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At least 1,261 records · Page 70Linked to original sources
USGS2022

Using microbial source tracking to identify fecal contamination sources in Great South Bay on Long Island, New York

The U.S. Geological Survey worked in cooperation with the New York State Department of Environmental Conservation to assess the potential sources of fecal contamination entering a part of Great South Bay (referred to as Great South Bay for the purposes of this report) near the hamlets of West Sayville, Sayville, and Bayport on the southern shore of Suffolk County on Long Island, New York. Water samples are routinely collected by the New York State Department of Environmental Conservation in the bay and analyzed for fecal coliform bacteria, an indicator of fecal contamination, to determine the need for closure of shellfish beds for harvest and consumption. Fecal coliform and other bacteria are an indicator of the potential presence of pathogenic (disease-causing) bacteria. However, indicator bacteria alone cannot determine the biological or geographical sources of contamination; therefore, microbial source tracking was implemented to determine various biological sources of contamination. In addition, information such as the location, weather and season, and surrounding land use where a sample was collected help determine the geographical source and conveyance of land-based water to the embayment. Analysis revealed that the most substantial source of fecal contamination to Great South Bay was discharge from sites draining ponds and wetlands into the tributaries sampled, Brown and Green Creeks, particularly during the summer months. Fecal coliform bacteria at sites where ponds and wetlands drain are increased by stormwater runoff, which is another substantial source of fecal contamination. Sites with high concentrations of fecal coliform bacteria in the summer exacerbated by stormwater include the Brown Creek Culvert at Middle Road, Mill Pond Culvert near South Street, and Green Creek Culvert near Montauk Highway sites. The canine Bacteroides (BacCan) marker was the most frequently detected microbial source tracking marker with 15 positive detections in surface water across the landscape, followed by the waterfowl Helicobacter (GFD) marker with 9 detections and the human Bacteroides (HF183) marker with 4 detections in surface water (excluding 2 detections in sediment). The ruminant Bacteroides (Rum2Bac) marker was not detected in any samples collected during this study. The detection frequency of BacCan was similar for all sampling conditions and seasons, suggesting canine influence is unrelated to weather events and is a year-round occurrence. BacCan was detected in 14 of 16 source samples and only 1 of 16 receptor samples, which suggests that canine fecal contamination is likely diluted in the bay. There was a similar amount of marker detections when comparing weather condition (wet or dry) and season (winter or summer), suggesting that fecal contamination was unrelated to weather events or time of year. Eight waterfowl marker detections were in samples collected during the winter, and only one during the summer, implicating seasonal avian fecal contamination throughout the embayment. The human marker was detected in only one surface-water receptor sample, during the wet winter sampling event at the Green Creek Mid-Bay site. Three of four human marker detections were in the samples collected during the wet winter sampling event, indicating that weather and season may influence the presence of human markers in Great South Bay, but human markers are not overly prevalent.

New York↗
USGS2017

Relative abundance of deformed wing virus, Varroa destructor virus 1, and their recombinants in honey bees (Apis mellifera) assessed by kmer analysis of public RNA-Seq data

Deformed wing virus (DWV) is a major pathogen of concern to apiculture, and recent reports have indicated the local predominance and potential virulence of recombinants between DWV and a related virus, Varroa destructor virus 1 (VDV). However, little is known about the frequency and titer of VDV and recombinants relative to DWV generally. In this study, I assessed the relative occurrence and titer of DWV and VDV in public RNA-seq accessions of honey bee using a rapid, kmer-based approach. Three recombinant types were detectable graphically and corroborated by de novo assembly. Recombination breakpoints did not disrupt the capsid-encoding region, consistent with previous reports, and both VDV- and DWV-derived capsids were observed in recombinant backgrounds. High abundance of VDV kmers was largely restricted to recombinant forms. Non-metric multidimensional scaling identified genotypic clusters among DWV isolates, which was corroborated by read mapping and consensus generation. The recently described DWV-C lineage was not detected in the searched accessions. The data further highlight the utility of high-throughput sequencing to monitor viral polymorphisms and statistically test biological predictors of titer, and point to the need for consistent methodologies and sampling schemes.

Journal of Invertebrate Pathology↗
USGS2023

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

Spiny lizards (genus Sceloporus ) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis , is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis , as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis , the species status of the California endemic island fence lizard ( S. becki ), and the spectacular radiation of Sceloporus lizards.

California↗
USGS1951

Ground-water conditions in the Dutch Flats area, Scotts Bluff and Sioux Counties, Nebraska, with a section on chemical quality of the ground water

The U.S. Department of the Interior (DOI) studied contamination induced by irrigation drainage in 26 areas of the Western United States during 1986-95. Comprehensive compilation, synthesis, and evaluation of the data resulting from these studies were initiated by DOI in 1992. Soils and ground water in irrigated areas of the West can contain high concentrations of selenium because of (1) residual selenium from the soil's parent rock beneath irrigated land; (2) selenium derived from rocks in mountains upland from irrigated land by erosion and transport along local drainages, and (3) selenium brought into the area in surface water imported for irrigation. Application of irrigation water to seleniferous soils can dissolve and mobilize selenium and create hydraulic gradients that cause the discharge of seleniferous ground water into irrigation drains. Given a source of selenium, the magnitude of selenium contamination in drainage-affected aquatic ecosystems is strongly related to the aridity of the area and the presence of terminal lakes and ponds. Marine sedimentary rocks and deposits of Late Cretaceous or Tertiary age are generally seleniferous in the Western United States. Depending on their origin and history, some Tertiary continental sedimentary deposits also are seleniferous. Irrigation of areas associated with these rocks and deposits can result in concentrations of selenium in water that exceed criteria for the protection of freshwater aquatic life. Geologic and climatic data for the Western United States were evaluated and incorporated into a geographic information system (GIS) to produce a map identifying areas susceptible to irrigation-induced selenium contamination. Land is considered susceptible where a geologic source of selenium is in or near the area and where the evaporation rate is more than 2.5 times the precipitation rate. In the Western United States, about 160,000 square miles of land, which includes about 4,100 square miles (2.6 million acres) of land irrigated for agriculture, has been identified as being susceptible. Biological data were used to evaluate the reliability of the map. In 12 of DOI's 26 study areas, concentrations of selenium measured in bird eggs were elevated sufficiently to significantly reduce hatchability of the eggs. The GIS map identifies 9 of those 12 areas. Deformed bird embryos having classic symptoms of selenium toxicosis were found in four of the study areas, and the map identifies all four as susceptible to irrigation-induced selenium contamination. The report describes the geography, geology, and ground-water resources of the Dutch Flats area in Scotts Bluff and Sioux Counties, Nebr. The area comprises about 60 square miles and consists predominantly of relatively flat-lying terraces. Farming is the principal occupation in the area. The farm lands are irrigated largely from surface water; ground water is used only as a supplementary supply during drought periods. The climate in the area is semiarid, and the mean annual precipitation is about 16 inches. The rocks exposed in the Dutch Flats area are of Tertiary sad Quaternary age. A map showing the areas of outcrop of the rock formations is included in the report. Sufficient unconfined ground water for irrigation supplies is contained in the deposits of the .third terrace, and wells that yield 1,000 to 2,000 gallons a minute probably could be developed. The depth to water in the area ranges from a few feet to about 80 feet sad averages about 30 feet. The depth to water varies throughout the year; it is least in the late summer when the recharge from irrigation is greatest, sad it is greatest in the early spring before irrigation is begun. A map showing the depth to water in September 1949 is included in the report. The ground-water reservoir is recharged by seepage from irrigation canals and laterals, by seepage from irrigation water applied to the farms, and, to a much lesser extent, by precipitation. In the area b

Nebraska↗
USGS2017

The concurrent use of novel soil surface microclimate measurements to evaluate CO2 pulses in biocrusted interspaces in a cool desert ecosystem

Carbon cycling associated with biological soil crusts, which occupy interspaces between vascular plants in drylands globally, may be an important part of the coupled climate-carbon cycle of the Earth system. A major challenge to understanding CO 2 fluxes in these systems is that much of the biotic and biogeochemical activity occurs in the upper few mm of the soil surface layer (i.e., the ‘mantle of fertility’), which exhibits highly dynamic and difficult to measure temperature and moisture fluctuations. Here, we report a multi-sensor approach to simultaneously measuring temperature and moisture of this biocrust surface layer (0–2 mm), and the deeper soil profile, concurrent with automated measurement of surface soil CO 2 effluxes. Our results illuminate robust relationships between biocrust water content and field CO 2 pulses that have previously been difficult to detect and explain. All observed CO 2 pulses over the measurement period corresponded to surface wetting events, including when the wetting events did not penetrate into the soil below the biocrust layer (0–2 mm). The variability of temperature and moisture of the biocrust surface layer was much greater than even in the 0–5 cm layer of the soil beneath the biocrust, or deeper in the soil profile. We therefore suggest that coupling surface measurements of biocrust moisture and temperature to automated CO 2 flux measurements may greatly improve our understanding of the climatic sensitivity of carbon cycling in biocrusted interspaces in our study region, and that this method may be globally relevant and applicable.

Biogeochemistry↗
USGS2001

A preliminary survey of marine contamination from mining-related activities on Marinduque Island, Philippines: porewater toxicity and chemistry results from a field trip, October 14-19, 2000

As a follow-up of an initial overview of environmental problems caused by mining activities on Marinduque Island, Philippines, USGS and TAMU-CC scientists went to Marinduque in October 2000 to do a preliminary assessment of potential impacts of mining-related activities on the marine environment. Like the previous visit in May 2000, the marine assessment was conducted at the invitation of Philippine Congressman Edmund O. Reyes. In this report we present the results of sediment porewater toxicity tests and chemical analyses. Toxicity tests consist of laboratory analyses for the assessment of adverse effects caused by environmental contaminants to animals or plants. Sediments (sand or mud) are known to accumulate contaminants (e.g., copper and other heavy metals). Therefore, it is common to perform toxicity tests using different phases of the sedimentary environment in order to analyze adverse effects of contaminants accumulated in the sediment. Sediment pore water (or interstitial water, i.e., the water distributed among the sediment grains) is a sedimentary phase which controls the bioavailability of contaminants to bottom dwelling aquatic organisms (both plants and animals). There are several different kinds of organisms with which toxicity tests can be performed. Among those, tests with sea urchin early life stages (gametes and embryos) are very common due to their high sensitivity to contaminants, ease of maintenance under laboratory conditions, and ecological importance, particularly in coral reefs. The basis of these tests is the exposure of gametes or embryos to the pore water to be analyzed for toxicity. If the pore water contains contaminants in levels that can adversely affect a number of marine species, fertilization and/or embryological development of sea urchins is inhibited. Chemical analyses provide additional information and aid in the interpretation of the toxicity test results. For the current study, chemical analyses were performed for the measurement of porewater concentrations of several heavy metals associated with copper mining activities. Pore waters for toxicological and chemical analyses were collected at several stations on the coast of Marinduque, near the mouths of the Boac and Mogpog rivers, and near the causeways formed by mine tailings disposal. Porewater samples were also collected at the Tres Reyes Marine Reserve, so that these non-contaminated samples could serve as a reference for test performance. Sea urchin embryological development and fertilization were only significantly impaired by two porewater samples, suggesting the presence of contaminants in toxic amounts at those stations. The toxic samples were collected near the up current side of the Calancan (Marcopper) mine tailings causeway (stations 2 and 3 – see figure 10). The pore water from station 2 also had the highest levels of heavy metals, particularly cadmium, cobalt, copper, nickel, lead and zinc (Table 5). The concentrations of cobalt, nickel and zinc were also elevated 2 at station 3. Copper concentrations were also elevated at the two river mouth stations (8 and 9) and near the CMI tailings causeway (station 7). Visual observations also indicated biological degradation due to heavy siltation and smothered coral at a gradient off the Calancan causeway, suggesting that siltation might also be causing a physical impact. This preliminary survey suggests that effects related to past mining activities are still evident and warrant a more comprehensive study to assess their severity and areal extent.

Open-File Report↗
USGS1995

Proceedings of the second biennial conference on research in Colorado Plateau National Parks

On 25-28 October 1993 in Flagstaff, Arizona, the National Biological Service Colorado Plateau Research Station (formerly National Park Service Cooperative Park Studies Unit) and Northern Arizona University hosted the Second Biennial Conference of Research on the Colorado Plateau. The conference theme focused on research, inventory, and monitoring on the federal, state, and private lands in the Colorado Plateau biogeographic province.

Utah;Colorado;Arizona;New Mexico↗
USGS2012

American Oystercatcher (Haematopus palliatus)

The American Oystercatcher is a large, conspicuous shorebird, common in coastal salt marshes and along sand beaches throughout the central part of its range. One of the few birds to specialize on bivalve mollusks living in saltwater, this species is completely restricted to marine habitats. Two races breed in North America—the eastern nominate race along the Atlantic coast from southern Maine south, and a second race along the Pacific coast from northwestern Baja California south. While the eastern race has been studied extensively across its range both during winter and the breeding season, the biology of the western race is poorly known and this population may also be at risk both from coastal development and hybridization with the American Black Oystercatcher ( H. bachmani ). Eastern oystercatchers regularly winter in large flocks, from Virginia south along the Atlantic and Gulf coasts.

Report↗
USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California↗
USGS2008

USGS Workshop on Scientific Aspects of a Long-Term Experimental Plan for Glen Canyon Dam, April 10-11, 2007, Flagstaff, Arizona

Executive Summary Glen Canyon Dam is located in the lower reaches of Glen Canyon National Recreation Area on the Colorado River, approximately 15 miles upriver from Grand Canyon National Park (fig. 1). In 1992, Congress passed and the President signed into law the Grand Canyon Protection Act (GCPA; title XVIII, sec. 1801?1809, of Public Law 102-575), which seeks ?to protect, mitigate adverse impacts to, and improve the values for which Grand Canyon National Park and Glen Canyon National Recreation Area were established.? The Glen Canyon Dam Adaptive Management Program (GCDAMP) was implemented as a result of the 1996 Record of Decision on the Operation of Glen Canyon Dam Final Environmental Impact Statement to ensure that the primary mandate of the GCPA is met through advances in information and resources management (U.S. Department of the Interior, 1995). On November 3, 2006, the Bureau of Reclamation (Reclamation) announced it would develop a long-term experimental plan environmental impact statement (LTEP EIS) for operational activities at Glen Canyon Dam and other management actions on the Colorado River. The purpose of the long-term experimental plan is twofold: (1) to increase the scientific understanding of the ecosystem and (2) to improve and protect important downstream resources. The proposed plan would implement a structured, longterm program of experimentation to include dam operations, potential modifications to Glen Canyon Dam intake structures, and other management actions such as removal of nonnative fish species. The development of the long-term experimental plan continues efforts begun by the GCDAMP to protect resources downstream of Glen Canyon Dam, including Grand Canyon, through adaptive management and scientific experimentation. The LTEP EIS will rely on the extensive scientific studies that have been undertaken as part of the adaptive management program by the U.S. Geological Survey?s (USGS) Grand Canyon Monitoring and Research Center (GCMRC), one of the four research stations within the USGS Southwest Biological Science Center. On April 10 and 11, 2007, at the behest of Reclamation, the GCMRC convened a workshop with scientific experts to identify one or more scientifically credible, long-term experimental options for Reclamation to consider for the LTEP EIS that would be consistent with the purpose and need for the plan. Workshop participants included government, academic, and private scientists with broad experience in the Colorado River in Grand Canyon and regulated rivers around the world. Resource managers and GCDAMP participants were also present on the second day of the workshop. In advance of the workshop, Reclamation and LTEP EIS cooperating agencies identified 14 core scientific questions. Workshop participants were asked to consider how proposed options would address these questions, which fall primarily into four areas: (1) conservation of endangered humpback chub (Gila cypha) and other high-priority biological resources, (2) conservation of sediment resources, (3) enhancement of recreational resources, and (4) preservation of cultural resources. A secondary objective of the workshop was the evaluation of four long-term experimental options developed by the GCDAMP Science Planning Group (SPG) (appendix B). The flow and nonflow treatments called for in the four experimental options were an important starting point for workshop discussions. At the beginning of the workshop, participants were provided with the final LTEP EIS scoping report prepared by Reclamation. Participants were also advised that Reclamation had committed to ?make every effortEto ensure that a new population of humpback chub is established in the mainstem or one or more of the tributaries within Grand Canyon? in the 1995 Operation of Glen Canyon Dam Final Environmental Impact Statement (U.S. Department of the Interior, 1995). This decision was consistent with the U.S. Fish and Wildlife Service?s 1995 bi

Open-File Report↗
USGS2009

Sample collection of ash and burned soils from the October 2007 southern California Wildfires

Between November 2 through 9, 2007 scientists from the U.S. Geological Survey (USGS) collected samples of ash and burned soils from 28 sites in six areas burned as a result of the Southern California wildfires of October 2007, including the Harris, Witch, Santiago, Ammo, Canyon, and Grass Valley Fires. The primary goal of this sampling and analysis effort was to understand how differences in ash and burned soil composition relate to vegetation type, underlying bedrock geology, burn intensity, and residential versus wildland. Sampling sites were chosen with the input of local experts from the USGS Water Resources and Biological Resources Disciplines to help understand possible effects of the fires on water supplies, ecosystems, and endangered species. The sampling was also carried out in conjunction with detailed field analysis of the spectral reflectance characteristics of the ash, so that chemical and mineralogical characteristics of the field samples could be used to help interpret data collected as part of an airborne, hyperspectral remote-sensing survey of several of the burned areas in mid-late November, 2007. This report presents an overview of the field sampling methodologies used to collect the samples, includes representative photos of the sites sampled, and summarizes important characteristics of each of the collection sites. In this report we use the term “ash” to refer collectively to white mineral ash, which results from full combustion of vegetation and black charred organic matter from partial combustion of vegetation or other materials. These materials were found to be intermingled as a deposited residue on the soil surface following the Southern California fires of 2007.

Open-File Report↗
USGS2002

Potential effects of structural controls and street sweeping on stormwater loads to the lower Charles River, Massachusetts

The water quality of the lower Charles River is periodically impaired by combined sewer overflows (CSOs) and non-CSO stormwater runoff. This study examined the potential non-CSO load reductions of suspended solids, fecal coliform bacteria, total phosphorus, and total lead that could reasonably be achieved by implementation of stormwater best management practices, including both structural controls and systematic street sweeping. Structural controls were grouped by major physical or chemical process; these included infiltration-filtration (physical separation), biofiltration-bioretention (biological mechanisms), or detention-retention (physical settling). For each of these categories, upper and lower quartiles, median, and average removal efficiencies were compiled from three national databases of structural control performance. Removal efficiencies obtained indicated a wide range of performance. Removal was generally greatest for infiltration-filtration controls and suspended solids, and least for biofiltration-bioretention controls and fecal coliform bacteria. Street sweeping has received renewed interest as a water-quality control practice because of reported improvements in sweeper technology and the recognition that opportunities for implementing structural controls are limited in highly urbanized areas. The Stormwater Management Model that was developed by the U.S. Geological Survey for the lower Charles River Watershed was modified to simulate the effects of street sweeping in a single-family land-use basin. Constituent buildup and washoff variable values were calibrated to observed annual and storm-event loads. Once calibrated, the street sweeping model was applied to various permutations of four sweeper efficiencies and six sweeping frequencies that ranged from every day to once every 30 days. Reduction of constituent loads to the lower Charles River by the combined hypothetical practices of structural controls and street sweeping was estimated for a range of removal efficiencies because of their inherent variability and uncertainty. This range of efficiencies, with upper and lower estimates, provides reasonable bounds on the load that could be removed by the practices examined. The upper estimated load reduction from combined street sweeping and structural controls, as a percentage of the total non-CSO load entering the lower Charles River downstream of Watertown Dam, was 44 percent for suspended solids, 34 percent for total lead, 14 percent for total phosphorus, and 17 percent for fecal coliform bacteria. The lower estimated load reduction from combined street sweeping and structural controls from non-CSO sources downstream of Watertown Dam, was 14 percent for suspended solids, 11 percent for total lead, 4.9 percent for total phosphorus, and 7.5 percent for fecal coliform bacteria. Load reductions by these combined management practices can be a small as 1.4 percent for total phosphorus to about 4 percent for the other constituents if the total load above Watertown Dam is added to the load from below the dam. Although the reductions in stormwater loads to the lower Charles River from the control practices examined appear to be minor, these practices would likely provide water-quality benefits to portions of the river during those times that they are most impaired-during and immediately after storms. It should also be recognized that only direct measurements of changes in stormwater loads before and after implementation of control practices can provide definitive evidence of the beneficial effects of these practices on water-quality conditions in the lower Charles River.

Massachusetts↗
USGS1996

U. S. Geological Survey programs in Michigan

For more than 100 years, the United States Geological Survey (USGS) has provided earth-science information on which managers, scientists, and other interested citizens base decisions regarding Michigan’s natural resources and natural hazards. The non-regulatory and scientific nature of the USGS work ensures that our products are technically sound, unbiased, and equally accessible and available to all interested parties. The various programs of the USGS in Michigan reflect a response to the citizens of Michigan and their need for geologic, topographic, biologic, and hydrologic information. Much of the work of the USGS in Michigan is part of cooperative programs in which the diversity of interests among local, regional, State, Tribal, and Federal agencies is accommodated through joint planning and funding.

Michigan↗
USGS2015

Chesapeake Bay impact structure: A blast from the past

About 35 million years ago, a 2-mile-wide meteorite smashed into Earth in what is now the lower Chesapeake Bay in Virginia. The oceanic impact vaporized, melted, fractured, and displaced rocks and sediments and sent billions of tons of water, sediments, and rocks into the air. Glassy particles of solidified melt rock rained down as far away as Texas and the Caribbean. Large tsunamis affected most of the North Atlantic basin. The resulting impact structure is more than 53 miles wide and has a 23-mile-wide, filled central crater surrounded by collapsed sediments. Now buried by hundreds of feet of younger sediments, the Chesapeake Bay impact structure is among the 20 largest known impact structures on Earth. Since its discovery in the early 1990s, scientists have conducted deep drilling and geophysical surveys of the impact structure to find out more about its size, composition, structure, age, and biological effects and to understand its lingering influences on the regional groundwater system. These efforts culminated in the drilling of a 1-mile-deep, continuously sampled corehole in 2005 by an international group of scientists and agencies.

Chesapeake Bay↗
USGS2009

Salton Sea Ecosystem Monitoring Project

The Salton Sea is critically important for wintering and breeding waterbirds, but faces an uncertain future due to water delivery reductions imposed by the Interstate and Federal Quantification Settlement Agreement of 2003. The current preferred alternative for wetland restoration at the Salton Sea is saline habitat impoundments created to mitigate the anticipated loss of wetland habitat. In 2006, a 50-hectare experimental complex that consisted of four inter-connected, shallow water saline habitat ponds (SHP) was constructed at the southeastern shoreline of the Salton Sea and flooded with blended waters from the Alamo River and Salton Sea. The present study evaluated ecological risks and benefits of the SHP concept prior to widespread restoration actions. This study was designed to evaluate (1) baseline chemical, nutrient, and contaminant measures from physical and biological constituents, (2) aquatic invertebrate community structure and colonization patterns, and (3) productivity of and contaminant risks to nesting waterbirds at the SHP. These factors were evaluated and compared with those of nearby waterbird habitat, that is, reference sites.

Open-File Report↗
USGS2013

Significance of headwater streams and perennial springs in ecological monitoring in Shenandoah National Park

Shenandoah National Park has been monitoring water chemistry and benthic macroinvertebrates in stream ecosystems since 1979. These monitoring efforts were designed to assess the status and trends in stream condition associated with atmospheric deposition (acid rain) and changes in forest health due to gypsy moth infestations. The primary objective of the present research was to determine whether the current long-term macroinvertebrate and water-quality monitoring program in Shenandoah National Park was failing to capture important information on the status and trends in stream condition by not sufficiently representing smaller, headwater streams. The current benthic-macroinvertebrate and water-chemistry sampling designs do not include routine collection of data from streams with contributing watershed areas smaller than 100 hectares, even though these small streams represent the overwhelming proportion of total stream length in the park. In this study, we sampled headwater sites, including headwater stream reaches (contributing watershed area approximately 100 hectares (ha) and perennial springs, in the park for aquatic macroinvertebrates and water chemistry and compared the results with current and historical data collected at long-term ecological monitoring (LTEM) sites on larger streams routinely sampled as part of ongoing monitoring efforts. The larger purpose of the study was to inform ongoing efforts by park managers to evaluate the effectiveness and efficiency of the current aquatic monitoring program in light of other potential stressors (for example, climate change) and limited resources. Our results revealed several important findings that could influence management decisions regarding long-term monitoring of park streams. First, we found that biological indicators of stream condition at headwater sites and perennial springs generally were more indicative of lower habitat quality and were more spatially variable than those observed at sites on routinely monitored larger streams. We hypothesized that poorer stream condition observed in smaller streams was due to stream drying that occurs more frequently in headwater areas. We also found that biological and water-chemistry measures responded differently to landscape drivers. Variation in most biological endpoints was driven primarily by stream size and was only secondarily associated with bedrock geology. In contrast, water chemistry showed essentially the opposite pattern, with underlying geology explaining much of the variation and stream size being of secondary importance. Therefore, expanding the LTEM program to include headwater areas would yield substantially different biological information, whereas broad inferences regarding spatial patterns in water chemistry would probably not change. Although significant differences in community composition were observed among streams of different sizes, no taxa were unique to headwater sites. All taxa collected at the 45 headwater sites also had been collected at one or more LTEM sites during one or more years. This observation indicates that headwater sites in the park may be structured by biotic nestedness; consequently, focusing management efforts on preserving the species pool at the larger LTEM sites would likely result in the protection of most taxa parkwide. Finally, linkages (correlations) between water chemistry and biological measures of stream condition were signficantly stronger when assessed at the LTEM sites than when assessed at the springs or headwater sites, indicating that conditions at downstream sites may be better indicators of water-quality trends.

Virginia↗
USGS2017

Skagit River coho salmon life history model—Users’ guide

Natural resource management is conducted in the context of multiple anthropogenic stressors and is further challenged owing to changing climate. Experiments to determine the effects of climate change on complex ecological systems are nearly impossible. However, using a simulation model to synthesize current understanding of key ecological processes through the life cycle of a fish population can provide a platform for exploring potential effects of and management responses to changing conditions. Potential climate-change scenarios can be imposed, responses can be observed, and the effectiveness of potential actions can be evaluated. This approach is limited owing to future conditions likely deviating in range and timing from conditions used to create the model so that the model is expected to become obsolete. In the meantime, however, the modeling process explicitly states assumptions, clarifies information gaps, and provides a means to better understand which relationships are robust and which are vulnerable to changing climate by observing whether and why model output diverges from actual observations through time. The purpose of the model described herein is to provide such a decision-support tool regarding coho ( Oncorhynchus kisutch ) salmon for the Sauk-Suiattle Indian Tribe of Washington State. The Skagit coho salmon model is implemented in a system dynamics format and has three primary stocks—(1) predicted smolts, (2) realized smolts, and (3) escapement. “Predicted smolts” are the number of smolts expected based on the number of spawners in any year and the Ricker production curve. Pink salmon ( Oncorhynchus gorbuscha ) return to the Skagit River in odd years, and when they overlap with juvenile rearing coho salmon, coho smolt production is substantially higher than in non-pink years. Therefore, the model uses alternative Ricker equations to predict smolts depending on whether their juvenile year was a pink or non-pink year. The stock “realized smolts” is calculated based on the expected effect of streamflow conditions to alter the productivity predicted by the Ricker curve. Adverse conditions include scouring flow events that occur when redds are present; high-flow events during winter on juveniles, which can cause fish displacement and adverse water turbidity; and extremely low flows in summer. The stock “escapement” represents the fish remaining after accounting for ocean mortality and harvest. Ocean mortality has been linked with indices of ocean conditions, which are related to ocean biological productivity. Ocean survival also may have a density-dependent component such that lower survival is associated with higher numbers of smolts. The model allows the user to change certain model parameters and inputs, and choose among alternative predictors for certain modeled relations.

Washington↗
USGS1972

Effects of acid mine drainage on fish and macroinvertebrates of the Tioga River, Pennsylvania and New York

Acid water from abandoned coal mines in the vicinity of Morris Run and Blossburg, Pa., severely alter the aquatic environment of the Tioga River. From Morris Run to Crooked Creek, a reach of 19 miles, the river bed is influenced by a smothering blanket of heavy metal precipitates and highly acidic water. Biologically, this reach of the river is devoid of fishlife and nearly devoid of benthic macroinvertebrates. Downstream from Crooked Creek the water quality and biota are slowly restored. At Presho, N.Y., the river again supports an abundant and diversified population of fish and bottom-dwelling organisms.

New York, Pennsylvania↗