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USGS2011

Characterization of winter foraging locations of Adélie penguins along the Western Antarctic Peninsula, 2001–2002

In accord with the hypotheses driving the Southern Ocean Global Ocean Ecosystems Dynamics (SO GLOBEC) program, we tested the hypothesis that the winter foraging ecology of a major top predator in waters off the Western Antarctic Peninsula (WAP), the Adélie penguin ( Pygoscelis adeliae ), is constrained by oceanographic features related to the physiography of the region. This hypothesis grew from the supposition that breeding colonies in the WAP during summer are located adjacent to areas of complex bathymetry where circulation and upwelling processes appear to ensure predictable food resources. Therefore, we tested the additional hypothesis that these areas continue to contribute to the foraging strategy of this species throughout the non-breeding winter season. We used satellite telemetry data collected as part of the SO GLOBEC program during the austral winters of 2001 and 2002 to characterize individual penguin foraging locations in relation to bathymetry, sea ice variability within the pack ice, and wind velocity and divergence (as a proxy for potential areas with cracks and leads). We also explored differences between males and females in core foraging area overlap. Ocean depth was the most influential variable in the determination of foraging location, with most birds focusing their effort on shallow (<200 m) waters near land and on mixed-layer (200–500 m) waters near the edge of deep troughs. Within-ice variability and wind (as a proxy for potential areas with cracks and leads) were not found to be influential variables, which is likely because of the low resolution satellite imagery and model outputs that were available. Throughout the study period, all individuals maintained a core foraging area separated from other individuals with very little overlap. However, from a year with light sea ice to one with heavy ice cover (2001–2002), we observed an increase in the overlap of individual female foraging areas with those of other birds, likely due to restricted access to the water column, reduced prey abundance, or higher prey concentration. Male birds maintained separate core foraging areas with the same small amount of overlap, showing no difference in overlap between the years. While complex bathymetry was an important physical variable influencing the Adélie penguin's foraging, the analysis of sea ice data of a higher resolution than was available for this study may help elucidate the role of sea ice in affecting Adélie penguin winter foraging behavior within the pack ice.

Deep-Sea Research Part II: Topical Studies in Ocea↗

USGS2019

Igneous rocks in the Fish Creek Mountains and environs, Battle Mountain area, north-central Nevada: A microcosm of Cenozoic igneous activity in the northern Great Basin, Basin and Range Province, USA

The Great Basin of the western United States, the northern component of the Basin and Range Province, is a region of Cenozoic lithospheric extension with multiple periods and types of igneous activity. The composition and volume of Cenozoic magmas reflect a complex interaction between mantle-derived magmas and highly diverse crust, where both mantle sources and magmatic processes were modulated by tectonic environment. The Fish Creek Mountains in north-central Nevada underwent multiple igneous events ranging from ca. 40 Ma to 1 Ma that span all of the complex Cenozoic tectono-magmatic episodes of the Great Basin. The Fish Creek Mountains, therefore, is an ideal location to evaluate the different sources and processes involved in magma generation. Many plutons were emplaced in the region between about 40 and 38 Ma, several of which host base and precious metal deposits. Between 36 and 33 Ma, lava fields and calderas of the 37–19 Ma Ignimbrite Flare-up were emplaced. Both these and the preceding plutons resulted from southwestward rollback of the Farallon plate beneath North America during by far the most voluminous phase of Cenozoic magmatism. The lavas range from rare basalt and basaltic andesite to andesite, dacite, and rhyolite, have continental arc-like incompatible element patterns, and high initial 87 Sr/ 86 Sr and low εNd that require a metasomatized lithospheric mantle source combined with minor crustal component. Ignimbrites of the 34.4 Ma Cove Mine (trachydacite to rhyolite) and 34.0 Ma Caetano calderas (rhyolite to high-silica rhyolite) are abundantly porphyritic, include hydrous phases, were largely derived from partial melts of crustal rocks, but likely include 20–30% of a mantle-derived component. Igneous activity ceased in the region as the rollback-arc migrated to the southwest, but at 24.9 Ma a new caldera formed in the southern Fish Creek Mountains that was filled by ignimbrites of the Fish Creek Mountains Tuff. Intracaldera rhyolite ignimbrites range from aphyric, pumice-rich deposits at the base to progressively more quartz-feldspar phyric ignimbrites at higher levels; all flow units lack hydrous phases. No contemporaneous mafic or intermediate igneous activity accompanied caldera formation, but initial 87 Sr/ 86 Sr values in the Fish Creek Mountains tuffs are lower than in the Caetano Tuff, suggesting a greater mantle contribution to the 24.9 Ma ignimbrites. After another hiatus in igneous activity, the region was intruded and overlain by basalt to rhyolite dykes and lavas of the northern Nevada rift between 16.8 and 15.1 Ma. The primarily tholeiitic igneous suite is of the same age, chemistry, and isotopic composition as the Grande Ronde Formation of the Columbia River flood basalts, and evolved members (trachydacite and rhyolite) are crustally contaminated. The youngest northern Nevada rift lava is an alkali olivine basalt with isotopic affinity to basalts of the eastern Snake River Plain. After 10 Ma of quiescence, the region was locally covered by mafic lava flows with high-alumina olivine tholeiite compositions, represented by the 5.4 Ma Pumpernickel Valley flows. Their mid-ocean ridge-like incompatible element compositions indicate a depleted mantle source for the lavas, but radiogenic isotopic compositions indicate that the lavas of this region include a significant contribution from a mafic to ultramafic, high- 87 Sr/ 86 Sr source. The final igneous event in the Fish Creek Mountains region, the 4.0 to 1.0 Ma Buffalo Valley volcanic field, includes flows and spatter cones of transitional to alkalic basalt that are divided into two geochemical groups with identical isotopic compositions. They represent variable, low percent partial melts of the asthenosphere at different depths, yielding different rare earth element characteristics. Similar to the Lunar Crater volcanic field, the Buffalo Valley rocks represent a rare case where the lithosphere in the central Great Basin is now thin enough to allow melting of the underlying asthenosphere. Cenozoic magmatism in the northern Great Basin exhibits several transitions in magma sources and tectonic setting with time. Magmatism began as pre-extension, subduction-related, primarily lithospherically-derived magmas emplaced on/in tectonically-thickened crust. The onset of extension was partially driven by impingement of the Yellowstone plume that resulted in emplacement of rift-related volcanic and intrusive rocks in the northern Nevada rift, followed by the eruption of extension-related HAOT lavas along the northwest margin of the Great Basin. Finally, lithospheric thinning allowed for partial melting of the asthenosphere and eruption of alkaline basaltic lavas.

Nevada↗

USGS2021

Simulation of dissolved organic carbon flux in the Penobscot Watershed, Maine

Dissolved organic carbon (DOC) is an important component of the carbon cycle as a measure of the hydrological transport of carbon between terrestrial carbon pools into soil pools and eventually into streams. As a result, changes in DOC in rivers and streams may indicate alterations in the storage of terrestrial carbon. Exploring the complex interactions between biogeochemical cycling and hydrologic processes, as well as the micro-climate variabilities that impact the rate of DOC fluxes, are challenging because the information is not readily available from in-situ measurements or from empirical models alone. This is particularly true of large-scale watersheds. The Penobscot Watershed is the largest watershed of the Gulf of Maine and the second largest in New England. Its typical soils, with high organic matter and a large forested and wetland landscape, result in higher DOC fluxes than what has been observed previously for most rivers in the northern temperate or boreal zones (Hope et al., 1994; Mulholland, 1997; Aitkenhead and McDowell, 2000). In this study, we emphasized the simulation of streamflow and DOC fluxes from the Penobscot Watershed (and several tributaries within the Penobscot Watershed) using the spatially distributed process-based Regional Hydro-Ecological Simulation System (RHESSys) model. Simulated results were evaluated using field measurements (streamflow, DOC fluxes) and remotely sensed products (Net Primary Production (NPP) and Leaf Area Index (LAI) from Moderate Resolution Imaging Spectroradiometer (MODIS). The average DOC flux for the Penobscot Watershed during 2004-2012 using the RHESSys model was 69 kg C/ha/year. The RHESSys simulated DOC flux is shown to correlate well with observed values, as well as with results previously reported from the empirical Load Estimator (LOADEST) model (71 kg C/ha/year) for 2004-2007 ( Huntington and Aiken, 2013). Our simulated results also show a temporal variation in the amount of DOC flux, indicating that the antecedent DOC concentration from one year can impact the DOC export in following years. Thus, DOC concentration is positively correlated with streamflow and antecedent precipitation, in agreement with previous studies (Ågren et al., 2010; Huntington and Aiken, 2013; Tian et al., 2013 ). The successful application of the rigorous RHESSys model in the Penobscot Watershed makes it a reasonable platform to test future scenarios impacting the hydrology and biogeochemistry within similar large complex watersheds.

Maine↗

USGS2012

The effects of drought and disturbance on the growth and developmental instability of loblolly pine ( Pinus taeda L.)

Ecological indicators provide early warning of adverse environmental change, helping land managers adaptively manage their resources while minimizing costly remediation. In 1999 and 2000, we studied two such indicators, growth and developmental instability, of loblolly pine ( Pinus taeda L.) influenced by mechanized infantry training at Fort Benning, Georgia. Disturbed areas were used for military training; tracked and wheeled vehicles damaged vegetation and soils. Highly disturbed sites had fewer trees, diminished ground cover, warmer soils in the summer, and more compacted soils with a shallower A-horizon. We hypothesized that disturbance would decrease the growth of needles, branches, and tree rings, increase the complexity of tree rings, and increase the developmental instability of needles. Contrary to our expectations, however, disturbance enhanced growth in the first year of the study, possibly by reducing competition. In the second year, a drought reduced growth of branches and needles, eliminating the stimulatory effect of disturbance. Growth-ring widths increased with growing-season precipitation, and decreased with growing-season temperature over the last 40 years. Disturbance had no effect on tree-ring complexity, as measured by the Hurst exponent. Within-fascicle variation of current-year needle length, a measure of developmental instability, differed among the study populations, but appeared unrelated to mechanical disturbance or drought.

Ecological Indicators↗

USGS2019

Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets

Diatom data have been collected in large-scale biological assessments in the United States, such as the U.S. Environmental Protection Agency’s National Rivers and Streams Assessment (NRSA). However, the effectiveness of diatoms as indicators may suffer if inconsistent taxon identifications across different analysts obscure the relationships between assemblage composition and environmental variables. To reduce these inconsistencies, we harmonized the 2008–2009 NRSA data from nine analysts by updating names to current synonyms and by statistically identifying taxa with high analyst signal (taxa with more variation in relative abundance explained by the analyst factor, relative to environmental variables). We then screened a subset of samples with QA/QC data and combined taxa with mismatching identifications by the primary and secondary analysts. When these combined “slash groups” did not reduce analyst signal, we elevated taxa to the genus level or omitted taxa in difficult species complexes. We examined the variation explained by analyst in the original and revised datasets. Further, we examined how revising the datasets to reduce analyst signal can reduce inconsistency, thereby uncovering the variation in assemblage composition explained by total phosphorus (TP), an environmental variable of high priority for water managers. To produce a revised dataset with the greatest taxonomic consistency, we ultimately made 124 slash groups, omitted 7 taxa in the small naviculoid (e.g., Sellaphora atomoides ) species complex, and elevated Nitzschia , Diploneis , and Tryblionella taxa to the genus level. Relative to the original dataset, the revised dataset had more overlap among samples grouped by analyst in ordination space, less variation explained by the analyst factor, and more than double the variation in assemblage composition explained by TP. Elevating all taxa to the genus level did not eliminate analyst signal completely, and analyst remained the most important predictor for the genera Sellaphora , Mayamaea , and Psammodictyon , indicating that these taxa present the greatest obstacle to consistent identification in this dataset. Although our process did not completely remove analyst signal, this work provides a method to minimize analyst signal and improve detection of diatom association with TP in large datasets involving multiple analysts. Examination of variation in assemblage data explained by analyst and taxonomic harmonization may be necessary steps for improving data quality and the utility of diatoms as indicators of environmental variables.

Ecological Indicators↗

USGS2021

Amphibian population responses to mitigation: Relative importance of wetland age and design

Wetland creation is a common practice to mitigate for the loss of natural wetlands. However, there is still uncertainty about how effectively created wetlands replace habitat provided by natural wetlands. This uncertainty is due in part because post-construction monitoring of biological communities, and vertebrates especially, is rare and typically short-term (<5 years). We estimated occupancy of 4 amphibian species in 8 created mitigation wetlands, 7 impacted wetlands, and 7 reference wetlands in the Greater Yellowstone Ecosystem in Wyoming, USA. Mitigation wetlands were created to replace wetland habitat that was lost during road construction and ranged in age from 1 to 10 years when sampled. Impacted wetlands were natural wetlands partially filled by road construction and were adjacent to a highway. We sampled for amphibian larvae during 6 summers from 2013 to 2020 and used multi-species occupancy models that estimated detection and occupancy of each of 4 amphibian species to determine how amphibian responses changed over time, especially in mitigation wetlands. Occupancy did not differ between impacted and reference wetlands for any of the 4 amphibian species. Western Toads ( Anaxyrus boreas ) were most common (although briefly) in created wetlands, and occupancy of Columbia Spotted Frogs ( Rana luteiventris ), Western Tiger Salamanders ( Ambystoma mavortium ), and Boreal Chorus Frogs ( Pseudacris maculata ) was lower in created wetlands than in impacted or reference wetlands. Individual wetland area was positively associated with occupancy for all 4 species and wetland vegetation cover was positively associated with Boreal Chorus Frog and Columbia Spotted Frog occupancy; these results emphasize the importance of design characteristics when planning mitigation wetlands. The link between wetland age and occupancy was complex and included threshold and quadratic relationships for three of the four species, but only Boreal Chorus Frog occupancy was still increasing slowly at the end of our study. Our results indicate created wetlands did not attain the suitability of impacted and natural wetlands for local amphibians, even several years after construction. The complex relationships between wetland age and species-specific occupancy illustrate the importance of long-term monitoring in describing population responses to the construction of wetlands as mitigation for wetland loss.

Ecological Indicators↗

USGS2015

Markov decision processes in natural resources management: observability and uncertainty

The breadth and complexity of stochastic decision processes in natural resources presents a challenge to analysts who need to understand and use these approaches. The objective of this paper is to describe a class of decision processes that are germane to natural resources conservation and management, namely Markov decision processes, and to discuss applications and computing algorithms under different conditions of observability and uncertainty. A number of important similarities are developed in the framing and evaluation of different decision processes, which can be useful in their applications in natural resources management. The challenges attendant to partial observability are highlighted, and possible approaches for dealing with it are discussed.

Ecological Modelling↗

USGS2009

Simulation modeling to understand how selective foraging by beaver can drive the structure and function of a willow community

Beaver-willow (Castor-Salix) communities are a unique and vital component of healthy wetlands throughout the Holarctic region. Beaver selectively forage willow to provide fresh food, stored winter food, and construction material. The effects of this complex foraging behavior on the structure and function of willow communities is poorly understood. Simulation modeling may help ecologists understand these complex interactions. In this study, a modified version of the SAVANNA ecosystem model was developed to better understand how beaver foraging affects the structure and function of a willow community in a simulated riparian ecosystem in Rocky Mountain National Park, Colorado (RMNP). The model represents willow in terms of plant and stem dynamics and beaver foraging in terms of the quantity and quality of stems cut to meet the energetic and life history requirements of beaver. Given a site where all stems were equally available, the model suggested a simulated beaver family of 2 adults, 2 yearlings, and 2 kits required a minimum of 4 ha of willow (containing about10 stems m -2 ) to persist in a steady-state condition. Beaver created a willow community where the annual net primary productivity (ANPP) was 2 times higher and plant architecture was more diverse than the willow community without beaver. Beaver foraging created a plant architecture dominated by medium size willow plants, which likely explains how beaver can increase ANPP. Long-term simulations suggested that woody biomass stabilized at similar values even though availability differed greatly at initial condition. Simulations also suggested that willow ANPP increased across a range of beaver densities until beaver became food limited. Thus, selective foraging by beaver increased productivity, decreased biomass, and increased structural heterogeneity in a simulated willow community.

Ecological Modelling↗

USGS2009

Sensitivity of system stability to model structure

A community is stable, and resilient, if the levels of all community variables can return to the original steady state following a perturbation. The stability properties of a community depend on its structure, which is the network of direct effects (interactions) among the variables within the community. These direct effects form feedback cycles (loops) that determine community stability. Although feedback cycles have an intuitive interpretation, identifying how they form the feedback properties of a particular community can be intractable. Furthermore, determining the role that any specific direct effect plays in the stability of a system is even more daunting. Such information, however, would identify important direct effects for targeted experimental and management manipulation even in complex communities for which quantitative information is lacking. We therefore provide a method that determines the sensitivity of community stability to model structure, and identifies the relative role of particular direct effects, indirect effects, and feedback cycles in determining stability. Structural sensitivities summarize the degree to which each direct effect contributes to stabilizing feedback or destabilizing feedback or both. Structural sensitivities prove useful in identifying ecologically important feedback cycles within the community structure and for detecting direct effects that have strong, or weak, influences on community stability. The approach may guide the development of management intervention and research design. We demonstrate its value with two theoretical models and two empirical examples of different levels of complexity. ?? 2009 Elsevier B.V. All rights reserved.

Ecological Modelling↗

USGS2019

Selecting ecological models using multi-objective optimization

Choices in ecological research and natural resource management require balancing multiple, often competing objectives. Examples include maximizing species persistence in a wildlife conservation context, while minimizing cost, or balancing opposing stakeholder objectives when managing wildlife populations. Multiple-objective optimization (MOO) provides a unifying framework for solving multiple objective problems. Model selection is a critical component of ecological inference and prediction and requires balancing the competing objectives of model fit and model complexity. The tradeoff between model fit and model complexity provides a basis for describing the model-selection problem within the MOO framework. We discuss MOO and two strategies for solving the MOO problem; modeling preferences pre-optimization and post-optimization. Most conventional model selection methods can be formulated as solutions of MOO problems via specification of pre-optimization preferences. We reconcile model selection within the MOO framework. We also consider model selection using post-optimization specification of preferences. That is, by first identifying Pareto optimal solutions, and then selecting among them. We demonstrate concepts with an ecological application of model selection using avian species richness data in the continental United States.

Ecological Modelling↗

USGS2023

Evaluations of Lagrangian egg drift models: From a laboratory flume to large channelized rivers

To help better interpret computational models in predicting drift of carp eggs in rivers, we present a series of model assessments for the longitudinal egg dispersion. Two three-dimensional Lagrangian particle tracking models, SDrift and FluEgg, are evaluated in a series of channels with increasing complexity. The model evaluation demonstrates that both models are able to accommodate channel complexity and provide a wide range of dispersion coefficients: K l = 0 (1 − 100) Hu ∗ with H being water depth and u ∗ being shear velocity. In a straight channel with K l = 0 (1) Hu ∗ SDrift predicts weaker longitudinal dispersion than FluEgg in the early stage as a result of weak vertical mixing associated with smooth wall turbulence. With sufficient time, SDrift and FluEgg predict similar egg dispersion, accounting for the differential advection due to the vertical velocity profile. In an idealized curved channel with K l = 0 (10) Hu ∗ , dispersion is driven by both vertical and transverse velocity profiles. SDrift yields slightly larger dispersion coefficients than FluEgg. In a real river with channel-training structures and having K l = 0 (100) Hu ∗ SDrift predicts a stronger longitudinal dispersion than FluEgg due to substantial local turbulent eddies and velocity gradients. To summarize, FluEgg shows good performance in capturing dispersion due to vertical velocity profiles and cross-channel velocity gradients. SDrift shows excellent model capabilities of revealing various dispersion mechanisms in addition to the vertical and cross-channel velocity variations. They include the initial turbulent diffusion stage with growing dispersion coefficients and strong dispersion due to in-stream hydraulic structures and localized turbulence.

Missouri↗

USGS2019

Mississippi river sediment diversions and coastal wetland sustainability: Synthesis of responses to freshwater, sediment, and nutrient inputs

Management and restoration of coastal wetlands require insight into how inundation, salinity, and the availability of mineral sediment and nutrients interact to influence ecosystem functions that control sustainability. The Mississippi River Delta, which ranks among the world's largest and most productive coastal wetland complexes, has experienced extensive deterioration over the last century due, in large part, to enhanced vulnerability to relative sea-level rise and lateral erosion caused by a combination of natural processes and anthropogenic modifications of hydrology. This land loss crisis has prompted the State of Louisiana to develop a comprehensive restoration plan that includes constructing and implementing a series of large-scale sediment diversions that will reconnect sediment- and nutrient-rich Mississippi River water to adjacent bays, estuaries, and wetlands. Sediment loading through diversions is predicted to enhance the long-term sustainability of coastal wetlands; however, the additive effects of increased inundation, abrubt changes in the salinity regime, and high nutrient loads on wetland plant growth and organic matter (SOM) decomposition rates, which help regulate accretion and elevation change, is uncertain. Therefore, this review attempts to synthesize existing information to inform predictions of the interactive effects of diversions on these drivers of coastal wetland sustainability. The data suggest that sediment deposition within an optimal elevation range will increase the overall productivity of existing wetlands where prolonged flooding does not counter this effect by limiting plant growth. A reduction in salinity may increase plant productivity and cause vegetation shifts to less salt tolerant species, but seasonal swings in salinity may have unforeseen consequences. Nutrient-loading is predicted to lead to greater aboveground productivity, which, in turn, can facilitate additional sediment trapping; however, belowground productivity may decline, particularly in areas where sediment deposition is limited. In areas experiencing net deposition, nutrient-enrichment is predicted to enhance belowground growth into new sediment and contribute to positive effects on soil organic matter accumulation, accretion, and elevation change. Thus, we contend that sediment input is essential for limiting the negative effects of flooding and nutrient-enrichment on wetland processes. These conclusions are generally supported by the biophysical feedbacks occurring in existing prograding deltas of the Mississippi River Delta complex.

Louisiana↗

USGS2007

Study of a prehistoric landslide using seismic reflection methods integrated with geological data in the Wasatch Mountains, Utah, USA

An integration of geological and geophysical techniques characterizes the internal and basal structure of a landslide along the western margin of the Wasatch Mountains in northern Utah, USA. The study area is within a region of planned and continuing residential development. The Little Valley Landslide is a prehistoric landslide as old as 13??ka B.P. Drilling and trenching at the site indicate that the landslide consists of chaotic and disturbed weathered volcanic material derived from Tertiary age volcanic rocks that comprise a great portion of the Wasatch Range. Five short high-resolution common mid-point seismic reflection profiles over selected portions of the site examine the feasibility of using seismic reflection to study prehistoric landslides in the Wasatch Mountain region. Due to the expected complexity of the near-surface geology, we have pursued an experimental approach in the data processing, examining the effects of muting first arrivals, frequency filtering, model-based static corrections, and seismic migration. The results provide a framework for understanding the overall configuration of the landslide, its basal (failure) surface, and the structure immediately underlying this surface. A glide surface or de??collement is interpreted to underlie the landslide suggesting a large mass movement. The interpretation of a glide surface is based on the onset of coherent reflectivity, calibrated by information from a borehole located along one of the seismic profiles. The glide surface is deepest in the center portion of the landslide and shallows up slope, suggesting a trough-like feature. This study shows that seismic reflection techniques can be successfully used in complex alpine landslide regions to (1) provide a framework in which to link geological data and (2) reduce the need for an extensive trenching and drilling program. ?? 2007 Elsevier B.V. All rights reserved.

Engineering Geology↗

USGS2011

Methods for assessing the stability of slopes during earthquakes-A retrospective

During the twentieth century, several methods to assess the stability of slopes during earthquakes were developed. Pseudostatic analysis was the earliest method; it involved simply adding a permanent body force representing the earthquake shaking to a static limit-equilibrium analysis. Stress-deformation analysis, a later development, involved much more complex modeling of slopes using a mesh in which the internal stresses and strains within elements are computed based on the applied external loads, including gravity and seismic loads. Stress-deformation analysis provided the most realistic model of slope behavior, but it is very complex and requires a high density of high-quality soil-property data as well as an accurate model of soil behavior. In 1965, Newmark developed a method that effectively bridges the gap between these two types of analysis. His sliding-block model is easy to apply and provides a useful index of co-seismic slope performance. Subsequent modifications to sliding-block analysis have made it applicable to a wider range of landslide types. Sliding-block analysis provides perhaps the greatest utility of all the types of analysis. It is far easier to apply than stress-deformation analysis, and it yields much more useful information than does pseudostatic analysis.

Engineering Geology↗

USGS2017

Prior knowledge-based approach for associating contaminants with biological effects: A case study in the St. Croix River basin, MN, WI, USA

Evaluating potential adverse effects of complex chemical mixtures in the environment is challenging. One way to address that challenge is through more integrated analysis of chemical monitoring and biological effects data. In the present study, water samples from five locations near two municipal wastewater treatment plants in the St. Croix River basin, on the border of MN and WI, USA, were analyzed for 127 organic contaminants. Known chemical-gene interactions were used to develop site-specific knowledge assembly models (KAMs) and formulate hypotheses concerning possible biological effects associated with chemicals detected in water samples from each location. Additionally, hepatic gene expression data were collected for fathead minnows ( Pimephales promelas ) exposed in situ , for 12 d, at each location. Expression data from oligonucleotide microarrays were analyzed to identify functional annotation terms enriched among the differentially-expressed probes. The general nature of many of the terms made hypothesis formulation on the basis of the transcriptome-level response alone difficult. However, integrated analysis of the transcriptome data in the context of the site-specific KAMs allowed for evaluation of the likelihood of specific chemicals contributing to observed biological responses. Thirteen chemicals (atrazine, carbamazepine, metformin, thiabendazole, diazepam, cholesterol, p-cresol, phenytoin, omeprazole, ethyromycin, 17β-estradiol, cimetidine, and estrone), for which there was statistically significant concordance between occurrence at a site and expected biological response as represented in the KAM, were identified. While not definitive, the approach provides a line of evidence for evaluating potential cause-effect relationships between components of a complex mixture of contaminants and biological effects data, which can inform subsequent monitoring and investigation.

Minnesota, Wisconsin↗

USGS2026

Performance evaluation and methods comparison of transcriptomic-based approaches for the characterization of wastewater treatment effluent

Wastewater treatment effluents (WWTE) present complex risks to aquatic ecosystems that are difficult to characterize using traditional methods. This study systematically evaluated the consistency and performance of transcriptomic-based approaches over time with repeated sampling and with differing experimental approaches (selection of reference condition, grab vs. composite sampling, deployed vs. laboratory exposed). RNA-seq was performed on larval fathead minnow (FHM) exposed in the laboratory to moderately hard reconstituted water (MRHW) or individual grab samples collected from an upstream site and a WWTE in the morning and afternoon over two successive days, as well as FHM deployed concurrently with grab sampling at the same sites. Composite transcriptional profiles were generated by pooling count data from grab sample exposures. The choice of comparator significantly affected results. The use of the upstream site as the reference consistently yielded fewer differentially expressed genes (DEGs) and minimal overlap compared to DEG sets from the other comparisons. Using MRHW as a comparator, DEG sets showed high consistency across grab samples, with morning samples demonstrating larger, highly consistent gene expression sets (96 % overlap) compared to afternoon samples, revealing clear and consistent within-day expression patterns. With the MHRW comparator, DEG sets from grab sample composites and deployments also overlapped substantially, indicating that transcriptional profiles accurately reflect WWTE composition regardless of exposure method. Comparisons with non-targeted (NTA) and targeted analytical datasets confirmed that gene expression interpretations aligned with effluent composition while highlighting limitations of relying solely on targeted analyte sets for connecting expression to specific chemicals. Though highly dependent on experimental design, these results demonstrate that transcriptomic-based methods provide significant utility for characterizing the bioactivity of complex environmental mixtures, and when paired with NTA datasets, have the potential to deliver a comprehensive assessment of their environmental risk.

Environmental Pollution↗

USGS2010

Sharing the floodplain: Mediated modeling for environmental management

Complex ecosystems, such as the Upper Mississippi River (UMR), present major management challenges. Such systems often provide a range of ecosystem services that are differentially valued by stakeholders representing distinct interests (e.g., agriculture, conservation, navigation) or institutions (e.g., federal and state agencies). When no single entity has the knowledge or authority to resolve conflicts over shared resource use, stakeholders may struggle to jointly understand the scope of the problem and to reach reasonable compromises. This paper explores mediated modeling as a group consensus building process for understanding relationships between ecological, economic and cultural well-being in the UMR floodplain. We describe a workshop structure used to engage UMR stakeholders that may be extended to resource use conflicts in other complex ecosystems. We provide recommendations for improving on these participatory methods in structuring future efforts. In conclusion, we suggest that tools which facilitate collaborative learning, such as mediated modeling, need to be incorporated at an institutional level as a vital element of integrated ecosystem management. ?? 2008 Elsevier Ltd.

Environmental Modelling and Software↗

USGS2018

Input data processing tools for the integrated hydrologic model GSFLOW

Integrated hydrologic modeling (IHM) encompasses a vast number of processes and specifications, variable in time and space, and development of models can be arduous. Model input construction techniques have not been formalized or made easily reproducible. Creating the input files for integrated hydrologic models requires complex GIS processing of raster and vector datasets from various sources. Developing stream network topology that is consistent with the model grid-scale digital elevation model (DEM) is important for robust simulation of surface water and groundwater exchanges. Distribution of meteorological data over the model domain is difficult in complex terrain at the model-grid scale, but is necessary for realistic simulations. As model development requires extensive GIS and computer programming expertise, the use of IHMs has mostly been limited to research groups with available financial, human, and technical resources. Here we present a series of open-source Python scripts that are combined with ESRI ArcGIS to provide a formalized technique for the parameterization and development of inputs for the readily available IHM called GSFLOW. This Python toolkit automates many of the necessary and laborious processes of parameterization, including stream network development, land coverages, and meteorological distribution over the model domain. The final products of the toolkit are PRMS ready Parameter Files, along with several input parameters for a MODFLOW model, including input for the Streamflow Routing Package. A demonstration of the toolkit is provided to illustrate its capabilities.

Environmental Modelling and Software↗

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