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USGS2000

Assessing the Kansas water-level monitoring program: An example of the application of classical statistics to a geological problem

Geologists may feel that geological data are not amenable to statistical analysis, or at best require specialized approaches such as nonparametric statistics and geostatistics. However, there are many circumstances, particularly in systematic studies conducted for environmental or regulatory purposes, where traditional parametric statistical procedures can be beneficial. An example is the application of analysis of variance to data collected in an annual program of measuring groundwater levels in Kansas. Influences such as well conditions, operator effects, and use of the water can be assessed and wells that yield less reliable measurements can be identified. Such statistical studies have resulted in yearly improvements in the quality and reliability of the collected hydrologic data. Similar benefits may be achieved in other geological studies by the appropriate use of classical statistical tools.

The Compass: Earth Science Journal of Sigma Gamma ↗

USGS2024

Influence of irrigation water and soil on annual mercury dynamics in Sacramento Valley rice fields

Methylmercury (MeHg) is a human and environmental toxin produced in flooded soils. Little is known about MeHg in rice ( Oryza Sativa L.) fields in Sacramento Valley, California. The objectives of this study were to quantify mercury fractions in irrigation water and within rice fields and to determine their mercury pools in surface water, soil, and grain. Soil, grain, and surface water (dissolved and particulate) MeHg and total mercury (THg) were monitored in six commercial rice fields throughout a winter fallow season and subsequent growing season. Both dissolved and particulate mercury fractions were higher in fallow season rice field water. Total suspended solids and particulate mercury concentrations were positively correlated ( r = 0.99 and 0.98 for THg and MeHg, respectively), suggesting that soil MeHg was suspended in the water column and potentially exported. Dissolved THg and MeHg concentrations were positively correlated with absorbance at 254 nm ( r = 0.47 and 0.58, respectively) in fallow season field water. In the growing season, fields with higher irrigation water MeHg concentrations (due to recycled water use) had elevated field-water MeHg ( r = 0.86) and grain MeHg concentrations ( r = 0.96). Based on a mass balance analysis, soil mercury pools were orders of magnitude larger than surface water or grain mercury pools; however, fallow season drainage and grain harvest were the primary pathways for MeHg export. Based on these findings, reducing (1) discharge when water is turbid, (2) straw inputs, and (3) use of recycled irrigation water could help reduce mercury exports in rice field drainage water.

California↗

USGS2015

U.S. recreational water quality criteria: a vision for the future

This manuscript evaluates the U.S. Recreational Water Quality Criteria (RWQC) of 2012, based upon discussions during a conference held 11–13 March 2013, in Honolulu, Hawaii. The RWQC of 2012 did not meet expectations among the research community because key recommended studies were not completed, new data to assess risks to bathers exposed to non-point sources of fecal indicator bacteria (FIB) were not developed, and the 2012 RWQC did not show marked improvements in strategies for assessing health risks for bathers using all types of recreational waters. The development of the 2012 RWQC was limited in scope because the epidemiologic studies at beach sites were restricted to beaches with point sources of pollution and water samples were monitored for only enterococci. The vision for the future is development of effective RWQC guidelines based on epidemiologic and quantitative microbial risk assessment (QMRA) studies for sewage specific markers, as well as human enteric pathogens so that health risks for bathers at all recreational waters can be determined. The 2012 RWQC introduced a program for states and tribes to develop site-specific water quality criteria, and in theory this approach can be used to address the limitations associated with the measurements of the traditional FIB.

International Journal of Environmental Research an↗

USGS2017

The Bayesian group lasso for confounded spatial data

Generalized linear mixed models for spatial processes are widely used in applied statistics. In many applications of the spatial generalized linear mixed model (SGLMM), the goal is to obtain inference about regression coefficients while achieving optimal predictive ability. When implementing the SGLMM, multicollinearity among covariates and the spatial random effects can make computation challenging and influence inference. We present a Bayesian group lasso prior with a single tuning parameter that can be chosen to optimize predictive ability of the SGLMM and jointly regularize the regression coefficients and spatial random effect. We implement the group lasso SGLMM using efficient Markov chain Monte Carlo (MCMC) algorithms and demonstrate how multicollinearity among covariates and the spatial random effect can be monitored as a derived quantity. To test our method, we compared several parameterizations of the SGLMM using simulated data and two examples from plant ecology and disease ecology. In all examples, problematic levels multicollinearity occurred and influenced sampling efficiency and inference. We found that the group lasso prior resulted in roughly twice the effective sample size for MCMC samples of regression coefficients and can have higher and less variable predictive accuracy based on out-of-sample data when compared to the standard SGLMM.

Journal of Agricultural, Biological, and Environme↗

USGS2007

Evaluation of the status of anurans on a refuge in suburban Maryland

Because many anurans have well-defined breeding seasons and male anurans produce loud advertisement calls, surveys of these breeding choruses are believed to provide a dependable means of monitoring population trends. The Patuxent Research Refuge initiated such a calling survey in the spring of 1997, which uses volunteers to collect anuran (frog and toad) calling survey data. The primary goal of initiating the calling surveys at the Patuxent Refuge was to obtain baseline information on anuran populations, such as species occurrence, frequency of occurrence, and relative abundance over time. In this paper, we used the calling survey data to develop models for the "proportion of area occupied" by individual anuran species, a method in which analysis is focused on the proportion of sites that are occupied by a species, instead of the number of individuals present in the population. This type of analysis is ideal for use in large-scale monitoring programs focused on species that are difficult to count, such as anurans or birds. We considered models for proportion of area occupied that allow for imperfect detection (that is, a species may be present but go undetected during sampling) by incorporating parameters that describe detection probability and the response of detection probability to various environmental and sampling covariates. Our results indicate that anuran populations on the Patuxent Research Refuge have high rates of occupancy compared to areas nearby and that extinction and colonization rates are stable. The potential uses for "proportion of area occupied" analyses are far-reaching and will allow for more accurate quantification of data and better-informed management decisions for calling surveys on a larger scale.

Maryland↗

USGS2024

Predicting Lake Huron Dreissena spp. spatial distribution patterns from environmental characteristics

Invasive dreissenid mussels ( Dreissena polymorpha and Dreissena rostriformis bugensis ) have altered Great Lakes ecosystems through a multitude of effects on benthic habitats, food web structure, and nutrient cycling. This study explores whether spatially continuous geographic data of environmental factors can be utilized to predict Dreissena spp. spatial distributions on a lake-wide scale. Categorical variables were also assessed for significant relationships with Dreissena spp. biomass. Point observations from the 2017 Lake Huron benthic survey under the Cooperative Science and Monitoring Initiative (CSMI) were utilized for in situ measurements of dreissenid presence and biomass at 119 sites across Lake Huron. Basin, bathymetric zone, and tributary influence were found to have statistically significant relationships to dreissenid biomass. A boosted regression tree (BRT) model (ROC score 0.707) was developed to spatially predict dreissenid presence probability across Lake Huron from six environmental explanatory variables: April, May, and October chlorophyll, June dissolved organic carbon, January bottom temperature, and May bottom temperature. The importance of food availability and bottom temperature illuminated relationships between dreissenid mussels and periods of benthic-pelagic mixing in the spring and fall seasons. Future models could be improved through advancements in survey technology for improved geographic characterization of mussel habitat characteristics and environmental constraints.

Lake Huron↗

USGS2007

Temporal trends in concentrations of DBCP and nitrate in groundwater in the eastern San Joaquin Valley, California, USA

Temporal monitoring of the pesticide 1,2-dibromo-3-chloropropane (DBCP) and nitrate and indicators of mean groundwater age were used to evaluate the transport and fate of agricultural chemicals in groundwater and to predict the long-term effects in the regional aquifer system in the eastern San Joaquin Valley, California. Twenty monitoring wells were installed on a transect along an approximate groundwater flow path. Concentrations of DBCP and nitrate in the wells were compared to concentrations in regional areal monitoring networks. DBCP persists at concentrations above the US Environmental Protection Agency's maximum contaminant level (MCL) at depths of nearly 40 m below the water table, more than 25 years after it was banned. Nitrate concentrations above the MCL reached depths of more than 20 m below the water table. Because of the intensive pumping and irrigation recharge, vertical flow paths are dominant. High concentrations (above MCLs) in the shallow part of the regional aquifer system will likely move deeper in the system, affecting both domestic and public-supply wells. The large fraction of old water (unaffected by agricultural chemicals) in deep monitoring wells suggests that it could take decades for concentrations to reach MCLs in deep, long-screened public-supply wells, however. ?? Springer-Verlag 2007.

Hydrogeology Journal↗

USGS2019

Investigation of recent decadal-scale cyclical fluctuations in salinity in the lower Colorado river

Beginning in the late 1970s, 10- to 15-year cyclical oscillations in salinity were observed at lower Colorado River monitoring sites, moving upstream from the international border with Mexico, above Imperial Dam, below Hoover Dam, and at Lees Ferry. The cause of these cyclical trends in salinity was unknown. These salinity cycles complicate the U.S. Bureau of Reclamation's (Reclamation) responsibility for managing salinity in the river for delivery of water to Mexico to meet treaty obligations. This study develops a conceptual model of the salinity cycles from time-series water quality, streamflow, and precipitation data in both the lower and upper Colorado River Basins in order to provide Reclamation the ability to understand, anticipate, and manage future salinity cycles in the lower river. Compared with the Lees Ferry record, both maximum and minimum salinity levels increase downstream by about 25% at Hoover Dam, by about 49% at Imperial Dam, and by about 69% at the northern international boundary with Mexico. In the upper basin, cyclical salinity trends are evident at the outflow of three major tributaries, where salinity is also noted to be inversely related to streamflow. Time series trends in precipitation within the catchments of the three upper basin tributaries indicate cyclical periods with above normal precipitation and periods with below normal precipitation. Periods of greater than normal precipitation in the contributing areas correspond with declines in salinity at the catchment monitoring sites and periods of less than normal precipitation correspond with rising salinity at the sites. Based on the conceptual model developed in this investigation, a multiple linear regression model was developed using a stepwise variable selection procedure to simulate salinity in Lake Powell inflow. Important variables in the explanation of salinity entering Lake Powell include flow from the three upper basin tributaries, seasonality, and mean precipitation in the upper basin, among others. The root mean square error of prediction for the MLR model was 31.48 mg/L (5.7%).

Arizona, Colorado, Nevada, New Mexico, Utah, Wyomi↗

USGS2021

Review: “Jacob’s Zoo”— How using Jacob’s method for aquifer testing leads to more intuitive understanding of aquifer characteristics

The interpretation of aquifer responses to pumping tests is an important tool for assessing aquifer geometry and properties, which are critical in the assessment of water resources or in environmental remediation. However, the responses of aquifers, measured by time-drawdown relationships in monitoring wells, are nonunique solutions that are affected by many factors. Jacob’s Zoo is a collection of graphical interpretations that allows students and practitioners to develop an intuitive feel for how natural hydrogeological systems work, and develop a set of skills that provide a better understanding of aquifer properties far beyond interpretation of pumping tests. Jacob’s Zoo, based on the work of Jacob (1950), fosters a deeper understanding, although few practitioners realize the full utility of the method. Jacob CE (1950) Flow of groundwater, In: Rouse H (ed) Engineering Hydraulics, Wiley, New York. P 321–386.

Hydrogeology Journal↗

USGS2004

Landsat yesterday and today: An American vision and an old challenge

Since the late 1960s, the United States government has invested more than $1 billion in designing, launching, and operating the Landsat (land satellite) series of Earth-observing satellites. Global change researchers, geologists, and environmental scientists have used images gathered by the satellites for purposes ranging from human health research, energy exploration, and pollution detection to agricultural assessments, urban growth monitoring, and earthquake lineament studies. The earliest data were captured on a digital medium called wide-band video tape (WBVT). However, two decades of unsound media storage conditions and a poorly maintained processing system have left the physically deteriorating WBVTs with no mechanism for interpretation. A national treasure was in jeopardy. With seed money from the National Aeronautics and Space Administration (NASA), the U.S. Geological Survey (USGS) began a project to rescue the data. More than 21,000 tapes from the 1970s have been transcribed to stable, archival media, preserving the data for future studies in Earth System Science.

Journal of Map & Geography Libraries↗

USGS2016

Methods of soil resampling to monitor changes in the chemical concentrations of forest soils

Recent soils research has shown that important chemical soil characteristics can change in less than a decade, often the result of broad environmental changes. Repeated sampling to monitor these changes in forest soils is a relatively new practice that is not well documented in the literature and has only recently been broadly embraced by the scientific community. The objective of this protocol is therefore to synthesize the latest information on methods of soil resampling in a format that can be used to design and implement a soil monitoring program. Successful monitoring of forest soils requires that a study unit be defined within an area of forested land that can be characterized with replicate sampling locations. A resampling interval of 5 years is recommended, but if monitoring is done to evaluate a specific environmental driver, the rate of change expected in that driver should be taken into consideration. Here, we show that the sampling of the profile can be done by horizon where boundaries can be clearly identified and horizons are sufficiently thick to remove soil without contamination from horizons above or below. Otherwise, sampling can be done by depth interval. Archiving of sample for future reanalysis is a key step in avoiding analytical bias and providing the opportunity for additional analyses as new questions arise.

Journal of Visualized Experiments↗

USGS1998

Seasonal and spatial patterns of nitrate and silica concentrations in Canajoharie Creek, New York

The impact of nonpoint-source pollution on surface waters in agricultural watersheds is an emerging environmental issue. As part of the U.S. Geological Survey National Water Quality Assessment program in the Hudson River Basin, Canajoharie Creek was monitored for seasonal and spatial patterns of nutrient chemistry from March 1993 to January 1996. Nitrate and silica concentrations in Canajoharie Creek suggest that seasonal and spatial variations of these nutrients are dominated by biological processes, particularly uptake by phytoplankton. Observed concentration patterns were more typical of those observed in much larger, low-gradient streams. The median nitrate and silica concentrations in Canajoharie Creek were significantly lower from April through November than during winter. Concentrations of both constituents declined downstream from the headwaters during base-flow conditions in June 1995. Groundwater and surface water chemistry data support biological causes for downstream decreases in silica. The strong correlation between nitrate and silica in samples collected along the mainstem suggests that most of the nitrate decrease is due to uptake by diatoms. Downstream patterns of chlorophyll-a in phytoplankton strongly suggest the conversion of in-stream nutrients to algal biomass. Data collected from Canajoharie Creek outlet during the northeast drought of 1995 indicate that silica concentrations in May had possibly declined to a level that adversely affected the diatom community. This decline in the diatom population and subsequent resurgence is inferred from a sharp rise in silica concentrations between May and July and a reversal of this trend from mid-July through October without associated changes in hydrology.

Journal of Environmental Quality↗

USGS2021

Evidence of successful river spawning by lake trout (Salvelinus namaycush) in the lower Niagara River, Lake Ontario

Restoration of a wild-produced lake trout Salvelinus namaycush population in Lake Ontario has not been successful despite the adult population often meeting or exceeding restoration targets. Lack of high-quality spawning habitat in Lake Ontario is suggested as one impediment to recruitment of wild lake trout, although the quantity and location of spawning habitat is poorly understood. If high-quality spawning habitat is limited in Lake Ontario, lake trout may be using uncommon spawning locations such as rivers. Anecdotal angler accounts point to the Niagara River as a lake trout spawning location. To better understand the potential of the Niagara River as a spawning location, egg and juvenile fish collections were conducted 12–14 river kilometers from the mouth of the Niagara River from 2010 to 2012; and mature female lake trout with surgically implanted acoustic tags were monitored from 2015 to 2019. Genetic analyses confirmed 60% of collected eggs and 93% of collected post-hatch juvenile fish in the Niagara River were lake trout. Tagged female lake trout returned to the Niagara River over consecutive years during the spawning season. The short duration of lake trout presence in the river (mean = 56 days/year) suggests female lake trout use the Niagara River primarily for spawning. Diversity in spawning locations may provide lake trout population’s resilience against environmental variability through a portfolio effect. Improved identification of riverine spawning locations, including their overall contribution to wild recruitment, may be a useful tool for managers to restore a wild-produced population of lake trout in Lake Ontario.

New York, Ontario↗

USGS2017

Development of a robust analytical framework for assessing landbird trends, dynamics and relationships with environmental covariates in the North Coast and Cascades Network

During 2015-2016, we completed development of a new analytical framework for landbird population monitoring data from the National Park Service (NPS) North Coast and Cascades Inventory and Monitoring Network (NCCN). This new tool for analysis combines several recent advances in modeling population status and trends using point-count data and is designed to supersede the approach previously slated for analysis of trends in the NCCN and other networks, including the Sierra Nevada Network (SIEN). Advances supported by the new model-based approach include 1) the use of combined data on distance and time of detection to estimate detection probability without assuming perfect detection at zero distance, 2) seamless accommodation of variation in sampling effort and missing data, and 3) straightforward estimation of the effects of downscaled climate and other local habitat characteristics on spatial and temporal trends in landbird populations. No changes in the current field protocol are necessary to facilitate the new analyses. We applied several versions of the new model to data from each of 39 species recorded in the three mountain parks of the NCCN, estimating trends and climate relationships for each species during 2005-2014. Our methods and results are also reported in a manuscript in revision for the journal Ecosphere (hereafter, Ray et al.). Here, we summarize the methods and results outlined in depth by Ray et al., discuss benefits of the new analytical framework, and provide recommendations for its application to synthetic analyses of long-term data from the NCCN and SIEN. All code necessary for implementing the new analyses is provided within the Appendices to this report, in the form of fully annotated scripts written in the open-access programming languages R and JAGS.

Natural Resource Report↗

USGS2013

Next generation of global land cover characterization, mapping, and monitoring

Land cover change is increasingly affecting the biophysics, biogeochemistry, and biogeography of the Earth's surface and the atmosphere, with far-reaching consequences to human well-being. However, our scientific understanding of the distribution and dynamics of land cover and land cover change (LCLCC) is limited. Previous global land cover assessments performed using coarse spatial resolution (300 m–1 km) satellite data did not provide enough thematic detail or change information for global change studies and for resource management. High resolution (∼30 m) land cover characterization and monitoring is needed that permits detection of land change at the scale of most human activity and offers the increased flexibility of environmental model parameterization needed for global change studies. However, there are a number of challenges to overcome before producing such data sets including unavailability of consistent global coverage of satellite data, sheer volume of data, unavailability of timely and accurate training and validation data, difficulties in preparing image mosaics, and high performance computing requirements. Integration of remote sensing and information technology is needed for process automation and high-performance computing needs. Recent developments in these areas have created an opportunity for operational high resolution land cover mapping, and monitoring of the world. Here, we report and discuss these advancements and opportunities in producing the next generations of global land cover characterization, mapping, and monitoring at 30-m spatial resolution primarily in the context of United States, Group on Earth Observations Global 30 m land cover initiative (UGLC).

International Journal of Applied Earth Observation↗

USGS2006

Effects of watershed-scale land use change on stream nitrate concentrations

The Walnut Creek Watershed Monitoring Project was conducted from 1995 through 2005 to evaluate the response of stream nitrate concentrations to changing land use patterns in paired 5000-ha Iowa watersheds. A large portion of the Walnut Creek watershed is being converted from row crop agriculture to native prairie and savanna by the U.S. Fish and Wildlife Service at the Neal Smith National Wildlife Refuge (NSNWR). Before restoration, land use in both Walnut Creek (treatment) and Squaw Creek (control) watersheds consisted of 70% row crops. Between 1990 and 2005, row crop area decreased 25.4% in Walnut Creek due to prairie restoration but increased 9.2% in Squaw Creek due to Conservation Reserve Program (CRP) grassland conversion back to row crop. Nitrate concentrations ranged between <0.5 to 14 mg L-1 at the Walnut Creek outlet and 2.1 to 15 mg L-1 at the downstream Squaw Creek outlet. Nitrate concentrations decreased 1.2 mg L-1 over 10 yr in the Walnut Creek watershed but increased 1.9 mg L-1 over 10 yr in Squaw Creek. Changes in nitrate were easier to detect and more pronounced in monitored subbasins, decreasing 1.2 to 3.4 mg L-1 in three Walnut Creek subbasins, but increasing up to 8.0 and 11.6 mg L-1 in 10 yr in two Squaw Creek subbasins. Converting row crop lands to grass reduced stream nitrate levels over time in Walnut Creek, but stream nitrate rapidly increased in Squaw Creek when CRP grasslands were converted back to row crop. Study results highlight the close association of stream nitrate to land use change and emphasize that grasslands or other perennial vegetation placed in agricultural settings should be part of a long-term solution to water quality problems. ?? ASA, CSSA, SSSA.

Journal of Environmental Quality↗

USGS2023

AIMS for wildlife: Developing an automated interactive monitoring system to integrate real-time movement and environmental data for true adaptive management

To effectively manage species and habitats at multiple scales, population and land managers require rapid information on wildlife use of managed areas and responses to landscape conditions and management actions. GPS tracking studies of wildlife are particularly informative to species ecology, habitat use, and conservation. Combining GPS data with administrative data and a diverse suite of remotely sensed, geo-referenced environmental (e.g., climatic) data, would more comprehensively inform how animals interact with and utilize habitats and ecosystems and our goal was to create a conceptual model for a system that would accomplish this – the ‘Automated Interactive Monitoring System (AIMS) for Wildlife’. Our objective for this study was to develop a Customized Wildlife Report (CWR) - the first AIMS for Wildlife deliverable product. CWRs collate and summarize our 8-year GPS tracking dataset of ∼11 million locations from 1338 individual (16 species) avifauna and make actionable, real-time data on animal movements and trends in a specific area of interest available to managers and stakeholders for rapid application in day-to-day management. The CWR exemplar presented in this paper was developed to address needs identified by habitat managers of Sacramento National Wildlife Refuge and illustrates the highly specific, information offered and how it contributes to assessing the efficacy of conservation actions while allowing for near real-time adaptive management. The report can be easily customized for any of the thousands of wildlife refuges or regional areas of interest in the United States, emphasizing the broad application of an animal movement data stream. Utilizing diverse, extensive telemetry data streams through scientific collaboration can aid managers and conservation stakeholders with short and long-term research and conservation planning and help address a cadre of issues from local-scale habitat management to improving the understanding of landscape level impacts like drought, wildfire, and climate change on wildlife populations.

Journal of Environmental Management↗

USGS2017

Predicting intensity of white-tailed deer herbivory in the Central Appalachian Mountains

In eastern North America, white-tailed deer ( Odocoileus virginianus ) can have profound influences on forest biodiversity and forest successional processes. Moderate to high deer populations in the central Appalachians have resulted in lower forest biodiversity. Legacy effects in some areas persist even following deer population reductions or declines. This has prompted managers to consider deer population management goals in light of policies designed to support conservation of biodiversity and forest regeneration while continuing to support ample recreational hunting opportunities. However, despite known relationships between herbivory intensity and biodiversity impact, little information exists on the predictability of herbivory intensity across the varied and spatially diverse habitat conditions of the central Appalachians. We examined the predictability of browsing rates across central Appalachian landscapes at four environmental scales: vegetative community characteristics, physical environment, habitat configuration, and local human and deer population demographics. In an information - theoretic approach, we found that a model fitting the number of stems browsed relative to local vegetation characteristics received most (62%) of the overall support of all tested models assessing herbivory impact. Our data suggest that deer herbivory responded most predictably to differences in vegetation quantity and type. No other spatial factors or demographic factors consistently affected browsing intensity. Because herbivory, vegetation communities, and productivity vary spatially, we suggest that effective broad-scale herbivory impact assessment should include spatially-balanced vegetation monitoring that accounts for regional differences in deer forage preference. Effective monitoring is necessary to avoid biodiversity impacts and deleterious changes in vegetation community composition that are difficult to reverse and/or may not be detected using traditional deer-density based management goals.

Appalachian Mountains↗