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Fort Collins Science Center

The U.S. Geological Survey's Fort Collins Science Center (FORT) is one of 17 USGS biological science centers nationwide. FORT conducts research and develops technical applications to assist land managers in understanding and managing biological resources, habitats, and ecosystems. Although the majority of FORT's activities are conducted within the 15-state Central Region of the USGS, many FORT projects are national or international in scope. FORT serves all Department of the Interior land management bureaus and other natural resource agencies. In addition, FORT scientists partner with DOI and other federal entities such as CDC, DOE, EPA, NASA, NIH, and USDA to share expertise and resources. FORT also partners with several universities and works cooperatively with states and nongovernmental organizations. Products and services include reports and publications, predictive models and software, maps and GIS products, and other technical assistance in the form of meetings, workshops, training, field visits, and needs assessments.

Fact Sheet↗

Predicting water quality by relating secchi-disk transparency and chlorophyll a measurements to Landsat satellite imagery for Michigan inland lakes, 2001-2006

The State of Michigan has more than 11,000 inland lakes; approximately 3,500 of these lakes are greater than 25 acres. The USGS, in cooperation with the Michigan Department of Environmental Quality (MDEQ), has been monitoring the quality of inland lakes in Michigan through the Lake Water Quality Assessment monitoring program. Approximately 100 inland lakes will be sampled per year from 2001 to 2015. Volunteers coordinated by MDEQ started sampling lakes in 1974, and continue to sample to date approximately 250 inland lakes each year through the Cooperative Lakes Monitoring Program (CLMP), Michigan’s volunteer lakes monitoring program. Despite this sampling effort, it is still impossible to physically collect the necessary water-quality measurements for all 3,500 Michigan inland lakes. Therefore, a technique was used by USGS, modeled after Olmanson and others (2001), in cooperation with MDEQ that uses satellite remote sensing to predict water quality in unsampled inland lakes greater than 25 acres. Water-quality characteristics that are associated with water clarity can be predicted for Michigan inland lakes by relating sampled measurements of secchi-disk transparency (SDT) and chlorophyll a concentrations (Chl- a ), to satellite imagery. The trophic state index (TSI) which is an indicator of the biological productivity can be calculated based on SDT measurements, Chl- a concentrations, and total phosphorus (TP) concentrations measured near the lake’s surface. Through this process, unsampled inland lakes within the fourteen Landsat satellite scenes encompassing Michigan can be translated into estimated TSI from either predicted SDT or Chl- a (fig. 1).

Michigan↗

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory-Processing, taxonomy, and quality control of benthic macroinvertebrate samples

Qualitative and quantitative methods to process benthic macroinvertebrate (BMI) samples have been developed and tested by the U.S. Geological Survey?s National Water Quality Laboratory Biological Group. The qualitative processing method is based on visually sorting a sample for up to 2 hours. Sorting focuses on attaining organisms that are likely to result in taxonomic identifications to lower taxonomic levels (for example, Genus or Species). Immature and damaged organisms are also sorted when they are likely to result in unique determinations. The sorted sample remnant is scanned briefly by a second person to determine if obvious taxa were missed. The quantitative processing method is based on a fixed-count approach that targets some minimum count, such as 100 or 300 organisms. Organisms are sorted from randomly selected 5.1- by 5.1-centimeter parts of a gridded subsampling frame. The sorted remnant from each sample is resorted by a second individual for at least 10 percent of the original sort time. A large-rare organism search is performed on the unsorted remnant to sort BMI taxa that were not likely represented in the sorted grids. After either qualitatively or quantitatively sorting the sample, BMIs are identified by using one of three different types of taxonomic assessment. The Standard Taxonomic Assessment is comparable to the U.S. Environmental Protection Agency Rapid Bioassessment Protocol III and typically provides Genus- or Species-level taxonomic resolution. The Rapid Taxonomic Assessment is comparable to the U.S. Environmental Protection Agency Rapid Bioassessment Protocol II and provides Familylevel and higher taxonomic resolution. The Custom Taxonomic Assessment provides Species-level resolution whenever possible for groups identified to higher taxonomic levels by using the Standard Taxonomic Assessment. The consistent use of standardized designations and notes facilitates the interpretation of BMI data within and among water-quality studies. Taxonomic identifications are quality assured by verifying all referenced taxa and randomly reviewing 10 percent of the taxonomic identifications performed weekly by Biological Group taxonomists. Taxonomic errors discovered during this review are corrected. BMI data are reviewed for accuracy and completeness prior to release. BMI data are released phylogenetically in spreadsheet format and unprocessed abundances are corrected for laboratory and field subsampling when necessary.

Open-File Report↗

Some limnological aspects of 20 selected lakes in Eagan and Apple Valley, Minnesota

Selected physical, chemical, and biological parameters were determined to assess the quality of 20 lakes in the cities of Eagan and Apple Valley, Minn. All the lakes are eutrophic except Holland and Fish Lakes, which are mesotrophic. Some lakes (including Fish Lake) have storm sewer inlets but are not discernibly different in quality than lakes with no such inlets.

Minnesota↗

1978 Water Quality Laboratory services catalog

The information in this catalog is provided to assist field personnel in the selection of determinations, the estimation of costs, the calculation of sample volume requirements, the identification of the necessary sample treatment and in the evaluation of the precision of the laboratory data. The major section of the catalog is the table of determinations which includes the cost, required sample volume, sample treatment, and precision. This table is divided into three sections: Inorganic determinations, organic determinations, and biological determinations. The "Inorganic determinations" are subdivided into major ions, major nutrients, trace constituents, physical parameters, and radiochemical measurements. The "Organic determinations" are subdivided into gross measures, pesticides, and munition products. The "Biological determinations" are subdivided into gross measures, periphyton, phytoplankton and benthic invertebrates. Regardless of the outline form attempted, exceptions and gray areas were encountered. Generally, exceptions were placed into the groups based on a sample designation. As a result, frequent use of the index may be required until users become familiar with the catalog.

Open-File Report↗

Physical, chemical, and biological data for detailed study of irrigation drainage in the Klamath Basin, California and Oregon, 1990-92

Physical, chemical, and biological data were collected between 1990 and 1992 as part of a detailed study by the U.S. Department of Interior of the effects of irrigation drainage on aquatic resources in the Klamath Basin of California and Oregon. Most of the sites for data collection were in and around the upper and lower sump of Tule Lake, in the Tule Lake National Wildlife Refuge, and along major drains in Lower Klamath National Wildlife Refuge. The physical and chemical data consist of particle-size determinations and concentrations of carbon, mercury, arsenic, chlorophenoxy acid, and organochlorine, organophosphate, and carbamate pesticides in bottom sediment; and concentrations of organophosphate, carbamate, and pyrethroid pesticides, major and trace inorganic constituents, nitrogen, phosphorus, and organic carbon in water. Continuous dissolved oxygen, pH, specific conduc- tance, and temperature data from selected sites in 1991 and 1992 are presented in graphical form to summarize the diel water-quality conditions. The biological data consists of concentrations of inorganic constituents and organochlorine pesticides in tissue, invertebrate and fish population surveys, fish health surveys, frog call surveys, egg shell thickness of avian eggs, and in situ and static toxicity bioassay data collected in 1991 and 1992 using aquatic bacteria, plants, invertebrates, fish, and bird species as test organisms.

Open-File Report↗

Endocrine active chemicals and endocrine disruption in Minnesota streams and lakes: Implications for aquatic resources, 1994-2008

The U.S. Geological Survey, in cooperation with St. Cloud State University, Minnesota Department of Health, Minnesota Pollution Control Agency, Minnesota Department of Natural Resources, Metropolitan Council Environmental Services, and the University of Minnesota, has conducted field monitoring studies and laboratory research to determine the presence of endocrine active chemicals and the incidence of endocrine disruption in Minnesota streams and lakes during 1994–2008. Endocrine active chemicals are chemicals that interfere with the natural regulation of endocrine systems, and may mimic or block the function of natural hormones in fish or other organisms. This interference commonly is referred to as endocrine disruption. Indicators of endocrine disruption in fish include vitellogenin (female egg yolk protein normally expressed in female fish) in male fish, oocytes present in male fish testes, reduced reproductive success, and changes in reproductive behavior. The results from a series of studies during 1994–2008 demonstrate that endocrine active chemicals are present in Minnesota surface waters, indicating that aquatic organism exposure is likely. Endocrine active chemicals have been identified in wastewater-treatment plant effluent and surface waters downstream from discharge of wastewater-treatment plant effluent throughout Minnesota at low concentrations. Biological indicators of endocrine disruption have been detected in wild fish throughout Minnesota at sites directly downstream from wastewater-treatment plant effluent, indicating that endocrine active chemicals in effluent contribute to endocrine disruption in fish. This finding was confirmed in a controlled study exposing fathead minnows to wastewater-treatment plant effluent at an onsite fish exposure laboratory. During this controlled study, changes in biological responses coincided with changes in wastewater-treatment plant effluent composition demonstrating that effluent effects on fish endocrine systems are temporally variable. Although chemicals contributing to endocrine disruption in fish are complex, several laboratory studies have further confirmed that certain classes of chemicals, such as hormones and alkylphenols, which are components of wastewater-treatment plant effluent, affect the endocrine systems of fish through biochemical, structural, and behavioral disruption. Although these studies indicate that wastewater-treatment plant effluent is a conduit for endocrine active chemicals to surface waters, endocrine active chemicals also were present in surface waters with no obvious wastewater-treatment plant effluent sources. Endocrine active chemicals were detected and indicators of endocrine disruption in fish were measured at numerous sites upstream from discharge of wastewater-treatment plant effluent. These observations indicate that other unidentified sources of endocrine active chemicals exist, such as runoff from land surfaces, atmospheric deposition, inputs from onsite septic systems, or other groundwater sources. Alternatively, some endocrine active chemicals may not yet have been identified or measured. The presence of biological indicators of endocrine disruption in male fish indicates that the fish are exposed to endocrine active chemicals. However indicators of endocrine disruption in male fish does not indicate an effect on fish reproduction or changes in fish populations.

Minnesota↗

Snakes in the wrong places: Gordon Rodda’s career in invasive species research

When USGS research zoologist Gordon G. Rodda was a graduate student at Cornell University studying behavioral biology of alligators —or later, completing a post-doc at the Smithsonian Institute studying the social behavior of green iguanas in Venezuela or following that, as a statistics and sociobiology instructor at the University of Tennessee—he did not foresee that his professional future was in snakes. Lots of snakes, and in places they don’t belong.

Report↗

Fish stocking in protected areas: Summary of a workshop

Native and nonnative sport fish have been introduced into the majority of historically fishless lakes in wilderness, generating conflicts between managing wilderness as natural ecosystems and providing opportunities for recreation. Managers faced with controversial and difficult decisions about how to manage wilderness lakes may not always have ready access to research relevant to these decisions. To address this problem, and to expose scientists to the concerns and constraints of managers and wilderness users, a workshop was held in October 1998 at the Flathead Lake Biological Station in Polson, Montana. Participants included 43 scientists, state and federal managers, wilderness users and advocates and students. Four subject areas were addressed: federal, state, tribal and user perspectives, community and ecosystem effects, species effects and management recommendations. Papers from the workshop are being developed for an issue of the journal Ecosystems.

Proceedings↗

The United States National Climate Assessment - Alaska Technical Regional Report

The Alaskan landscape is changing, both in terms of effects of human activities as a consequence of increased population, social and economic development and their effects on the local and broad landscape; and those effects that accompany naturally occurring hazards such as volcanic eruptions, earthquakes, and tsunamis. Some of the most prevalent changes, however, are those resulting from a changing climate, with both near term and potential upcoming effects expected to continue into the future. Alaska's average annual statewide temperatures have increased by nearly 4°F from 1949 to 2005, with significant spatial variability due to the large latitudinal and longitudinal expanse of the State. Increases in mean annual temperature have been greatest in the interior region, and smallest in the State's southwest coastal regions. In general, however, trends point toward increases in both minimum temperatures, and in fewer extreme cold days. Trends in precipitation are somewhat similar to those in temperature, but with more variability. On the whole, Alaska saw a 10-percent increase in precipitation from 1949 to 2005, with the greatest increases recorded in winter. The National Climate Assessment has designated two well-established scenarios developed by the Intergovernmental Panel on Climate Change (Nakicenovic and others, 2001) as a minimum set that technical and author teams considered as context in preparing portions of this assessment. These two scenarios are referred to as the Special Report on Emissions Scenarios A2 and B1 scenarios, which assume either a continuation of recent trends in fossil fuel use (A2) or a vigorous global effort to reduce fossil fuel use (B1). Temperature increases from 4 to 22°F are predicted (to 2070-2099) depending on which emissions scenario (A2 or B1) is used with the least warming in southeast Alaska and the greatest in the northwest. Concomitant with temperature changes, by the end of the 21st century the growing season is expected to lengthen by 15-25 days in some areas of Alaska, with much of that corresponding with earlier spring snow melt. Future projections of precipitation (30-80 years) over Alaska show an increase across the State, with the largest changes in the northwest and smallest in the southeast. Because of increasing temperatures and growing season length, however, increased precipitation may not correspond with increased water availability, due to temperature related increased evapotranspiration. The extent of snow cover in the Northern Hemisphere has decreased by about 10 percent since the late 1960s, with stronger trends noted since the late 1980s. Alaska has experienced similar trends, with a strong decrease in snow cover extent occurring in May. When averaged across the State, the disappearance of snow in the spring has occurred from 4 to 6 days earlier per decade, and snow return in fall has occurred approximately 2 days later per decade. This change appears to be driven by climate warming rather than a decrease in winter precipitation, with average winter temperatures also increasing by about 2.5°F. The extent of sea ice has been declining, as has been widely published in both national and scientific media outlets, and is projected to continue to decline during this century. The observed decline in annual sea ice minimum extent (September) has occurred more rapidly than was predicted by climate models and has been accompanied by decreases in ice thickness and in the presence of multi-year ice. This decrease was first documented by satellite imagery in the late 1970s for the Bering and Chukchi Seas, and is projected to continue, with the potential for the disappearance of summer sea ice by mid- to late century. A new phenomenon that was not reported in previous assessments is ocean acidification. Uptake of carbon dioxide (CO2) by oceans has a significant effect on marine biogeochemistry by reducing seawater pH. Ocean acidification is of particular concern in Alaska, because cold sea water absorbs CO2 more rapidly than warm water, and a decrease in sea ice extent has allowed increased sea surface exposure and more uptake of CO2 into these northern waters. Ocean acidification will likely affect the ability of organisms to produce and maintain shell material, such as aragonite or calcite (calcium carbonate minerals structured from carbonate ions), required by many shelled organism, from mollusks to corals to microscopic organisms at the base of the food chain. Direct biological effects in Alaska further along the food chain have yet to be studied and may vary among organisms. Some of the potentially most significant changes to Alaska that could result from a changing climate are the effects on the terrestrial cryosphere - particularly glaciers and permafrost. Alaskan glaciers are changing at a rapid rate, the primary driver appearing to be temperature. Statewide, glaciers lost 13 cubic miles of ice annually from the 1950s to the 1990s, and that rate doubled in the 2000s. However, like temperature and precipitation, glacier ice loss is not spatially uniform; most glaciers are losing mass, yet some are growing (for example Hubbard Glacier in southeast Alaska). Alaska glaciers with the most rapid loss are those terminating in sea water or lakes. With this increasing rate of melt, the contribution of surplus fresh water entering into the oceans from Alaska's glaciers, as well as those in neighboring British Columbia, Canada, is approximately 20 percent of that contributed by the Greenland Ice Sheet. Permafrost degradation (that is, the thawing of ice-rich soils) is currently (2012) impacting infrastructure and surface-water availability in areas of both discontinuous and continuous ground ice. Over most of the State, the permafrost is warming, with increasing temperatures broadly consistent with increasing air temperatures. On the Arctic coastal plain of Alaska, permafrost temperatures showed some cooling in the 1950s and 1960s but have been followed by a roughly 5°F increase since the 1980s. Many areas in the continuous permafrost zone have seen increases in temperature in the seasonally active layer and a decrease in re-freezing rates. Changes in the discontinuous permafrost zone are initially much more observable due to the resulting thermokarst terrain (land surface formed as ice rich permafrost thaws), most notable in boreal forested areas. Climate warming in Alaska has potentially broad implications for human health and food security, especially in rural areas, as well as increased risk for injury with changing winter ice conditions. Additionally, such warming poses the potential for increasing damage to existing water and sanitation facilities and challenges for development of new facilities, especially in areas underlain by permafrost. Non-infectious and infectious diseases also are becoming an increasing concern. For example, from 1999 to 2006 there was a statistically significant increase in medical claims for insectbite reactions in five of six regions of Alaska, with the largest percentage increase occurring in the most northern areas. The availability and quality of subsistence foods, normally considered to be very healthy, may change due to changing access, changing habitats, and spoilage of meat in food storage cellars. These and other trends and potential outcomes resulting from a changing climate are further described in this report. In addition, we describe new science leadership activities that have been initiated to address and provide guidance toward conducting research aimed at making available information for policy makers and land management agencies to better understand, address, and plan for changes to the local and regional environment. This report cites data in both metric and standard units due to the contributions by numerous authors and the direct reference of their data.

Alaska↗

Spatial and temporal patterns in streamflow, water chemistry, and aquatic macroinvertebrates of selected streams in Fairfax County, Virginia, 2007–18

Urbanization substantially alters the landscape in ways that can impact stream hydrology, water chemistry, and the health of aquatic communities. Stormwater best management practices (BMPs) are the primary tools used to mitigate the effects of urban stressors such as increased runoff, decreased baseflow, and increased nutrient and sediment transport. To date, Fairfax County Virginia’s stormwater management program has made substantial investments into the implementation of both structural and nonstructural BMPs aimed at restoring and protecting watersheds. The U.S. Geological Survey (USGS), in cooperation with Fairfax County, Virginia, established a long-term water-resources monitoring program to evaluate the watershed-scale effects of these investments. Monitoring began at 14 stations in 2007 and was expanded to 20 stations in 2013. This report utilized the first 10 years of data collection to (1) assess water quantity and quality, as well as ecological condition; (2) compute annual nutrient and sediment loads; and (3) evaluate trends in streamflow, water quality, and ecological condition. Efforts are underway to link the biotic and abiotic patterns described herein to watershed management practices as well as factors such as land use change, public works infrastructure, and climate. Hydrologic, chemical, and benthic macroinvertebrate community conditions in the streams monitored were similar to those observed in other studies of urban streams. Multidecadal trends in baseflow indices and runoff ratios at long-term Chesapeake Bay Non-tidal Network streamgages (CB-NTN) indicate a decrease in groundwater recharge and increase in storm runoff as a result of urbanization. Streamflow yields varied spatially with land cover, geology, and soil characteristics, whereas flashiness was positively related to impervious area. Dissolved oxygen typically was lowest in the Coastal Plain and across all Triassic Lowlands streams, and highest in the Piedmont. Dissolved oxygen concentrations generally were above Virginia’s minimum criterion of 4.0 milligrams per liter (mg/L), most violations occurred at Paul Spring Branch in the Coastal Plain during the warmest months of the year owing to increased chemical and biological oxygen demand. Typical pH values of the monitored streams centered on neutrality (pH = 7); however, diurnal fluctuations were most prevalent in the continuous pH data at Flatlick Branch (FLAT; a Triassic Lowlands station), as a result of increased photosynthesis catalyzed by phosphorus-rich geology. Specific conductance (SC) varied spatially owing to geology (highest at Triassic Lowlands stations) and anthropogenic disturbance (watersheds with high impervious land cover). Specific conductance typically was inversely related to streamflow except in winter months following deicing road salt applications, when values increased by several orders of magnitude. A significant increase in SC of about 2 percent per year was observed from the combined trend result of all monitoring stations over the 10-year period. Significant SC increases occurred at nearly all monitoring stations. Increasing trends were observed during winter and nonwinter months, which suggests that salts applied to deice roadways and other impervious surfaces are stored in the environment and released year-round. Suspended-sediment (SS) concentrations in monthly samples did not vary significantly between most stations, but typically were highest in the spring and lowest in the fall as a result of seasonal differences in streamflow and climate. Suspended-sediment yields ranged from 62 to 1,428 tons per square mile (ton/mi 2 ), with a median of 302 ton/mi 2 . Annual loads were greatest during the wettest water years (October 1-September 30; 2008, 2011, and 2014), with the greatest interannual variability occurring at Difficult Run above Fox Lake (DIFF) and South Fork Little Difficult Run (SFLIL). Suspended sediment was primarily composed of silts and clays; however, the proportion of sand in suspended sediment was related positively to streamflow. Cross-correlation analyses suggested the dominant sources of SS were streambank erosion and resuspension of in-channel material at DIFF and FLAT; whereas, upland sources and erosion of upper streambanks were more common at Dead Run (DEAD), Long Branch (LONG), and SFLIL. Median total phosphorus (TP) concentrations ranged from 0.016 to 0.077 mg/L, with a networkwide median of 0.022 mg/L, were highest in the warm season (April-September), and were composed primarily of dissolved phosphorous. Although TP concentrations were relatively low across the network, the highest concentrations were consistently at stations located in the Triassic Lowlands, owing to phosphorous-rich geology, and in the Coastal Plain, owing to the low-phosphorous sorptive capacity of those soils. A significant increase in TP concentration occurred in a few stations, but the combined trend results from all stations demonstrated a significant increase of about 4 percent per year. Networkwide increases were also observed in total dissolved phosphorus, orthophosphate, and total particulate phosphorus. The composition of TP shifted from dissolved to particulate as streamflow increased and for this reason loads primarily were composed of particulate phosphorous. Median annual TP loads were highest at FLAT and DEAD and ranged from 247 to 642 pounds per square mile (lbs/mi 2 ) networkwide. Interannual variability in phosphorous yields was apparent at most stations; the highest loading years were also the wettest years during the study period and coincident with the highest peak annual flows. Total nitrogen (TN) concentrations typically were low throughout the network with exceptions occurring at stations located in watersheds with a high density of septic infrastructure. Elevated TN concentrations also were observed in some watersheds without a high density of septic systems and may be attributable to geologic and soil properties that limit denitrification as well as other unknown anthropogenic inputs. Total nitrogen typically was dominated by nitrate during baseflows; however, the proportion of particulate nitrogen increased during stormflows. Total nitrogen yields were similar across stations, with medians ranging from about 3,600 to 6,300 lbs/mi 2 and were related to annual streamflow volume. Total nitrogen concentrations and flow-normalized concentrations decreased over the 10-year period at 7 stations, with median reductions of about 2.5 percent. Increasing trends were observed at the two stations with the highest median TN concentration (Captain Hickory Run and SFLIL, 3–5 mg/L), both watersheds contain a high density of septic infrastructure. The combined trend results from all stations revealed no trend in TN and a declining trend in nitrate of about 2 percent per year. Overall, benthic community metrics indicated that streams throughout Fairfax County were initially of poor health; however, many metrics show an improving trend (from poor to fair based on the Fairfax County Index of Biological Integrity [IBI]). Significant increasing trends in IBI occurred at the network-scale and at 4 individual stations; additionally, scores improved by at least 1 qualitative category (for example, poor to fair, fair to good) at 11 of the 14 stations between 2009 (the first year all 14 stations were sampled) and 2017. Changes in all metrics suggest that the biodiversity, function, and condition of streams in Fairfax County are improving, but some of these improvements are driven by increased diversity and percent composition of organisms that are tolerant of the urban environment.

Virginia↗

2011 Georgiana Slough non-physical barrier performance evaluation project report

The Sacramento River and its tributaries support populations of anadromous fish species including winter-run, spring-run, fall-run, and late fall–run Chinook salmon ( Oncorhynchus tshawytscha ); and steelhead ( O. mykiss ). Several of these species are listed as threatened or endangered under the California Endangered Species Act (CESA), federal Endangered Species Act (ESA), or both. These species spawn and rear in Sacramento River tributaries; adults use the mainstem Sacramento River for primarily upstream migration and juveniles use it for downstream migration. Juvenile Chinook salmon and steelhead migrate through the lower river during winter and spring. During their downstream migration, juvenile salmonids encounter alternative pathways, such as Sutter and Steamboat Sloughs, the Sacramento–San Joaquin Delta (Delta), Delta Cross Channel (DCC), and Georgiana Slough. Likewise, sturgeon juveniles migrate downstream in the Sacramento River basin to the Delta, utilizing the distributary channels to rear within and migrate through the system. Georgiana Slough is a natural channel that allows water and fish to move into the interior Delta. Previous studies have demonstrated that juvenile Chinook salmon experience greater mortality when migrating into Georgiana Slough than those juveniles that continue to migrate downstream in the Sacramento River (Perry 2010). Movement and/or diversion of these fish into the interior and south Delta increases the likelihood of losses through predation, entrainment into non-project Delta diversions, and mortality associated with the State Water Project (SWP) and Central Valley Project (CVP) pumping facilities in the south Delta (Perry 2010; NMFS 2009). Figure ES-1 shows the migration pathways in the lower Sacramento River and Delta for outmigrating anadromous salmonids, and the location of the DCC, and the SWP and CVP pumping facilities in the south Delta. Passage of juvenile salmonids from the Sacramento River into the interior Delta through the DCC can be reduced through seasonal closure of the radial gates (February through May); however, no similar protection is available to reduce the movement of juvenile salmonids from the Sacramento River into the interior Delta through Georgiana Slough. Flows into Georgiana Slough improve water quality and flushing in the interior Delta and free access encourages use by recreational boaters. Because of these benefits, alternatives to the installation of a physical barrier (i.e. radial gates), are being investigated. Under the ESA, the National Marine Fisheries Service (NMFS) issued the 2009 Biological and Conference Opinion for the Long‐Term Operations of the Central Valley Project and State Water Project (BO) for Chinook salmon and other listed anadromous fish species (NMFS 2009). Reasonable and Prudent Alternative (RPA) Action IV.1.3 of the BO requires the California Department of Water Resources (DWR) and the U.S. Bureau of Reclamation (Reclamation) to consider engineering solutions to reduce the diversion of juvenile salmonids from the Sacramento River into the interior and south Delta. DWR implemented the 2011 Georgiana Slough NonPhysical Barrier (GSNPB) Study to test the effectiveness of using a non-physical barrier, referred to as a behavioral Bio-Acoustic Fish Fence (BAFF), that combines three stimuli to deter juvenile Chinook salmon from entering Georgiana Slough: sound, high-intensity modulated light (previously known as stroboscopic light), and a bubble curtain. This report presents the results of the experimental tests conducted in 2011.

California↗

Water-quality data for the Talkeetna River and four streams in National Parks, Cook Inlet basin, Alaska, 1998

Five streams in the Cook Inlet Basin, Alaska, were sampled in 1998 to provide the National Park Service with baseline information on water quality. Four of these streams drain National Park Service land: Costello and Colorado Creeks in Denali National Park and Preserve, Johnson River in Lake Clark National Park and Preserve, and Kamishak River in Katmai National Park and Preserve. The fifth site was on the Talkeetna River, outside of national park boundaries. Samples of stream water, streambed sediments, and fish tissues were collected for chemical analyses. Biological and geomorphic information was also collected at each site. Nutrient concentrations in stream water were low and commonly were less than analytical detection limits. Analyses of fish tissues for 28 organochlorine compounds at Talkeetna River and Costello Creek produced just one detection. Hexachlorobenzene was detected at a concentration of 5.70 micrograms per kilogram in slimy sculpin from the Talkeetna River. Streambed sediment samples from the Talkeetna River had three organochlorine compounds at detectable levels; hexachlorobenzene was measured at 13 micrograms per kilogram and two other compounds were below the minimum reporting levels. At Colorado Creek, Johnson River, and Kamishak River, where fish samples were not collected, no organochlorine compounds were detected in streambed sediment samples. Several semivolatile organic compounds were detected at Colorado Creek and Costello Creek. Only one compound, dibenzothiophene, detected at Costello Creek at a concentration of 85 micrograms per kilogram was above the minimum reporting limit. No semivolatile organic compounds were detected at the Talkeetna, Kamishak, or Johnson Rivers. Trace elements were detected in both fish tissues and streambed sediments. Macroinvertebrate and fish samples contained few taxa at all sites. Total numbers of macroinvertebrate taxa ranged from 19 at the Johnson River to 38 at the Talkeetna River. Diptera were the most abundant and diverse order of macroinvertebrates at all sites. Total numbers of diptera taxa ranged from 8 at the Kamishak River to 19 at the Talkeetna River. Fish communities were represented by a maximum of nine taxa at the Talkeetna River and were absent at Colorado Creek. The Johnson River sampling site produced small numbers of juvenile Dolly Varden, and Costello Creek produced small numbers of both juvenile Dolly Varden and slimy sculpin.

Alaska↗

A new database on contaminant exposure and effects in terrestrial vertebrates for natural resource managers

The Biomonitoring of Environmental Status and Trends (BEST) program of the Department of the Interior is focused to identify and understand effects of contaminant stressors on biological resources under their stewardship. Despite the desire of many to continuously monitor the environmental health of our estuaries, much can be learned by summarizing existing temporal, geographic, and phylogenetic contaminant information. To this end, retrospective contaminant exposure and effects data for amphibians, reptiles, birds, and mammals residing within 30 km of Atlantic coast estuaries are being assembled through searches of published literature (e.g., Fisheries Review, Wildlife Review, BIOSIS Previews) and databases (e.g., US EPA Ecological Incident Information System; USGS Diagnostic and Epizootic Databases), and compilation of summary data from unpublished reports of government natural resource agencies, private conservation groups, and universities. These contaminant exposure and effect data for terrestrial vertebrates (CEE-TV) are being summarized using Borland dBASE in a 96- field format, including species, collection time and site coordinates, sample matrix, contaminant concentration, biomarker and bioindicator responses, and source of information (N>1500 records). This CEE-TV database has been imported into the ARC/INFO geographic information system (GIS), for purposes of examining geographic coverage and trends, and to identify critical data gaps. A preliminary risk assessment will be conducted to identify and characterize contaminants and other stressors potentially affecting terrestrial vertebrates that reside, migrate through or reproduce in these estuaries. Evaluations are underway, using specific measurement and assessment endpoints, to rank and prioritize estuarine ecosystems in which terrestrial vertebrates are potentially at risk for purposes of prediction and focusing future biomonitoring efforts.

Book chapter↗

An assessment of stream habitat and nutrients in the Elwha River basin: implications for restoration

The Elwha River was once famous for its 10 runs of anadromous salmon which included chinook that reportedly exceeded 45 kilograms. These runs either ceased to exist or were significantly depleted after the construction of the Elwha (1912) and Glines Canyon (1927) Dams, which resulted in the blockage of more than 113 kilometers of mainstem river and tributary habitat. In 1992, in response to the loss of the salmon runs in the Elwha River Basin, President George Bush signed the Elwha River Ecosystem and Fisheries Restoration Act, which authorizes the Secretary of the Interior to remove both dams for ecosystem restoration. The objective of this U.S. Geological Survey (USGS) study was to begin describing baseline conditions for assessing changes that will result from restoration. The first step was to review available physical, chemical, and biological information on the Elwha River Basin. We found that most studies have focused on anadromous fish and habitat and that little information is available on water quality, habitat classification, geomorphic processes, and riparian and aquatic biological communities. There is also a lack of sufficient data on baseline conditions for assessing future changes if restoration occurs. The second component of this study was to collect water-quality and habitat data, filling information gaps. This information will permit a better understanding of the relation between physical habitat and nutrient conditions and changes that may result from salmon restoration. We collected data in the fall of 1997 and found that the concentrations of nitrogen and phosphorous were generally low, with most samples having concentrations below detection limits. Detectable concentrations of nitrogen were associated with sites in the lower reach of the Elwha River, whereas the few detections of phosphorus were at sites throughout the basin. Nutrient data indicate that the Elwha River and its tributaries are oligotrophic. Results of the stream classification indicated that most of the habitat that would be usable by salmon is found in the mainstem of the Elwha River due to natural gradient barriers at the lower end of most tributaries. Habitat is diverse in the mainstem due to large woody debris accumulations and the existence of secondary channels. We concluded that restoring salmon runs to the Elwha River system will affect the ecosystem profoundly. Decaying carcasses of migrating salmon will be the source of large quantities of nutrients to the Elwha River. The complex instream habitat of the mainstem will enhance cycling of these nutrients because carcasses will be retained long enough to be assimilated thereby increasing primary and secondary production, size of immature salmonids, and overall higher salmon recruitment.

Washington↗

Ecological requirements for pallid sturgeon reproduction and recruitment in the Missouri River—A synthesis of science, 2005 to 2012

This report is intended to synthesize the state of the scientific understanding of pallid sturgeon ecological requirements to provide recommendations for future science directions and context for Missouri River restoration and management decisions. Recruitment of pallid sturgeon has been low to non-existent throughout its range. Emerging understanding of the genetic structure of pallid sturgeon populations sets a broad framework for species and river management decisions, including decisions about managing the future genetic diversity of the species, but also decisions about where and what type of river restoration actions will be effective for subpopulations of this highly migratory species. Adult pallid sturgeon may migrate hundreds of kilometers (km) to spawn and their progeny may disperse even greater distances downstream as drifting free embryos. As a result of their complex life history pallid sturgeon naturally exploit a wide range of habitats during their life cycles. The construction of dams and reservoirs has fragmented habitats and may have shifted Missouri River subpopulations downstream. Research has not identified one primary biological or ecological constraint that appears to limit populations of the pallid sturgeon. With the present (2013) state of knowledge many life stages and life-stage transitions cannot be ruled out as contributing to recruitment failure. Biological opinions in 2000 (and amended in 2003) presented the dominant hypotheses for recruitment failure that existed at that time. Emphasis was on the role of the flow regime, specifically spring flow pulses (“spring rises”), to condition spawning substrate and cue reproductive aggregations and migrations, and on low flows and additional slow, shallow-water area to serve as rearing habitat for age-0 to juvenile pallid sturgeon. Studies on spawning habitat dynamics have documented that habitat patches selected for spawning by fish in the Lower Missouri River (Missouri River downstream from Gavins Point Dam to the confluence with the Mississippi River) are dominantly on outside, revetted bends in the deepest, fastest, and most turbulent water. Studies in more natural habitat on the Yellowstone River have documented spawning in convergent flow in the middle of the channel on discrete patches of gravel within a sand-dominated channel, an arrangement that may be more effective in attracting aggregations of reproductive fish compared to the nearly continuous revetment on the Lower Missouri River. Pallid sturgeon spawn in the spring and early summer during periods of increasing day length. Water temperature consistently exerts a threshold effect for spawning at 16–18 °C. In addition, the role of water temperature is indicated by pauses and reversals in upstream migrations that have been associated with cold weather fronts that create a transient decrease in water temperature. From 2005 to 2012 on the Lower Missouri River, no obvious relations between flow pulses and fish movements and spawning behaviors have been apparent. However, pallid sturgeon tracking at the Upper Missouri–Yellowstone confluence indicates that in most years, most telemetered pallid sturgeon migrate out of the Missouri River and into the Yellowstone River in the June–July timeframe in association with the spring pulse. This pattern was disrupted in 2011 when a high flow pulse with warm temperatures and high turbidity emanated from the Milk River, followed by record releases from Fort Peck Dam, and 36–39 percent of the telemetered population migrated up the Upper Missouri. This result supports the hypothesis that sufficiently large flow pulses may trigger migration and aggregation but it is not clear that functional pulses are within reservoir management authorities. Notably, a pallid sturgeon free embryo was captured on the Upper Missouri River in 2011 and another single, genetically confirmed embryo was captured on the Yellowstone River in 2012. Research on free-embryo drift has indicated the potential for hundreds of miles of downstream dispersal. Lack of distance to accommodate the extended downstream dispersal period of free embryos on the Upper Missouri and Yellowstone Rivers is the predominant hypothesis for recruitment failure in the upper basin. Long drift distances in the Lower Missouri River may be responsible for shifting Lower Missouri River sub-populations further into the Middle Mississippi River. Physical understanding of drift processes indicates that mean velocities could be slowed through decreased discharges or increased channel hydraulic radius (width and topographic diversity) to reduce free-embryo dispersal distances. In addition, the probability that free embryos are transported into and retained in channel-margin habitats is theoretically amenable to channel re-engineering that would increase cross-channel secondary currents in bends or channel expansions. Considerable uncertainty persists, however, about whether extended drift of Lower Missouri River larvae is responsible for recruitment failure. If drift distance is limiting, it is important to discern whether it would be advisable to retain larvae within the Missouri River, and where along the river restoration projects should be placed to optimize survival and growth of age-0 and juvenile sturgeon. Longitudinal differences in female pallid sturgeon fecundity lend support to the hypothesis that recruitment failure may be due, in part, to fish having insufficient nutrition to produce the numbers of gametes needed for the population to grow, perhaps because of simultaneous declines in prey-fish populations and their habitats. Establishing a chain of causality from habitat decline, to prey-fish populations, to sturgeon diets, to sturgeon fecundity, and to pallid sturgeon population growth presents a considerable scientific challenge. In addition to the dominant hypotheses relating pallid sturgeon populations to changes in flow regime and channel morphology, other factors have been identified that might be sources of stress and contribute to recruitment failure. Among these are water quality and contaminants. Ambient water-quality monitoring on the Missouri River has demonstrated summer episodes when dissolved oxygen dips below 5 milligrams per liter, a threshold that may be stressful especially to age-0 and juvenile sturgeon. Documented cases of intersex in shovelnose and pallid sturgeon indicate that agricultural and municipal sources of endocrine disrupting chemicals also may have a role in pallid sturgeon recruitment failure. Scientific understanding of the ecological requirements of pallid sturgeon has increased almost exponentially in the last two decades, and efforts are now turning from understanding fundamental biology of the species to quantifying how population dynamics relate to potential management actions. Progress in developing the science needed to inform management actions on the Missouri River may benefit from continuation of monitoring of reproductive cycles, reproductive movements, growth, and survival of telemetry tagged adults, increased emphasis on focused, complementary field and laboratory studies of factors influencing early life history, implementation of studies to resolve the role of food limitations in growth, survival, and reproductive condition, and implementation of studies designed specifically to parameterize models linking management to populations.

Missouri River↗

USGS Mineral Resources Program: International Activities

The USGS is the country's leading earth science organization. Since 1879, USGS scientists have gathered and analyzed data and disseminated the results of their research on the geology, cartography, hydrology, and, more recently biology, of every continent and ocean on Earth. Multidisciplinary research both in the United States and in the international arena has been an important part of the USGS mission. The USGS Mineral Resources Program is the sole Federal agency program that provides high-quality scientific information, objective resource assessments, and unbiased research results on mineral issues

Fact Sheet↗

Relationships between the health of Alaska Native communities and our environment -- phase 1, exploring and communicating

Alaska Natives depend on local natural resources for nutritional and, for many, spiritual health. As a result, public health in Alaska is strongly influenced by the relationship between people and their surrounding physical, chemical, and biological environments. Alaska is vast with diverse wildlife and plant communities that are valued as subsistence foods (fig. 1). These resources are supported by equally diverse ecosystems and their underpinning landforms and geologies. The U.S. Geological Survey (USGS) is attempting to integrate physical, chemical, and biological information to better describe current (2013) environments and project scenarios for the future. Integrating ecological data into the public health dialogue is challenging for the more than 280 rural communities of Alaska. This fact sheet reviews a recent USGS effort, the Geographic Information System (GIS) Native Health Project, to better incorporate scientific information into such dialogue.

Alaska↗