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Purpose, processes, partnerships, and products: four Ps to advance participatory socio-environmental modeling

Including stakeholders in environmental model building and analysis is an increasingly popular approach to understanding ecological change. This is because stakeholders often hold valuable knowledge about socio-environmental dynamics and collaborative forms of modeling produce important boundary objects used to collectively reason about environmental problems. Although the number of participatory modeling (PM) case studies and the number of researchers adopting these approaches has grown in recent years, the lack of standardized reporting and limited reproducibility have prevented PM's establishment and advancement as a cohesive field of study. We suggest a four-dimensional framework (4P) that includes reporting on dimensions of (1) the Purpose for selecting a PM approach (the why ); (2) the Process by which the public was involved in model building or evaluation (the how ); (3) the Partnerships formed (the who ); and (4) the Products that resulted from these efforts (the what ). We highlight four case studies that use common PM software-based approaches (fuzzy cognitive mapping, agent-based modeling, system dynamics, and participatory geospatial modeling) to understand human–environment interactions and the consequences of ecological changes, including bushmeat hunting in Tanzania and Cameroon, agricultural production and deforestation in Zambia, and groundwater management in India. We demonstrate how standardizing communication about PM case studies can lead to innovation and new insights about model-based reasoning in support of ecological policy development. We suggest that our 4P framework and reporting approach provides a way for new hypotheses to be identified and tested in the growing field of PM.

Ecological Applications

Distinguishing brackish lacustrine from brackish marine deposits in the stratigraphic record: A case study from the late Miocene and early Pliocene Bouse Formation, Arizona and California, USA

Brackish marine and brackish continental environments are fundamentally different from a compositional perspective. Brackish water is often defined as having salinity lower than that of standard seawater but higher than that of freshwater, but less regard is given to the origin of the salts involved. The simple dilution of standard seawater by freshwater in a coastal or estuarine setting constitutes a brackish environment, but so do lakes where continental fresh water is impounded and becomes more saline through a variety of solute evolution pathways. The range of potential compositions of brackish lake water is diverse and includes water with “seawater-like” compositions. Isolated brackish lake environments located hundreds of kilometers inland can evolve towards sodium chloride-dominated, low alkalinityenvironments that mimic the composition of brackish seawater environments. These types of lakes can harbor a variety of continentally invasive but typically marine organisms, including but not limited to algae, foraminifers, mollusks, diatoms, and crustaceans . Distinguishing brackish marine from brackish lake environments in the geologic record can be difficult. In this paper, the enigmatic late Miocene and early Pliocene southern Bouse Formation of southern Arizona and California, USA, considered by many to represent a marine transgression along the lower Colorado River corridor, is discussed within a broad framework that incorporates hydrochemical, biogeographical, and species niche concepts. A brackish lake interpretation provides a powerful platform that can comprehensively account for the enigmatic mixed marine and continental fossil assemblage and possible tidal rhythmites that feature prominently in the southern Bouse Formation controversy. A review of the broader regional (paleo)environmental context for the southern Bouse supports a sodium chloride-dominated, low alkalinity, mildly brackish (10-5 ppt) Colorado River-fed lake depositional environment that was populated by an intriguing but predictable array of euryhaline, opportunistic, and continentally invasive marginal marine organisms.

Arizona, California

Revisiting 228Th as a tool for determining sedimentation and mass accumulation rates

The use of 228Th has seen limited application for determining sedimentation and mass accumulation rates in coastal and marine environments. Recent analytical advances have enabled rapid, precise measurements of particle-bound 228Th using a radium delayed coincidence counting system (RaDeCC). Herein we review the 228Th cycle in the marine environment and revisit the historical use of 228Th as a tracer for determining sediment vertical accretion and mass accumulation rates in light of new measurement techniques. Case studies comparing accumulation rates from 228Th and 210Pb are presented for a micro-tidal salt marsh and a marginal sea environment. 228Th and 210Pb have been previously measured in mangrove, deltaic, continental shelf and ocean basin environments, and a literature synthesis reveals that 228Th (measured via alpha or gamma spectrometry) derived accumulation rates are generally equal to or greater than estimates derived from 210Pb, reflecting different integration periods. Use of 228Th is well-suited for shallow (<15 cm) cores over decadal timescales. Application is limited to relatively homogenous sediment profiles with minor variations in grain size and minimal bioturbation. When appropriate conditions are met, complimentary use of 228Th and 210Pb can demonstrate that the upper layers of a core are undisturbed and can improve spatial coverage in mapping accumulation rates due to the higher sample throughput for sediment 228Th.

Massachusetts

What to do when invaders are out of control?

Biological invasions threaten species and ecosystems worldwide. Impacts from invasions are especially prevalent in freshwaters, where managers have struggled to contain the problem. Conventional approaches to managing invaders focus on prevention and control. In practice, these measures have proven to be variably effective. Control or eradication of established invaders is particularly difficult and, even if ecologically feasible, it may not be socially desirable. Here we propose a new alternative to managing invasive species: managing impact modifiers (MIM). The MIM approach focuses on managing impacts, rather than controlling the invader directly. We reviewed the literature for the world's worst invasive fishes in freshwaters to show there is strong evidence to support the potential for MIM as an effective means of managing impacts of invasions. This included evidence pointing to characteristics of the environment or species themselves that modify impacts of invasions. Detail of three case studies reinforces the potential for MIM as a viable option. Although MIM appears promising, effective application could involve significant investment in an information gathering phase to identify impact modifiers and the means to manage them. Accordingly, MIM is best incorporated into management plans that include a strong learning or adaptive component. Ultimately, MIM may be one of the only viable alternatives for managing invasive species that are truly out of control.

WIREs Water

Prior knowledge-based approach for associating contaminants with biological effects: A case study in the St. Croix River basin, MN, WI, USA

Evaluating potential adverse effects of complex chemical mixtures in the environment is challenging. One way to address that challenge is through more integrated analysis of chemical monitoring and biological effects data. In the present study, water samples from five locations near two municipal wastewater treatment plants in the St. Croix River basin, on the border of MN and WI, USA, were analyzed for 127 organic contaminants. Known chemical-gene interactions were used to develop site-specific knowledge assembly models (KAMs) and formulate hypotheses concerning possible biological effects associated with chemicals detected in water samples from each location. Additionally, hepatic gene expression data were collected for fathead minnows ( Pimephales promelas ) exposed in situ , for 12 d, at each location. Expression data from oligonucleotide microarrays were analyzed to identify functional annotation terms enriched among the differentially-expressed probes. The general nature of many of the terms made hypothesis formulation on the basis of the transcriptome-level response alone difficult. However, integrated analysis of the transcriptome data in the context of the site-specific KAMs allowed for evaluation of the likelihood of specific chemicals contributing to observed biological responses. Thirteen chemicals (atrazine, carbamazepine, metformin, thiabendazole, diazepam, cholesterol, p-cresol, phenytoin, omeprazole, ethyromycin, 17β-estradiol, cimetidine, and estrone), for which there was statistically significant concordance between occurrence at a site and expected biological response as represented in the KAM, were identified. While not definitive, the approach provides a line of evidence for evaluating potential cause-effect relationships between components of a complex mixture of contaminants and biological effects data, which can inform subsequent monitoring and investigation.

Minnesota, Wisconsin

The protectiveness of aquatic life criteria for threatened or endangered aquatic species: Cadmium in California

In the United States, conflicts can arise between the processes to derive aquatic life criteria (ALC) for chemicals under the Clean Water Act (CWA) and the evaluation procedures used in Endangered Species Act (ESA) consultations on the protectiveness of those criteria for protected species. This paper examines the roots of, and possible reconciliation of, one longstanding conflict over cadmium aquatic life criteria in California. This case study includes 1) an overview of occurrences of cadmium in the aquatic environment, 2) factors affecting toxicity of cadmium to aquatic life, 3) a contrast between the analytical procedures of CWA aquatic life criteria derivation and ESA consultation, 4) quantitative estimates of no-effect concentrations of cadmium for 44 ESA listed species in comparison with updated aquatic life criteria, and 5) concludes with suggestions to update California’s aquatic life criteria for cadmium that would be more protective of sensitive ESA listed species. A root cause of conflict is the different levels of biological organization that are the focus of CWA and ESA procedures. The CWA ALC are intended to protect diverse ecosystems by protecting at least 95% of the species richness in communities, allowing that it is acceptable for some species in the residual most sensitive 5% of the community richness to be harmed or even locally extirpated so long as they are not societally important species. The ESA is charged with minimizing harm to individual organisms and disallows increasing risk of extinction or impeding recovery of protected species. With cadmium in California, these procedures converge because some of the most sensitive species to cadmium happen to be surrogates for protected species (acute responses of steelhead/rainbow trout, Oncorhynchus mykiss , and chronic responses of threespine stickleback, Gasterosteus aculeatus ). The present review concludes that while the superseded 1996 cadmium criteria versions would not be fully protective for up to half of the 44 ESA listed aquatic species in California, the updated 2016 versions would be more protective. Still, the review shows that the updated acute criteria would only fully protect the less sensitive half of the distribution of data for steelhead/rainbow trout sensitivity to cadmium, and the chronic criterion still would not protect the listed threespine stickleback. With a data rich species such as rainbow trout, instead of defining acute criteria using a central tendency statistic such as the geometric mean of multiple test responses, using a lower statistic such as the 10th percentile would ensure that the vast majority of a sensitive, protected species (and all less sensitive species) would be protected. Available data for the stickleback indicate it may be highly sensitive to cadmium, but no threshold can be derived from existing data. Additional testing with cadmium and stickleback would be needed to suggest an alternative, quantitative approach.

California

Alkylcyclohexanes in environmental geochemistry

The n-alkylated cyclohexanes (CHs) are a homologous series of hydrocarbon compounds that are commonly present in crude oil and refinery products such as diesel fuel. These compounds exhibit specific distribution patterns for different fuel types, providing useful fingerprints for characterizing petroleum products, especially after degradation of n-alkanes has occurred. However, there are no published data to show how these compounds are altered in the environment after long-term spillage of petroleum products. This paper presents two case studies of oil spills that demonstrate the changing distribution patterns resulting from long-term anaerobic microbial degradation. These spills are the 1979 crude-oil spill in Bemidji, Minnesota, and a chronic diesel-fuel spillage from 1953-1991 at Mandan, North Dakota. The alkyl CHs in both spilled oil products are affected by similar biodegradative processes in which the compounds undergo a consistent pattern of loss from the high molecular weight end of the homolog distribution. Degradation results in a measurable increase in the concentrations of the homologs in the lower molecular weight range, a gradual lowering in carbon number of the homolog maximum, and a gradual decrease of the total homolog range from the high molecular weight end. This pattern is the opposite of low-end loss expected with weathering and aerobic biodegradation. The enhancement of the low molecular mass alkyl CH homologs, if not recognized as a degradative pathway of diesel fuel in an anaerobic environment, can potentially be misinterpreted in fuel-oil fingerprinting as deriving from lower distillation-range fuels or admixture of diesel with other fuels.

Environmental Forensics

Assessment of coastal and fluvial morphodynamic changes using Structure-for-Motion: A case study of the Sfȃntu Gheorghe Mouth (Danube Delta, Romania)

The ability to accurately map erosion, flooding, and habitat loss in coastal environments is crucial for formulating national strategies aimed at preventing and mitigating the impacts of natural disasters. A fundamental component of this process is the implementation of coastal morphodynamics monitoring through Structure-from-Motion (SfM) techniques, utilizing high-resolution 2D/3D data obtained from aerial photogrammetry. To assess morphodynamic changes over a three-year period (2022 – 2024), several SfM-based photogrammetric studies were conducted, each year, in the Romanian sector of the Danube-Black Sea coastal zone, specifically at the mouth of one of the Danube River distributaries (Sf Gheorghe branch) into the Black Sea, and along the left bank, near Sf Gheorghe locality, located within the Danube Delta Biosphere Reserve (DDBR). The essential equipment for aerial photogrammetry comprises Unmanned Aerial Vehicles (UAVs) and Global Navigation Satellite Systems (GNSS). In this study, the UAV used was a DJI Mavic 3T (Enterprise/Thermal) drone, complemented by two Trimble R12i and R4 GNSS systems, as well as approximately 10 Ground Control Points (GCPs). Data acquisition and processing were carried out using specialized photogrammetric software (Agisoft Metashape) along with various GIS tools (e.g., Blue Marble Geographics Global Mapper and ESRI ArcMap). The photogrammetric products generated for the study, as detailed in this paper, include Digital Elevation Models (DEMs), Digital Terrain Models (DTMs), orthomosaics (orthophotos), and others. At Sfântu Gheorghe beach, a comparison between 2023 and 2024 photogrammetric surveys revealed that the left bank of the Sf. Gheorghe Arm, at the river mouth into the Black Sea, suffered from a twist (erosion) of up to 64 metres. Additionally, on the selected perimetre (total area of 31,910 square meters ) from the beach and dune zone of Sf. Gheorghe, an area of up to 16,202 square meters was eroded between 2023 and 2024. This contrasts with the period between 2022 and 2023, during which deposition predominated. Erosion at the Danube mouths and the adjacent Black Sea coastline is driven by a complex interaction of natural and anthropogenic factors. Natural processes, including subsidence, sea-level rise, and episodic extreme storm events, contribute significantly to coastal dynamics. Meanwhile, human-induced factors, such as upstream hydrotechnical works that limits sediment transport, cutting of navigation canals, as well as the exacerbating effects of climate change, further accelerate erosion. The recent Structure-from-Motion (SfM) surveys provide essential quantitative data, enabling a detailed analysis of both short-term and long-term morphodynamic changes influenced by seasonal variations and extreme hydrometeorological events in this highly dynamic coastal system.

Sfȃntu Gheorghe Mouth (Danube Delta)

Urban sprawl leaves its PAH signature

The increasing vehicle traffic associated with urban sprawl in the United States is frequently linked to degradation of air quality, but its effect on aquatic sediment is less well-recognized. This study evaluates trends in PAHs, a group of contaminants with multiple urban sources, in sediment cores from 10 reservoirs and lakes in six U.S. metropolitan areas. The watersheds chosen represent a range in degree and age of urbanization. Concentrations of PAHs in all 10 reservoirs and lakes increased during the past 20-40 years. PAH contamination of the most recently deposited sediment at all sites exceeded sediment-quality guidelines established by Environment Canada, in some cases by several orders of magnitude. These results add a new chapter to the story told by previous coring studies that reported decreasing concentrations of PAHs after reaching highs in the 1950s. Concurrent with the increase in concentrations is a change in the assemblage of PAHs that indicates the increasing trends are driven by combustion sources. The increase in PAH concentrations tracks closely with increases in automobile use, even in watersheds that have not undergone substantial changes in urban land-use levels since the 1970s.The increasing vehicle traffic associated with urban sprawl in the United States is frequently linked to degradation of air quality, but its effect on aquatic sediment is less well-recognized. This study evaluates trends in PAHs, a group of contaminants with multiple urban sources, in sediment cores from 10 reservoirs and lakes in six U.S. metropolitan areas. The watersheds chosen represent a range in degree and age of urbanization. Concentrations of PAHs in all 10 reservoirs and lakes increased during the past 20-40 years. PAH contamination of the most recently deposited sediment at all sites exceeded sediment-quality guidelines established by Environment Canada, in some cases by several orders of magnitude. These results add a new chapter to the story told by previous coring studies that reported decreasing concentrations of PAHs after reaching highs in the 1950s. Concurrent with the increase in concentrations is a change in the assemblage of PAHs that indicates the increasing trends are driven by combustion sources. The increase in PAH concentrations tracks closely with increases in automobile use, even in watersheds that have not undergone substantial changes in urban land-use levels since the 1970s.

Environmental Science & Technology

Using the Maxent program for species distribution modelling to assess invasion risk

MAXENT is a software package used to relate known species occurrences to information describing the environment, such as climate, topography, anthropogenic features or soil data, and forecast the presence or absence of a species at unsampled locations. This particular method is one of the most popular species distribution modelling techniques because of its consistent strong predictive performance and its ease to implement. This chapter discusses the decisions and techniques needed to prepare a correlative climate matching model for the native range of an invasive alien species and use this model to predict the potential distribution of this species in a potentially invaded range (i.e. a novel environment) by using MAXENT for the Burmese python ( Python molurus bivittatus ) as a case study. The chapter discusses and demonstrates the challenges that are associated with this approach and examines the inherent limitations that come with using MAXENT to forecast distributions of invasive alien species.

Book chapter

Heterogeneous occupancy and density estimates of the pathogenic fungus Batrachochytrium dendrobatidis in waters of North America

Biodiversity losses are occurring worldwide due to a combination of stressors. For example, by one estimate, 40% of amphibian species are vulnerable to extinction, and disease is one threat to amphibian populations. The emerging infectious disease chytridiomycosis, caused by the aquatic fungus Batrachochytrium dendrobatidis ( Bd ), is a contributor to amphibian declines worldwide. Bd research has focused on the dynamics of the pathogen in its amphibian hosts, with little emphasis on investigating the dynamics of free-living Bd . Therefore, we investigated patterns of Bd occupancy and density in amphibian habitats using occupancy models, powerful tools for estimating site occupancy and detection probability. Occupancy models have been used to investigate diseases where the focus was on pathogen occurrence in the host. We applied occupancy models to investigate free-living Bd in North American surface waters to determine Bd seasonality, relationships between Bd site occupancy and habitat attributes, and probability of detection from water samples as a function of the number of samples, sample volume, and water quality. We also report on the temporal patterns of Bd density from a 4-year case study of a Bd -positive wetland. We provide evidence that Bd occurs in the environment year-round. Bd exhibited temporal and spatial heterogeneity in density, but did not exhibit seasonality in occupancy. Bd was detected in all months, typically at less than 100 zoospores L −1 . The highest density observed was ∼3 million zoospores L −1 . We detected Bd in 47% of sites sampled, but estimated that Bd occupied 61% of sites, highlighting the importance of accounting for imperfect detection. When Bd was present, there was a 95% chance of detecting it with four samples of 600 ml of water or five samples of 60 mL. Our findings provide important baseline information to advance the study of Bd disease ecology, and advance our understanding of amphibian exposure to free-living Bd in aquatic habitats over time.

California, Colorado, Idaho, Maine, Minnesota, Nev

Optimal exploitation strategies for an animal population in a stochastic serially correlated environment

Optimal exploitation strategies were studied for an animal population in a stochastic, serially correlated environment. This is a general case and encompasses a number of important cases as simplifications. Data on the mallard (Anas platyrhynchos) were used to explore the exploitation strategies and test several hypotheses because relatively much is known concerning the life history and general ecology of this species and extensive empirical data are available for analysis. The number of small ponds on the central breeding grounds was used as an index to the state of the environment. Desirable properties of an optimal exploitation strategy were defined. A mathematical model was formulated to provide a synthesis of the existing literature, estimates of parameters developed from an analysis of data, and hypotheses regarding the specific effect of exploitation on total survival. Both the literature and the analysis of data were inconclusive concerning the effect of exploitation on survival. Therefore, alternative hypotheses were formulated: (1) exploitation mortality represents a largely additive form of mortality, or (2 ) exploitation mortality is compensatory with other forms of mortality, at least to some threshold level. Models incorporating these two hypotheses were formulated as stochastic dynamic programming models and optimal exploitation strategies were derived numerically on a digital computer. Optimal exploitation strategies were found to exist under rather general conditions. Direct feedback control was an integral component in the optimal decision-making process. Optimal exploitation was found to be substantially different depending upon the hypothesis regarding the effect of exploitation on the population. Assuming that exploitation is largely an additive force of mortality, optimal exploitation decisions are a convex function of the size of the breeding population and a linear or slightly concave function of the environmental conditions. Optimal exploitation under this hypothesis tends to reduce the variance of the size of the population. Under the hypothesis of compensatory mortality forces, optimal exploitation decisions are approximately linearly related to the size of the breeding population. Environmental variables may be somewhat more important than the size of the breeding population to the production of young mallards. In contrast, the size of the breeding population appears to be more important in the exploitation process than is the state of the environment. The form of the exploitation strategy appears to be relatively insensitive to small changes in the production rate. In general, the relative importance of the size of the breeding population may decrease as fecundity increases. The optimal level of exploitation in year t must be based on the observed size of the population and the state of the environment in year t unless the dynamics of the population, the state of the environment, and the result of the exploitation decisions are completely deterministic. Exploitation based on an average harvest, harvest rate, or designed to maintain a constant breeding population size is inefficient.

Book

Optimal exploitation strategies for an animal population in a stochastic serially correlated environment

Optimal exploitation strategies were studied for an animal population in a stochastic, serially correlated environment. This is a general case and encompasses a number of important cases as simplifications. Data on the mallard (Anas platyrhynchos) were used to explore the exploitation strategies and test several hypotheses because relatively much is known concerning the life history and general ecology of this species and extensive empirical data are available for analysis. The number of small ponds on the central breeding grounds was used as an index to the state of the environment. Desirable properties of an optimal exploitation strategy were defined. A mathematical model was formulated to provide a synthesis of the existing literature, estimates of parameters developed from an analysis of data, and hypotheses regarding the specific effect of exploitation on total survival. Both the literature and the analysis of data were inconclusive concerning the effect of exploitation on survival. Therefore, alternative hypotheses were formulated: (1) exploitation mortality represents a largely additive form of mortality, or (2 ) exploitation mortality is compensatory with other forms of mortality, at least to some threshold level. Models incorporating these two hypotheses were formulated as stochastic dynamic programming models and optimal exploitation strategies were derived numerically on a digital computer. Optimal exploitation strategies were found to exist under rather general conditions. Direct feedback control was an integral component in the optimal decision-making process. Optimal exploitation was found to be substantially different depending upon the hypothesis regarding the effect of exploitation on the population. Assuming that exploitation is largely an additive force of mortality, optimal exploitation decisions are a convex function of the size of the breeding population and a linear or slightly concave function of the environmental conditions. Optimal exploitation under this hypothesis tends to reduce the variance of the size of the population. Under the hypothesis of compensatory mortality forces, optimal exploitation decisions are approximately linearly related to the size of the breeding population. Environmental variables may be somewhat more important than the size of the breeding population to the production of young mallards. In contrast, the size of the breeding population appears to be more important in the exploitation process than is the state of the environment. The form of the exploitation strategy appears to be relatively insensitive to small changes in the production rate. In general, the relative importance of the size of the breeding population may decrease as fecundity increases. The optimal level of exploitation in year t must be based on the observed size of the population and the state of the environment in year t unless the dynamics of the population, the state of the environment, and the result of the exploitation decisions are completely deterministic. Exploitation based on an average harvest, harvest rate, or designed to maintain a constant breeding population size is inefficient.

Dissertation Abstracts International

Whiting events in SW Florida coastal waters: a case study using MODIS medium-resolution data

Whitings, floating patches of calcium carbonate mud, have been found in both shallow carbonate banks and freshwater environments around the world. Although these events have been studied for many decades, much of their characteristics remain unknown. Recent sightings of whitings near Ten Thousand Islands, Florida suggest a phenomenon that has not previously been documented in this area. Using medium-resolution (250-m) data collected by the Moderate Resolution Imaging Spectroradiometer (MODIS) from December 2010 to November 2013, we documented whiting events and their spatial and temporal patterns in this region. Classification rules were first established, and then applied to all 474 cloud-free and sun glint-free MODIS images. Whiting occurrences were found between 25°46′N and 25°20′N and less than 40 km from the southwest Florida coastline. Over the 3-year period, whiting occurrence peaked in spring and autumn and reached a minimum during the winter and summer months. Further field and laboratory research are needed to explain driving force(s) behind these events.

Florida

Applied Geochemistry Special Issue on Environmental geochemistry of modern mining

Environmental geochemistry is an integral part of the mine-life cycle, particularly for modern mining. The critical importance of environmental geochemistry begins with pre-mining baseline characterization and the assessment of environmental risks related to mining, continues through active mining especially in water and waste management practices, and culminates in mine closure. The enhanced significance of environmental geochemistry to modern mining has arisen from an increased knowledge of the impacts that historical and active mining can have on the environment, and from new regulations meant to guard against these impacts. New regulations are commonly motivated by advances in the scientific understanding of the environmental impacts of past mining. The impacts can be physical, chemical, and biological in nature. The physical challenges typically fall within the purview of engineers, whereas the chemical and biological challenges typically require a multidisciplinary array of expertise including geologists, geochemists, hydrologists, microbiologists, and biologists. The modern mine-permitting process throughout most of the world now requires that potential risks be assessed prior to the start of mining. The strategies for this risk assessment include a thorough characterization of pre-mining baseline conditions and the identification of risks specifically related to the manner in which the ore will be mined and processed, how water and waste products will be managed, and what the final configuration of the post-mining landscape will be. In the Fall 2010, the Society of Economic Geologists held a short course in conjunction with the annual meeting of the Geological Society of America in Denver, Colorado (USA) to examine the environmental geochemistry of modern mining. The intent was to focus on issues that are pertinent to current and future mines, as opposed to abandoned mines, which have been the focus of numerous previous short courses. The geochemical challenges of current and future mines share similarities with abandoned mines, but differences also exist. Mining and ore processing techniques have changed; the environmental footprint of waste materials has changed; environmental protection has become a more integral part of the mine planning process; and most historical mining was done with limited regard for the environment. The 17 papers in this special issue evolved from the Society of Economic Geologists’ short course. The relevant geochemical processes encompass the source, transport, and fate of contaminants related to the life cycle of a mine. Contaminants include metals and other inorganic species derived from geologic sources such as ore and solid mine waste, and substances brought to the site for ore processing, such as cyanide to leach gold. Factors, such as mine-waste mineralogy, hydrologic setting, mine-drainage chemistry, and microbial activity, that affect the hydrochemical risks from mining are reviewed by Nordstrom et al. In another paper, Nordstrom discusses baseline characterization at mine sites in a regulatory framework, and emphasizes the influence of mineral deposits in producing naturally elevated concentrations of many trace elements in surface water and groundwater. Surface water quality in mineralized watersheds is influenced by a number of processes that act on daily (diel) cycles and can produce dramatic variations in trace element concentrations as described by Gammons et al. Pre-mining baseline characterization studies should strive to capture the magnitude of these diel variations. Desbarats et al., using a case study of mine drainage from a gold mine, illustrate how elements that commonly occur as negatively charged species (anions) in solution, such as arsenic as arsenate, behave in an opposite fashion than most metals, which occur as positively charged species (cations). Significant improvement in the understanding of factors that influence the toxicity of metals to aquatic organisms in surface water has highlighted the importance of aqueous chemistry, particularly dissolved organic carbon, as described by Smith et al. Stream sediment contamination is another important pathway for affecting aquatic organisms, as reviewed by Besser et al. Understanding and predicting environmental consequences from mining begins with knowing the mineralogy and mineral reactivity of the ore, the wastes, and of secondary minerals formed later. Jamieson et al. review the importance of mineralogical studies in mine planning and remediation. A number of types of site-specific studies are needed to identify environmental risks related to individual mines. Lapakko reviews the general framework of mine waste characterization studies that are integral to the mine planning process. Hageman et al. present a comparative study of several static tests commonly used to characterize mine waste. The mining and ore processing practices employed at a specific mine site will vary on the basis of the commodities being targeted, the geology of the deposit, the geometry of the deposit, and the mining and ore processing methods used. Thus, these factors, in addition to the waste management practices used, can result in a variety of end-member mine waste features, each of which has its own set of challenges. Open pit mines and underground mines require waste rock to be removed to access ore. Waste rock presents unique problems because the rock is commonly mineralized at sub-economic grades and has not been processed to remove potentially problematic minerals, such as pyrite. Amos et al. examine the salient aspects of the geochemistry of waste rock. Mill tailings – the waste material after ore minerals have been removed – are a volumetrically important solid waste at many mine sites. Their fine grain size and the options for their management make their behavior in the environment distinct from that of waste rock. Lindsay et al. describe some of these differences through three case-study examples. Subaqueous disposal of tailings is another option described by Moncur et al. Cyanide leaching for gold extraction is a common method throughout the world. Johnson describes environmental aspects of cyanidation. Uranium mining presents unique environmental challenges, particularly since in-situ recovery has seen widespread use. Campbell et al. review the environmental geochemistry of uranium mining and current research on bioremediation. Ore concentrates from many types of metal mining undergo a pyrometallurgical technique known as smelting to extract the metal. Slag is the result of smelting, and it may be an environmental liability or a valuable byproduct, as described by Piatak et al. Finally, the open pits that result from surface mining commonly reach below the water table. At the end of mining, these pits may fill to form lakes that become part of the legacy of the mine. Castendyk et al., in two papers, review theoretical aspects of the environmental limnology of pit lakes. They also describe approaches that have been used to model pit lake water balance, wall-rock contributions to pit lake chemistry, pit lake water quality, and limnological processes, such as vertical mixing, through the use of three case studies.

Applied Geochemistry

The applicability of terrestrial visitor impact management strategies to the protection of coral reefs

A dramatic expansion in nature-based tourism to tropical coastal destinations has occurred in the past 20 years. Tourism development, combined with intense recreational pressures, has irreversibly transformed and degraded many popular scenic natural environments. This paper examines the management of recreational impacts to coral reefs using Virgin Islands National Park as a case study. A review of terrestrial recreational ecology research explores the implications and potential applicability of some principal findings to the protection of coral reefs. Visitor impact management recommendations for the protection of coral reefs are offered. Managers can minimize coral reef recreational impacts by (1) restricting high-impact uses, (2) containing rather than dispersing recreational use, (3) encouraging the use of resistant environments, (4) teaching low-impact recreational practices, and (5) enforcing park rules and regulations.

Ocean and Coastal Management

Optimal exploitation strategies for an animal population in a Markovian environment: A theory and an example

Optimal exploitation strategies were studied for an animal population in a Markovian (stochastic, serially correlated) environment. This is a general case and encompasses a number of important special cases as simplifications. Extensive empirical data on the Mallard (Anas platyrhynchos) were used as an example of general theory. The number of small ponds on the central breeding grounds was used as an index to the state of the environment. A general mathematical model was formulated to provide a synthesis of the existing literature, estimates of parameters developed from an analysis of data, and hypotheses regarding the specific effect of exploitation on total survival. The literature and analysis of data were inconclusive concerning the effect of exploitation on survival. Therefore, two hypotheses were explored: (1) exploitation mortality represents a largely additive form of mortality, and (2) exploitation mortality is compensatory with other forms of mortality, at least to some threshold level. Models incorporating these two hypotheses were formulated as stochastic dynamic programming models and optimal exploitation strategies were derived numerically on a digital computer. Optimal exploitation strategies were found to exist under the rather general conditions. Direct feedback control was an integral component in the optimal decision—making process. Optimal exploitation was found to be substantially different depending upon the hypothesis regarding the effect of exploitation on the population. If we assume that exploitation is largely an additive force of mortality in Mallards, then optimal exploitation decisions are a convex function of the size of the breeding population and a linear or slight concave function of the environmental conditions. Under the hypothesis of compensatory mortality forces, optimal exploitation decisions are approximately linearly related to the size of the Mallard breeding population. Dynamic programming is suggested as a very general formulation for realistic solutions to the general optimal exploitation problem. The concepts of state vectors and stage transformations are completely general. Populations can be modeled stochastically and the objective function can include extra—biological factors. The optimal level of exploitation in year t must be based on the observed size of the population and the state of the environment in year t unless the dynamics of the population, the state of the environment, and the result of the exploitation decisions are completely deterministic. Exploitation based on an average harvest, or harvest rate, or designed to maintain a constant breeding population size is inefficient.

Ecology

Integrated synoptic surveys of the hydrodynamics and water-quality distributions in two Lake Michigan rivermouth mixing zones using an autonomous underwater vehicle and a manned boat

The U.S. Geological Survey (USGS), in cooperation with the National Monitoring Network for U.S. Coastal Waters and Tributaries, launched a pilot project in 2010 to determine the value of integrated synoptic surveys of rivermouths using autonomous underwater vehicle technology in response to a call for rivermouth research, which includes study domains that envelop both the fluvial and lacustrine boundaries of the rivermouth mixing zone. The pilot project was implemented at two Lake Michigan rivermouths with largely different scales, hydrodynamics, and settings, but employing primarily the same survey techniques and methods. The Milwaukee River Estuary Area of Concern (AOC) survey included measurements in the lower 2 to 3 miles of the Milwaukee, Menomonee, and Kinnickinnic Rivers and inner and outer Milwaukee Harbor. This estuary is situated in downtown Milwaukee, Wisconsin, and is the most populated basin that flows directly into Lake Michigan. In contrast, the Manitowoc rivermouth has a relatively small harbor separating the rivermouth from Lake Michigan, and the Manitowoc River Watershed is primarily agricultural. Both the Milwaukee and Manitowoc rivermouths are unregulated and allow free exchange of water with Lake Michigan. This pilot study of the Milwaukee River Estuary and Manitowoc rivermouth using an autonomous underwater vehicle (AUV) paired with a manned survey boat resulted in high spatial and temporal resolution datasets of basic water-quality parameter distributions and hydrodynamics. The AUV performed well in these environments and was found primarily well-suited for harbor and nearshore surveys of three-dimensional water-quality distributions. Both case studies revealed that the use of a manned boat equipped with an acoustic Doppler current profiler (ADCP) and multiparameter sonde (and an optional flow-through water-quality sampling system) was the best option for riverine surveys. To ensure that the most accurate and highest resolution velocity data were collected concurrently with the AUV surveys, the pilot study used a manned boat equipped with an ADCP. Combining the AUV and manned boat datasets resulted in datasets that are essentially continuous from the fluvial through the lacustrine zones of a rivermouth. Whereas the pilot studies were completed during low flows on the tributaries, completion of surveys at higher flows using the same techniques is possible, but the use of the AUV would be limited to areas with relatively low velocities (less than 2 feet per second) such as the harbors and nearshore zones of Lake Michigan. Overall, this pilot study aimed at evaluation of AUV technology for integrated synoptic surveys of rivermouth mixing zones was successful, and the techniques and methods employed in this pilot study should be transferrable to other sites with similar success. The use of the AUV provided significant time savings compared to traditional sampling techniques. For example, the survey of outer Milwaukee Harbor using the AUV required less than 7 hours for approximately 600 profiles compared to the 150 hours it would have taken using traditional methods in a manned boat (a 95 percent reduction in man-hours). The integrated datasets resulting from the AUV and manned survey boat are of high value and present a picture of the mixing and hydrodynamics of these highly dynamic, highly variable rivermouth mixing zones from the relatively well-mixed fluvial environment through the rivermouth to the stratified lacustrine receiving body of Lake Michigan. Such datasets not only allow researchers to understand more about the physical processes occurring in these rivermouths, but they provide high spatial resolution data required for interpretation of relations between disparate point samples and calibration and validation of numerical models.

Wisconsin