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USGS2010

Grassland birds wintering at U.S. Navy facilities in southern Texas

Grassland birds have undergone widespread decline throughout North America during the past several decades. Causes of this decline include habitat loss and fragmentation because of conversion of grasslands to cropland, afforestation in the East, brush and shrub invasion in the Southwest and western United States, and planting of exotic grass species to enhance forage production. A large number of exotic plant species, including grasses, have been introduced in North America, but most research on the effects of these invasions on birds has been limited to breeding birds, primarily those in northern latitudes. Research on the effects of exotic grasses on birds in winter has been extremely limited. This is the first study in southern Texas to examine and compare winter bird responses to native and exotic grasslands. This study was conducted during a period of six years (2003–2009) on United States Navy facilities in southern Texas including Naval Air Station–Corpus Christi, Naval Air Station–Kingsville, Naval Auxiliary Landing Field Waldron, Naval Auxiliary Landing Field Orange Grove, and Escondido Ranch, all of which contained examples of native grasslands, exotic grasslands, or both. Data from native and exotic grasslands were collected and compared for bird abundance and diversity; ground cover, vegetation density, and floristic diversity; bird and vegetation relationships; diversity of insects and arachnids; and seed abundance and diversity. Effects of management treatments in exotic grasslands were evaluated by comparing numbers and diversity of birds and small mammals in mowed, burned, and control areas. To determine bird abundance and bird species richness, birds were surveyed monthly (December–February) during the winters of 2003–2008 in transects (100 meter × 20 meter) located in native and exotic grasslands distributed at all five U.S. Navy facilities. To compare vegetation in native and exotic grasslands, vegetation characteristics were measured during 2003–2008 in the same transects used for bird surveys and included five measures of ground cover, plus estimates of plant species richness, vegetation density (visual obstruction) at two different heights, and shrub numbers. These data, plus seasonal rainfall, were then used to evaluate components of variation in native and exotic grasslands. Relations between total bird numbers and bird species richness with environmental variation in native and exotic grasslands were compared. To compare diversity of arthropods in native and exotic grasslands, insects and arachnids were collected using three different methodologies (standardized sweep-net, random sweep-net, and pitfall traps) during four seasons, (2005–2006), at Naval Air Station–Corpus Christi, Naval Auxiliary Landing Field Waldron, and Naval Air Station–Kingsville. To compare seed abundance and diversity between native and exotic grasslands, seeds were collected for two winters (2004–2006) at Naval Air Station–Corpus Christi and Naval Air Station–Kingsville. To evaluate effects of management on grassland vertebrates, abundance and diversity of birds and small mammals were estimated and compared in exotic grasses subjected to mowing, burning, or no active management (control) for one full year (2008–2009). Observations were made of 1,044 birds of 30 species in grassland transects during five winters. The Savannah Sparrow ( Passerculus sandwichensis ) was the most common bird, which, with 644 detections, accounted for 63 percent of all individuals identified to species. Meadowlarks ( Sturnella spp. ) and Le Conte’s Sparrows ( Ammodramus leconteii ) were the second (10 percent) and third (7 percent) most abundant bird species, respectively. Six of the seven most abundant species detected in grasslands were grassland species, and their numbers accounted for 87 percent of all birds, but 20 of the 30 species (67 percent) that used grasslands were not grassland species. Seven species observed in grassland transects during the study were Species of Conservation Concern: Le Conte’s Sparrow, Sedge Wren ( Cistothorus platensis ), Grasshopper Sparrow ( Ammodramus savannarum ), Long-billed Curlew ( Numenius americanus ), Sprague’s Pipit ( Anthus spragueii ), Cassin’s Sparrow ( Aimophila cassinii ), and Loggerhead Shrike ( Lanius ludovicianus ). Native grasslands consistently supported greater bird species richness than exotic grasslands. In one winter, exotic grasslands supported more birds than native grasslands. Native grasslands were determined to have more forb cover, more bare ground, and greater plant species richness than exotic grasslands, whereas exotic grasslands were characterized by more grass cover and relatively greater vegetation density during dry years. Not only did these individual measures differ between native and exotic grasslands, but components of variation also differed. In native grasslands, grass density and cover contributed more to variation, whereas in exotic grasslands, non-grass vegetation was a greater component of variation. Total bird numbers and bird species richness in native grasslands were related to the principal component that contained a measure of litter cover. Total bird numbers and bird species richness in exotic grasslands indicated no significant relationships with any of the principal components of variation. The two most common insect orders in native grasslands were Hymenoptera and Coleoptera, which accounted for 42 percent of all insects. The two most common insect orders in exotic grasslands were Hemiptera and Homoptera, which accounted for about 80 percent of all insects. Insect family richness was greater in exotic grasslands than in native grasslands in two of four seasons. Proportions of arachnid families were similar in native and exotic grasslands, but arachnid family richness was greater in exotic grasslands than in native grasslands. Abundance of seeds was greater in exotic than in native grasslands. However, seed diversity was greater in native grasslands than in exotic grasslands. Among the three types of management (mowed, burned, and control) applied to exotic grasses, birds were most abundant in the mowed area. Sedge Wrens, however, were never encountered in mowed sites. Meadowlarks were similarly abundant in all treatments, but Le Conte’s Sparrows were detected only in the control (unmanaged) area. Hispid cotton rats ( Sigmodon hispidus ) accounted for 93 percent of all rodent captures, with the number of captures peaking December through February. Hispid cotton rat numbers and total rodent numbers were greatest in control and pre-burn areas, and lowest in the mowed area. Mammal diversity, however, was greatest in the mowed habitat. Native and exotic grasslands differed essentially in all categories (bird numbers and diversity, vegetation characteristics, components of variation, diversity of insects and arachnids, and seed abundance and diversity) used to measure and compare them. This indicates that fundamental ecosystem processes have been altered after native grasslands have undergone invasion and ultimate domination by exotic grass species. Future research in Texas grassland ecosystems is essential because: 1) Texas sustains more area in grasslands than any other state or province in the Central Flyway; 2) Texas serves as the winter destination or migration pathway for hundreds of species of birds, including winter residents and Neotropical migrants; 3) ecology, distribution, and numbers of grassland birds wintering in southern latitudes of the United States remains poorly understood; and 4) climate change threatens to further accelerate advances of invading grass species.

Open-File Report↗

USGS2020

Geochemical and mineralogical study of the Red Mountain porphyry copper-molybdenum deposit and vicinity, Santa Cruz County, Arizona

The Red Mountain porphyry copper-molybdenum deposit (Cu-Mo deposit or PCD) is located in the northern part of the Patagonia Mountains, Santa Cruz County, Arizona. Extensive core drilling has delineated a large, deep-seated, structurally intact mineral system that extends from the present surface to depths of more than 1,765 meters. This system is hosted in a thick complex of predominantly felsic to andesitic volcanic rocks of the Cretaceous Period. This complex was intruded by scattered bodies of the Tertiary Period that are predominantly quartz monzonite porphyry; no major associated source intrusion has yet been found at depth. A total of 818 samples of core were analyzed for as many as 44 elements. The abundances and distributions at depth of at least 17 of these elements (silver [Ag], arsenic [As], gold [Au], boron [B], bismuth [Bi], copper [Cu], mercury [Hg], potassium [K], molybdenum [Mo], lead [Pb], sulfur [S], antimony [Sb], tin [Sn], tellurium [Te], thallium [Tl], tungsten [W], and zinc [Zn]) are related mostly to events that generated the Red Mountain system. Many of these same samples were also analyzed by X-ray diffraction for a suite of minerals. The multielement and mineralogical analyses of the core samples provide important information about the concentrations, associations, and distributions of select elements and minerals, including zoning patterns that may not be apparent from visual examination of core samples. The distributions of selected elements and minerals in these samples reveal an unusually complete mineral system that extends from a typical PCD with potassic alteration at depth to peripheral zones of phyllic and advanced argillic alteration as well as a copper-rich supergene enriched zone and the remnants of a leached cap. R-mode factor analysis was run with 34 elements for a set of samples from the deep part of the hypogene Cu-Mo deposit and another set from the part of the supergene zone with the highest copper enrichment. For the hypogene zone dataset, five factors are related to the PCD: (1) Ag, Cu, Mo, S, and Te; (2) As, B, Hg, and Sb; (3) Au and sodium (Na); (4) manganese (Mn), Pb, and Zn; and (5) K and Tl. For the supergene dataset, the deposit-related factors include (1) Cu, Mo, S, and Te; (2) Ag, As, Hg, Pb, Sb, and Tl; (3) Au and Na; and (4) K and rubidium (Rb). The changes in element associations between the two datasets indicate that some of these new associations are a result of formation of several suites of hypogene minerals in the deep part of the deposit and different hypogene mineral suites in the peripheral part of the deposit. Some changes may be because of the effects of supergene processes. Zones containing deposit-related elements and minerals common to many PCDs are present at Red Mountain. These zones include a crude, inverted cup-shaped shell containing anomalous copper accompanied by high concentrations of Ag, Au, K, Mo, total S, sulfate S, Sb, Te, and Tl, as well as local concentrations of As, B, Hg, Pb, and Zn. Hydrothermal minerals spatially associated with the deep hypogene Cu-Mo deposit include chalcopyrite, molybdenite, pyrite, plagioclase, orthoclase, biotite, magnetite, calcite, quartz, and anhydrite. Many of the hydrothermally deposited elements that are spatially related to the deposit are also concentrated in zones above the deep part of the deposit, including Ag, As, K, Pb, Sb, Te, Tl, and Zn. These elements are concentrated either (1) in generally wide, flat zones present in the upper part of the system or (2) in crudely arcuate peripheral zones found mainly in the middle part of the system and surrounding the deep part of the deposit. Near-surface, restricted hypogene anomalies are present for bismuth, mercury, tin, and tungsten. The upper part of the deposit has been subjected to supergene enrichment and weathering. Deposit-related elements that remain anomalous in this area include Ag, As, Au, B, Bi, cobalt (Co), Cu, Hg, Mo, Pb, S, Sb, Sn, Te, Tl, uranium (U), and W. These positive concentrations indicate that, with the exception of copper and possibly mercury and uranium, these elements had relatively low chemical mobilities in the supergene enrichment and later weathering environments at Red Mountain. Most may have been deposited during one or more hypogene events and then redistributed locally during later events. Zinc is the only deposit-related element that has clearly been depleted as a result of supergene and (or) weathering events. Minerals that are common in the unweathered upper part of the system include chalcocite, pyrite, quartz, sericite, alunite, and pyrophyllite, as well as less common covellite, enargite, tennantite, tourmaline, barite, anglesite, and other sulfide or sulfate minerals. Subsequent to formation of the Red Mountain Cu-Mo deposit and supergene enrichment, chemical weathering produced an area of pervasive hematite and other iron oxides in the near-surface part of the deposit to form a leached cap. These iron-rich minerals formed primarily as a result of the oxidation of pyrite. This event was accompanied by losses of cobalt, mercury, magnesium, and zinc, as well as destruction of sericite, plagioclase, pyrite, clay minerals, and pyrophyllite. A total of 122 rock samples, 119 soil samples, and samples of three plant species (57 mesquite, 108 oak, and 68 juniper) were collected over and around Red Mountain. For the rock and soil samples, the distributions of anomalous Ag, As, Bi, Cu, Fe, Mo, Pb, Sb, Te, and Tl best delineated the exposed part of the deposit. The highest concentrations of many of these elements are centered on one or both of two main areas with exposures of quartz monzonite porphyry. The high concentrations of arsenic in the deposit area (as much as 390 parts per million (ppm) in rock and 1,500 ppm in soil) and of lead (as much as 2,370 ppm in rock and 1,490 ppm in soil) are particularly noteworthy. The concentrations of various elements in the plant ash vary widely among the three species and are species dependent. Many of the deposit-related elements are either nonessential for plant growth or are considered toxic at certain concentration ranges. In spite of this, the distributions of potentially toxic Ag, As, Bi, Cd, Cu, Mo, Pb, Sb, selenium (Se), and Zn produce deposit-related anomalies for one or more of the three species. Vegetation sampling offered no advantage over rock or soil sampling as an exploration tool. From an environmental standpoint, however, the plant analyses provide baseline data for both essential and nonessential elements that might be useful, for example, for selecting native plant species for revegetating mine waste areas. The exposed part of the Red Mountain deposit has not been greatly disturbed as a result of mining and other activities. However, some of the rock, soil, and plant samples that were collected near the Harshaw Creek and Alum Gulch drainages, which are peripheral to Red Mountain, are also anomalous for various deposit-related elements. These anomalies are probably the result of dispersion of stream sediments contaminated with material from past mining.

Arizona↗

USGS2024

An update of hydrologic conditions and distribution of selected constituents in water, eastern Snake River aquifer and perched groundwater zones, Idaho National Laboratory, Idaho, emphasis 2019–21

Since 1952, wastewater discharged to infiltration ponds (also called “percolation ponds”) and disposal wells at the Idaho National Laboratory (INL) has affected water quality in the eastern Snake River Plain (ESRP) aquifer and perched groundwater zones underlying the INL. The U.S. Geological Survey (USGS), in cooperation with the U.S. Department of Energy (DOE), maintains groundwater-monitoring networks at the INL to determine hydrologic trends and to delineate the movement of radiochemical and chemical wastes in both the aquifer and perched groundwater zones. This report presents an analysis of water-level and water-quality data collected from the ESRP aquifer and perched groundwater wells from the USGS groundwater monitoring networks during 2019–21. From March–May 2018 to March–May 2021, water levels in wells completed in the ESRP aquifer increased in the northern part of the INL and decreased in the southwestern part. Water-level increases ranged from 0.02 to 1.04 feet in the northern part and decreases ranged from 0.03 to 2.94 feet in the southwestern part of the INL. Detectable concentrations of radiochemical constituents in water samples from wells in the ESRP aquifer at the INL generally decreased or remained constant during 2019–21. Decreases in concentrations were attributed to radioactive decay, changes in waste-disposal methods, and dilution from recharge and underflow. In 2021, tritium was detected above reporting levels in water samples collected from 46 of 105 aquifer wells and ranged from 150±50 to 4,280±150 picocuries per liter (pCi/L). Tritium concentrations from eight wells completed in deep perched groundwater near the Advanced Test Reactor Complex (ATRC) generally were greater than or equal to the reporting level during at least one sampling event during 2019–21, and concentrations ranged from 160±50 to 2,097±107 pCi/L. Concentrations of strontium-90 in water from 12 of 45 aquifer wells sampled in 2021 exceeded the reporting level, and concentrations ranged from 2.5±0.7 to 299±6 pCi/L. During 2021, concentrations of strontium-90 from five wells completed in deep perched groundwater at the ATRC equaled or exceeded the reporting levels, and concentrations ranged from 3±0.9 pCi/L to 27.8±1.3 pCi/L. Concentrations of cesium-137 were less than the reporting level in all but one aquifer well, and concentrations of plutonium-238, plutonium-239, -240 (undivided), and americium-241 were less than the reporting level in water samples from all aquifer wells sampled during this study period. Dissolved chromium concentrations in water samples from 64 ESRP aquifer wells ranged from less than (<) 0.5 to 76.4 micrograms per liter (μg/L). During 2019–21, dissolved chromium was detected in water from wells completed in deep perched groundwater above the ESRP aquifer at the ATRC, and concentrations ranged from <1 to 82.1 μg/L. In 2021, concentrations of dissolved sodium in water from most ESRP aquifer wells in the southern part of the INL were greater than the western tributary groundwater background concentration of 8.3 milligrams per liter (mg/L). During 2021, dissolved sodium concentrations in water from 15 wells completed in deep perched groundwater ranged from 11.7 to 122.5 mg/L. Variations in sodium concentrations in aquifer wells and perched groundwater zones are attributed to either migration of remnant water from the former chemical-waste ponds or disposal volume and composition variability in percolation ponds installed in 2008. In 2021, concentrations of chloride in most water samples from ESRP aquifer wells south of the Idaho Nuclear Technology and Engineering Center (INTEC) and at the Central Facilities Area (CFA) exceeded background concentrations. Chloride concentrations in water from wells south of the INTEC have generally decreased because of discontinued chloride disposal to the legacy percolation ponds since 2002 when the discharge of wastewater was discontinued. During 2019–21, dissolved chloride concentrations in deep perched groundwater above the ESRP aquifer from 18 wells at the ATRC ranged from 8.15 to 231 mg/L. In 2021, sulfate concentrations in water samples from ESRP aquifer wells in the south-central part of the INL that exceeded the background concentration of sulfate, ranged from 21 to 141 mg/L. The greater-than-background concentrations in water from these wells are attributed to sulfate disposal at the ATRC infiltration ponds or the legacy INTEC percolation ponds. In 2021, sulfate concentrations in water samples from aquifer wells near the Radioactive Waste Management Complex (RWMC) were mostly greater than background concentrations. The maximum dissolved sulfate concentration in shallow perched groundwater near the ATRC was 575 mg/L in 2021. During 2021, dissolved sulfate concentrations in water from wells completed in deep perched groundwater near the cold waste ponds at the ATRC ranged from 22.3 to 519 mg/L. In 2021, concentrations of nitrate in water from most ESRP aquifer wells at and near the INTEC exceeded the western tributary groundwater background concentration of 0.655 mg/L. Concentrations of nitrate in aquifer wells southwest of INTEC and farther away from the influence of disposal areas and the Big Lost River, in intermittent source of surface water recharge to the aquifer, show a general decrease in nitrate concentration over time. Two aquifer wells south of INTEC show increasing trends that could result from wastewater beneath the INTEC tank farm being mobilized to the aquifer. During 2019–21, water samples from several ESRP aquifer wells were collected and analyzed for volatile organic compounds (VOCs). Twelve VOCs were detected, and 1–4 VOCs were detected in water samples from 10 wells. The most frequently detected VOCs include carbon tetrachloride (tetrachloromethane), trichloromethane, tetrachloroethene, 1,1,1-trichloroethane, and trichloroethene. In 2019–21, concentrations for all VOCs were less than their respective maximum contaminant levels (MCLs) for drinking water, except carbon tetrachloride in one well, trichloroethene in two wells, and vinyl chloride in one well. During 2019–21, variability and bias were evaluated from 34 replicate and 14 blank quality-assurance samples. Results from replicate analyses were investigated to evaluate sample variability. Constituents with acceptable reproducibility were major ions, trace elements, nutrients, and VOCs. All radiochemical constituents including gross alpha- and beta- radioactivity, strontium-90, cesium-137, and tritium, had acceptable reproducibility. Bias from sample contamination was evaluated from equipment, field, and source-solution blanks. Chloride and sulfate were detected slightly above their respective method detection limits in equipment and field blanks, but at concentrations well below the co-collected sample for that well. These chloride and sulfate detections in the field and equipment blanks were inconsequential because they weren’t detected above the analysis-specific variability for those constituents as determined by replicate sample result evaluation. None of the detections of nutrients and trace inorganic constituents were high enough to indicate environmental sample or analytical procedure bias.

Idaho↗

USGS2022

Use case development for earth monitoring, analysis, and prediction (EarthMAP)—A road map for future integrated predictive science at the U.S. Geological Survey

Executive Summary The U.S. Geological Survey (USGS) 21st-century science strategy 2020–30 promotes a bureau-wide strategy to develop and deliver an integrated, predictive science capability that works at the scales and timelines needed to inform societally relevant resource management and protection and public safety and environmental health decisions (U.S. Geological Survey, 2021). This is the overarching goal of the USGS Earth Monitoring, Analysis, and Prediction (EarthMAP) vision, which consists of three components: (1) integrated data and information, (2) integrated predictive science, and (3) actionable information—all designed and delivered to respond to user needs. To launch this vision and help shape the design and implementation of integrated predictive science, the USGS Regional Offices each developed a set of use cases (hereafter Use Cases)—short descriptions of potential science applications that could clearly address high priority decision-making needs of our stakeholders and that align with an integrated science focus. Use Cases are not actionable science planning documents, nor stand-alone scholarly works, but should be considered as innovative, next-generation science ideas that can be considered as potential components of science plans still under development. The goal of Use Case development was to (1) identify and characterize existing USGS scientific capacities and expertise that can support science goals and products, (2) identify opportunities to leverage current capacities for next-generation science, and (3) foster engagement across the entire Bureau to further refine the USGS strategy for EarthMAP and integrated predictive science. The Use Case development effort documented in this report was coordinated by the Use Case Development Team (UCDT), consisting of representatives from each region. The UCDT undertook five tasks: (1) develop a unified approach to engage bureau scientists consistently across all regions in aspirational thinking about what can be accomplished; (2) work with the regions and their Science Centers to generate an initial set of Use Cases, authored directly by scientists; (3) characterize, summarize, and document the initial set of Use Case submissions from authors to illuminate bureau-level demand for integrated science; (4) compare existing and needed capacities from the Use Case descriptions with preliminary results of the EarthMAP Capacity Assessment (Keisman and others, 2021); and (5) describe lessons learned from the Use Case development process and provide recommendations to inform future efforts to generate integrated science activities. This report outlines the approach the UCDT developed to solicit Use Cases from the regions and summarizes the high-level qualitative findings from this first-round effort. The UCDT received 36 Use Cases from the regions and identified potential points of convergence and commonalities considered useful in making connections among the participating scientists. The Southwest (SW) Region and the Rocky Mountain (RM) Region asked scientists to give special consideration to Use Cases with applicability to the Colorado River Basin, and seven of the Use Cases specifically named that geographic area as a focus. Coastal hazards and coastal resilience were identified in Use Cases from the Alaska (AK), Northeast (NE), and Southeast (SE) Regions. Aspects of wildfire and post-wildfire response were part of Uses Cases from AK, RM, and SW Regions. The greatest convergence of Use Case themes was related to conservation of public lands and waters, which is a powerful linkage lending strength to future collaborative efforts. The most common type of stakeholder decisions that would be informed by the Use Case science applications were related to adaptation, mitigation, and response (for example, how to increase the resilience of coastal communities to climate-related stressors and how to prevent or respond to harmful algal blooms). Other common types of decisions included water and land management decisions (including operational water management decisions such as reservoir operations and land use planning in the sagebrush biome), decisions about how to manage and conserve habitats and species, and risk management decisions (such as managing the post-wildfire flood risks). These decision types are not exclusive because many Use Cases cross categories. Use Case authors identified existing and needed science and technology capabilities required for Use Case implementation, which were then aligned to capabilities assessed in the EarthMAP Capacity Assessment (Keisman and others, 2021). Strong alignment was found for data and information integration approaches, modeling and prediction approaches, and capabilities related to delivery of actionable information. A majority of Use Cases indicated insufficient current capacity for needed data collection methods, data integration, and modeling and prediction approaches, whereas only 25 percent indicated insufficient capacity for actionable information delivery. Overall, many Use Case capacity demand gaps could potentially be met by existing bureau-wide capacity. In addition, nearly half of the Use Cases could potentially be implemented within 3 years if funding, capabilities, and personnel impediments were removed and science priorities were realigned. Several challenges emerged during the Use Case development process. The first challenge was developing an approach that was flexible enough to accommodate regional differences in planning and implementation, while also ensuring enough guidance to promote meaningful summary analyses. The UCDT encountered a strong demand for continuous communication and education to improve overall understanding of the integrated predictive science strategy. Another challenge was managing expectations about EarthMAP activities as a design effort that was not aligned to an immediate funding opportunity. Connecting the Use Cases to stakeholder needs without the opportunity for direct stakeholder engagement was also challenging. The last notable challenge was in obtaining consistent interpretation and characterization of the qualitative data housed in the narrative descriptions of Use Cases, written in different styles. Overall, the 36 Use Cases can serve as components of a road map for advancing integrated monitoring and predictive science throughout the USGS by revealing opportunities to (1) encourage cross-region initiatives that address shared interests in common themes by integrating similar Use Cases and through direct involvement of stakeholders in identifying needs and designing effective responses, (2) leverage the Use Cases to target investments that are aligned with the Bureau and Department of the Interior (DOI) priorities, (3) connect Use Cases and the results of the companion EarthMAP Capacity Assessment (Keisman and others, 2021) to identify potential priorities for capacity building investments, and (4) raise awareness of common integrated and interdisciplinary science interests within and across the regions through Use Case and Capacity Assessment summary outreach activities.

Open-File Report↗

USGS2013

Review of revised Klamath River Total Maximum Daily Load models from Link River Dam to Keno Dam, Oregon

Flow and water-quality models are being used to support the development of Total Maximum Daily Load (TMDL) plans for the Klamath River downstream of Upper Klamath Lake (UKL) in south-central Oregon. For riverine reaches, the RMA-2 and RMA-11 models were used, whereas the CE-QUAL-W2 model was used to simulate pooled reaches. The U.S. Geological Survey (USGS) was asked to review the most upstream of these models, from Link River Dam at the outlet of UKL downstream through the first pooled reach of the Klamath River from Lake Ewauna to Keno Dam. Previous versions of these models were reviewed in 2009 by USGS. Since that time, important revisions were made to correct several problems and address other issues. This review documents an assessment of the revised models, with emphasis on the model revisions and any remaining issues. The primary focus of this review is the 19.7-mile Lake Ewauna to Keno Dam reach of the Klamath River that was simulated with the CE-QUAL-W2 model. Water spends far more time in the Lake Ewauna to Keno Dam reach than in the 1-mile Link River reach that connects UKL to the Klamath River, and most of the critical reactions affecting water quality upstream of Keno Dam occur in that pooled reach. This model review includes assessments of years 2000 and 2002 current conditions scenarios, which were used to calibrate the model, as well as a natural conditions scenario that was used as the reference condition for the TMDL and was based on the 2000 flow conditions. The natural conditions scenario included the removal of Keno Dam, restoration of the Keno reef (a shallow spot that was removed when the dam was built), removal of all point-source inputs, and derivation of upstream boundary water-quality inputs from a previously developed UKL TMDL model. This review examined the details of the models, including model algorithms, parameter values, and boundary conditions; the review did not assess the draft Klamath River TMDL or the TMDL allocations. Attention to the details of a model is one of the best ways to identify potential problems, correct them if possible, and begin to assess the magnitude of potential model errors and uncertainty. Model users need to determine the level of acceptable uncertainty associated with their objectives, identify all sources of potential uncertainty (model uncertainty, data uncertainty, etc.), and assess their approach and results accordingly. In the draft Klamath River TMDL, the Oregon Department of Environmental Quality identified the upstream boundary conditions as the largest source of uncertainty for both the current and natural conditions scenarios, not the model algorithms or choice of model parameters. We agree that the upstream boundary conditions are one of the largest, if not the largest, source of model uncertainty; therefore, the derivation of upstream boundary conditions may be more important to the TMDL than some other model-related issues identified in this review. The revised models contain a number of changes, some of which were done to solve small problems and are largely inconsequential to model results, but others of which are important and affect model predictions of instream concentrations. A consistent version of the model is now applied to all scenarios, and an error in the source code was corrected that had inadvertently discarded 20 percent of the incoming solar radiation in the original model. The baseline light-extinction coefficient for water was decreased and set to a consistent and defensible value across all models of reservoir reaches. Inconsistencies among the values of certain parameters in the original models, such as the ammonia nitrification rate and the decomposition rates of organic matter, have been eliminated, although the reasoning behind the final selections was not documented. The dependence of the rate of sediment oxygen demand (SOD) on temperature was modified such that the SOD rate was substantially decreased at temperatures less than 20°C, causing the model to predict higher dissolved oxygen (DO) concentrations in spring, autumn, and winter. Although that change to the temperature dependence function was done to make the function more similar to the model’s default, this change was not accompanied by any documentation of recalibration or sensitivity exercises. The maximum SOD rate for the 2002 current conditions scenario was decreased from 3.0 grams per square meter per day (g/m 2 /d) in the original model to 2.0 g/m 2 /d in the revised model, a considerable adjustment that appears to have been needed to offset effects of a change to another variable (O2LIM) that would have resulted in a substantial increase in the effective SOD rate for 2002. A 50-percent decrease in the SOD rate over a 2-year period, however, is not likely to be mirrored by field measurements, so this change may be compensating for some process that is not represented correctly in the DO budget for the current conditions scenarios. Several important changes were made to the natural conditions scenario. First, the elevation of the Keno reef was corrected; the elevation specified in the original model was 1 foot too high, which affected the volume of the pooled reach and the travel time through it. The most important changes to this scenario were to the upstream boundary inputs of organic matter and algae, which affect incoming fluxes of nitrogen and phosphorus. Algal biomass inputs were increased by approximately 60 percent during summer because of a change in the way those inputs were derived from results of the UKL TMDL model. Non-algal organic matter inputs were decreased, particularly in summer to correct a problem attributed to double-counting of phosphorus in the original inputs. The distribution of non-algal organic matter was changed from 20 percent dissolved in the original model to 90 percent dissolved in the revised model in response to review comments and published data. The overall sum of algal biomass and non-living organic matter was decreased, which resulted in lower inputs of total phosphorus and nitrogen. Total phosphorus inputs were less than 0.03 mg/L, and although the inputs were derived from selected results of the UKL TMDL model, these concentrations seem too low to be representative of a historically eutrophic system surrounded by extensive wetlands, peat soils, and a groundwater system high in phosphorus. The draft TMDL states that the upstream boundary conditions are the greatest source of uncertainty, greater than any uncertainty associated with the models. Efforts to improve existing models of algal growth and nutrient cycling in UKL, therefore, would provide a substantial benefit to downstream modeling efforts on the Klamath River. Although many improvements were made in revising the Klamath River TMDL models, some issues and uncertainties remain. Several errors in the model source code remain, but do not affect model results for this application as long as certain options and rates are not changed; future users of these models should be aware of these issues. Although the distribution of dissolved and particulate organic matter was modified for the natural conditions scenario, that distribution was not changed for the current conditions scenarios. Recent data on that distribution and the likely rates of organic matter decomposition could be used to improve these models in the future. Nitrate predictions at Keno (Highway 66) still are too high for the current conditions scenarios; future efforts should re-evaluate the model’s denitrification rates and the release rate of ammonia from anoxic sediments. Possibly the most important of the remaining issues are tied to the two-state (healthy/unhealthy) hypothesis for the algae population that was coded into the model. Some of the rates and conversion functions could be refined to make them more acceptable; currently, the published literature does not support the concept of moderately low dissolved-oxygen concentrations as a stressor of algae in the ranges used by the model. More research is needed before these algorithms can be truly tested. The algorithms currently appear to help the model fit the patterns in the available data, and that is useful and perhaps sufficient for some purposes, but those algorithms are not truly predictive or reliable for certain purposes until they can be tested through well-designed experiments and research. In summary, the TMDL models used to simulate Link and Klamath Rivers from Link River Dam to Keno Dam were revised to fix several problems and address various issues. The resulting models are an improvement over those that were reviewed by USGS in 2009, and represent a useful advance in the simulation of a complex system that is difficult to model. However, several issues remain that cause increased uncertainty in the model results. Depending on the objectives of the modeling, now or in the future, these remaining issues could be more or less important. For the Klamath River TMDL, the upstream boundary conditions may be a larger source of uncertainty than the concerns with model algorithms and model parameters identified in this review. Efforts to re-evaluate the available models of algal growth and nutrient cycling in UKL would be highly beneficial to downstream modeling efforts in the Klamath River.

Oregon;California↗