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Results for “Nature Methods”

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USGS2005

Mathematical analysis demonstrates that interferons-β and -γ Interact in a multiplicative manner to disrupt herpes simplex virus replication

Several studies suggest that the innate interferons (IFNs), IFN- α and IFN- β , can act in concert with IFN- γ to synergistically inhibit the replication of cytomegalovirus and herpes simplex virus type 1 (HSV-1). The significance of this observation is not yet agreed upon in large part because the nature and magnitude of the interaction between IFN- α/β and IFN- γ is not well defined. In the current study, we resolve this issue by demonstrating three points. First, the hyperbolic tangent function, tanh ( x ), can be used to describe the individual effects of IFN- β or IFN- γ on HSV-1 replication over a 320,000-fold range of IFN concentration. Second, pharmacological methods prove that IFN- β and IFN- γ interact in a greater-than-additive manner to inhibit HSV-1 replication. Finally, the potency with which combinations of IFN- β and IFN- γ inhibit HSV-1 replication is accurately predicted by multiplying the individual inhibitory effects of each cytokine. Thus, IFN- β and IFN- γ interact in a multiplicative manner. We infer that a primary antiviral function of IFN- γ lies in its capacity to multiply the potency with which IFN- α/β restricts HSV-1 replication in vivo. This hypothesis has important ramifications for understanding how T lymphocyte-secreted cytokines such as IFN- γ can force herpesviruses into a latent state without destroying the neurons or leukocytes that continue to harbor these viral infections for the lifetime of the host.

Journal of Theoretical Biology↗

USGS2019

A comparison of the Trojan Y Chromosome strategy to harvesting models for eradication of nonnative species

The Trojan Y Chromosome strategy (TYC) is a promising eradication method for biological control of nonnative species. The strategy works by manipulating the sex ratio of a population through the introduction of supermales that guarantee male offspring. In the current study, we compare the TYC method with a pure harvesting strategy. We also analyze a hybrid harvesting model that mirrors the TYC strategy. The dynamic analysis leads to results on stability of solutions and bifurcations of the model. Several conclusions about the different strategies are established via optimal control methods. In particular, the results affirm that either a pure harvesting or hybrid strategy may work better than the TYC method at controlling a nonnative species population. Recommendations for resource managers Where harvesting is feasible, it is as effective if not more effective than the classical TYC method. Therein managers may attempt harvesting female fish while stocking males or harvesting both male and female fishes. Managers may attempt linear harvesting, saturating density‐dependent harvesting, and unbounded density‐dependent harvesting. Linear harvesting is seen to be the most effective. We caution against the outright use of harvesting due to various density‐dependent effects that may arise. To this end hybrid models that involve a combination of harvesting and TYC‐type methods might be a better strategy. One may also use harvesting as a tool in mesocosm settings to predict the efficacy of the TYC strategy in the wild.

Natural Resource Modeling↗

USGS2021

Emerging control strategies for integrated pest management of invasive carps

Invasive carps are ecologically and economically problematic fish species in many large river basins in the United States and pose a threat to aquatic ecosystems throughout much of North America. Four species of invasive carps: black carp ( Mylopharyngodon piceus ), grass carp ( Ctenopharyngodon idella ), silver carp ( Hypophthalmichthys molitrix ) and bighead carp ( Hypophthalmichthys nobilis ), are particularly concerning for native ecosystems because they occupy and disrupt a variety of food and habitat niches. In response, natural resource agencies are developing integrated pest management (IPM) plans to mitigate invasive carps. Control tools are one key component within a successful IPM program and have been a focal point for development by governmental agencies and academic researchers. For example, behavioural deterrents and barriers that block migratory pathways could limit carps range expansion into new areas, while efficient removal methods could suppress established carp populations. However, control tools are sometimes limited in practice due to uncertainty with deployment, efficacy and availability. This review provides an overview of several emerging modelling approaches and control technologies that could inform and support future invasive carp IPM programs.

Journal of Vertebrate Biology↗

USGS2009

Groundwater quality data for the Tahoe-Martis study unit, 2007: Results from the California GAMA Program

Groundwater quality in the approximately 460-square-mile Tahoe–Martis study unit was investigated in June through September 2007 as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Project was developed in response to the Groundwater Quality Monitoring Act of 2001 and is being conducted by the U.S. Geological Survey (USGS) in cooperation with the California State Water Resources Control Board (SWRCB). The study was designed to provide a spatially unbiased assessment of the quality of raw groundwater used for public water supplies within the Tahoe–Martis study unit (Tahoe–Martis) and to facilitate statistically consistent comparisons of groundwater quality throughout California. Samples were collected from 52 wells in El Dorado, Placer, and Nevada Counties. Forty-one of the wells were selected using a spatially distributed, randomized grid-based method to provide statistical representation of the study area (grid wells), and 11 were selected to aid in evaluation of specific water-quality issues (understanding wells). The groundwater samples were analyzed for a large number of synthetic organic constituents (volatile organic compounds [VOC], pesticides and pesticide degradates, and pharmaceutical compounds), constituents of special interest (perchlorate and N -nitrosodimethylamine [NDMA]), naturally occurring inorganic constituents (nutrients, major and minor ions, and trace elements), radioactive constituents, and microbial indicators. Naturally occurring isotopes (tritium, carbon-14, strontium isotope ratio, and stable isotopes of hydrogen and oxygen of water), and dissolved noble gases also were measured to help identify the sources and ages of the sampled groundwater. In total, 240 constituents and water-quality indicators were investigated. Three types of quality-control samples (blanks, replicates, and samples for matrix spikes) each were collected at 12 percent of the wells, and the results obtained from these samples were used to evaluate the quality of the data for the groundwater samples. Field blanks rarely contained detectable concentrations of any constituent, suggesting that data for the groundwater samples were not compromised by possible contamination during sample collection, handling or analysis. Differences between replicate samples were within acceptable ranges. Matrix spike recoveries were within acceptable ranges for most compounds. This study did not attempt to evaluate the quality of water delivered to consumers; after withdrawal from the ground, raw water typically is treated, disinfected, or blended with other waters to maintain water quality. Regulatory thresholds apply to water that is served to the consumer, not to raw groundwater. However, to provide some context for the results, concentrations of constituents measured in the raw groundwater were compared with regulatory and nonregulatory health-based thresholds established by the U.S. Environmental Protection Agency (USEPA) and the California Department of Public Health (CDPH), and with aesthetic and technical thresholds established by CDPH. Comparisons between data collected for this study and drinking-water thresholds are for illustrative purposes only and do not indicate of compliance or noncompliance with regulatory thresholds. The concentrations of most constituents detected in groundwater samples from the Tahoe–Martis wells were below drinking-water thresholds. Organic compounds (VOCs and pesticides) were detected in about 40 percent of the samples from grid wells, and most concentrations were less than 1/100th of regulatory and nonregulatory health-based thresholds, although the conentration of perchloroethene in one sample was above the USEPA maximum contaminant level (MCL-US). Concentrations of all trace elements and nutrients in samples from grid wells were below regulatory and nonregulatory health-based thresholds, with five exceptions. Concentrations of arsenic were above the MCL-US in 20 percent of the samples from grid wells. Gross alpha particle activity (MCL-US), boron (CDPH notification level, NL-CA), and molybdenum (USEPA lifetime health advisory, HAL-US) were each detected above thresholds in two of the samples from grid wells, and radon (proposed alternative MCL-US) was detected above the threshold in one sample from a grid well. Most of the samples from Tahoe–Martis grid wells had concentrations of major elements, total dissolved solids, and trace elements below the CDPH secondary maximum contaminant levels, nonenforceable thresholds set for aesthetic and technical concerns. Fifteen percent of the samples from grid wells contained iron, manganese, or total dissolved solids at concentrations above these levels.

California, Nevada↗

USGS2009

Groundwater quality data in the Mojave study unit, 2008: Results from the California GAMA Program

Groundwater quality in the approximately 1,500 square-mile Mojave (MOJO) study unit was investigated from February to April 2008, as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Project was developed in response to the Groundwater Quality Monitoring Act of 2001 and is being conducted by the U.S. Geological Survey (USGS) in cooperation with the California State Water Resources Control Board (SWRCB). MOJO was the 23rd of 37 study units to be sampled as part of the GAMA Priority Basin Project. The MOJO study was designed to provide a spatially unbiased assessment of the quality of untreated ground water used for public water supplies within MOJO, and to facilitate statistically consistent comparisons of groundwater quality throughout California. Samples were collected from 59 wells in San Bernardino and Los Angeles Counties. Fifty-two of the wells were selected using a spatially distributed, randomized grid-based method to provide statistical representation of the study area (grid wells), and seven were selected to aid in evaluation of specific water-quality issues (understanding wells). The groundwater samples were analyzed for a large number of organic constituents [volatile organic compounds (VOCs), pesticides and pesticide degradates, and pharmaceutical compounds], constituents of special interest (perchlorate and N-nitrosodimethylamine [NDMA]) naturally occurring inorganic constituents (nutrients, dissolved organic carbon [DOC], major and minor ions, silica, total dissolved solids [TDS], and trace elements), and radioactive constituents (gross alpha and gross beta radioactivity, radium isotopes, and radon-222). Naturally occurring isotopes (stable isotopes of hydrogen, oxygen, and carbon, stable isotopes of nitrogen and oxygen in nitrate, and activities of tritium and carbon-14), and dissolved noble gases also were measured to help identify the sources and ages of the sampled ground water. In total, over 230 constituents and water-quality indicators (field parameters) were investigated. Three types of quality-control samples (blanks, replicates, and matrix spikes) each were collected at approximately 5–8 percent of the wells, and the results for these samples were used to evaluate the quality of the data for the groundwater samples. Field blanks rarely contained detectable concentrations of any constituent, suggesting that contamination was not a significant source of bias in the data for the groundwater samples. Differences between replicate samples generally were within acceptable ranges, indicating acceptable analytical reproducibility. Matrix spike recoveries were within acceptable ranges for most compounds. This study did not attempt to evaluate the quality of water delivered to consumers; after withdrawal from the ground, untreated groundwater typically is treated, disinfected, or blended with other waters to maintain water quality. Regulatory thresholds apply to water that is served to the consumer, not to untreated ground water. However, to provide some context for the results, concentrations of constituents measured in the untreated ground water were compared with regulatory and non-regulatory health-based thresholds established by the U.S. Environmental Protection Agency (USEPA) and California Department of Public Health (CDPH) and thresholds established for aesthetic and technical concerns by CDPH. Comparisons between data collected for this study and thresholds for drinking-water are for illustrative purposes only, and are not indicative of compliance or non-compliance with those thresholds. Most constituents that were detected in groundwater samples in the 59 wells in MOJO were found at concentrations below drinking-water thresholds. In MOJO’s 52 grid wells, volatile organic compounds (VOCs) were detected in 40 percent of the wells, and pesticides and pesticide degradates were detected in 23 percent of the grid wells. Results for health-based thresholds in MOJO grid wells showed that all of the detections of organic compounds in samples from MOJO grid wells were below health-based thresholds, with the exception of a single detection of NDMA above the California Department of Public Health notification level (NL-CA). Trace elements and radioactive constituents were sampled for at 19 MOJO grid wells and most detections were below health-based thresholds. Exceptions include: six detections of arsenic above the USEPA maximum contaminant level (MCL-US), two detections of boron and one detection of vanadium above the NL-CA, one detection each of molybdenum and strontium that were above the USEPA lifetime health advisory level (HAL-US), and one detection of fluoride just above the MCL-CA of 2 µg/L. Most detections of radioactive constituents in the MOJO grid wells were below health-based thresholds, with the exception of one detection of gross alpha radioactivity (72-hour count and 30-day count) above the MCL-CA, and 17 grid wells (of 19 sampled) that had activities of radon-222 above the proposed MCL-US of 300 pCi/L, but all were below the proposed alternative MCL-US of 4,000 pCi/L. All of the samples collected from the 19 MOJO grid wells for trace elements, and most of the samples for major ions and total dissolved solids (TDS), had measured concentrations below the non-enforceable thresholds set for aesthetic concerns. Four grid wells had TDS concentrations above the California Department of Public Health secondary maximum contaminant level (SMCL-CA) recommended threshold of 500 mg/L, and three of these wells were also above the SMCL-CA upper threshold of 1,000 mg/L. Four grid wells (of 19 sampled) had sulfate measured at concentrations above the recommended SMCL-CA threshold of 250 mg/L, and one of these detections was also above the upper SMCL-CA threshold of 500 mg/L. One grid well had chloride levels at a concentration above the upper SMCL-CA threshold of 500 mg/L. Eleven grid wells (of 52 sampled) had pH values outside of the SMCL-US range for pH.

California↗

USGS2009

Groundwater-quality data in the South Coast Interior Basins study unit, 2008: Results from the California GAMA Program

Groundwater quality in the approximately 653-square-mile South Coast Interior Basins (SCI) study unit was investigated from August to December 2008, as part of the Priority Basins Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basins Project was developed in response to Legislative mandates (Supplemental Report of the 1999 Budget Act 1999-00 Fiscal Year; and, the Groundwater-Quality Monitoring Act of 2001 [Sections 10780-10782.3 of the California Water Code, Assembly Bill 599]) to assess and monitor the quality of groundwater used as public supply for municipalities in California, and is being conducted by the U.S. Geological Survey (USGS) in cooperation with the California State Water Resources Control Board (SWRCB). SCI was the 27th study unit to be sampled as part of the GAMA Priority Basins Project. This study was designed to provide a spatially unbiased assessment of the quality of untreated groundwater used for public water supplies within SCI, and to facilitate statistically consistent comparisons of groundwater quality throughout California. Samples were collected from 54 wells within the three study areas [Livermore, Gilroy, and Cuyama] of SCI in Alameda, Santa Clara, San Benito, Santa Barbara, Ventura, and Kern Counties. Thirty-five of the wells were selected using a spatially distributed, randomized grid-based method to provide statistical representation of the study unit (grid wells), and 19 were selected to aid in evaluation of specific water-quality issues (understanding wells). The groundwater samples were analyzed for organic constituents [volatile organic compounds (VOCs), pesticides and pesticide degradates, polar pesticides and metabolites, and pharmaceutical compounds], constituents of special interest [perchlorate and N-nitrosodimethylamine (NDMA)], naturally occurring inorganic constituents [trace elements, nutrients, major and minor ions, silica, total dissolved solids (TDS), and alkalinity], and radioactive constituents [gross alpha and gross beta radioactivity and radon-222]. Naturally occurring isotopes [stable isotopes of hydrogen, oxygen, and carbon, and activities of tritium and carbon-14] and dissolved noble gases also were measured to help identify the sources and ages of the sampled groundwater. In total, 288 constituents and water-quality indicators (field parameters) were investigated. Three types of quality-control samples (blanks, replicates, and matrix spikes) each were collected at approximately 4–11 percent of the wells, and the results for these samples were used to evaluate the quality of the data for the groundwater samples. Field blanks rarely contained detectable concentrations of any constituent, suggesting that contamination was not a significant source of bias in the data obtained from the groundwater samples. Differences between replicate samples generally were less than 10 percent relative standard deviation, indicating acceptable analytical reproducibility. Matrix spike recoveries were within the acceptable range (70 to 130 percent) for most compounds. This study did not attempt to evaluate the quality of water delivered to consumers; after withdrawal from the ground, untreated groundwater typically is treated, disinfected, and/or blended with other waters to maintain water quality. Regulatory thresholds apply to water that is served to the consumer, not to untreated groundwater. However, to provide some context for the results, concentrations of constituents measured in the untreated groundwater were compared with regulatory and nonregulatory health-based thresholds established by the U.S. Environmental Protection Agency (USEPA) and California Department of Public Health (CDPH), and to nonregulatory thresholds established for aesthetic and technical concerns by CDPH. Comparisons between data collected for this study and thresholds for drinking water are for illustrative purposes only, and are not indicative of compliance or noncompliance with those thresholds. Most inorganic constituents that were detected in groundwater samples from the 35 grid wells in the SCI study unit were found at concentrations below drinking-water thresholds; additionally, all detections of organic constituents in SCI grid well samples were below health-based thresholds.

California↗

USGS1984

Water-table contours, directions of ground-water movement, and measurements of inflow to American Falls Reservoir, southeastern Idaho, April 1984

In 1978 the U.S. Geological Survey began a 5-year study of the High Plains regional aquifer system to provide hydrologic information for evaluating the effects of long-term development of the aquifer and to develop a capability for predicting aquifer response to alternative changes in ground-water management. By use of a digital model, this report presents a quantitative description of the High Plains aquifer in Oklahoma. The High Plains aquifer consists predominantly of the Tertiary Ogallala Formation and overlying Quaternary alluvium and terrace deposits which are hydraulically connected to the High Plains aquifer. Much of the aquifer is underlain by formations of Permian through Cretaceous age, which generally have very small hydraulic conductivities. In some areas parts of underlying Triassic, Jurassic, or Cretaceous rocks are hydraulically connected with the aquifer. The High Plains aquifer is a water-table aquifer in which water moves generally to the east-southeast. Before the beginning of extensive irrigation of the 1960's, the aquifer was essentially in dynamic equilibrium with recharge from precipitation balanced by natural discharge from the aquifer. Ground-water discharge appeared in streams leaving the area or was returned to the atmosphere through evapotranspiration. Accurate records of irrigation pumpage are not available from the High Plains. In order to estimate irrigation pumpage, published records of crop distribution were used and a consumptive use was assigned to each principal irrigated crop. This method gave an estimated irrigation demand. Pumpage was taken as a percentage of the total irrigation demand. Irrigation has decreased ground-water discharge from the High Plains aquifer. Ground-water discharge was estimated as approximately 118 cubic feet per second in 1980. A finite-difference digital model was used to simulate flow in the High Plains aquifer. The recharge was adjusted so that 1980 ground-water discharge was 118 cubic feet per second, the estimated ground-water discharge for 1980. Recharge in the eastern half of the modeled area was 0.45 inch per year; one-half this value was used in the western half of the modeled area. Hydraulic conductivity was divided into three zones: 19.3 feet per day in the eastern zone; 16.2 feet per day in the central zone; and 8.28 feet per day in the western zone. A specific yield of 14.7 percent was used in the model. Using all these parameters, the model was calibrated so that the mean difference between predevelopment modeled and measured head was -0.044 foot. Following the calibration procedure, the model was used to predict the volumes of water in storage and distribution of saturated thickness in 1993 and 2020 using the 1980 pumping rates. The calculated quantity of water in storage in the aquifer in 1941 (predevelopment) was approximately 135.2 million acre-feet; in 1980, approximately 121.9 million acre-feet; in 1993 approximately 112.7 million acre-feet; and in 2020, approximately 96.2 million acre-feet. The High Plains aquifer in Oklahoma will continue to be an important source of water past the year 2000. As withdrawals continue from the aquifer at the present rate, the water table will continue to decline and when the water table drops below the streambed in any part of the area, ground-water discharge to streams will cease in that area. Based on the calculated volumes of water in storage, the volume of water remaining in storage as compared to the predevelopment volume is as follows: 90 percent in 1980, 83 percent in 1993, and 71 percent in 2020.

Idaho↗

USGS2016

Estimating peak-flow frequency statistics for selected gaged and ungaged sites in naturally flowing streams and rivers in Idaho

The U.S. Geological Survey, in cooperation with the Idaho Transportation Department, updated regional regression equations to estimate peak-flow statistics at ungaged sites on Idaho streams using recent streamflow (flow) data and new statistical techniques. Peak-flow statistics with 80-, 67-, 50-, 43-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities (1.25-, 1.50-, 2.00-, 2.33-, 5.00-, 10.0-, 25.0-, 50.0-, 100-, 200-, and 500-year recurrence intervals, respectively) were estimated for 192 streamgages in Idaho and bordering States with at least 10 years of annual peak-flow record through water year 2013. The streamgages were selected from drainage basins with little or no flow diversion or regulation. The peak-flow statistics were estimated by fitting a log-Pearson type III distribution to records of annual peak flows and applying two additional statistical methods: (1) the Expected Moments Algorithm to help describe uncertainty in annual peak flows and to better represent missing and historical record; and (2) the generalized Multiple Grubbs Beck Test to screen out potentially influential low outliers and to better fit the upper end of the peak-flow distribution. Additionally, a new regional skew was estimated for the Pacific Northwest and used to weight at-station skew at most streamgages. The streamgages were grouped into six regions (numbered 1_2, 3, 4, 5, 6_8, and 7, to maintain consistency in region numbering with a previous study), and the estimated peak-flow statistics were related to basin and climatic characteristics to develop regional regression equations using a generalized least squares procedure. Four out of 24 evaluated basin and climatic characteristics were selected for use in the final regional peak-flow regression equations. Overall, the standard error of prediction for the regional peak-flow regression equations ranged from 22 to 132 percent. Among all regions, regression model fit was best for region 4 in west-central Idaho (average standard error of prediction=46.4 percent; pseudo-R 2 >92 percent) and region 5 in central Idaho (average standard error of prediction=30.3 percent; pseudo-R 2 >95 percent). Regression model fit was poor for region 7 in southern Idaho (average standard error of prediction=103 percent; pseudo-R 2 <78 percent) compared to other regions because few streamgages in region 7 met the criteria for inclusion in the study, and the region’s semi-arid climate and associated variability in precipitation patterns causes substantial variability in peak flows. A drainage area ratio-adjustment method, using ratio exponents estimated using generalized least-squares regression, was presented as an alternative to the regional regression equations if peak-flow estimates are desired at an ungaged site that is close to a streamgage selected for inclusion in this study. The alternative drainage area ratio-adjustment method is appropriate for use when the drainage area ratio between the ungaged and gaged sites is between 0.5 and 1.5. The updated regional peak-flow regression equations had lower total error (standard error of prediction) than all regression equations presented in a 1982 study and in four of six regions presented in 2002 and 2003 studies in Idaho. A more extensive streamgage screening process used in the current study resulted in fewer streamgages used in the current study than in the 1982, 2002, and 2003 studies. Fewer streamgages used and the selection of different explanatory variables were likely causes of increased error in some regions compared to previous studies, but overall, regional peak‑flow regression model fit was generally improved for Idaho. The revised statistical procedures and increased streamgage screening applied in the current study most likely resulted in a more accurate representation of natural peak-flow conditions. The updated, regional peak-flow regression equations will be integrated in the U.S. Geological Survey StreamStats program to allow users to estimate basin and climatic characteristics and peak-flow statistics at ungaged locations of interest. StreamStats estimates peak-flow statistics with quantifiable certainty only when used at sites with basin and climatic characteristics within the range of input variables used to develop the regional regression equations. Both the regional regression equations and StreamStats should be used to estimate peak-flow statistics only in naturally flowing, relatively unregulated streams without substantial local influences to flow, such as large seeps, springs, or other groundwater-surface water interactions that are not widespread or characteristic of the respective region.

Idaho↗

USGS2002

Comparison of traditional and molecular methods for detection of Renibacterium salmoninarum

Bacterial kidney disease (BKD) caused by Renibacterium salmoninarum occurs in most parts of the world where wild or cultured salmonid fishes are present. Several extensive reviews have been written on the pathogen and the disease (Fryer and Sanders, 1981; Austin and Austin, 1987; Elliott et al ., 1989; Evelyn, 1993; Evenden et al ., 1993; Fryer and Lannan, 1993). Bacterial kidney disease can cause serious mortality in juvenile salmonids in both fresh water and seawater, and also in prespawning adults. Although the chronic nature of the disease has hindered accurate estimates of fish losses, particularly in feral fish populations, BKD is one the most important bacterial diseases affecting cultured salmonids, with reported losses as high as 80% in stocks of Pacific salmon ( Oncorhynchus spp.) and 40% in stocks of Atlantic salmon ( Salmo salar ) (Evenden et al ., 1993).

Book chapter↗

USGS2020

Using NASA Earth observations and Google Earth Engine to map winter cover crop conservation performance in the Chesapeake Bay watershed

Winter cover crops such as barley, rye, and wheat help to improve soil structure by increasing porosity, aggregate stability, and organic matter, while reducing the loss of agricultural nutrients and sediments into waterways. The environmental performance of cover crops is affected by choice of species, planting date, planting method, nutrient inputs, temperature, and precipitation. The Maryland Department of Agriculture (MDA) oversees an agricultural cost-share program that provides farmers with funding to cover costs associated with planting winter cover crops, and the U.S. Geological Survey (USGS) and the U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) have partnered with the MDA to develop satellite remote sensing techniques for measuring cover crop performance. The MDA has developed the capacity to digitize field boundaries for all fields enrolled in their cover crop programs (>26,000 fields per year) to support a remote sensing performance analysis at a statewide scal,e and has requested assistance with the associated imagery processing from the National Aeronautics and Space Administration (NASA). Using the Google Earth Engine (GEE) cloud computing platform, scripts were developed to process Landsat 5/7/8 and Harmonized Sentinel-2 imagery to measure winter cover crop performance. We calibrated cover crop performance models using linear regression between satellite vegetation indices and USGS / USDA-ARS field sampling data collected on Maryland farms between 2006 and 2012 (1298 samples). Satellite-derived Normalized Difference Vegetation Index (NDVI) values showed significant correlation with the natural logarithm of cover crop biomass ( p ≤0.01, R 2 = 0.56) and with observed percent vegetative ground cover (p ≤0.01, R 2 = 0.68). The GEE scripts were used to composite seasonal maximum NDVI values for each enrolled cover crop field and calculate performance metrics for the winter and spring seasons of three enrollment years (2014–15, 2015–16, and 2017–18) for four Maryland counties. Results from winter 2017–18 demonstrate that rye and barley fields had higher biomass than wheat fields, and that early planting, along with planting methods that increase seed-soil contact, increased performance. The processing capabilities of GEE will support the MDA in scaling up remote sensing performance analysis statewide, providing information to evaluate the environmental outcomes associated with various agronomic management strategies. The tool can be modified for different seasonal cutoffs, utilize new sensors to capture phenology in winter and spring, and scale to larger regions for use in adaptive management of winter cover crops planted for environmental benefit.

Maryland↗

USGS2004

Ecoregions and ecoregionalization: geographical and ecological perspectives

Ecoregions, i.e., areas exhibiting relative homogeneity of ecosystems, are units of analysis that are increasingly important in environmental assessment and management. Ecoregions provide a holistic framework for flexible, comparative analysis of complex environmental problems. Ecoregions mapping has intellectual foundations in both geography and ecology. However, a hallmark of ecoregions mapping is that it is a truly interdisciplinary endeavor that demands the integration of knowledge from a multitude of sciences. Geographers emphasize the role of place, scale, and both natural and social elements when delineating and characterizing regions. Ecologists tend to focus on environmental processes with special attention given to energy flows and nutrient cycling. Integration of disparate knowledge from the many key sciences has been one of the great challenges of ecoregions mapping, and may lie at the heart of the lack of consensus on the “optimal” approach and methods to use in such work. Through a review of the principal existing US ecoregion maps, issues that should be addressed in order to advance the state of the art are identified. Research related to needs, methods, data sources, data delivery, and validation is needed. It is also important that the academic system foster education so that there is an infusion of new expertise in ecoregion mapping and use.

Environmental Management↗

USGS2016

A new look at liming as an approach to accelerate recovery from acidic deposition effects

Acidic deposition caused by fossil fuel combustion has degraded aquatic and terrestrial ecosystems in North America for over four decades. The only management option other than emissions reductions for combating the effects of acidic deposition has been the application of lime to neutralize acidity after it has been deposited on the landscape. For this reason, liming has been a part of acid rain science from the beginning. However, continued declines in acidic deposition have led to partial recovery of surface water chemistry, and the start of soil recovery. Liming is therefore no longer needed to prevent further damage, so the question becomes whether liming would be useful for accelerating recovery of systems where improvement has lagged. As more is learned about recovering ecosystems, it has become clear that recovery rates vary with watershed characteristics and among ecosystem components. Lakes appear to show the strongest recovery, but recovery in streams is sluggish and recovery of soils appears to be in the early stages. The method in which lime is applied is therefore critical in achieving the goal of accelerated recovery. Application of lime to a watershed provides the advantage of increasing Ca availability and reducing or preventing mobilization of toxic Al, an outcome that is beneficial to both terrestrial and aquatic ecosystems. However, the goal should not be complete neutralization of soil acidity, which is naturally produced. Liming of naturally acidic areas such as wetlands should also be avoided to prevent damage to indigenous species that rely on an acidic environment.

Science of the Total Environment↗

USGS1987

Age-specificity of black-capped chickadee survival rates: Analysis of capture-recapture data

The ornithological literature indicates a widespread belief in two generalizations about the age—specificity of avian survival rates: (1) survival rates of young birds for some period following fledging are lower than those of adults, and (2) after reaching adulthood survival rates are constant for birds of all ages. There is a growing body of evidence in support of the first generalization, although little is known about how long the survival difference between young and adults lasts. This latter question can be addressed with capture—recapture or band recovery studies based on birds marked in the winter, but the inability to determine age in many species during winter has prevented the use of standard methods. There is very little evidence supporting the second generalization, and we are in need of methods and actual analyses that address this question. In the present paper we restate the two generalizations as hypotheses and test them using data from a wintering Black—capped Chickadee (Parus atricapillus) population in Connecticut, which has been studied by Loery for 26 yr. We use a cohort—based Jolly—Seber approach, which should be useful in other investigations of this nature. We found strong evidence of lower survival rates in 1st—yr birds than in adults, but could not determine whether this was the result of higher mortality rates, higher emigration rates, or a combination of the two. We also found evidence that survival rates of adult birds were not constant with age but decreased at a rate of ° 3.5%/yr. As adult birds are very faithful to their wintering areas, we believe that almost all this decrease can be attributed to an increase in mortality with age. Simulation results suggest that heterogeneity of capture probabilities could not explain the magnitude of the decrease in survival with age. Age—dependent tag loss is also discussed as an alternative explanation, but is dismissed as very unlikely in this situation. This analysis thus provides some of the first evidence of declining adult survival probabilities with age for any bird species.

Ecology↗

USGS2009

Groundwater quality data for the northern Sacramento Valley, 2007: Results from the California GAMA Program

Groundwater quality in the approximately 1,180-square-mile Northern Sacramento Valley study unit (REDSAC) was investigated in October 2007 through January 2008 as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Project was developed in response to the Groundwater Quality Monitoring Act of 2001, and is being conducted by the U.S. Geological Survey (USGS) in cooperation with the California State Water Resources Control Board (SWRCB). The study was designed to provide a spatially unbiased assessment of the quality of raw groundwater used for public water supplies within REDSAC and to facilitate statistically consistent comparisons of groundwater quality throughout California. Samples were collected from 66 wells in Shasta and Tehama Counties. Forty-three of the wells were selected using a spatially distributed, randomized grid-based method to provide statistical representation of the study area (grid wells), and 23 were selected to aid in evaluation of specific water-quality issues (understanding wells). The groundwater samples were analyzed for a large number of synthetic organic constituents (volatile organic compounds [VOC], pesticides and pesticide degradates, and pharmaceutical compounds), constituents of special interest (perchlorate and N-nitrosodimethylamine [NDMA]), naturally occurring inorganic constituents (nutrients, major and minor ions, and trace elements), radioactive constituents, and microbial constituents. Naturally occurring isotopes (tritium, and carbon-14, and stable isotopes of nitrogen and oxygen in nitrate, stable isotopes of hydrogen and oxygen of water), and dissolved noble gases also were measured to help identify the sources and ages of the sampled ground water. In total, over 275 constituents and field water-quality indicators were investigated. Three types of quality-control samples (blanks, replicates, and sampmatrix spikes) were collected at approximately 8 to 11 percent of the wells, and the results for these samples were used to evaluate the quality of the data obtained from the groundwater samples. Field blanks rarely contained detectable concentrations of any constituent, suggesting that contamination was not a noticeable source of bias in the data for the groundwater samples. Differences between replicate samples were within acceptable ranges for nearly all compounds, indicating acceptably low variability. Matrix-spike recoveries were within acceptable ranges for most compounds. This study did not attempt to evaluate the quality of water delivered to consumers; after withdrawal from the ground, raw groundwater typically is treated, disinfected, or blended with other waters to maintain water quality. Regulatory thresholds apply to water that is served to the consumer, not to raw ground water. However, to provide some context for the results, concentrations of constituents measured in the raw groundwater were compared with regulatory and nonregulatory health-based thresholds established by the U.S. Environmental Protection Agency (USEPA) and California Department of Public Health (CDPH) and with aesthetic and technical thresholds established by CDPH. Comparisons between data collected for this study and drinking-water thresholds are for illustrative purposes only and do not indicate compliance or noncompliance with those thresholds. The concentrations of most constituents detected in groundwater samples from REDSAC were below drinking-water thresholds. Volatile organic compounds (VOC) and pesticides were detected in less than one-quarter of the samples and were generally less than a hundredth of any health-based thresholds. NDMA was detected in one grid well above the NL-CA. Concentrations of all nutrients and trace elements in samples from REDSAC wells were below the health-based thresholds except those of arsenic in three samples, which were above the USEPA maximum contaminant level (MCL-US). However, none of these wells were public-supply wells. Concentrations of all radioactive constituents were below health-based thresholds except radon-222, which was detected above the proposed MCL-US of 300 pCi/L in samples from 11 grid wells. Most of the samples from REDSAC wells had concentrations of major elements, total dissolved solids, and trace elements below the non-enforceable thresholds set for aesthetic or technical concerns. A few samples contained iron, manganese, or pH at levels above the SMCL-CA or SMCL-US thresholds.

California↗

USGS1993

Water-quantity, water-quality, soil, and sediment data collected at Goose Egg Spring, Natrona County, Wyoming, May and July 1992

Recent, apparent increases in sediment accumulation in Goose Egg Spring, southwest of Casper, Wyoming, may have been the result of natural environmental processes or quarry operations near the spring in late 1991. Goose Egg Spring is the sole source of water for the Dan Speas Fish Rearing Station. This facility is operated by the Wyoming Game and Fish Commission and produces about 77,000 kilograms of stockable fish annually. Samples of the spring water, surrounding soils, and bottom sediment were collected. Methods used in obtaining all samples are discussed. Results of chemical analyses of the spring water, stratigraphic description of core samples, particle-size distribution analysis, visual mineralogical assessment, and X-ray diffraction analysis were used to characterize Goose Egg Spring and the immediately surrounding area in May and July 1992.

Open-File Report↗

USGS2024

U.S. Geological Survey Tunison Laboratory of Aquatic Science research to rehabilitate native prey fish of the Lake Ontario fish community—Coregonine fishes

Restoration of native coregonines to Lake Ontario of the Laurentian Great Lakes will improve the diversity of forage for salmonid predators and ecological function in the lake, but efficacy of experimental releases for native species restoration must be evaluated. The Coregonine Research Program at the U.S. Geological Survey Tunison Laboratory of Aquatic Science encompassed a diverse array of research, with an emphasis on improved culture methods and field assessments of experimentally released juvenile coregonines. This research was carried out to support the Fish Community Objectives of the Lake Ontario Committee, is funded largely by the Great Lakes Restoration Initiative, and was done in collaboration with other laboratories and agencies, particularly, the U.S. Fish and Wildlife Service; New York State Department of Environmental Conservation; Ontario Ministry of Natural Resources and Forestry; and other U.S. Geological Survey laboratories. The Tunison Laboratory of Aquatic Science and partners have developed new and innovative hatchery techniques to raise cisco and bloater to life stages suitable for survival in Lake Ontario; assessed adult bloater survival in Lake Ontario; and evaluated survival, return rate, and reproduction of adult cisco in historic spawning locations in Lake Ontario embayments. Successes, challenges, and research needs are discussed.

Lake Ontario↗

USGS2022

Identifying shared priorities for a bioregional approach to restoration in the Northern Gulf of Mexico

Natural resource management is often challenged with a mismatch between the scale of decision-making and the scale of the biological, ecological, and physical processes that control a system. Bioregional approaches to adaptive management have emerged as an approach to inform natural resource management at ecologically relevant scales and across multi-level governance structures. The implementation of adaptive management requires the determination of ecological and social priorities that can inform a desired system state across multiple governing bodies. We use the Northern Gulf of Mexico, United States, as a case study for a bioregional approach to adaptive management and illustrate a method for developing objectives and management priorities across programs and jurisdictions. Through this synthesis, using qualitative coding methods to develop a shared vocabulary across the diverse dataset, we identified commonalities and differences in ecological and human community priorities across the five states which line the Northern Gulf of Mexico. Using these shared priorities, we conceptualize a network of priority-focused objectives as a starting point for further stakeholder engagement and effectively monitoring and evaluating progress across boundaries. This approach serves as a framework for cross-program adaptive management by illustrating a desired system state that reflects the shared priorities among decision-making authorities in this region and offering individual programs or projects a method to articulate their contributions to the broader set of shared priorities Gulf-wide. This method can be used by restoration managers in any region of the world to align project objectives within cross-jurisdictional boundaries and illustrate the value of a bioregional approach to restoration.

Gulf of Mexico↗

USGS2001

Kullback-Leibler information in resolving natural resource conflicts when definitive data exist

Conflicts often arise in the management of natural resources. Often they result from differing perceptions, varying interpretations of the law, and self-interests among stakeholder groups (for example, the values and perceptions about spotted owls and forest management differ markedly among environmental groups, government regulatory agencies, and timber industries). We extend the conceptual approach to conflict resolution of Anderson et al. (1999) by using information-theoretic methods to provide quantitative evidence for differing stakeholder positions. Importantly, we assume that relevant empirical data exist that are central to the potential resolution of the conflict. We present a hypothetical example involving an experiment to assess potential effects of a chemical on monthly survival probabilities of the hen clam (Spisula solidissima). The conflict centers on 3 stakeholder positions: 1) no effect, 2) an acute effect, and 3) an acute and chronic effect of the chemical treatment. Such data were given to 18 analytical teams to make independent analyses and provide the relative evidence for each of 3 stakeholder positions in the conflict. The empirical evidence strongly supports only one of the 3 positions in the conflict: the application of the chemical causes acute and chronic effects on monthly survival, following treatment. Formal inference from all the stakeholder positions is provided for the 2 key parameters underlying the hen clam controversy. The estimates of these parameters were essentially unbiased (the relative bias for the control and treatment group's survival probability was -0.857% and 1.400%, respectively) and precise (coefficients of variation were 0.576% and 2.761%, respectively). The advantages of making formal inference from all the models, rather than drawing conclusions from only the estimated best model, is illustrated. Finally, we contrast information-theoretic and Bayesian approaches in terms of how positions in the controversy enter the formal analysis.

Wildlife Society Bulletin↗