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At least 163 records · Page 9Linked to original sources
USGS2023

A novel approach to assessing natural resource injury with Bayesian networks

Quantifying the effects of environmental stressors on natural resources is problematic because of complex interactions among environmental factors that influence endpoints of interest. This complexity, coupled with data limitations, propagates uncertainty that can make it difficult to causally associate specific environmental stressors with injury endpoints. The Natural Resource Damage Assessment and Restoration (NRDAR) regulations under the Comprehensive Environmental Response, Compensation, and Liability Act and Oil Pollution Act aim to restore natural resources injured by oil spills and hazardous substances released into the environment; exploration of alternative statistical methods to evaluate effects could help address NRDAR legal claims. Bayesian networks (BNs) are statistical tools that can be used to estimate the influence and interrelatedness of abiotic and biotic environmental variables on environmental endpoints of interest. We investigated the application of a BN for injury assessment using a hypothetical case study by simulating data of acid mine drainage (AMD) affecting a fictional stream-dwelling bird species. We compared the BN-generated probability estimates for injury with a more traditional approach using toxicity thresholds for water and sediment chemistry. Bayesian networks offered several distinct advantages over traditional approaches, including formalizing the use of expert knowledge, probabilistic estimates of injury using intermediate direct and indirect effects, and the incorporation of a more nuanced and ecologically relevant representation of effects. Given the potential that BNs have for natural resource injury assessment, more research and field-based application are needed to determine their efficacy in NRDAR. We expect the resulting methods will be of interest to many US federal, state, and tribal programs devoted to the evaluation, mitigation, remediation, and/or restoration of natural resources injured by releases or spills of contaminants

Integrated Environmental Assessment and Management↗
USGS2021

Modern Mars' geomorphological activity, driven by wind, frost, and gravity

Extensive evidence of landform-scale martian geomorphic changes has been acquired in the last decade, and the number and range of examples of surface activity have increased as more high-resolution imagery has been acquired. Within the present-day Mars climate, wind and frost/ice are the dominant drivers, resulting in large avalanches of material down icy, rocky, or sandy slopes; sediment transport leading to many scales of aeolian bedforms and erosion; pits of various forms and patterned ground; and substrate material carved out from under subliming ice slabs. Due to the ability to collect correlated observations of surface activity and new landforms with relevant environmental conditions with spacecraft on or around Mars, studies of martian geomorphologic activity are uniquely positioned to directly test surface-atmosphere interaction and landform formation/evolution models outside of Earth. In this paper, we outline currently observed and interpreted surface activity occurring within the modern Mars environment, and tie this activity to wind, seasonal surface CO2 frost/ice, sublimation of subsurface water ice, and/or gravity drivers. Open questions regarding these processes are outlined, and then measurements needed for answering these questions are identified. In the final sections, we discuss how many of these martian processes and landforms may provide useful analogs for conditions and processes active on other planetary surfaces, with an emphasis on those that stretch the bounds of terrestrial-based models or that lack terrestrial analogs. In these ways, modern Mars presents a natural and powerful comparative planetology base case for studies of Solar System surface processes, beyond or instead of Earth.

Geomorphology↗
USGS2021

The influence of legacy contamination on the transport and bioaccumulation of mercury within the Mobile River Basin

Past industrial use and subsequent release of mercury (Hg) into the environment have resulted in severe cases of legacy contamination that still influence contemporary Hg levels in biota. While the bioaccumulation of legacy Hg is commonly assessed via concentration measurements within fish tissue, this practice becomes difficult in regions of high productivity and methylmercury (MeHg) production, like the Mobile River Basin, Alabama in the southeastern United States. This study applied Hg stable isotope tracers to distinguish legacy Hg from regional deposition sources in sediments, waters, and fish within the Mobile River. Sediments and waters displayed differences in δ 202 Hg between industrial and background sites, which corresponded to drastic differences in Hg concentration. Sites that were affected by legacy Hg, as defined by δ 202 Hg, produced largemouth bass with lower MeHg content (59–70%) than those captured in the main rivers (>85%). Direct measurements of Hg isotopes and mathematical estimates of MeHg isotope pools in fish displayed similar distinctions between legacy and watershed sources as observed in other matrices. These results indicate that legacy Hg can accumulate directly into fish tissue as the inorganic species and may also be available for methylation within contaminated zones decades after the initial release.

Alabama↗
USGS2014

Pluvial lakes in the Great Basin of the western United States: a view from the outcrop

Paleo-lakes in the western United States provide geomorphic and hydrologic records of climate and drainage-basin change at multiple time scales extending back to the Miocene. Recent reviews and studies of paleo-lake records have focused on interpretations of proxies in lake sediment cores from the northern and central parts of the Great Basin. In this review, emphasis is placed on equally important studies of lake history during the past ∼30 years that were derived from outcrop exposures and geomorphology, in some cases combined with cores. Outcrop and core records have different strengths and weaknesses that must be recognized and exploited in the interpretation of paleohydrology and paleoclimate. Outcrops and landforms can yield direct evidence of lake level, facies changes that record details of lake-level fluctuations, and geologic events such as catastrophic floods, drainage-basin changes, and isostatic rebound. Cores can potentially yield continuous records when sampled in stable parts of lake basins and can provide proxies for changes in lake level, water temperature and chemistry, and ecological conditions in the surrounding landscape. However, proxies such as stable isotopes may be influenced by several competing factors the relative effects of which may be difficult to assess, and interpretations may be confounded by geologic events within the drainage basin that were unrecorded or not recognized in a core. The best evidence for documenting absolute lake-level changes lies within the shore, nearshore, and deltaic sediments that were deposited across piedmonts and at the mouths of streams as lake level rose and fell. We review the different shorezone environments and resulting deposits used in such reconstructions and discuss potential estimation errors. Lake-level studies based on deposits and landforms have provided paleohydrologic records ranging from general changes during the past million years to centennial-scale details of fluctuations during the late Pleistocene and Holocene. Outcrop studies have documented the integration histories of several important drainage basins, including the Humboldt, Amargosa, Owens, and Mojave river systems, that have evolved since the Miocene within the active tectonic setting of the Great Basin; these histories have influenced lake levels in terminal basins. Many pre-late Pleistocene lakes in the western Great Basin were significantly larger and record wetter conditions than the youngest lakes. Outcrop-based lake-level data provide important checks on core-based proxy interpretations; we discuss four such comparisons. In some cases, such as for Lakes Owens and Manix, outcrop and core data synthesis yields stronger and more complete records; in other cases, such as for Bonneville and Lahontan, conflicts point toward reconsideration of confounding factors in interpretation of core-based proxies.

Great Basin↗
USGS2007

Monitoring and modeling ice-rock avalanches from ice-capped volcanoes: A case study of frequent large avalanches on Iliamna Volcano, Alaska

Iliamna is an andesitic stratovolcano of the Aleutian arc with regular gas and steam emissions and mantled by several large glaciers. Iliamna Volcano exhibits an unusual combination of frequent and large ice-rock avalanches in the order of 1 ?? 106??m3 to 3 ?? 107??m3 with recent return periods of 2-4??years. We have reconstructed an avalanche event record for the past 45??years that indicates Iliamna avalanches occur at higher frequency at a given magnitude than other mass failures in volcanic and alpine environments. Iliamna Volcano is thus an ideal site to study such mass failures and its relation to volcanic activity. In this study, we present different methods that fit into a concept of (1) long-term monitoring, (2) early warning, and (3) event documentation and analysis of ice-rock avalanches on ice-capped active volcanoes. Long-term monitoring methods include seismic signal analysis, and space-and airborne observations. Landsat and ASTER satellite data was used to study the extent of hydrothermally altered rocks and surface thermal anomalies at the summit region of Iliamna. Subpixel heat source calculation for the summit regions where avalanches initiate yielded temperatures of 307 to 613??K assuming heat source areas of 1000 to 25??m2, respectively, indicating strong convective heat flux processes. Such heat flow causes ice melting conditions and is thus likely to reduce the strength at the base of the glacier. We furthermore demonstrate typical seismic records of Iliamna avalanches with rarely observed precursory signals up to two hours prior to failure, and show how such signals could be used for a multi-stage avalanche warning system in the future. For event analysis and documentation, space- and airborne observations and seismic records in combination with SRTM and ASTER derived terrain data allowed us to reconstruct avalanche dynamics and to identify remarkably similar failure and propagation mechanisms of Iliamna avalanches for the past 45??years. Simple avalanche flow modeling was able to reasonably replicate Iliamna avalanches and can thus be applied for hazard assessments. Hazards at Iliamna Volcano are low due to its remote location; however, we emphasize the transfer potential of the methods presented here to other ice-capped volcanoes with much higher hazards such as those in the Cascades or the Andes. ?? 2007 Elsevier B.V. All rights reserved.

Journal of Volcanology and Geothermal Research↗
USGS1995

USGS Tracks Acid Rain

The U.S. Geological Survey (USGS) has been actively studying acid rain for the past 15 years. When scientists learned that acid rain could harm fish, fear of damage to our natural environment from acid rain concerned the American public. Research by USGS scientists and other groups began to show that the processes resulting in acid rain are very complex. Scientists were puzzled by the fact that in some cases it was difficult to demonstrate that the pollution from automobiles and factories was causing streams or lakes to become more acidic. Further experiments showed how the natural ability of many soils to neutralize acids would reduce the effects of acid rain in some locations--at least as long as the neutralizing ability lasted (Young, 1991). The USGS has played a key role in establishing and maintaining the only nationwide network of acid rain monitoring stations. This program is called the National Atmospheric Deposition Program/National Trends Network (NADP/NTN). Each week, at approximately 220 NADP/NTN sites across the country, rain and snow samples are collected for analysis. NADP/NTN site in Montana. The USGS supports about 72 of these sites. The information gained from monitoring the chemistry of our nation's rain and snow is important for testing the results of pollution control laws on acid rain.

Fact Sheet↗
USGS2023

Reduction of paraoxonase expression followed by inactivation across independent semiaquatic mammals suggests stepwise path to pseudogenization

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 ( Pon1 ) gene among aquatic mammal lineages— Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3 , a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1 , there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.

Molecular Biology and Evolution↗
USGS2017

Ecosystem services from transborder migratory species: Implications for conservation governance

This article discusses the conservation challenges of volant migratory transborder species and conservation governance primarily in North America. Many migratory species provide ecosystem service benefits to society. For example, insectivorous bats prey on crop pests and reduce the need for pesticides; birds and insects pollinate food plants; and birds afford recreational opportunities to hunters and birdwatchers. Migration is driven by the seasonal availability of resources; as resources in one area become seasonally scarce, individuals move to locations where resources have become seasonally abundant. The separation of the annual lifecycle means that species management and governance is often fractured across international borders. Because migratory species depend on habitat in different locations, their ability to provide ecosystem services in one area depends on the spatial subsidies, or support, provided by habitat and ecological processes in other areas. This creates telecouplings, or interconnections across geographic space, of areas such that impacts to the habitat of a migratory species in one location will affect the benefits enjoyed by people in other locations. Information about telecoupling and spatial subsidies can be used to craft new governance arrangements such as Payment for Ecosystem Services programs that target specific stakeholder groups and locations. We illustrate these challenges and opportunities with three North American case studies: the Duck Stamp Program, Mexican free-tailed bats ( Tadarida brasiliensis mexicana ), and monarch butterflies ( Danaus plexippus ).

Annual Review of Environment and Resources↗
USGS2019

Spatial sampling bias and model complexity in stream-based species distribution models: A case study of Paddlefish (Polyodon spathula) in the Arkansas River basin, USA

Leveraging existing presence records and geospatial datasets, species distribution modeling has been widely applied to informing species conservation and restoration efforts. Maxent is one of the most popular modeling algorithms, yet recent research has demonstrated Maxent models are vulnerable to prediction errors related to spatial sampling bias and model complexity. Despite elevated rates of biodiversity imperilment in stream ecosystems, the application of Maxent models to stream networks has lagged, as has the availability of tools to address potential sources of error and calculate model evaluation metrics when modeling in nonraster environments (such as stream networks). Herein, we use Maxent and customized R code to estimate the potential distribution of paddlefish ( Polyodon spathula ) at a stream-segment level within the Arkansas River basin, USA, while accounting for potential spatial sampling bias and model complexity. Filtering the presence data appeared to adequately remove an eastward, large-river sampling bias that was evident within the unfiltered presence dataset. In particular, our novel riverscape filter provided a repeatable means of obtaining a relatively even coverage of presence data among watersheds and streams of varying sizes. The greatest differences in estimated distributions were observed among models constructed with default versus AIC C -selected parameterization. Although all models had similarly high performance and evaluation metrics, the AIC C -selected models were more inclusive of westward-situated and smaller, headwater streams. Overall, our results solidified the importance of accounting for model complexity and spatial sampling bias in SDMs constructed within stream networks and provided a roadmap for future paddlefish restoration efforts in the study area.

Arkansas, Colorado, Kansas, Missouri, Nebraska, Ne↗
USGS2017

Genomics of Arctic cod

The Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. To better understand the population genetic structure and the role of natural selection acting on the maternally-inherited mitochondrial genome (mitogenome), a molecule often associated with adaptations to temperature, we analyzed genetic data collected from 11 biparentally-inherited nuclear microsatellite DNA loci and nucleotide sequence data from from the mitochondrial DNA (mtDNA) cytochrome b (cytb) gene and, for a subset of individuals, the entire mitogenome. In addition, due to potential of species misidentification with morphologically similar Polar cod (Arctogadus glacialis), we used ddRAD-Seq data to determine the level of divergence between species and identify species-specific markers. Based on the findings presented here, Arctic cod across the Pacific Arctic (Bering, Chukchi, and Beaufort Seas) comprise a single panmictic population with high genetic diversity compared to other gadids. High genetic diversity was indicated across all 13 protein-coding genes in the mitogenome. In addition, we found moderate levels of genetic diversity in the nuclear microsatellite loci, with highest diversity found in the Chukchi Sea. Our analyses of markers from both marker classes (nuclear microsatellite fragment data and mtDNA cytb sequence data) failed to uncover a signal of microgeographic genetic structure within Arctic cod across the three regions, within the Alaskan Beaufort Sea, or between near-shore or offshore habitats. Further, data from a subset of mitogenomes revealed no genetic differentiation between Bering, Chukchi, and Beaufort seas populations for Arctic cod, Saffron cod (Eleginus gracilis), or Walleye pollock (Gadus chalcogrammus). However, we uncovered significant differences in the distribution of microsatellite alleles between the southern Chukchi and central and eastern Beaufort Sea samples of Arctic cod. Finally, using ddRAD-Seq data, we identified species-specific markers and in conjunction with mitogenome data, identified an Arctic cod x Polar cod hybrid in western Canadian Beaufort Sea. Overall, the lack of genetic structure among Arctic cod within the Bering, Chukchi and Beaufort seas of Alaska is concordant with the absence of geographic barriers to dispersal and typical among marine fishes. Arctic cod may exhibit a genetic pattern of isolation-by-distance, whereby populations in closer geographic proximity are more genetically similar than more distant populations. As this signal is only found between our two fartherest localities, data from populations elsewhere in the species’ global range are needed to determine if this is a general characteristic. Further, tests for selection suggested a limited role for natural selection acting on the mitochondrial genome of Arctic cod, but do not exclude the possibility of selection on genes involved in nuclear-mitogenome interactions. Unlike previous genetic assessment of Arctic cod sampled from the Chukchi Sea, the high levels of genetic diversity found in Arctic cod assayed in this study, across regions, suggests that the species in the Beaufort and Chukchi seas does not suffer from low levels of genetic variation, at least at neutral genetic markers. The large census size of Arctic cod may allow this species to retain high levels of genetic diversity. In addition, we discovered the presence of hybridization between Arctic and Polar cod (although low in frequency). Hybridization is expected to occur when environmental changes modify species distributions that result in contact between species that were previously separated. In such cases, hybridization may be an evolutionary mechanism that promotes an increase in genetic diversity that may provide species occupying changing environments with locally-adapted genotypes and, therefore, phenotypes. Natural selection can only act on the standing genetic variation present within a population. Therefore, given its higher levels of genetic diversity in combination with a large population size, Arctic cod may be resilient to current and future environmental change, as high genetic diversity is expected to increase opportunities for positive selection to act on genetic variants beneficial in different environments, regardless of the source of that genetic variation.

OCS Study↗
USGS2025

Causal networks to inform decisions for ecological restoration

The release of contaminants into the environment can occur from anthropogenic activities, such as oil extraction and transportation, mining, and industrial processes. Remediation associated with reducing contaminant concentrations, and restoration that improves animals and supporting habitat, are often needed to restore ecosystems to their pre-release, baseline condition. We demonstrated the application of Bayesian Decision Networks (BDNs) with two Natural Resource Damage Assessment and Restoration (NRDAR) case studies. We use a stylized case study of riparian restoration following the remediation of a mine-impacted site to evaluate proposed restoration actions aimed at restoring Song Sparrow ( Melospiza melodia ) populations to baseline conditions. We then use a settled NRDAR case with implemented restoration in the Upper Arkansas River (UAR, Colorado, USA) to demonstrate the application of BDNs to evaluate and forecast restoration effectiveness for Brown Trout ( Salmo trutta ) (i.e., restoration effectiveness assessment). The riparian restoration model showed differences in the effects of restoration actions on Song Sparrow populations, with the time to reach baseline generally reduced with increased restoration costs, indicating trade-offs between costs and expected recovery. The UAR model showed recovery of Brown Trout populations (i.e., uplift) in response to improved instream habitat restoration, along with forecasted improvements. While the BDNs we developed were specific to two case studies, the structure is adaptable to a diversity of sites, resources, and actions. We suggest that causal network modeling can provide restoration practitioners with a decision advisory tool useful for a wide range of projects.

Environmental Management↗
USGS2008

Relationship between remotely-sensed vegetation indices, canopy attributes and plant physiological processes: What vegetation indices can and cannot tell us about the landscape

Vegetation indices (VIs) are among the oldest tools in remote sensing studies. Although many variations exist, most of them ratio the reflection of light in the red and NIR sections of the spectrum to separate the landscape into water, soil, and vegetation. Theoretical analyses and field studies have shown that VIs are near-linearly related to photosynthetically active radiation absorbed by a plant canopy, and therefore to light-dependent physiological processes, such as photosynthesis, occurring in the upper canopy. Practical studies have used time-series VIs to measure primary production and evapotranspiration, but these are limited in accuracy to that of the data used in ground truthing or calibrating the models used. VIs are also used to estimate a wide variety of other canopy attributes that are used in Soil-Vegetation-Atmosphere Transfer (SVAT), Surface Energy Balance (SEB), and Global Climate Models (GCM). These attributes include fractional vegetation cover, leaf area index, roughness lengths for turbulent transfer, emissivity and albedo. However, VIs often exhibit only moderate, non-linear relationships to these canopy attributes, compromising the accuracy of the models. We use case studies to illustrate the use and misuse of VIs, and argue for using VIs most simply as a measurement of canopy light absorption rather than as a surrogate for detailed features of canopy architecture. Used this way, VIs are compatible with “Big Leaf” SVAT and GCMs that assume that canopy carbon and moisture fluxes have the same relative response to the environment as any single leaf, simplifying the task of modeling complex landscapes.

Arizona↗
USGS2022

The silence of the clams: Forestry registered pesticides as multiple stressors on soft-shell clams

Contaminants are ubiquitous in the environment, often reaching aquatic systems. Combinations of forestry use pesticides have been detected in both water and aquatic organism tissue samples in coastal systems. Yet, most toxicological studies focus on the effects of these pesticides individually, at high doses, and over acute time periods, which, while key for establishing toxicity and safe limits, are rarely environmentally realistic. We examined chronic (90 days) exposure by the soft-shell clam, Mya arenaria , to environmentally relevant concentrations of four pesticides registered for use in forestry (atrazine, 5 μg/L; hexazinone, 0.3 μg/L; indaziflam, 5 μg/L; and bifenthrin, 1.5 μg/g organic carbon (OC)). Pesticides were tested individually and in combination, except bifenthrin, which was tested only in combination with the other three. We measured shell growth and condition index every 30 days, as well as feeding rates, mortality, and chemical concentrations in tissue from a subset of clams at the end of the experiment to measure contaminant uptake. Indaziflam caused a high mortality rate (max. 36%), followed by atrazine (max. 27%), both individually as well as in combination with other pesticides. Additionally, indaziflam concentrations in tissue (61.70–152.56 ng/g) were higher than those of atrazine (26.48–48.56 ng/g), despite equal dosing concentrations, indicating higher tissue accumulation. Furthermore, clams exposed to indaziflam and hexazinone experienced reduced condition index and clearance rates individually and in combination with other compounds; however, the two combined did not result in significant mortality. These two compounds, even at environmentally relevant concentrations, affected a non-target organism and, in the case of the herbicide indaziflam, accumulated in clam tissue and appeared more toxic than other tested pesticides. These findings underscore the need for more comprehensive studies combining multiple compounds at relevant concentrations to understand their impacts on aquatic ecosystems.

Science of the Total Environment↗
USGS2015

Sequential decision making in computational sustainability via adaptive submodularity

Many problems in computational sustainability require making a sequence of decisions in complex, uncertain environments. Such problems are generally notoriously difficult. In this article, we review the recently discovered notion of adaptive submodularity, an intuitive diminishing returns condition that generalizes the classical notion of submodular set functions to sequential decision problems. Problems exhibiting the adaptive submodularity property can be efficiently and provably near-optimally solved using simple myopic policies. We illustrate this concept in several case studies of interest in computational sustainability: First, we demonstrate how it can be used to efficiently plan for resolving uncertainty in adaptive management scenarios. Secondly, we show how it applies to dynamic conservation planning for protecting endangered species, a case study carried out in collaboration with the US Geological Survey and the US Fish and Wildlife Service.

AI Magazine↗
USGS2009

Thatcher Bay, Washington, Nearshore Restoration Assessment

The San Juan Archipelago, located at the confluence of the Puget Sound, the Straits of Juan de Fuca in Washington State, and the Straits of Georgia, British Columbia, Canada, provides essential nearshore habitat for diverse salmonid, forage fish, and bird populations. With 408 miles of coastline, the San Juan Islands provide a significant portion of the available nearshore habitat for the greater Puget Sound and are an essential part of the regional efforts to restore Puget Sound (Puget Sound Shared Strategy 2005). The nearshore areas of the San Juan Islands provide a critical link between the terrestrial and marine environments. For this reason the focus on restoration and conservation of nearshore habitat in the San Juan Islands is of paramount importance. Wood-waste was a common by-product of historical lumber-milling operations. To date, relatively little attention has been given to the impact of historical lumber-milling operations in the San Juan Archipelago. Thatcher Bay, on Blakely Island, located near the east edge of the archipelago, is presented here as a case study on the restoration potential for a wood-waste contaminated nearshore area. Case study components include (1) a brief discussion of the history of milling operations. (2) an estimate of the location and amount of the current distribution of wood-waste at the site, (3) a preliminary examination of the impacts of wood-waste on benthic flora and fauna at the site, and (4) the presentation of several restoration alternatives for the site. The history of milling activity in Thatcher Bay began in 1879 with the construction of a mill in the southeastern part of the bay. Milling activity continued for more than 60 years, until the mill closed in 1942. Currently, the primary evidence of the historical milling operations is the presence of approximately 5,000 yd3 of wood-waste contaminated sediments. The distribution and thickness of residual wood-waste at the site was determined by using sediment coring and GIS-based interpolation techniques. Additionally, pilot studies were conducted to characterize in place sediment redox, organic composition, and sulfide impacts to nearshore flora and fauna. We found that the presence of wood-waste in Thatcher Bay may alter the quality of the benthic habitat by contributing to elevated levels of total organic composition (TOC) of the sediment. Increased TOC favors anaerobic respiration in marine sediments, and sulfide, a toxic by-product of this process, was found at levels as high as 17.5 mg L-1 in Thatcher Bay. The Thatcher Bay sulfide levels are several orders of magnitude higher than those known to impact benthic invertebrates. Eelgrass, Zostera marina, located on the western margin of Thatcher Bay, was surveyed by using underwater video surveys. This baseline distribution will in part be used to measure the impact of any future remediation efforts. Additionally, the distribution and survey data can provide an estimate of propagule source for future colonization of restored sediment. Three restoration alternatives were considered, and a ranking matrix was developed to score each alternative against site-specific and regional criteria. The process identified the removal of wood-waste from a water-based platform as the preferred alternative. Our multidisciplinary investigation identified the location, thickness, and potential impacts of wood-waste that has persisted in the nearshore environment of Thatcher Bay since at least 1942. We also provide a process to efficiently evaluate alternatives to remediate the impact of this historical disturbance and to potentially contribute to an increase of nearshore diversity and productivity at this site. Elements of this approach could inform restoration planning at similarly impacted sites throughout the region.

Open-File Report↗
USGS2008

Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

The steps necessary to conduct a pitfall trapping survey for small terrestrial vertebrates are presented. Descriptions of the materials needed and the methods to build trapping equipment from raw materials are discussed. Recommended data collection techniques are given along with suggested data fields. Animal specimen processing procedures, including toe- and scale-clipping, are described for lizards, snakes, frogs, and salamanders. Methods are presented for conducting vegetation surveys that can be used to classify the environment associated with each pitfall trap array. Techniques for data storage and presentation are given based on commonly use computer applications. As with any study, much consideration should be given to the study design and methods before beginning any data collection effort.

Techniques and Methods↗
USGS2005

Determination of uranyl incorporation into biogenic manganese oxides using X-ray absorption spectroscopy and scattering

Βiogenic manganese oxides are common and an important source of reactive mineral surfaces in the environment that may be potentially enhanced in bioremediation cases to improve natural attenuation. Experiments were performed in which the uranyl ion, UO 2 2+ (U(VI)), at various concentrations was present during manganese oxide biogenesis. At all concentrations, there was strong uptake of U onto the oxides. Synchrotron-based extended X-ray absorption fine structure (EXAFS) spectroscopy and X-ray diffraction (XRD) studies were carried out to determine the molecular-scale mechanism by which uranyl is incorporated into the oxide and how this incorporation affects the resulting manganese oxide structure and mineralogy. The EXAFS experiments show that at low concentrations (<0.3 mol % U, <1 μM U(VI) in solution), U(VI) is present as a strong bidentate surface complex. At high concentrations (>2 mol % U, >4 μM U(VI) in solution), the presence of U(VI) affects the stability and structure of the Mn oxide to form poorly ordered Mn oxide tunnel structures, similar to todorokite. EXAFS modeling shows that uranyl is present in these oxides predominantly in the tunnels of the Mn oxide structure in a tridentate complex. Observations by XRD corroborate these results. Structural incorporation may lead to more stable U(VI) sequestration that may be suitable for remediation uses. These observations, combined with the very high uptake capacity of the Mn oxides, imply that Mn-oxidizing bacteria may significantly influence dissolved U(VI) concentrations in impacted waters via sorption and incorporation into Mn oxide biominerals.

Environmental Science & Technology↗
USGS2005

Genetic divergence of rabies viruses from bat species of Colorado, USA

Molecular epidemiological studies have linked many cryptic human rabies cases in the United States with exposure to rabies virus (RV) variants associated with insectivorous bats. In Colorado, bats accounted for 98% of all reported animal rabies cases between 1977 and 1996. The genetic divergence of RV was investigated in bat and terrestrial animal specimens that were submitted for rabies diagnosis to the Colorado Department of Public Health and Environment (CDPHE), Colorado, USA. RV isolates from animal specimens across the United States were also included in the analysis. Phylogenetic analyses were performed on partial nucleoprotein (N) gene sequences, which revealed seven principal clades. RV associated with the colonial big brown bat, Eptesicus fuscus , an bats of the genus Myotis were found to segregate into two distinct clades (I and IV). Clade I was harbored by E. fuscus and Myotis species, but was also identified in terrestrial animals such as domestic cats and striped skunks ( Mephitis mephitis ). Clade IV was divided into subclades IVA, IVB, and IVC; IVA was identified in E. fuscus, and Myotis species bats, and also in a fox; subclades IVB and IVC circulated predominantly in E. fuscus . Clade II was formed by big free-tailed bat ( Nyctinomops macrotis ) and striped skunk ( Mephitis mephitis ) samples. Clade III included RVs that are maintained by generally solitary, migratory bats such as the silver-haired bat ( Lasionycteris noctivagans ) and bats of the genus Lasiurus . Big brown bats were found to harbor this RV variant. None of the Colorado specimens segregated with clades V and VII that harbor RVs associated with terrestrial animals. Different species of bats had the same RV variant, indicating active inter-species rabies transmission. In Colorado, animal rabies occurs principally in bats, and the identification of bat RVs in cat, gray fox Urocyon cinereoargenteus ), and striped skunks demonstrated the importance of rabies spillover from bats to domestic and terrestrial wildlife species.

Vector-Borne and Zoonotic Diseases↗