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USGS2023

Sharing land via keystone structure: Retaining naturally regenerated trees may efficiently benefit birds in plantations

Meeting food/wood demands with increasing human population and per-capita consumption is a pressing conservation issue, and is often framed as a choice between land sparing and land sharing. Although most empirical studies comparing the efficacy of land sparing and sharing supported land sparing, land sharing may be more efficient if its performance is tested by rigorous experimental design and habitat structures providing crucial resources for various species––keystone structures––are clearly involved. We launched a manipulative experiment to retain naturally regenerated broad-leaved trees when harvesting conifer plantations in central Hokkaido, northern Japan. We surveyed birds in harvested treatments, unharvested plantation controls and natural forest references one-year before the harvest and for three consecutive post-harvest years. We developed a hierarchical community model separating abundance and space-use (territorial proportion overlapping treatment plots) subject to imperfect detection to assess population consequences of retention harvesting. Application of the model to our data showed that retaining some broad-leaved trees increased total abundance of forest birds over the harvest rotation cycle. Specifically, pre-harvest survey showed that the amount of broad-leaved trees increased forest bird abundance in a concave manner (i.e., in a form of diminishing-return). After harvesting, a small amount of retained broad-leaved trees mitigated negative harvesting impacts on abundance though retention harvesting reduced the space-use. Nevertheless, positive retention effects on the post-harvest bird density as the product of abundance and space-use exhibited a concave form. Thus, small profit reductions were shown to yield large increases in forest bird abundance. The difference in bird abundance between clear-cutting and low amounts of broad-leaved tree retention increased slightly from the first to second post-harvesting years. We conclude that retaining a small amount of broad-leaved trees may be a cost-effective on-site conservation approach for the management of conifer plantations. Retention of 20-30 broad-leaved trees per ha may be sufficient to maintain higher forest bird abundance than clear-cutting over the rotation cycle. Retention approaches can be incorporated into management systems using certification schemes and best management practices. Developing an awareness of the roles and values of naturally regenerated trees is needed to diversify plantations.

Ecological Applications↗

USGS2009

Fire rehabilitation effectiveness: a chronosequence approach for the Great Basin

Federal land management agencies have invested heavily in seeding vegetation for emergency stabilization and rehabilitation (ES&R) of non-forested lands. ES&R projects are implemented to reduce post-fire dominance of non-native annual grasses, minimize probability of recurrent fire, quickly recover lost habitat for sensitive species, and ultimately result in plant communities with desirable characteristics including resistance to invasive species and resilience or ability to recover following disturbance. Land managers lack scientific evidence to verify whether seeding non-forested lands achieves their desired long-term ES&R objectives. The overall objective of our investigation is to determine if ES&R projects increase perennial plant cover, improve community composition, decrease invasive annual plant cover and result in a more desirable fuel structure relative to no treatment following fires while potentially providing habitat for Greater Sage-Grouse, a species of management concern. In addition, we provide the locations and baseline vegetation data for further studies relating to ES&R project impacts. We examined effects of seeding treatments (drill and broadcast) vs. no seeding on biotic and abiotic (bare ground and litter) variables for the dominant climate regimes and ecological types within the Great Basin. We attempted to determine seeding effectiveness to provide desired plant species cover while restricting non-native annual grass cover relative to post-treatment precipitation, post-treatment grazing level and time-since-seeding. Seedings were randomly sampled from all known post-fire seedings that occurred in the four-state area of Idaho, Nevada, Oregon and Utah. Sampling locations were stratified by major land resource area, precipitation, and loam-dominated soils to ensure an adequate spread of locations to provide inference of our findings to similar lands throughout the Great Basin. Nearly 100 sites were located that contained an ES&R project. Of these sites, 61 were seeded by using a drill, 27 were broadcast aerially, and 12 had a combination of both. We randomly sampled three burned and seeded, burned and unseeded, and unburned and unseeded locations in the vicinity of the fire, each within the same ecological site. We measured foliar cover of all plant functional groups (perennial or annual, shrub, grass, forb, native or introduced), biological soil crusts, and abiotic (bare soil and litter) variables using the line-point intercept protocol. Fuel loads and horizontal fuel continuity were measured. We applied linear mixed models to response variables (cover and density of plant groups) relative to the dependent variables (seeding treatments and precipitation/temperature relationships. Post-fire strengths with native perennial grasses or shrubs in mixes did not increase density or cover of these groups significantly relative to unseeded, burned areas. Seeded non-native perennial grasses and the shrub Bassia prostrata were effective in providing more cover in aerial and drill seedings. Seeded non-native perennial grass cover increased with increased annual precipitation regardless of seeding type. Seeding native shrubs, particularly Artemisia tridentata, did not significantly increase shrub cover in burned areas. Cover of undesirable non-native annual grasses was lower in drill seedings relative to unseeded areas but only at higher elevations. Seeding effectiveness after wildfire is unpredictable in drier, low elevation environments, and our findings indicate management objectives are more likely met when focusing efforts on higher elevation or higher precipitation locations where establishment of perennial grasses is more likely. On sites where potential for invasion and dominance of non-native annuals is high, such as lower and drier sites, intensive methods of restoration that include invasive plant control before seeding may be required. Where establishment of native perennial plants is the goal, managers might consider using native-only seed mixtures, because we found that the non-native perennials typically used in Great Basin restoration efforts are selected for their competitive nature and may reduce establishment of less competitive native species. Although we attempted to include information on livestock grazing history after seedings, we were unable to extract sufficient data from files to address this topic that may play an additional role in understanding native plant abundance post-fire seeding. Evaluation of drill and aerial seeding effects on fuel characteristics focused on two metrics that are standard inputs for fire behavior models, fuel load and fuel continuity. Fuel loads were evaluated separately for total fuel load biomass, and the individual components that sum to total biomass, namely herbaceous, shrub, shrub:herbaceous ratio, litter, 10-hour, and 100-hour fuel biomasses. Fuel continuity was evaluated using the following cover categories, total, annual grass, annual forb, perennial forb perennial grass, shrub, litter, vegetative interspace, and perennial interspace. Drill seeding did not affect fuel loads, except to reduce 10-hour fuels, probably due to mechanical destruction of dead and down fuels by the drill seeding equipment. Drill seeding did affect fuel continuity, specifically decreasing total plant cover by increasing perennial grass cover which suppressed annual grass and litter production resulting in a net decrease in continuity, but only at the elevations above approximately 1500m. Aerial seeding had no effect on any fuel load or fuel continuity category. For the Greater Sage-Grouse habitat study, we developed multi-scale empirical models of sage-grouse occupancy in 211 randomly located plots within a 40 million ha portion of the species’ range. We then used these models to predict sage-grouse habitat quality at 101 ES&R seeding projects. We compared conditions at restoration sites to published habitat guidelines. Sage-grouse occupancy was positively related to plot- and landscape-level dwarf sagebrush (Artemisia arbuscula, A. nova, A. tripartita) and big sagebrush steppe, and negatively associated with non-native grass and human development. The predicted probability of sage-grouse occupancy at treated plots was low on average (0.07–0.09) and was not significantly different from burned areas that had not been treated. Restoration was more often successful at higher elevation sites with low annual temperatures, high spring precipitation, and high plant diversity. No plots seeded after fire (n=313) met all overstory guidelines for breeding habitats, but approximately 50% met understory guidelines, particularly for perennial grasses. This trend was similar for summer habitat. Ninety-eight percent of treated plots did not meet winter habitat guidelines. Restoration actions in burned areas did not increase the probability of meeting most guideline criteria. The probability of meeting guidelines was influenced by a latitudinal gradient, local climate, and topography. Post-fire seeding treatments in Great Basin sagebrush shrublands generally have not created high quality habitat for sage-grouse. Understory conditions are more likely to be adequate than those of overstory, but in unfavorable climates, establishing forbs and reducing cheatgrass dominance is unlikely. Reestablishing sagebrush cover will require more than 20 years using the restoration methods of the past two decades. Given current fire frequencies and restoration capabilities, protection of landscapes containing a mix of dwarf sagebrush and big sagebrush steppe, minimal human development, and low non-native plant cover may provide the best opportunity for conservation of sage-grouse habitats. Our database of ES&R locations has used the Land Treatment Digital Library to archive data and location information regarding our study (see Pilliod and Welty 2013). This has contributed to two additional studies. One examined the potential spread of Bassia prostrata (aka Kochia prostrata; forage kochia) from ES&R project locations (Gray and Muir 2013). The second used remote sensing to determine the phenology of vegetation green-up on post-fire seeded sites (Sankey et al. 2013).

California;Idaho;Oregon;Utah↗

USGS2009

Character and Trends of Water Quality in the Blue River Basin, Kansas City Metropolitan Area, Missouri and Kansas, 1998 through 2007

Water-quality and ecological character and trends in the metropolitan Blue River Basin were evaluated from 1998 through 2007 to provide spatial and temporal resolution to factors that affect the quality of water and biota in the basin and provide a basis for assessing the efficacy of long-term combined sewer control and basin management plans. Assessments included measurements of stream discharge, pH, dissolved oxygen, specific conductance, turbidity, nutrients (dissolved and total nitrogen and phosphorus species), fecal-indicator bacteria (Escherichia coli and fecal coliform), suspended sediment, organic wastewater and pharmaceutical compounds, and sources of these compounds as well as the quality of stream biota in the basin. Because of the nature and myriad of factors that affect basin water quality, multiple strategies are needed to decrease constituent loads in streams. Strategies designed to decrease or eliminate combined sewer overflows (CSOs) would substantially reduce the annual loads of nutrients and fecal-indicator bacteria in Brush Creek, but have little effect on Blue River loadings. Nonpoint source reductions to Brush Creek could potentially have an equivalent, if not greater, effect on water quality than would CSO reductions. Nonpoint source reductions could also substantially decrease annual nutrient and bacteria loadings to the Blue River and Indian Creek. Methods designed to decrease nutrient loads originating from Blue River and Indian Creek wastewater treatment plants (WWTPs) could substantially reduce the overall nutrient load in these streams. For the main stem of the Blue River and Indian Creek, primary sources of nutrients were nonpoint source runoff and WWTPs discharges; however, the relative contribution of each source varied depending on how wet or dry the year was and the number of upstream WWTPs. On Brush Creek, approximately two-thirds of the nutrients originated from nonpoint sources and the remainder from CSOs. Nutrient assimilation processes, which reduced total nitrogen loads by approximately 13 percent and total phosphorus loads by double that amount in a 20-kilometer reach of the Blue River during three synoptic base-flow sampling events between August through September 2004 and September 2005, likely are limited to selected periods during any given year and may not substantially reduce annual nutrient loads. Bacteria densities typically increased with increasing urbanization, and bacteria loadings to the Blue River and Indian Creek were almost entirely the result of nonpoint source runoff. WWTPs contributed, on average, less than 1 percent of the bacteria to these reaches, and in areas of the Blue River that had combined sewers, CSOs contributed only minor amounts (less than 2 percent) of the total annual load in 2005. The bulk of the fecal-indicator bacteria load in Brush Creek also originated from nonpoint sources with the remainder from CSOs. From October 2002 through September 2007, estimated daily mean Escherichia coli bacteria density in upper reaches of the Blue River met the State of Missouri secondary contact criterion standard approximately 85 percent of the time. However, in lower Blue River reaches, the same threshold was exceeded approximately 45 percent of the time. The tributary with the greatest number of CSO discharge points, Brush Creek, contributed approximately 10 percent of the bacteria loads to downstream reaches. The tributary Town Fork Creek had median base-flow Escherichia coli densities that were double that of other basin sites and stormflow densities 10 times greater than those in other parts of the basin largely because approximately one-fourth of the runoff in the Town Fork Creek Basin is believed to originate in combined sewers. Genotypic source typing of bacteria indicated that more than half of the bacteria in this tributary originated from human sources with two storms contributing the bulk of all bacteria sourced as human. However, areas outsid

Scientific Investigations Report↗

USGS2018

Groundwater contributions to excessive algal growth in the East Fork Carson River, Carson Valley, west-central Nevada, 2010 and 2012

Excessive algal growth and low dissolved oxygen concentrations were observed during low streamflow conditions during summer months along a 5,800-foot reach of the East Fork Carson River in Carson Valley, west-central Nevada. Algal growth from nutrient enrichment of a stream reduces aquatic diversity, threatens fish ecology and stream health, and can be a recreational nuisance. In response to concerns that groundwater discharging to the 5,800-foot reach of the East Fork Carson River may be a source of nutrients to the stream, the U.S. Geological Survey, in cooperation with the Carson Water Subconservancy District and the Nevada Division of Environmental Protection, conducted studies during the summers of 2010 and 2012 to gain an improved understanding of the contributions of nutrients to the stream from groundwater, characterize algal conditions and algal effects on water quality, assess potential sources of nitrate in groundwater discharging to the stream, and evaluate nitrate reduction in groundwater from denitrification. A reconnaissance study in the summer of 2010 along the 5,800-foot study reach located a subreach with clear evidence of nutrient-rich groundwater discharging to the stream. At the subreach, nitrate plus nitrite (referred to hereafter as nitrate) concentrations in groundwater discharging to the stream were high (average 2.75 milligrams per liter as nitrogen) along the right bank. The stream at this location had the highest stream nitrate concentrations (average 0.056 milligrams per liter as nitrogen) compared to other locations upstream and downstream of the subreach. As a result, the 2012 study focused on a 405-foot subreach of the East Fork Carson River centered where results from the 2010 study found the highest stream and groundwater concentrations of nitrate, as well as the greatest observed contributions of groundwater discharge to the stream. Groundwater nutrient concentrations were much higher than stream nutrient concentrations during the summer of 2012 during low streamflow conditions at the 405-foot subreach of the East Fork Carson River. Average groundwater nitrate and orthophosphate concentrations along the right bank of the 405‑foot subreach were 9 and 12 times higher, respectively, than in the stream at this subreach. Groundwater discharge rates to the study reach based on different methods varied from 0.09 to 1.2 cubic feet per second per mile. Estimated groundwater discharge rates to the right bank of the study subreach were used to calculate groundwater nutrient load estimates to the subreach right bank, which were found to be low when compared to stream nutrient loads. Elevated algal biomass levels above nuisance thresholds were observed during the summers of 2010 and 2012. The study reach was characterized as mesotrophic-eutrophic during the 2010 study and eutrophic during the 2012 study. The presence of algae caused daily dissolved oxygen and pH fluctuations in the stream, resulting in exceedances of the State of Nevada water-quality standards owing to low dissolved oxygen concentrations and high pH concentrations, although the standards might not have been applicable during 2012 because of extremely low streamflow. The addition of nutrients to the stream from the constant supply in groundwater discharge sustains the growth of algae during low streamflow conditions. In the summer when streamflow is low or very low, nutrient-rich groundwater discharge enters the stream through the sediment-water interface at the streambed. Because the attached algae is thick and stream velocity is low, the nutrient-rich water pools at the sediment-water interface. Higher nutrient concentrations at the streambed create a favorable microenvironment for algae attached to the substrate to consume available nutrients from the groundwater before the groundwater mixes with overlying stream water. The source of nitrate in groundwater in this subreach is anthropogenic because nitrate concentrations are greater than background groundwater nitrate concentrations in Douglas County, high groundwater nitrate concentrations are only found at the right bank of the stream near a housing development, and organic wastewater compounds indicative of human-derived sources were also detected in groundwater wells on the right bank of the stream. Nitrogen and oxygen isotope concentrations of nitrate in shallow groundwater were used to determine the specific source of the nitrate, but the isotopic values indicated denitrification was occurring. Further investigation is needed to determine the specific anthropogenic source of the nitrate in the groundwater because the denitrification present in all samples obscures the original source of nitrogen.

Nevada↗

USGS1999

The ecological condition of estuaries in the Gulf of Mexico

The Gulf of Mexico is a vast natural resource encompassing the coastal areas of western Florida, Alabama, Mississippi, Louisiana, and Texas, as well as a portion of Mexico. Many estuaries flow into the Gulf of Mexico and serve as nursery grounds for fish, habitat for a wide variety of wildlife, shipping routes, and a source of recreation. Estuarine-dependent species constitute more than 95 percent of the commercial fishery harvests from the Gulf of Mexico, and many important recreational fishery species depend on estuaries during some part of their life cycle. Gulf estuaries are diverse and productive ecosystems that provide a variety of valuable resources, including fish and shellfish, recreation, transportation, and water supply. Assessing the overall condition of Gulf of Mexico estuaries required incorporating data from other federal, state, and local monitoring programs to augment the information on ecological indicators collected by the U.S. Environmental Protection Agency’s (USEPA) Environmental Monitoring and Assessment Program (EMAP). The resulting document would provide a synthesis of the available knowledge about the condition of Gulf of Mexico estuaries. This document is intended for use by scientists and other citizens concerned with the ecological condition of estuaries, as well as by managers and lawmakers interested in the sustained use of estuaries for commercial and recreational purposes. It also addresses public concerns about the aesthetic quality of coastal areas vital to tourism and recreation. By producing this report on the ecological condition of estuaries in the Gulf of Mexico, we have taken one step in assessing the health of this environmental resource. We have produced an environmental “report card” to be used as a guide in the evaluation of management decisions and research directions. This report is organized in three parts: (1) an introduction that gives background information on the Gulf of Mexico, estuarine ecology, and the factors that impact estuaries in the gulf, (2) the main section on priority ecological indicators used to measure the condition of estuaries in the gulf and (3) an ecological report card that summarizes the data on ecological indicators and provides a rating of the condition of estuaries in each gulf state and for gulf estuaries overall. Many of the ratings were based on the percent area of estuaries in each state exhibiting degraded or adverse levels of an indicator. Eutrophication, a condition of high nutrients often resulting in low oxygen levels and other adverse effects, is an important water quality concern for estuaries along the gulf coast. The National Oceanic and Atmospheric Administration (NOAA) has compared the Gulf of Mexico to other coastal regions like the middle Atlantic and has ranked the Gulf of Mexico as having the highest number of point sources of nutrients and the highest percentage of land use devoted to agriculture. We evaluated monitoring data for nitrogen, chlorophyll, and dissolved oxygen as indicators of eutrophication. Although most of the estuaries exhibited high nitrogen or chlorophyll or low dissolved oxygen concentrations at least once during a survey, many times these conditions were observed in small rivers or bayous rather than in the entire estuary. Often, the percent area affected was low. The gulf estuaries had moderate conditions overall for nutrients and dissolved oxygen. Definite nutrient problems were observed in >25% of the estuarine area in Louisiana and Texas and definite dissolved oxygen problems were observed in Alabama. Contaminants in estuarine sediments provide evidence of the accumulation of chemicals from anthropogenic sources. We compared the concentrations of sediment contaminants to established guideline values to determine the proportion of estuarine area that could have potential adverse effects on living organisms. Although detectable levels of contaminants were measured in almost every estuary in the Gulf of Mexico, <25% of the estuarine area in all states had contaminant concentrations that exceeded these guidelines. Wetlands are integral parts of estuarine systems. Declining acreage means habitat loss that may be the result of commercial and residential development, hydrologic alterations, or dredge and fill operations. The Gulf of Mexico region contains more than 50% of the coastal wetland acreage in the U.S. and yet it also has the highest rate of coastal wetland loss. Nine of the top ten estuarine drainage areas ranked by total wetland area are in the Gulf of Mexico region. The most current estimates of total wetland loss over the past 200 years range from 41% to 54% for the gulf states. Although coastal wetlands continue to be altered or destroyed, some estimates indicate that the rate of loss has slowed. All gulf states were rated as having severe problems with wetland loss. The condition of benthic (bottom-dwelling) invertebrates, fish and shellfish, birds, and threatened and endangered species was used to evaluate the health of estuarine fauna. Degraded benthic communities inhabited <25% of the estuarine area in all gulf states except for Texas. Commercial fish and shellfish landings may be used as an indicator of population stability while fish biomarkers are used to measure the health of individuals in the population. Commercial landings of the top four fisheries (shrimp, menhaden, blue crab, and oyster) are stable in the gulf states while fish biomarkers indicate fair to poor fish health in Alabama and Texas and good fish health elsewhere. Coastal and marine bird populations appear to be in good condition throughout the gulf. Four threatened or endangered species inhabit coastal areas in the Gulf of Mexico: brown pelican, Gulf sturgeon, manatee, and Kemp’s ridley sea turtle. In general, populations of these species are in good to fair condition in the gulf states. Public health indicators include shellfish bed closures and chemicals found in edible fish tissue. Harvest of shellfish (primarily oyster in the Gulf of Mexico) is restricted or prohibited when concentrations of bacteria or other pathogens reach levels that could impair human health. The gulf states contain the most acreage of shellfish-growing waters in the U.S. but also have the most acreage restricted for harvest. All gulf states except Mississippi have >25% of their shellfish-growing waters restricted for harvest, mostly due to pollution from wastewater treatment plants or other upstream sources. Advisories may be issued that limit consumption when the concentrations of chemicals in fish tissue exceed levels known to be harmful to humans. Although seafood consumption advisories have been issued in all gulf states, the percent of the fish population with high concentrations of contaminants is relatively low in the gulf overall.

Alabama, Florida, Louisiana, Mississippi, Texas↗

USGS2020

Fate and behavior tools related to inland spill response—Workshop on the U.S. Geological Survey’s role in Federal science support

Executive Summary There is a growing body of tools available for science support for determining the fate and behavior of industrial and agricultural chemicals that are rapidly injected (“spilled”) into aquatic environments. A 2-day roundtable-style workshop was held by the U.S. Geological Survey (USGS) in Middleton, Wisconsin, in December 2017 to describe and explore existing Federal science support for spill fate and behavior tools used for inland spills, ongoing and new fate and behavior studies, and science gaps in planning and response tools as part of the USGS Midcontinent Region’s efforts to include spill response as part of its strategic plans. A total of 28 attendees representing a variety of Federal, State, and regional entities presented on programs and tools used in various aspects of spill response. Most programs and tools discussed were for spills in riverine environments but tools and applications for spills in lakes, on land surfaces, in urban storm sewer networks, and groundwater also were discussed. A primary workshop focus was to facilitate communication and increase potential for future collaboration among agencies for inland spill science support. The role and need for more USGS science support within the inland spill community was discussed. Enhanced communication is needed within the USGS and the U.S. Department of the Interior science programs, as well as within and among other agencies that do emergency planning and response. A main conclusion of the workshop was that there are untapped resources of the USGS outlined in the agency’s science strategy that could strengthen science support for fate and behavior tools in inland areas, especially in the Upper Mississippi River, Ohio River, and Great Lakes Basins where large freshwater resources overlap with dense corridors of oil and hazardous substances, with transportation networks, and with large populations centers. Fate and behavior tools are being developed quickly for inland spill response by multiple Federal agencies in partnership with local and regional entities. Applicability of these tools ranges from planning and preparedness, to the early stages of spill response for protection of human life and property, and to the application of monitoring and models to assess the long-term consequences of spills. Key findings from the workshop, with an emphasis on potential further development of USGS science support, include the following: •The national and regional response to spills occurs within an established system that must be respected by all parties involved in spill response. The USGS’s role is to support spill responders who are physically working at a spill scene, deploying booms and using other efforts to contain and recover spilled materials. •The USGS has tools that have been used throughout spill response operations, from early response to recovery and restoration. Developing a more formal role for the USGS to participate in science support for inland spills on a consistent basis is a desired outcome. This will require the USGS to improve internal and external communication and would be best accomplished by assigning one or more coordinator positions within the agency to plan and oversee USGS spill-response efforts. More involvement of the USGS on National and Regional Response Teams, especially in the realm of the Science and Technology Subcommittees, will gofar in increasing external communication and integration of fate and behavior tools. •Rapid response to spills requires modeling and mapping of plumes and associated time-of-travel estimation for a range of stream sizes across the United States. Many existing models use USGS streamgage data and the USGS National Hydrography Dataset. Nearly all existing models would benefit from updated linkages to USGS StreamStats and its soon-to-be released time-of-travel estimates,real-time velocity, stream morphology, and slope data. Integrating USGS tools with those from other agencies could be done to better serve the larger spill response community. • A problem is that existing models to rapidly predict plume extent, as well as more followup/longer-term fate and transport models, can be unknown or unavailable to spill responders. Thus, creating and strengthening linkages among USGS scientists skilled at using these tools is needed to support spill response with the on-scene responders. • Research for inland spill fate and behavior done outside of an immediate spill response can assist with spill planning and preparedness by (1) revealing sites likely to experience spills in the future (high-risk sites) and (2) understanding how a spilled substance might behave under a range of environmental conditions. However, USGS research on this topic has been scarce and subject to funding availability. Examples include the 2010 Line 6B Spill release into the Kalamazoo River in Michigan, where the USGS provided science support for a variety of fate and behavior tools for stream and impoundment environments. A long-term research site in Bemidji, Minnesota, provides important insights into transformations and longevity of spilled oil in groundwater and groundwater-surface water interactions. • Linking stream models to other components of this inland environment, including groundwater, overland flow, and karst, is needed. Stream network data can be linked to underground conduits such as storm sewers and karst groundwater systems. Stream models can also be linked with geospatial data such as that contained in U.S. Environmental Protection Agency’s interactive mapping tools. • The USGS is uniquely qualified to collect water-quality data during spills in the United States because of its many geographically dispersed water science centers, its knowledge and preparedness for flood measurement and documentation, and its cadre of skilled water-quality employees. Rapid-deployment gages, used for floods, could also be used for spills if they included spill-specific sensors. Coordinated expertise at USGS water and environmental science centers can be used for monitoring spill effects and for assessing risk to water quality and ecological communities. • Scientists at the USGS have proven capable of providing science coordination and technical assistance within the Incident Command Structure at the request of the lead on-scene coordinator. This external coordination, as well as internal communication within USGS Water, Hazards, and Ecosystems Mission Areas, could be improved by establishing and naming a USGS spills coordinator. Scott Morlock, Jo Ellen Hinck, and Faith Fitzpatrick are currently (2017) serving in informal coordination roles in addition to their traditional duties.

Open-File Report↗

USGS2003

Irrigation-induced contamination of water, sediment, and biota in the western United States-synthesis of data from the National Irrigation Water Quality Program

In October 1985 the U.S. Department of the Interior (DOI), through the National Irrigation Water Quality Program (NIWQP), began a series of field investigations at 26 areas in the Western United States to determine whether irrigation drainage has had harmful effects on fish, wildlife, and humans or has reduced beneficial uses of water. In 1992 NIWQP initiated the Data Synthesis Project to evaluate data collected during the field investigations. Geologic, climatologic, and hydrologic data were evaluated and water, sediment, and biota from the 26 areas were analyzed to identify commonalities and dominant factors that result in irrigation-induced contamination of water and biota. Data collected for the 26 area investigations have been compiled and merged into a common data base. The structure of the data base is designed to enable assessment of relations between contaminant concentrations in water, sediment, and biota. The data base is available to the scientific community through the World Wide Web at URL http://www.usbr.gov/niwqp . Analysis of the data base for the Data Synthesis included use of summary statistics, factor analysis, and logistic regression. A Geographic Information System was used to store and analyze spatially oriented digital data such as land use, geology and evaporation rates. In the U.S. Department of the Interior (DOI) study areas, samples of water, bottom sediment, and biota were collected for trace-element and pesticide analysis. Contaminants most commonly associated with irrigation drainage were identified by comparing concentrations in water with established criteria. For surface water, the criteria used were typically chronic criteria for the protection of freshwater aquatic life. Because ground water can discharge to the surface where wildlife can be exposed to it, the criteria used for ground water were both the maximum contaminant levels (MCL's) for drinking water and the chronic criteria for the protection of freshwater aquatic life. Data collected by the NIWQP studies indicated that, in surface water, filtered and unfiltered samples had nearly the same concentrations of arsenic, boron, molybdenum, and selenium for concentrations greater than about 10 micrograms per liter. Therefore, in this concentration range, filtered concentrations can be directly compared to biological-effect levels developed for unfiltered samples. In the range of 1 to 10 micrograms per liter there may be a tendency for unfiltered arsenic concentrations to be greater than filtered concentrations. For selenium, however, the data suggest differences from equality in that range result from analytical imprecision and not a general tendency for unfiltered concentrations to be greater than filtered concentrations. This relation may not be true in lentic, nutrient-rich waters because in such settings algae can bioaccumulate large amounts of selenium and other trace elements. Selenium was the trace element in surface water that most commonly exceeded chronic criteria for the protection of freshwater aquatic life; more than 40 percent of the selenium concentrations in surface-water samples exceeded the U.S. Environmental Protection Agency (USEPA) aquatic-life chronic criterion (5 micrograms per liter). In 12 of the 26 areas at least 25 percent of the surface water-samples had selenium concentrations that either equaled or exceeded the chronic criterion (5 micrograms per liter). More than 28 percent of boron concentrations and almost 17 percent of the molybdenum concentrations exceeded the aquatic life criteria established by the State of California (550 and 19 micrograms per liter, respectively). In ground water, more than 22 percent of the arsenic concentrations and more than 35 percent of the selenium concentrations exceeded the MCL (10 and 50 micrograms per liter, respectively). Few samples of uranium in surface water exceeded a criterion for the protection of aquatic life (300 micrograms per liter), but 44 percent of the uranium concentrations in ground water exceeded the MCL (30 micrograms per liter). Molybdenum, selenium and uranium were the trace elements most commonly found in bottom-sediment samples that exceeded the upper limit of the 95th percentile expected range in soils of the Western United States. Selenium is the only trace element for which ecological sediment guidelines are used in this report. Selenium concentrations commonly exceeded the ecological sediment guideline of two micrograms per gram. DDT and its degradation products DDD and DDE were the most common pesticide residues found in surface water at concentrations exceeding criteria. However, almost all the samples exceeding the criteria were from a single study area, the Owyhee-Vale Reclamation Project areas in Oregon and Idaho. The organochlorine pesticide chlordane was detected in 30 percent of the bottom-sediment samples, and undegraded DDT was detected in 21 percent. DDT or its degradation products were detected in all 21 study areas where bottom-sediment samples were analyzed for organochlorine pesticides. A principal-components analysis indicated that elevated selenium concentrations in surface water are not associated with elevated boron, molybdenum, or arsenic concentrations. The occurrence of selenium is associated with sulfate and uranium. The association of boron and molybdenum with chloride suggests that evaporative processes control their concentrations. Arsenic is not associated with any other measured trace element and is associated negatively with selenium. This report focuses on selenium because it was the trace element most frequently found at concentrations exceeding criteria for the protection of aquatic life. Selenium concentrations in water are dynamic, and, at a given site, the selenium concentration can change by an order of magnitude during a year and from one year to another. In some areas, selenium contamination may not occur during normal or wet periods. However, during a drought, reduced water deliveries may result in selenium contamination by evaporative concentration. Marine sedimentary rocks, especially those of Late Cretaceous age, are likely to be seleniferous. Irrigation of soils derived from them can contribute large amounts of selenium to drainwater; shallow wells in and near irrigated areas contained hundreds to thousands of micrograms per liter of selenium. The median selenium concentration in surface-water samples from NIWQP sites associated with Upper Cretaceous marine sedimentary rocks is 7 micrograms per liter (range less than 1 to 8,300 micrograms per liter) and from sites not associated with such rocks is 0.4 micrograms per liter (range less than 1 to 390 micrograms per liter). Irrigation-induced selenium contamination has been observed only in arid or semiarid areas. In those NIWQP study areas having local geologic sources of selenium, typically more than 25 percent of the surface-water samples exceed the chronic criterion for selenium if the evaporation rate is 3.0 times greater than the annual precipitation. In terminal water bodies, selenium accumulates and is not flushed out. In both terminal and flow-through lakes and ponds, the median selenium concentrations in surface water for samples collected from June through August are nearly the same (1.0 and 0.8 micrograms per liter, respectively). However, the 75th-percentile selenium concentration for terminal water bodies (24 µg/L) is significantly higher than for flow-through systems (4 µg/L). Selenium concentrations in biota were compared with concentrations that have been demonstrated to have adverse effects on similar species (the effect level) or to have adverse effects on another species if consumed (the dietary effect level). Twenty-five percent of the plant samples had selenium concentrations exceeding the dietary effect level (3 micrograms per gram dry weight) whereas more than 57 percent of the invertebrate samples and 61 percent of the fish samples exceeded the dietary effect level. Of the more than 2,000 bird eggs collected, 44 percent had selenium concentrations exceeding 6 micrograms per gram, a threshold value for reduced hatchability. In 14 areas, selenium concentrations in eggs from some populations of birds exceeded 6 micrograms per gram. Selenium-caused deformities of bird embryos were found in four of the NIWQP study areas; however, most study areas were not systematically surveyed for such deformities. Eggs were sampled from 34 species of birds belonging to 10 orders. Nearly all the eggs collected come from aquatic species of birds, with American coots, mallards, and American avocets being the three species most frequently collected. Of the 34 species, at least one set of eggs from 16 species had a geometric-mean selenium concentration of at least 12.5 micrograms per gram, a high-risk threshold. All three species of grebes yielded at least one set of high risk eggs, as did four of five species of shorebirds and five of eleven species of waterfowl. Egg-set data were examined to determine if some feeding guilds are more at risk to selenium poisoning than others. Analysis of data for waterbird eggs from the study areas where the 75th percentile selenium concentration in surface water exceeded 5 µg/L suggests that herbivorous birds may bioaccumulate less selenium than insect- and fish-eating birds. For birds from these study areas, selenium concentrations for 39 percent of the egg sets from herbivorous birds fell in the normal range (less than 3 µg/g) while only 7 and 0 percent, respectively, of egg sets from insect- and fish-eating birds fall in the normal range. Although herbivorous birds may bioaccumulate less selenium, it does not appear that any waterbird feeding guilds are particularly well buffered from exposure to selenium contamination. Predictive tools were developed to aid managers in identifying specific land areas at risk for irrigation-induced selenium contamination. The tools range from identifying broad geographic regions where selenium contamination is likely, to assessing the probability that selenium concentrations in a specific stream or lake exceed the chronic criterion for selenium. A geographic information system was used to prepare a map that identifies land areas in the Western United States that are susceptible to selenium contamination if irrigated. On the basis of the 75th percentile, selenium concentration in surface water, 12 of the 26 NIWQP study areas were classified as contaminated, two as seleniferous, and 12 as uncontaminated. The map correctly identified both seleniferous areas and 10 of 12 selenium-contaminated areas as susceptible; 10 of 12 uncontaminated areas were correctly identified as not being susceptible. About 160,000 square miles are identified as being susceptible; of that area, about 4,100 square miles have been identified by satellite imagery as actively being irrigated. Principal-components analysis and pattern-recognition techniques indicate that major-ion chemistry of water samples alone can be used to identify selenium- and nonselenium-producing areas in the Western United States. Water samples composed of simple salts of sulfate typically have concentrations of selenium that exceed 3 µg/g, whereas samples composed of simple salts of chloride or carbonate typically have low selenium concentrations. Weathering of soils that contain reduced-sulfur minerals, such as pyrite, mobilizes sulfur and selenium because selenium commonly substitutes for sulfur in these minerals. In areas where the bedrock is composed of Upper Cretaceous marine sedimentary rocks, logistic regression of data from the NIWQP sites indicates that if the dissolved-solids concentration equals 1,000 milligrams per liter, the probability is about 69 percent that the selenium concentration will exceed 5 micrograms per liter, the U.S. Environmental Protection Agency chronic criterion. In areas where the bedrock is not composed of such rocks, the probability is only about 10 percent. The avian-egg data within the biotic data base were used to make a quantitative toxicological risk assessment. Of the 23 study areas where avian eggs were sampled, 14 areas yielded at least one egg containing 6 µg/g selenium, the threshold for embryotoxicity. However, only 6 of the study areas yielded eggs containing enough selenium to expect selenium-induced teratogenesis of duck embryos. Predicted probabilities of discovering embryo teratogenesis matched field observations in 13 of the 14 study areas reporting results of embryo assessments. Bird eggs were collected from 161 individual sampling sites and at 79 of those sites selenium concentrations in one or more eggs exceeded 6 µg/g. At the 79 sites where biological effects are expected on the basis of selenium concentrations in the eggs, the median rate was 3.9 percent of the hens losing at least one egg to selenium-induced embryotoxicity. This corresponds to about 1.2 percent selenium-induced egg inviability among otherwise viable eggs. Across all NIWQP study areas, the overall rate of hens projected to lose at least one egg to selenium-induced embryotoxicity is estimated to be 1.9 percent, which corresponds to about 0.3 percent selenium-induced egg inviability among otherwise viable eggs. After accounting for increased mortality of selenium poisoned-hatchlings due to other factors such as weather and predators, it was estimated that that increases of 0.3 and 1.2 percent in inviable eggs would cause approximately a 1.4 and 5.4 percent depression in nesting success. Regional surveys of nesting success among ducks revealed that duck populations commonly exist near their demographic break-even point. The vulnerable demographic condition of North American duck populations during the mid-1960's to mid-1980's was primarily due to noncontaminant factors, such as poor-quality nesting habitat and dry climatic cycles. Under such conditions, rates of 1.4- to 5.4-percent depression in nesting success caused by exposure to selenium from irrigation projects can be crucial for avian populations already close to their demographic break-even point. Even the worst-case levels of contaminant effects, however, could be tolerated by populations of ducks existing just modestly above demographic break-even points. This suggests the biotic risk to ducks could be addressed by reducing irrigation-induced water pollution but more effectively by restoring high-quality (more predator-safe) nesting habitat. An analysis at the nesting-site level was made of the relation between selenium content of water and bird eggs. Eggs from 93 bird populations were collected from nesting sites where the water sample collected during April-July contained less than 5 µg/L selenium. The average selenium concentration in egg sets was embryotoxic in 19 of the 93 populations. Of the populations collected at sites where the selenium in the water was less than 1 microgram per liter, only four of 54 populations contained embryotoxic concentrations. Eggs from 65 populations of birds were collected from nesting sites where selenium concentrations in water samples collected during April-July equaled or exceeded 5 µg/L, and 55 of those 65 populations contained embryotoxic concentrations of selenium in the eggs. An analysis at the study-area level was made of the relation between selenium contamination of water and selenium contamination of the food chain and egg loss due to selenium poisoning. Most food organisms, particularly aquatic invertebrates and fish, contained potentially harmful amounts of selenium in study areas where selenium concentrations in more than 25 percent of the water samples exceed 5 µg/L. The analysis also indicates that some hens are predicted to lose eggs to selenium poisoning in all study areas where selenium concentrations in more than 25 percent of the water samples exceed 5 µg/L. These results suggest that areas where selenium contamination of the food chain and loss of eggs to selenium poisoning is occurring may be identified using the same methods developed to identify areas where selenium contamination of water is likely to occur.

western United States↗

USGS2016

Wildfire may increase habitat quality for spring Chinook salmon in the Wenatchee River subbasin, WA, USA

Pacific Northwest salmonids are adapted to natural disturbance regimes that create dynamic habitat patterns over space and through time. However, human land use, particularly long-term fire suppression, has altered the intensity and frequency of wildfire in forested upland and riparian areas. To examine the potential impacts of wildfire on aquatic systems, we developed stream-reach-scale models of freshwater habitat for three life stages (adult, egg/fry, and juvenile) of spring Chinook salmon ( Oncorhynchus tshawytscha ) in the Wenatchee River subbasin, Washington. We used variables representing pre- and post-fire habitat conditions and employed novel techniques to capture changes in in-stream fine sediment, wood, and water temperature. Watershed-scale comparisons of high-quality habitat for each life stage of spring Chinook salmon habitat suggested that there are smaller quantities of high-quality juvenile overwinter habitat as compared to habitat for other life stages. We found that wildfire has the potential to increase quality of adult and overwintering juvenile habitat through increased delivery of wood, while decreasing the quality of egg and fry habitat due to the introduction of fine sediments. Model results showed the largest effect of fire on habitat quality associated with the juvenile life stage, resulting in increases in high-quality habitat in all watersheds. Due to the limited availability of pre-fire high-quality juvenile habitat, and increased habitat quality for this life stage post-fire, occurrence of characteristic wildfires would likely create a positive effect on spring Chinook salmon habitat in the Wenatchee River subbasin. We also compared pre- and post-fire model results of freshwater habitat for each life stage, and for the geometric mean of habitat quality across all life stages, using current compared to the historic distribution of spring Chinook salmon. We found that spring Chinook salmon are currently distributed in stream channels in which in-stream habitat for most life stages has a consistently positive response to fire. This compares to the historic distribution of spring Chinook, in which in-stream habitat exhibited a variable response to fire, including decreases in habitat quality overall or for specific life stages. This suggests that as the distribution of spring Chinook has decreased, they now occupy those areas with the most positive potential response to fire. Our work shows the potentially positive link between wildfire and aquatic habitat that supports forest managers in setting broader goals for fire management, perhaps leading to less fire suppression in some situations.

Washington↗

USGS2008

A multi-model framework for simulating wildlife population response to land-use and climate change

Reliable assessments of how human activities will affect wildlife populations are essential for making scientifically defensible resource management decisions. A principle challenge of predicting effects of proposed management, development, or conservation actions is the need to incorporate multiple biotic and abiotic factors, including land-use and climate change, that interact to affect wildlife habitat and populations through time. Here we demonstrate how models of land-use, climate change, and other dynamic factors can be integrated into a coherent framework for predicting wildlife population trends. Our framework starts with land-use and climate change models developed for a region of interest. Vegetation changes through time under alternative future scenarios are predicted using an individual-based plant community model. These predictions are combined with spatially explicit animal habitat models to map changes in the distribution and quality of wildlife habitat expected under the various scenarios. Animal population responses to habitat changes and other factors are then projected using a flexible, individual-based animal population model. As an example application, we simulated animal population trends under three future land-use scenarios and four climate change scenarios in the Cascade Range of western Oregon. We chose two birds with contrasting habitat preferences for our simulations: winter wrens (Troglodytes troglodytes), which are most abundant in mature conifer forests, and song sparrows (Melospiza melodia), which prefer more open, shrubby habitats. We used climate and land-use predictions from previously published studies, as well as previously published predictions of vegetation responses using FORCLIM, an individual-based forest dynamics simulator. Vegetation predictions were integrated with other factors in PATCH, a spatially explicit, individual-based animal population simulator. Through incorporating effects of landscape history and limited dispersal, our framework predicted population changes that typically exceeded those expected based on changes in mean habitat suitability alone. Although land-use had greater impacts on habitat quality than did climate change in our simulations, we found that small changes in vital rates resulting from climate change or other stressors can have large consequences for population trajectories. The ability to integrate bottom-up demographic processes like these with top-down constraints imposed by climate and land-use in a dynamic modeling environment is a key advantage of our approach. The resulting framework should allow researchers to synthesize existing empirical evidence, and to explore complex interactions that are difficult or impossible to capture through piecemeal modeling approaches. ?? 2008 Elsevier B.V.

Ecological Modelling↗

USGS2011

Threshold responses of songbirds to long-term timber management on an active industrial forest

Forest managers often seek to balance economic benefits from timber harvesting with maintenance of habitat for wildlife, ecosystem function, and human uses. Most research on the relationship between avian abundance and active timber management has been short-term, lasting one to two years, creating the need to investigate long-term avian responses and to identify harvest thresholds when a small change in habitat results in a disproportionate response in relative abundance and nest success. Our objectives were to identify trends in relative abundance and nest success and to identify landscape-scale disturbance thresholds for avian species and habitat guilds in response to a variety of harvest treatments (clear-cuts, heavy and light partial harvests) over 14 years. We conducted point counts and monitored nests at an industrial forest in the central Appalachians of West Virginia during 1996–1998, 2001–2003, and 2007–2009. Early successional species increased in relative abundance across all three time periods, whereas interior-edge and forest-interior guilds peaked in relative abundance mid-study after which the forest-interior guild declined. Of 41 species with >10 detections, four (10%) declined significantly, 13 (32%) increased significantly (only three species among all periods), and 9 (22%) peaked in abundance mid-study (over the entire study period, four species had no significant change in abundance, four declined, and one increased). Based on piecewise linear models, forest-interior and interior-edge guilds’ relative abundance harvest thresholds were 28% total harvests (all harvests combined), 10% clear-cut harvests, and 18% light partial harvests, after which abundances declined. Harvest thresholds for the early successional guild were 42% total harvests, 11% clear-cut harvest, and 10% light partial harvests, and relative abundances increased after surpassing thresholds albeit at a reduced rate of increase after the clear-cut threshold. Threshold confidence intervals for individual species overlapped their guild threshold intervals 91% of the time. Even though relative abundance of most species (80%) did not decline as the area affected by timber management increased, implementing management at or below our approximate forest-interior and interior-edge harvest thresholds would reduce the number of declining species by half, maintain higher relative abundances of four species with a net decline in abundance but that peaked in abundance mid-study, and maintain higher relative abundances of ten additional species. In contrast, this management strategy also would prevent the increase in relative abundance of seven species and limit the increase in abundance of three species that increased throughout the study.

West Virginia↗

USGS2007

Status review of the Marbled Murrelet (Brachyramphus marmoratus) in Alaska and British Columbia

The Marbled Murrelet ( Brachyramphus marmoratus ) is a small, diving seabird inhabiting inshore waters of the Northeastern Pacific Ocean. This species feeds on small, schooling fishes and zooplankton, and nests primarily on the moss-covered branches of large, old-growth conifers, and also, in some parts of its range, on the ground. We reviewed existing information on this species to evaluate its current status in the northern part of its range—Alaska (U.S.) and British Columbia (Canada). Within the southern part of its range (Washington, Oregon, and California, U.S.), the Marbled Murrelet was listed as a threatened species under the Endangered Species Act (ESA) in 1993, and the U.S. Fish and Wildlife Service (USFWS) needed information on the species throughout its range for ESA deliberations. We compiled published information on the conservation status, population biology, foraging ecology, population genetics, population status and trends, demography, marine and nesting habitat characteristics, threats, and ongoing conservation efforts for Marbled Murrelets in Alaska and British Columbia. We conducted a new genetic study using samples from a segment of the range that had not been included in previous studies (Washington, Oregon) and additional nuclear intron and microsatellite markers. We also analyzed available at-sea survey data from several locations for trend. To understand the reasonableness of the empirical trend data, we developed demographic models incorporating stochasticity to discern what population trends were possible by chance. The genetic studies substantially confirmed previous findings on population structure in the Marbled Murrelet. Our present work finds three populations: (1) one comprising birds in the central and western Aleutian Islands; (2) one comprising birds in central California; and (3) one comprising birds within the center of the range from the eastern Aleutians to northern California. Our knowledge of genetic structure within this central population is limited and it requires additional study. Compiling available abundance information, we estimated that in the recent past, Marbled Murrelets in Alaska numbered on the order of 1 million birds. We were unable to generate a similar estimate for historical population size in British Columbia. Using trend information from at-sea surveys spanning a wide geographic range in Alaska, murrelet numbers declined significantly at five of eight trend sites at annual rates of -5.4 to -12.7 percent since the early 1990s. Applying these rates of decline to the historical population estimate, the current murrelet population in Alaska is projected to be on the order of 270,000 birds. This represents an overall population decline of about 70 percent during the past 25 years. In British Columbia, available trend data indicate that murrelet populations there have experienced similar declines. We updated a recent (2002) population estimate for British Columbia, concluding that there are now between 54,000 and 92,000 murrelets in British Columbia. The rates of decline we observed are within, but at the high end of, a range of rates expected by chance. Given that declines were estimated for sites over essentially the entire northern range of the species, there is cause for concern about the species’ status. In their marine habitats, Marbled Murrelets overlap with salmon (Oncorhynchus sp.) gillnetting operations in British Columbia and in Alaska (especially in Prince William Sound and Southeast Alaska), and annual bycatch mortality is likely in the low thousands per year, although bycatch rates are difficult to measure. The species’ inshore distribution coincides with high levels of vessel traffic and makes them especially vulnerable to both chronic oil pollution and to catastrophic spills (e.g., the 1989 Exxon Valdez oil spill [EVOS] in south-central Alaska, which is estimated to have killed 12,000 to 15,000 murrelets). In their forested nesting habitats, Marbled Murrelets have lost about 15 percent of their suitable nesting habitat in Southeast Alaska, and 33 to 49 percent in British Columbia, from industrial-scale logging within the past half century. Increased predation also may be a threat to murrelet populations, related to fragmentation and edge effects from logging and development, and recent population increases observed for some important murrelet predators, including Bald Eagles ( Haliaeetus leucocephalus ), Common Ravens ( Corvus corax ), and Steller’s Jays ( Cyanocitta stelleri ). Nesting habitat losses cannot explain the declines observed in areas where industrial logging has not occurred on a large scale (e.g., Prince William Sound) or at all (Glacier Bay). The apparent change in population size and rates of decline reported for the Marbled Murrelet are large, and we therefore considered alternative explanations and precedents for changes of similar magnitude in other marine wildlife populations in the Northeastern Pacific Ocean. The declines are likely real, and related to combined and cumulative effects from climate-related changes in the marine ecosystem (most likely the 1977 regime shift) and human activities (logging, gillnet bycatch, oil pollution). Much uncertainty about the decline could be alleviated by continuing to repeat boat surveys in Prince William Sound and lower Cook Inlet, and by repeating the boat survey of Southeast Alaska that was conducted in 1994. This survey used a statistically sound design and covered the region that has been and likely remains the center of the species’ abundance. Important questions remain to be addressed about methods for measuring population status and change, adult mortality (major sources, density dependence, seasonal concordance), and the movements of wintering populations.

Alaska, British Columbia↗

USGS2021

Satellite remote sensing to assess cyanobacterial bloom frequency across the United States at multiple spatial scales

Cyanobacterial blooms can have negative effects on human health and local ecosystems. Field monitoring of cyanobacterial blooms can be costly, but satellite remote sensing has shown utility for more efficient spatial and temporal monitoring across the United States. Here, satellite imagery was used to assess the annual frequency of surface cyanobacterial blooms, defined for each satellite pixel as the percentage of images for that pixel throughout the year exhibiting detectable cyanobacteria . Cyanobacterial frequency was assessed across 2,196 large lakes in 46 states across the continental United States (CONUS) using imagery from the European Space Agency’s Ocean and Land Colour Instrument for the years 2017 through 2019. In 2019, across all satellite pixels considered, annual bloom frequency had a median value of 4% and a maximum value of 100%, the latter indicating that for those satellite pixels, a cyanobacterial bloom was detected by the satellite sensor for every satellite image considered. In addition to annual pixel-scale cyanobacterial frequency, results were summarized at the lake- and state-scales by averaging annual pixel-scale results across each lake and state. For 2019, average annual lake-scale frequencies also had a maximum value of 100%, and Oregon and Ohio had the highest average annual state-scale frequencies at 65% and 52%. Pixel-scale frequency results can assist in identifying portions of a lake that are more prone to cyanobacterial blooms, while lake- and state-scale frequency results can assist in the prioritization of sampling resources and mitigation efforts. Satellite imagery is limited by the presence of snow and ice, as imagery collected in these conditions are quality flagged and discarded. Thus, annual bloom frequencies within nine climate regions were investigated to determine whether missing data biased results in climate regions more prone to snow and ice, given that their annual summaries would be weighted toward the summer months when cyanobacterial blooms tend to occur. Results were unbiased by the time period selected in most climate regions, but a large bias was observed for the Northwest Rockies and Plains climate region. Moderate biases were observed for the Ohio Valley and the Southeast climate regions. Finally, a clustering analysis was used to identify areas of high and low cyanobacterial frequency across CONUS based on average annual lake-scale cyanobacterial frequencies for 2019. Several clusters were identified that transcended state, watershed, and eco-regional boundaries. Combined with additional data, results from the clustering analysis may offer insight regarding large-scale drivers of cyanobacterial blooms.

Ecological Indicators↗

USGS2003

The Role of stocking in the reestablishment and augmentation of native fish in the Lower Colorado River mainstream (1998-2002)

The Colorado River has experienced dramatic physical and biological change. Rated as the fifth largest river in the USA by volume, today its waters seldom reach the sea. Water diversions gradually reduce its flow to a point where its last remaining waters are diverted at Morales Dam leaving nearly 100 km of historic channel dry. In contrast, lower basin storage reservoirs cover 36% of the historic channel. Remaining portions of the flowing river have been channelized and straightened to a point where it now resembles a large canal. Levees, mechanical dredging, and the natural forces of erosion have degraded the river channel nearly 2 m in some locations, isolating it from its floodplain and affecting local water tables. The river no longer functions as a natural stream system characteristic of spring run-off, summer spates, and droughts. Today it serves as a water storage and conveyance system to meet human needs. Physical change has been severe, but not as devastating as the biological pollution. More than 80 nonnative fish species have been introduced to the lower basin. Today, over 20 fish species have established, many forming economically important sport fisheries. As these alien species expanded their range, native communities rapidly declined and disappeared from much of their historic range. By 1930, most had become rare. The last remnant populations of bonytail, razorback sucker, and Colorado pikeminnow in the lower basin were taken downstream of Davis Dam during the 1960’s and 1970’s. Today, Colorado pikeminnow, and it appears, wild bonytail are extirpated downstream of Glen Canyon Dam, and wild razorback suckers are extremely rare. The Colorado River and its fish assemblage is a totally different ecosystem than it was a century ago. State and federal agencies have been attempting to reestablish native communities for nearly three decades. More than 12 million razorback suckers, most of them small, were stocked between 1981 and 1991. Few of these fish survived and during the past decade managers have switched to stocking larger suckers to improve survival. Since 1995, nearly 18,000 bonytail and 30,000 large razorback suckers have been stocked in Lake Havasu. There was also a single stocking (611) of flannelmouth suckers in 1976. These programs have produced mixed results. The single introduction of flannelmouth sucker has resulted in a thriving community, estimated at more than 4,000 fish. This success spirited hopes by many that other natives would respond similarly but unfortunately, that has not occurred. Initial stocking returns suggest that stocking survival of bonytail and razorback sucker is relatively poor (<12%) and the absence of any detectable recruitment indicates present reintroduction efforts are falling short of anticipated survival or potential recovery. In contrast, the single introduction of wild flannelmouth sucker, out-performed millions of hatchery produced razorback sucker. This suggests hatchery reared fish may be inferior to wild fish in terms of survival skills, which has been found to be the case for terrestrial animal introductions. A review of culturing, stocking, and repatriation techniques is warranted which examines ways to better prepare fish to convert to natural foods, recognize predators, and be physically conditioned to cope with currents and hopefully avoid or escape predators. Comparison of flannelmouth sucker success and the razorback sucker’s failure provides compelling evidence that helps explain the dramatic physical habitat changes that have occurred and the possible role of habitat selection and predator communities. It mimics conditions observed in portions of the upper basin where flannelmouth suckers are still common but razorback suckers have been extirpated. Both sucker species are successfully spawning in the lower basin, however, recruitment can only be detected for flannelmouth. Habitat preference and associated predation pressure of those habitats appear to be the primary factors responsible for recruitment. Flannelmouth suckers prefer channel habitat that supports a fraction of the predators found in off-channel habitats where razorback suckers reside. The dependence of razorback sucker young on slack water habitat puts the species at a much higher predation risk. Through a process of trial and error during the past two decades, managers are now stocking large natives to increase their survival. Small native fish simply have not survived. While this improves short-term stocking survival, it ignores or at least delays dealing with the predation issue. Current stocking programs have reestablished or augmented relatively small populations of bonytail, razorback, and flannelmouth suckers between Davis and Parker Dams. All three species are better off than they were a decade ago in this section of the river. Unfortunately, bonytail and razorback sucker will only maintain a presence in the Colorado River main stem through continued stocking and it remains to be seen if management agencies will make that long-term commitment. While the gains for the bonytail and razorback sucker have been difficult, the successful reintroduction of flannelmouth sucker highlights the ecological changes that have taken place and suggests this, and possibly other channel oriented species (i.e., Gila robusta) could be established. In contrast, there is no evidence to suggest we can expect similar recruitment or expansions for bonytail and razorback sucker. Their dependence on slack water habitat leaves their young vulnerable to overwhelming predation. Recovery in the main stem will only be accomplished with a dramatic decrease and possibly a total removal of nonnative species. After ten years and over $6 million in expenditures to remove nonnative fish it appears this philosophy is neither technically nor politically viable. In the meantime, stocking is the only alternative available to insure these species don’t disappear. The only viable option appears the creation and maintenance of small, isolated refuge communities where these species have shown they can produce young.

Arizona, California, Nevada↗

USGS2012

Preliminary assessment of channel stability and bed-material transport in the Tillamook Bay tributaries and Nehalem River basin, northwestern Oregon

This report summarizes a preliminary study of bed-material transport, vertical and lateral channel changes, and existing datasets for the Tillamook (drainage area 156 square kilometers [km 2 ]), Trask (451 km 2 ), Wilson (500 km 2 ), Kilchis (169 km 2 ), Miami (94 km 2 ), and Nehalem (2,207 km 2 ) Rivers along the northwestern Oregon coast. This study, conducted in coopera-tion with the U.S. Army Corps of Engineers and Oregon Department of State Lands to inform permitting decisions regarding instream gravel mining, revealed that: Study areas along the six rivers can be divided into reaches based on tidal influence and topography. The fluvial (nontidal or dominated by riverine processes) reaches vary in length (2.4-9.3 kilometer [km]), gradient (0.0011-0.0075 meter of elevation change per meter of channel length [m/m]), and bed-material composition (a mixture of alluvium and intermittent bedrock outcrops to predominately alluvium). In fluvial reaches, unit bar area (square meter of bar area per meter of channel length [m 2 /m]) as mapped from 2009 photographs ranged from 7.1 m 2 /m on the Tillamook River to 27.9 m 2 /m on the Miami River. In tidal reaches, all six rivers flow over alluvial deposits, but have varying gradients (0.0001-0.0013 m/m) and lengths affected by tide (1.3-24.6 km). The Miami River has the steepest and shortest tidal reach and the Nehalem River has the flattest and longest tidal reach. Bars in the tidal reaches are generally composed of sand and mud. Unit bar area was greatest in the Tidal Nehalem Reach, where extensive mud flats flank the lower channel. Background factors such as valley and channel confinement, basin geology, channel slope, and tidal extent control the spatial variation in the accumulation and texture of bed material. Presently, the Upper Fluvial Wilson and Miami Reaches and Fluvial Nehalem Reach have the greatest abundance of gravel bars, likely owing to local bed-material sources in combination with decreasing channel gradient and valley confinement. Natural and human-caused disturbances such as mass movements, logging, fire, channel modifications for navigation and flood control, and gravel mining also have varying effects on channel condition, bed-material transport, and distribution and area of bars throughout the study areas and over time. Existing datasets include at least 16 and 18 sets of aerial and orthophotographs that were taken of the study areas in the Tillamook Bay tributary basins and Nehalem River basin, respectively, from 1939 to 2011. These photographs are available for future assessments of long-term changes in channel condition, bar area, and vegetation establishment patterns. High resolution Light Detection And Ranging (LiDAR) surveys acquired in 2007-2009 could support future quantitative analyses of channel morphology and bed-material transport in all study areas. A review of deposited and mined gravel volumes reported for instream gravel mining sites shows that bed-material deposition tends to rebuild mined bar surfaces in most years. Mean annual deposition volumes on individual bars exceeded 3,000 cubic meters (m 3 ) on Donaldson Bar on the Wilson River, Dill Bar on the Kilchis River, and Plant and Winslow Bars on the Nehalem River. Cumulative reported volumes of bed-material deposition were greatest at Donaldson and Dill Bars, totaling over 25,000 m 3 per site from 2004 to 2011. Within this period, reported cumulative mined volumes were greatest for the Donaldson, Plant, and Winslow Bars, ranging from 24,470 to 33,940 m 3 . Analysis of historical stage-streamflow data collected by the U.S. Geological Survey on the Wilson River near Tillamook (14301500) and Nehalem River near Foss (14301000) shows that these rivers have episodically aggraded and incised, mostly following high flow events, but they do not exhibit systematic, long-term trends in bed elevation. Multiple cross sections show that channels near bridge crossings in all six study areas are dynamic with many subject to incision and aggradation as well as lateral shifts in thalweg position and bank deposition and erosion. In fluvial reaches, unit bar area declined a net 5.3-83.6 percent from 1939 to 2009. The documented reduction in bar area may be attributable to several factors, including vegetation establishment and stabilization of formerly active bar surfaces, lateral channel changes and resulting alterations in sediment deposition and erosion patterns, and streamflow and/or tide differences between photographs. Other factors that may be associated with the observed reduction in bar area but not assessed in this reconnaissance level study include changes in the sediment and hydrology regimes of these rivers over the analysis period. In tidal reaches, unit bar area increased on the Tillamook and Nehalem Rivers (98.0 and 14.7 percent, respectively), but declined a net 24.2 to 83.1 percent in the other four tidal reaches. Net increases in bar area in the Tidal Tillamook and Nehalem Reaches were possibly attributable to tidal differences between the photographs as well as sediment deposition behind log booms and pile structures on the Tillamook River between 1939 and 1967. The armoring ratio (ratio of the median grain sizes of a bar's surface and subsurface layers) was 1.6 at Lower Waldron Bar on the Miami River, tentatively indicating a relative balance between transport capacity and sediment supply at this location. Armoring ratios, however, ranged from 2.4 to 5.5 at sites on the Trask, Wilson, Kilchis, and Nehalem Rivers; these coarse armor layers probably reflect limited bed-material supply at these sites. On the basis of mapping results, measured armoring ratios, and channel cross section surveys, preliminary conclusions are that the fluvial reaches on the Tillamook, Trask, Kilchis, and Nehalem Rivers are currently sediment supply-limited in terms of bed material - that is, the transport capacity of the channel generally exceeds the supply of bed material. The relation between transport capacity and sediment is more ambiguous for the fluvial reaches on the Wilson and Miami Rivers, but transport-limited conditions are likely for at least parts of these reaches. Some of these reaches have possibly evolved from sediment supply-limited to transport-limited over the last several decades in response to changing basin and climate conditions. Because of exceedingly low gradients, all the tidal reaches are transport-limited. Bed material in these reaches, however, is primarily sand and finer grain-size material and probably transported as suspended load from upstream reaches. These reaches will be most susceptible to watershed conditions affecting the supply and transport of fine sediment. Compared to basins on the southwestern Oregon coast, such as the Chetco and Rogue River basins, these six basins likely transport overall less gravel bed material. Although tentative in the absence of actual transport measurements, this conclusion is supported by the much lower area and frequency of bars and longer tidal reaches along all the northcoast rivers examined in this study. Previous studies suggest that the expansive and largely unvegetated bars visible in the 1939 photographs are primarily associated with voluminous sedimentation starting soon after the first Tillamook Burn fire in 1933. However, USGS studies of temporal bar trends in other Oregon coastal rivers unaffected by the Tillamook Burn show similar declines in bar area over approximately the same analysis period. In the Umpqua and Chetco River basins, historical declines in bar area are associated with long-term decreases in flood magnitude. Other factors may include changes in the type and volume of large wood and riparian vegetation. Further characterization of hydrology patterns in these basins and possible linkages with climate factors related to flood peaks, such as the Pacific Decadal Oscillation, could support inferences of expected future changes in vegetation establishment and channel planform and profile. More detailed investigations of bed-material transport rates and channel morphology would support assessments of lateral and vertical channel condition and longitudinal trends in bed material. Such assessments would be most practical for the fluvial study areas on the Wilson, Kilchis, Miami, and Nehalem Rivers and relevant to several ongoing management and ecological issues pertaining to sand and gravel transport. Tidal reaches may also be logical subjects for indepth analysis where studies would be more relevant to the deposition and transport of fine sediment (and associated channel and riparian conditions and processes) rather than coarse bed material.

Oregon↗

USGS2012

Preliminary assessment of channel stability and bed-material transport in the Rogue River basin, southwestern Oregon

This report summarizes a preliminary assessment of bed-material transport, vertical and lateral channel changes, and existing datasets for the Rogue River basin, which encompasses 13,390 square kilometers (km 2 ) along the southwestern Oregon coast. This study, conducted to inform permitting decisions regarding instream gravel mining, revealed that: The Rogue River in its lowermost 178.5 kilometers (km) alternates between confined and unconfined segments, and is predominately alluvial along its lowermost 44 km. The study area on the mainstem Rogue River can be divided into five reaches based on topography, hydrology, and tidal influence. The largely confined, active channel flows over bedrock and coarse bed material composed chiefly of boulders and cobbles in the Grants Pass (river kilometers [RKM] 178.5–152.8), Merlin (RKM 152.8–132.7), and Galice Reaches (RKM 132.7–43.9). Within these confined reaches, the channel contains few bars and has stable planforms except for locally wider segments such as the Brushy Chutes area in the Merlin Reach. Conversely, the active channel flows over predominately alluvial material and contains nearly continuous gravel bars in the Lobster Creek Reach (RKM 43.9–6.7). The channel in the Tidal Reach (RKM 6.7–0) is also alluvial, but tidally affected and unconfined until RKM 2. The Lobster Creek and Tidal Reaches contain some of the most extensive bar deposits within the Rogue River study area. For the 56.6-km-long segment of the Applegate River included in this study, the river was divided into two reaches based on topography. In the Upper Applegate River Reach (RKM 56.6–41.6), the confined, active channel flows over alluvium and bedrock and has few bars. In the Lower Applegate River Reach (RKM 41.6–0), the active channel alternates between confined and unconfined segments, flows predominantly over alluvium, shifts laterally in unconfined sections, and contains more numerous and larger bars. The 6.5-km segment of the lower Illinois River included in this study was treated as one reach. This stretch of the Illinois River is fully alluvial, with nearly continuous gravel bars flanking the channel. The width of the active channel is confined by the narrow topography of the valley. The primary human activities that have likely influenced channel condition, bed-material transport, and the extent and area of bars are (1) historical gold mining throughout the basin, (2) historical and ongoing gravel mining from instream sites in the Tidal Reach and floodplain sites such as those in the Lower Applegate River Reach, (3) hydropower and flow control structures, (4) forest management and fires throughout the basin, and (5) dredging. These anthropogenic activities likely have varying effects on channel condition and the transport and deposition of sediment throughout the study area and over time. Several vertical (aspect) aerial photographs (including the complete coverages of the study area taken in 1995, 2000, 2005, and 2009 and the partial coverages taken in 1967, 1968, 1969, and 1990) are available for assessing long-term changes in attributes such as channel condition, bar area, and vegetation cover. A Light Detection And Ranging (LiDAR) survey performed in 2007–2008 provides 1-m resolution topographic data for sections of the Grants Pass (RKM 178.5–167.6) and Lobster Creek (RKM 17.8–12 and 10–6.7) Reaches and the entire Tidal Reach. Previous studies provide information for specific locations, including (1) an estimated average annual bed-material load of 76,000 m 3 at the former Savage Rapids Dam site (RKM 173.1, Grants Pass Reach), (2) over 490 m of channel shifting from 1965 to 1991 in the Brushy Chutes area (RKM 142–141, Merlin Reach), (3) active sediment transport and channel processes in the Lobster Creek Reach, (4) lateral channel migration in the Tidal Reach, and (5) up to 1.8 m of bar aggradation from the town of Agness (RKM 45.1) to the Rogue River mouth following the flood in water year 1997. Review of the repeat surveys conducted at the instream gravel-mining sites on Elephant and Wedderburn Bars tentatively indicated that these bars (1) experience some bed-material deposition in most years and more substantial deposition following high flows such as those in water years 1997 and 2006, and (2) are dynamic and subject to local scour and deposition. Results from the specific gage analyses completed for five long-term USGS streamflow-gaging stations showed that only the Grants Pass station on the Rogue River (RKM 164.4, Grants Pass Reach) experienced substantial changes in the stage–discharge relationship across a range of flows from 1938 to 2009. Observed changes indicate channel incision at this site. The Rogue and Applegate Rivers are dynamic and subject to channel shifting, aggradation, and incision, as indicated by channel cross sections surveyed during 2000–2010 on the Rogue River and 1933–2010 on the Applegate River. The elevation of the riverbed changed substantially (defined here as more than a net 0.5 m of incision or aggradation) at three locations on the Rogue River (near RKM 164.5, 139.2, and 1.3) and two on the Applegate River (near RKM 42 and 13.5). Systematic delineation of bar features from vertical photographs taken in 1967–69, 2005, and 2009 indicated that most of the repeat mapping sites had a net loss in bar area over the analysis period, ranging from 22 percent at the Oak Flat site (Illinois River Reach) to 69 percent at the Thompson Creek site (Upper Applegate River Reach). Bar area remained stable at the Williams Creek site (Lower Applegate River Reach), but increased 11 percent at the Elephant Rock site (Tidal Reach). The declines in bar area were associated primarily with the establishment of vegetation on upper bar surfaces lacking obvious vegetation in the 1960s. Some of the apparent changes in bar area may also owe to some differences in streamflow and tide levels between the vertical photographs. On the mainstem Rogue River, the median diameter of surface particles varied from 21 mm at the Wedderburn Bar in the Tidal Reach to more than 100 millimeters (mm) at some of the coarsest bars in the Galice Reach. Low armoring ratios tentatively indicated that sediment supply likely exceeds transport capacity at Orchard (Lobster Creek Reach) and Wedderburn (Tidal Reach) Bars. Conversely, relatively higher armoring ratios indicated that transport capacity likely is in balance with sediment supply at Roberston Bridge Bar (Merlin Reach) and exceeds sediment supply at Rogue River City (Grants Pass Reach), Solitude Riffle (Galice Reach), and Hooks Gulch (Galice Reach) Bars. Limited particle data were collected in the study areas on the Applegate and Illinois Rivers. Particle size measurements and armoring ratios tentatively show that sediment supply likely exceeds transport capacity at Bakery Bar in the Lower Applegate Reach. Also, the bed material exiting the Applegate River is likely finer than the bed material in the Rogue River, whereas bed material exiting the Illinois River is likely coarser than the bed material in the Rogue River. Together, these observations and findings indicate that (1) the size, area, and overall position of bars in the Rogue River study area are determined largely by valley physiography, such that unconfined alluvial sections have large channel-flanking bars, whereas confined sections have fewer and smaller bars, (2) segments within the Grants Pass, Merlin, Tidal, Upper Applegate River, and Lower Applegate River Reaches are prone to vertical and/or lateral channel adjustments, and (3) the balance between transport capacity and sediment supply varies throughout the study area. High winter flows and the steep, confined character of much of the Rogue River within the study area result in a river corridor with a high capacity to transport bed material. In the Grants Pass and Galice Reaches, the extensive in-channel bedrock as well as the sparse number and coarse texture of bars indicate that these reaches are likely supply-limited, meaning that the river’s transport capacity exceeds the supply of bed material. In contrast, the Lobster Creek and Tidal Reaches and perhaps portions of the Merlin Reach receive bed-material inputs that more closely balance or even exceed the river’s transport capacity. The lowermost reaches on the Illinois and Applegate Rivers are fully alluvial segments that are likely transport limited, meaning sediment supply likely exceeds the river's transport capacity. However, the steeper Upper Applegate River Reach is likely supply-limited as indicated by the sparse number and area of bars mapped in this reach and the intermittent bedrock outcrops in the channel. The sediment loads derived from these large tributaries draining the Klamath Mountains are probably important contributions to the overall transport of bed material in the Rogue River basin. Compared to the slightly smaller Umpqua River basin (drainage area 12,103 km 2 ) to the north, the Rogue River (13,390 km 2 ) likely transports more bed material. Although this conclusion of greater bed-material transport in the Rogue River is tentative in the absence of either actual transport measurements or transport capacity calculations, empirical evidence, including the much greater area and frequency of bars along most of the Rogue River as well as the much shorter tidal reach on the Rogue River (6.7 km) compared to the Umpqua River (40 km) supports this inference. More detailed investigations of bed-material transport rates and channel morphology would support assessments of channel condition, longitudinal trends in particle size, the relation between sediment supply and transport capacity, and the potential causes of bar area loss (such as vegetation establishment and potential changes in peak flow patterns). The reaches most practical for such assessments and relevant to several management and ecological issues are (1) the lower Rogue River basin, including the Lobster Creek and Tidal Reaches of the Rogue River as well as the Illinois River Reach and (2) the Lower Applegate River Reach.

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