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National Park Service Vegetation Mapping Inventory Program: Appalachian National Scenic Trail vegetation mapping project

The National Park Service (NPS) Vegetation Mapping Inventory (VMI) Program classifies, describes, and maps existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VMI Program is managed by the NPS I&M Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey Upper Midwest Environmental Sciences Center, NatureServe, NPS Northeast Temperate Network, and NPS Appalachian National Scenic Trail (APPA) have completed vegetation classification and mapping of APPA for the NPS VMI Program. Mappers, ecologists, and botanists collaborated to affirm vegetation types within the U.S. National Vegetation Classification (USNVC) of APPA and to determine how best to map the vegetation types by using aerial imagery. Analyses of data from 1,618 vegetation plots were used to describe USNVC associations of APPA. Data from 289 verification sites were collected to test the field key to vegetation associations and the application of vegetation associations to a sample set of map polygons. Data from 269 validation sites were collected to assess vegetation mapping prior to submitting the vegetation map for accuracy assessment (AA). Data from 3,265 AA sites were collected, of which 3,204 were used to test accuracy of the vegetation map layer. The collective of these datasets affirmed 280 USNVC associations for the APPA vegetation mapping project. To map the vegetation and land cover of APPA, 169 map classes were developed. The 169 map classes consist of 150 that represent natural (including ruderal) vegetation types in the USNVC, 11 that represent cultural (agricultural and developed) vegetation types in the USNVC, 5 that represent natural landscapes with catastrophic disturbance or some other modification to natural vegetation preventing accurate classification in the USNVC, and 3 that represent nonvegetated water (non-USNVC). Features were interpreted from viewing 4-band digital aerial imagery using digital onscreen three-dimensional stereoscopic workflow systems in geographic information systems (GIS). (Digital aerial imagery was collected each fall during 2009–11 to capture leaf-phenology change of hardwood trees across the latitudinal range of APPA.) The interpreted data were digitally and spatially referenced, thus making the spatial-database layers usable in GIS. Polygon units were mapped to either a 0.5-hectare (ha) or 0.25-ha minimum mapping unit, depending on vegetation type or scenario; however, polygon units were mapped to 0.1 ha for alpine vegetation. A geodatabase containing various feature-class layers and tables provide locations and support data to USNVC vegetation types (vegetation map layer), vegetation plots, verification sites, validation sites, AA sites, project boundary extent and zones, and aerial image centers and flight lines. The feature-class layer and related tables of the vegetation map layer provide 30,395 polygons of detailed attribute data covering 110,919.7 ha, with an average polygon size of 3.6 ha; the vegetation map coincides closely with the administrative boundary for APPA. Summary reports generated from the vegetation map layer of the map classes representing USNVC natural (including ruderal) vegetation types apply to 28,242 polygons (92.9% of polygons) and cover 106,413.0 ha (95.9%) of the map extent for APPA. The map layer indicates APPA to be 92.4% forest and woodland (102,480.8 ha), 1.7% shrubland (1866.3 ha), and 1.8% herbaceous cover (2,065.9 ha). Map classes representing park-special vegetation (undefined in the USNVC) apply to 58 polygons (0.2% of polygons) and cover 404.3 ha (0.4%) of the map extent. Map classes representing USNVC cultural types apply to 1,777 polygons (5.8% of polygons) and cover 2,516.3 ha (2.3%) of the map extent. Map classes representing nonvegetated water (non-USNVC) apply to 332 polygons (1.1% of polygons) and cover 1,586.2 ha (1.4%) of the map extent.

Appalachian National Scenic Trail↗

Death Valley regional groundwater flow system, Nevada and California: Hydrogeologic framework and transient groundwater flow model

A numerical three-dimensional (3D) transient groundwater flow model of the Death Valley region was developed by the U.S. Geological Survey for the U.S. Department of Energy programs at the Nevada Test Site and at Yucca Mountain, Nevada. Decades of study of aspects of the groundwater flow system and previous less extensive groundwater flow models were incorporated and reevaluated together with new data to provide greater detail for the complex, digital model. A 3D digital hydrogeologic framework model (HFM) was developed from digital elevation models, geologic maps, borehole information, geologic and hydrogeologic cross sections, and other 3D models to represent the geometry of the hydrogeologic units (HGUs). Structural features, such as faults and fractures, that affect groundwater flow also were added. The HFM represents Precambrian and Paleozoic crystalline and sedimentary rocks, Mesozoic sedimentary rocks, Mesozoic to Cenozoic intrusive rocks, Cenozoic volcanic tuffs and lavas, and late Cenozoic sedimentary deposits of the Death Valley regional groundwater flow system (DVRFS) region in 27 HGUs. Information from a series of investigations was compiled to conceptualize and quantify hydrologic components of the groundwater flow system within the DVRFS model domain and to provide hydraulic-property and head-observation data used in the calibration of the transient-flow model. These studies reevaluated natural groundwater discharge occurring through evapotranspiration (ET) and spring flow; the history of groundwater pumping from 1913 through 1998; groundwater recharge simulated as net infiltration; model boundary inflows and outflows based on regional hydraulic gradients and water budgets of surrounding areas; hydraulic conductivity and its relation to depth; and water levels appropriate for regional simulation of prepumped and pumped conditions within the DVRFS model domain. Simulation results appropriate for the regional extent and scale of the model were provided by acquiring additional data, by reevaluating existing data using current technology and concepts, and by refining earlier interpretations to reflect the current understanding of the regional groundwater flow system. Groundwater flow in the Death Valley region is composed of several interconnected, complex groundwater flow systems. Groundwater flow occurs in three subregions in relatively shallow and localized flow paths that are superimposed on deeper, regional flow paths. Regional groundwater flow is predominantly through a thick Paleozoic carbonate rock sequence affected by complex geologic structures from regional faulting and fracturing that can enhance or impede flow. Spring flow and ET are the dominant natural groundwater discharge processes. Groundwater also is withdrawn for agricultural, commercial, and domestic uses. Groundwater flow in the DVRFS was simulated using MODFLOW-2000, the U.S. Geological Survey 3D finitedifference modular groundwater flow modeling code that incorporates a nonlinear least-squares regression technique to estimate aquifer parameters. The DVRFS model has 16 layers of defined thickness, a finite-difference grid consisting of 194 rows and 160 columns, and uniform cells 1,500 meters (m) on each side. Prepumping conditions (before 1913) were used as the initial conditions for the transient-state calibration. The model uses annual stress periods with discrete recharge and discharge components. Recharge occurs mostly from infiltration of precipitation and runoff on high mountain ranges and from a small amount of underflow from adjacent basins. Discharge occurs primarily through ET and spring discharge (both simulated as drains) and water withdrawal by pumping and, to a lesser amount, by underflow to adjacent basins simulated by constant-head boundaries. All parameter values estimated by the regression are reasonable and within the range of expected values. The simulated hydraulic heads of the final calibrated transient model generally fit observed heads reasonably well (residuals with absolute values less than 10 meters) with two exceptions: in most areas of nearly flat hydraulic gradient the fit is considered moderate (residuals with absolute values of 10 to 20 meters), and in areas of steep hydraulic gradient along the Eleana Range and western part of Yucca Flat, southern part of the Owlshead Mountains, southern part of the Bullfrog Hills, and the north-northwestern part of the model domain (residuals with absolute values greater than 20 meters). Groundwater discharge residuals are fairly random, with as many areas where simulated flows are less than observed flows as areas where simulated flows are greater. The highest unweighted groundwater discharge residuals occur at Death Valley, Sarcobatus Flat (northeastern area), Tecopa, and early observations at Manse Spring in Pahrump Valley. High weighted-discharge residuals were computed in Indian Springs Valley and parts of Death Valley. Most of these inaccuracies in head and discharge can be attributed to insufficient representation of the hydrogeology in the HFM and(or) discharge estimates, misrepresentation of water levels, and(or) model error associated with grid-cell size. The model represents the large and complex groundwater flow system of the Death Valley region at a greater degree of refinement and accuracy than has been possible previously. The representation of detail provided by the 3D digital hydrogeologic framework model and the numerical groundwater flow model enabled greater spatial accuracy in every model parameter. The lithostratigraphy and structural effects of the hydrogeologic framework; recharge estimates from simulated net infiltration; discharge estimates from ET, spring flow, and pumping; and boundary inflow and outflow estimates all were reevaluated, some additional data were collected, and accuracy was improved. Uncertainty in the results of the flow model simulations can be reduced by improving on the quality, interpretation, and representation of the water-level and discharge observations used to calibrate the model and improving on the representation of the HGU geometries, the spatial variability of HGU material properties, the flow model physical framework, and the hydrologic conditions.

California, Nevada↗

Environmental fate and effects of the lampricide Bayluscide: A review

Bayluscide is an additive to TFM that increases the effectiveness of TFM as a lampricide. A review of the literature was undertaken to determine the environmental fate and effects of Bayluscide. Niclosamide (2′, 5-dichloro-4′-nitrosalicylanilide), the active ingredient of Bayluscide, degrades rapidly in natural water and sediment systems, however, the rate of degradation is very slow in autoclaved samples. This difference suggests that degradation under laboratory conditions is dependent on microbial activity and hydrolysis plays a minor role in degradation of niclosamide. The major degradation product of niclosamide has been reported to be aminoniclosamide (2′,5-dichloro-4′-aminosalicylanilide), which represented more than 50% of the residues extractable from sediments. Significantly more of the chemical is adsorbed to sediments with higher organic content and at lower pH's. The mobility of niclosamide in soil can be characterized as slight to medium; the estimated leaching distance would range from 0 to > 25 cm depending on the soil type and pH. The active ingredient of Bayluscide (niclosamide) is decomposed by ultra-violet light depending on the intensity and duration of the exposure. The uptake of residues by most invertebrates exposed to 14 C-niclosamide is fairly rapid and equilibrium is reached within 24 h. About 90% of the accumulated residues were lost within 48 h after the organisms were transferred to clean flowing water. As with invertebrates, fish rapidly accumulate and eliminate residues of niclosamide. Three distinct residues were isolated from the extracts of edible fillet tissue; parent niclosamide, the glucuronide conjugate of niclosamide, and the sulfate ester of niclosamide. Aquatic plants and agricultural crops do not appear to be adversely affected at concentrations of Bayluscide used for lamprey or snail control. Mayflies ( Hexagenia sp .). tend to be susceptible to TFM, but are relatively resistant to the effects of exposure to Bayluscide. Bayluscide was originally developed as a molluscicide to eliminate snails. Therefore, it is not surprising that mollusks are extremely sensitive to Bayluscide. Oral, dermal, and ocular administration of Bayluscide to mammals resulted in no clinical signs of systemic toxicity. Tests of the chronic effects of Bayluscide indicated that it is not mutagenic or carcinogenic. Bayluscide is not persistent in the environment; it breaks down in natural water and sediment systems through hydrolysis, photolysis, and microbial degradation. Given the limited use and tight control maintained by the U.S. Fish and Wildlife Service during applications of lampricides, Bayluscide presents minimal risk to human health and safety of the environment.

Conference Paper↗

Availability and distribution of low flow in Anahola Stream, Kauaʻi, Hawaiʻi

Anahola Stream is a perennial stream in northeast Kauaʻi, Hawaiʻi, that supports agricultural, domestic, and cultural uses within its drainage basin. Beginning in the late 19th century, Anahola streamflow was diverted by Makee Sugar Company at altitudes of 840 feet (upper intake) and 280 feet (lower intake) for irrigating sugarcane in the Keālia area. When sugarcane cultivation in the Keālia area ceased in 1988, part of the Makee Sugar Company’s surface-water collection system (Makee diversion system) in the Anahola drainage basin was abandoned. In an effort to better manage available surface-water resources, the State of Hawaiʻi Department of Hawaiian Home Lands is considering using the existing ditches in the Anahola Stream drainage basin to provide irrigation water for Native Hawaiian farmers in the area. To provide information needed for successful management of the surface-water resources, the U.S. Geological Survey investigated the availability and distribution of natural low flow in Anahola Stream and also collected low-flow data in Goldfish Stream, a stream that discharges into Kaneha Reservoir, which served as a major collection point for the Makee diversion system. Biological surveys of Anahola Stream were conducted as part of a study to determine the distribution of native and nonnative aquatic stream fauna. Results of the biological surveys indicated the presence of the following native aquatic species in Anahola Stream: ʻoʻopu ʻakupa (Sandwich Island sleeper) and ʻoʻopu naniha (Tear-drop goby) in the lower stream reaches surveyed; and ʻoʻopu nākea (Pacific river goby), ʻoʻopu nōpili (Stimpson’s goby), and ʻōpae kalaʻole (Mountain shrimp) in the middle and upper stream reaches surveyed. Nonnative aquatic species were found in all of the surveyed stream reaches along Anahola Stream. The availability and distribution of natural low flow were determined using a combination of discharge measurements made from February 2011 to May 2012 at low-flow partial-record and seepage-run stations established at locations of interest along study-area streams. Upstream of the upper intake, the estimated natural (undiverted) median flow in Anahola Stream is 2.7 million gallons per day, and the flow is expected to be greater than or equal to 0.97 million gallons per day 95 percent of the time. About 0.7 mile upstream of the lower intake and downstream from the confluence with Keaʻoʻopu Stream, the estimated natural (undiverted) median flow in Anahola Stream is 6.3 million gallons per day, and the flow is expected to be greater than or equal to 2.7 million gallons per day 95 percent of the time. In Goldfish Stream, about 0.4 mile upstream from the point of discharge into Kaneha Reservoir, the estimated natural median flow is 0.54 million gallons per day, and the flow is expected to be greater than or equal to 0.23 million gallons per day 95 percent of the time. The discharge estimates are representative of low-flow conditions in the study-area streams, and they are applicable to the base period (water years 1961–2011) over which they have been computed. The distribution of natural low flow in Anahola Stream was characterized through data collected during wet- and dry-season seepage runs. Seepage-run results show that Anahola Stream was generally a gaining stream under natural low-flow conditions. During the wet-season seepage run, Anahola Stream at the station located upstream of tributary Kaʻalula Stream had more than five times the flow that was measured upstream from the upper intake. The estimated total gain (including tributary inflow) in the 6.1-mile seepage-run reach was 6.97 million gallons per day; about 42 percent of that gain was groundwater discharge to the main channel of Anahola Stream. During the dry-season seepage run, about 34 percent of the estimated total gain of 3.93 million gallons per day in the same seepage-run reach was groundwater discharge to the main channel of Anahola Stream. A 15-percent seepage loss was estimated in a 0.3-mile reach downstream from the confluence of Anahola and Keaʻoʻopu Streams. The report summarizes scenarios that describe (1) surface-water availability under regulated conditions of Anahola Stream if the upper and lower intakes are restored in the future; and (2) amount of flow available for agricultural use at the upper intake under a variety of potential instream-flow standards that may be established by the State of Hawaiʻi for the protection of instream uses.

Hawai'i↗

Environmental fate and effects of the lampricide bayluscide: a review

Bayluscide is an additive to TFM that increases the effectiveness of TFM as a lampricide. A review of the literature was undertaken to determine the environmental fate and effects of Bayluscide. Niclosamide (2', 5-dichloro-4'-nitrosalicylanilide), the active ingredient of Bayluscide, degrades rapidly in natural water and sediment systems, however, the rate of degradation is very slow in autoclaved samples. This difference suggests that degradation under laboratory conditions is dependent on microbial activity and hydrolysis plays a minor role in degradation of niclosamide. The major degradation product of niclosamide has been reported to be aminoniclosamide (2',5-dichloro-4'-aminosalicylanilide), which represented more than 50% of the residues extractable from sediments. Significantly more of the chemical is adsorbed to sediments with higher organic content and at lower pH's. The mobility of niclosamide in soil can be characterized as slight to medium; the estimated leaching distance would range from 0 to > 25 cm depending on the soil type and pH. The active ingredient of Bayluscide (niclosamide) is decomposed by ultra-violet light depending on the intensity and duration of the exposure. The uptake of residues by most invertebrates exposed to super(14)C-niclosamide is fairly rapid and equilibrium is reached within 24 h. About 90% of the accumulated residues were lost within 48 h after the organisms were transferred to clean flowing water. As with invertebrates, fish rapidly accumulate and eliminate residues of niclosamide. Three distinct residues were isolated from the extracts of edible fillet tissue; parent niclosamide, the glucuronide conjugate of niclosamide, and the sulfate ester of niclosamide. Aquatic plants and agricultural crops do not appear to be adversely affected at concentrations of Bayluscide used for lamprey or snail control. Mayflies (Hexagenia sp.). tend to be susceptible to TFM, but are relatively resistant to the effects of exposure to Bayluscide. Bayluscide was originally developed as a molluscicide to eliminate snails. Therefore, it is not surprising that mollusks are extremely sensitive to Bayluscide. Oral, dermal, and ocular administration of Bayluscide to mammals resulted in no clinical signs of systemic toxicity. Tests of the chronic effects of Bayluscide indicated that it is not mutagenic or carcinogenic. Bayluscide is not persistent in the environment; it breaks down in natural water and sediment systems through hydrolysis, photolysis, and microbial degradation. Given the limited use and tight control maintained by the U.S. Fish and Wildlife Service during applications of lampricides, Bayluscide presents minimal risk to human health and safety of the environment.

Journal of Great Lakes Research↗

Groundwater-flow model of the Treasure Valley, southwestern Idaho, 1986–2015

Most of the population of the Treasure Valley and the surrounding area of southwestern Idaho and easternmost Oregon depends on groundwater for domestic supply, either from domestic or municipal-supply wells. Current and projected rapid population growth in the area has caused concern about the long-term sustainability of the groundwater resource. In 2016, the U.S. Geological Survey, in cooperation with the Idaho Water Resource Board and the Idaho Department of Water Resources, began a project to construct a numerical groundwater-flow model of the westernmost portion of the western Snake River Plain aquifer system, called the Treasure Valley. The development of the model was guided by several objectives, including: to improve the understanding of groundwater and surface water interactions; to facilitate conjunctive water management; to provide a tool for water resources planning; and to provide a tool for water allocation. The model was constructed with a spatial scale and level of detail that aimed to meet these objectives while balancing the sometimes-competing goals of fast runtimes, numerical stability, usability, and parsimony. The Treasure Valley Groundwater Flow Model (TVGWFM) is a three-dimensional finite-difference numerical model constructed using MODFLOW 6 (Langevin and others, 2017, Documentation for the MODFLOW 6 Groundwater Flow Model: U.S. Geological Survey Techniques and Methods, book 6, chap. A55, 197 p., https://doi.org/10.3133/tm6A55 ). The model covers the westernmost portion of the western Snake River Plain and is discretized into a regular grid of 64 by 65 cells with a side length of 1 mile and 6 layers of varying depth and active area. A historical model period was developed consisting of 360 month-long stress periods for 1986–2015. The model builds upon previous modeling efforts by adding a transient period, incorporating new head and discharge observations to constrain parameters, incorporating information from the hydrogeologic framework model (HFM) of Bartolino (2019, Hydrogeologic framework of the Treasure Valley and surrounding area, Idaho and Oregon: U.S. Geological Survey Scientific Investigations Report 2019–5138, https://doi.org/10.3133/sir20195138 ) and incorporating refined estimates of evapotranspiration and irrigation classification of lands in the study area. The TVGWFM includes all significant components of recharge to and discharge from the aquifer. Inflows include canal seepage, irrigation and precipitation recharge, mountain-front recharge, rivers and stream seepage, and seepage from Lake Lowell. Outflows include discharge to agricultural drainage ditches, discharge to rivers and streams, pumping, and discharge to Lake Lowell. Each recharge or discharge component is represented separately using individual MODFLOW 6 packages. Parameter values were derived with a combination of trial-and-error steps and automated parameter estimation using PEST software (Doherty, J.E., 2005, PEST, model-independent parameter estimation–User manual: Watermark Numerical Computing, https://pesthomepage.org/documentation ). Parameter estimates were constrained with several types of observation data, including water levels, water level changes, vertical water level differences, drain discharges, change in drain discharges, river seepage, seepage from Lake Lowell, and change in seepage from Lake Lowell. Material properties from the hydrogeologic framework were also used to assign the minimum and maximum values of some parameters. A final parameter realization was reached that minimized residuals between the observed and modelled values for the various observation groups. Mean residuals for the observation groups were 15.4 feet (ft) for water levels, 0.2 ft for water level changes, 19.4 ft for vertical water level differences, −3.9 cubic feet per second (ft 3 /s) for drain discharges, 0.0 ft 3 /s for changes in drain discharge, 45.0 ft 3 /s for river seepage, −40.1 ft 3 /s for Lake Lowell seepage, and 126.3 ft 3 /s for changes in Lake Lowell seepage. The quality of the model’s fit to observations varied spatially, with notable areas of under- or over-simulation of water levels present to the northwest and southwest of Lake Lowell, in the foothills along the eastern model boundary, and near the City of Eagle. Trends were observed in the residuals of many of the observation groups, indicating that the model is missing or not fully reproducing some phenomena that are observed in the system. The TVGWFM can be used as a tool for water resource planning, for understanding the interactions of groundwater and surface water at a basin scale, and for facilitating conjunctive management, but may lack the precision needed for water rights administration at a local scale. Additional sources of uncertainty or limitations of the model are noted. The quantity and spatial distribution of canal seepage and infiltration of irrigation water recharge, the largest sources of recharge to the system, are unknown and approximated indirectly. There is poor understanding of how canal seepage and incidental recharge change as land is converted from agricultural (irrigated) to suburban (semi-irrigated). These uncertainties will affect any scenarios that investigate changes to land use or irrigation practices. Finally, the model has relatively high water-level residuals around and to the southwest of Lake Lowell and should not be used to estimate water level effects in that region. The model was built with multiple, broadly expressed objectives and did not optimize performance for specific uses. However, the model and the tools included in an associated data release provide ample flexibility to improve the model for future uses. Adjustments and improvements could be made by refining the model in an area of interest, collecting additional calibration data, applying more rigorous boundary conditions, or re-estimating model parameters to optimize model performance for a specific model forecast.

Idaho↗

Comparison of nitrate, pesticides, and volatile organic compounds in samples from monitoring and public-supply wells, Kirkwood-Cohansey aquifer system, southern New Jersey

The number and total concentration of volatile organic compounds (VOCs) per sample were significantly greater in water from public-supply wells than in water from shallow and moderate-depth monitoring wells in the surficial Kirkwood-Cohansey aquifer system in the Glassboro area of southern New Jersey. In contrast, concentrations of nitrate (as nitrogen) and the number and total concentration of pesticides per sample were statistically similar in samples from shallow and moderate-depth monitoring wells and those from public-supply wells. VOCs in ground water typically are derived from point sources, which commonly exist in urban areas and which result in spatially variable contaminant concentrations near the water table. Because larger volumes of water are withdrawn from public-supply wells than from monitoring wells, their contributing areas are larger and, therefore, they are more likely to intercept water flowing from VOC point sources. Additionally, public-supply wells intercept flow paths that span a large temporal interval. Public-supply wells in the Glassboro study area withdraw water flowing along short paths, which contains VOCs that recently entered the aquifer system, and water flowing along relatively long paths, which contains VOCs that originated from the degradation of parent compounds or that are associated with past land uses. Because the volume of water withdrawn from monitoring wells is small and because shallow monitoring wells are screened near the water table, they generally intercept only relatively short flow paths. Therefore, samples from these wells represent relatively recent, discrete time intervals and contain both fewer VOCs and a lower total VOC concentration than samples from public-supply wells. Nitrate and pesticides in ground water typically are derived from nonpoint sources, which commonly are found in both agricultural and urban areas and typically result in lowlevel, relatively uniform concentrations near the water table. Because nonpoint sources are diffuse and because processes such as degradation or sorption/dispersion do not occur at rates sufficient to prevent detection of these constituents in parts of the aquifer used for domestic and public supply in the study area, concentrations of nitrate and pesticides and numbers of pesticide compounds are likely to be similar in samples from shallow monitoring wells and samples from public-supply wells. Results of a comparison of (1) the general characteristics of, and water-quality data from, public-supply wells in the Glassboro study area to available data from public-supply wells screened in the Kirkwood-Cohansey aquifer system outside the study area, and (2) land-use settings, soil characteristics, and aquifer properties in and outside the study area indicate that the findings of this study likely are applicable to the entire extent of the Kirkwood- Cohansey aquifer system in southern New Jersey.

New Jersey↗

Simulating groundwater flow in the Mississippi Alluvial Plain with a focus on the Mississippi Delta

The Mississippi Alluvial Plain has become one of the most important agricultural regions in the United States but relies heavily on groundwater for irrigation. On average, more than 12 billion gallons are withdrawn daily from the Mississippi River Valley alluvial aquifer. Declining groundwater levels, especially in the Delta region of northwest Mississippi and the Cache and Grand Prairie regions of eastern Arkansas, have led to concerns about future sustainability. The U.S. Geological Survey Mississippi Alluvial Plain Project is focused on quantifying the groundwater system in the alluvial plain and the response of groundwater resources to future development. A key objective of the project is to provide updated groundwater flow models supported by extensive data collection and analyses. MODFLOW 6, PEST++, and several open-source python packages were used to develop a simplified, faster running version of the Mississippi Embayment Regional Aquifer Study model that can provide boundary conditions for local inset models, including the Mississippi Delta model described in this report. An automated workflow was used for model construction, history matching, and development of baseline future climate scenarios. The models incorporate information from a Soil-Water-Balance code simulation of the terrestrial water balance, metering-based estimates of water use from thousands of wells, measured and estimated streamflow and stages, and the largest airborne electromagnetic survey flown to date in the United States. Baseline scenarios for the Mississippi Delta under potential future climates were constructed using recharge, surface runoff and irrigation pumping forcings from a future version of the Soil-Water-Balance model, driven by downscaled temperature and precipitation output from 10 general circulation model simulations, including high and moderate carbon emissions pathways. Results indicate a complex water balance that varies in time and space in terms of the terrestrial recharge, stream leakage, and regional groundwater flow components, which are affected by seasonal forcings, human activity, and alluvial geomorphology. The general circulation model outputs indicate a continued rise in average temperatures but no clear precipitation trend. Increased crop water demand is anticipated from the higher temperatures, resulting in increased irrigation withdrawals to sustain current levels of irrigated agriculture. Simulated drawdowns in groundwater levels at the mid-21st century vary greatly. Under moderate or wet climate scenarios, and in parts of the aquifer that are well connected to surface water, little to no additional drawdown is anticipated. Under dry or warm scenarios, drawdowns of as much as 10 meters or more are possible in parts of the aquifer that are relatively disconnected from surface water. Under dry or warm scenarios, the portion of the Delta with greater than 60 feet of saturated thickness could be reduced from near 100 percent currently (2018) to 80–90 percent by mid-century. Future simulations with the model could include alternative management scenarios to identify options for improving groundwater sustainability. The automated model construction workflows are designed to facilitate regular updating, making this a “living” framework that the Mississippi Department of Environmental Quality and other stakeholders can use for adaptive management going forward.

Arkansas, Louisiana, Mississippi↗

Infrared remote sensing for monitoring rainfall

Evaluations of thermal infrared satellite data from TIROS-N and the Heat Capacity Mapping Mission (HCMM) showed that rainfall distribution patterns could be reliably detected on images acquired up to at least three days after the event. The temperature relationship decreased eight days after the event when soil variations influenced the signal. A time-series analysis reduced thermal variability normally observed over diverse landscapes and increased the sensitivity of the procedures. The method of repetitive low-resolution thermal observations could be operationally employed over large geographic regions with currently available satellite systems. The results would augment the existing rain gauge stations by increasing the spatial sensitivity and the reliability of detection and mapping individual rainfall events.

Agricultural Water Management↗

Virulence evolution of a salmonid virus following a host jump

Emergent viral diseases remain a critical obstacle to welfare across landscapes and species, encompassing humans, wildlife, and agriculture. Following a jump to a novel host, the severity of disease resulting from infection is a critical determinant of the overall emergent pathogen threat. Conventional wisdom posits that virulence, defined here as host mortality, attenuates to intermediate levels as a pathogen adapts to a novel host, but this is largely based on data from just one system, myxoma virus, which was intentionally introduced as a biocontrol agent in rabbits ( Oryctolagus cuniculus ) in mid-1900s Australia. In this study, we demonstrate that infectious hematopoietic necrosis virus (IHNV), which made a host jump from sockeye salmon ( Oncorhynchus nerka , ancestral host) to rainbow trout ( O. mykiss , novel host), has not conformed to classical theory. We quantified virulence in the ancestral and novel hosts using common garden in vivo experiments with 16 archival IHNV isolates collected from 1972-2017, which span the period from shortly after the host jump and the subsequent 45 years of host adaptation. These virus isolates also represent two distinct phylogenetic genogroups, each associated with either the ancestral or novel host. The experiments were replicated across two research facilities, two challenges dosages, and two temperatures. While isolates from the ancestral genogroup showed no temporal change in virulence in either host, isolates from the novel viral genogroup displayed a significant increase in virulence over time in the novel host. Some possible indication of a virus temperature adaption after the host jump was also present. Potential drivers of virulence evolution are discussed. This represents one of only a handful of systems in which the evolution of increased virulence has been empirically characterized after a host jump and subsequent adaptation. It contributes to a growing body of evidence that contradicts the classical case study of myxoma virus attenuation after adaptation.

PLoS Pathogens↗

Population viability and connectivity of the Louisiana black bear ( Ursus americanus luteolus )

In 1992, the U.S. Fish and Wildlife Service (USFWS) granted Ursus americanus luteolus (Louisiana black bear) threatened status under the U.S. Endangered Species Act of 1973, listing loss and fragmentation of habitat as the primary threats. A study was developed by the U.S. Geological Survey in cooperation with the University of Tennessee, the Louisiana Department of Wildlife and Fisheries, and the USFWS to estimate demographic rates and genetic structure of Louisiana black bear populations; evaluate relations between environmental and anthropogenic factors and demographic, genetic, and movement characteristics of Louisiana black bear populations; and develop data-driven stochastic population projection models to assess long-term persistence of individual subpopulations and the overall black bear population in Louisiana. Data were collected with non-invasive DNA sampling, live capture, winter den visits, and radio monitoring from 2002 to 2012 in the four areas supporting breeding subpopulations in Louisiana: Tensas River Basin (TRB), Upper Atchafalaya River Basin (UARB), Lower Atchafalaya River Basin (LARB), and Three Rivers Complex (TRC). Bears were live trapped and radio collared in the TRB and TRC to estimate survival and reproductive rates, deterministic matrix models were used to estimate asymptotic growth rates, and stochastic population models were used to estimate long-term viability. DNA extracted from hair collected at baited, barbed-wire enclosures in the TRB, UARB, and LARB and capture-mark-recapture (CMR) analysis based on Bayesian hierarchical modeling methods were used to estimate apparent survival ( φ ), per capita recruitment ( γ ), abundance ( N ), realized growth rate ( λ ), and long-term viability. From 2002 to 2012, we radio monitored 86 adult females greater than (>) 2 years old within the TRB, and 43 adult females were monitored in the TRC. The mean annual survival rate estimate ranged from 0.97 to 0.99 for the TRB and from 0.93 to 0.97 for the TRC. Fecundity and yearling recruitment in the TRB were 0.47 and 0.15, respectively, whereas estimates for the TRC were 0.37 and 0.18. Depending on estimated carrying capacity, the strength of the density dependence, level of uncertainty, and the treatment of unresolved signals, persistence probabilities for the TRC subpopulation ranged from 0.295 to 0.999. Estimates of N for females in the TRB ranged from 140 to 163 during 2006–12 when detection heterogeneity was assumed to follow a logistic-normal distribution (Model 1) and from 133 to 158 when a 2-point finite mixture distribution was assumed (Model 2). Annual estimates of γ ranged from 0.00 to 0.16 and from 0 to 0.22, depending on the model, and estimates of φ ranged from 0.87 to 0.93 during that period. In the UARB, estimates of N for females ranged from 25 to 44 during the study period, regardless of heterogeneity model. Estimated γ ranged from 0.00 to 0.41, and φ ranged from 0.88 to 0.90 during that period. Estimated N for females in the LARB was from 78 to 97 from 2010 to 2012 based on Model 1 and from 68 to 84 based on Model 2. Estimates of γ were 0.00 for 2010–11 regardless of heterogeneity model and ranged from 0.24 to 0.31 for 2011–12, depending on the model assumptions. We estimated φ as 0.81 for 2010–11, and from 0.84 to 0.85 for 2011–12, depending on model assumptions. We estimated Φ as 0.81 for 2010–11, ranging and from 0.84 to 0.85 for 2011–12, depending on model assumptions. On the basis of vital rate estimates from Model 1 of the CMR analysis, probability of persistence over 100 years for the TRB population was >0.999, 0.975, and 0.958 for process-only, 50-percent (%) credible interval (CI), and 95% CI projections, respectively. Similarly, the probability of persistence based on Model 2 was >0.999, 0.982, and 0.958. For the UARB, probabilities of persistence based on Model 1 were >0.999, 0.971, and 0.958 for process-only, 50% CI, and 95% CI projections, respectively, and 0.993, 0.929, and 0.849 for Model 2. Using the telemetry and reproductive data from the TRC, probabilities of persistence were greater than or equal to 0.95 only for projections based on the most optimistic set of assumptions. Assuming that the dynamics of the TRB, TRC, and UARB populations were independent and using the most pessimistic population-specific persistence probabilities (that is, 0.958, 0.295, and 0.849, respectively), the overall probability of persistence for bears in that population system was 0.996. Genetic methods were used to estimate interchange and structure between subpopulations in Louisiana and in Minnesota (MINN); Mississippi (MISS); and the White River Basin (WRB), Arkansas. Results from the all-population and the WRB–TRB clustering analyses indicate at least five genetically distinct populations. The genetic clustering and migrant analyses combined with capture data provided direct evidence that interchange has occurred from the WRB to the TRB and MISS, from the TRB to MISS, from the UARB to the TRC, and from the TRC to the TRB. Indirect evidence that interchange occurred from the UARB to the TRC and from the UARB to the TRB by way of the TRC was documented. No evidence was found of interchange from any of the subpopulations to the WRB, UARB, or LARB. From April 2010 to April 2012, global positioning system (GPS) radio collars were placed on 8 female and 23 male bears ranging from 1 to 11 years of age to develop a step-selection function model to predict routes and rates of interchange. For both males and females, the probability of a step being selected increased as the distance to natural land cover and agriculture at the end of the step decreased and as distance from roads at the end of a step increased. Of 4,000 correlated random walks, the least potential interchange was between TRB and TRC and between UARB and LARB, but the relative potential for natural interchange between UARB and TRC was high. The step-selection model predicted that dispersals between the LARB and UARB populations were infrequent but possible for males and nearly nonexistent for females. No evidence of natural female dispersal between subpopulations has been documented thus far, which is also consistent with model predictions.

Louisiana↗

Simulation of groundwater flow and the interaction of groundwater and surface water in the Willamette Basin and Central Willamette subbasin, Oregon

Full appropriation of tributary streamflow during summer, a growing population, and agricultural needs are increasing the demand for groundwater in the Willamette Basin. Greater groundwater use could diminish streamflow and create seasonal and long-term declines in groundwater levels. The U.S. Geological Survey (USGS) and the Oregon Water Resources Department (OWRD) cooperated in a study to develop a conceptual and quantitative understanding of the groundwater-flow system of the Willamette Basin with an emphasis on the Central Willamette subbasin. This final report from the cooperative study describes numerical models of the regional and local groundwater-flow systems and evaluates the effects of pumping on groundwater and surface‑water resources. The models described in this report can be used to evaluate spatial and temporal effects of pumping on groundwater, base flow, and stream capture. The regional model covers about 6,700 square miles of the 12,000-square mile Willamette and Sandy River drainage basins in northwestern Oregon—referred to as the Willamette Basin in this report. The Willamette Basin is a topographic and structural trough that lies between the Coast Range and the Cascade Range and is divided into five sedimentary subbasins underlain and separated by basalts of the Columbia River Basalt Group (Columbia River basalt) that crop out as local uplands. From north to south, these five subbasins are the Portland subbasin, the Tualatin subbasin, the Central Willamette subbasin, the Stayton subbasin, and the Southern Willamette subbasin. Recharge in the Willamette Basin is primarily from precipitation in the uplands of the Cascade Range, Coast Range, and western Cascades areas. Groundwater moves downward and laterally through sedimentary or basalt units until it discharges locally to wells, evapotranspiration, or streams. Mean annual groundwater withdrawal for water years 1995 and 1996 was about 400 cubic feet per second; irrigation withdrawals accounted for about 80 percent of that total. The upper 180 feet of productive aquifers in the Central Willamette and Southern Willamette subbasins produced about 70 percent of the total pumped volume. In this study, the USGS constructed a three-dimensional numerical finite-difference groundwater-flow model of the Willamette Basin representing the six hydrogeologic units, defined in previous investigations, as six model layers. From youngest to oldest, and [generally] uppermost to lowermost they are the: upper sedimentary unit, Willamette silt unit, middle sedimentary unit, lower sedimentary unit, Columbia River basalt unit, and basement confining unit. The high Cascade unit is not included in the groundwater-flow model because it is not present within the model boundaries. Geographic boundaries are simulated as no-flow (no water flowing in or out of the model), except where the Columbia River is simulated as a constant hydraulic head boundary. Streams are designated as head-dependent-flux boundaries, in which the flux depends on the elevation of the stream surface. Groundwater recharge from precipitation was estimated using the Precipitation-Runoff Modeling System (PRMS), a watershed model that accounts for evapotranspiration from the unsaturated zone. Evapotranspiration from the saturated zone was not considered an important component of groundwater discharge. Well pumping was simulated as specified flux and included public supply, irrigation, and industrial pumping. Hydraulic conductivity values were estimated from previous studies through aquifer slug and permeameter tests, specific capacity data, core analysis, and modeling. Upper, middle and lower sedimentary unit horizontal hydraulic conductivity values were differentiated between the Portland subbasin and the Tualatin, Central Willamette, and Southern Willamette subbasins based on preliminary model results.

Oregon↗

Generalized water-table and water-level data at the US Air Force plant 42 and vicinity, Palmdale, California, March-April, 1997

The U.S. Air Force Plant 42 (Plant 42) which is in the Antelope Valley about 1.5 miles northeast of Palmdale and 3 miles southeast of Lancaster in Los Angeles County. Historically, ground water has been the primary source of water owing, in large part, to the scarcity of surface water in the region. Since 1972, supplemental surface water has been imported from the California Water Project to help meet the demand for water. Despite the importation of surface water, ground-water withdrawal for both municipal and agricultural uses is affecting ground-water levels in the vicinity of Plant 42. To better understand the effects of ground-water withdrawal on ground-water levels and movement in the area, the U.S. Geological Survey (USGS), in cooperation with the U.S. Air Force, constructed a generalized water-table-contour map of the aquifer system underlying Plant 42 and the surrounding area.

Water-Resources Investigations Report↗

Spatial and temporal variation of stream chemistry associated with contrasting geology and land-use patterns in the Chesapeake Bay watershed—Summary of results from Smith Creek, Virginia; Upper Chester River, Maryland; Conewago Creek, Pennsylvania; and Difficult Run, Virginia, 2010–2013

Despite widespread and ongoing implementation of conservation practices throughout the Chesapeake Bay watershed, water quality continues to be degraded by excess sediment and nutrient inputs. While the Chesapeake Bay Program has developed and maintains a large-scale and long-term monitoring network to detect improvements in water quality throughout the watershed, fewer resources have been allocated for monitoring smaller watersheds, even though water-quality improvements that may result from the implementation of conservation practices are likely to be first detected at smaller watershed scales. In 2010, the U.S. Geological Survey partnered with the U.S. Environmental Protection Agency and the U.S. Department of Agriculture to initiate water-quality monitoring in four selected small watersheds that were targeted for increased implementation of conservation practices. Smith Creek watershed is an agricultural watershed in the Shenandoah Valley of Virginia that is dominated by cattle and poultry production, and the Upper Chester River watershed is an agricultural watershed on the Eastern Shore of Maryland that is dominated by row-cropping activities. The Conewago Creek watershed is an agricultural watershed in southeastern Pennsylvania that is characterized by mixed agricultural activities. The fourth watershed, Difficult Run, is a suburban watershed in northern Virginia that is dominated by medium density residential development. The objective of this study was to investigate spatial and temporal variations in water chemistry and suspended sediment in these four relatively small watersheds that represent a range of land-use patterns and underlying geology to (1) characterize current water-quality conditions in these watersheds, and (2) identify the dominant sources, sinks, and transport processes in each watershed. The general study design involved two components. The first included intensive routine water-quality monitoring at an existing streamgage within each study area (including continuous water-quality monitoring as well as discrete water-quality sampling) to develop a detailed understanding of the temporal and hydrologic variability in stream chemistry and sediment transport in each watershed. The second component involved extensive water-quality monitoring at various sites throughout each watershed to develop a detailed understanding of spatial patterns. Both components were used to improve understanding of sources and transport processes affecting stream chemistry, including nutrients and suspended sediments, and their implications for detecting long-term trends related to best management practices. This report summarizes the results of monitoring that was performed from April 2010 through September 2013. Individual Small Watershed Summaries Summaries for each of the four small watersheds are presented below. Each watershed has a more descriptive and detailed section in the report, but these summaries may be particularly useful for some watershed managers and stakeholders desiring slightly less technical detail. Smith Creek Smith Creek is a 105.39-mi 2 watershed within the Shenandoah Valley that drains to the North Fork Shenandoah River. The long-term Smith Creek base-flow index is 72.3 percent, indicating that on average, approximately 72 percent of Smith Creek flow was base flow, which suggests that Smith Creek streamflow is dominated by groundwater discharge rather than stormwater runoff. A series of cluster and principal components analyses demonstrated that the majority of the variability in Smith Creek water quality could be attributed to hydrologic and seasonal variability. Statistically significant positive correlations with flow were observed for turbidity, suspended sediments, total nitrogen, ammonium, orthophosphate, iron, total phosphorus, and the ratio of calcium to magnesium. Statistically significant inverse correlations with flow were observed for specific conductance, magnesium, δ 15 N of nitrate, pH, bicarbonate, calcium, and δ 18 O of nitrate. Of particular note, flow and nitrate were not statistically significantly correlated, likely because of the relatively complex concentration-discharge relationship observed in continuous and discrete datasets. Statistically significant seasonal patterns were observed for numerous water-quality constituents: water temperature, turbidity, orthophosphate, total phosphorus, suspended-sediment concentration, and silica were higher during the warm season, but pH, dissolved oxygen, and sulfate were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient loads in Smith Creek using the continuous water-quality monitors. The mean Smith Creek in-stream sediment load was approximately 6,900 tons per year, with nearly 90 percent of the sediment load over the 3-year study period contributed during the eight largest storm events during that period. The Smith Creek total phosphorus load was approximately 21,000 pounds of phosphorus per year, with the majority of the load contributed during stormflow periods, although a substantial phosphorus load still occurs during base-flow conditions. The Smith Creek total nitrogen load was approximately 400,000 pounds per year, with total nitrogen accumulation less dominated by stormflow contributions (as was the case for sediment and total phosphorus) and strongly affected by base-flow export of nitrogen from the basin. Extensive water-quality monitoring throughout the Smith Creek watershed revealed how the complex geology and hydrology interacted to result in variable water chemistry. During relatively dry and low base-flow periods, much of the discharge in Smith Creek was contributed by a single dominant spring—Lacey Spring. During wetter base-flow periods, the flows in Smith Creek were largely generated by a mixture of headwater springs and forested mountain tributaries with very different geochemical composition. The headwater springs generally issued from limestone bedrock and were characterized as having relatively high nitrate, specific conductance, calcium, and magnesium, as well as relatively low concentrations of phosphorus, ammonium, iron, and manganese. The undeveloped, high-gradient, forested mountain sites were generally characterized by low ionic strength waters with low nutrient concentrations. Nitrate isotope data from the limestone springs generally were consistent with manure-derived nitrogen sources (such as cattle and poultry), although the possibility of other mixed sources cannot be excluded. Nitrate isotope data from the undeveloped, high-gradient forested mountain sites were more consistent with nitrogen from undisturbed soils, atmospheric deposition, or nitrogen fixation. Regardless of the nitrogen source, oxygen isotope data indicate that the nitrate was largely a result of nitrification. Land-use data indicate that manure sources of nitrogen dominated watershed nitrogen inputs. Phosphorus sources were less well studied. The presence of a single point-source discharge near the town of New Market contributed the majority of the phosphorus to Smith Creek under base-flow conditions, but nonpoint sources of phosphorus dominated the loading to Smith Creek during stormflow periods. Implementation of conservation practices increased in the Smith Creek watershed during the study period, and even though a broad range of practice types was implemented, the most common practices included stream fencing (for cattle exclusion), the development of nutrient management plans, conservation crop rotation, and the planting of cover crops. While the implementation of these conservation practices is encouraging, results indicate small increases in nitrate concentrations at the streamgage over the last 29 years, concurrent with small decreases in nitrate fluxes. It will likely be years before the cumulative effect of these practices can be detected in the Smith Creek water quality, and the magnitude of the effect of these conservation practices detected in Smith Creek will depend largely on whether nutrient loading (of manure and commercial fertilizer) is reduced over time. Upper Chester River The Upper Chester River watershed includes the 36-square-mile (mi 2 ) watershed area around several nontidal tributaries that drain into the tidal Chester River. The streamgage is on Chesterville Branch, the largest nontidal tributary (approximately 6.12 mi 2 ) and is the site for continuous water-quality monitoring for this project. The base-flow index at Chesterville Branch is about 72 percent and indicates that, as in most of the Coastal Plain, groundwater is the greatest contributor to streamflow. As such, more than 90 percent of the nitrogen in the stream is in the form of nitrate from groundwater. Continuous and discrete data collected at Chesterville Branch show the effects of streamflow and season on water quality. Significantly positive correlations with flow were observed for ammonium, dissolved and total phosphorus, sediment, and turbidity as runoff carried these constituents from the land surface into Chesterville Branch. Other constituents that increased significantly with flow include potassium, sulfate, iron, and manganese, which are likely contributed from near-stream areas and ponds with high organic-matter content. Total nitrogen, pH, and specific conductance, along with chemical constituents associated with groundwater inputs including nitrate, calcium, ratio of calcium to magnesium, silica, bicarbonate, and sodium, were negatively correlated with flow because concentrations of these constituents were diluted by runoff. Seasonal differences in water chemistry, which are most likely related to increased biologic effects on the uptake and release of chemicals in the stream and near-stream areas, also were observed. Water temperature, orthophosphate, δ 15 N of nitrate, bicarbonate, sodium, and the ratio of sodium to chloride were higher during the warm season, and dissolved oxygen, total nitrogen, nitrate, magnesium, sulfate, and manganese were higher during the cool season. Surrogate-regression models developed by using continuous water-quality data showed that the annual sediment load for the 2013 water year was about 2,600 tons, with more than 90 percent of this sediment contributed during two storms. The total phosphorus load in 2013 was about 13,000 pounds with more than 90 percent contributed during the same two storms as sediment. The load of total nitrogen, 140,000 pounds, accumulated steadily throughout the 2013 water year as nitrate in groundwater continuously discharged into the stream. The same two large storms that contributed 90 percent of the suspended-sediment and total phosphorus load only contributed about 20 percent of the annual total nitrogen load. Extensive water-quality monitoring of stream base flow throughout the Upper Chester River watershed identified how differences in land use and hydrogeology affected water chemistry. In parts of the watershed with well-drained soil and thick sandy aquifer sediments, concentrations of nitrate and other chemicals associated with fertilizer and lime application increased in streams as agricultural land use increased. More than 90 percent of the nitrogen in streams from these areas was in the form of nitrate, and concentrations ranged from about 5 milligrams per liter (mg/L) to 8 mg/L as nitrogen in the two largest tributaries. Stream nitrate concentrations were about 1 mg/L as nitrogen where soils were more poorly drained, the surficial aquifer sediments were thinner, and forests and wetlands were more widespread than agriculture. Nitrate isotope data were consistent with inorganic fertilizers ± atmospheric deposition and N 2 fixation as sources of nitrogen, and with nitrification as the dominant nitrate-forming process. Nitrate reduction was indicated by elevated δ 15 N and δ 18 O values in some samples from streams draining watersheds with poorly drained soils. An analysis of land-use data and SPARROW modeling input data attributed almost 90 percent of the nitrogen sources in the Upper Chester River watershed to inorganic fertilizer and fixation of atmospheric nitrogen by legumes, which is in agreement with the isotopic characteristics of nitrate in this watershed. Local sources of manure are limited in this area. Total phosphorus concentrations during base flow ranged from below detection to about 0.2 mg/L. Stream phosphorus concentrations during base flow were generally lower than those measured during storms because most phosphorus transport likely occurs as phosphorus attached to sediment particles during runoff. Because manure is not widely used in this area, the major source of phosphorus is likely fertilizer. The implementation of conservation practices in the Upper Chester River watershed increased substantially during the study period, with a total implementation of 1,194 U.S. Department of Agriculture-compliant practices. The most frequently used practices were oriented towards nutrient and sediment control, including cover crops, nutrient management planning, conservation crop rotation, conservation tillage, and irrigation management. The current Chesapeake Bay model for this area predicts that implementation of best management practices should result in a 13-percent decrease in overall delivery of nitrogen to the Upper Chester River. Because most nitrogen travels through the groundwater system for years to decades before being discharged to streams, the time period of monitoring was not sufficient to see the effects of these practices on water quality. The magnitude of the effect that may eventually be detected will depend on the degree to which nitrate leaching into the groundwater system is reduced over time. Loadings of phosphorus and sediment are primarily transported during large runoff events and are difficult to control and analyze for trends because of their timing and episodic nature. Conewago Creek Conewago Creek has two primary monitoring locations—one near the middle of the 47-mi 2 watershed and the other near the outlet just upstream of the Susquehanna River. The base-flow index was 47.3 percent for 2012–2013, indicating that on average, approximately 53 percent of the streamflow in Conewago Creek exited the watershed as surface flow, which suggests that the stormwater runoff was somewhat greater than groundwater discharge (base flow). A series of cluster and principal components analyses demonstrated that the majority of the variability in the Conewago Creek water quality could be attributed to hydrologic and seasonal variability. Statistically significant positive correlations with flow were observed at both monitoring sites for ammonium, total phosphorus, orthophosphate, iron, and manganese; additionally, at the upstream monitoring station, total nitrogen demonstrated a statistically significant positive correlation with flow. Statistically significant inverse correlations with flow were observed at both sites for water temperature, specific conductance (at the downstream site only), sulfate, chloride, calcium, and magnesium. Statistically significant seasonal patterns were observed for several water-quality constituents. Water temperature, phosphorus (upstream site only), and orthophosphate were higher during the warm season, and nitrate and total nitrogen (upstream site only) were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient load in Conewago Creek by using the continuous water-quality monitors and water-quality samples. Conewago Creek sediment load was approximately 9,900 tons in 2012 and approximately 18,900 tons in 2013, with nearly 80 percent of the sediment load in 2013 contributed by the three largest storm events. Annual total nitrogen loads could not be estimated due to poor model performance. The addition of continued monitoring or a continuously recording nitrate sensor could improve estimates of total nitrogen loads. During 2012 and 2013, phosphorus loads in Conewago Creek were approximately 50,000 pounds in each year. Combining data from one high-flow synoptic sampling with the data from routine sampling revealed how the geology and hydrology interact to result in variable water chemistry throughout the Conewago Creek watershed. The areas above the upstream gage in the headwaters are generally underlain by forested non-carbonate bedrock and are characterized by relatively low nitrate, specific conductance, calcium, and magnesium, as well as relatively low concentrations of phosphorus, ammonium, iron, and manganese. The more developed, agricultural areas below the upstream site were generally characterized by higher ionic strength waters with higher nutrient and metal concentrations. An analysis of land-use data and SPAtially Referenced Regressions On Watershed (SPARROW) modeling data indicates that manure sources of nitrogen dominate the input of nitrogen to the watershed. Implementation of conservation practices increased in the Conewago Creek watershed during the study period, and while a broad range of practice types were implemented, the most common practices included residue and tillage management, cover crops, nutrient management, terracing, and stream fencing (for animal exclusion or bank restoration). While the implementation of these conservation practices is encouraging, the cumulative effects of these practices probably will not be detected in Conewago Creek water quality for several years. The magnitude of the effects of these conservation practices on water quality in Conewago Creek will depend largely on the extent to which nutrient loading (septic, manure, and commercial fertilizer) and sediment-producing activities are reduced over time. Difficult Run The Difficult Run watershed is a 57.82-mi 2 watershed that drains to the Potomac River. The long-term Difficult Run base-flow index (from 1936 to 2010) was 57.9, indicating that approximately 58 percent of streamflow exited the watershed as base flow and 42 percent as stormflow; however, with continued development and urbanization of the watershed, the base-flow index has decreased to 50 percent during the last 20 years. This base-flow index was less than those of the other watersheds evaluated in this study, likely because the Difficult Run watershed largely is underlain by crystalline piedmont metamorphic rocks and has a greater proportion of impervious urban land cover. A series of cluster and principal components analyses indicated that most of the variability in Difficult Run water quality could be attributed to hydrologic variability and seasonality. Statistically significant positive correlations with flow were observed for turbidity, dissolved oxygen, suspended sediments, ammonium, orthophosphate, iron, and total phosphorus. Statistically significant inverse correlations with flow were observed for water temperature, pH, specific conductance, bicarbonate, calcium, magnesium, nitrate, δ 15 N of nitrate, and silica. Statistically significant seasonal patterns were observed for numerous water-quality constituents: water temperature, ammonium, orthophosphate, and δ 15 N of nitrate were higher during the warm season, and dissolved oxygen, nitrate, and manganese were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient loading rates. The Difficult Run sediment load was approximately 8,000 tons per year, with greater than 95 percent of the sediment load in the 2013 water year contributed by the seven largest storm events. The total phosphorus load in Difficult Run was approximately 14,000 pounds of phosphorus per year, with the majority of the load contributed during stormflow periods. The total nitrogen load in Difficult Run is estimated to have been approximately 140,000 pounds per year, with total nitrogen accumulation less dominated by stormflow contributions than that of phosphorus and strongly affected by base-flow export of nitrogen from the basin. Extensive water-quality monitoring throughout the Difficult Run watershed revealed relatively uniform generation of flow per unit of watershed area, as well as spatial variation in water quality that is strongly related to land-use activities. Elevated nitrate concentrations were observed in a subset of monitoring sites that are inversely correlated with population density and positively correlated to the septic system density within each subwatershed. The majority of the elevated nitrate concentrations for these sites are hypothesized to be caused by nitrate leaching from septic systems, more so than homeowner fertilizer usage among these subwatersheds that have lower population densities than other parts of the watershed. Nitrate isotope data, temporal patterns in the water-quality data, mass-balance computations, and a separate land-use analysis all generally indicate that leachate from septic systems was the likely source of the elevated nitrate. Another group of water-quality sites have relatively low nitrogen concentrations, are located in areas that are served by city sewer lines, and have experienced stream restoration activities. A final group of sites drained the areas with the highest imperviousness and had strongly elevated specific conductance, chloride, and sodium, which were likely caused by a combination of road salting and other anthropogenic sources draining these urbanized areas in the watershed. A fourth group of sites represents a mixture of water sources and had water quality similar to that at the Difficult Run streamgage. Analysis of the nitrate isotope data generally indicates a broad range of composition indicative of mixed natural and anthropogenic nitrogen sources. Implementation of conservation practices increased in the Difficult Run watershed during the study period, and while a broad range of practice types was implemented, the most common practices included stream restoration. While the implementation of these conservation practices is encouraging, the cumulative effect of these practices probably will not be detected in Difficult Run water quality for several years.

Maryland, Pennsylvania, Virginia↗

Toward a comprehensive information system to assist invasive species management in Hawaii and Pacific Islands

The need for coordinated regional and global electronic databases to assist prevention, early detection, rapid response, and control of biological invasions is well accepted. The Pacific Basin Information Node (PBIN), a node of the National Biological Information Infrastructure, has been increasingly engaged in the invasive species enterprise since its establishment in 2001. Since this time, PBIN has sought to support frontline efforts at combating invasions, through working with stakeholders in conservation, agriculture, forestry, health, and commerce to support joint information needs. Although initial emphasis has been on Hawaii, cooperative work with other Pacific islands and countries of the Pacific Rim is already underway and planned.

Weed Science↗

Mitigating the effects of landscape development on streams in urbanizing watersheds

This collaborative study examined urbanization and impacts on area streams while using the best available sediment and erosion control (S&EC) practices in developing watersheds in Maryland, United States. During conversion of the agricultural and forested watersheds to urban land use, land surface topography was graded and vegetation was removed creating a high potential for sediment generation and release during storm events. The currently best available S&EC facilities were used during the development process to mitigate storm runoff water quality, quantity, and timing before entering area streams. Detailed Geographic Information System (GIS) maps were created to visualize changing land use and S&EC practices, five temporal collections of LiDAR (light detection and ranging) imagery were used to map the changing landscape topography, and streamflow, physical geomorphology, and habitat data were used to assess the ability of the S&EC facilities to protect receiving streams during development. Despite the use of the best available S&EC facilities, receiving streams experienced altered flow, geomorphology, and decreased biotic community health. These impacts on small streams during watershed development affect sediment and nutrient loads to larger downstream aquatic ecosystems such as the Chesapeake Bay.

Maryl↗

Occurrence of bacteria in Blue Marsh Lake and selected tributaries, Berks County, Pennsylvania: September-October 2001

The Commonwealth of Pennsylvania has water-quality standards that limit the number of specific bacteria in water that is considered safe for recreational use. Bacteria such as fecal streptococci, fecal coliforms, and Escherichia coli (E. coli ) are used to assess recreational water quality because they usually live in the intestines of warm-blooded animals. Fecal indicator bacteria commonly are associated with waterborne disease-causing organisms (pathogens). These indicator bacteria are used routinely as a measure of the quality of water for recreational activities such as swimming, boating, and water skiing. If the indicator bacteria are present, effective measures could be taken to prevent the transmission or epidemic outbreak of waterborne diseases as a result of contamination of these waters from human or animal waste. Blue Marsh Lake is on Tulpehocken Creek in Berks County, Pa., and drains a largely agricultural basin. Land use in the basin is approximately 60 percent cropland, and 85 percent of the farms are livestock and poultry farms. The potential sources of fecal bacteria are: geese that inhabit the recreational areas of the lake, humans that visit the Dry Brooks Day Use Area (swimming area), and farm animals, wastewater facilities, and household septic systems in the basin (bacteria from these sources could enter the lake through tributaries). To meet the recreational water-quality standard, lake water may not have more than 200 colony-forming units (CFU) of fecal coliforms per 100 milliliters (mL). During the week of July 23, 2001, data collected by the U.S. Army Corps of Engineers (USACE) at the swimming area at Blue Marsh Lake showed concentrations of fecal coliforms in the water exceeding the standard. To determine the extent of elevated concentrations of fecal indicator bacteria, further study of the lake and selected tributaries was needed.

Pennsylvania↗

Rio Grande transboundary integrated hydrologic model and water-availability analysis, New Mexico and Texas, United States, and Northern Chihuahua, Mexico

Errata **September 28, 2018: The purpose of a USGS Open-file report (OFR) is dissemination of information that must be released immediately to fill a public need or information that is not sufficiently refined to warrant publication in one of the other USGS series. As part of that refinement process, an error was discovered in one of the input data sets of the Rio Grande Transboundary Integrated Hydrologic Model (RGTIHM) that this OFR was based upon. The error involved the assignment of storage properties to “phantom cells.” Phantom cells are required for most variants of MODFLOW that use a structured finite-difference grid when individual stratigraphic layers are represented as separate layers. Using phantom cells is a common practice that allows separate model layers to be maintained without having to combine stratigraphic layers into equivalent model layers or to use an unstructured grid. Typically, phantom cell horizontal hydraulic conductivities and storage properties are set to a small number and vertical hydraulic conductivities are set to a number large enough to allow vertical flow between the vertically adjacent layers. In the RGTIHM, the specific storage properties of the phantom cells for the upper (RGTIHM layers 3 and 4), middle (RGTIHM layers 5 and 6), and lower (RGTIHM layers 7 and 8) members of the Santa Fe Group were inadvertently assigned a value of 1 feet -1 . The revision of these specific storage values to a small number (1.0 x 10 -09 feet -1 ) required additional trial-and-error model calibration and a new sensitivity analysis. After calibration, the overall model fit remained similar to the fit described in the OFR, but the fit for many individual features such as project water available for diversions at the American Canal and Acequia Madre improved due to the reduction in flow coming from lower layers. Overall, there is still an average net depletion of groundwater flow, and the conclusions of the report are not changed. The revised average annual groundwater flow depletion simulated for the period 1953-2014 is -1,480 acre-feet/year for the entire model region, and -3,660 acre-feet/year for the portion of the model in the United States. The final version of the model will be the basis of the USGS Scientific Investigations Report that will supersede this OFR. An updated Model Archive of RGTIHM is available upon request to the USGS California Water Science Center. The corrected version of the model WAS the basis for the USGS Scientific Investigations Report that SUPERSEDED this Open-File Report.** Abstract Changes in population, agricultural development and practices (including shifts to more water-intensive crops), and climate variability are increasing demands on available water resources, particularly groundwater, in one of the most productive agricultural regions in the Southwest—the Rincon and Mesilla Valley parts of Rio Grande Valley, Doña Ana and Sierra Counties, New Mexico, and El Paso County, Texas. The goal of this study was to produce an integrated hydrological simulation model to help evaluate water-management strategies, including conjunctive use of surface water and groundwater for historical conditions, and to support long-term planning for the Rio Grande Project. This report describes model construction and applications by the U.S. Geological Survey, working in cooperation and collaboration with the Bureau of Reclamation. This model, the Rio Grande Transboundary Integrated Hydrologic Model, simulates the most important natural and human components of the hydrologic system, including selected components related to variations in climate, thereby providing a reliable assessment of surface-water and groundwater conditions and processes that can inform water users and help improve planning for future conditions and sustained operations of the Rio Grande Project (RGP) by the Bureau of Reclamation. Model development included a revision of the conceptual model of the flow system, construction of a Transboundary Rio Grande Watershed Model (TRGWM) water-balance model using the Basin Characterization Model (BCM), and construction of an integrated hydrologic flow model with MODFLOW-One-Water Hydrologic Flow Model (referred to as One Water). The hydrologic models were developed for and calibrated to historical conditions of water and land use, and parameters were adjusted so that simulated values closely matched available measurements (calibration). The calibrated model was then used to assess the use and movement of water in the Rincon Valley, Mesilla Basin, and northern part of the Conejos-Médanos Basin, with the entire region referred to as the “Transboundary Rio Grande” or TRG. These tools provide a means to understand hydrologic system response to the evolution of water use in the region, its availability, and potential operational constraints of the RGP. The conceptual model identified surface-water and groundwater inflows and outflows that included the movement and use of water both in natural and in anthropogenic systems. The groundwater-flow system is characterized by a layered geologic sedimentary sequence combined with the effects of groundwater pumping, operation of the RGP, natural runoff and recharge, and the application of irrigation water at the land surface that is captured and reused in an extensive network of canals and drains as part of the conjunctive use of water in the region. Historical groundwater-level fluctuations followed a cyclic pattern that were aligned with climate cycles, which collectively resulted in alternating periods of wet or dry years. Periods of drought that persisted for one or more years are associated with low surface-water availability that resulted in higher rates of groundwater-level decline. Rates of groundwater-level decline also increased during periods of agricultural intensification, which necessitated increasing use of groundwater as a source of irrigation water. Agriculture in the area was initially dominated by alfalfa and cotton, but since 1970 more water-intensive pecan orchards and vegetable production have become more common. Groundwater levels substantially declined in subregions where drier climate combined with increased demand, resulting in periods of reduced streamflows. Most of the groundwater was recharged in the Rio Grande Valley floor, and most of the pumpage and aquifer storage depletion was in Mesilla Basin agricultural subregions. A cyclic imbalance between inflows and outflows resulted in the modeled cyclic depletion (groundwater withdrawals in excess of natural recharge) of the groundwater basin during the 75-year simulation period of 1940–2014. Changes in groundwater storage can vary considerably from year to year, depending on land use, pumpage, and climate conditions. Climatic drivers of wet and dry years can greatly affect all inflows, outflows, and water use. Although streamflow and, to a minor extent, precipitation during inter-decadal wet-year periods replenished the groundwater historically, contemporary water use and storage depletion could have reduced the effects of these major recharge events. The average net groundwater flow-rate deficit for 1953–2014 was estimated to be about 8,990 acre-feet per year.

New Mexico, Northern Chihuahua, Texas↗