeaking that considers both negative and positive externalities. The results imply that most individuals prefer stronger restrictions on short-term regulations to mitigate local environmental impacts. Individuals especially value improvements in recreational use, fish stocks, and the ecological state. On the other hand, potential increases in CO 2 emissions are linked with a clear disutility. The estimated benefits obtained from an improved state of the river environment due to such restrictions exceed the disutility caused by increased CO 2 emissions. Furthermore, the results also reveal unobserved preference heterogeneity among individuals, which should be accounted for in the willingness-to-pay (WTP) estimation using a model specification with correlated utility coefficients. Overall, the findings can inform policy-makers and environmental managers on the economic value of hydropeaking externalities and further guide the sustainable management of rivers regulated for hydropower generation.

13 HYDRO ENERGY↗

Temperature-dependent oxygen isotope fractionation in otoliths of juvenile Chinook salmon ( Oncorhynchus tshawytscha )

Oxygen thermometry has become a widely used technique for reconstructing thermal history in calcifying organisms but interpretation can be subject to predictive error from vital effects. To better understand these processes in Chinook salmon (Oncorhynchus tshawytscha) we experimentally constructed a temperature-dependent, otolith–water fractionation relationship for oxygen isotopes (δ 18 O) by rearing post-yolk absorptive juvenile fish at nominal temperatures from 6 to 21 °C. Temperature and otolith precipitation rate had significant effects on the otolith–water δ 18 O fractionation, but somatic growth rate did not. The slope of the δ 18 O fractionation equation also differed significantly from that of synthetic aragonite. Furthermore, our results suggest the expression of kinetic effects on δ 18 O fractionation in otoliths of Chinook salmon that are increasingly constrained at higher temperatures by other physical and physiological processes involved in mineral formation. Species-specific δ 18 O fractionation equations have considerable utility to reconstruct temperature history in Pacific salmon, but applications should recognize the potential for inferential uncertainty arising from interacting vital effects.

59 BASIC BIOLOGICAL SCIENCES↗

Germplasm cryopreservation of macroalgae for aquaculture breeding and natural resource conservation: A review

The expansion of the global macroalgal aquaculture and climate change creates the need for germplasm preservation of valuable aquaculture strains and maintenance of natural biodiversity. Compared to the large number of studies in fish and shellfish species, relative few studies have been conducted on the macroalgal germplasm cryopreservation. The first cryopreservation of macroalgae to –75 °C was reported on Neopyropia tenera (formerly called Porphyra tenera) in 1964. To date, a total of 34 studies reported germplasm cryopreservation in 33 species, including Chlorophyta (7 species), Ochrophyta (14 species), and Rhodophyta (12 species). Here, the goal of this review was to summarize the published studies on macroalgal germplasm cryopreservation, compare the reported protocols for the cryopreservation process, and identify the factors affecting post-thaw viability. Overall, macroalgal germplasm cryopreservation included haploid or diploid thalli, spores, and gametes. Cryotubes (1.5-ml or 2-ml) have been widely used to package germplasm samples for cooling and storage in most studies, and the 0.5-ml straws and 5-ml cryotubes have been used in several studies. Two approaches (programmable controlled cooling and vitrification) were employed for macroalgal germplasm cryopreservation. A two-step programmable controlled cooling (e.g., from initial culture temperature to a frozen temperature, such as –40 °C, and then directly plunging into liquid nitrogen at –196 °C) was determined to be an effective cooling strategy. Vitrification, a super rapid cooling for a sample to form non-crystalline amorphous solid, was applied on macroalgal germplasm cryopreservation with sample encapsulation and dehydration. Survival of post-thaw samples varied significantly in different studies. Based on research updates, recommendations are made for future research. It is expected that this review can serve as a foundation for future germplasm banking of macroalgae for aquaculture and biodiversity preservation.

59 BASIC BIOLOGICAL SCIENCES↗

Interactions between U.S. biofuels policy and the Endangered Species Act

The Renewable Fuel Standard (RFS) is the primary policy governing the use of biofuels in the United States. Following the 2007 enactment of the RFS, there has been substantial expansion in the use of cropland to produce biofuel feedstocks, including corn and soybeans. Both the conversion of land and the ongoing cultivation of these crops can, depending on management practices, lead to negative environmental outcomes including degraded water quality, increased water use, increased greenhouse gas emissions, and loss or degradation of wildlife habitat. These outcomes have the potential to affect threatened and endangered species protected under the U.S. Endangered Species Act (ESA). The ESA requires federal agencies to consult with the U.S. Fish and Wildlife Service or the National Marine Fisheries Service to ensure that an agency's actions are not likely to jeopardize the existence of imperiled species, nor result in the destruction or adverse modification of their habitat. However, formal consultation has not yet been completed between the U.S. Environmental Protection Agency—the agency charged with implementing the RFS—and the wildlife services, thereby hindering mitigation or remediation of potential impacts. This analysis explores the likely effects of the RFS on land use changes and critical habitat, illustrates example pathways by which threatened and endangered species may be affected, and proposes solutions to help redress this harm. The findings suggest a need for further consultation and assessment of the interactions between the RFS and ESA as well as additional research to support the species-conservation and policymaking processes.

09 BIOMASS FUELS↗

Discovery of additional ancient genome duplications in yeasts

Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages, preceding adaptive radiations in vertebrates, teleost fish, and angiosperms. In contrast to the many known ancient WGDs in animals, and especially plants, we are aware of evidence for only four WGDs in fungi. The oldest of these occurred ∼100 million years ago (mya) and is shared by ∼60 extant Saccharomycetales species, including the baker’s yeast Saccharomyces cerevisiae. Notably, this is the only known ancient WGD event in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery. Some studies have suggested that fungal lineages that experience chromosome and genome duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGDs is due to an absence of data. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species, with three additional long-read assemblies, we discovered three novel WGD events. Although the functions of retained duplicate genes originating from these events are broad, they bear similarities to the well-known WGD that occurred in the Saccharomycetales. In conclusion, our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.

convergent evolution↗

Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon ( Oncorhynchus tshawytscha ) production in the Sacramento Valley

Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem health and valuation methods to predict ecosystem response to restoration actions. This process is particularly challenging for anadromous fish species such as California's Sacramento River winter-run Chinook salmon, due to their limited geographic range and diverse life history habitat requirements. Tools, such as life-cycle models, are needed to manage population dynamics and quantify the composite effects of processes across space and time. Nevertheless, complex institutions can hinder result interpretation and communication, and limit model use in decision-making. This paper focuses on the federally endangered and endemic Sacramento River winter-run Chinook (Oncorhynchus tshawytscha) by developing a Winter-Run Habitat-based Population Model (WRHAP). Additionally, WRHAP is a conceptual, freshwater rearing stage model that includes alternative rearing habitats reported in the literature (e.g., floodplains, off-channel and tributaries), defines rules of habitat use based on instream conditions, and incorporates a juvenile growth module that combines bioenergetics modeling with empirical growth rates. Model outputs reasonably follow observed out-migration patterns and provide a realistic smolt size distribution arriving at the San Francisco Bay. This effort demonstrates the importance of currently “non-critical” habitats (as defined by the Endangered Species Act) for juvenile development, with floodplain habitat contributing to a quarter of out-migrating biomass (despite < 18% availability and <10% of total rearing days), and off-channel growth being one of the most sensitive parameters (explaining ~13% of average juvenile weight variance). The model shows the utility of a simple population model to explore relationships between habitat quality/quantity and juvenile development, and to assist water/environmental management and decision-making processes focused on species recovery.

54 ENVIRONMENTAL SCIENCES↗

Hydropower and environmental flow management: System-level trade-offs at Glen Canyon Dam

The research focuses on the Colorado River Basin, specifically examining the Glen Canyon Dam (GCD) and its influence on surrounding aquatic ecosystems. This area is crucial due to its role in hydropower production and its impact on downstream environments, including the Grand Canyon National Park. This study explores the integration of environmental factors into hydro dispatch modeling at GCD to tackle ecological challenges posed by the invasive smallmouth bass (SMB). Utilizing the GTMax SL and SERM models, the research assesses the effects of SMB control experiments on hydropower generation, economic value, and grid stability. The study examines the financial and economic impacts of bypass flows designed to release colder water to prevent SMB spawning, which can significantly reduce hydropower output and increase costs. The research identifies that declining reservoir levels and rising water temperatures in Lake Powell have facilitated SMB spawning, posing a threat to native fish populations like the endangered humpback chub. The findings highlight the importance of adaptive management strategies to balance ecological preservation with hydropower generation amid long-term weather-related challenges. The study underscores the need for comprehensive assessments of flow options to prevent SMB establishment below GCD, considering the broader implications for sediment dynamics and ecological interactions.

Ecological impact assessment↗

Integrating in situ environmental covariates in an American lobster catch model to improve impact assessment

The installation and operation of floating offshore wind power is an integral component of societal transition to renewable energy generation where fixed bottom offshore wind is not possible. However, it will cause unique ecosystem changes. To disentangle the effects of offshore wind installations from the concurrent effects of climate change and the fishing practices on commercially significant resources, we must develop detailed characterizations of the resources before development occurs. In the Gulf of Maine, American lobster is the most commercially and culturally important fishery. At the time of writing, this is the largest fishery by value in North America. Our understanding of baseline localized parameters (such as catch per trap at the spatial scale of individual turbines) should be informed by relationships to environmental, biological, and survey-specific functional drivers of catch. A more mechanistic understanding of catch will allow for strategic adjustments to Post- Deployment fishery responses and ultimately, the development of research- and commercial-scale floating offshore wind development. Here, we used survey data from the New England Aqua Ventus Pre-Construction Commercial Trapping Survey to develop Generalized Additive Models describing seasonal catch per trap for legal and sublegal lobsters. We found fall catch to be nearly twice that of spring. Bottom temperature dynamics could be used to predict catch, and the Fall survey was associated with a warmer temperature regime. By using analytical tools that incorporate environmental heterogeneity, we developed monitoring methods from preconstruction baseline data that will be applicable over the post-construction operating period of an offshore wind farm.

BACI↗

Cecropin P1 antimicrobial peptide modulates differential expression of immune relevant genes in rainbow trout ( Oncorhynchus mykiss ) gill cell line, RTgill-W1

Accumulated evidence indicates that antimicrobial peptides modulate immune activities in fish. In this study, we profiled the differential expression patterns of representative immune relevant genes in an epithelial-like cell line of rainbow trout gill, RTgill-W1, in response to exposure of cecropin P1 antimicrobial peptide. RTgill-W1 cells were treated with synthetic cecropin P1 over time (0, 2, 4 and 24 h) with or without the present of lipopolysaccharide (LPS) or polyinosinic polycytidylic acid (PolyI:C). The relative abundances of each mRNA were measured by real-time quantitative PCR. The dose-response study revealed significant perturbations of mRNA levels of genes related to pro-inflammation, acute phase, surface proteins and transcription factors at 30 μM of cecropin P1. In addition, cecropin P1 altered the differential expression patterns that were induced by LPS or PolyI:C, at different time points in RTgill-W1. Overall, our results indicate that cecropin P1 exhibits pro-inflammation activity, modulate cell-cell interaction and cytokine signal transduction in rainbow trout gill cell, and may suggest a potential application of this peptide as an immune adjuvant for disease control in aquaculture.

59 BASIC BIOLOGICAL SCIENCES↗

The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome

Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L⁻¹) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. Furthermore, this culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.

CyanoHABs↗

SubTSBR to tackle high noise and outliers for data-driven discovery of differential equations

Data-driven discovery of differential equations has been an emerging research topic. We propose a novel algorithm subsampling-based threshold sparse Bayesian regression (SubTSBR) to tackle high noise and outliers. The subsampling technique is used for improving the accuracy of the Bayesian learning algorithm. It has two parameters: subsampling size and the number of subsamples. When the subsampling size increases with fixed total sample size, the accuracy of our algorithm goes up and then down. When the number of subsamples increases, the accuracy of our algorithm keeps going up. We demonstrate how to use our algorithm step by step and compare our algorithm with threshold sparse Bayesian regression (TSBR) for the discovery of differential equations. We show that our algorithm produces better results. We also discuss the merits of discovering differential equations from data and demonstrate how to discover models with random initial and boundary condition as well as models with bifurcations. The numerical examples are: (1) predator-prey model with noise, (2) shallow water equations with outliers, (3) heat diffusion with random initial and boundary condition, and (4) fish-harvesting problem with bifurcations.

97 MATHEMATICS AND COMPUTING↗

Best practices for predictions of radionuclide activity concentrations and total absorbed dose rates to freshwater organisms exposed to uranium mining/milling

Predictions of radionuclide dose rates to freshwater organisms can be used to evaluate the radiological environmental impacts of releases from uranium mining and milling projects. These predictions help inform decisions on the implementation of mitigation measures. The objective of this study was to identify how dose rate modelling could be improved to reduce uncertainty in predictions to non-human biota. For this purpose, we modelled the activity concentrations of 210 Pb, 210 Po, 226 Ra, 230 Th, and 238 U downstream of uranium mines and mills in northern Saskatchewan, Canada, together with associated weighted absorbed dose rates for a freshwater food chain using measured activity concentrations in water and sediments. Differences in predictions of radionuclide activity concentrations occurred mainly from the different default partition coefficient and concentration ratio values from one model to another and including all or only some 238 U decay daughters in the dose rate assessments. Consequently, we recommend a standardized best-practice approach to calculate weighted absorbed dose rates to freshwater biota whether a facility is at the planning, operating or decommissioned stage. At the initial planning stage, the best-practice approach recommend using conservative site-specific baseline activity concentrations in water, sediments and organisms and predict conservative incremental activity concentrations in these media by selecting concentration ratios based on species similarity and similar water quality conditions to reduce the uncertainty in dose rate calculations. At the operating and decommissioned stages, the best-practice approach recommends relying on measured activity concentrations in water, sediment, fish tissue and wholebody of small organisms to further reduce uncertainty in dose rate estimates. This approach would allow for more realistic but still conservative dose assessments when evaluating impacts from uranium mining projects and making decision on adequate controls of releases.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Uptake and elimination of 137Cs in aquatic biota inhabiting a contaminated effluent canal

Radiocesium (137Cs) is among the most prevalent and concerning radionuclide released from anthropogenic activities due to its relatively slow decay time and high bioavailability. Numerous studies have reported activity concentrations of 137Cs in exposed biota, but few have assessed detailed toxicokinetics. The objective of our study was to quantify and compare the uptake and elimination of 137Cs in aquatic taxa from multiple classes with different ecological roles inhabiting a canal contaminated from nuclear production activities on the Savannah River Site in South Carolina, USA. We tracked accumulation and elimination of 137Cs in four understudied aquatic species: one aquatic macrophyte [American white water lily (Nymphae odorata), two benthic associated omnivorous species (American bullfrog (Lithobates catesbeianus) and red swamp crayfish (Procambarus clarkii), and one pelagic carnivorous fish (Eastern mosquitofish (Gambusia holbrooki)]. We monitored accumulation of 137Cs from initial exposure until equilibrium for biota restricted within the canal and subsequently tracked elimination of 137Cs over time by moving organisms from the canal to a nearby reference pond. Results indicated bullfrog tadpoles reached 95 % equilibrium in approximately 9 days, the fastest among the species evaluated. After bullfrog tadpoles, the next fastest time to equilibrium was achieved by red swamp crayfish (51 days) followed by mosquitofish (86 days). At equilibrium, bullfrog tadpoles were found to have similar 137Cs activity concentrations to mosquitofish (3.16 and 3.57 Bq/g, respectively), and both were significantly higher than red swamp crayfish (1.77 Bq/g). For elimination, we found biological half-lives to range between 8 and 43 days with bullfrog tadpoles eliminating 137Cs the fastest followed by water lilies, mosquitofish, and red swamp crayfish. Overall, we found the uptake and elimination of 137Cs to vary widely among our studied species, but benthic organisms are not at an increased risk to accumulate 137Cs compared to organisms in less frequent contact with the sediment.

Benthic organism Bioaccumulation Bioindicator Elim↗

Comparison of fiber-optic distributed temperature sensing and high-sensitivity sensor spatial surveying of stream temperature

Measuring surface water temperature spatial variability is needed to estimate the interaction between surface water and groundwater, evaluate fish habitat and thermal inertia, and to estimate streamflow frequency and duration. Fiber optic distributed temperature sensing (FO-DTS) has been used in rivers and lakes, providing high-resolution and sensitive temperature monitoring over large temporal and spatial scales. However, in streams with cobbly or bedrock-lined streambeds and variable bathymetry, use of FO-DTS to measure temperature close to the surface water and groundwater interface can be challenging if even feasible. FO-DTS can also be costly, involve difficult installations, and require an advanced understanding of the technology, calibration, and data processing. In this study, we compared FO-DTS stream temperature survey results to an alternative temperature survey method employing a towed transect of high-resolution temperature loggers spaced at 1-m and transported in the stream along the study reach, to measure the spatial distribution of stream-water temperature in East Fork Poplar Creek near Oak Ridge, Tennessee, USA. We assessed the applicability and limitations of the two methods, and quantitatively compared in-situ temperature survey results measured simultaneously with each method. Regression results showed strong temporal and spatial correlation between the two methods. Differences were only elevated near the stream banks in areas that were coincident with correlation slope deviations from unity, which was attributed to shallower water and lower data density. Kriging standard errors were also low at channel center with minor increases near the stream banks. Furthermore, the results suggested that the array of the individual temperature sensors can provide a practical alternative to FO-DTS for thermal characterization of surface water, providing slightly lower spatial and temporal resolution, but with higher accuracy of temperature measurement, with greater simplicity, and with a broader range of conditions where it may be applied.

54 ENVIRONMENTAL SCIENCES↗

Development of sustainable low carbon Engineered Cementitious Composites with waste polyethylene fiber, sisal fiber and carbonation curing

Engineered cementitious composites (ECC) is an advanced fiber-reinforced cementitious composite with high tensile ductility. However, the binder and fiber system in ECC incur high economic and environmental cost. In this study, a low carbon ECC was developed by substituting virgin polyethylene fiber with waste polyethylene fiber (WPE) from waste marine fishing nets. Carbonation curing was applied to further reduce embodied carbon footprint via direct CO 2 mineralization. This research examined the low carbon ECC’s mechanical properties, including compressive strength and tensile strength and ductility. The CO 2 footprint and material costs of ECC were also investigated. The objective was to develop an ECC competitive to normal concrete economically and environmentally while maintain the unique ductile performance of ECC. Results suggest that carbonation-cured WPE reinforced ECC possesses 50% of the CO 2 footprint and 37% of the cost of traditional concrete. Meanwhile, this low carbon ECC maintains at least 4 MPa tensile strength and 6% tensile ductility. This research demonstrates the feasibility of developing construction materials with low environmental impact while maintaining high performance for civil infrastructure applications. As a result, the adoption of WPE in ECC provides a plausible pathway to recycle marine waste into the construction industry that urgently needs to be decarbonized.

42 ENGINEERING↗