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USGS2008

Modeling axisymmetric flow and transport

Unmodified versions of common computer programs such as MODFLOW, MT3DMS, and SEAWAT that use Cartesian geometry can accurately simulate axially symmetric ground water flow and solute transport. Axisymmetric flow and transport are simulated by adjusting several input parameters to account for the increase in flow area with radial distance from the injection or extraction well. Logarithmic weighting of interblock transmissivity, a standard option in MODFLOW, can be used for axisymmetric models to represent the linear change in hydraulic conductance within a single finite-difference cell. Results from three test problems (ground water extraction, an aquifer push-pull test, and upconing of saline water into an extraction well) show good agreement with analytical solutions or with results from other numerical models designed specifically to simulate the axisymmetric geometry. Axisymmetric models are not commonly used but can offer an efficient alternative to full three-dimensional models, provided the assumption of axial symmetry can be justified. For the upconing problem, the axisymmetric model was more than 1000 times faster than an equivalent three-dimensional model. Computational gains with the axisymmetric models may be useful for quickly determining appropriate levels of grid resolution for three-dimensional models and for estimating aquifer parameters from field tests.

Ground Water↗

USGS2010

Solute and heat transport model of the Henry and Hilleke laboratory experiment

SEAWAT is a coupled version of MODFLOW and MT3DMS designed to simulate variable-density ground water flow and solute transport. The most recent version of SEAWAT, called SEAWAT Version 4, includes new capabilities to represent simultaneous multispecies solute and heat transport. To test the new features in SEAWAT, the laboratory experiment of Henry and Hilleke (1972) was simulated. Henry and Hilleke used warm fresh water to recharge a large sand-filled glass tank. A cold salt water boundary was represented on one side. Adjustable heating pads were used to heat the bottom and left sides of the tank. In the laboratory experiment, Henry and Hilleke observed both salt water and fresh water flow systems separated by a narrow transition zone. After minor tuning of several input parameters with a parameter estimation program, results from the SEAWAT simulation show good agreement with the experiment. SEAWAT results suggest that heat loss to the room was more than expected by Henry and Hilleke, and that multiple thermal convection cells are the likely cause of the widened transition zone near the hot end of the tank. Other computer programs with similar capabilities may benefit from benchmark testing with the Henry and Hilleke laboratory experiment. Journal Compilation ?? 2009 National Ground Water Association.

Ground Water↗

USGS2009

Representing pump-capacity relations in groundwater simulation models

The yield (or discharge) of constant-speed pumps varies with the total dynamic head (or lift) against which the pump is discharging. The variation in yield over the operating range of the pump may be substantial. In groundwater simulations that are used for management evaluations or other purposes, where predictive accuracy depends on the reliability of future discharge estimates, model reliability may be enhanced by including the effects of head-capacity (or pump-capacity) relations on the discharge from the well. A relatively simple algorithm has been incorporated into the widely used MODFLOW groundwater flow model that allows a model user to specify head-capacity curves. The algorithm causes the model to automatically adjust the pumping rate each time step to account for the effect of drawdown in the cell and changing lift, and will shut the pump off if lift exceeds a critical value. The algorithm is available as part of a new multinode well package (MNW2) for MODFLOW.

Ground Water↗

USGS2010

Viruses and bacteria in karst and fractured rock aquifers in east Tennessee, USA

A survey of enteric viruses and indicator bacteria was carried out in eight community water supply sources (four wells and four springs) in East Tennessee. Seven sites derived their water from carbonate aquifers and one from fractured sandstone. Four of the sites were deemed "low-risk" based on prior monitoring of fecal indicators and factors such as presence of thick layers of overlying sediments. The remaining sites were deemed "high-risk." Enteric viruses (enterovirus and reovirus) were detected by cell culture at least once in seven of the eight wells or springs including all but one of the four low-risk sites. Viral RNA, however, was not detected in any of the samples by reverse transcription-polymerase chain reaction. Conventional indicators of microbial contamination (Escherichia coli and total coliform bacteria) were detected together with culturable viruses in seven of nine virus positive samples. Bacteroides, an alternative fecal indicator which has not previously been used in groundwater investigations, was also detected in all but one of the samples containing E. coli or total coliform bacteria, as well as in one sample where viruses were present in the absence of other bacterial indicators. The study highlights some of the challenges involved in surveys of virus occurrence and indicates that culturable enteric viruses in East Tennessee karst aquifers may be more widespread than previously observed in studies of karst aquifers in Pennsylvania (8%), the Ozark region of Missouri (< 1%), or several other states covered in a national microbial water quality survey conducted by the U.S. Environmental Protection Agency (43%). Copyright ?? 2010 The Author(s). Journal compilation ?? 2010 National Ground Water Association.

Ground Water↗

USGS2011

Evaluation of MODFLOW-LGR in connection with a synthetic regional-scale model

This work studies costs and benefits of utilizing local‐grid refinement (LGR) as implemented in MODFLOW‐LGR to simulate groundwater flow in a buried tunnel valley interacting with a regional aquifer. Two alternative LGR methods were used: the shared‐node (SN) method and the ghost‐node (GN) method. To conserve flows the SN method requires correction of sources and sinks in cells at the refined/coarse‐grid interface. We found that the optimal correction method is case dependent and difficult to identify in practice. However, the results showed little difference and suggest that identifying the optimal method was of minor importance in our case. The GN method does not require corrections at the models' interface, and it uses a simpler head interpolation scheme than the SN method. The simpler scheme is faster but less accurate so that more iterations may be necessary. However, the GN method solved our flow problem more efficiently than the SN method. The MODFLOW‐LGR results were compared with the results obtained using a globally coarse (GC) grid. The LGR simulations required one to two orders of magnitude longer run times than the GC model. However, the improvements of the numerical resolution around the buried valley substantially increased the accuracy of simulated heads and flows compared with the GC simulation. Accuracy further increased locally around the valley flanks when improving the geological resolution using the refined grid. Finally, comparing MODFLOW‐LGR simulation with a globally refined (GR) grid showed that the refinement proportion of the model should not exceed 10% to 15% in order to secure method efficiency.

Ground Water↗

USGS2011

Dissolved oxygen as an indicator of bioavailable dissolved organic carbon in groundwater

Concentrations of dissolved oxygen (DO) plotted vs. dissolved organic carbon (DOC) in groundwater samples taken from a coastal plain aquifer of South Carolina (SC) showed a statistically significant hyperbolic relationship. In contrast, DO-DOC plots of groundwater samples taken from the eastern San Joaquin Valley of California (CA) showed a random scatter. It was hypothesized that differences in the bioavailability of naturally occurring DOC might contribute to these observations. This hypothesis was examined by comparing nine different biochemical indicators of DOC bioavailability in groundwater sampled from these two systems. Concentrations of DOC, total hydrolysable neutral sugars (THNS), total hydrolysable amino acids (THAA), mole% glycine of THAA, initial bacterial cell counts, bacterial growth rates, and carbon dioxide production/consumption were greater in SC samples relative to CA samples. In contrast, the mole% glucose of THNS and the aromaticity (SUVA 254 ) of DOC was greater in CA samples. Each of these indicator parameters were observed to change with depth in the SC system in a manner consistent with active biodegradation. These results are uniformly consistent with the hypothesis that the bioavailability of DOC is greater in SC relative to CA groundwater samples. This, in turn, suggests that the presence/absence of a hyperbolic DO-DOC relationship may be a qualitative indicator of relative DOC bioavailability in groundwater systems.

South Carolina↗

USGS2007

Field methods for measurement of ground water redox chemical parameters

An inexpensive, versatile, and portable system is presented, which facilitates rapid field determinations of redox potentials, pH, conductivity, ferrous and total iron, nitrite, specific conductance, dissolved oxygen, and temperature. Accuracy is facilitated by on‐site measurements of most parameters using specially constructed flow‐through cells and, for several analyses, sealed reagent ampoules, which can be broken and developed inside a flowing stream of ground water. Coupled with laboratory analyses of more stable ground water parameters, this system can provide accurate and relatively inexpensive determinations of redox conditions in ground water.

Groundwater Monitoring & Remediation↗

USGS2007

Verification of the Rhea-orographic-precipitation model

ABSTRACT: Observed April 1 snowpack accumulations within and near the Gunnison River basin in southwestern Colorado are compared with simulations from the Rhea-orographic-precipitation model to determine if the model simulates reliable magnitudes and temporal and spatial variability in winter precipitation for the basin. Twenty simulations of the Rhea model were performed using‘optimal’parameter sets determined for 10-kilometer (km) grids (10-km by 10-km grid cells) through stochastic calibration. Comparisons of Rhea-model simulations of winter precipitation with April 1 snowpack accumulations at 32 snowcourse stations were performed for the years 1972–1990. For most stations and most years the Rhea model reliably simulates the temporal and spatial variability in April 1 snowpack accumulations. However, in general, the Rhea-model underestimates April 1 snowpack accumulations in the Gunnison River basin area, and the underestimation is greatest for locations that receive the largest amount of snow. A significant portion of the error in Rhea-model simulations is due to the calibration of the Rhea model using gauge-catch precipitation measurements which can be as much as 50 percent below actual snowfall accumulations. Additional error in the Rhea-model simulations is a result of the comparison of gridded precipitation values to observed values measured at points.

Journal of the American Water Resources Associatio↗

USGS2008

Global daily reference evapotranspiration modeling and evaluation

Accurate and reliable evapotranspiration (ET) datasets are crucial in regional water and energy balance studies. Due to the complex instrumentation requirements, actual ET values are generally estimated from reference ET values by adjustment factors using coefficients for water stress and vegetation conditions, commonly referred to as crop coefficients. Until recently, the modeling of reference ET has been solely based on important weather variables collected from weather stations that are generally located in selected agro-climatic locations. Since 2001, the National Oceanic and Atmospheric Administration’s Global Data Assimilation System (GDAS) has been producing six-hourly climate parameter datasets that are used to calculate daily reference ET for the whole globe at 1-degree spatial resolution. The U.S. Geological Survey Center for Earth Resources Observation and Science has been producing daily reference ET (ETo) since 2001, and it has been used on a variety of operational hydrological models for drought and streamflow monitoring all over the world. With the increasing availability of local station-based reference ET estimates, we evaluated the GDAS-based reference ET estimates using data from the California Irrigation Management Information System (CIMIS). Daily CIMIS reference ET estimates from 85 stations were compared with GDAS-based reference ET at different spatial and temporal scales using five-year daily data from 2002 through 2006. Despite the large difference in spatial scale (point vs . ∼100 km grid cell) between the two datasets, the correlations between station-based ET and GDAS-ET were very high, exceeding 0.97 on a daily basis to more than 0.99 on time scales of more than 10 days. Both the temporal and spatial correspondences in trend/pattern and magnitudes between the two datasets were satisfactory, suggesting the reliability of using GDAS parameter-based reference ET for regional water and energy balance studies in many parts of the world. While the study revealed the potential of GDAS ETo for large-scale hydrological applications, site-specific use of GDAS ETo in complex hydro-climatic regions such as coastal areas and rugged terrain may require the application of bias correction and/or disaggregation of the GDAS ETo using downscaling techniques.

Journal of the American Water Resources Associatio↗

USGS2008

A fully distributed implementation of mean annual streamflow regional regression equations

Estimates of mean annual streamflow are needed for a variety of hydrologic assessments. Away from gage locations, regional regression equations that are a function of upstream area, precipitation, and temperature are commonly used. Geographic information systems technology has facilitated their use for projects, but traditional approaches using the polygon overlay operator have been too inefficient for national scale applications. As an alternative, the Elevation Derivatives for National Applications (EDNA) database was used as a framework for a fully distributed implementation of mean annual streamflow regional regression equations. The raster “flow accumulation” operator was used to efficiently achieve spatially continuous parameterization of the equations for every 30 m grid cell of the conterminous United States (U.S.). Results were confirmed by comparing with measured flows at stations of the Hydro-Climatic Data Network, and their applications value demonstrated in the development of a national geospatial hydropower assessment. Interactive tools at the EDNA website make possible the fast and efficient query of mean annual streamflow for any location in the conterminous U.S., providing a valuable complement to other national initiatives (StreamStats and the National Hydrography Dataset Plus).

Journal of the American Water Resources Associatio↗

USGS2009

Hematology of healthy Florida manatees (Trichechus manatus)

Background: Hematologic analysis is an important tool in evaluating the general health status of free-ranging manatees and in the diagnosis and monitoring of rehabilitating animals. Objectives: The purpose of this study was to evaluate diagnostically important hematologic analytes in healthy manatees (Trichechus manatus) and to assess variations with respect to location (free ranging vs captive), age class (small calves, large calves, subadults, and adults), and gender. Methods: Blood was collected from 55 free-ranging and 63 captive healthy manatees. Most analytes were measured using a CELL-DYN 3500R; automated reticulocytes were measured with an ADVIA 120. Standard manual methods were used for differential leukocyte counts, reticulocyte and Heinz body counts, and plasma protein and fibrinogen concentrations. Results: Rouleaux, slight polychromasia, stomatocytosis, and low numbers of schistocytes and nucleated RBCs (NRBCs) were seen often in stained blood films. Manual reticulocyte counts were higher than automated reticulocyte counts. Heinz bodies were present in erythrocytes of most manatees. Compared with free-ranging manatees, captive animals had slightly lower MCV, MCH, and eosinophil counts and slightly higher heterophil and NRBC counts, and fibrinogen concentration. Total leukocyte, heterophil, and monocyte counts tended to be lower in adults than in younger animals. Small calves tended to have higher reticulocyte counts and NRBC counts than older animals. Conclusions: Hematologic findings were generally similar between captive and free-ranging manatees. Higher manual reticulocyte counts suggest the ADVIA detects only reticulocytes containing large amounts of RNA. Higher reticulocyte and NRBC counts in young calves probably reflect an increased rate of erythropoiesis compared with older animals. ?? 2009 American Society for Veterinary Clinical Pathology.

Veterinary Clinical Pathology↗

USGS2016

Natural inactivation of Escherichia coli in anoxic and reduced groundwater

Aims Inactivation rates of E. coli in groundwater have most often been determined in aerobic and oxidized systems. This study examined E. coli inactivation rates in anaerobic and extremely reduced groundwater systems that have been identified as recharge zones. Methods and Results Groundwater from six artesian wells was diverted to above ground, flow through mesocosms that contained laboratory grown E. coli in diffusion chambers. All groundwater was anaerobic and extremely reduced (ORP < - 300 mV). Cells were plated onto mTEC agar during 21 day incubation periods. All data fit a bi-phasic inactivation model, with > 95% of the E. coli population being inactivated < 11.0 hrs (mean k = 0.488± 0.188 h −1 ). Conclusions The groundwater geochemical conditions enhanced the inactivation of E. coli to rates approximately 21-fold greater than previously published inactivation rate in groundwater (mean k = 0.023 ± 0.030 h −1 ). Also, mTEC agar inhibits E. coli growth following exposure to anaerobic and reduced groundwater. Significance and Impact of the Study Aquifer recharge zones with geochemical characteristics observed in this study complement above ground engineered processes (e.g., filtration, disinfection), while increasing the overall indicator microorganism log-reduction rate of a facility.

Journal of Applied Microbiology↗

USGS2014

Evidence against a Pleistocene desert refugium in the Lower Colorado River Basin

Aim The absence of Sonoran Desert plants in late Pleistocene-aged packrat middens has led to speculation that they survived glacial episodes either in refugia as intact associations (Clementsian community concept) or in dry microsites within chaparral or woodland according to individualistic species responses (Gleasonian community concept). To test these hypotheses, we developed a midden record from one likely refugium in north-eastern Baja California, Mexico. We also measured stomatal guard cell size in fossil leaves to further evaluate site-level individualistic responses of Larrea tridentata (creosote bush) ploidy races to climatic changes, including monsoonal history, over the late Quaternary. Location Sierra Juárez, Lower Colorado River Basin, north-eastern Baja California, Mexico. Methods Packrat ( Neotoma ) middens were collected from <300 m elevation on the eastern piedmont of the Sierra Juárez. Plant macrofossils and pollen were analysed from 50 dated middens, including determination of Larrea tridentata ploidy races. Results Pleistocene middens dating back to >55,000 cal. yr BP contained a mix of extralocal species characteristic of chaparral and pinyon–juniper–oak woodland, along with some modern desert elements. Many other desert taxa were absent during the Pleistocene, although most had arrived by the beginning of the Holocene 11,700 years ago. Main conclusions The assemblage of chaparral, woodland and select desert elements refutes the hypothesis that the Lower Colorado River Basin served as a late Pleistocene refugium for Sonoran Desert flora. The rapid arrival of most missing desert species by the early Holocene suggests they did not have far to migrate. They probably survived the last glacial period as smaller, disparate populations in dry microsites within chaparral and pinyon–juniper–oak woodlands. Diploid and tetraploid races of Larrea tridentata were present during the Pleistocene, but hexaploids did not appear until the mid-Holocene. This demonstrates that individualistic responses to climate involved genetic variants, in this case cytotypes, and not just species.

Baja California↗

USGS2015

Piscine reovirus, but not Jaundice Syndrome, was transmissible to Chinook Salmon, Oncorhynchus tshawytscha (Walbaum), Sockeye Salmon, Oncorhynchus nerka (Walbaum), and Atlantic Salmon, Salmo salar L.

A Jaundice Syndrome occurs sporadically among sea-pen-farmed Chinook Salmon in British Columbia, the westernmost province of Canada. Affected salmon are easily identified by a distinctive yellow discolouration of the abdominal and periorbital regions. Through traditional diagnostics, no bacterial or viral agents were cultured from tissues of jaundiced Chinook Salmon; however, piscine reovirus (PRV) was identified via RT-rPCR in all 10 affected fish sampled. By histopathology, Jaundice Syndrome is an acute to peracute systemic disease, and the time from first clinical signs to death is likely <48 h; renal tubular epithelial cell necrosis is the most consistent lesion. In an infectivity trial, Chinook Salmon, Sockeye Salmon and Atlantic Salmon, intraperitoneally inoculated with a PRV-positive organ homogenate from jaundiced Chinook Salmon, developed no gross or microscopic evidence of jaundice despite persistence of PRV for the 5-month holding period. The results from this study demonstrate that the Jaundice Syndrome was not transmissible by injection of material from infected fish and that PRV was not the sole aetiological factor for the condition. Additionally, these findings showed the Pacific coast strain of PRV, while transmissible, was of low pathogenicity for Atlantic Salmon, Chinook Salmon and Sockeye Salmon.

British Columbia↗

USGS2026

Melanoma and other melanistic lesions in brown bullhead Ameiurus nebulosus from waterbodies in the northeastern United States and Canada: Identification of risk factors

Melanistic lesions, including non-raised black areas due to proliferations of melanocytes and melanomacrophages in the dermis and epidermis, as well as raised black areas consistent with melanoma, are described in brown bullhead (BBH) Ameiurus nebulosus from three water bodies in the northeastern United States and Quebec, Canada. First observed in the Vermont portion of Lake Memphremagog, Vermont, USA and Quebec, Canada, the prevalence of melanistic lesions during 2014–2020 was greater than 30% in BBH 200 mm and longer. In 2023, seven sites throughout the lake were assessed, and prevalence ranged from 18% to 42%. In Hermon Pond, Maine, the prevalence was 29% in 2024, and in Village Pond, New Hampshire, lesions occurred in 22% of BBH in 2025. Compared to skin from visibly normal BBH, skin with melanistic lesions had significantly higher concentrations of seven metals, including arsenic, a known carcinogen and zinc. Lesions associated with oxidative damage, such as the accumulation of ceroid/lipofuscin, were also observed in the gill, spleen and kidney tissue of both affected and visibly normal BBH. The progression of lesions, observed by histopathology, ranged from inflammation, signs of oxidative damage, proliferation and necrosis of club cells, and the presence of melanomacrophages and melanocytes in the epidermis to invasive melanoma and suggests chronic exposure of BBH to environmental initiators and promoters of carcinogenesis.

New Hampshire, New York, Quebec, Vermont↗

USGS2022

Streamlined approach for assessing embedded consumption of lithium and cobalt in the United States

In today's complex global supply chains, time and data intensive analyses are required to understand global flows of mineral commodities from mine to consumer, particularly for mineral commodities in products (electronics, automobiles, etc.) that contain multiple parts with many mineral commodities. National and regional analyses require additional time and data to incorporate international trade flows. However, data limitations and time constraints often prohibit global and national material flow analyses for minor metals. Here we present a methodological approach to circumvent these constraints by utilizing readily available industry-level global data from the United Nations Statistics Division and national industrial data to estimate total requirements for a mineral commodity. We apply this approach to lithium and cobalt use in the United States for the year 2018 and distinguish between apparent raw material consumption versus inferred embedded consumption of lithium and cobalt materials in all forms. The results show that more than half of the United States’ total requirements for both lithium and cobalt is in parts and products that were manufactured outside the United States. In large part, this is due to limited US manufacturing capability for lithium-ion battery materials and cells and the United States’ high import reliance for electronics that use those batteries.

Journal of Industrial Ecology↗

USGS2019

Temperature mediates secondary dormancy in resting cysts of Pyrodinium bahamense (Dinophyceae)

High‐biomass blooms of the toxic dinoflagellate Pyrodinium bahamense occur most summers in Tampa Bay, Florida, USA, posing a recurring threat to ecosystem health. Like many dinoflagellates, P. bahamense forms immobile resting cysts that can be deposited on the seafloor—creating a seed bank that can retain the organism within the ecosystem and initiate future blooms when cysts germinate. In this study, we examined changes in the dormancy status of cysts collected from Tampa Bay and applied lessons from plant ecology to explore dormancy controls. Pyrodinium bahamense cysts incubated immediately after field collection displayed a seasonal pattern in dormancy and germination that matched the pattern of cell abundance in the water column. Newly deposited (surface) cysts and older (buried) cysts exhibited similar germination patterns, suggesting that a common mechanism regulates dormancy expression in new and mature cysts. Extended cool‐ and warm‐temperature conditioning of field‐collected cysts altered the cycle of dormancy compared with that of cysts in nature, with the duration of cool temperature exposure being the best predictor of when cysts emerged from dormancy. Extended warm conditioning, on the other hand, elicited a return to dormancy, or secondary dormancy, in nondormant cysts. These results directly demonstrate environmental induction of secondary dormancy in dinoflagellates—a mechanism common and thoroughly documented in higher plants with seasonal growth cycles. Our findings support the hypothesis that a seasonal cycle in cyst germination drives P. bahamense bloom periodicity in Tampa Bay and point to environmentally induced secondary dormancy as an important regulatory factor of that cycle.

Florida↗

USGS2022

Bet-hedging and best-bet strategies shape seed dormancy

Seed dormancy (i.e. delayed germination even when conditions are favourable) is a key plant characteristic that occurs among many species worldwide. But, what selective pressures led to seed dormancy? A recent study provides a major analysis of the factors driving this trait at the global scale (Zhang et al ., 2022 ). Using c. 12 000 species and 10 million records across the globe, they conclude that dormancy is a strategy for plants living under ‘seasonal/unpredictable’ environments; and suggest that bet-hedging could be the major mechanism behind the pattern. To reach their conclusions the authors relate the proportion of species with dormant seeds in a grid-cell global map against climate variables related to annual precipitation, temperature and seasonality. Then they showed that the most significant variables were those related to climate seasonality that they equate with unpredictable climates (although seasonal climates usually are highly predictable in their seasonal cycles).

New Phytologist↗