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DOE OSTI2023

Establishing connectivity patterns of eastern oysters ( Crassostrea virginica ) on regional oceanographic scales

Localized depletion of marine and estuarine populations often results from large-scale natural and anthropogenic disturbances (e.g., hurricanes, oil spills) as well as overharvest of fisheries resources. Understanding how such localized depletions may affect populations at larger regional scales requires knowledge of connectivity among local populations within the larger regional landscape or metapopulation. Efforts to restore populations following such decreases require similar knowledge. During the 2010 Deepwater Horizon oil spill, dramatic declines of oysters occurred throughout estuaries west and east of the Mississippi River. We examined trajectories of particles, which were parameterized to mimic oyster larvae, using the ADvanced CIRCulation (ADCIRC; https://adcirc.org ) model to evaluate potential connectivity within and among embayments from Western Louisiana to Alabama. Patterns of larval settlement, which we defined as the intersection of a larval particle with known or expected oyster habitat at any point 13–21 days post-release, reflected much greater local contributions, with 50%–90% of settled particles originating within the same subdivision of embayments. Exchange among subdivision was much less (0%–40%) and settlement originating from outside the embayment of release was trivial under most scenarios (0%–14%). Connectivity between adjacent basins was greatest for larvae released in the southern portions of the embayment, whereas connectivity among nonadjacent basins was not predicted under the scenarios modeled. Because most local populations are relatively isolated on ecological timescales, areas suffering from extensive local depletion are likely to require extensive time to recover due to the lack of larval subsidy from the overall regional population. Restoration would require building stepping-stone populations or reefs within and among basin to restore a high degree of connectivity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Advancing the understanding of coastal disturbances with a network-of-networks approach

Coastal ecosystems are at the nexus of many high priority challenges in environmental sciences, including predicting the influences of compounding disturbances exacerbated by climate change on biogeochemical cycling. Extreme events such as hurricanes, flooding, landslides, and wildfires influence biogeochemical cycling in these systems. However, while research in coastal science is fundamentally transdisciplinary – as drivers of biogeochemical and ecological processes often span scientific and environmental domains – traditional place-based approaches are still often employed to understand coastal ecosystems. In this perspective, we argue that integration among distributed research sites from a macrosystem perspective is crucial to understand how compounding disturbances affect coastal ecosystems. We identify a roadmap for the implementation of an integrated network-of-networks framework that leverages existing research network sites in coastal ecosystems to advance continental-scale process understanding for studying extreme events and global change. We also identify specific ways that existing research efforts can maximize mutual benefit, and where additional infrastructure investments might increase return-on-investment along the coast, using the coastal continental US as a case study.

Myers-Pigg, Allison N. [BATTELLE (PACIFIC NW LAB)]↗

DOE OSTI2021

Functional traits driving species role in the structure of terrestrial vertebrate scavenger networks

Abstract Species assemblages often have a non‐random nested organization, which in vertebrate scavenger (carrion‐consuming) assemblages is thought to be driven by facilitation in competitive environments. However, not all scavenger species play the same role in maintaining assemblage structure, as some species are obligate scavengers (i.e., vultures) and others are facultative, scavenging opportunistically. We used a database with 177 vertebrate scavenger species from 53 assemblages in 22 countries across five continents to identify which functional traits of scavenger species are key to maintaining the scavenging network structure. We used network analyses to relate ten traits hypothesized to affect assemblage structure with the “role” of each species in the scavenging assemblage in which it appeared. We characterized the role of a species in terms of both the proportion of monitored carcasses on which that species scavenged, or scavenging breadth (i.e., the species “normalized degree”), and the role of that species in the nested structure of the assemblage (i.e., the species “paired nested degree”), therefore identifying possible facilitative interactions among species. We found that species with high olfactory acuity, social foragers, and obligate scavengers had the widest scavenging breadth. We also found that social foragers had a large paired nested degree in scavenger assemblages, probably because their presence is easier to detect by other species to signal carcass occurrence. Our study highlights differences in the functional roles of scavenger species and can be used to identify key species for targeted conservation to maintain the ecological function of scavenger assemblages.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Predicting responses to climate change using a joint species, spatially dependent physiologically guided abundance model

Abstract Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species–environment correlations to climatic conditions not currently experienced by a species, which can result in unrealistic predictions. For poikilotherms, incorporating species' thermal physiology to inform extrapolations under novel thermal conditions can result in more realistic predictions. Furthermore, models that incorporate species and spatial dependencies may improve predictions by capturing correlations present in ecological data that are not accounted for by predictor variables. Here, we present a joint species, spatially dependent physiologically guided abundance (jsPGA) model for predicting multispecies responses to climate warming. The jsPGA model uses a basis function approach to capture both species and spatial dependencies. We apply the jsPGA model to predict the response of eight fish species to projected climate warming in thousands of lakes in Minnesota, USA. By the end of the century, the cold‐adapted species was predicted to have high probabilities of extirpation across its current range—with 10% of lakes currently inhabited by this species having an extirpation probability >0.90. The remaining species had varying levels of predicted changes in abundance, reflecting differences in their thermal physiology. Though the model did not identify many strong species dependencies, the variation in estimated spatial dependence across species suggested that accounting for both dependencies was important for predicting the abundance of these fishes. The jsPGA model provides a new tool for predicting changes in the abundance, distribution, and extirpation probability of poikilotherms under novel thermal conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Emerging Rare Earth Element Separation Technologies

Rare earth elements are essential for numerous clean energy applications, yet their mining, separation, and processing pose significant environmental challenges. Traditional separation processes often result in ecological damage, highlighting the critical need for innovative techniques that reduce environmental impacts. This article reviews recent advancements in rare earth separation technologies, with a particular focus on the role of neutral organic compounds. It explores how these compounds change selectivity across the rare earth series, offering promising strategies for designing more effective rare earth element separation systems. Furthermore, the article points out research areas requiring additional investigation to improve the sustainability of these critical processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Grain size estimation in fluvial gravel bars using uncrewed aerial vehicles: A comparison between methods based on imagery and topography

Abstract Grain size assessments are necessary for understanding the various geomorphological, hydrological and ecological processes that occur within rivers. Recent research has shown that the application of Structure‐from‐Motion (SfM) photogrammetry to imagery from uncrewed aerial vehicles (UAVs) shows promise for rapidly characterising grain sizes along rivers in comparison to traditional field‐based methods. Here, we evaluated the applicability of different methods for estimating grain sizes in gravel bars along a study reach in the Olentangy River in Columbus, Ohio. We collected imagery of these gravel bars with a UAV and processed those images with SfM photogrammetry software to produce three‐dimensional point clouds and orthomosaics. Our evaluation compared statistical models calibrated on topographic roughness, which was computed from the point clouds, and to those based on image texture, which was computed from the orthomosaics. Our results showed that statistical models calibrated on image texture were more accurate than those based on topographic roughness. This might be because of site‐specific patterns of grain size, shape and imbrication. Such patterns would have complicated the detection of topographic signatures associated with individual grains. Our work illustrates that UAV‐SfM approaches show potential to be used as an accessible method for characterising surface grain sizes along rivers at higher spatial and temporal resolutions than those provided by traditional methods.

Wong, Tyler↗

DOE OSTI2020

Rewilding of Fukushima's human evacuation zone

There is substantial interest in understanding the ecological impacts of the nuclear accidents at the Chernobyl and Fukushima Daiichi nuclear power plants. However, population‐level data for large mammals have been limited, and there remains much speculation regarding the status of wildlife species in these areas. Using a network of remote cameras placed along a gradient of radiological contamination and human presence, we collected data on population‐level impacts to wildlife (that is, abundance and occupancy patterns) following the 2011 Fukushima Daiichi nuclear accident. We found no evidence of population‐level impacts in mid‐ to large‐sized mammals or gallinaceous birds, and show several species were most abundant in human‐evacuated areas, despite the presence of radiological contamination. These data provide unique evidence of the natural rewilding of the Fukushima landscape following human abandonment, and suggest that if any effects of radiological exposure in mid‐ to large‐sized mammals in the Fukushima Exclusion Zone exist, they occur at individual or molecular scales, and do not appear to manifest in population‐level responses.

Lyons, Phillip C.↗

DOE OSTI2021

Responding to the US national pollinator plan: a case study in Michigan

The long‐term health of pollinators is a critical issue for the functioning of natural habitats and for agricultural production. In response to widespread public concern about the future of these ecologically and economically important animals, in 2015 the US Government released a national strategy to support pollinators, including research priorities, directives for funding, and timelines for achieving three overarching goals. Five years after this strategic plan was released, we evaluate progress toward the national targets for improved honey bee ( Apis mellifera ) overwintering survival, expanded pollinator habitat, and larger monarch butterfly ( Danaus plexippus ) populations, and find that the three goals of the plan have not yet been reached. Our research and extension programs to improve the health of honey bees, wild bees, and monarch butterflies in the US state of Michigan are described, providing opportunities to contribute to the national pollinator goals.

Bloom, Elias H.↗

DOE OSTI2025

Resist! : Sustaining forest carbon sequestration and wood production after insect disturbance

Disturbances from insect pests threaten ecologically and economically important goods and services supplied by forests, including wood production and carbon sequestration. We highlight the factors that influence these services’ resistance, a term quantifying the initial response to disturbance. Insects inflict damage through a range of mechanisms, prompting distinct plant physiological responses that scale to influence ecosystem processes and, with time, goods and services. The degree and timing of tree mortality and defoliation affect the amount of residual vegetation available to support compensatory wood production and influence carbon sequestration by changing rates of detritus-fueled decomposition. Compounding, or sequential, insect attacks may prime a forest for additional disturbance, further eroding wood production and carbon sequestration. Forest management practices that promote biological and structural diversity, and augment or retain limiting biological and nutrient resources, may buffer against the effects of insect pests on wood production and carbon sequestration.

Gough, Christopher M. [Virginia Commonwealth Univ.↗

DOE OSTI2023

Climate Change Risks to Freshwater Subsistence Fisheries in Arctic Alaska: Insights and Uncertainty from Broad Whitefish Coregonus nasus

Arctic freshwater ecosystems and fish populations are largely shaped by seasonal and long-term watershed hydrology. In this paper, we hypothesize how changing air temperature and precipitation will alter freeze and thaw processes, hydrology, and instream habitat to assess potential indirect effects, such as the change to the foraging and behavioral ecology, on Arctic fishes, using Broad Whitefish Coregonus nasus as an indicator species. Climate change is expected to continue to alter hydrologic pathways, flow regimes, and, therefore, habitat suitability, connectivity, and availability for fishes. Warming and lengthening of the growing season will likely increase fish growth rates; however, the exceedance of threshold stream temperatures will likely increase physiological stress and alter life histories. We expect these changes to have mixed effects on Arctic subsistence fishes and fisheries. Management and conservation approaches focused on preserving the processes that create heterogeneity in aquatic habitats, genes, and communities will help maintain the resilience of Broad Whitefish and other important subsistence fisheries. Long-term effects are uncertain, so filling scientific knowledge gaps, such as identifying important habitats or increasing knowledge of abiotic variables in priority watersheds, is key to understanding and potentially mitigating likely impacts to Arctic fishes in a rapidly changing landscape.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

The Wasatch Environmental Observatory: A mountain to urban research network in the semi‐arid western US

Abstract The 2085 km 2 Jordan River Basin, and its seven sub‐catchments draining the Central Wasatch Range immediately east of Salt Lake City, UT, are home to an array of hydrologic, atmospheric, climatic and chemical research infrastructure that collectively forms the Wasatch Environmental Observatory (WEO). WEO is geographically nested within a wildland to urban land‐use gradient and built upon a strong foundation of over a century of discharge and climate records. A 2200 m gradient in elevation results in variable precipitation, temperature and vegetation patterns. Soil and subsurface structure reflect systematic variation in geology from granitic, intrusive to mixed sedimentary clastic across headwater catchments, all draining to the alluvial or colluvial sediments of the former Lake Bonneville. Winter snowfall and spring snowmelt control annual hydroclimate, rapid population growth dominates geographic change in lower elevations and urban gas and particle emissions contribute to episodes of severe air pollution in this closed‐basin. Long‐term hydroclimate observations across this diverse landscape provide the foundation for an expanding network of infrastructure in both montane and urban landscapes. Current infrastructure supports both basic and applied research in atmospheric chemistry, biogeochemistry, climate, ecology, hydrology, meteorology, resource management and urban redesign that is augmented through strong partnerships with cooperating agencies. These features allow WEO to serve as a unique natural laboratory for addressing research questions facing seasonally snow‐covered, semi‐arid regions in a rapidly changing world and an excellent facility for providing student education and research training.

Follstad Shah, Jennifer J.↗

DOE OSTI2022

Advancing river corridor science beyond disciplinary boundaries with an inductive approach to catalyse hypothesis generation

Abstract A unified conceptual framework for river corridors requires synthesis of diverse site‐, method‐ and discipline‐specific findings. The river research community has developed a substantial body of observations and process‐specific interpretations, but we are still lacking a comprehensive model to distill this knowledge into fundamental transferable concepts. We confront the challenge of how a discipline classically organized around the deductive model of systematically collecting of site‐, scale‐, and mechanism‐specific observations begins the process of synthesis. Machine learning is particularly well‐suited to inductive generation of hypotheses. In this study, we prototype an inductive approach to holistic synthesis of river corridor observations, using support vector machine regression to identify potential couplings or feedbacks that would not necessarily arise from classical approaches. This approach generated 672 relationships linking a suite of 157 variables each measured at 62 locations in a fifth order river network. Eighty four percent of these relationships have not been previously investigated, and representing potential (hypothetical) process connections. We document relationships consistent with current understanding including hydrologic exchange processes, microbial ecology, and the River Continuum Concept, supporting that the approach can identify meaningful relationships in the data. Moreover, we highlight examples of two novel research questions that stem from interpretation of inductively‐generated relationships. This study demonstrates the implementation of machine learning to sieve complex data sets and identify a small set of candidate relationships that warrant further study, including data types not commonly measured together. This structured approach complements traditional modes of inquiry, which are often limited by disciplinary perspectives and favour the careful pursuit of parsimony. Finally, we emphasize that this approach should be viewed as a complement to, rather than in place of, more traditional, deductive approaches to scientific discovery.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Seasonal and tidal variations in hydrologic inputs drive salt marsh porewater nitrate dynamics

Salt marshes remove terrestrially derived nutrients en route to coasts. While these systems play a critical role in improving water quality, we still have a limited understanding of the spatiotemporal variability of biogeochemically reactive solutes and processes within salt marshes. We implemented a high-frequency sampling system to monitor sub-hourly nitrate (NO$^{–}_{3}$) concentrations in salt marsh porewater at Elkhorn Slough in central California, USA. We instrumented three marsh positions along an elevation gradient subjected to different amounts of tidal inundation, which we predicted would lead to varied biogeochemical characteristics and hydrological interactions. At each marsh position, we continuously monitored porewater NO$^{–}_{3}$ concentrations at depths of 10, 30, and 50 cm and porewater levels measured at 70 cm depth over seven deployments of ~10 days each that spanned seasonal wet/dry periods common to Mediterranean climates. We quantified tidal event hysteresis between NO$^{–}_{3}$ and water level to understand how NO$^{–}_{3}$ concentrations and sources fluctuate across tidal cycles. In dry periods, the NO$^{–}_{3}$-porewater level relationship indicated that the NO$^{–}_{3}$ source was likely estuarine surface water that flooded the transect during high tides and the salt marsh was a NO$^{–}_{3}$ sink. In wet periods, the NO$^{–}_{3}$-porewater level relationship suggested the salt marsh was a source of NO$^{–}_{3}$. Finally, these findings suggest that tidal and seasonal hydrologic fluxes together control NO$^{–}_{3}$ porewater dynamics and export and influence ecological processes in coastal environments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Warmer incubation temperatures and later lay–orders lead to shorter telomere lengths in wood duck ( Aix sponsa ) ducklings

The environment that animals experience during development shapes phenotypic expression. In birds, two important aspects of the early-developmental environment are lay-order sequence and incubation. Later-laid eggs tend to produce weaker offspring, sometimes with compensatory mechanisms to accelerate their growth rate to catch-up to their siblings. Further, small decreases in incubation temperature slow down embryonic growth rates and lead to wide-ranging negative effects on many post-hatch traits. Recently, telomeres, non-coding DNA sequences at the end of chromosomes, have been recognized as a potential proxy for fitness because longer telomeres are positively related to lifespan and individual quality in many animals, including birds. Although telomeres appear to be mechanistically linked to growth rate, little is known about how incubation temperature and lay-order may influence telomere length. We incubated wood duck (Aix sponsa) eggs at two ecologically-relevant temperatures (34.9 and 36.2ºC) and measured telomere length at hatch and one week after. We found that ducklings incubated at the lower temperature had longer telomeres than those incubated at the higher temperature both at hatch and one week later. Further, we found that later-laid eggs produced ducklings with shorter telomeres than those laid early in the lay-sequence, although lay-order was not related to embryonic developmental rate. Furthermore, this study contributes to our broader understanding of how parental effects can affect telomere length early in life. More work is needed to determine if these effects on telomere length persist until adulthood, and if they are associated with effects on fitness in this precocial species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Morphology and composition of Goldeye (Hiodontidae; Hiodon alosoides) otoliths

In this work, we provide up-todate morphological and compositional data on otoliths of the osteoglossomorph Goldeye (Hiodon alosoides). Using computed tomography (CT) X-ray, we documented the location of each of the three pairs of otoliths (lapilli, sagittae, and asterisci) in relation to the swim bladder, which extended forward in close proximity to the sagittae and asterisci. The lappili were the largest otoliths in terms of surface area and volume, but the sagittae were highly modified, appearing spiral in shape when viewed dorsally, with a surface area to volume ratio more than double that of the lapilli. Using scanning electron microscopy, the surface of each otolith was viewable in great detail, and small otoconia (~10.5 μm diameter) were observed on each, but were most numerous on the sagittae. Additionally, on scanning electron micrographs, the sagittae appeared to be bi-lobed, with asymmetrical lobes each oriented in the same general direction. Using neutron and X-ray diffraction methods, we found three polymorphs of calcium carbonate crystals (aragonite, vaterite, and calcite), sometimes all within the same otolith. However, in general, lapilli and sagittae were composed predominately of aragonite whereas asterisci were composed chiefly of vaterite. With these results, we provide information on a unique species, whose inclusion in future studies would benefit our understanding of fish hearing, fish evolution, and fisheries ecology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

A Step-by-Step Protocol from METASPACE to Biological Interpretation

Mass spectrometry imaging (MSI) represents an exceptional tool for exploring complex biological systems spatially at the molecular level. However, due to its multidimensional nature and large-scale data output, it presents considerable challenges when it comes to extracting meaningful biological insights. Recent advancements, such as the METASPACE platform, have enabled researchers to efficiently process, annotate, and interpret MSI datasets by leveraging machine learning and cloud-based infrastructure. In this tutorial, we present a detailed and user-friendly R-pipeline designed to help METASPACE users navigate untargeted metabolomic annotations and transform them into practical insights about their biological systems. By combining METASPACE annotations with rapid R-based screening, this workflow not only streamlined the analytical process but also enhanced the understanding of spatial molecular distribution, especially for complex systems. Here, this easy-to-follow approach has the potential for applications in diagnostics, drug discovery, environmental and ecological processes, and more. We envision this pipeline to be particularly useful for newcomers to the field of MSI and

Moreno Pedraza, Abigail↗

DOE OSTI2021

BrazilClim : The overcoming of limitations of pre‐existing bioclimate data

Abstract Species distribution modelling has become instrumental in assessing the influence of environmental conditions on the occurrence or abundance of taxa. The set of environmental layers used for this purpose is a crucial aspect, for which different climate‐based (bioclimatic) datasets have been recently developed. These bioclimatic variables result from combinations of precipitation and temperatures surfaces. Here, we explored both the performance and possibility of improving some of the currently available bioclimatic databases, through an evaluation of the precipitation and temperatures surfaces used to generate them. For this purpose, we used a combination of statistic and graphic approaches. We focused on Brazil, not only due to its natural megadiversity, but also due to its continental size and orographic heterogeneity: an excellent ground for refining methods replicable elsewhere. We found a better match between the climatic data measured on‐field and Tropical Rainfall Measuring Mission (TRMM 3B43 v7) in the case of precipitation, and the surfaces provided by the National Oceanic and Atmospheric Administration (NOAA) in the case of temperatures, sources uncommonly used for species niche modelling. We gauge‐calibrated the best performing surfaces using machine‐learning algorithms and generated corrected surfaces that allowed us to create BrazilClim: a database of bioclimatic variables, based on improved primary surfaces, which will result in more assertive predicted distributions and more actual pictures of the species' ecological requirements for megadiverse Brazil, an approach replicable elsewhere. All primary and bioclimatic surfaces generated for this study may be freely downloaded.

Ramoni‐Perazzi, Paolo↗

DOE OSTI2022

Deficient precipitation sensitivity to Sahel land surface forcings among CMIP5 models

Abstract The overall performance of the simulated seasonal precipitation response to local terrestrial forcings, namely vegetation abundance and soil moisture, in the Sahel among the Coupled Model Intercomparison Project Phase Five (CMIP5) Earth System Models (ESMs) is systematically investigated and compared with its observational counterpart using a multivariate statistical method. The observed seasonal precipitation response is evaluated against a large ensemble of observational, reanalysis, and satellite data sets to provide quantification of uncertainties. The behaviour of models with and without a Dynamic Global Vegetation Model (DGVM) component is also explored, along with the mechanisms responsible for terrestrial feedback on rainfall. In general, the CMIP5 models can reasonably capture the seasonal evolution of Sahel precipitation and soil moisture, albeit with wet biases during the pre‐monsoon period and dry biases during the peak monsoon period. The non‐DGVM ESMs simulate comparable leaf area indices (LAIs) with observations, while DGVM‐enabled ESMs simulate too much year‐round LAI. The variance of precipitation that is attributed to oceanic forcings in CMIP5 is comparable with observations; however, the variance of precipitation that is attributed to terrestrial forcings is smaller in CMIP5 models than observed, especially for non‐DGVM ESMs. CMIP5 models, especially those without DGVMs, undervalue precipitation's observed response strength to soil moisture anomalies. In both observations and CMIP5 models, none of the atmospheric variables show significant responses to direct vegetation forcing, except for the response in transpiration. Although vegetation has minimal direct effect on the atmospheric state, it can affect the atmosphere by modifying soil moisture and transpiration rate indirectly, which helps explain the more realistic simulation of rainfall in DGVM‐enabled ESMs than non‐DGVM ESMs. Coupling of an ESM to a DGVM is critical in generating reasonable land–atmosphere feedback and examining future ecological and climatic changes over the Sahel.

54 ENVIRONMENTAL SCIENCES↗