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USGS2023

Reproducibility starts at the source: R, Python, and Julia Packages for retrieving USGS hydrologic data

Much of modern science takes place in a computational environment, and, increasingly, that environment is programmed using R, Python, or Julia. Furthermore, most scientific data now live on the cloud, so the first step in many workflows is to query a cloud database and load the response into a computational environment for further analysis. Thus, tools that facilitate programmatic data retrieval represent a critical component in reproducible scientific workflows. Earth science is no different in this regard. To fulfill that basic need, we developed R, Python, and Julia packages providing programmatic access to the U.S. Geological Survey’s National Water Information System database and the multi-agency Water Quality Portal. Together, these packages create a common interface for retrieving hydrologic data in the Jupyter ecosystem, which is widely used in water research, operations, and teaching. Source code, documentation, and tutorials for the packages are available on GitHub. Users can go there to learn, raise issues, or contribute improvements within a single platform, which helps foster better engagement and collaboration between data providers and their users.

Water↗

USGS2015

Influence of ecological factors on prevalence of meningeal worm ( Parelaphostrongylus tenuis infection in South Dakota, USA

The meningeal worm ( Parelaphostrongylus tenuis ) is a nematode parasite that commonly infects white-tailed deer ( Odocoileus virginianus ; WTD) throughout the deciduous forest biome and deciduous-coniferous ecotone of eastern and central North America; the species is not known to occur west of the grassland biome of central North America. We used county-specific prevalence data to evaluate potential effects of landscape and climatologic factors on the spatial distribution of meningeal worm infection in South Dakota, US. Probability of infection increased 4-fold between eastern and western South Dakota and 1.3-fold for each 1-cm increase in summer precipitation. Sixty-three percent of WTD had only a single worm in the cranium. Expansion of meningeal worm infection across western South Dakota may be inherently low due to the combined effects of arid climate and potential attributes of the Missouri River that limit regional movements by infected WTD. Use of landscape genetic analyses to identify potential relationships between landscape features and population genetic structure of infected deer and parasites may contribute to a greater understanding of regional heterogeneity in meningeal worm infection rates across South Dakota, particularly in counties adjacent to the Missouri River. Future research evaluating heterogeneity in prevalence and intensity of infection between fawn and yearling deer, and the potential role of yearling male deer as dispersal agents of meningeal worms across the Missouri River, also is warranted.

South Dakota↗

USGS1982

Liming of acidified waters: issues and research - a report of the International Liming Workshop

Acidic deposition is a problem of significant national and international concern. It is strongly suspected that acidic deposition has adversely affected aquatic resources in Scandinavia and North America. While substantial resources are being devoted to understanding the causative factors associated with surface water acidification, much less research is being conducted on mitigative strategies. Mitigative techniques involving liming may be useful for short-term protection of specific component of aquatic communities or for renovation of seriously impacted aquatic ecosystems. The selection of effective liming strategies is based on an integrated understanding of the following key factors: biological systems, water chemistry, sediment chemistry, hydrology, and watershed characteristics, effectiveness of neutralizing materials, and application techniques. Research in Scandinavia, Canada, and the U.S. has led to a partial understanding of some of the key factors for successful neutralization of surface waters (Bengtsson, 1982; Fraser and Britt, 1982). However, conflicting results of liming operations and experiments have been reported. (Fraser et al., 1982; Fraser and Britt, 1982; Sverdrup and Bjerle, 1982). Additional research is required to improve the ability of scientists and resource managers to select effective liming strategies. An International Liming workshop was convened during 19-25 September 1982 at the University of Washington's Friday Harbor Laboratories. The major objective of this workshop were: - To identify the most critical deficiencies in the scientific understanding of liming techniques and their long-term consequences. - To develop and document a research strategy to address information deficiencies that are pertinent to the protection or renovation of acidic surface waters in the United States. The participants who contributed to this workshop are listed in Table 1.

FWS/OBS↗

USGS2002

Basis and methods of NASA airborne topographic mapper lidar surveys for coastal studies

This paper provides an overview of the basic principles of airborne laser altimetry for surveys of coastal topography, and describes the methods used in the acquisition and processing of NASA Airborne Topographic Mapper (ATM) surveys that cover much of the conterminous US coastline. This form of remote sensing, also known as "topographic lidar", has undergone extremely rapid development during the last two decades, and has the potential to contribute within a wide range of coastal scientific investigations. Various airborne laser surveying (ALS) applications that are relevant to coastal studies are being pursued by researchers in a range of Earth science disciplines. Examples include the mapping of "bald earth" land surfaces below even moderately dense vegetation in studies of geologic framework and hydrology, and determination of the vegetation canopy structure, a key variable in mapping wildlife habitats. ALS has also proven to be an excellent method for the regional mapping of geomorphic change along barrier island beaches and other sandy coasts due to storms or long-term sedimentary processes. Coastal scientists are adopting ALS as a basic method in the study of an array of additional coastal topics. ALS can provide useful information in the analysis of shoreline change, the prediction and assessment of landslides along seacliffs and headlands, examination of subsidence causing coastal land loss, and in predicting storm surge and tsunami inundation.

Journal of Coastal Research↗

USGS2020

Memorial to Jack B. Epstein 1935-2020

Jack Burton Epstein, a career geologist with the U.S. Geological Survey (USGS) passed away in May 2020 at his home in Great Falls, Virginia. His career and contributions to the USGS spanned more than 60 years from his time as a summer field assistant while attending college, through 40 years as a research geologist, and more than 15 years as an emeritus scientist. Jack was born December 27, 1935 in Brooklyn, New York and attended CUNY- Brooklyn College where he received his Bachelor of Science degree in geology in 1956. He earned his Master of Science degree in 1958 from the University of Wyoming, and his doctorate degree in geology in 1970 from The Ohio State University. His master’s thesis was geologic mapping of the Fanny Peak quadrangle, Black Hills of Wyoming and South Dakota, and his Ph. D. dissertation focused on the geology of the Stroudsburg quadrangle and adjacent areas, Pennsylvania and New Jersey.

Geological Society of America Memorials↗

USGS2023

Attributes of Upper Mississippi River System contiguous forest areas

Floodplain forests are important features of river systems as they create habitat for a variety of wildlife species as well as influence water quality by sequestering nutrients. The ecological conditions found within forested areas can vary greatly from place to place, contributing to spatial variability in species diversity, animal use of the floodplain, and other ecological functions. For this reason, it is important for managers and researchers to identify and map existing forest conditions for use in restoration practices or research studies. A number of forest attributes have been identified as useful in predicting the local ecological conditions found within forested areas. For example, attributes related to the size, shape and configuration of forest patches have been linked to susceptibility to invasion by exotic species, animal and plant dispersal patterns, population distributions, and species diversity (Zuidema and others, 1996; Laurance and others, 2001; Weathers and others, 2001; Lindenmayer and Franklin 2002; Harper and others, 2005; Ramaharitra 2006). In floodplain forests, patterns of inundation have been shown to influence local soil conditions as well as plant species composition and diversity (De Jager and others, 2012). Knowing the land-use history of forest areas has also been shown to be important in understanding present day ecological conditions of forested areas (Turner and others, 2004). To support floodplain forest research and management actions on the Upper Mississippi River System (UMRS), we identified contiguous forested areas (i.e., areas of forest cover that were separated from each other by other land or water cover types) in the floodplain and calculated a wide range of attributes that define basic ecosystem conditions within such forested areas. The data allows users to query on a set of attributes (e.g., size, shape, inundation characteristics, etc.) to visualize the distribution of various ecological conditions. In addition, the data allows for future data analyses of relationships among different ecological conditions and other data, such as animal and plant population distributions.

Upper Mississippi River system↗

USGS2015

Organic contaminant transport and fate in the subsurface: evolution of knowledge and understanding

Toxic organic contaminants may enter the subsurface as slightly soluble and volatile nonaqueous phase liquids (NAPLs) or as dissolved solutes resulting in contaminant plumes emanating from the source zone. A large body of research published in Water Resources Research has been devoted to characterizing and understanding processes controlling the transport and fate of these organic contaminants and the effectiveness of natural attenuation, bioremediation, and other remedial technologies. These contributions include studies of NAPL flow, entrapment, and interphase mass transfer that have advanced from the analysis of simple systems with uniform properties and equilibrium contaminant phase partitioning to complex systems with pore-scale and macroscale heterogeneity and rate-limited interphase mass transfer. Understanding of the fate of dissolved organic plumes has advanced from when biodegradation was thought to require oxygen to recognition of the importance of anaerobic biodegradation, multiple redox zones, microbial enzyme kinetics, and mixing of organic contaminants and electron acceptors at plume fringes. Challenges remain in understanding the impacts of physical, chemical, biological, and hydrogeological heterogeneity, pore-scale interactions, and mixing on the fate of organic contaminants. Further effort is needed to successfully incorporate these processes into field-scale predictions of transport and fate. Regulations have greatly reduced the frequency of new point-source contamination problems; however, remediation at many legacy plumes remains challenging. A number of fields of current relevance are benefiting from research advances from point-source contaminant research. These include geologic carbon sequestration, nonpoint-source contamination, aquifer storage and recovery, the fate of contaminants from oil and gas development, and enhanced bioremediation.

Water Resources Research↗

USGS2014

High-resolution geophysical data collected aboard the U.S. Geological Survey research vessel Rafael to supplement existing datasets from Buzzards Bay and Vineyard Sound, Massachusetts

Geophysical and geospatial data were collected in Buzzards Bay, in the shallow-water areas of Vineyard Sound, and in the nearshore areas off the eastern Elizabeth Islands and northern coast of Martha's Vineyard, Massachusetts, on the U.S. Geological Survey research vessel Rafael between 2007 and 2011, in a collaborative effort between the U.S. Geological Survey and the Massachusetts Office of Coastal Zone Management. This report describes results of this collaborative effort, which include mapping the geology of the inner shelf zone of the Elizabeth Islands and the sand shoals of Vineyard Sound and studying geologic processes that contribute to the evolution of this area. Data collected during these surveys include: bathymetry, acoustic backscatter, seismic-reflection profiles, sound velocity profiles, and navigation. The long-term goals of this project are (1) to provide high-resolution geophysical data that will support research on the influence of sea-level change and sediment supply on coastal evolution and (2) to inventory subtidal marine habitats and their distribution within the coastal zone of Massachusetts.

Massachusetts↗

USGS2025

Decision-support modeling and research priorities for establishing baseline conditions for outstandingly remarkable values, Obed Wild and Scenic River, Tennessee

The Obed River is the last undammed river in Tennessee. The Obed Wild and Scenic River is managed by the National Park Service and covers a protected area of the Obed River headwaters (including four contributing tributaries). The Obed Wild and Scenic River supports a unique ecosystem with eight federally listed species. The National Park Service is responsible for preserving the baseline free-flowing condition of the river and associated outstandingly remarkable values (ORVs). Previous studies have been mostly project-based with differing methods, thus complicating efforts to quantify long-term changes in environmental conditions. This report presents a science plan summarizing (1) ORV conditions, (2) recent results of a decision-support hydrologic model for OBRI, and (3) possible future research priorities. The decision-support model was created to model streamflow conditions and changes in the ORVs since park establishment in 1976 and during three additional time periods. Established baseline conditions could help with management of ORVs not dependent on streamflow.

Tennessee↗

USGS2016

Observed and simulated hydrologic response for a first-order catchment during extreme rainfall 3 years after wildfire disturbance

Hydrologic response to extreme rainfall in disturbed landscapes is poorly understood because of the paucity of measurements. A unique opportunity presented itself when extreme rainfall in September 2013 fell on a headwater catchment (i.e., <1 ha) in Colorado, USA that had previously been burned by a wildfire in 2010. We compared measurements of soil-hydraulic properties, soil saturation from subsurface sensors, and estimated peak runoff during the extreme rainfall with numerical simulations of runoff generation and subsurface hydrologic response during this event. The simulations were used to explore differences in runoff generation between the wildfire-affected headwater catchment, a simulated unburned case, and for uniform versus spatially variable parameterizations of soil-hydraulic properties that affect infiltration and runoff generation in burned landscapes. Despite 3 years of elapsed time since the 2010 wildfire, observations and simulations pointed to substantial surface runoff generation in the wildfire-affected headwater catchment by the infiltration-excess mechanism while no surface runoff was generated in the unburned case. The surface runoff generation was the result of incomplete recovery of soil-hydraulic properties in the burned area, suggesting recovery takes longer than 3 years. Moreover, spatially variable soil-hydraulic property parameterizations produced longer duration but lower peak-flow infiltration-excess runoff, compared to uniform parameterization, which may have important hillslope sediment export and geomorphologic implications during long duration, extreme rainfall. The majority of the simulated surface runoff in the spatially variable cases came from connected near-channel contributing areas, which was a substantially smaller contributing area than the uniform simulations.

Water Resources Research↗

USGS2013

The contribution of cold winter temperatures to the 2003 alewife population collapse in Lake Huron

The Lake Huron ecosystem has recently undergone dramatic changes. As part of those changes, the once highly abundant non-native alewife Alosa pseudoharengus population crashed in 2003 and has yet to recover. The purpose of this study was to evaluate whether temperature played a role in the population crash, because historically alewife have been subject to die-off events in response to cold temperatures in other lakes. Long-term climate data (1973–2009) showed that the winter of 2002–2003 exhibited the largest drop in degree days relative to the previous year, had the most extensive average March ice coverage, and was among the coldest years on record. However, since 2003, winter temperatures have not been overly cold, and air temperature has shown an increasing trend. Also, the relationship between temperature and alewife abundance between 1975 and 2006 was non-significant. Therefore, although we found evidence that cold winter temperatures contributed to the abrupt decline of alewife in 2003, they could not explain why the population failed to recover as it had after previous cold winters. Historically, Chinook salmon abundance contributed to long-term trends in alewife abundance, however, we found predation by Chinook to play a lesser role on the 2003 alewife collapse. In the absence of direct estimates of food availability, analyses of alewife length data suggest that a declining prey base altered the ecosystem conditions for alewife, possibly contributing to their collapse and lack of recovery.

Journal of Great Lakes Research↗

USGS1981

The Earth Resources Observation Systems data center's training technical assistance, and applications research activities

The Earth Resources Observation Systems (EROS) Data Center (EDO, administered by the U.S. Geological Survey, U.S. Department of the Interior, provides remotely sensed data to the user community and offers a variety of professional services to further the understanding and use of remote sensing technology. EDC reproduces and sells photographic and electronic copies of satellite images of areas throughout the world. Other products include aerial photographs collected by 16 organizations, including the U.S. Geological Survey and the National Aeronautics and Space Administration. Primary users of the remotely sensed data are Federal, State, and municipal government agencies, universities, foreign nations, and private industries. The professional services available at EDC are primarily directed at integrating satellite and aircraft remote sensing technology into the programs of the Department of the Interior and its cooperators. This is accomplished through formal training workshops, user assistance, cooperative demonstration projects, and access to equipment and capabilities in an advanced data analysis laboratory. In addition, other Federal agencies, State and local governments, universities, and the general public can get assistance from the EDC Staff. Since 1973, EDC has contributed to the accelerating growth in development and operational use of remotely sensed data for land resource problems through its role as educator and by conducting basic and applied remote sensing applications research. As remote sensing technology continues to evolve, EDC will continue to respond to the increasing demand for timely information on remote sensing applications. Questions most often asked about EDC's research and training programs include: Who may attend an EDC remote sensing training course? Specifically, what is taught? Who may cooperate with EDC on remote sensing projects? Are interpretation services provided on a service basis? This report attempts to define the goals and objectives of and policies on the following EDC services: Training Program. User Assistance. Data Analysis Laboratory. Cooperative Demonstration Projects. Research Projects.

Open-File Report↗

USGS2020

Biological soil crusts in ecological restoration: Emerging research and perspectives

Drylands encompass over 40% of terrestrial ecosystems and face significant anthropogenic degradation causing a loss of ecosystem integrity, services, and deterioration of social‐ecological systems. To combat this degradation, some dryland restoration efforts have focused on the use of biological soil crusts (biocrusts): complex communities of cyanobacteria, algae, lichens, bryophytes, and other organisms living in association with the top millimeters of soil. Biocrusts are common in many ecosystems and especially drylands. They perform a suite of ecosystem functions: stabilizing soil surfaces to prevent erosion, contributing carbon through photosynthesis, fixing nitrogen, and mediating the hydrological cycle in drylands. Biocrusts have emerged as a potential tool in restoration; developing methods to implement effective biocrust restoration has the potential to return many ecosystem functions and services. Although culture‐based approaches have allowed researchers to learn about the biology, physiology, and cultivation of biocrusts, transferring this knowledge to field implementation has been more challenging. A large amount of research has amassed to improve our understanding of biocrust restoration, leaving us at an opportune time to learn from one another and to join approaches for maximum efficacy. The articles in this special issue improve the state of our current knowledge in biocrust restoration, highlighting efforts to effectively restore biocrusts through a variety of different ecosystems, across scales and utilizing a variety of lab and field methods. This collective work provides a useful resource for the scientific community as well as land managers.

Restoration Ecology↗

USGS1999

Quality of life on the Colorado Plateau: A report to camera-survey collaborators in southeast Utah

What constitutes quality of life among community residents in southeastern and central Utah? What critical areas, elements, and special outdoor places are essential to quality of life in those areas? Answering these questions was the goal of this "quality-of-life" research collaboration in the Colorado Plateau region. Collaborators include the Utah Travel Council (UTC), Canyon Country Partnership, Utah State University, and the county governments of Carbon, Emery, Grand, San Juan, and Wayne counties. In recent years, the goal of the UTC has changed from simply encouraging tourism development to understanding the relationship between tourism and community quality of life. Elements of the new UTC mission include: “make Utah a better place to live by increasing the economic contribution of tourism,” and “protect base resources and maintain quality of life for residents and visitors alike” (Utah Division of Travel Development, 1997). The Social, Economic, and Institutional Analysis Section [SEIAS]/ Midcontinent Ecological Science Center/U.S. Geological Survey conducted this research in late spring through winter of 1997 in an effort to answer those questions posed by the collaboration. This report provides an overview of the research and presents summary results.

Utah↗

USGS2024

Characterizing variability in geochemistry and mineralogy of western US dust sources

Dust events originate from multiple sources in arid and semi-arid regions, making it difficult to quantify source contributions. Dust geochemical/mineralogical composition, if the sources are sufficiently distinct, can be used to quantify the contributions from different sources. To test the viability of using geochemical and mineralogical measurements to separate dust-emitting sites, we used dust samples collected between 2018 and 2020 from ten National Wind Erosion Research Network (NWERN) sites that are representative of western United States (US) dust sources. Dust composition varied seasonally at many of the sites, but within-site variability was smaller than across-site variability, indicating that the geochemical signatures are robust over time. It was not possible to separate all the sites using commonly applied principal component analysis (PCA) and cluster analysis because of overlap in dust geochemistry. However, a linear discriminant analysis (LDA) successfully separated all sites based on their geochemistry, suggesting that LDA may prove useful for separating dust sources that cannot be separated using PCA or other methods. Further, an LDA based on mineralogical data separated most sites using only a limited number of mineral phases that were readily explained by the local geologic setting. Taken together, the geochemical and mineralogical measurements generated distinct signatures of dust emissions across NWERN sites. If expanded to include a broader range of sites across the western US, a library of geochemical and mineralogical data may serve as a basis to track and quantify dust contributions from these sources.

Aeolian Research↗

USGS2021

A U.S.-China EcoPartnership study of disturbed wetland vegetation in West Dongting Lake, China

West Dongting Lake in China is important for human livelihoods and habitat of migratory waterfowl and other wildlife. The waterway re-engineering and agriculture intensification have contributed to changes in hydrology, sediment, and vegetation on the floodplain. This paper describes an EcoPartnership program conducted by the U.S. Geological Survey, Wetland and Aquatic Research Center, and Beijing Forestry University. It focused on the development of a wetland ecosystem network in West Dongting Lake with technical support from the U.S. partner using a number of related studies to examine wetland vegetation dynamics from upstream to downstream along the tributaries. The results of U.S. studies showed that the regeneration potential of species might be altered by changes in climate and local environment, and seed bank depletion by germination may be a major conservation threat in a future with recurring droughts in swamps of the southeastern United States. In the monsoonal wetlands of West Dongting Lake, the soil seed bank could be used as a seed source for revegetation after hydrologic restoration with the introduction of certain foundational species and the removal of poplar plantations. Also, West Dongting Lake is at high ecological risk of mercury pollution. Wetland ecosystem monitoring may allow managers to use the information to predict effects of climate change, water level and flow changes on sedimentation, and to manage for desired vegetation to support waterfowl and ecosystem services. The cooperation of two countries through the EcoPartnership program is now well established and poised for extensive research projects in the future.

West Dongting Lake↗

USGS2019

Review of and recommendations for monitoring contaminants and their effects in the San Francisco Bay−Delta

Legacy and current-use contaminants enter into and accumulate throughout the San Francisco Bay−Delta (Bay−Delta), and are present at concentrations with known effects on species important to this diverse watershed. There remains major uncertainty and a lack of focused research able to address and provide understanding of effects across multiple biological scales, despite previous and ongoing emphasis on the need for it. These needs are challenging specifically because of the established regulatory programs that often monitor on a chemical- by-chemical basis, or in which decisions are grounded in lethality-based endpoints. To best address issues of contaminants in the Bay−Delta, monitoring efforts should consider effects of environmentally relevant mixtures and sub- lethal impacts that can affect ecosystem health. These efforts need to consider the complex environment in the Bay−Delta including variable abiotic (e.g., temperature, salinity) and biotic (e.g., pathogens) factors. This calls for controlled and focused research, and the development of a multi-disciplinary contaminant monitoring and assessment program that provides information across biological scales. Information gained in this manner will contribute toward evaluating parameters that could alleviate ecologically detrimental outcomes. This review is a result of a Special Symposium convened at the University of California−Davis (UCD) on January 31, 2017 to address critical information needed on how contaminants affect the Bay−Delta. The UCD Symposium focused on new tools and approaches for assessing multiple stressor effects to freshwater and estuarine systems. Our approach is similar to the recently proposed framework laid out by the U.S. Environmental Protection Agency (USEPA) that uses weight of evidence to scale toxicological responses to chemical contaminants in a laboratory, and to guide the conservation of priority species and habitats. As such, we also aimed to recommend multiple endpoints that could be used to promote a multi-disciplinary understanding of contaminant risks in Bay−Delta while supporting management needs.

California↗

USGS2007

Understanding Ecosystems and Predicting Ecosystem Change

In 2007, the U.S. Geological Survey (USGS) developed a science strategy outlining the major natural science issues facing the Nation in the next decade. The science strategy consists of six science directions of critical importance, focusing on areas where natural science can make a substantial contribution to the well-being of the Nation and the world. This fact sheet focuses on understanding ecosystems and predicting ecosystem change, and how USGS research can strengthen the Nation with information needed to meet the challenges of the 21st century.

Fact Sheet↗