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Metropolitan land cover inventory using multiseasonal Landsat data

As a part of the Pacific Northwest Land Resources Inventory Demonstration Project (PNLRIDP), planners from State, regional, and local agencies in Oregon are working with scientists from the EROS Data Center (USGS), Ames Research Center (NASA), and the Jet Propulsion Laboratory (California Institute of Technology) to obtain practical training and experience in the analysis of remotely sensed data collected from air and spacecraft. A 4,000 km2 area centered on metropolitan Portland was chosen as the demonstration site, and a four-date Landsat temporal overlay was created which contained January, April, July, and October data collected in 1973. Digital multispectral analysis of single dates and two-date combinations revealed that the spring-summer and summer-fall combinations were the most satisfactory for land cover inventory. Residential, commercial and industrial, improved open space, water, forested, and agriculture land cover categories were obtained consistently in the majority of classification iterations. Census tract and traffic zone boundaries were digitized and registered with the Landsat data to facilitate integration of the land cover information with socioeconomic and environmental data already available to Oregon planners.

Open-File Report↗

Seven recommendations to make your invasive alien species data more useful

Science-based strategies to tackle biological invasions depend on recent, accurate, well-documented, standardized and openly accessible information on alien species. Currently and historically, biodiversity data are scattered in numerous disconnected data silos that lack interoperability. The situation is no different for alien species data, and this obstructs efficient retrieval, combination, and use of these kinds of information for research and policy-making. Standardization and interoperability are particularly important as many alien species related research and policy activities require pooling data. We describe seven ways that data on alien species can be made more accessible and useful, based on the results of a European Cooperation in Science and Technology (COST) workshop: (1) Create data management plans; (2) Increase interoperability of information sources; (3) Document data through metadata; (4) Format data using existing standards; (5) Adopt controlled vocabularies; (6) Increase data availability; and (7) Ensure long-term data preservation. We identify four properties specific and integral to alien species data (species status, introduction pathway, degree of establishment, and impact mechanism) that are either missing from existing data standards or lack a recommended controlled vocabulary. Improved access to accurate, real-time and historical data will repay the long-term investment in data management infrastructure, by providing more accurate, timely and realistic assessments and analyses. If we improve core biodiversity data standards by developing their relevance to alien species, it will allow the automation of common activities regarding data processing in support of environmental policy. Furthermore, we call for considerable effort to maintain, update, standardize, archive, and aggregate datasets, to ensure proper valorization of alien species data and information before they become obsolete or lost.

Frontiers in Applied Mathematics and Statistics↗

It’s time for focused in situ studies of planetary surface-atmosphere interactions

A critical gap in planetary observations has been in situ characterization of extra-terrestrial, present-day atmospheric and surface environments and activity. While some surface activity has been observed and some in situ meteorological measurements have been collected by auxiliary instruments on Mars, existing information is insufficient to conclusively characterize the natural processes via concurrent and high-resolution measurement of environmental drivers and activity. Thus, many atmospheric, aeolian, and other surface processes models – which are used to generate key constraints on science and exploration in many areas of planetary investigation—such as surface exposure/erosion estimates, landscape interpretation, and modeling dust storm development—remain untested under non-Earth conditions. Analogous terrestrial processes are often studied intensively via numerical modeling that integrates empirical results from laboratory and/or field studies of process-response interactions between the atmosphere and relevant surface landforms. Incorporation of such in situ measurements into model development has significantly advanced our understanding of atmosphere-surface interactions and related geomorphic processes on Earth, and is poised to do so on other planets. However, to date, such testing and refinement have not been possible in other planetary environments, partially because investigations of this sort require new technologies, mission architectures, and operations designs (e.g., different from large rovers focused on geochemical investigations) to fully address the key gaps in our understanding while keeping cost and risk low. Fortunately, technological developments in the areas of surface access, instrumentation, and onboard processing/memory now enable small spacecraft to accommodate meteorological and aeolian instrumentation that could collect the needed measurements to fill this critical gap while remaining within typical small spacecraft resource budgets. Furthermore, maturity of our understanding of the broader geologic and atmospheric context on Mars provides a ready framework for ingestion of discrete ground truth measurements into our understanding of the broader and multi-scale martian natural systems and processes. These advancements make addressing key science questions with novel mission concepts feasible, promising results that would significantly advance our understanding of extraterrestrial surface-atmosphere interactions. This summary follows from a community-generated white paper for the ongoing Planetary Science/Astrobiology Decadal Survey, small spacecraft concept development at JPL, and numerous JPL and community discussions.

Conference Paper↗

U.S. Geological Survey shrub/grass products provide new approach to shrubland monitoring

In the Western United States, shrubland ecosystems provide vital ecological, hydrological, biological, agricultural, and recreational services. However, disturbances such as livestock grazing, exotic species invasion, conversion to agriculture, climate change, urban expansion, and energy development are altering these ecosystems. Improving our understanding of how shrublands are distributed, where they are changing, the extent of the historical change, and likely future change directions is critical for successful management of these ecosystems. Remote-sensing technologies provide the most likely data source for large-area monitoring of ecosystem disturbance—both near-real time and historically. A monitoring framework supported by remote-sensing data can offer efficient and accurate analysis of change across a range of spatial and temporal scales. The U.S. Geological Survey has been working to develop new remote-sensing data, tools, and products to characterize and monitor these changing shrubland landscapes. Nine individual map products (components) have been developed that quantify the percent of shrub, sagebrush, big sagebrush, herbaceous, annual herbaceous, litter, bare ground, shrub height, and sagebrush height at 1-percent intervals in each 30-meter grid cell. These component products are designed to be combined and customized to widely support different applications in rangeland monitoring, analysis of wildlife habitat, resource inventory, adaptive management, and environmental review.

Fact Sheet↗

Sediments, structural framework, petroleum potential, environmental conditions, and operational considerations of the United States North Atlantic Outer Continental Shelf

The area designated for possible oil and gas lease sale as modified from BLM memorandum 3310 #42 (722) and referred to therein as the North Atlantic Outer Continental Shelf (OCS) contains about 58,300 sq km of shelf beneath water depths of less than 200 m and lies chiefly within the Georges Bank basin. The oldest sediments drilled or dredged on the bordering Continental Slope are sandstone, clay, and silt of Upper Cretaceous age. In Upper Cretaceous exposures, on Marthas Vineyard and nearby New England islands, the predominant lithology appears to be clay. About 125 km northeast of the eastern tip of Georges Bank, the Shell B-93 well penetrated clays and silts of Upper and Lower Cretaceous age above dense Jurassic carbonate rocks which overlie a basement of lower Paleozoic slate, schist, quartzite, and granite. Structurally, the Georges Bank basin is a westerly trending trough which opens to the west-southwest. Post-Paleozoic sediments are more than 8 km thick in parts of the basin. Major structural features appear to be directly related to basement structures. Local anticlines, probably caused by differential compaction over basement flexures and horst blocks or by later uplift along basement faults are reflected principally in Lower Cretaceous and older sediments, though some of these features continue upward to within 0.7 of a second (about 650 m) of the seafloor. Tertiary deposits in the Georges Bank basin are probably up to a kilometre thick and are made up of poorly consolidated sand, silt, and clay. The Cretaceous section is inferred to be up to 3.5 km thick and to be mainly clastics -- shale, siltstone, calcareous shale, changing to limestone in the lowest part of the system. Jurassic rocks in the deepest part of the basin appear to be about 3.6 to 4.0 km thick and probably consist mainly of dense carbonates. Potential source rocks in the Georges Bank basin may include organic-rich Cretaceous shale and carbonaceous Jurassic limestone. By analogy with the Scotian Shelf, Cretaceous sandstones are considered to be potential reservoir rocks. Local zones of porous dolomite are believed to be present in carbonate rocks of Jurassic age and should not be overlooked as potential reservoirs. Structural highs related to draping and differential compaction over basement blocks could be important potential petroleum traps. Additional traps may include reef structures near the shelf edge, updip pinchouts, and stratigraphic traps in both clastic and carbonate sediment. A statistical mean for the undiscovered recoverable petroleum resources is calculated to be 0.9 billion barrels of oil and 4.2 trillion cubic feet of gas. At the 5 percent probability level (1 in 20 chance) the undiscovered recoverable petroleum resources are calculated to be 2.4 billion barrels of oil and 12.5 trillion cubic feet of gas. These undiscovered recoverable petroleum resources are those quantities of oil and gas that may be reasonably expected to exist in favorable settings, but which have not yet been identified by drilling. Such estimates, therefore, carry a high degree of uncertainty. Environmental studies of Georges Bank indicated a low-moderate risk from petroleum development. However, the risk estimate is based on very limited data. Drift bottle returns used to infer oil spill trajectories show about a 2% overall recovery rate. Meteorologic data comes mainly from nearby land areas and from ships attempting to avoid storms. Seismicity on Georges Bank is low. This may reflect, in large part, the difficulty of land-based stations in recording earthquakes far from the coast. Direct data on the engineering properties of shallow buried sediment comes mainly from two Texas Tower surveys of limited areas on Georges Shoal and Nantucket Shoals made in the early 1950's. The 17 holes (most less than 30 m deep) reveal some silty layers below loose sand and much lateral variability in sediment type over short distances. The technology for exploration at the required water depths (20 m - 200 m) is available. Mobil drilling units are in great demand around the world and will have to be brought in from other areas along with skilled manpower. Our highest estimates indicate 50 platforms, 800 producing wells, 1,100 km of pipeline, and 5 onshore terminals may be needed. The time frame for production, using our high estimates (5% probability) for the undiscovered recoverable resources, could include 4-5 years for significant development, 6-7 years until production commences, and 18 years until peak production.

Open-File Report↗

International Watershed Technology: Improving Water Quality and Quantity at the Local, Basin, and Regional Scales

This article introduces the five papers in the “International Watershed Technology” collection. These papers were selected from 60 technical presentations at the fifth biennial ASABE 21st Century Watershed Technology Conference and Workshop: Improving the Quality of Water Resources at Local, Basin, and Regional Scales, held in Quito, Ecuador, on 3-9 December 2016. The conference focused on solving spatial and temporal water quality and quantity problems and addressed topics such as watershed management in developing countries, aquatic ecology and ecohydrology, ecosystem services, climate change mitigation strategies, flood forecasting, remote sensing, and water resource policy and management. While diverse, the presentation topics reflected the continuing evolution of the “data mining” and “big data” themes of past conferences related to geospatial data applications, with increasing emphasis on practical solutions. The papers selected for this collection represent applications of spatial data analyses toward practical ends with a theme of “tools and techniques for sustainability.” The papers address a range of topics, including the matching of crops with water availability, and assessing the environmental impacts of agricultural production. The papers identify some of the latest tools and techniques for improving sustainability in watershed resource management that are relevant to both developing and developed countries.

Transactions of the ASABE↗

Restoration monitoring metric framework: Integrating innovative remote-sensing technologies: Comparisons between field and remotely sensed vegetation surveys of restored forested and grassland sites in Ohio

Restoration monitoring is generally perceived as costly and time-consuming, yet the concept of universal restoration monitoring metrics is trending for evaluation of restoration performance across spatial scales, project boundaries, and jurisdictions. Natural Resource Damage Assessment and Restoration (NRDAR) practitioners seek to restore natural resources injured by oil spills or hazardous substance releases into the environment. Therefore, a multiagency team [US Army Engineer Research and Development Center (ERDC), US Department of the Interior (DOI), and US Department of Energy (DOE)] developed and field-tested a multitiered monitoring framework, illustrating a range of field and remote-sensing techniques and methodologies. The restoration monitoring framework and field demonstration offer a unique methodology to acquire and evaluate simultaneously collected, multiscale/multiplatform data. The result of this research provides new insights to (1) assist planning, implementing, and monitoring restoration progress and effectiveness; and (2) apply common monitoring methods, endpoints, and metrics to other types of ecosystem restoration initiatives. Although the aim was to inform monitoring and management of areas that had been injured, these methods could also be used to inform restoration monitoring practices in a broader context, benefiting environmental stewardship missions of all project partners.

Final Technical Report↗

NetCDF-CF-OPeNDAP: Standards for ocean data interoperability and object lessons for community data standards processes

It is generally recognized that meeting society's emerging environmental science and management needs will require the marine data community to provide simpler, more effective and more interoperable access to its data. There is broad agreement, as well, that data standards are the bedrock upon which interoperability will be built. The path that would bring the marine data community to agree upon and utilize such standards, however, is often elusive. In this paper we examine the trio of standards 1) netCDF files; 2) the Climate and Forecast (CF) metadata convention; and 3) the OPeNDAP data access protocol. These standards taken together have brought our community a high level of interoperability for "gridded" data such as model outputs, satellite products and climatological analyses, and they are gaining rapid acceptance for ocean observations. We will provide an overview of the scope of the contribution that has been made. We then step back from the information technology considerations to examine the community or "social" process by which the successes were achieved. We contrast the path by which the World Meteorological Organization (WMO) has advanced the Global Telecommunications System (GTS) - netCDF/CF/OPeNDAP exemplifying a "bottom up" standards process whereas GTS is "top down". Both of these standards are tales of success at achieving specific purposes, yet each is hampered by technical limitations. These limitations sometimes lead to controversy over whether alternative technological directions should be pursued. Finally we draw general conclusions regarding the factors that affect the success of a standards development effort - the likelihood that an IT standard will meet its design goals and will achieve community-wide acceptance. We believe that a higher level of thoughtful awareness by the scientists, program managers and technology experts of the vital role of standards and the merits of alternative standards processes can help us as a community to reach our interoperability goals faster.

Conference Paper↗

Rare-earth elements

The rare-earth elements (REEs) are 15 elements that range in atomic number from 57 (lanthanum) to 71 (lutetium); they are commonly referred to as the “lanthanides.” Yttrium (atomic number 39) is also commonly regarded as an REE because it shares chemical and physical similarities and has affinities with the lanthanides. Although REEs are not rare in terms of average crustal abundance, the concentrated deposits of REEs are limited in number. Because of their unusual physical and chemical properties, the REEs have diverse defense, energy, industrial, and military technology applications. The glass industry is the leading consumer of REE raw materials, which are used for glass polishing and as additives that provide color and special optical properties to the glass. Lanthanum-based catalysts are used in petroleum refining, and cerium-based catalysts are used in automotive catalytic converters. The use of REEs in magnets is a rapidly increasing application. Neodymium-iron-boron magnets, which are the strongest known type of magnets, are used when space and weight are restrictions. Nickel-metal hydride batteries use anodes made of a lanthanum-based alloys. China, which has led the world production of REEs for decades, accounted for more than 90 percent of global production and supply, on average, during the past decade. Citing a need to retain its limited REE resources to meet domestic requirements as well as concerns about the environmental effects of mining, China began placing restrictions on the supply of REEs in 2010 through the imposition of quotas, licenses, and taxes. As a result, the global rare-earth industry has increased its stockpiling of REEs; explored for deposits outside of China; and promoted new efforts to conserve, recycle, and substitute for REEs. New mine production began at Mount Weld in Western Australia, and numerous other exploration and development projects noted in this chapter are ongoing throughout the world. The REE-bearing minerals are diverse and often complex in composition. At least 245 individual REE-bearing minerals are recognized; they are mainly carbonates, fluorocarbonates, and hydroxylcarbonates (n = 42); oxides (n = 59); silicates (n = 85); and phosphates (n = 26). Many of the world’s significant REE deposits occur in carbonatites, which are carbonate igneous rocks. The REEs also have a strong genetic association with alkaline magmatism. The systematic geologic and chemical processes that explain these observations are not well understood. Economic or potentially economic REE deposits have been found in (a) carbonatites, (b) peralkaline igneous systems, (c) magmatic magnetite-hematite bodies, (d) iron oxide-copper-gold (IOCG) deposits, (e) xenotime-monazite accumulations in mafic gneiss, (f) ion-absorption clay deposits, and (g) monazite-xenotime-bearing placer deposits. Carbonatites have been the world’s main source for the light REEs since the 1960s. Ion-adsorption clay deposits in southern China are the world’s primary source of the heavy REEs. Monazite-bearing placer deposits were important sources of REEs before the mid-1960s and may be again in the future. In recent years, REEs have been produced from large carbonatite bodies mined at the Mountain Pass deposit in California and, in China, at the Bayan Obo deposit in Nei Mongol Autonomous Region, the Maoniuping deposit in Sichuan Province, the Daluxiang deposit in Sichuan Province, and the Weishan deposit in Anhui Province. Alkaline igneous complexes have recently been targeted for exploration because of their enrichments in the heavy REEs. Information relevant to the environmental aspects of REE mining is limited. Little is known about the aquatic toxicity of REEs. The United States lacks drinking water standards for REEs. The concentrations of REEs in environmental media are influenced by their low abundances in crustal rocks and their limited solubility in most groundwaters and surface waters. The scarcity of sulfide minerals, including pyrite, minimizes or eliminates concerns about acid-mine drainage for carbonatite-hosted deposits and alkaline-intrusion-related REE deposits. For now, insights into environmental responses of REE mine wastes must rely on predictive models.

Professional Paper↗

Instream water use in the United States: water laws and methods for determining flow requirements

Water use generally is divided into two primary classes - offstream use and instream use. In offstream use, sometimes called out-of-stream or diversionary use, water is withdrawn (diverted) from a stream or aquifer and transported to the place of use. Examples are irrigated agriculture, municipal water supply, and industrial use. Each of these offstream uses, which decreases the volume of water available downstream from the point of diversion, is discussed in previous articles in this volume. Instream use, which generally does not diminish the flow downstream from its point of use, and its importance are described in this article. One of the earliest instream uses of water in the United States was to turn the water wheels that powered much of the Nation's industry in the 18th and 19th centuries. Although a small volume of water might have been diverted to a mill near streamside, that water usually was returned to the stream near the point of diversion and, thus, the flow was not diminished downstream from the mill. Over time, the generation of hydroelectric power replaced mill wheels as a means of converting water flow into energy. Since the 1920's, the generation of hydroelectric power increasingly has become a major instream use of water. By 1985, more than 3 billion acre-feet of water (3,050,000 million gallons per day) was used annually for hydropower generation (Solley and others, 1988, p. 45)-enough water to cover the State of Colorado to a depth of 51 feet. Navigation is another instream use with a long history. The Lewis and Clark expedition journals and many of Mark Twain's novels illustrate the extent to which the Nation originally depended on adequate streamfiows for basic transportation. Navigation in the 1980's is still considered to be an instream use; however, it often is based upon a stream system that has been modified greatly through channelization, diking, and construction of dams and locks. The present (1987) inland water navigation system in the conterminous United States consists of about 12,000 miles of maintained waterways, over which about 500 million tons of cargo is carried each year (U.S. Army Corps of Engineers, 1988, p. 16). Although not so widely practiced in recent years, streams have been used to dispose of raw waste products from homes, communities, and factories. This use has been discouraged by law and public policy because of public health concerns and the damage it causes to the environment. Beginning in the mid-1960's, other instream uses gained new prominence in the water-resources arena-the assertion of a legal right to a free-flowing stream for biological, recreational, and esthetic purposes. These uses themselves, however, are not new. Riverine habitat always has produced fish, and the beauty of flowing water always has evoked a strong sense of esthetic appreciation. What is new is the emerging legitimacy and awareness of these noneconomic uses under State and Federal laws and regulations. In the past, environmental uses of flowing water were ignored, for the most part, under a long-standing legal tradition that favored offstream uses and certain instream uses that had a strong economic basis. The history of instream-flow policy debate really concerns those recently recognized types of interim uses. Although the more transitional water uses have been protected by law, the recognition of other in stream uses has resulted in substantial changes in State water laws. Although methods for determining the volume of water needed for most traditional water uses are relatively straight-forward and well-established, methods for determining water requirements for the in stream uses have been developed only recently and are continuing to evolve. Water laws that have favored the more traditional water uses, the inherent nature of conflict between instream and offstream water uses, and the special kinds of technological and philosophical problems posed by the "newer" types of instream uses are described below. Water laws that have been passed to accommodate the more recently recognized instream uses are summarized.

Report↗

Iodine-129 in the Snake River Plain Aquifer at and Near the Idaho National Laboratory, Idaho, 2003 and 2007

From 1953 to 1988, wastewater containing approximately 0.94 curies of iodine-129 (129I) was generated at the Idaho National Laboratory (INL) in southeastern Idaho. Almost all of this wastewater was discharged at or near the Idaho Nuclear Technology and Engineering Center (INTEC) on the INL site. Most of the wastewater was discharged directly into the eastern Snake River Plain aquifer through a deep disposal well until 1984; however, some wastewater also was discharged into unlined infiltration ponds or leaked from distribution systems below the INTEC. In 2003, the U.S. Geological Survey (USGS), in cooperation with the U.S. Department of Energy, collected samples for 129I from 36 wells used to monitor the Snake River Plain aquifer, and from one well used to monitor a perched zone at the INTEC. Concentrations of 129I in the aquifer ranged from 0.0000066 +- 0.0000002 to 0.72 +- 0.051 picocuries per liter (pCi/L). Many wells within a 3-mile radius of the INTEC showed decreases of as much as one order of magnitude in concentration from samples collected during 1990-91, and all of the samples had concentrations less than the Environmental Protection Agency's Maximum Contaminant Level (MCL) of 1 pCi/L. The average concentration of 129I in 19 wells sampled during both collection periods decreased from 0.975 pCi/L in 1990-91 to 0.249 pCi/L in 2003. These decreases are attributed to the discontinuation of disposal of 129I in wastewater after 1988 and to dilution and dispersion in the aquifer. Although water from wells sampled in 2003 near the INTEC showed decreases in concentrations of 129I compared with data collected in 1990-91, some wells south and east of the Central Facilities Area, near the site boundary, and south of the INL showed slight increases. These slight increases may be related to variable discharge rates of wastewater that eventually moved to these well locations as a mass of water from a particular disposal period. In 2007, the USGS collected samples for 129I from 36 wells that are used to monitor the aquifer south of INTEC and from 2 wells that are used to monitor perched zones at INTEC. Concentrations of 129I in the eastern Snake River Plain aquifer ranged from 0.000026 +- 0.000002 to 1.16 +- 0.04 pCi/L, and the concentration at one well exceeded the maximum contaminant level (1 pCi/L) for public drinking water supplies. The average concentration of 19 wells sampled in 2003 and 2007 did not differ; however, slight increases and decreases of concentrations in several areas around the INTEC were evident in the aquifer. The decreases are attributed to the discontinued disposal and to dilution and dispersion in the aquifer. The increases may be due to the movement into the aquifer of remnant perched water below the INTEC. In 2007, the USGS also collected samples from 31 zones in 6 wells equipped with multi-level WestbayTM packer sampling systems to help define the vertical distribution of 129I in the aquifer. Concentrations ranged from 0.000011 +- 0.0000005 to 0.0167 +- 0.0007 pCi/L. For three wells, concentrations of 129I between zones varied one to two orders of magnitude. For two wells, concentrations varied for one zone by more than an order of magnitude from the wells' other zones. Similar concentrations were measured from all five zones sampled in one well. All of the 31 zones had concentrations two or more magnitudes below the maximum contaminant level.

Scientific Investigations Report↗

Variation in detection distance of Eastern Black Rail (Laterallus jamaicensis jamaicensis) vocalizations by autonomous recording units

Autonomous recording units (ARUs) are an emerging technology that allows for passive monitoring of soniferous animals and soundscapes. Over the past decade, ARUs have become a popular tool for monitoring birds for their potential to reduce the labor and costs of traditional in-person sampling procedures. However, uncertainty surrounding factors affecting detection of avian taxa using ARUs can inhibit their monitoring efficacy. Eastern Black Rails ( Laterallus jamaicensis jamaicensis ) are a secretive marsh bird listed as a federally threatened species in the U.S.A. Eastern Black Rail vocalizations are difficult to detect by field personnel, and numerous in-person surveys can be required to confirm their presence at a site. While ARUs are an alternative for detecting Eastern Black Rails, it is unknown at what maximum distance an ARU can detect their vocalizations. We evaluated factors affecting the detection distance of simulated vocalizations for ARUs in four marsh vegetation types under a range of environmental conditions. Detection distances varied across models, vocalization and vegetation types, and call volume. Kickeedo vocalizations were detected at greater distances, and detection distances increased for all vocalization types in open vegetation. High relative humidity increased detection distances, while louder background noise decreased detection distances. High wind speeds in cordgrass ( Spartina spp .) decreased detection probability disproportionately relative to other vegetation types. Based on these results, considerations of survey area, vegetation type, and site condition can allow land managers and researchers to optimize Eastern Black Rail monitoring using ARUs. Given the substantial staff time needed to monitor this species, ARUs may increase the likelihood of detection and provide an efficient alternative to in-person monitoring.

Waterbirds↗

Genetics

In the current context of environmental changes, it is easy to see how extrinsic factors, such as shifts in sea surface temperature, food availability and accumulation of pollutants, can impact the health of marine mammals. However, intrinsic factors, including the genetic constitution of an individual, are also largely responsible for shaping health, particularly in terms of immune system effectiveness. In the previous edition of this book, the chapter on genetics thoroughly addressed the techniques available for identification of species, populations, stocks and individuals, studying social organization, and determining the relationships among individuals in a group. We have written the current chapter with an emphasis on how each individual’s genetic constitution and the prevalence of particular genetic variants is relevant to marine mammal health and disease. The chapter first presents a brief conceptual framework for understanding how genetics shape health and disease. We next outline common genetic techniques and current tools and technologies that are emerging in marine mammal health studies. Finally, the scope, pitfalls and limitations of these tools are discussed.

Book chapter↗

Geochemical modeling for mine site characterization and remediation

Geochemical Modeling for Mine Site Characterization and Remediation is the fourth of six volumes in the Management Technologies for Metal Mining Infl uenced Water series about technologies for management of metal mine and metallurgical process drainage. This handbook describes the important components of hydrogeochemical modeling for mine environments, primarily those mines where sulfi de minerals are present—metal mines and coal mines. It provides general guidelines on the strengths and limitations of geochemical modeling and an overview of its application to the hydrogeochemistry of both unmined mineralized sites and those contaminated from mineral extraction and mineral processing. The handbook includes an overview of the models behind the codes, explains vital geochemical computations, describes several modeling processes, provides a compilation of codes, and gives examples of their application, including both successes and failures. Hydrologic modeling is also included because mining contaminants most often migrate by surface water and groundwater transport, and contaminant concentrations are a function of water residence time as well as pathways. This is an indispensable resource for mine planners and engineers, environmental managers, land managers, consultants, researchers, government regulators, nongovernmental organizations, students, stakeholders, and anyone with an interest in mining influenced water.

Book↗

An experimental evaluation of the efficacy of imaging flow cytometry (FlowCam) for detecting invasive Dreissened and Corbiculid bivalve veligers

Zebra ( Dreissena polymorpha ) and quagga ( D. bugensis ) mussels, first introduced from central Asia into the Great Lakes of North America in the late 1980s, have crossed the continental divide and more recently spread across western North America. At the same time, several new technologies have been developed for the early detection of dreissenids, including the FlowCam, a digital imaging-in-flow instrument, intended to detect dreissenid planktonic larvae (veligers). However, the efficacy of this technology has rarely been tested. We experimentally evaluated the FlowCam’s ability to capture identifiable images of quagga mussel veligers under 2 different types of conditions: (i) deionized water, and (ii) Columbia River Basin water (CRBW), including natural sediment and native plankton. We further evaluated the FlowCam’s ability to distinguish between dreissenid veligers and corbiculid veligers (Asian clam, Corbicula fluminea ). We interpret our results to indicate that the FlowCam can consistently detect dreissenid veligers across a range of veliger densities. Moreover, the presence of other plankton and detritus only slightly affected dreissenid detection by the FlowCam. However, the orientation of individual bivalve veligers as they were imaged by the FlowCam precluded specific identification of a substantial proportion (24.8%) of veligers as either dreissenid or corbiculid. We suggest that the FlowCam is an important detection tool best utilized as part of a multifaceted approach, including traditional microscopy and possibly environmental DNA.

Lake and Reservoir Management↗

The effects of sediment and mercury mobilization in the South Yuba River and Humbug Creek confluence area, Nevada County, California: Concentrations, speciation, and environmental fate – Part 1: Field characterization

Millions of pounds of mercury (Hg) were deposited in the river and stream channels of the Sierra Nevada from placer and hard-rock mining operations in the late 1800s and early 1900s. The resulting contaminated sediments are relatively harmless when buried and isolated from the overlying aquatic environment. The entrained Hg in the sediment constitutes a potential risk to human and ecosystem health should it be reintroduced to the actively cycling portion of the aquatic system, where it can become methylated and subsequently bioaccumulated in the food web. Each year, sediment is mobilized within these fluvial systems during high stormflows, transporting hundreds of tons of Hg-laden sediment downstream. The State of California and resource-management agencies, including the Bureau of Land Management (BLM) and the U.S. Forest Service, are concerned about additional disturbances, such as from suction gold dredging activities, which have the potential to mobilize Hg associated with buried sediment layers elevated in Hg that are otherwise likely to remain buried under normal storm conditions. The BLM initiated a study looking at the feasibility of removing Hg-contaminated sediment at the confluence of the South Yuba River and Humbug Creek in the northern Sierra Nevada of California by using standard suction-dredge technology. Additionally, the California State Water Resources Control Board (SWRCB) supported a comprehensive characterization of the intended dredge site. Together, the BLM and SWRCB supported a comprehensive characterization of Hg contamination at the site and the potential effects of sediment disturbance at locations with historical hydraulic mining debris on downstream environments. The comprehensive study consisted of two primary components: field studies and laboratory experiments. The field component, described in this report, had several study elements: 1) a preliminary, smallscale, in-stream dredge test; 2) comprehensive characterization of grain size distribution, Hg speciation, and mineralogy of bed and suspended sediment; 3) a determination of the past and current sources of sediment in the study area; 4) an assessment of Hg bioaccumulation in the local invertebrate population; and 5) a comparison of potential Hg transport caused by natural storm disturbances with potential Hg mobilization caused by suction dredging as a method of Hg removal at the study site. The laboratory component of the study assessed the potential influence of the disturbance of Hg-contaminated sediment through experiments designed to simulate in-stream transport, deposition, and potential methylation of Hg, described in a companion report (see Marvin-DiPasquale and others, 2011). Results of the field studies indicate that the fine-grained fraction (silt-clay, less than 0.063 millimeters) contains the greatest concentration of Hg in contaminated sediment. Because the fine-grained fraction is the most susceptible to longrange fluvial transport, disturbance of Hg-contaminated sediment is likely to increase the concentration and load of Hg in downstream waters. The preliminary, small-scale dredge test showed an increase in the concentration of fine particles and Hg in the water column caused by the dredge activity, despite relatively low concentrations of fine particles and Hg (about 300 nanograms per gram) at the dredge site. Characterization of sediment from two test pits and other sites in the vicinity of the confluence of the South Yuba River and Humbug Creek revealed a highly variable distribution of fine- and coarse-grained sediment. The highest levels of Hg contamination (up to 11,100 ng/g) were associated with the fine-grained fraction of sediment from the bedrock contact zone of Pit 2, a horizon which also yielded grains of gold and gold-Hg amalgam. A closed-circuit tank experiment with a venturi dredge at the base of Pit 1, in a gravel bar within the South Yuba River, resulted in fine-grained suspended sediment remaining in suspension more than 40 hours following the disturbance simulation. Although the volumetric concentration of Hg declined over time as particles settled out, the concentration of Hg on the suspended particles increased over time as the suspended material became finer grained, because Hg is preferentially adsorbed on to clay-sized particles. Mineralogical and chemical analyses indicated that the buried fine-grained material with the greatest Hg contamination was derived from hydraulic mining debris, which consist primarily of Eocene gravels mined in the Malakoff Diggins, North Bloomfield, and Lake City areas within the South Yuba River watershed. Coarse material and more recently deposited sediment were derived primarily from upstream sources on the South Yuba River. The biota assessment indicated that invertebrate taxa collected from all sites on the South Yuba River in 2007, including lower Humbug Creek, had elevated concentrations of total mercury (THg) and methylmercury (MeHg) compared to a reference site on the Bear River, upstream of mining effects. Differences with the reference site were less pronounced in 2008 when a significant reduction in MeHg concentrations was observed in biota across all taxa from concentrations in 2007. It is possible that the inter-annual variation was related to the fact that suction dredging was active in the South Yuba River in 2007 but not in 2008 when a local moratorium was imposed by the BLM. There were significant variations among taxa for both THg and MeHg concentrations, with the water striders (Gerridae) having the highest concentrations of both THg and MeHg; variation among sites was not as strong as between years or among taxa. These results suggest that additional monitoring would be helpful to investigate the possible linkage between variations in MeHg bioaccumulation and levels of suction dredge activity in areas of historical gold mining. Results from the field studies indicate that disturbance of the finegrained Hg-contaminated sediment would likely lead to enhanced mobilization of Hg to downstream environments; therefore, the use of suction dredging to remove Hg at the South Yuba River and Humbug Creek confluence area would likely result in enhanced Hg transport downstream relative to natural conditions.

California↗

Effects of coal-mine discharges on the quality of the Stonycreek River and its tributaries, Somerset and Cambria counties, Pennsylvania

This report describes the results of a study by the U.S. Geological Survey, done in cooperation with the Somerset Conservation District, to locate and sample abandoned coal-mine discharges in the Stonycreek River Basin, to prioritize the mine discharges for remediation, and to determine the effects of the mine discharges on water quality of the Stonycreek River and its major tributaries. From October 1991 through November 1994, 270 abandoned coal-mine discharges were located and sampled. Discharges from 193 mines exceeded U.S. Environmental Protection Agency effluent standards for pH, discharges from 122 mines exceeded effluent standards for total-iron concentration, and discharges from 141 mines exceeded effluent standards for total-manganese concentration. Discharges from 94 mines exceeded effluent standards for all three constituents. Only 40 mine discharges met effluent standards for pH and concentrations of total iron and total manganese. A prioritization index (PI) was developed to rank the mine discharges with respect to their loading capacity on the receiving stream. The PI lists the most severe mine discharges in a descending order for the Stonycreek River Basin and for subbasins that include the Shade Creek, Paint Creek, Wells Creek, Quemahoning Creek, Oven Run, and Pokeytown Run Basins. Passive-treatment systems that include aerobic wetlands, compost wetlands, and anoxic limestone drains (ALD's) are planned to remediate the abandoned mine discharges. The successive alkalinity-producing-system treatment combines ALD technology with the sulfate reduction mechanism of the compost wetland to effectively remediate mine discharge. The water quality and flow of each mine discharge will determine which treatment system or combination of treatment systems would be necessary for remediation. A network of 37 surface-water sampling sites was established to determine stream-water quality during base flow. A series of illustrations show how water quality in the mainstem deteriorates downstream because of inflows from tributaries affected by acidic mine discharges. From the upstream mainstem site (site 801) to the outflow mainstem site (site 805), pH decreased from 6.8 to 4.2, alkalinity was completely depleted by inflow acidities, and total-iron discharges increased from 30 to 684 pounds per day. Total-manganese and total-sulfate discharges increased because neither constituent precipitates readily. Also, discharges of manganese and sulfate entering the mainstem from tributary streams have a cumulative effect. Oven Run and Pokeytown Run are two small tributary streams significantly affected by acidic mine drainage (AMD) that flow into the Stonycreek River near the town of Hooversville. The Pokeytown Run inflow is about 0.5 mile downstream from the Oven Run inflow. These two streams are the first major source of AMD flowing into the Stonycreek River. Data collected on the Stonycreek River above the Oven Run inflow and below the Pokeytown Run inflow show a decrease in pH from 7.6 to 5.1, a decrease in alkalinity concentration from 42 to 2 milligrams per liter, an increase in total sulfate discharge from 18 to 41 tons per day, and an increase in total iron discharge from 29 to 1,770 pounds per day. Data collected at three mainstem sites on the Stonycreek River below Oven Run and Pokeytown Run show a progressive deterioration in river water quality from AMD. Shade Creek and Paint Creek are other tributary streams to the Stonycreek River that have a significant negative effect on water quality of the Stonycreek River. One third of the abandoned-mine discharges sampled were in the Shade Creek and Paint Creek Basins.

Pennsylvania↗

Nature . . . an environmental yardstick

To one who has spent his professional career in geologic science, conservation always has had special meaning. In the measurements so necessary to his work the geologist develops an integrity in the use of numbers and in the qualifications attending the validity of numbers. Scientific analysis of geologic events and sequence develops a keen sense of what is coincidental, correlative, and consequential. The geologist applies his science in evaluating hazards to man as natural catastrophes and/or benefits to man such as earth materials that form the resource base of his society. But more than these the geologist has acquired a deep appreciation for the planet as a whole, its inner structure, its landscape, and the living things that abound.

Information and Technology Report↗