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Results for “Developments in Biological Standardization”

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At least 145 records · Page 8Linked to original sources
USGS1980

Handbook of acute toxicity of chemicals to fish and aquatic invertebrates : summaries of toxicity tests conducted at Columbia National Fisheries Research Laboratory, 1965-78

Acute toxicity is a major subject of research at Columbia National Fisheries Research Laboratory for evaluating the impact of toxic chemicals on fishery resources. The Laboratory has played a leading role in developing research technology for toxicity testing and data interpretation. In 1965-78, more than 400 chemicals were tested against a variety of invertebrates and fish species representative of both cold- and warm-water climates. The use of acute toxicity tests for assessing the potential hazard of chemical contaminants to aquatic organisms is well documented (Boyd 1957; Henderson et al. 1960; Sanders and Cope 1966; Macek and McAllister 1970). Static acute toxicity tests provide rapid and (within limits) reproducible concentration-response curves for estimating toxic effects of chemicals on aquatic organisms. These tests provide a database for determining relative toxicity of a large number of chemicals to a variety of species and for estimating acute effects of chemical spills on natural aquatic systems; they also assist in determining priority and design of additional toxicity studies. Acute toxicity tests usually provide estimates of the exposure concentration causing 50% mortality (LC50) to test organisms during a specified period of time. For certain invertebrates, the effective concentration is based on immobilization, or some other identifiable endpoint, rather than on lethality. The application of the LC50 has gained acceptance among toxicologists and is generally the most highly rated test for assessing potential adverse effects of chemical contaminants to aquatic life (Brungs and Mount 1978; American Institute for Biological Sciences 1978 a ). The literature contains numerous papers dealing with the acute toxicity of chemicals to freshwater organisms. However, there is a tremendous need for a concise compendium of toxicity data covering a large variety of chemicals and test species. This Handbook is a compilation of a large volume of acute toxicity data from the Columbia Laboratory and its field laboratories. It presents definitive acute toxicity data on 271 chemicals tested against a variety of freshwater invertebrates and fishes. The chemicals represent all major groups of pesticides, as well as numerous industrial chemicals. This compilation should serve as a useful database for the many agencies and organizations dealing with research and management programs concerned with the impact of chemicals on aquatic resources. The Columbia Laboratory has played a major role in developing currently used standard methodology for static acute toxicity testing. The use of standardized methodology greatly reduces variation in results. The data presented here have been carefully scrutinized to eliminate tests that failed to follow acceptable procedures. Handling of test organisms and procedures for static toxicity tests followed those described by Lennon and Walker (1964) and Macek and McAllister (1970), and conform well with those recommended by Brauhn and Schoettger (1975) and the Committee on Methods for Toxicity Tests with Aquatic Organisms (1975). The species of fish and invertebrates that were tested are listed in phylogenetic order in Tables 1 and 2. Fish were obtained from Federal and State hatcheries as either eggs or fry. Original stocks of invertebrates were collected and cultured from wild populations with no known source of contamination; these populations were replenished regularly. The invertebrates were cultured in the Laboratory by methods similar to those described by Sanders and Cope (1966). Test chemicals usually consisted of technical or analytical grade samples of known purity. Formulations of the chemicals were also tested when available. When purity of test chemicals was known, all calculated concentrations were based on percent active ingredients. Stock solutions were prepared immediately before each test, with commercial grade acetone as the carrier solvent. Occasionally, ethanol or dimethyl-formamide was substituted. Solvent concentrations did not exceed 0.5 mL/L in final dilution water. Test water (dilution water) was reconstituted from deionized water of at least 10 6 ohms resistivity by the addition of appropriate reagent grade chemicals (Marking 1969). Water was buffered to maintain a pH of 7.2 to 7.5, an alkalinity of 30 to 35 mg/L, and a hardness of 40 to 50 mg/L as CaCO 3 . Test water was mixed thoroughly and aerated before transfer into test chambers. Fish were acclimated to dilution water by gradually changing the water in acclimated tanks from 100% well water to 100% reconstituted water over a 1- to 3-day period at the desired testing temperature. Invertebrates were acclimated from well water to dilution water over a 4- to 6-h period. Toxicity tests were conducted under static conditions without aeration, and the organisms were not fed during acclimation or testing. Temperature of test solutions was maintained within ± 1°C of that required for a given test. Toxicity tests with fish were conducted in 18.9-liter (5-gal) wide-mouthed jars containing 15 liters of test solution. Fingerling fish weighing 0.2 to 1.5 g were tested at each concentration. Caution was taken not to exceed 0.8 g of test organisms per liter of solution. Duplicate test chambers were used to accommodate larger fish. Test chambers varied in size for invertebrates, depending on the species used; volume of test solution ranged from 0.25 to 4 liters. At least 10 organisms were exposed to each concentration for all definitive tests. At least six concentrations were used per toxicity test. The tests began upon initial exposure to the toxicant and continued for 96 h. Immobilization tests with invertebrates were conducted for only 48 h. The number of dead or affected organisms in each test chamber were recorded and the dead organisms were removed every 24 h; general observations on the condition of test organisms were also recorded at these times. Toxicity data were analyzed by a statistical method described by Litchfield and Wilcoxon (1949) to determine LC50 (theoretical estimate of the concentration lethal to 50% of the test animals) and 95% confidence intervals. This method is recommended by the American Public Health Association (1971) and by Sprague (1969) for determining median lethal concentrations. The procedure is easily modified for computing a single LC50 when replicate tests are performed.

Resource Publication↗
USGS2011

Exploring sensitivity of a multistate occupancy model to inform management decisions

1. Dynamic occupancy models are often used to investigate questions regarding the processes that influence patch occupancy and are prominent in the fields of population and community ecology and conservation biology. Recently, multistate occupancy models have been developed to investigate dynamic systems involving more than one occupied state, including reproductive states, relative abundance states and joint habitat‐occupancy states. Here we investigate the sensitivities of the equilibrium‐state distribution of multistate occupancy models to changes in transition rates. 2. We develop equilibrium occupancy expressions and their associated sensitivity metrics for dynamic multistate occupancy models. To illustrate our approach, we use two examples that represent common multistate occupancy systems. The first example involves a three‐state dynamic model involving occupied states with and without successful reproduction (California spotted owl Strix occidentalis occidentalis ), and the second involves a novel way of using a multistate occupancy approach to accommodate second‐order Markov processes (wood frog Lithobates sylvatica breeding and metamorphosis). 3. In many ways, multistate sensitivity metrics behave in similar ways as standard occupancy sensitivities. When equilibrium occupancy rates are low, sensitivity to parameters related to colonisation is high, while sensitivity to persistence parameters is greater when equilibrium occupancy rates are high. Sensitivities can also provide guidance for managers when estimates of transition probabilities are not available. 4. Synthesis and applications. Multistate models provide practitioners a flexible framework to define multiple, distinct occupied states and the ability to choose which state, or combination of states, is most relevant to questions and decisions about their own systems. In addition to standard multistate occupancy models, we provide an example of how a second‐order Markov process can be modified to fit a multistate framework. Assuming the system is near equilibrium, our sensitivity analyses illustrate how to investigate the sensitivity of the system‐specific equilibrium state(s) to changes in transition rates. Because management will typically act on these transition rates, sensitivity analyses can provide valuable information about the potential influence of different actions and when it may be prudent to shift the focus of management among the various transition rates.

Journal of Applied Ecology↗
USGS2020

Predictive relations between acid-base chemistry and fish assemblages in streams of the Adirondack Mountains

Surface waters across much of New York State’s Adirondack Mountains were acidified in the late 20th century but began to recover following the 1990 Title IV Amendments to the Clean Air Act. Previous assessments of acidification recovery in the Adirondacks have generally been based on surface water chemistry data and inferred relationships to fish and other aquatic biota. Little data, however, has been available to characterize biological impacts and predict recovery of fish assemblages in streams of the region. Here, we use quantitative fish surveys combined with chemistry data from 48 headwater streams sampled during summer 2014–2016 to develop logistic (probability) models that characterize the status of contemporary fish assemblages and predict how different N and S deposition loads may affect future fish assemblages. Statistical models for inorganic aluminum (Al i ) and richness ≥1 species; and for acid neutralizing capacity (ANC) and total density >400 fish/0.1 ha, total biomass >1500 g/0.1 ha, brook trout Salvelinus fontinalis density >0 or >200 fish/0.1 ha, and brook trout biomass >1000 g/0.1 ha were suitable for evaluating community and population responses to changes in acid-base chemistry. Predictions of fish-assemblage responses using several of these models demonstrated that anticipated changes in national (U.S.) secondary standards for atmospheric emissions of NO x and SO x to achieve target N and S deposition loads are likely to alter the acid-base chemistry and the probabilities of observing various levels of brook trout population and fish-community metrics in streams across the region and elsewhere.

New York↗
USGS2023

Temperature and winter duration requirements for reproductive success in johnny darter Etheostoma nigrum in the South Platte River basin, Colorado

Changes in water temperature and its seasonal timing influences the physiological processes of many aquatic ectotherms. Wastewater treatment plants (WWTP) contribute to warmer and more consistent water temperatures in streams draining the North American Great Plains, particularly during winter months. Reduced variation in seasonal water temperature may adversely affect fishes that rely on temperature fluctuation or specific overwintering temperatures for reproductive cues. We used johnny darter Etheostoma nigrum (Family Percidae), a thermally sensitive species native to the South Platte River Basin, as a focal species to assess the effects of winter water temperature regulations in Colorado. Our objective was to evaluate the effects of winter stream temperature and winter duration on reproductive success of johnny darter in the laboratory to inform development of water quality criteria for the South Platte River Basin. Winter duration (60, 90 or 120 days) and temperature (4 or 12°C) were crossed in a factorial design of six treatments that simulated warmed effluent-impacted streams as well as streams with a more natural thermal regime. We defined reproductive success in johnny darter by examining four reproductive endpoints: (1) spawning timing, (2) egg and larvae production, (3) egg success, and (4) egg development. Across the four endpoints, seven main response variables were measured: spawning initiation date, eggs per gram of female per week, live larvae per gram of female per week, fertilisation success, hatching success, egg-to-larva survival and days to hatch. Winter temperature and duration influenced spawning timing and egg development. Earlier spawning initiation dates were observed in fish exposed to 12°C winters and was associated with a higher number of days to hatch. Eggs per gram of female per week, live larvae per gram of female per week, fertilisation success, hatching success, and egg-to-larva survival were similar among winter treatments. Although the State of Colorado chronic winter water temperature standard of 12°C appears to be adequate for egg and larvae production in johnny darter, our results showed that fish exposed to the standard began spawning significantly earlier than fish exposed to 4°C winters. Evaluating reproductive output in the context of seasonal timing is valid because spawning timing has the potential to affect overall production and egg development, and consequently recruitment and population sustainability. Therefore, spawning timing should be considered when making management decisions and revising water temperature standards. The warming of streams and rivers from WWTP effluent is a global issue, especially in areas that are undergoing rapid urbanisation. Fishes are particularly sensitive to water temperature and many fishes worldwide are likely to be experiencing changes in important physiological processes, affecting both reproduction and survival. Our study indicates that reproductive timing could be influenced by stream warming and stresses the need for further studies on the influence of anthropogenic effects on stream warming.

Colorado↗
USGS2023

The Coastal Carbon Library and Atlas: Open source soil data and tools supporting blue carbon research and policy

Quantifying carbon fluxes into and out of coastal soils is critical to meeting greenhouse gas reduction and coastal resiliency goals. Numerous ‘blue carbon’ studies have generated, or benefitted from, synthetic datasets. However, the community those efforts inspired does not have a centralized, standardized database of disaggregated data used to estimate carbon stocks and fluxes. In this paper, we describe a data structure designed to standardize data reporting, maximize reuse, and maintain a chain of credit from synthesis to original source. We introduce version 1.0.0. of the Coastal Carbon Library, a global database of 6723 soil profiles representing blue carbon-storing systems including marshes, mangroves, tidal freshwater forests, and seagrasses. We also present the Coastal Carbon Atlas, an R-shiny application that can be used to visualize, query, and download portions of the Coastal Carbon Library. The majority (4815) of entries in the database can be used for carbon stock assessments without the need for interpolating missing soil variables, 533 are available for estimating carbon burial rate, and 326 are useful for fitting dynamic soil formation models. Organic matter density significantly varied by habitat with tidal freshwater forests having the highest density, and seagrasses having the lowest. Future work could involve expansion of the synthesis to include more deep stock assessments, increasing the representation of data outside of the U.S., and increasing the amount of data available for mangroves and seagrasses, especially carbon burial rate data. We present proposed best practices for blue carbon data including an emphasis on disaggregation, data publication, dataset documentation, and use of standardized vocabulary and templates whenever appropriate. To conclude, the Coastal Carbon Library and Atlas serve as a general example of a grassroots F.A.I.R. (Findable, Accessible, Interoperable, and Reusable) data effort demonstrating how data producers can coordinate to develop tools relevant to policy and decision-making.

Global Change Biology↗
USGS2022

Gaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database

To advance national efforts for the detection and biosurveillance of aquatic invasive species (AIS), we employed a community consensus process to enable the incorporation of environmental DNA (eDNA) detection data into the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species (NAS) database (https://nas.er.usgs.gov/eDNA/). Our goal was to identify minimum standards and best practices for the verification of eDNA data by working closely with AIS eDNA community practitioners and natural resource managers across government, private and academic sectors. To better inform management decisions, verified AIS eDNA data will be displayed on a separate mapping layer alongside visual sighting data with the inclusion of additional information on the eDNA methods employed to collect and produce the data. To allow for eDNA data display, we produced consensus derived online documents including a submission application and data submission template and are developing a guidance document for detailing the eDNA data submission process. We also developed a communication plan including a mechanism for reporting detections to appropriate managers for consideration prior to display. The products of these efforts are an application and data submission process that will be used in the new environmental DNA data layer on the Nonindigenous Aquatic Species (NAS) database. Herein, we detail how we engaged the eDNA community for consensus of our standards, share lessons learned from the process, and describe the benefits of such an approach at instilling confidence among the research and decision-maker community.

Management of Biological Invasions↗
USGS2011

Catfish science: Status and trends in the 21st century

Catfish science, the study of the fish order Siluriformes, is a diverse and expanding field in terms of advances and breadth of topics. We compiled literature from primary fisheries journals as an index of interest and advances in catfish science to examine temporal trends in the field. The number of catfish scientific publications varied over the past century with strong peaks during 1975–1979 and 2005–2010, which may be the result of interactive scientific and societal influences. Catfish biology was the predominant publication topic until the late 1990s, when ecology, techniques, and management publications became more prevalent. Articles on catfish ecology were most numerous in both the first and second international catfish symposia, but publications on techniques and conservation were more numerous in the second catfish symposium than the first. We summarize the state of knowledge, recent advances, and areas for future attention among topics in catfish science, including sampling and aging techniques, population dynamics, ecology, fisheries management, species diversity, nonnative catfish, and human dimensions, with an emphasis on the gains in this second symposium. Areas that we expect to be pursued in the future are development of new techniques and validation of existing methods; expansion of research to less-studied catfish species; broadening temporal, spatial, and organizational scales; interdisciplinary approaches; and research on societal views and constituent demands. Meeting these challenges will require scientists to span beyond their professional comfort zones to effectively reach higher standards. We look forward to the coming decade and the many advances in the conservation, ecology, and management of catfish that will be shared.

Conference Paper↗
USGS2012

Physical setting and natural sources of exposure to carcinogenic trace elements and radionuclides in Lahontan Valley, Nevada

In Lahontan Valley, Nevada, arsenic, cobalt, tungsten, uranium, radon, and polonium-210 are carcinogens that occur naturally in sediments and groundwater. Arsenic and cobalt are principally derived from erosion of volcanic rocks in the local mountains and tungsten and uranium are derived from erosion of granitic rocks in headwater reaches of the Carson River. Radon and 210Po originate from radioactive decay of uranium in the sediments. Arsenic, aluminum, cobalt, iron, and manganese concentrations in household dust suggest it is derived from the local soils. Excess zinc and chromium in the dust are probably derived from the vacuum cleaner used to collect the dust, or household sources such as the furnace. Some samples have more than 5 times more cobalt in the dust than in the local soil, but whether the source of the excess cobalt is anthropogenic or natural cannot be determined with the available data. Cobalt concentrations are low in groundwater, but arsenic, uranium, radon, and 210 Po concentrations often exceed human-health standards, and sometime greatly exceed them. Exposure to radon and its decay products in drinking water can vary significantly depending on when during the day that the water is consumed. Although the data suggests there have been no long term changes in groundwater chemistry that corresponds to the Lahontan Valley leukemia cluster, the occurrence of the very unusual leukemia cluster in an area with numerous 210 Po and arsenic contaminated wells is striking, particularly in conjunction with the exceptionally high levels of urinary tungsten in Lahontan Valley residents. Additional research is needed on potential exposure pathways involving food or inhalation, and on synergistic effects of mixtures of these natural contaminants on susceptibility to development of leukemia.

Nevada↗
USGS2019

The status of mussel health assessment and a path forward

Declines of freshwater mussel (order Unionida) populations worldwide are attributed to habitat degradation, pollution, and invasive species, among other factors. However, these purported causes do not fully explain the enigmatic decline and large-scale die-offs of mussels that have occurred in assumedly “healthy” streams across a wide geographic region. The roles of the microbiota and pathogens in mussel health has been understudied, and, as a result, few references exist to compare the microbiota of healthy mussels to that of stressed or dying mussels. Captive propagation and stocking programs have expanded across the globe without standard diagnostic protocols to assess health or potential diseases in hatchery-reared or wild stocks. Introduction of nonindigenous species, contaminants of emerging concern and anthropogenic climate change could adversely alter underlying variables that support mussel health such as nutrient and microbial composition, in addition to increased risk for outbreaks of opportunistic disease and emergent diseases in freshwater mussel populations. We suggest a coordinated, collaborative, and multidisciplinary effort to advance methods for assessing freshwater mussel health. We identify research and resources needed to answer central questions surrounding mussel health including identifying potential agents of disease, defining clinical signs of declining condition, refining stress-specific biomarkers for health assessment, and developing protocols specific for mussels.

Freshwater Mollusk Biology and Conservation↗
USGS2006

Some potentials and limits of the leucocrit test as a fish health assessment method

The sensitivity of the leucocrit as a stress tolerance and fish health assessment method was evaluated by subjecting juvenile coho salmon, Oncorhynchus kisutch , or steelhead trout, Salmo gairdneri , to standardized crowding, handling, temperature and disease challenges. The leucocrit was a sensitive indicator of the physiological stress resulting from crowding at population densities of 0·2–0·4 kg l −1 , and to the stress of handling and to temperature changes. It was relatively insensitive to physiological sampling procedures which supports its continued development as a stress assessment method. In the case of fish diseases, subclinical or active Renibacterium salmoninarum and Yersinia ruckeri infections had essentially no effect on leucocrit values. In contrast, active Aeromonas salmonicida infections significantly depressed the leucocrit. However, no change was seen during the subclinical (incubation) phase prior to the development of an epizootic. Thus, the potential of the leucocrit as a fish health assessment method appears limited.

Journal of Fish Biology↗
USGS2015

Evaluating unsupervised methods to size and classify suspended particles using digital in-line holography

Substantial information can be gained from digital in-line holography of marine particles, eliminating depth-of-field and focusing errors associated with standard lens-based imaging methods. However, for the technique to reach its full potential in oceanographic research, fully unsupervised (automated) methods are required for focusing, segmentation, sizing and classification of particles. These computational challenges are the subject of this paper, in which we draw upon data collected using a variety of holographic systems developed at Plymouth University, UK, from a significant range of particle types, sizes and shapes. A new method for noise reduction in reconstructed planes is found to be successful in aiding particle segmentation and sizing. The performance of an automated routine for deriving particle characteristics (and subsequent size distributions) is evaluated against equivalent size metrics obtained by a trained operative measuring grain axes on screen. The unsupervised method is found to be reliable, despite some errors resulting from over-segmentation of particles. A simple unsupervised particle classification system is developed, and is capable of successfully differentiating sand grains, bubbles and diatoms from within the surf-zone. Avoiding miscounting bubbles and biological particles as sand grains enables more accurate estimates of sand concentrations, and is especially important in deployments of particle monitoring instrumentation in aerated water. Perhaps the greatest potential for further development in the computational aspects of particle holography is in the area of unsupervised particle classification. The simple method proposed here provides a foundation upon which further development could lead to reliable identification of more complex particle populations, such as those containing phytoplankton, zooplankton, flocculated cohesive sediments and oil droplets.

Journal of Atmospheric and Oceanic Technology↗
USGS2022

California Deepwater Investigations and Groundtruthing (Cal DIG) I, volume 3 — Benthic habitat characterization offshore Morro Bay, California

Coastal and Marine Ecological Classification Standard (CMECS) geoform, substrate, and biotic component geographic information system (GIS) products were developed for the U.S. Exclusive Economic Zone (U.S. EEZ) of south-central California in the region of Santa Lucia Bank motivated by interest in development of offshore wind-energy capacity and infrastructure. The Bureau of Ocean Energy Management (BOEM), in coordination with the State of California and many other members of the California Task Force, issued calls for information in 2018 for the study area offshore of Morro Bay, California. The study area is in depths of 500 to 1,200 meters (m) and adjacent to a decommissioned nuclear power plant with a developed electric grid connection, and in an area of high wind resource. BOEM is the lead agency responsible for planning and leasing in the U.S. EEZ and funded this project to assess baseline conditions of, and the potential effects on, the seafloor environment. This project, carried out by the U.S. Geological Survey (USGS), resulted in three reports: one on biological analysis of seafloor video data, one on analysis of the geologic framework and hazards, and this report on seafloor habitat. The study area consists of 8,424 square kilometers (km 2 ) of multibeam echo sounder (MBES) data acquired during five surveys from 2016 to 2019. Remotely operated vehicle (ROV) video was acquired in 2019 to supervise the classification of the MBES data into habitats. Derivatives of the MBES data were classified into 16 unique biotopes, 6 substrate types, 28 modifier groups, and 22 geoforms. The study area substrate is predominantly soft sediment (mud and fine sand) covering 7,804 km 2 (92.7 percent) of the area. Mixed substrate areas on rocky banks, channel scarps, and the shelf break comprise 404 km 2 (4.8 percent) of the study area. Hard substrate areas are found predominantly on the tops and flanks of banks and on bank ridges that separate canyons incising the banks. Hard substrates comprise 211 km 2 of the study area (2.5 percent). After the bathymetry and backscatter raster images (rasters) were classified, manual editing was also done to remove noise artifacts. This effort was not completely successful and there are numerous erroneous small areas in the rasters that have been passed on to the CMECS polygon product. Nearly 120,000 annotations of organisms and their habitat were made from 25 video transects selected from 185 hours of ROV video. In total, 2,714 km 2 of seafloor were successfully assigned to biotopes. Some biotopes were assigned to separate areas spatially distant from the transects that define the biotope. Expected relations between physical habitat and biota such as the number of species and the substrate induration and rugosity were verified. Slope is typically a predictive variable and was used in the classification of habitat, but the ground truth used for biotic component analysis included very little steeply sloping area. Ground-truth ROV operations were reduced by the sea state; additional ground truth could improve the biotic results and increase confidence in the spatial distribution of classifications reported here.

California↗
USGS1998

Simulating transport of volatile organic compounds in the unsaturated zone using the computer model R-UNSAT

Subsurface spills of gasoline and other petroleum products are a common environmental problem throughout the industrialized world. The U.S. Environmental Protection Agency has estimated that 40 percent of the more than 200,000 retail service stations in the United States have had accidental releases of petroleum hydrocarbons to the subsurface (U.S. Environmental Protection Agency, 1991). Restoration of a contaminated aquifer to regulatory standards is a technically difficult problem even when best engineering strategies are applied. Natural attenuation, a remediation strategy that relies on intrinsic physical, chemical, and biological processes to decrease contaminant concentrations, is gaining widespread acceptance in aquifer restoration efforts (Tremblay and others, 1995). The potential for successful remediation by natural attenuation depends on the fate of the organic constituents of the spilled product, which may include additives such as methyl tert-butyl ether (MTBE). These compounds can dissolve in ground water, adsorb to subsurface sediments, volatilize and diffuse through the unsaturated zone, or undergo chemical and biological reactions (fig. 1). Volatilization and biodegradation near the water table are two processes that can contribute significantly to the natural attenuation of volatile organic compounds (VOCs) in shallow ground water (McAllister and Chiang, 1994). To date, quantitative information on the rates at which these processes occur has been limited. R-UNSAT, a computer model designed for quantifying rates of volatilization and biodegradation of organic compounds near the water table, was developed and documented by the U.S. Geological Survey (USGS) and is now available to the public. R-UNSAT also can be applied, however, to other unsaturated-zone transport problems that involve gas diffusion, such as radon migration, and the deposition of compounds from the atmosphere to shallow ground water. This fact sheet describes the transport model and demonstrates its capabilities through applications to point- and nonpoint-source contamination.

Fact Sheet↗
USGS2018

Flow-ecology relationships are spatially structured and differ among flow regimes

In streams, hydrology is a predominant driver of ecological structure and function. Providing adequate flows to support aquatic life, or environmental flows, is therefore a top management priority in stream systems. Flow regime classification is a widely accepted approach for establishing environmental flow guidelines. However, it is surprisingly difficult to quantify relationships between hydrology and ecology (flow–ecology relationships) while describing how these relationships vary across classified flow regimes. Developing such relationships is complicated by several sources of spatial bias, such as autocorrelation due to spatial design, flow regime classification and other environmental or ecological sources of spatial bias. We used mixed moving‐average spatial stream network models to develop flow–ecology relationships across classified flow regimes and to assess spatial patterns of these relationships. We compared relationships between fish traits and life‐history strategies with hydrologic metrics across flow regimes and assessed whether spatial autocorrelation influenced these relationships. Trait–hydrology relationships varied between flow regimes and across all streams combined. Some relationships between traits and hydrologic metrics fit predictions based on life‐history theory, while others exhibited unexpected relationships with hydrology. Spatial factors described a large proportion of variability in fish traits and different patterns of spatial autocorrelation were observed in different flow regimes. Synthesis and applications. Further work is needed to understand why flow–ecology relationships vary across classified flow regimes and why these relationships may not fit predictions based on life‐history theories. Managers determining environmental flow standards need to be aware that different hydrologic metrics are often important drivers of fish trait diversity in different flow regimes. Flow–ecology relationships may therefore be confounded by spatial structure inherent in flow regime classification and much existing biological data. Complex patterns of spatial bias should be considered when managing stream systems within an environmental flows framework.

Journal of Applied Ecology↗
USGS2006

Summary of Environmental Monitoring and Assessment Program (EMAP) activities in South Dakota, 2000–2004

The U.S. Environmental Protection Agency (USEPA) initiated data-collection activities for the Environmental Monitoring and Assessment Program-West (EMAP-West) in South Dakota during 2000. The objectives of the study were to develop the monitoring tools necessary to produce unbiased estimates of the ecological condition of surface waters across a large geographic area of the western United States, and to demonstrate the effectiveness of those tools in a large-scale assessment. In 2001, the U.S. Geological Survey (USGS) and the South Dakota Department of Game, Fish and Parks (GF&P) established a cooperative agreement and assumed responsibility for completing the remaining assessments for the perennial, wadable streams of the EMAP-West in the State. Stream assessment sites were divided into two broad categories-the first category of sites was randomly selected and assigned by the USEPA for South Dakota. The second category consisted of sites that were specifically selected because they appeared to have reasonable potential for representing the best available physical, chemical, and biological conditions in the State. These sites comprise the second category of assessment sites and were called 'reference' sites and were selected following a detailed evaluation process. Candidate reference site data will serve as a standard or benchmark for assessing the overall ecological condition of the randomly selected sites. During 2000, the USEPA completed 22 statewide stream assessments in South Dakota. During 2001-2003, the USGS and GF&P completed another 42 stream assessments bringing the total of randomly selected stream assessments within South Dakota to 64. In addition, 18 repeat assessments designed to meet established quality-assurance/quality-control requirements were completed at 12 of these 64 sites. During 2002-2004, the USGS in cooperation with GF&P completed stream assessments at 45 candidate reference sites. Thus, 109 sites had stream assessments completed in South Dakota for EMAP-West (2000-2004). Relatively early in the EMAP-West stream-assessment process, it became apparent that for some streams in south-central South Dakota, in-stream conditions varied considerably over relatively short distances of only a few miles. These changes appeared to be a result of geomorphic changes associated with changes in the underlying geology. For these streams, moving stream assessment sites short distances upstream or downstream had the potential to provide substantially different bioassessment data. In order to obtain a better understanding of how geology influences stream conditions, two streams located in south-central South Dakota were chosen for multiple stream sampling at sites located along their longitudinal profile at points where notable changes in geomorphology were observed. Subsequently, three sites on Bear-in-the-Lodge Creek and three sites on Black Pipe Creek were selected for multiple stream sampling using EMAP-West protocols so that more could be learned about geologic influences on stream conditions. Values for dissolved oxygen and specific conductance generally increased from upstream to downstream locations on Bear-in-the-Lodge Creek. Values for pH and water temperature generally decreased from upstream to downstream locations. Decreasing water temperature could be indicative of ground-water inflows. Values for dissolved oxygen, pH, and water temperature generally increased from upstream to downstream locations on Black Pipe Creek. The increase in temperature at the lower sites is a result of less dense riparian cover, and the warmer water also could account for the lower concentrations of dissolved oxygen found in the lower reaches of Black Pipe Creek. Values for specific conductance were more than three times greater at the lower site (1,342 microsiemens per centimeter (?S/cm)) than at the upper site (434 ?S/cm). The increase probably occurs when the stream transitions from contacting the underlying Ar

South Dakota↗
USGS2006

Comparative performance of fixed-film biological filters: Application of reactor theory

Nitrification is classified as a two-step consecutive reaction where R1 represents the rate of formation of the intermediate product NO2-N and R2 represents the rate of formation of the final product NO3-N. The relative rates of R1 and R2 are influenced by reactor type characterized hydraulically as plug-flow, plug-flow with dispersion and mixed-flow. We develop substrate conversion models for fixed-film biofilters operating in the first-order kinetic regime based on application of chemical reactor theory. Reactor type, inlet conditions and the biofilm kinetic constants Ki (h-1) are used to predict changes in NH4-N, NO2-N, NO3-N and BOD5. The inhibiting effects of the latter on R1 and R2 were established based on the ?? relation, e.g.:{A formula is presented}where BOD5,max is the concentration that causes nitrification to cease and N is a variable relating Ki to increasing BOD5. Conversion models were incorporated in spreadsheet programs that provided steady-state concentrations of nitrogen and BOD5 at several points in a recirculating aquaculture system operating with input values for fish feed rate, reactor volume, microscreen performance, make-up and recirculating flow rates. When rate constants are standardized, spreadsheet use demonstrates plug-flow reactors provide higher rates of R1 and R2 than mixed-flow reactors thereby reducing volume requirements for target concentrations of NH4-N and NO2-N. The benefit provided by the plug-flow reactor varies with hydraulic residence time t as well as the effective vessel dispersion number, D/??L. Both reactor types are capable of providing net increases in NO2-N during treatment but the rate of decrease in the mixed-flow case falls well behind that predicted for plug-flow operation. We show the potential for a positive net change in NO2-N increases with decreases in the dimensionless ratios K2, (R2 )/K1,( R1 ) and [NO2-N]/[NH4-N] and when the product K1, (R1) t provides low to moderate NH4-N conversions. Maintaining high levels of the latter reduces the effective reactor utilization rate (%) defined here as (RNavg/RNmax)100 where RNavg is the mean reactive nitrogen concentration ([NH4-N] + [NO2-N]) within the reactor, and RNmax represents the feed concentration of the same. Low utilization rates provide a hedge against unexpected increases in substrate loading and reduce water pumping requirements but force use of elevated reactor volumes. Further ?? effects on R1 and R2 can be reduced through use of a tanks-in-series versus a single mixed-flow reactor configuration and by improving the solids removal efficiency of microscreen treatment.

Aquacultural Engineering↗
USGS2004

National Wildlife Refuge System: Ecological context and integrity

The Refuge Improvement Act of 1997 established a statutory mission and management standards for the National Wildlife Refuge system. The U.S. Fish and Wildlife Service subsequently issued a policy for ensuring the biological integrity, diversity, and environmental health of the system. This policy requires understanding the management objectives of each refuge in a local, regional, and national context. An assessment of the refuge system in a national and regional context reveals that refuges are typically smaller than many conservation holdings and are unevenly distributed across the conterminous U.S. Western rangelands, coastal wetlands, and northern grasslands; wetlands are the best-represented ecosystems, while temperate forests have the poorest representation. In contrast to other agency holdings or management designations in the national protected areas network (e.g., national parks, national forests, wilderness areas), refuges tend to occupy sites at lower elevations and that have higher productivity and soil quality. This difference points to the important contribution of the refuges in providing much needed ecological balance within the national protected areas network. However, the ecological integrity of the refuge system is challenged by the proximity of individual refuges to development. Overall, the refuges are becoming islands in a landscape matrix of urban and agricultural development. This creates future challenges for meeting management objectives to ensure the biological integrity, diversity, and environmental health of the system. If the policy to ensure biological integrity, diversity, and environmental health of the refuge system is to be successful, it may be more important to address issues about what happens on adjacent lands than uses within refuges.

Natural Resources Journal↗
USGS2012

Advancing global marine biogeography research with open-source GIS software and cloud-computing

Across many scientific domains, the ability to aggregate disparate datasets enables more meaningful global analyses. Within marine biology, the Census of Marine Life served as the catalyst for such a global data aggregation effort. Under the Census framework, the Ocean Biogeographic Information System was established to coordinate an unprecedented aggregation of global marine biogeography data. The OBIS data system now contains 31.3 million observations, freely accessible through a geospatial portal. The challenges of storing, querying, disseminating, and mapping a global data collection of this complexity and magnitude are significant. In the face of declining performance and expanding feature requests, a redevelopment of the OBIS data system was undertaken. Following an Open Source philosophy, the OBIS technology stack was rebuilt using PostgreSQL, PostGIS, GeoServer and OpenLayers. This approach has markedly improved the performance and online user experience while maintaining a standards-compliant and interoperable framework. Due to the distributed nature of the project and increasing needs for storage, scalability and deployment flexibility, the entire hardware and software stack was built on a Cloud Computing environment. The flexibility of the platform, combined with the power of the application stack, enabled rapid re-development of the OBIS infrastructure, and ensured complete standards-compliance.

Transactions in GIS↗