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USGS2017

U.S. Geological Survey Karst Interest Group Proceedings, San Antonio, Texas, May 16–18, 2017

Introduction and Acknowledgments Karst aquifer systems are present throughout parts of the United States and some of its territories, and have developed in carbonate rocks (primarily limestone and dolomite) and evaporites (gypsum, anhydrite, and halite) that span an interval of time encompassing more than 550 million years. The depositional environments, diagenetic processes, post-depositional tectonic events, and geochemical weathering processes that form karst aquifers are varied and complex. These factors involve biological, chemical, and physical changes that when combined with the diverse climatic regimes in which karst development has taken place, result in the unique dual- or triple-porosity nature of karst aquifers. These complex hydrogeologic systems typically represent challenging and unique conditions to scientists attempting to study groundwater flow and contaminant transport in these terrains. The dissolution of carbonate rocks and the subsequent development of distinct and beautiful landscapes, caverns, and springs have resulted in the most exceptional karst areas being designated as national or state parks. Tens of thousands of similar areas in the United States have been developed into commercial caverns and known privately owned caves. Both public and private properties provide access for scientists to study the flow of groundwater in situ . Likewise, the range and complexity of landforms and groundwater flow systems associated with karst terrains are enormous, perhaps more than for any other aquifer type. Karst aquifers and landscapes that form in tropical areas, such as the cockpit karst along the north coast of Puerto Rico, differ greatly from karst landforms in more arid climates, such as the Edwards Plateau in west-central Texas or the Guadalupe Mountains near Carlsbad, New Mexico, where hypogenic processes have played a major role in speleogenesis. Many of these public and private lands also contain unique flora and fauna associated with these karst hydrogeologic systems. As a result, numerous federal, state, and local agencies have a strong interest in the study of karst terrains. Many of the major springs and aquifers in the United States have developed in carbonate rocks, such as the Floridan aquifer system in Florida and parts of Alabama, Georgia, and South Carolina; the Ozark Plateaus aquifer system in parts of Arkansas, Kansas, Missouri, and Oklahoma; and the Edwards-Trinity aquifer system in west-central Texas. These aquifers, and the springs that discharge from them, serve as major water-supply sources and form unique ecological habitats. Competition for the water resources of karst aquifers is common, and urban development and the lack of attenuation of contaminants in karst areas due to dissolution features that form direct pathways into karst aquifers can impact the ecosystem and water quality associated with these aquifers. The concept for developing a platform for interaction among scientists within the U.S. Geological Survey (USGS) working on karst-related studies evolved from the November 1999 National Groundwater Meeting of the USGS. As a result, the Karst Interest Group (KIG) was formed in 2000. The KIG is a loose-knit, grass-roots organization of USGS and non-USGS scientists and researchers devoted to fostering better communication among scientists working on, or interested in, karst science. The primary mission of the KIG is to encourage and support interdisciplinary collaboration and technology transfer among scientists working in karst areas. Additionally, the KIG encourages collaborative studies between the different mission areas of the USGS as well as with other federal and state agencies, and with researchers from academia and institutes. To accomplish its mission, the KIG has organized a series of workshops that have been held near nationally important karst areas. To date (2017) seven KIG workshops, including the workshop documented in this report, have been held. The workshops typically include oral and poster sessions on selected karst-related topics and research, as well as field trips to local karst areas. To increase non-USGS participation an effort was made for the workshops to be held at a university or institute beginning with the fourth workshop. Proceedings of the workshops are published by the USGS and are available online at the USGS publications warehouse https://pubs.er.usgs.gov/ by using the search term “karst interest group.” The first KIG workshop was held in St. Petersburg, Florida, in 2001, in the vicinity of the large springs and other karst features of the Floridan aquifer system. The second KIG workshop was held in 2002, in Shepherdstown, West Virginia, in proximity to the carbonate aquifers of the northern Shenandoah Valley, and highlighted an invited presentation on karst literature by the late Barry F. Beck of P.E. LaMoreaux and Associates. The third KIG workshop was held in 2005, in Rapid City, South Dakota, near evaporite karst features in limestones of the Madison Group in the Black Hills of South Dakota. The Rapid City KIG workshop included field trips to Wind Cave National Park and Jewel Cave National Monument, and featured a presentation by Thomas Casadevall, then USGS Central Region Director, on the status of Earth science at the USGS. The fourth KIG workshop in 2008 was hosted by the Hoffman Environmental Research Institute and Center for Cave and Karst Studies at Western Kentucky University in Bowling Green, Kentucky, near Mammoth Cave National Park and karst features of the Chester Upland and Pennyroyal Plateau. The workshop featured a late-night field trip into Mammoth Cave led by Rickard Toomey and Rick Olsen, National Park Service. The fifth KIG workshop in 2011 was a joint meeting of the USGS KIG and University of Arkansas HydroDays, hosted by the Department of Geosciences at the University of Arkansas in Fayetteville. The workshop featured an outstanding field trip to the unique karst terrain along the Buffalo National River in the southern Ozarks, and a keynote presentation on paleokarst in the United States was delivered by Art and Peggy Palmer. The sixth KIG workshop was hosted by the National Cave and Karst Research Institute (NCKRI) in 2014, in Carlsbad, New Mexico. George Veni, Director of the NCKRI, served as a co-chair of the workshop with Eve Kuniansky of the USGS. The workshop featured speaker Dr. Penelope Boston, Director of Cave and Karst Studies at New Mexico Tech, Socorro, and Academic Director at the NCKRI, who addressed the future of karst research. The field trip on evaporite karst of the lower Pecos Valley was led by Lewis Land (NCKRI karst hydrologist), and the field trip on the geology of Carlsbad Caverns National Park was led by George Veni. This current seventh KIG workshop is being held in San Antonio at the University of Texas at San Antonio (UTSA). This 2017 workshop is being hosted by the Department of Geological Sciences’ Student Geological Society (SGS), and student chapters of the American Association of Petroleum Geologists (AAPG) and Association of Engineering Geologists (AEG), with support by the UTSA Department of Geological Sciences and Center for Water Research. The UTSA student chapter presidents, Jose Silvestre (SGS), John Cooper (AAPG), and Tyler Mead (AEG) serve as co-chairs of the 2017 workshop with Eve Kuniansky of the USGS. The technical session committee is chaired by Eve Kuniansky, USGS, and includes Michael Bradley, Tom Byl, Rebecca Lambert, John Lane, and James Kaufmann, all USGS, and Patrick Tucci, retired USGS. The logistics committee includes Amy Clark, Yongli Gao, and Lance Lambert (Department Chair), UTSA Department of Geological Sciences; and Ryan Banta and Allan Clark, USGS, San Antonio, Texas. The field trip committee is chaired by Allan Clark and includes Amy Clark, Yongli Gao, and Keith Muehlestein, UTSA; Marcus Gary, Edwards Aquifer Authority and University of Texas at Austin; Ron Green, Southwest Research Institute; Geary Schindel, Edwards Aquifer Authority; and George Veni, NCKRI. Additionally, two organizations have assisted the UTSA student chapters in hosting the meeting by donating funds to the chapters: the Edwards Aquifer Authority, San Antonio, Texas, and the Barton Springs Edwards Aquifer Authority, Austin, Texas. Additionally, Yongli Gao, Center for Water Research and Department of Geological Sciences, UTSA, helped develop sessions on cave and karst research in China for this workshop. These proceedings could not have been accomplished without the assistance of Lawrence E. Spangler as co-editor who not only has subject matter expertise, but also serves as an editor with the USGS Science Publishing Network. We sincerely hope that this workshop continues to promote future collaboration among scientists of varied and diverse backgrounds, and improves our understanding of karst aquifer systems in the United States and its territories. The extended abstracts of USGS authors were peer reviewed and approved for publication by the USGS. Articles submitted by university researchers and other federal and state agencies did not go through the formal USGS peer review and approval process, and therefore may not adhere to USGS editorial standards or stratigraphic nomenclature. However, all articles had a minimum of two peer reviews and were edited for consistency of appearance in the proceedings. The use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The USGS Water Availability and Use Science Program funded the publication costs of the proceedings.

Scientific Investigations Report↗

USGS2014

Methane hydrates in nature - Current knowledge and challenges

Recognizing the importance of methane hydrate research and the need for a coordinated effort, the United States Congress enacted the Methane Hydrate Research and Development Act of 2000. At the same time, the Ministry of International Trade and Industry in Japan launched a research program to develop plans for a methane hydrate exploratory drilling project in the Nankai Trough. India, China, the Republic of Korea, and other nations also have established large methane hydrate research and development programs. Government-funded scientific research drilling expeditions and production test studies have provided a wealth of information on the occurrence of methane hydrates in nature. Numerous studies have shown that the amount of gas stored as methane hydrates in the world may exceed the volume of known organic carbon sources. However, methane hydrates represent both a scientific and technical challenge, and much remains to be learned about their characteristics and occurrence in nature. Methane hydrate research in recent years has mostly focused on: (1) documenting the geologic parameters that control the occurrence and stability of methane hydrates in nature, (2) assessing the volume of natural gas stored within various methane hydrate accumulations, (3) analyzing the production response and characteristics of methane hydrates, (4) identifying and predicting natural and induced environmental and climate impacts of natural methane hydrates, (5) analyzing the methane hydrate role as a geohazard, (6) establishing the means to detect and characterize methane hydrate accumulations using geologic and geophysical data, and (7) establishing the thermodynamic phase equilibrium properties of methane hydrates as a function of temperature, pressure, and gas composition. The U.S. Department of Energy (DOE) and the Consortium for Ocean Leadership (COL) combined their efforts in 2012 to assess the contributions that scientific drilling has made and could continue to make to advance our understanding of methane hydrates in nature. COL assembled a Methane Hydrate Project Science Team with members from academia, industry, and government. This Science Team worked with COL and DOE to develop and host the Methane Hydrate Community Workshop, which surveyed a substantial cross section of the methane hydrate research community for input on the most important research developments in our understanding of methane hydrates in nature and their potential role as an energy resource, a geohazard, and/or as an agent of global climate change. Our understanding of how methane hydrates occur in nature is still growing and evolving, and it is known with certainty that field, laboratory, and modeling studies have contributed greatly to our understanding of hydrates in nature and will continue to be a critical source of the information needed to advance our understanding of methane hydrates.

Journal of Chemical and Engineering Data↗

USGS2000

Use of chlorine-36 to determine regional-scale aquifer dispersivity, eastern Snake River Plain aquifer, Idaho/USA

Chlorine-36 (36Cl) derived from processed nuclear waste that was disposed at the US Department of Energy's Idaho National Engineering and Environmental Laboratory (INEEL) through a deep injection well in 1958, was detected 24-28 yr later in groundwater monitoring wells approximately 26 km downgradient from the source. Groundwater samples covering the period 1966-1995 were selected from the US Geological Survey's archived-sample library at the INEEL and analyzed for 36Cl by accelerator mass spectrometry (AMS). The smaller 36Cl peak concentrations in water from the far-field monitoring wells relative to the input suggest that aquifer dispersivity may be large. However, the sharpness of the 1958 disposal peak of 36Cl is matched by the measured 36Cl concentrations in water from these wells. This implies that a small aquifer dispersivity may be attributed to preferential groundwater flowpaths. Assuming that tracer arrival times at monitoring wells are controlled by preferential flow, a 1-D system-response model was used to estimate dispersivity by comparing the shape of predicted 36Cl-concentration curves to the shape of 36Cl-concentration curves measured in water from these observation wells. The comparisons suggest that a 1-D dispersivity of 5 m provides the best fit to the tracer data. Previous work using a 2-D equivalent porous-media model concluded that longitudinal dispersivity (equivalent to 1-D dispersivity in our model) was 90 m (Ackerman, 1991). A 90 m dispersivity value eliminates the 1958 disposal peak in our model output curves. The implications of the arrival of 36Cl at downgradient monitoring wells are important for three reasons: (1) the arrival times and associated 36Cl concentrations provide quantitative constraints on residence times, velocities, and dispersivities in the aquifer; (2) they help to refine our working hypotheses of groundwater flow in this aquifer and (3) they may suggest a means of estimating the distribution of preferential flowpaths in the aquifer. ?? 2000 Elsevier Science B.V. All rights reserved.

Nuclear Instruments and Methods in Physics Researc↗

USGS2003

The National Map: from geography to mapping and back again

When the means of production for national base mapping were capital intensive, required large production facilities, and had ill-defined markets, Federal Government mapping agencies were the primary providers of the spatial data needed for economic development, environmental management, and national defense. With desktop geographic information systems now ubiquitous, source data available as a commodity from private industry, and the realization that many complex problems faced by society need far more and different kinds of spatial data for their solutions, national mapping organizations must realign their business strategies to meet growing demand and anticipate the needs of a rapidly changing geographic information environment. The National Map of the United States builds on a sound historic foundation of describing and monitoring the land surface and adds a focused effort to produce improved understanding, modeling, and prediction of land-surface change. These added dimensions bring to bear a broader spectrum of geographic science to address extant and emerging issues. Within the overarching construct of The National Map, the U.S. Geological Survey (USGS) is making a transition from data collector to guarantor of national data completeness; from producing paper maps to supporting an online, seamless, integrated database; and from simply describing the Nation’s landscape to linking these descriptions with increased scientific understanding. Implementing the full spectrum of geographic science addresses a myriad of public policy issues, including land and natural resource management, recreation, urban growth, human health, and emergency planning, response, and recovery. Neither these issues nor the science and technologies needed to deal with them are static. A robust research agenda is needed to understand these changes and realize The National Map vision. Initial successes have been achieved. These accomplishments demonstrate the utility of The National Map to the Nation and give confidence in evolving its future applications.

Photogrammetric Engineering and Remote Sensing↗

USGS2013

Data management challenges in species distribution modeling

An important component in the fields of ecology and conservation biology is understanding the environmental conditions and geographic areas that are suitable for a given species to inhabit. A common tool in determining such areas is species distribution modeling which uses computer algorithms to determine the spatial distribution of organisms. Most commonly the correlative relationships between the organism and environmental variables are the primary consideration. The data requirements for this type of modeling consist of known presence and possibly absence locations of the species as well as the values of environmental or climatic covariates thought to define the species habitat suitability at these locations. These covariate data are generally extracted from remotely sensed imagery, interpolated/gridded historical climate data, or downscaled climate model output. Traditionally, ecologists and biologists have constructed species distribution models using workflows and data that reside primarily on their local workstations or networks. This workflow is becoming challenging as scientists increasingly try to use these modeling techniques to inform management decisions under different climate change scenarios. This challenge stems from the fact that remote sensing products, gridded historical climate, and downscaled climate models are not only increasing in spatial and temporal resolution but proliferating as well. Any rigorous assessment of uncertainty requires a computationally intensive sensitivity analysis accounting for various sources of uncertainty. The scientists fitting these models generally do not have the background in computer science required to take advantage of recent advances in web-service based data acquisition, remote high-powered data processing, or scientific workflow systems. Ecologists in the field of modeling are in need of a tractable platform that abstracts the inherent computational complexity required to incorporate the burgeoning field of coupled climate and ecological response modeling. In this paper we describe the computational challenges in species distribution modeling and solutions using scientific workflow systems. We focus on the Software for Assisted Species Modeling (SAHM) a package within VisTrails, an open-source scientific workflow system.

Bulletin of the Technical Committee on Data Engine↗

USGS2022

Contaminants of emerging concern in the Great Lakes: Science to inform management practices for protecting the health and integrity of wildlife populations from adverse effects: GLRI action plan I, focus area 1, goal 5

Executive Summary: Under Action Plan I (2010-2014) of the Great Lakes Restoration Initiative (GLRI), Federal and Academic partners began an investigation of the presence and distribution of contaminants of emerging concern (CECs) in the Great Lakes and potential impacts on fish and wildlife. The term CECs is applied to a broad range of chemicals that are currently in use but for which we currently lack good understanding of whether fish, wildlife, or humans are being exposed and/or whether negative health or environmental effects are expected if exposure occurs. Pharmaceuticals, personal care products, flame retardants, many current use pesticides, and poly- and perfluorinated chemicals are some well-known groups of CECs, but there is no definitive or comprehensive list that can be used to support the management of CECs to reduce impacts on the Great Lakes ecosystem. Four overarching goals were identified for this collaborative investigation: 1. Evaluate the sources, occurrence, and distribution of CECs across the Great Lakes Basin. 2. Examine associations between the distribution of CECs and land-use patterns. 3. Review both scientific literature and field-generated data to determine the potential for CECs to cause adverse effects on Great Lakes fish and wildlife populations. 4. Develop efficient strategies to survey and/or monitor for threats that CECs may pose in order to take effective management actions before those threats evolve into large scale impacts on Great Lakes ecosystems or the services they provide. Achievement of these goals ensures progress towards Focus Area 1: Toxic Substances and Areas of Concern from GLRI Action Plan I, Goal 5: “ The health and integrity of wildlife populations and habitat are protected from adverse chemical and biological effects associated with the presence of toxic substances in the Great Lakes Basin ”. This large-scale research effort was comprised of individual and collaborative projects from multiple federal agencies and academic institutions, involving over 85 investigators, and overseen by the U.S. Environmental Protection Agency (EPA) Region 5, Great Lakes National Program Office. Partners include the United States Geological Survey, the National Oceanic and Atmospheric Administration, U.S. Fish and Wildlife Service, Saint Cloud State University, the U.S. EPA Office of Research and Development, and the U.S. Army Corps of Engineers. Key findings: 1. Contaminants of emerging concern were found throughout the monitored Great Lakes tributaries, but types and concentrations vary in association with regional land use. CECs were detected in nearly all samples collected. The type and concentration of the specific contaminants detected varied considerably among field sites and in association with land use type, such as urban, agricultural, wetland, 2 or forest. Contaminants were detected in the water column, sediment, and tissues of all species surveyed in the current work (mussels, aquatic insects, fish, and insect-eating birds). 2. There were over 20 contaminants for which CEC concentrations approached or exceeded those reported to cause toxicity in laboratory experiments. This was based on detection in water, sediments and or biota at one or more field sites. These contaminants represent compounds that warrant further investigation and monitoring with respect to potential impacts in certain areas of the Great Lakes basin. Based on the present investigation, compounds of greatest concern include: polycyclic aromatic hydrocarbons, associated with oil-based products and combustion of organic matter; atrazine, an herbicide; dichlorvos, an insecticide; and ibuprofen and venlafaxine, both pharmaceuticals. 3. Results suggest that mixtures of CECs presently found in most Great Lakes tributary locations surveyed may elicit subtle biological effects, but likely are not, alone, causing obvious detriment to current communities of fish and wildlife. CECs detected in the Great Lakes were associated with subtle biological effects like changes in gene expression, altered circulating glucose, etc. in both wild-caught and laboratory-reared organisms. These effects were generally not indicative of reproductive failure or mortality. However, the effects may have more serious implications when combined with other sources of stress like habitat degradation, changing climate conditions, and competition with invasive species. Due to limited historical data, it is unknown whether severe CEC-related impacts have already affected aquatic communities in waterbodies that have received long-term inputs of these contaminants. Likewise, under Action Plan I, biological effects were not necessarily evaluated at the sites where CEC concentrations exceeding laboratory toxicity thresholds were detected. As a result, strategic, ongoing surveillance and monitoring of CECs is warranted. This collaborative investigation resulted in new tools, approaches, and data that can be used to inform and support the management of CECs to reduce their impacts on Great Lakes natural resources. The following products of this research effort are available through https://communities.geoplatform.gov/glri/ or by contacting the investigators (see technical chapters found in Appendices A-F): 1. Database of CEC occurrence and concentrations in US tributary streams. The database includes CEC detections in water, sediment, and fish and wildlife tissues, and represents the most comprehensive survey of CECs in the Great Lakes Region. 2. Synopses of results and key findings. Integrated summaries of results, conclusions, and management implications of the CEC research are available through reports, topical fact sheets, and presentations. 3. Technical publications: This collaborative research effort has resulted in over 50 peer-reviewed publications, agency reports, and data releases that can be of use to resource managers, the scientific community, and members of the public. 4. Innovative tools. Innovative monitoring devices, sampling equipment, conceptual frameworks, and software applications were developed over the course of this 3 research. These tools are transferable to stakeholders via internet accessibility or via specifications, instructions, and demonstration detailed in technical publications. Hypotheses to guide CECs research under Action Plan II. Findings from 2010-2014 were used to guide further research in 2015-2018 for basin-wide surveillance of CECs and for sites warranting further study of potential biological impacts of CECs. Additional surveillance included both evaluation of additional classes of contaminants and expanded lists for chemical classes shown to be of greatest concern. Mixtures of some of the most frequently detected contaminants were also tested in laboratory studies to understand whether long term exposures to multiple contaminants may result in effects not evident from uncontrolled, short-term field experiments.

Great Lakes↗

USGS2003

The U.S. Geological Survey Land Remote Sensing Program

In 2002, the U. S. Geological Survey (USGS) launched a program to enhance the acquisition, preservation, and use of remotely sensed data for USGS science programs, as well as for those of cooperators and customers. Remotely sensed data are fundamental tools for studying the Earth's land surface, including coastal and near-shore environments. For many decades, the USGS has been a leader in providing remotely sensed data to the national and international communities. Acting on its historical topographic mapping mission, the USGS has archived and distributed aerial photographs of the United States for more than half a century. Since 1972, the USGS has acquired, processed, archived, and distributed Landsat and other satellite and airborne remotely sensed data products to users worldwide. Today, the USGS operates and manages the Landsats 5 and 7 missions and cooperates with the National Aeronautics and Space Administration (NASA) to define and implement future satellite missions that will continue and expand the collection of moderate-resolution remotely sensed data. In addition to being a provider of remotely sensed data, the USGS is a user of these data and related remote sensing technology. These data are used in natural resource evaluations for energy and minerals, coastal environmental surveys, assessments of natural hazards (earthquakes, volcanoes, and landslides), biological surveys and investigations, water resources status and trends analyses and studies, and geographic and cartographic applications, such as wildfire detection and tracking and as a source of information for The National Map. The program furthers these distinct but related roles by leading the USGS activities in providing remotely sensed data while advancing applications of such data for USGS programs and a wider user community.

Fact Sheet↗

USGS2021

Physics-guided machine learning for scientific discovery: An application in simulating lake temperature profiles

Physics-based models are often used to study engineering and environmental systems. The ability to model these systems is the key to achieving our future environmental sustainability and improving the quality of human life. This article focuses on simulating lake water temperature, which is critical for understanding the impact of changing climate on aquatic ecosystems and assisting in aquatic resource management decisions. General Lake Model (GLM) is a state-of-the-art physics-based model used for addressing such problems. However, like other physics-based models used for studying scientific and engineering systems, it has several well-known limitations due to simplified representations of the physical processes being modeled or challenges in selecting appropriate parameters. While state-of-the-art machine learning models can sometimes outperform physics-based models given ample amount of training data, they can produce results that are physically inconsistent. This article proposes a physics-guided recurrent neural network model (PGRNN) that combines RNNs and physics-based models to leverage their complementary strengths and improves the modeling of physical processes. Specifically, we show that a PGRNN can improve prediction accuracy over that of physics-based models (by over 20% even with very little training data), while generating outputs consistent with physical laws. An important aspect of our PGRNN approach lies in its ability to incorporate the knowledge encoded in physics-based models. This allows training the PGRNN model using very few true observed data while also ensuring high prediction accuracy. Although we present and evaluate this methodology in the context of modeling the dynamics of temperature in lakes, it is applicable more widely to a range of scientific and engineering disciplines where physics-based (also known as mechanistic) models are used.

ACM/IMS Transactions on Data Science↗

USGS2014

Bioaccumulation and toxicity of CuO nanoparticles by a freshwater invertebrate after waterborne and dietborne exposures

The incidental ingestion of engineered nanoparticles (NPs) can be an important route of uptake for aquatic organisms. Yet, knowledge of dietary bioavailability and toxicity of NPs is scarce. Here we used isotopically modified copper oxide ( 65 CuO) NPs to characterize the processes governing their bioaccumulation in a freshwater snail after waterborne and dietborne exposures. Lymnaea stagnalis efficiently accumulated 65 Cu after aqueous and dietary exposures to 65 CuO NPs. Cu assimilation efficiency and feeding rates averaged 83% and 0.61 g g –1 d –1 at low exposure concentrations (<100 nmol g –1 ), and declined by nearly 50% above this concentration. We estimated that 80–90% of the bioaccumulated 65 Cu concentration in L. stagnalis originated from the 65 CuO NPs, suggesting that dissolution had a negligible influence on Cu uptake from the NPs under our experimental conditions. The physiological loss of 65 Cu incorporated into tissues after exposures to 65 CuO NPs was rapid over the first days of depuration and not detectable thereafter. As a result, large Cu body concentrations are expected in L. stagnalis after exposure to CuO NPs. To the degree that there is a link between bioaccumulation and toxicity, dietborne exposures to CuO NPs are likely to elicit adverse effects more readily than waterborne exposures.

Environmental Science & Technology↗

USGS2008

EAARL coastal topography - Northern Gulf of Mexico

These remotely sensed, geographically referenced elevation measurements of Lidar-derived coastal topography were produced as a collaborative effort between the U.S. Geological Survey (USGS), Florida Integrated Science Center (FISC), St. Petersburg, FL and the National Aeronautics and Space Administration (NASA), Wallops Flight Facility, VA. One objective of this research is to create techniques to survey areas for the purposes of geomorphic change studies following major storm events. The USGS Coastal and Marine Geology Program's National Assessment of Coastal Change Hazards project is a multi-year undertaking to identify and quantify the vulnerability of U.S. shorelines to coastal change hazards such as effects of severe storms, sea-level rise, and shoreline erosion and retreat. Airborne Lidar surveys conducted during periods of calm weather are compared to surveys collected following extreme storms in order to quantify the resulting coastal change. Other applications of high-resolution topography include habitat mapping, ecological monitoring, volumetric change detection, and event assessment. The purpose of this project is to provide highly detailed and accurate datasets of the northern Gulf of Mexico coastal areas, acquired on September 19, 2004, immediately following Hurricane Ivan. The datasets are made available for use as a management tool to research scientists and natural resource managers. An innovative airborne Lidar instrument originally developed at the NASA Wallops Flight Facility, and known as the Experimental Airborne Advanced Research Lidar (EAARL), was used during data acquisition. The EAARL system is a raster-scanning, waveform-resolving, green-wavelength (532 nanometer) Lidar designed to map near-shore bathymetry, topography, and vegetation structure simultaneously. The EAARL sensor suite includes the raster-scanning, water-penetrating full-waveform adaptive Lidar, a down-looking RGB (red-green-blue) digital camera, a high-resolution multi-spectral color infrared (CIR) camera, two precision dual-frequency kinematic carrier-phase GPS receivers and an integrated miniature digital inertial measurement unit which provide for sub-meter georeferencing of each laser sample. The nominal EAARL platform is a twin-engine Cessna 310 aircraft, but the instrument may be deployed on a range of light aircraft. A single pilot, a Lidar operator, and a data analyst constitute the crew for most survey operations. This sensor has the potential to make significant contributions in measuring sub-aerial and submarine coastal topography within cross-environmental surveys. Elevation measurements were collected over the survey area using the EAARL system on September 19, 2004. The survey resulted in the acquisition of 3.2 gigabytes of data. The data were processed using the Airborne Lidar Processing System (ALPS), a custom-built processing system developed in a NASA-USGS collaboration. ALPS supports the exploration and processing of Lidar data in an interactive or batch mode. Modules for pre-survey flight line definition, flight path plotting, Lidar raster and waveform investigation, and digital camera image playback have been developed. Processing algorithms have been developed to extract the range to the first and last significant return within each waveform. ALPS is routinely used to create maps that represent submerged or sub-aerial topography. Specialized filtering algorithms have been implemented to determine the 'bare earth' under vegetation from a point cloud of 'last return' elevations.

Alabama, Florida, Mississippi↗

USGS2003

The saturated zone at Yucca Mountain: An overview of the characterization and assessment of the saturated zone as a barrier to potential radionuclide migration

The US Department of Energy is pursuing Yucca Mountain, Nevada, for the development of a geologic repository for the disposal of spent nuclear fuel and high-level radioactive waste, if the repository is able to meet applicable radiation protection standards established by the US Nuclear Regulatory Commission and the US Environmental Protection Agency (EPA). Effective performance of such a repository would rely on a number of natural and engineered barriers to isolate radioactive waste from the accessible environment. Groundwater beneath Yucca Mountain is the primary medium through which most radionuclides might move away from the potential repository. The saturated zone (SZ) system is expected to act as a natural barrier to this possible movement of radionuclides both by delaying their transport and by reducing their concentration before they reach the accessible environment. Information obtained from Yucca Mountain Site Characterization Project activities is used to estimate groundwater flow rates through the site-scale SZ flow and transport model area and to constrain general conceptual models of groundwater flow in the site-scale area. The site-scale conceptual model is a synthesis of what is known about flow and transport processes at the scale required for total system performance assessment of the site. This knowledge builds on and is consistent with knowledge that has accumulated at the regional scale but is more detailed because more data are available at the site-scale level. The mathematical basis of the site-scale model and the associated numerical approaches are designed to assist in quantifying the uncertainty in the permeability of rocks in the geologic framework model and to represent accurately the flow and transport processes included in the site-scale conceptual model. Confidence in the results of the mathematical model was obtained by comparing calculated to observed hydraulic heads, estimated to measured permeabilities, and lateral flow rates calculated by the site-scale model to those calculated by the regional-scale flow model. In addition, it was confirmed that the flow paths leaving the region of the potential repository are consistent with those inferred from gradients of measured head and those independently inferred from water-chemistry data. The general approach of the site-scale SZ flow and transport model analysis is to calculate unit breakthrough curves for radionuclides at the interface between the SZ and the biosphere using the three-dimensional site-scale SZ flow and transport model. Uncertainties are explicitly incorporated into the site-scale SZ flow and transport abstractions through key parameters and conceptual models. ?? 2002 Elsevier Science B.V. All rights reserved.

Journal of Contaminant Hydrology↗

USGS2002

Meeting ecological and societal needs for freshwater

Human society has used freshwater from rivers, lakes, groundwater, and wetlands for many different urban, agricultural, and industrial activities, but in doing so has overlooked its value in supporting ecosystems. Freshwater is vital to human life and societal well-being, and thus its utilization for consumption, irrigation, and transport has long taken precedence over other commodities and services provided by freshwater ecosystems. However, there is growing recognition that functionally intact and biologically complex aquatic ecosystems provide many economically valuable services and long-term benefits to society. The short-term benefits include ecosystem goods and services, such as food supply, flood control, purification of human and industrial wastes, and habitat for plant and animal life—and these are costly, if not impossible, to replace. Long-term benefits include the sustained provision of those goods and services, as well as the adaptive capacity of aquatic ecosystems to respond to future environmental alterations, such as climate change. Thus, maintenance of the processes and properties that support freshwater ecosystem integrity should be included in debates over sustainable water resource allocation. The purpose of this report is to explain how the integrity of freshwater ecosystems depends upon adequate quantity, quality, timing, and temporal variability of water flow. Defining these requirements in a comprehensive but general manner provides a better foundation for their inclusion in current and future debates about allocation of water resources. In this way the needs of freshwater ecosystems can be legitimately recognized and addressed. We also recommend ways in which freshwater ecosystems can be protected, maintained, and restored. Freshwater ecosystem structure and function are tightly linked to the watershed or catchment of which they are a part. Because riverine networks, lakes, wetlands, and their connecting groundwaters, are literally the “sinks” into which landscapes drain, they are greatly influenced by terrestrial processes, including many human uses or modifications of land and water. Freshwater ecosystems, whether lakes, wetlands, or rivers, have specific requirements in terms of quantity, quality, and seasonality of their water supplies. Sustainability normally requires these systems to fluctuate within a natural range of variation. Flow regime, sediment and organic matter inputs, thermal and light characteristics, chemical and nutrient characteristics, and biotic assemblages are fundamental defining attributes of freshwater ecosystems. These attributes impart relatively unique characteristics of productivity and biodiversity to each ecosystem. The natural range of variation in each of these attributes is critical to maintaining the integrity and dynamic potential of aquatic ecosystems; therefore, management should allow for dynamic change. Piecemeal approaches cannot solve the problems confronting freshwater ecosystems. Scientific definitions of the requirements to protect and maintain aquatic ecosystems are necessary but insufficient for establishing the appropriate distribution between societal and ecosystem water needs. For scientific knowledge to be implemented science must be connected to a political agenda for sustainable development. We offer these recommendations as a beginning to redress how water is viewed and managed in the United States: (1) Frame national and regional water management policies to explicitly incorporate freshwater ecosystem needs, particularly those related to naturally variable flow regimes and to the linking of water quality with water quantity; (2) Define water resources to include watersheds, so that freshwaters are viewed within a landscape, or systems context; (3) Increase communication and education across disciplines, especially among engineers, hydrologists, economists, and ecologists to facilitate an integrated view of freshwater resources; (4) Increase restoration efforts, using well-grounded ecological principles as guidelines; (5) Maintain and protect the remaining freshwater ecosystems that have high integrity; and (6) Recognize the dependence of human society on naturally functioning ecosystems.

Ecological Applications↗

USGS2000

Interim report on the scientific investigations in the Animas River watershed, Colorado to facilitate remediation decisions by the U.S. Bureau of Land Management and the U.S. Forest Service, March 29, 2000 meeting, Denver, Colo.

INTRODUCTION The joint U.S. Department of the Interior and U.S. Department of Agriculture Abandoned Mine Lands Initiative (AMLI) was developed as a collaborative effort between the Federal land management agencies (FLMA, that is the U.S. Bureau of Land Management and the U.S. Forest Service) and the U.S. Geological Survey (USGS) in 1996. The stated goal of the AML Initiative was to develop a strategy for gathering and communicating the scientific information needed to develop effective and cost-efficient remediation of abandoned mines within the framework of a watershed. Four primary objectives of the AMLI are to: 1. Provide the scientific information needed (in the short-term) by the FLMAs to make decisions related to the design and implementation of cleanup actions, 2. Develop a multi-disciplined, multi-division approach that integrates geologic, hydrologic, geochemical and ecological information into a knowledge base for sound decision making, 3. Transfer technologies developed within the scientific programs of the USGS to the field and demonstrate their suitability to solve real, practical problems, and 4. Establish working relationships among involved members of land management and regulatory agencies within the framework of a watershed approach to the cleanup of abandoned mines. Long-term process-based research, including development of analytical tools, is recognized as being critical to the long-term success in remediating watersheds impacted by historical mining activities (AML 5-year plan, http://amli.usgs.gov/amli). In a meeting of Federal agencies (U.S. Bureau of Land Management [BLM], U.S. Bureau of Reclamation [BOR], U.S. National Park Service [NPS], U.S. Forest Service [USFS], the U.S. Environmental Protection Agency [EPA], the U.S. Fish and Wildlife Service [F&WS]), and State agencies (Colorado Division of Public Health and Environment, Colorado Division of Mines and Geology), several watersheds were examined within the state whose water quality was presumed to be impacted by historical mining activities. The Animas River watershed (fig. 1) was selected by the State and Federal agencies as one of two watersheds in the U.S. to be studied in detail by the USGS in the AML Initiative. Beginning in October 1997, each of the four Divisions of the USGS (Water Resources, Geologic, Biological Resources, and National Mapping) initiated a collaborative integrated science study of the watershed. Funds were provided from USGS base funding to each of the four Divisions in response to the priorities set by Congressional action and within the flexibility provided by the budgetary framework funding individual research programs. The AML Initiative provides for a five-year focused scientific effort in the two watersheds with final synthesis of the scientific results from each to be published in 2001. Publications are released on the AML web site on a regular basis (http://amli.usgs.gov/amli). On March 29, 2000, the USGS hosted a meeting for the BLM and USFS to discuss remediation options that were under consideration for the summer of 2000. The purpose of this report is to provide an overview of the scientific rational provided by the USGS to meet objective one above, and to summarize our preliminary interpretations of our data. Additional information from sites on private lands have been collected by the State of Colorado, EPA, and the ARSG. Unfortunately, these data have not been fully supplied to the USGS so our conclusions are based only upon our data. These interpretations provide science-based constraints on possible remediation options to be considered by the FLMA, the State, and local property owners in the Animas River watershed. The report is presented in outline format to facilitate discussion of remediation options at the March 29, 2000 meeting. Not all historical mining sites within the watershed are on public lands. This should not be construed to be a final report of the USGS

Denver↗

USGS2007

Strategic Plan for the North American Breeding Bird Survey: 2006-2010

Executive Summary The mission of the North American Breeding Bird Survey (BBS) is to provide scientifically credible measures of the status and trends of North American bird populations at continental and regional scales to inform biologically sound conservation and management actions. Determining population trends, relative abundance, and distributions of North American avifauna is critical for identifying conservation priorities, determining appropriate conservation actions, and evaluating those actions. The BBS program, jointly coordinated by the U.S. Geological Survey and Environment Canada’s Canadian Wildlife Service, provides the U.S. and Canadian Federal governments, state and provincial agencies, other conservation practitioners, and the general public with science-based avian population trend estimates and other information for regional and national species’ population assessments. Despite the demonstrated value of the BBS for furthering avian conservation across North America, its importance is often underappreciated, and it is underfunded compared with many other government-supported programs that report on status of the environment. Today, BBS resources, adjusted for inflation, are below the amount allocated in the 1970s and are still only sufficient to support two biologists. Yet the number of routes, participants, data, and data requests has quadrupled. Data and information management and delivery requirements and security concerns, non-existent in 1966, impose further demands on BBS resources. In addition, the Mexican expansion of the BBS offers new hope for a truly continental approach to avian conservation, but also brings additional challenges. Meeting the goals of this plan will take cooperation among myriad stakeholders; yet, even with collaboration, most objectives of this plan will be unattainable if BBS program support is not increased. The BBS developed this strategic plan to help set priorities and identify resources required for the program to continue to meet the evolving needs of the conservation community for information on bird population change. By setting clear goals, strategies, and measures of success, this plan provides a cohesive framework and vision for maintenance and development of the BBS. The plan identifies two major goals for the BBS, with a number of strategies and objectives to achieve these goals. Over the next 5 years, progress made in addressing each long-term goal and its associated 5-year strategies and objectives will gage the plan’s success. Specific actions, projected outcomes, and measures of success related to accomplishing these are outlined in Table 1, with a timeline in Table 2. The two main goals for the program, with a summary of the strategies to achieve them, are: Goal 1: Collect scientifically credible measures of the status and trends of North American bird populations at continental and regional scales. The North American Breeding Bird Survey will continue to support North American natural resource conservation through the collection of scientifically credible measures of the status and trends of continental bird populations. While doing this, the BBS will work to improve the science behind the program to better meet its mission and the changing needs of the avian conservation community. In partnership with collaborators, the BBS will address detection probability bias and habitat bias, improve analytical methods, and more fully assess and account for observer quality. Moreover, the BBS will improve the quality and breadth of avian population data through strategic increases in route density and the establishment of a Mexican BBS program. Goal 2: Ensure BBS data and analytical results are widely available and easily accessible for use by the avian conservation and management communities. At the heart of the BBS lies a four-million-record database containing more than 40 years of data on more than 600 bird species. These data are of no value if not well maintained, appropriately analyzed, and widely and easily accessible. The USGS has greatly improved data management and accessibility in recent years. Trend estimates were first made available via the Internet in the mid-1990s, followed closely by the raw data with baseline metadata and standard operating procedures. Nevertheless, numerous enhancements to data management and the usability of BBS results will greatly improve the ability of the BBS to serve avian conservation goals. The BBS needs to ensure that BBS data and results presented on the web site use the best data-management practices and statistical methods, with adequate documentation for users to understand them and any differences between different trend estimates. Moreover, the BBS needs to increase communication with BBS partners and stakeholders to ensure that it continues to meet the avian population status and trends needs of the conservation community and to encourage the development of new products. Working with collaborators, the BBS will develop tools for integrating environmental parameters like habitat change into the analyses, and for integrating BBS data with other avian survey results. In addition, the BBS will continue to improve data and database management through the incorporation of additional data and data fields, such as georeferenced stop locations and more complete metadata for the raw data and results, thus enhancing the uses that can be made of the data.

Circular↗

USGS2007

Surficial sediment character of the New York-New Jersey offshore continental shelf region: A GIS compilation

Broad continental shelf regions such as the New York Bight are the product of a complex geologic history and dynamic oceanographic processes, dominated by the Holocene marine transgression (>100 m sea-level rise) following the end of the last Pleistocene ice advance ~ 20,000 years ago. The area of the U.S. Exclusive Economic Zone (U.S. EEZ) territory, extending 200 nautical miles seaward from the coast, is larger than the continental U.S. and contains submerged landforms that provide a variety of natural functions and societal benefits, such as: critical habitats for fisheries, ship navigation and homeland security, and engineering activities (i.e. oil and gas platforms, pipeline and cable routes, potential wind-energy-generation sites). Some parts of the continental margins, particularly inner-continental shelf regions, also contain unconsolidated hard-mineral deposits such as sand and gravel that are regarded as potential aggregate resources to meet or augment needs not met by onshore deposits (Williams, 1992). The present distribution of surficial sediment off the northeastern United States is shaped from the deposits left by the last glaciation and reflects the cumulative effects of sediment erosion, transport, sorting, and deposition by storm and tidal processes during the Holocene rise in sea level. As a result, the sediments on the sea floor represent both an historical record of former conditions and a guide to possible future sedimentary environments. The U.S. Geological Survey (USGS) through the Coastal and Marine Geology Program, in cooperation with the University of Colorado and other partners, has compiled extant sediment character and textural data as well as other geologic information on the sea floor from all regions around the U.S. into the usSEABED data system (Reid and others, 2005; Buczkowski and others, 2006; Reid and others, 2006). The usSEABED system, which contains information on sediment grain size and lithology for more than 340,500 stations within the U.S. EEZ. has been developed and populated with data as part of the USGS Marine Aggregate Resources and Processes and the National Benthic Habitats projects in order to provide the base-line data needed to update the current maps of offshore surficial geologic character and sediment distribution. The maps are also used to characterize benthic sea floor environments important for marine ecosystems. U.S. Geological Survey, Data Series 118 (Reid and others, 2005), of the usSEABED data release series, represents the combined efforts of the USGS and several other government agencies to provide a unified resource for accessing and preserving records of U.S. east coast sea floor geologic information and sediment texture data. For this present report, we have chosen to focus on the New York-New Jersey region, an area that has been intensely studied by the USGS for many years to address many complex issues. This report illustrates the uses of the usSEABED database for GIS applications, while offering additional insight into the resources and data available from the USGS and its collaborative institutions. This report is based on data contained in U.S. Geological Survey Data Series 118 (Reid and others, 2005) and shows an assortment of example GIS products that are possible using usSEABED. All data are intended to be GIS-ready and should not require any additional cleanup, formatting, or renaming of fields in order to use the data in a Geographic Information System. This project employs the Environmental Systems Research Institute's (ESRI) ArcView™ software. Many of these maps were made as part of the ongoing USGS study to assess marine aggregate resources offshore New York and New Jersey, but these maps can serve many other purposes. The marine science community, educators, students and others are encouraged to use these data to generate GIS products for their own purposes. The objectives of the Marine Aggregate Resources and Processes project are to produce a series of new geologic maps and reports of the sea floor that will provide scientific insights into the character and geologic development of U.S. continental margins and to use these maps and information to assess the potential availability of offshore sand and gravel resources. The mapping and aggregate resource assessments are being conducted on a national scale using the usSEABED data base as described in Williams and others (2003). Potential uses for these data include: (1) defining the geological variability of the sea floor in relation to benthic habitat diversity; (2) improving our understanding of the processes that control the distribution and transport of bottom sediments and benthic habitats; (3) locating aggregate resources for beach nourishment and industrial applications; and (4) providing a detailed geospatial framework for future marine science research, monitoring, and management activities. The initial assessments are in progress for the New York Bight and Louisiana offshore areas.

New Jersey, New York↗

USGS2013

Geomorphic and vegetation processes of the Willamette River floodplain, Oregon: current understanding and unanswered science questions

This report summarizes the current understanding of floodplain processes and landforms for the Willamette River and its major tributaries. The area of focus encompasses the main stem Willamette River above Newberg and the portions of the Coast Fork Willamette, Middle Fork Willamette, McKenzie, and North, South and main stem Santiam Rivers downstream of U.S. Army Corps of Engineers dams. These reaches constitute a large portion of the alluvial, salmon-bearing rivers in the Willamette Basin. The geomorphic, or historical, floodplain of these rivers has two zones - the active channel where coarse sediment is mobilized and transported during annual flooding and overbank areas where fine sediment is deposited during higher magnitude floods. Historically, characteristics of the rivers and geomorphic floodplain (including longitudinal patterns in channel complexity and the abundance of side channels, islands and gravel bars) were controlled by the interactions between floods and the transport of coarse sediment and large wood. Local channel responses to these interactions were then shaped by geologic features like bedrock outcrops and variations in channel slope. Over the last 150 years, floods and the transport of coarse sediment and large wood have been substantially reduced in the basin. With dam regulation, nearly all peak flows are now confined to the main channels. Large floods (greater than 10-year recurrence interval prior to basinwide flow regulation) have been largely eliminated. Also, the magnitude and frequency of small floods (events that formerly recurred every 2–10 years) have decreased substantially. The large dams trap an estimated 50–60 percent of bed-material sediment—the building block of active channel habitats—that historically entered the Willamette River. They also trap more than 80 percent of the estimated bed material in the lower South Santiam River and Middle and Coast Forks of the Willamette River. Downstream, revetments further decrease bed-material supply by an unknown amount because they limit bank erosion and entrainment of stored sediment. The rivers, geomorphic floodplain, and vegetation within the study area have changed noticeably in response to the alterations in floods and coarse sediment and wood transport. Widespread decreases have occurred in the rates of meander migration and avulsions and the number and diversity of landforms such as gravel bars, islands, and side channels. Dynamic and, in some cases, multi-thread river segments have become stable, single-thread channels. Preliminary observations suggest that forest area has increased within the active channel, further reducing the area of unvegetated gravel bars. Alterations to floods and sediment transport and ongoing channel, floodplain, and vegetation responses result in a modern Willamette River Basin. Here, the floodplain influenced by the modern flow and sediment regimes, or the functional floodplain, is narrower and inset with the broader and older geomorphic floodplain. The functional floodplain is flanked by higher elevation relict floodplain features that are no longer inundated by modern floods. The corridor of present- day active channel surfaces is narrower, enabling riparian vegetation to establish on formerly active gravel bar surfaces. The modern Willamette River Basin with its fundamental changes in the flood, sediment transport, and large wood regimes has implications for future habitat conditions. System-wide future trends probably include narrower floodplains and a lower diversity of landforms and habitats along the Willamette River and its major tributaries compared to historical patterns and today. Furthermore, specific conditions and future trends will probably vary between geologically stable, anthropogenically stable, and dynamic reaches. The middle and lower segments of the Willamette River are geologically stable, whereas the South Santiam and Middle Fork Willamette Rivers were historically dynamic, but are now largely stable in response to flow regulation and revetment construction. The upper Willamette and North Santiam Rivers retain some dynamic characteristics, and provide the greatest diversity of aquatic and riparian habitats under the current flow and sediment regime. The McKenzie River has some areas that are more dynamic, whereas other sections are stable due to geology or revetments. Historical reductions in channel dynamism also have implications for ongoing and future recruitment and succession of floodplain forests. For instance, the succession of native plants like black cottonwood is currently limited by (1) fewer low-elevation gravel bars for stand initiation; (2) altered streamflow during seed release, germination, and stand initiation; (3) competition from introduced plant species; and (4) frequent erosion of young vegetation in some locations because scouring flows are concentrated within a narrow channel corridor. Despite past alterations, the Willamette River Basin has many of the physical and ecological building blocks necessary for highly functioning rivers. Management strategies, including environmental flow programs, river and floodplain restoration, revetment modifications, and reclamation of gravel mines, are underway to mitigate some historical changes. However, there are some substantial gaps in the scientific understanding of the modern Willamette basin that is needed to efficiently integrate these blocks and to establish realistic objectives for future conditions. Unanswered questions include: 1. What is the distribution and diversity of landforms and habitats along the Willamette River and its tributaries? 2. What is the extent of today’s functional floodplain—the part of the river corridor actively formed and modified by fluvial processes? 3. How are landforms and habitats in the Willamette River Basin created and sustained by present-day flow and sediment conditions? 4. How is the succession of native floodplain vegetation shaped by present-day flow and sediment conditions? Answering these questions will produce baseline data on the current distributions of landforms and habitats (question 1), the extent of the functional floodplain (question 2), and the effects of modern flow and sediment regimes on future floodplain landforms, habitats, and vegetation succession (questions 3 and 4). Addressing questions 1 and 2 is a logical next step because they underlie questions 3 and 4. Addressing these four questions would better characterize the modern Willamette Basin and help in implementing and setting realistic targets for ongoing management strategies, demonstrating their effectiveness at the site and basin scales, and anticipating future trends and conditions.

Oregon↗

USGS1999

Fishes of Missouri River, chute, and flood plain habitats: Chapter 4 in Initial biotic survey of Lisbon Bottom, Big Muddy National Fish and Wildlife Refuge

The Lisbon Bottom Unit of the Big Muddy National Fish and Wildlife Refuge (Refuge) is approximately 2,200 acres and is the first complete unit of the Refuge. Primary objectives of the Refuge are to create and restore diverse riverine aquatic habitats and reconnect the Missouri River to its flood plain where feasible. Management seeks to accomplish these objectives by encouraging natural processes of erosion, deposition, and succession to the greatest extent possible. One of the most salient aquatic features of the Lisbon Bottom Unit is a newly created 2-mile-long free-flowing chute, or side channel (Fig. 1). This chute began forming as a levee breech scour hole during the Great Flood of 1993. The chute continued to develop during the 1995 flood and finally cut through to a flowing side channel during the 1996 flood. Extensive erosion and bank sluffing continued during 1997 due to sustained high flows that occurred throughout most of the year. The chute has progressively become wider and deeper with a developing meander pattern and channel bars have begun to form. Lisbon Bottom also contains several seasonal and permanent wetlands and is subject to periodic flooding at high Missouri River stages. Eight studies have been completed or are ongoing to evaluate Missouri River fishes associated with various habitat components of Lisbon Bottom and adjacent Missouri River reaches (Table 1). Several are part of much larger investigations to evaluate fish use of flood-created habitat features, basinwide fish assessment, and endangered or candidate species concerns. At the Lisbon Bottom Unit or in the Missouri River adjacent to the unit 54 fish species were collected (Table 2). Eight of these species have either a protected status under State or Federal laws or biologists consider them to potentially qualify for protected status. The status of the following fish is listed in Table 2: pallid sturgeon x shovelnose sturgeon hybrid, paddlefish, northern pike, sturgeon chub, sicklefin chub, ghost shiner, western silvery minnow, plains minnow, and blue sucker. Equally important to note are fish species that were not collected. The flathead chub, currently listed as State endangered and proposed for Federal listing, were not collected in any of the studies. Common fish species, collected in all seven sampling studies, included gizzard shad, common carp, river carpsucker, and freshwater drum. Paddlefish, skipjack herring, silver carp, white sucker, redfin shiner, western silvery minnow, bullhead minnow, and black bullhead were each collected in only one of the seven studies. Pflieger (1971) developed a guild system for the fishes of Missouri based on distribution patterns and centers of abundance. Fish were assigned to one of four primary faunal groups: Ozark, Big River, Lowland, and Prairie. Two secondary groups (Ozark-prairie and Ozark-lowland) were defined for species equally abundant and distributed in two of the primary areas. Two Ozark-prairie species, shorthead redhorse and white sucker, were collected on or near the Lisbon Bottom Unit. Big River species are found primarily in the Missouri and Mississippi Rivers. The environmental factors controlling fish distribution in these rivers appear to be substrate, current velocity, and turbidity. On or near the Lisbon Bottom Unit 18 Big River species were collected (Table 2). Lowland species are intolerant of siltation and high turbidity. They inhabit standing or slow-moving water with sand, fine gravel, and organic debris substrates. Two Lowland species, bullhead minnow and mosquitofish, were collected in connected scours on the Lisbon Bottom Unit. Prairie species have broader ecological tolerances than the Ozark and Lowland species. They are largely absent in high gradient streams and cool, clear waters. Prairie species make up a significant proportion of Missouri and Mississippi River fishes. Seven Prairie species were collected on or near the Lisbon Bottom Unit (Table 2). The last group, Wide-ranging, was defined as the species more widespread than the other faunal groups with broader environmental tolerances. Most Wide-ranging species occur at least occasionally in all sections of the state. Nineteen Wide-ranging species were collected on or near the Lisbon Bottom Unit (Table 2). Kubisiak (1997) found that isolated scours in the Lower Missouri River were dominated by Wide-ranging species. Connected scours also held Wideranging species but they contained Prairie species and were dominated by Big River species. Faunal group diversity and species richness were compared between isolated (Study l) and connected (Studies 4, 5, 7, and 8) scours of the Lisbon Bottom Unit. Species richness was similar with 22 species collected in isolated scours and an average of 24.8 species collected in connected scours. Isolated scour fish catches were dominated by Wide-ranging fish (59%) with 14% Big River fishes and 14% Prairie fishes. Connected scours had a larger percentage of Big River fish (32%) and fewer Wide-ranging (36%) and Prairie (13%) species than the isolated scours. In the combined studies, Wide-ranging fish dominated the connected scours. A similar comparison was made of fish from chute habitats and the Missouri River. Chute habitats include the Lisbon Bottom Chute, the chute between the right bank and island located at river mile 219, and a shallow channel running between a large sandbar complex and the channel border adjacent to Lisbon Bottom. Species richness in the chutes (35 species) was greater than that of the adjacent river (23 species). Big River species (40%) dominated the chute samples, followed by Wide-ranging at 31% Cand Prairie Cut 14%. The river samples contained equal numbers of Wide-ranging species (35%) and Big River species (35%) with 17% Prairie species. Differences in fish guild diversity and species richness may be due to numerous factors including sampling effort and sampling season. River samples were collected only in Study 3 in October; chute samples were collected in July, August, and October. Fish may have been using the chute in July and August to spawn, feed, or escape high river levels. The Lisbon Bottom Chute is a truly unique feature of the Lower Missouri River. It is the first naturally created side channel to develop since the U.S. Army Corps of Engineers tamed the river. The Corps eliminated 89% of the islands in the Missouri River between 1879 and 1954 (Funk and Robinson 1974). The chutes between the islands and the shore were shallower with less current than the main channel. These areas provided diversity to the Missouri River fish habitat, serving as nursery and feeding areas. The Lisbon Bottom Unit of the Big Muddy National Fish and Wildlife Refuge will continue to be studied in an effort to understand the complex role these areas play in river systems.

Missouri↗

USGS2022

Fishway Entrance Palisade

This technical report summarizes the work that was conducted by the University of Massachusetts Amherst and the United States Geological Survey (USGS), along with other project partners, on the Fishway Entrance Palisade (EP), a projected funded through the Department of Energy’s (DOE) funding opportunity titled ‘Innovative Solutions for Fish Passage at Hydropower Dams’ (DE‐FOA‐0001662). The period of performance ranged from September 1, 2018 through September 30, 2021. The EP is a novel fish passage engineering technology designed to provide more favorable entry conditions for fish and to reduce costs relative to conventional fishway auxiliary water systems (AWS). The EP project has four primary components. First, the Northeast United States Auxiliary Water Systems Database was created (Northeast Fishway Auxiliary Water Systems Database Section). The database, developed with material provided by the U.S. Fish and Wildlife Service, contains information on fishway type (e.g., lift, Denil, pool and weir) and Auxiliary Water System (AWS) details (e.g., water conveyance method, diffuser type) for 60 hydroelectric sites in the region. Findings indicate that nearly 4 out of every 10 fishway in the region is a fish lift and approximately 1 out of every 4 is a Denil ladder. The remainder are a mix of vertical slot fishways, pool and weirs, and Ice Harbor fishways. Furthermore, over half of all AWS systems use floor diffusers to discharge the auxiliary (or attraction) water into the entrance of a fishway, whereas only 14% use wall diffusers. Second, limited experiments on a conventional AWS with live, actively migrating fish were conducted at the USGS Easter Ecological Science Center (EESC) S.O. Conte Research Laboratory (Conventional Auxiliary Water System Experiments Section). This study determined how water velocity through a wall diffuser, without turning vanes or timber baffles to distribute the flow, affects the behavior and passage of adult American shad, a conservative surrogate species for migratory fish on the East Coast. Two gross diffuser velocity treatments were examined, 0.5 ft/s and 1.0 ft/s. These wall diffuser velocities represented current (0.5 ft/s) and past (1.0 ft/s) design criteria guidelines set forth by the USFWS North Atlantic-Appalachian Region (Rojas 2020; USFWS 2019). Six trials with a total of 151 American Shad were conducted in June of 2019 for the two treatments. No differences in American shad passage efficiency were discovered between the two treatments, while approximately 3 in every 4 attempts were successful at passing the diffuser. While these results may appear to indicate that the generally accepted gross wall diffuser velocity criteria for American shad of 0.5 ft/s could be safely increased to 1.0 ft/s, further analysis is warranted. Furthermore, it is unknown how other migratory and resident fish species that traverse these structures would be impacted by such a change. Studying the wall diffuser hydraulics led to an important AWS observation. Without turning vanes or timber baffles in this study, doubling the diffuser area was insufficient at producing the type of flow field change one may expect by halving the gross diffuser velocity. Instead, the flow fields throughout each treatments study area were similar, which led to similar results in shad performance. This not only highlights the importance of installing flow guidance devices like turning vanes, but also to the importance of properly maintaining them, which can be costly. Third, more expansive experiments on the novel EP were conducted in the spring of 2019 and 2021 (Fishway Entrance Palisade Experiments). The goal of this study was to determine how adult American shad responded to a variety of conditions at a full-scale EP. A total of six treatments were examined by changing the average auxiliary channel velocity between 1.0 and 5.0 ft/s in intervals of 1.0 ft/s and by inserting/removing an entrance gate at the opening of the fishway. Thirty trials with a total of 1,273 shad were conducted over the two years. In all treatments, at least ~7 out of every 10 fish successfully passed the EP diffuser and swam into the entrance channel within the 3.5-hour long trial, highlighting the general effectiveness of the novel AWS technology. In both study years, lower velocities through the EP diffuser led to increased shad performance, though performance peaked for the 2 ft/s velocity treatment. This treatment condition represents an approximate six-fold increase in gross diffuser velocity relative to conventional auxiliary water systems, which in turn presents opportunities for cost savings (e.g., reduction in diffuser size). Shad performance, in general, was worse in 2019 than in 2021, potentially due to the different run timing when our trials were conducted (2019 trials occurred near the end of the migration season, unlike in 2021). Treatments in 2019 had approximately a 20% reduction in entrance efficiency by the trial end, including a 16.7% drop for the 3 ft/s velocity treatment in 2019 relative to 2021 (the only carryover treatment between years). Lastly, adding an entrance gate caused a significant delay to entry. The time to 25% entry raised ~20 minutes from the near instantaneous 25% entry that was reported for the other treatments conducted in the same year (2021). Though by the end of the 3.5-hour trial, the overall entrance efficiency nearly matched those of the other 2021 treatments. The fourth and final component of the EP project was an economic analysis that focused on the cost of attraction and environmental flows (Modeling Power Generation Losses Due to Environmental and Fish Passage Attraction Flows at a Run-Of-River Hydroelectric Operation in the Northeast). The study assessed the economic impact of meeting environmental flow requirements at a representative hydroelectric facility and fish lift in the Northeast. An initial finding of the study was that there is a paucity of published data on the costs of meeting attraction and environmental flows. This is due, in part, to the proprietary nature of this data. To explore the costs associated with these flows, three types of environmental flows were assessed: upstream fishway attraction flows, downstream fishway attraction flows, and habitat maintenance minimum flows. A physics-based model was developed and calibrated with three years of hourly generation and flow data as inputs. Gage flow inputs were adjusted and used to calculate power generated. To address hydrologic variability, the model was executed to simulate 30 years of historical flows. Results indicate that both interannual and seasonal climatic factors impact the costs of meeting environmental flow requirements. Generation potential is most strongly curtailed during dry years in terms of maximizing the capacity factor (the percent of time a plant generates at capacity). Dry years, and especially dry summers, have the most significant costs associated with mitigation flows. Of the three types of flows, habitat flows are most costly in terms of power production, followed by upstream attraction flows. Downstream attraction flows are least costly. This finding is the likely result of differences in both flow rates and duration of the seasonal requirement for each flow. Overall, environmental flows represented a 2-12% loss in annual generation, but losses during a dry summer can reach over 20%.

Final Technical Report↗