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USGS2014

Best practices for continuous monitoring of temperature and flow in wadeable streams

The United States Environmental Protection Agency (U.S. EPA) is working with its regional offices, states, tribes, river basin commissions and other entities to establish Regional Monitoring Networks (RMNs) for freshwater wadeable streams. To the extent possible, uninterrupted, biological, temperature and hydrologic data will be collected on an ongoing basis at RMN sites, which are primarily located on smaller, minimally disturbed forested streams. The primary purpose of this document is to provide guidance on how to collect accurate, year-round temperature and hydrologic data at ungaged wadeable stream sites. It addresses questions related to equipment needs, sensor configuration, sensor placement, installation techniques, data retrieval, and data processing. This guidance is intended to increase comparability of continuous temperature and hydrologic data collection at RMN sites and to ensure that the data are of sufficient quality to be used in future analyses. It also addresses challenges posed by year-round deployments. These data will be used for detecting temporal trends; providing information that will allow for a better understanding of relationships between biological, thermal, and hydrologic data; predicting and analyzing climate change impacts and quantifying natural variability.

Report↗
USGS2018

Prioritization framework for ranking riverine ecosystem stressors using example sites from the Tualatin River Basin, Oregon

As human populations increase, so does their influence over the environment. Altered terrain, degraded water quality, and threatened or endangered species are all-too-common consequences of a growing anthropogenic influence on the landscape. To help manage these effects, researchers have developed new ways to characterize current environmental conditions and help resource managers seek solutions to bring affected areas back to their best attainable health. Before an ecosystem can be improved, however, its current level of ecological stress must be determined. Characterizing environmental conditions at many sites across a landscape helps managers understand the range of current conditions and prioritize where they might focus restoration and protection efforts. This report details the development of a prioritization framework to score riverine ecosystem stressors in a watershed based on example sites from the Tualatin River Basin in northwestern Oregon. The framework incorporated the most influential site-specific stressors throughout the basin built on a long history of data collection. These stressors were characterized with 13 metrics that were organized into 4 groups: hydrologic, water quality, physical habitat, and biological. Each stressor metric used readily accessible data and was translated to a score between 0 and 10. The higher the score, the healthier the site. This initial application of the framework used field observations and measurements to rank site conditions at two Tualatin River sites and four Tualatin River tributary sites. Given the versatility of this framework, it easily could be expanded to include more sites or new metrics, if necessary. Because stressors varied by season, all metrics for the tributary sites were scored separately during the wet season (November through April) and dry season (May through October). Water-quality data were available over a prolonged period; therefore, water-quality metrics were assessed by season and by decade (1990–99 compared to 2000–12) to evaluate long-term stressor trends. Results for the Tualatin River Basin prioritization framework indicated that the urban tributaries demonstrated the greatest stress throughout the year, especially during the dry summer months. Spatially, the upper Tualatin River was healthier than the lower reaches of the river. Water-quality has improved in the last 10 years, mostly due to improvements in the dry period contaminant scores, but challenges remain with high water temperatures and low dissolved-oxygen conditions. The biggest challenge with this type of research derived from inconsistencies within the available data. Both spatial and temporal data gaps must be addressed to improve the prioritization. Incorporating both discrete and continuous datasets into the prioritization framework remains a challenge because the datasets have slightly different information and criteria and are not always comparable. Regardless, this report provides guidelines for developing a prioritization framework that ranks the ecological health of sites in a watershed and provides guidance on management actions for improving conditions by targeting factors that greatly affect the health of river ecosystems.

Oregon↗
USGS2014

Carbon isotope equilibration during sulphate-limited anaerobic oxidation of methane

Collectively, marine sediments comprise the largest reservoir of methane on Earth. The flux of methane from the sea bed to the overlying water column is mitigated by the sulphate-dependent anaerobic oxidation of methane by marine microbes within a discrete sedimentary horizon termed the sulphate–methane transition zone. According to conventional isotope systematics, the biological consumption of methane leaves a residue of methane enriched in 13 C (refs 1–3). However, in many instances the methane within sulphate–methane transition zones is depleted in 13 C, consistent with the production of methane, and interpreted as evidence for the intertwined anaerobic oxidation and production of methane 4–6 . Here, we report results from experiments in which we incubated cultures of microbial methane consumers with methane and low levels of sulphate, and monitored the stable isotope composition of the methane and dissolved inorganic carbon pools over time. Residual methane became progressively enriched in 13 C at sulphate concentrations above 0.5 mM, and progressively depleted in 13 C below this threshold. We attribute the shift to 13 C depletion during the anaerobic oxidation of methane at low sulphate concentrations to the microbially mediated carbon isotope equilibration between methane and carbon dioxide. We suggest that this isotopic e ect could help to explain the 13 C-depletion of methane in subseafloor sulphate–methane transition zones.

Nature Geoscience↗
USGS2000

Methodology for applying monitored natural attenuation to petroleum hydrocarbon-contaminated ground-water systems with examples from South Carolina

Natural attenuation processes such as dispersion, advection, and biogradation serve to decrease concentrations of disssolved contaminants as they are transported in all ground-water systems. However, the efficiency of these natural attenuation processes and the degree to which they help attain remediation goals, varies considerably from site to site. This report provides a methodology for quantifying various natural attenuation mechanisms. This methodology incorporates information on (1) concentrations of contaminants in space and/or time; (2) ambient reduction/oxidation (redox) conditions; (3) rates and directions of ground-water flow; (4) rates of contaminant biodegradation; and (5) demographic considerations, such as the presence of nearby receptor exposure points or property boundaries. This document outlines the hydrologic, geochemical, and biologic data needed to assess the efficiency of natural attenuation, provides a screening tool for making preliminary assessments, and provides examples of how to determine when natural attenuation can be a useful component of site remediation at leaking underground storage tank sites. At a site in the Piedmont Physiographic Province (Laurens, South Carolina), hydrologic and water-chemistry data indicate that the natural attenuation capacity for benzene is approximately 5 percent per foot of flowpath. As a result, benzene concentrations would decrease from about 28,000 micrograms per liter in ground water at the source area to less than 5 micrograms per liter 200 feet downgradient and prior to discharging to a stream. Because of this rapid attenuation, contaminants do not presently impact the stream downgradient of the site. In contrast, at a site in the coastal Plain Physiographic Province (Charleston, South Carolina), hydrologic and water-chemistry data indicate that, even thought the site has a substantial natural attenuation capacity, it may not be sufficient to fully protect a nearby point of ground-water discharge. These two sites illustrate how the efficiency of natural attenuation processes acting on petroleum hydrocarbons can be systematically evaluated using hydrologic, geochemical, and microbiologic methods. These methods, in turn, can be used to assess the role that the natural attenuation of petroleum hydrocarbons can play in achieving overall site remediation.

South Carolina↗
USGS2023

Community and citizen science on the Elwha River: Past, present, and future

This report reflects on the past, present, and potential future of community and citizen science (CCS) in the Elwha River watershed, with particular focus on the years before and after a major restoration event: the removal of two dams that had impacted the river system for a century. We ask: how does CCS feature in the Elwha story and how could it feature? We use the term CCS to reference the broad range of ways in which members of the public might participate in authentic science and monitoring processes, including students and both paid and unpaid interns: participants are individuals contributing to scientific projects without prior formal training in the topic. Removal of the Elwha dams was a large-scale, complex project, and communities had an important role to play: the Lower Elwha Klallam Tribe (LEKT) and other local groups were a large part of the original drive to remove the dams. Some funding and policy requirements for monitoring are ending, but there is still much to learn from the changes happening in the Elwha, requiring ongoing research and monitoring. In 2022, the Elwha scientific community came together in a multifaceted effort called the “Elwha ScienceScape” to mark the ten-year anniversary of dam removal and to plan for future monitoring. One of ScienceScape’s priorities is expanding CCS efforts, and because the Elwha dam removal is a powerful international symbol of large-scale watershed restoration, ScienceScape is well-positioned to inform and emphasize the potential role of CCS in dam removal worldwide. This report presents insights about Elwha CCS from an academic literature review and discussions with scientists and many others that have been working in the Elwha. We found that the history of CCS on the Elwha is important but understated, with few scientific papers acknowledging support by volunteers of various kinds. Recent and ongoing CCS projects on the Elwha tend to be focused on biological phenomena, and most are associated with educational opportunities (across many types of institutions) and paid internships. We also noted that most Elwha CCS projects required volunteers with particular pre-existing skill sets (e.g., botanical knowledge) or time to impart specialized training (e.g. boat use), leading many projects towards engagement with a smaller number of volunteers. Partners working in the Elwha are considering a wide range of potential new CCS projects, and these ideas are in varying stages of development. Many new projects would broaden public involvement in terms of the opportunities available and increase the variety of focal topics for research and monitoring. This increased breadth is promising: there are indications that the local community’s interests also range widely, from fish recovery after dam removal to dam removal impacts on humans. Elwha CCS projects have encountered some challenges and barriers, including the administrative burden of coordinating volunteers and managing liability concerns. But Elwha ScienceScape scientists are committed to the value that CCS brings both to the research itself as well as to those who participate in these projects. CCS can be a way to increase equity in science and engage people who would not otherwise participate in research, and in many cases the research simply wouldn’t be possible without their help. Support with project administration, volunteer management, and data management could help in expanding CCS efforts and broadening their inclusivity. More systematic tracking of CCS projects to assess how they contribute to research and to community and participant benefit could be helpful in establishing and maintaining a long-term CCS strategy in the Elwha.

Wshington↗
USGS2016

Diversity of fungal endophytes in non-native Phragmites australis in the Great Lakes

Plant–microbial interactions may play a key role in plant invasions. One common microbial interaction takes place between plants and fungal endophytes when fungi asymptomatically colonize host plant tissues. The objectives of this study were to isolate and sequence fungal endophytes colonizing non-native Phragmites australis in the Great Lakes region to evaluate variation in endophyte community composition among three host tissue types and three geographical regions. We collected entire ramets from multiple clones and populations, surface sterilized plant tissues, and plated replicate tissue samples from leaves, stems, and rhizomes on corn meal agar plates to culture and isolate fungal endophytes. Isolates were then subjected to Sanger sequencing of the ITS region of the nuclear ribosomal DNA. Sequences were compared to fungal databases to define operational taxonomic units (OTUs) that were analyzed statistically for community composition. In total, we obtained 173 endophyte isolates corresponding to 55 OTUs, 39 of which were isolated only a single time. The most common OTU corresponded most closely to Sarocladium strictum and comprised 25 % of all fungal isolates. More OTUs were found in stem tissues, but endophyte diversity was greatest in rhizome tissues. PERMANOVA analyses indicated significant differences in endophyte communities among tissue types, geographical regions, and the interaction between those factors, but no differences among individual ramets were detected. The functional role of the isolated endophytes is not yet known, but one genus isolated here ( Stagonospora ) has been reported to enhance Phragmites growth. Understanding the diversity and functions of Phragmites endophytes may provide targets for control measures based on disrupting host plant/endophyte interactions.

Great Lakes region↗
USGS2013

Bathymetric surveys of the Kootenai River near Bonners Ferry, Idaho, water year 2011

In 2009, the Kootenai Tribe of Idaho released and implemented the Kootenai River Habitat Restoration Master Plan. This plan aimed to restore, enhance, and maintain the Kootenai River habitat and landscape to support and sustain habitat conditions for aquatic species and animal populations. In support of these restoration efforts, the U.S. Geological Survey, in cooperation with the Kootenai Tribe of Idaho, conducted high-resolution multibeam echosounder bathymetric surveys in May, June, and July 2011, as a baseline bathymetric monitoring survey on the Kootenai River near Bonners Ferry, Idaho. Three channel patterns or reaches exist in the study area—braided, meander, and a transitional zone connecting the braided and meander reaches. Bathymetric data were collected at three study areas in 2011 to provide: (1) surveys in unmapped portions of the meander reach; (2) monitoring of the presence and extent of sand along planned lines within a section of the meander reach; and (3) monitoring aggradation and degradation of the channel bed at specific cross sections within the braided reach and transitional zone. The bathymetric data will be used to update and verify flow models, calibrate and verify sediment transport modeling efforts, and aid in the biological assessment in support of the Kootenai River Habitat Restoration Master Plan. The data and planned lines for each study reach were produced in ASCII XYZ format supported by most geospatial software.

Idaho↗
USGS2004

Hydrogeology and water quality of the Pepacton Reservoir Watershed in southeastern New York. Part 4. Quantity and quality of ground-water and tributary contributions to stream base flow in selected main-valley reaches

Estimates of the quantity and quality of ground-water discharge from valley-fill deposits were calculated for nine valley reaches within the Pepacton watershed in southeastern New York in July and August of 2001. Streamflow and water quality at the upstream and downstream end of each reach and at intervening tributaries were measured under base-flow conditions and used in mass-balance equations to determine quantity and quality of ground-water discharge. These measurements and estimates define the relative magnitudes of upland (tributary inflow) and valley-fill (ground-water discharge) contributions to the main-valley streams and provide a basis for understanding the effects of hydrogeologic setting on these contributions. Estimates of the water-quality of ground-water discharge also provide an indication of the effects of road salt, manure, and human wastewater from villages on the water quality of streams that feed the Pepacton Reservoir. The most common contaminant in ground-water discharge was chloride from road salt; concentrations were less than 15 mg/L. Investigation of ground-water quality within a large watershed by measurement of stream base-flow quantity and quality followed by mass-balance calculations has benefits and drawbacks in comparison to direct ground-water sampling from wells. First, sampling streams is far less expensive than siting, installing, and sampling a watershed-wide network of wells. Second, base-flow samples represent composite samples of ground-water discharge from the most active part of the ground-water flow system across a drainage area, whereas a well network would only be representative of discrete points within local ground-water flow systems. Drawbacks to this method include limited reach selection because of unfavorable or unrepresentative hydrologic conditions, potential errors associated with a large number of streamflow and water-quality measurements, and limited ability to estimate concentrations of nonconservative constituents such as nutrients. The total gain in streamflow from the upper end to the lower end of each valley reach was positively correlated with the annual-runoff volume calculated for the drainage area of the reach. This correlation was not greatly affected by the proportions of ground-water and tributary contributions, except at two reaches that lost much of their tributary flow after the July survey. In these reaches, the gain in total streamflow showed a negative departure from this correlation. Calculated ground-water discharge exceeded the total tributary inflow in each valley reach in both surveys. Groundwater discharge, as a percentage of streamflow gain, was greatest among reaches in wide valleys (about 1,000-ft wide valley floors) that contain permeable valley fill because tributary flows were seasonally diminished or absent as a result of streambed infiltration. Tributary inflows, as a percentage of streamflow gain, were highest in reaches of narrow valleys (200-500-ft wide valley floors) with little valley fill and high annual runoff. Stream-water and ground-water quality were characterized by major-ion type as either (1) naturally occurring water types, relatively unaffected by road salt, or (2) road-salt-affected water types having elevated concentrations of chloride and sodium. The naturally occurring waters were typically the calcium-bicarbonate type, but some contained magnesium and (or) sulfate as secondary ions. Magnesium concentration in base flow is probably related to the amount of till and its carbonate content, or to the amount of lime used on cultivated fields within a drainage area. Sulfate was a defining ion only in dilute waters (with short or unreactive flow paths) with low concentrations of bicarbonate. Nearly all tributary waters were classified as naturally occurring water types. Ground-water discharge from nearly all valley reaches that contain State or county highways had elevated concentrations of chloride and sodsodium. The mean chloride concentrations of ground-water discharge--from 8 to 13 milligrams per liter--did not exceed Federal or State standards, but were about 5 times higher than naturally occurring levels. Application of road salt along a valley bottom probably affects only the shallow ground water in the area between a road and a stream. The elevated concentrations of chloride and sodium in the base-flow samples from such reaches indicate that the concentrations in the affected ground water were high enough to offset the low concentrations in all unaffected ground water entering the reach. Nutrient (nitrate and orthophosphate) concentrations in base-flow samples collected throughout the valleyreach network could not generally be used to estimate their concentrations in ground-water discharge because these constituents can be transformed or removed from water through biological uptake, transformation, or by adsorption on sediments. Base-flow samples from streams with upgradient manure sources or villages served by septic systems consistently had the highest concentrations of these nutrients.

Scientific Investigations Report↗
USGS2014

Comparability among four invertebrate sampling methods, Fountain Creek Basin, Colorado, 2010-2012

The U.S. Geological Survey, in cooperation with Colorado Springs City Engineering and Colorado Springs Utilities, designed a study to determine if sampling method and sample timing resulted in comparable samples and assessments of biological condition. To accomplish this task, annual invertebrate samples were collected concurrently using four sampling methods at 15 U.S. Geological Survey streamflow gages in the Fountain Creek basin from 2010 to 2012. Collectively, the four methods are used by local (U.S. Geological Survey cooperative monitoring program) and State monitoring programs (Colorado Department of Public Health and Environment) in the Fountain Creek basin to produce two distinct sample types for each program that target single-and multiple-habitats. This study found distinguishable differences between single-and multi-habitat sample types using both community similarities and multi-metric index values, while methods from each program within sample type were comparable. This indicates that the Colorado Department of Public Health and Environment methods were compatible with the cooperative monitoring program methods within multi-and single-habitat sample types. Comparisons between September and October samples found distinguishable differences based on community similarities for both sample types, whereas only differences were found for single-habitat samples when multi-metric index values were considered. At one site, differences between September and October index values from single-habitat samples resulted in opposing assessments of biological condition. Direct application of the results to inform the revision of the existing Fountain Creek basin U.S. Geological Survey cooperative monitoring program are discussed.

Colorado↗
USGS2002

Streamflow and water-quality data for selected watersheds in the Lake Tahoe basin, California and Nevada, through September 1998

The U.S. Geological Survey, in cooperation with the Tahoe Regional Planning Agency, and the University of California, Davis-Tahoe Research Group, has monitored tributaries in the Lake Tahoe Basin since 1988. This monitoring has characterized streamflow and has determined concentrations of nutrients and suspended sediment, which may have contributed to loss of clarity in Lake Tahoe. The Lake Tahoe Interagency Monitoring Program was developed to collect water-quality data in the basin. In 1998, the tributary-monitoring program included 41 water-quality stations in 14 of the 63 watersheds totaling half the area tributary to Lake Tahoe. The monitored watershed areas range from 1.08 square miles for First Creek to 56.5 square miles for the Upper Truckee River.Annual and unit runoff for 20 primary and secondary streamflow gaging stations in 10 selected watersheds are described. Water years 1988-98 were used to compare runoff data. The Upper Truckee River at South Lake Tahoe, Calif., had the highest annual runoff and Logan House Creek near Glenbrook, Nev., had the lowest. Blackwood Creek near Tahoe City, Calif., had the highest unit runoff and Logan House Creek had the lowest. The highest instantaneous peak flow was recorded at Upper Truckee River at South Lake Tahoe during the January 2, 1997, flood event.Certain water-quality measurements were made in the field. Ranges and median values of those measurements are described for 41 stations. Water temperature ranged from 0 to 23?C. Specific conductance ranged from 13 to 900 microsiemens per centimeter at 25?C. pH ranged from 6.7 to 10.6. Dissolved-oxygen concentrations ranged from 5.2 to 12.6 mg/L and from 70 to 157 percent of saturation.Loads, yields, and trends of nutrients and suspended sediment during water years 1988-98 at the streamflow gaging stations also are described. The Upper Truckee River at South Lake Tahoe had the largest median monthly load for five of the six measured nutrients and of suspended sediment, while Trout Creek at South Lake Tahoe had the largest median monthly load for the remaining nutrient. Logan House Creek near Glenbrook had the smallest median monthly loads for all nutrients and suspended sediment. Seasonal load summaries at selected stations showed nutrient and suspended-sediment loads were greatest in the spring months of April, May and June and least in the summer months of July, August, and September. Monthly load comparisons also were described for five watersheds with multiple stations.Incline Creek had the highest combined rank for all nutrients and sediment. Incline Creek had the largest monthly yields for dissolved nitrite plus nitrate nitrogen and soluble reactive phosphorus. Third Creek had the second highest combined rank and had the largest monthly yields for total nitrogen, total phosphorus, biologically reactive iron, and suspended sediment. Edgewood Creek had the largest monthly yield for dissolved ammonia nitrogen. Logan House Creek had the lowest combined rank and the smallest monthly yields for all nutrients and sediment.Trends in concentrations are either decreasing or not significant for all nutrients in all sampled watersheds, with the exception of biologically reactive iron. Biologically reactive iron and suspended sediment show an increasing trend in three watersheds and decreasing or no significant trend in the other seven watersheds.

Water-Resources Investigations Report↗
USGS1999

Disease control operations

Individual disease outbreaks have killed many thousands of animals on numerous occasions. Tens of thousands of migratory birds have died in single die-offs with as many as 1,000 birds succumbing in 1 day. The ability to successfully combat such explosive situations is highly dependent on the readiness of field personnel to deal with them. Because many disease agents can spread through wildlife populations very quickly, advance preparation is essential for preventing infected animals from spreading disease to additional species and locations. Carefully thought-out disease contingency plans should be developed as practical working documents for field personnel and updated as necessary. Well-designed plans can prove invaluable in minimizing wildlife losses and the costs associated with disease control activities. Although requirements for disease control operations vary and must be tailored to each situation, all disease contingency planning involves general concepts and basic biological information. This chapter, which is intended to be a practical guide, identifies the major activities and needs of disease control operations, and relates them to disease contingency planning.

Information and Technology Report↗
USGS1989

Molybdenum Hazards to Fish, Wildlife, and Invertebrates: A Synoptic Review

Ecological and toxicological aspects of molybdenum (Mo) in the environment are briefly reviewed, with emphasis on fish and wildlife. Subtopics include sources and uses, chemical properties, mode of action, background concentrations in biological and nonbiological samples, and lethal and sublethal effects on terrestrial plants and invertebrates, aquatic organisms, birds, and mammals. Current recommendations for Mo and the protection of sensitive living resources are presented.

Contaminant Hazard Reviews↗
USGS2002

Cruise report RV Moana Wave Cruise M-1-02-GM bathymetry and acoustic backscatter of the mid and outer continental shelf, head of De Soto Canyon, northeastern Gulf of Mexico June 17, through July 9, 2002 Pensacola, FL to Pensacola, FL

The mid to outer continental shelf off Mississippi-Alabama and off northwest Florida were the focus of US Geological Survey (USGS) multibeam echosounder (MBES) mapping cruises in 2000 and 2001, respectively. These areas were mapped to investigate the extent of "deep-water reefs" first suggested by Ludwick and Walton (1957). The reefs off Mississippi and Alabama were initially described in water depths of 60 to 120 m (Ludwick and Walton, 1957) but the 2000 mapping found reef and hardgrounds to be much more extensive than previously thought (Gardner et al., 2001). The persistent trend of reef-like features along the outer shelf of Mississippi-Alabama suggested the trend might continue along the northwest Florida mid and outer shelf so a MBES-mapping effort was mounted in 2001 to test this suggestion. It is critical to determine the accurate location, geomorphology, and types of the ridges and reefs that occur in this region to understand the Quaternary history of the area and to assess their importance as benthic habitats for fisheries. The 2001 survey found a series of shelf-depth platforms with ridges (possibly reefs) constructed on their surfaces (Gardner et al., 2002). The area known as the "head of De Soto Canyon" is the large unmapped region between the 2000 and 2001 mapped areas. The head of De Soto Canyon is an outer shelf zone with a relatively steep western wall and a much gentler eastern wall. It was unknown prior to this cruise whether the reefs of the Mississippi-Alabama shelf continue eastward into the head of De Soto Canyon and connect with the ridges and reefs mapped on the northwest Florida outer shelf. The existence of carbonate-cemented latest Quaternary to Holocene sandstones along the western wall of the head of De Soto Canyon (Shipp and Hopkins, 1978; Benson et al., 1997; W.W. Schroeder, personnel comm., 2002) is of interest because of the potential benthic habitats they may represent. Precisely georeferenced high-resolution mapping of bathymetry is a fundamental first step in the study of an area suspected to be critical benthic habitats. Morphology is thought to be critical to define the distribution of dominant demersal plankton/planktivores communities. Community structure and trophodynamics of demersal fishes of the outer continental shelf of the northeastern Gulf of Mexico presently are focuses of a major USGS research project. A goal of the project is to answer questions concerning the relative roles played by morphology and surficial geology in controlling biological differentiation. Deep-water ridges, reefs, and outcrops are important because they are fish havens and key spawning sites, and are critical habitats for larval, juvenile, and economically important sport/food fishes.

Gulf of Mexico, head Of De Soto Canyon↗
USGS2002

Threats to desert tortoise populations: a critical review of the literature

Decision in resource management are generally based on a combination of sociopolitical, economic, and environmental factors, and may be biased by personal values. These three components often contradict each other resulting in controversy. Controversies can usually be reduced when solid scientific evidence is used to support or refute a decision. However, it is important to recognize that data often do little to alter antagonists' positions when differences in values are the bases if the dispute. But, supporting data can make the decision more defensible, both legally and ethically, especially if the data supporting all opposing viewpoints are included in the decision-making process. Resource management decisions must be made using the best scientific information currently available. However, scientific data vary in two important measures of quality: reliability and validity. The reliability of the data is a measure of the degree to which the observations or conclusion can be repeated. Validity of the data is a measure of the degree to which the observation or conclusion reflects what actually occurs in nature. How the data are collected strongly affects the reliability of validity of ecological conclusions that can be made. Research data potentially relevant to management come from different sources, and the source often provides clues to the reliability and, to a certain extent, validity of data. Understanding the quality of data being used to make management decisions helps to separate the philosophical or value-based aspects of arguments from the objective ones, thus helping to clarify the decisions and judgments that need to be made. The West Mojave Plan is a multispecies, bioregional plan for the management of natural resources within a 9.4 million-acre area of the Mojave Desert in California. The plan addresses the legal requirements for the recovery of the desert tortoise ( Gopherus agazzizii ), a threatened species, but also covers an additional approximately 80 species of plants and animals assigned special status by the Bureau of Land Management, U. S. Fish and Wildlife Service, and California Department of Fish and Game. Within the planning area, 28 separate jurisdictions (counties, cities, towns, military installations, etc.) seek programmatic prescriptions that will facilitate streamlined environmental review, result in expedited authorization for development projects, and protect listed and unlisted species into the foreseeable future to avoid or minimize conflicts between proposed development and species' conservation and recovery. All of the scientific data available concerning the biology and management of these approximately 80 species and their habitats must be evaluated to develop a scientifically credible plan. This document provides an overview and evaluation of the knowledge of the major threats to the persistence and recovery of desert tortoise populations. I was specifically asked to evaluate the scientific veracity of the data and reports available. I summarize the data presently available with particular focus on the West Mojave Desert, evaluate the scientific integrity of the data. and identify major gaps in the available knowledge. I do not attempt to provide in-depth details on each study or threat; for more details I encourage the reader to consult the individual papers or reports city throughout this report (many of which are available at most university libraries and at the West Mojave Plan office in Riverside, California). I also do not attempt to characterize or evaluate the past or present management actions, except where they have direct bearing on evaluation of threats, nor do I attempt, for the most part, to acquire, generate, or evaluate new or existing, but uninterpreted data.

California↗
USGS2023

Near-field receiving-water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California—2020

Trace-metal concentrations in sediment and in the clam Limecola petalum (World Register of Marine Species, 2020; formerly reported as Macoma balthica and M. petalum ), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer (km) south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in south San Francisco Bay, California. This report includes the data collected by the U.S. Geological Survey (USGS) for January 2020–December 2020 (Cain and others, 2022). These data append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2020 data within the context of the longer, multidecadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving- Water Monitoring Program, initiated in 1994. Silver and copper contamination substantially decreased at the site in the 1980s following the implementation by PARWQCP of advanced wastewater-treatment and source-control measures. Since the 1990s, concentrations of these elements in surface sediments have continued to decrease, although more slowly. For example, from 1994 to 2020, the minimum annual mean silver concentration—0.20 milligram per kilogram (mg/kg)—was observed in multiple years. In 2020, silver concentrations ranged from 0.18 to 0.28 mg/kg. These concentrations are 2 to 3 times higher than the regional background concentration. Presently (2020), sediment-copper concentrations appear to be near the regional background level. Over the same period (1994–2020), sedimentary iron and zinc exhibited modest decreases. Sedimentary aluminum, chromium, mercury, nickel, and selenium have not exhibited any trend. Since 1994, silver and copper concentrations in L. petalum have varied seasonally, apparently in response to a combination of site-specific metal exposures and cyclic growth and reproduction, as reported previously. Seasonal patterns for other elements, including chromium, mercury, nickel, selenium, and zinc, generally were similar in timing and magnitude as those for silver and copper. Downward trends in the silver and zinc concentrations in L. petalum during 1994–2020 were evident and appeared to be related to the general physiological condition of the clam, indicated by a condition index. Biological effects of elevated silver and copper contamination at the Palo Alto site have been interpreted from data collected during and after the recession of these contaminants. Concentrations of both elements in the soft tissues of L. petalum decreased with sedimentary copper and silver. This pattern was associated with changes in the reproductive activity of L. petalum , as well as the structure of the benthic invertebrate community. Reproductive activity of L. petalum increased as metal concentrations in L. petalum decreased (Hornberger and others, 2000), and presently is stable with almost all animals initiating reproduction in the fall and spawning the following spring. Analyses of the benthic community structure indicate that the infaunal invertebrate community has shifted from one dominated by several opportunistic species when silver and copper exposures were highest to one in which the species abundance is more evenly distributed, a pattern that indicates a more stable community that is subjected to fewer stressors. Importantly, this long-term change is unrelated to other metals and other measured environmental factors, including salinity and sediment composition. In addition, two of the opportunistic species ( Ampelisca abdita and Streblospio benedicti ) that brood their young and live on the surface of the sediment in tubes have shown a continual decrease in dominance coincident with the decrease in metals. Both species had short-lived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 2020. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly from 2011 to 2012 and returned to pre-2011 numbers in 2020. The reproductive mode of most species that were present in 2020 was indicative of species that were capable of movement either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2020 benthic community data, which showed that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of species that consume the sediment, or filter feed, those that have pelagic larvae that must survive landing on the sediment, and those that brood their young. The long-term recovery observed after the 1970s can be ascribed to the decrease in sediment pollutants.

California↗
USGS2023

Selenium hazards in the Salton Sea environment—Summary of current knowledge to inform future wetland management

Quaternary marine and continental shales in the western United States are sources of selenium that can be loaded into the aquatic environment through mining, agricultural, and energy production processes. The mobilization of selenium from shales through agricultural irrigation has been recognized since the 1930s; however, discovery of deformities in birds and other wildlife using agricultural habitats during the 1980s spurred studies to determine the extent and effects of the contamination. Through these early studies, researchers determined that biota in the Salton Sea drainage basin was at risk from legacy selenium contamination in the Colorado River watershed. The Salton Sea and its surrounding managed and unmanaged wetlands provide vital inland habitat and trophic support for diverse assemblages of resident and migratory wildlife, and understanding regional selenium hazards for these trust species is a priority for many Federal and State agencies. The modern Salton Sea is a shallow, landlocked saline lake in Riverside and Imperial Counties (not shown) of California that is sustained by irrigation return and perennial river inflow. Changes in water transfer agreements under the 2003 Quantification Settlement Agreement (QSA) have resulted in reduced irrigation flow, declining lake levels, and the evolution of unmanaged wetlands in areas where drains and rivers no longer reach the Salton Sea. These wetlands provide additional habitat for some species of concern, but their potential to increase selenium hazards for trust species is largely unknown. From the 1980s to 2020, efforts to document selenium contamination and effects throughout the region have resulted in a considerable amount of selenium data from the Salton Sea and its surrounding drainage basin; however, no long-term (greater than 20 years), consistent sampling program has been established, and all data have been collected by different entities using a variety of protocols and analytical techniques. This lack of coordination has been previously documented in regional management plans and has led to difficulty in reliably assessing selenium hazards in the Salton Sea environment. This report provides a summary of the available disparate selenium information collected from water, sediment, and biota in the Salton Sea region since the 1980s and to identify data gaps that need to be filled to understand the potential effects of selenium on species of concern, including federally endangered desert pupfish ( Cyprinodon macularius ) and Yuma Ridgway’s Rail ( Rallus obsoletus yumanensis; formerly Yuma Clapper Rail, Rallus longirostris yumanensis ). Available data from the Salton Sea drainage basin show that water from the Colorado River has the lowest selenium concentration of all surface water sources. All other surface water flowing into the Salton Sea has elevated selenium concentrations due to evaporation and evapotranspiration that occurs in agricultural fields and associated water delivery infrastructure or leaching of selenium from irrigated farmland soils. The Salton Sea has lower selenium concentrations because of various biogeochemical processes that recycle selenium into the sediment or volatilize it to the atmosphere; however, these mechanisms are not well defined, and it is not clear if selenium cycling will change in response to possible changes in the oxidation state of the Salton Sea bottom waters as water levels decline. Agricultural drains have the highest average selenium concentrations, but few drains have been sampled since changes in irrigation practices have occurred (due to the 2003 QSA). Groundwater selenium concentrations are variable; some wells south of the Salton Sea have selenium concentrations as high as 300 micrograms per liter (µg/L), whereas selenium concentrations are below detection in other wells. Groundwater and surface-water geothermal discharge zones around the margins of the Salton Sea and in unmanaged wetlands have not been studied in detail, and published selenium measurements are not available for these surface features. Selenium concentrations in the sediment of the Salton Sea drainage basin are highest in wetland particulate organic matter and the Salton Sea lakebed, indicating that removal of selenium from the water to the sediment has been a primary mechanism for keeping selenium concentrations low in the water column. Sediment selenium concentrations in wetlands are lower than in the Salton Sea but higher than inflowing drains and rivers, indicating the lentic wetland sites also may be important sinks for selenium because of biogeochemical processes. Sediment selenium data have not been collected in agricultural drains since changes in irrigation practices occurred (due to the 2003 QSA), and it is unknown if selenium sequestration from the water column has changed in these systems. We divided biological data into broad taxonomic categories, including primary producers, invertebrates, herpetofauna, mammals, fishes, and birds to facilitate evaluation of selenium concentrations and spatiotemporal trends observed in the Salton Sea. Overall, selenium concentrations were substantially greater in algae samples compared to all vascular plant samples combined. Median selenium concentrations in several invertebrate taxa (Chironomidae, Formicidae, Corixidae, Corbiculidae and Nereididae, and Decapoda) exceeded the maximum suggested dietary threshold of 3.0–4.0 micrograms per gram (µg/g) dry weight (dw) for predators consuming invertebrates in aquatic food webs. The greatest number of samples were collected from fish, and selenium distributions among species and locations showed that the range for most samples was lower than the U.S. Environmental Protection Agency selenium criterion for aquatic life (8.5 µg/g dw whole body, 11.3 µg/g dw fillets). The median selenium concentrations for whole body fish were below the selenium criterion in most locations, except for bairdiella ( Bairdiella icistia ) from the Salton Sea and irrigation drains, a few individual tilapia spp. (family Cichlidae, including genera Tilapia, Oreochromis , and their hybrids) from the river and river outlets, and several western mosquitofish ( Gambusia affinis ) and sailfin molly ( Poecilia latipinna ) from irrigation drain outlets. For avian samples combined among years and locations, median selenium concentrations in livers from all families except waders and Ibis (family Threskiornithidae) were higher than levels expected to cause selenium toxicosis (10–20 µg/g dw), and all median egg concentrations were above or near 6.0 μg/g dw, which is a conservative threshold value for reproductive impairment. Most knowledge gaps we identified for water, sediment, and biota were interrelated, and the use of integrated approaches to address knowledge gaps can provide greater insight into the drivers behind selenium hazards. Integrated water, sediment, and biota studies could help identify cost-effective management solutions that serve multiple purposes. A comprehensive analysis of the hydrology, biogeochemistry, and food-web processes in wetlands and other habitats can inform predictive models to identify drivers of selenium bioavailability, uptake from the environment and subsequent trophic transfer, ultimately forming the basis for experimental habitat management manipulations to minimize selenium hazards to wildlife. Furthermore, a comprehensive, long-term sampling and analytical laboratory plan would enable comparison of data among different entities that are sampling at the Salton Sea. Such efforts are well suited to help fill knowledge gaps that preclude understanding of selenium hazards and future management options for biota using Salton Sea habitats, including newly formed wetlands throughout the region. All data compiled for this report are available in two U.S. Geological Survey data releases: Groover and others (2022) for water and sediment samples and De La Cruz and others (2022) for biological samples. The data releases include all publicly available data for selenium concentrations in water, sediment, and biological samples collected in and around the Salton Sea, including the Coachella and Imperial Valleys. The data releases also include previously unpublished data.

California↗
USGS2013

Golden eagle records from the Midwinter Bald Eagle Survey: information for wind energy management and planning

The purpose of this Data Series report is to provide the occasions, locations, and counts when golden eagles were recorded during the annual Midwinter Bald Eagle Surveys. Golden eagles (Aquila chrysaetos) are protected by Federal statutes including the Bald and Golden Eagle Protection Act (BGEPA) (16 USC 668-668c) and the Migratory Bird Treaty Act (MBTA) (16 USC 703-12). The U.S. Fish and Wildlife Service (Service) manages golden eagles with the goal of maintaining stable or increasing breeding populations (U.S. Fish and Wildlife Service, 2009). Development for the generation of electricity from wind turbines is occurring in much of the range of the golden eagle in the western United States. Development could threaten population stability because golden eagles might be disturbed by construction and operation of facilities and they are vulnerable to mortality from collisions with wind turbines (Smallwood and Thelander, 2008). Therefore, the Service has proposed a process by which wind energy developers can collect information that could lead to Eagle Conservation Plans (ECP), mitigation, and permitting that allow for golden eagle management in areas of wind energy development (U.S. Fish and Wildlife Service, 2011). The Service recommends that ECP be developed in stages, and the first stage is to learn if golden eagles occur at the landscape level where potential wind facilities might be located. Information about where eagles occur can be obtained from technical literature, agency files, and other sources of information including on-line biological databases. The broad North American distribution of golden eagles is known, but there is a paucity of readily available information about intermediate geographic scales and site-specific scales, especially during the winter season (Kochert and others, 2002).

Data Series↗
USGS2012

Identification of the thiamin pyrophosphokinase gene in rainbow trout: Characteristic structure and expression of seven splice variants in tissues and cell lines and during embryo development

Thiamin pyrophosphokinase (TPK) converts thiamin to its active form, thiamin diphosphate. In humans, TPK expression is down-regulated in some thiamin deficiency related syndrome, and enhanced during pregnancy. Rainbow trout are also vulnerable to thiamin deficiency in wild life and are useful models for thiamin metabolism research. We identified the tpk gene transcript including seven splice variants in the rainbow trout. Almost all cell lines and tissues examined showed co-expression of several tpk splice variants including a potentially major one at both mRNA and protein levels. However, relative to other tissues, the longest variant mRNA expression was predominant in the ovary and abundant in embryos. During embryogenesis, total tpk transcripts increased abruptly in early development, and decreased to about half of the peak shortly after hatching. In rainbow trout, the tpk transcript complex is ubiquitously expressed for all tissues and cells examined, and its increase in expression could be important in the early-middle embryonic stages. Moreover, decimated tpk expression in a hepatoma cell line relative to hepatic and gonadal cell lines appears to be consistent with previously reported down-regulation of thiamin metabolism in cancer.

Comparative Biochemistry and Physiology, Part B: B↗