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Final Project Memorandum: Ecological implications of mangrove forest migration in the southeastern U.S.

Winter climate change has the potential to have a large impact on coastal wetlands in the southeastern United States. Warmer winter temperatures and reductions in the intensity of freeze events would likely lead to mangrove forest range expansion and salt marsh displacement in parts of the U.S. Gulf of Mexico and Atlantic coast. The objective of this research was to better evaluate the ecological implications of mangrove forest migration and salt marsh displacement. The potential ecological impacts of mangrove migration are diverse ranging from important biotic impacts (e.g., coastal fisheries, land bird migration; colonial-nesting wading birds) to ecosystem stability (e.g., response to sea level rise and drought; habitat loss; coastal protection) to biogeochemical processes (e.g., carbon storage; water quality). This research specifically investigated the impact of mangrove forest migration on coastal wetland soil processes and the consequent implications for coastal wetland responses to sea level rise and carbon storage.

Report↗

Simulation of ground-water flow in the High Plains aquifer, southern sandhills area, west-central Nebraska

A generalized ground-water flow model was prepared for the High Plains aquifer in the southern sandhills area of west-central Nebraska. A grid of 4- by 4-mile nodes was established over the study area. Steady-state water levels were simulated using a distribution of recharge from a soil-moisture budget model and from estimates of hydraulic conductivity obtained from logs of test holes in the area. The final calibrated simulation used hydraulic- conductivity values that were 122 percent, and recharge rates that were 89 percent of the original values used in the model. Sixty-seven percent of the simulated recharge to the High Plains aquifer discharges to rivers, streams, and lakes. Discharges through ground-water evapotranspiration and from pumping wells account for 20 percent, with the wells accounting for less than 10 percent of the total discharge, and subsurface boundary outflow accounts for 13 percent. Twenty years of simulated pumping, assuming one additional well would be added to each township annually for 10 years, and two wells per township would be added each year for the succeeding 10 years, produced a maximum simulated drawdown of less than 10 feet when a uniform specific yield of 16 percent for the aquifer in the study area was assumed.

Open-File Report↗

A novel member of the family Hepeviridae from cutthroat trout ( Oncorhynchus clarkii )

Beginning in 1988, the Chinook salmon embryo (CHSE-214) cell line was used to isolate a novel virus from spawning adult trout in the state of California, USA. Termed the cutthroat trout ( Oncorhynchus clarkii ) virus (CTV), the small, round virus was not associated with disease, but was subsequently found to be present in an increasing number of trout populations in the western USA, likely by a combination of improved surveillance activities and the shipment of infected eggs to new locations. Here, we report that the full length genome of the 1988 Heenan Lake isolate of CTV consisted of 7269 nucleotides of positive-sense, single-stranded RNA beginning with a 5' untranslated region (UTR), followed by three open reading frames (ORFs), a 3' UTR and ending in a polyA tail. The genome of CTV was similar in size and organization to that of Hepatitis E virus (HEV) with which it shared the highest nucleotide and amino acid sequence identities. Similar to the genomes of human, rodent or avian hepeviruses, ORF 1 encoded a large, non-structural polyprotein that included conserved methyltransferase, protease, helicase and polymerase domains, while ORF 2 encoded the structural capsid protein and ORF 3 the phosphoprotein. Together, our data indicated that CTV was clearly a member of the family Hepeviridae , although the level of amino acid sequence identity with the ORFs of mammalian or avian hepeviruses (13-27%) may be sufficiently low to warrant the creation of a novel genus. We also performed a phylogenetic analysis using a 262. nt region within ORF 1 for 63 isolates of CTV obtained from seven species of trout reared in various geographic locations in the western USA. While the sequences fell into two genetic clades, the overall nucleotide diversity was low (less than 8.4%) and many isolates differed by only 1-2 nucleotides, suggesting an epidemiological link. Finally, we showed that CTV was able to form persistently infected cultures of the CHSE-214 cell line that may have use in research on the biology or treatment of hepevirus infections of humans or other animals.

Virus Research↗

Completion Summary for Well NRF-16 near the Naval Reactors Facility, Idaho National Laboratory, Idaho

In 2009, the U.S. Geological Survey in cooperation with the U.S. Department of Energy's Naval Reactors Laboratory Field Office, Idaho Branch Office cored and completed well NRF-16 for monitoring the eastern Snake River Plain (SRP) aquifer. The borehole was initially cored to a depth of 425 feet below land surface and water samples and geophysical data were collected and analyzed to determine if well NRF-16 would meet criteria requested by Naval Reactors Facility (NRF) for a new upgradient well. Final construction continued after initial water samples and geophysical data indicated that NRF-16 would produce chemical concentrations representative of upgradient aquifer water not influenced by NRF facility disposal, and that the well was capable of producing sustainable discharge for ongoing monitoring. The borehole was reamed and constructed as a Comprehensive Environmental Response Compensation and Liability Act monitoring well complete with screen and dedicated pump. Geophysical and borehole video logs were collected after coring and final completion of the monitoring well. Geophysical logs were examined in conjunction with the borehole core to identify primary flow paths for groundwater, which are believed to occur in the intervals of fractured and vesicular basalt and to describe borehole lithology in detail. Geophysical data also were examined to look for evidence of perched water and the extent of the annular seal after cement grouting the casing in place. Borehole videos were collected to confirm that no perched water was present and to examine the borehole before and after setting the screen in well NRF-16. Two consecutive single-well aquifer tests to define hydraulic characteristics for well NRF-16 were conducted in the eastern SRP aquifer. Transmissivity and hydraulic conductivity averaged from the aquifer tests were 4.8 x 103 ft2/d and 9.9 ft/d, respectively. The transmissivity for well NRF-16 was within the range of values determined from past aquifer tests in other wells near NRF of 4.4 x 102 to 5.1 x 105 ft2/d. Water samples were analyzed for metals, nutrients, total organic carbon, volatile organic compounds, semi-volatile organic compounds, herbicides, pesticides, polychlorinated biphenols, and radionuclides. All chloride, nitrate, and sulfate concentrations were less than background concentrations for the eastern SRP aquifer north of the NRF. Concentrations in water samples for most of the organic compounds and radionuclides were less than the reporting limits and reporting levels.

Scientific Investigations Report↗

Parameter estimation method and updating of regional prediction equations for ungaged sites in the desert region of California

The U.S. Geological Survey (USGS) is currently updating at-site flood frequency estimates for USGS streamflow-gaging stations in the desert region of California. The at-site flood-frequency analysis is complicated by short record lengths (less than 20 years is common) and numerous zero flows/low outliers at many sites. Estimates of the three parameters (mean, standard deviation, and skew) required for fitting the log Pearson Type 3 (LP3) distribution are likely to be highly unreliable based on the limited and heavily censored at-site data. In a generalization of the recommendations in Bulletin 17B, a regional analysis was used to develop regional estimates of all three parameters (mean, standard deviation, and skew) of the LP3 distribution. A regional skew value of zero from a previously published report was used with a new estimated mean squared error (MSE) of 0.20. A weighted least squares (WLS) regression method was used to develop both a regional standard deviation and a mean model based on annual peak-discharge data for 33 USGS stations throughout California’s desert region. At-site standard deviation and mean values were determined by using an expected moments algorithm (EMA) method for fitting the LP3 distribution to the logarithms of annual peak-discharge data. Additionally, a multiple Grubbs-Beck (MGB) test, a generalization of the test recommended in Bulletin 17B, was used for detecting multiple potentially influential low outliers in a flood series. The WLS regression found that no basin characteristics could explain the variability of standard deviation. Consequently, a constant regional standard deviation model was selected, resulting in a log-space value of 0.91 with a MSE of 0.03 log units. Yet drainage area was found to be statistically significant at explaining the site-to-site variability in mean. The linear WLS regional mean model based on drainage area had a Pseudo- 2 R of 51 percent and a MSE of 0.32 log units. The regional parameter estimates were then used to develop a set of equations for estimating flows with 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities for ungaged basins. The final equations are functions of drainage area.Average standard errors of prediction for these regression equations range from 214.2 to 856.2 percent.

California↗

Spatial and temporal variation of stream chemistry associated with contrasting geology and land-use patterns in the Chesapeake Bay watershed—Summary of results from Smith Creek, Virginia; Upper Chester River, Maryland; Conewago Creek, Pennsylvania; and Difficult Run, Virginia, 2010–2013

Despite widespread and ongoing implementation of conservation practices throughout the Chesapeake Bay watershed, water quality continues to be degraded by excess sediment and nutrient inputs. While the Chesapeake Bay Program has developed and maintains a large-scale and long-term monitoring network to detect improvements in water quality throughout the watershed, fewer resources have been allocated for monitoring smaller watersheds, even though water-quality improvements that may result from the implementation of conservation practices are likely to be first detected at smaller watershed scales. In 2010, the U.S. Geological Survey partnered with the U.S. Environmental Protection Agency and the U.S. Department of Agriculture to initiate water-quality monitoring in four selected small watersheds that were targeted for increased implementation of conservation practices. Smith Creek watershed is an agricultural watershed in the Shenandoah Valley of Virginia that is dominated by cattle and poultry production, and the Upper Chester River watershed is an agricultural watershed on the Eastern Shore of Maryland that is dominated by row-cropping activities. The Conewago Creek watershed is an agricultural watershed in southeastern Pennsylvania that is characterized by mixed agricultural activities. The fourth watershed, Difficult Run, is a suburban watershed in northern Virginia that is dominated by medium density residential development. The objective of this study was to investigate spatial and temporal variations in water chemistry and suspended sediment in these four relatively small watersheds that represent a range of land-use patterns and underlying geology to (1) characterize current water-quality conditions in these watersheds, and (2) identify the dominant sources, sinks, and transport processes in each watershed. The general study design involved two components. The first included intensive routine water-quality monitoring at an existing streamgage within each study area (including continuous water-quality monitoring as well as discrete water-quality sampling) to develop a detailed understanding of the temporal and hydrologic variability in stream chemistry and sediment transport in each watershed. The second component involved extensive water-quality monitoring at various sites throughout each watershed to develop a detailed understanding of spatial patterns. Both components were used to improve understanding of sources and transport processes affecting stream chemistry, including nutrients and suspended sediments, and their implications for detecting long-term trends related to best management practices. This report summarizes the results of monitoring that was performed from April 2010 through September 2013. Individual Small Watershed Summaries Summaries for each of the four small watersheds are presented below. Each watershed has a more descriptive and detailed section in the report, but these summaries may be particularly useful for some watershed managers and stakeholders desiring slightly less technical detail. Smith Creek Smith Creek is a 105.39-mi 2 watershed within the Shenandoah Valley that drains to the North Fork Shenandoah River. The long-term Smith Creek base-flow index is 72.3 percent, indicating that on average, approximately 72 percent of Smith Creek flow was base flow, which suggests that Smith Creek streamflow is dominated by groundwater discharge rather than stormwater runoff. A series of cluster and principal components analyses demonstrated that the majority of the variability in Smith Creek water quality could be attributed to hydrologic and seasonal variability. Statistically significant positive correlations with flow were observed for turbidity, suspended sediments, total nitrogen, ammonium, orthophosphate, iron, total phosphorus, and the ratio of calcium to magnesium. Statistically significant inverse correlations with flow were observed for specific conductance, magnesium, δ 15 N of nitrate, pH, bicarbonate, calcium, and δ 18 O of nitrate. Of particular note, flow and nitrate were not statistically significantly correlated, likely because of the relatively complex concentration-discharge relationship observed in continuous and discrete datasets. Statistically significant seasonal patterns were observed for numerous water-quality constituents: water temperature, turbidity, orthophosphate, total phosphorus, suspended-sediment concentration, and silica were higher during the warm season, but pH, dissolved oxygen, and sulfate were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient loads in Smith Creek using the continuous water-quality monitors. The mean Smith Creek in-stream sediment load was approximately 6,900 tons per year, with nearly 90 percent of the sediment load over the 3-year study period contributed during the eight largest storm events during that period. The Smith Creek total phosphorus load was approximately 21,000 pounds of phosphorus per year, with the majority of the load contributed during stormflow periods, although a substantial phosphorus load still occurs during base-flow conditions. The Smith Creek total nitrogen load was approximately 400,000 pounds per year, with total nitrogen accumulation less dominated by stormflow contributions (as was the case for sediment and total phosphorus) and strongly affected by base-flow export of nitrogen from the basin. Extensive water-quality monitoring throughout the Smith Creek watershed revealed how the complex geology and hydrology interacted to result in variable water chemistry. During relatively dry and low base-flow periods, much of the discharge in Smith Creek was contributed by a single dominant spring—Lacey Spring. During wetter base-flow periods, the flows in Smith Creek were largely generated by a mixture of headwater springs and forested mountain tributaries with very different geochemical composition. The headwater springs generally issued from limestone bedrock and were characterized as having relatively high nitrate, specific conductance, calcium, and magnesium, as well as relatively low concentrations of phosphorus, ammonium, iron, and manganese. The undeveloped, high-gradient, forested mountain sites were generally characterized by low ionic strength waters with low nutrient concentrations. Nitrate isotope data from the limestone springs generally were consistent with manure-derived nitrogen sources (such as cattle and poultry), although the possibility of other mixed sources cannot be excluded. Nitrate isotope data from the undeveloped, high-gradient forested mountain sites were more consistent with nitrogen from undisturbed soils, atmospheric deposition, or nitrogen fixation. Regardless of the nitrogen source, oxygen isotope data indicate that the nitrate was largely a result of nitrification. Land-use data indicate that manure sources of nitrogen dominated watershed nitrogen inputs. Phosphorus sources were less well studied. The presence of a single point-source discharge near the town of New Market contributed the majority of the phosphorus to Smith Creek under base-flow conditions, but nonpoint sources of phosphorus dominated the loading to Smith Creek during stormflow periods. Implementation of conservation practices increased in the Smith Creek watershed during the study period, and even though a broad range of practice types was implemented, the most common practices included stream fencing (for cattle exclusion), the development of nutrient management plans, conservation crop rotation, and the planting of cover crops. While the implementation of these conservation practices is encouraging, results indicate small increases in nitrate concentrations at the streamgage over the last 29 years, concurrent with small decreases in nitrate fluxes. It will likely be years before the cumulative effect of these practices can be detected in the Smith Creek water quality, and the magnitude of the effect of these conservation practices detected in Smith Creek will depend largely on whether nutrient loading (of manure and commercial fertilizer) is reduced over time. Upper Chester River The Upper Chester River watershed includes the 36-square-mile (mi 2 ) watershed area around several nontidal tributaries that drain into the tidal Chester River. The streamgage is on Chesterville Branch, the largest nontidal tributary (approximately 6.12 mi 2 ) and is the site for continuous water-quality monitoring for this project. The base-flow index at Chesterville Branch is about 72 percent and indicates that, as in most of the Coastal Plain, groundwater is the greatest contributor to streamflow. As such, more than 90 percent of the nitrogen in the stream is in the form of nitrate from groundwater. Continuous and discrete data collected at Chesterville Branch show the effects of streamflow and season on water quality. Significantly positive correlations with flow were observed for ammonium, dissolved and total phosphorus, sediment, and turbidity as runoff carried these constituents from the land surface into Chesterville Branch. Other constituents that increased significantly with flow include potassium, sulfate, iron, and manganese, which are likely contributed from near-stream areas and ponds with high organic-matter content. Total nitrogen, pH, and specific conductance, along with chemical constituents associated with groundwater inputs including nitrate, calcium, ratio of calcium to magnesium, silica, bicarbonate, and sodium, were negatively correlated with flow because concentrations of these constituents were diluted by runoff. Seasonal differences in water chemistry, which are most likely related to increased biologic effects on the uptake and release of chemicals in the stream and near-stream areas, also were observed. Water temperature, orthophosphate, δ 15 N of nitrate, bicarbonate, sodium, and the ratio of sodium to chloride were higher during the warm season, and dissolved oxygen, total nitrogen, nitrate, magnesium, sulfate, and manganese were higher during the cool season. Surrogate-regression models developed by using continuous water-quality data showed that the annual sediment load for the 2013 water year was about 2,600 tons, with more than 90 percent of this sediment contributed during two storms. The total phosphorus load in 2013 was about 13,000 pounds with more than 90 percent contributed during the same two storms as sediment. The load of total nitrogen, 140,000 pounds, accumulated steadily throughout the 2013 water year as nitrate in groundwater continuously discharged into the stream. The same two large storms that contributed 90 percent of the suspended-sediment and total phosphorus load only contributed about 20 percent of the annual total nitrogen load. Extensive water-quality monitoring of stream base flow throughout the Upper Chester River watershed identified how differences in land use and hydrogeology affected water chemistry. In parts of the watershed with well-drained soil and thick sandy aquifer sediments, concentrations of nitrate and other chemicals associated with fertilizer and lime application increased in streams as agricultural land use increased. More than 90 percent of the nitrogen in streams from these areas was in the form of nitrate, and concentrations ranged from about 5 milligrams per liter (mg/L) to 8 mg/L as nitrogen in the two largest tributaries. Stream nitrate concentrations were about 1 mg/L as nitrogen where soils were more poorly drained, the surficial aquifer sediments were thinner, and forests and wetlands were more widespread than agriculture. Nitrate isotope data were consistent with inorganic fertilizers ± atmospheric deposition and N 2 fixation as sources of nitrogen, and with nitrification as the dominant nitrate-forming process. Nitrate reduction was indicated by elevated δ 15 N and δ 18 O values in some samples from streams draining watersheds with poorly drained soils. An analysis of land-use data and SPARROW modeling input data attributed almost 90 percent of the nitrogen sources in the Upper Chester River watershed to inorganic fertilizer and fixation of atmospheric nitrogen by legumes, which is in agreement with the isotopic characteristics of nitrate in this watershed. Local sources of manure are limited in this area. Total phosphorus concentrations during base flow ranged from below detection to about 0.2 mg/L. Stream phosphorus concentrations during base flow were generally lower than those measured during storms because most phosphorus transport likely occurs as phosphorus attached to sediment particles during runoff. Because manure is not widely used in this area, the major source of phosphorus is likely fertilizer. The implementation of conservation practices in the Upper Chester River watershed increased substantially during the study period, with a total implementation of 1,194 U.S. Department of Agriculture-compliant practices. The most frequently used practices were oriented towards nutrient and sediment control, including cover crops, nutrient management planning, conservation crop rotation, conservation tillage, and irrigation management. The current Chesapeake Bay model for this area predicts that implementation of best management practices should result in a 13-percent decrease in overall delivery of nitrogen to the Upper Chester River. Because most nitrogen travels through the groundwater system for years to decades before being discharged to streams, the time period of monitoring was not sufficient to see the effects of these practices on water quality. The magnitude of the effect that may eventually be detected will depend on the degree to which nitrate leaching into the groundwater system is reduced over time. Loadings of phosphorus and sediment are primarily transported during large runoff events and are difficult to control and analyze for trends because of their timing and episodic nature. Conewago Creek Conewago Creek has two primary monitoring locations—one near the middle of the 47-mi 2 watershed and the other near the outlet just upstream of the Susquehanna River. The base-flow index was 47.3 percent for 2012–2013, indicating that on average, approximately 53 percent of the streamflow in Conewago Creek exited the watershed as surface flow, which suggests that the stormwater runoff was somewhat greater than groundwater discharge (base flow). A series of cluster and principal components analyses demonstrated that the majority of the variability in the Conewago Creek water quality could be attributed to hydrologic and seasonal variability. Statistically significant positive correlations with flow were observed at both monitoring sites for ammonium, total phosphorus, orthophosphate, iron, and manganese; additionally, at the upstream monitoring station, total nitrogen demonstrated a statistically significant positive correlation with flow. Statistically significant inverse correlations with flow were observed at both sites for water temperature, specific conductance (at the downstream site only), sulfate, chloride, calcium, and magnesium. Statistically significant seasonal patterns were observed for several water-quality constituents. Water temperature, phosphorus (upstream site only), and orthophosphate were higher during the warm season, and nitrate and total nitrogen (upstream site only) were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient load in Conewago Creek by using the continuous water-quality monitors and water-quality samples. Conewago Creek sediment load was approximately 9,900 tons in 2012 and approximately 18,900 tons in 2013, with nearly 80 percent of the sediment load in 2013 contributed by the three largest storm events. Annual total nitrogen loads could not be estimated due to poor model performance. The addition of continued monitoring or a continuously recording nitrate sensor could improve estimates of total nitrogen loads. During 2012 and 2013, phosphorus loads in Conewago Creek were approximately 50,000 pounds in each year. Combining data from one high-flow synoptic sampling with the data from routine sampling revealed how the geology and hydrology interact to result in variable water chemistry throughout the Conewago Creek watershed. The areas above the upstream gage in the headwaters are generally underlain by forested non-carbonate bedrock and are characterized by relatively low nitrate, specific conductance, calcium, and magnesium, as well as relatively low concentrations of phosphorus, ammonium, iron, and manganese. The more developed, agricultural areas below the upstream site were generally characterized by higher ionic strength waters with higher nutrient and metal concentrations. An analysis of land-use data and SPAtially Referenced Regressions On Watershed (SPARROW) modeling data indicates that manure sources of nitrogen dominate the input of nitrogen to the watershed. Implementation of conservation practices increased in the Conewago Creek watershed during the study period, and while a broad range of practice types were implemented, the most common practices included residue and tillage management, cover crops, nutrient management, terracing, and stream fencing (for animal exclusion or bank restoration). While the implementation of these conservation practices is encouraging, the cumulative effects of these practices probably will not be detected in Conewago Creek water quality for several years. The magnitude of the effects of these conservation practices on water quality in Conewago Creek will depend largely on the extent to which nutrient loading (septic, manure, and commercial fertilizer) and sediment-producing activities are reduced over time. Difficult Run The Difficult Run watershed is a 57.82-mi 2 watershed that drains to the Potomac River. The long-term Difficult Run base-flow index (from 1936 to 2010) was 57.9, indicating that approximately 58 percent of streamflow exited the watershed as base flow and 42 percent as stormflow; however, with continued development and urbanization of the watershed, the base-flow index has decreased to 50 percent during the last 20 years. This base-flow index was less than those of the other watersheds evaluated in this study, likely because the Difficult Run watershed largely is underlain by crystalline piedmont metamorphic rocks and has a greater proportion of impervious urban land cover. A series of cluster and principal components analyses indicated that most of the variability in Difficult Run water quality could be attributed to hydrologic variability and seasonality. Statistically significant positive correlations with flow were observed for turbidity, dissolved oxygen, suspended sediments, ammonium, orthophosphate, iron, and total phosphorus. Statistically significant inverse correlations with flow were observed for water temperature, pH, specific conductance, bicarbonate, calcium, magnesium, nitrate, δ 15 N of nitrate, and silica. Statistically significant seasonal patterns were observed for numerous water-quality constituents: water temperature, ammonium, orthophosphate, and δ 15 N of nitrate were higher during the warm season, and dissolved oxygen, nitrate, and manganese were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient loading rates. The Difficult Run sediment load was approximately 8,000 tons per year, with greater than 95 percent of the sediment load in the 2013 water year contributed by the seven largest storm events. The total phosphorus load in Difficult Run was approximately 14,000 pounds of phosphorus per year, with the majority of the load contributed during stormflow periods. The total nitrogen load in Difficult Run is estimated to have been approximately 140,000 pounds per year, with total nitrogen accumulation less dominated by stormflow contributions than that of phosphorus and strongly affected by base-flow export of nitrogen from the basin. Extensive water-quality monitoring throughout the Difficult Run watershed revealed relatively uniform generation of flow per unit of watershed area, as well as spatial variation in water quality that is strongly related to land-use activities. Elevated nitrate concentrations were observed in a subset of monitoring sites that are inversely correlated with population density and positively correlated to the septic system density within each subwatershed. The majority of the elevated nitrate concentrations for these sites are hypothesized to be caused by nitrate leaching from septic systems, more so than homeowner fertilizer usage among these subwatersheds that have lower population densities than other parts of the watershed. Nitrate isotope data, temporal patterns in the water-quality data, mass-balance computations, and a separate land-use analysis all generally indicate that leachate from septic systems was the likely source of the elevated nitrate. Another group of water-quality sites have relatively low nitrogen concentrations, are located in areas that are served by city sewer lines, and have experienced stream restoration activities. A final group of sites drained the areas with the highest imperviousness and had strongly elevated specific conductance, chloride, and sodium, which were likely caused by a combination of road salting and other anthropogenic sources draining these urbanized areas in the watershed. A fourth group of sites represents a mixture of water sources and had water quality similar to that at the Difficult Run streamgage. Analysis of the nitrate isotope data generally indicates a broad range of composition indicative of mixed natural and anthropogenic nitrogen sources. Implementation of conservation practices increased in the Difficult Run watershed during the study period, and while a broad range of practice types was implemented, the most common practices included stream restoration. While the implementation of these conservation practices is encouraging, the cumulative effect of these practices probably will not be detected in Difficult Run water quality for several years.

Maryland, Pennsylvania, Virginia↗

Ultrahigh resolution topographic mapping of Mars with MRO HiRISE stereo images: Meter-scale slopes of candidate Phoenix landing sites

The objectives of this paper are twofold: first, to report our estimates of the meter‐to‐decameter‐scale topography and slopes of candidate landing sites for the Phoenix mission, based on analysis of Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) images with a typical pixel scale of 3 m and Mars Reconnaissance Orbiter (MRO) High Resolution Imaging Science Experiment (HiRISE) images at 0.3 m pixel −1 and, second, to document in detail the geometric calibration, software, and procedures on which the photogrammetric analysis of HiRISE data is based. A combination of optical design modeling, laboratory observations, star images, and Mars images form the basis for software in the U.S. Geological Survey Integrated Software for Imagers and Spectrometers (ISIS) 3 system that corrects the images for a variety of distortions with single‐pixel or subpixel accuracy. Corrected images are analyzed in the commercial photogrammetric software SOCET SET (® BAE Systems), yielding digital topographic models (DTMs) with a grid spacing of 1 m (3–4 pixels) that require minimal interactive editing. Photoclinometry yields DTMs with single‐pixel grid spacing. Slopes from MOC and HiRISE are comparable throughout the latitude zone of interest and compare favorably with those where past missions have landed successfully; only the Mars Exploration Rover (MER) B site in Meridiani Planum is smoother. MOC results at multiple locations have root‐mean‐square (RMS) bidirectional slopes of 0.8–4.5° at baselines of 3–10 m. HiRISE stereopairs (one per final candidate site and one in the former site) yield 1.8–2.8° slopes at 1‐m baseline. Slopes at 1 m from photoclinometry are also in the range 2–3° after correction for image blur. Slopes exceeding the 16° Phoenix safety limit are extremely rare.

Journal of Geophysical Research E: Planets↗

Detection and mapping of hydrocarbon deposits on Titan

We report the identification of compounds on Titan's surface by spatially resolved imaging spectroscopy methods through Titan's atmosphere, and set upper limits to other organic compounds. We present evidence for surface deposits of solid benzene (C 6 H 6 ), solid and/or liquid ethane (C 2 H 6 ), or methane (CH 4 ), and clouds of hydrogen cyanide (HCN) aerosols using diagnostic spectral features in data from the Cassini Visual and Infrared Mapping Spectrometer (VIMS). Cyanoacetylene (2-propynenitrile, IUPAC nomenclature, HC 3 N) is indicated in spectra of some bright regions, but the spectral resolution of VIMS is insufficient to make a unique identification although it is a closer match to the feature previously attributed to CO 2 . We identify benzene, an aromatic hydrocarbon, in larger abundances than expected by some models. Acetylene (C 2 H 2 ), expected to be more abundant on Titan according to some models than benzene, is not detected. Solid acetonitrile (CH 3 CN) or other nitriles might be candidates for matching other spectral features in some Titan spectra. An as yet unidentified absorption at 5.01- μ m indicates that yet another compound exists on Titan's surface. We place upper limits for liquid methane and ethane in some locations on Titan and find local areas consistent with millimeter path lengths. Except for potential lakes in the southern and northern polar regions, most of Titan appears “dry.” Finally, we find there is little evidence for exposed water ice on the surface. Water ice, if present, must be covered with organic compounds to the depth probed by 1–5- μ m photons: a few millimeters to centimeters.

Journal of Geophysical Research - Planets↗

Enhanced surveillance strategies for detecting and monitoring chronic wasting disease in free-ranging cervids

The purpose of this document is to provide wildlife management agencies with the foundation upon which they can build scientifically rigorous and cost-effective surveillance and monitoring programs for chronic wasting disease (CWD) or refine their existing programs. The first chapter provides an overview of potential demographic and spatial risk factors of susceptible wildlife populations that may be exploited for CWD surveillance and monitoring. The information contained in this chapter explores historic as well as recent developments in our understanding of CWD disease dynamics. It also contains many literature references for readers who may desire a more thorough review of the topics or CWD in general. The second chapter examines methods for enhancing efforts to detect CWD on the landscape where it is not presently known to exist and focuses on the efficiency and cost-effectiveness of the surveillance program. Specifically, it describes the means of exploiting current knowledge of demographic and spatial risk factors, as described in the first chapter, through a two-stage surveillance scheme that utilizes traditional design-based sampling approaches and novel statistical methods to incorporate information about the attributes of the landscape, environment, populations and individual animals into CWD surveillance activities. By accounting for these attributes, efficiencies can be gained and cost-savings can be realized. The final chapter is unique in relation to the first two chapters. Its focus is on designing programs to monitor CWD once it is discovered within a jurisdiction. Unlike the prior chapters that are more detailed or prescriptive, this chapter by design is considerably more general because providing comprehensive direction for creating monitoring programs for jurisdictions without consideration of their monitoring goals, sociopolitical constraints, or their biological systems, is not possible. Therefore, the authors draw upon their collective experiences implementing disease-monitoring programs to present the important questions to consider, potential tools, and various strategies for those wildlife management agencies endeavoring to create or maintain a CWD monitoring program. Its intent is to aid readers in creating efficient and cost-effective monitoring programs, while avoiding potential pitfalls. It is hoped that these three chapters will be useful tools for wildlife managers struggling to implement efficient and effective CWD disease management programs.

Open-File Report↗

Summary of significant results from studies of triazine herbicides and their degradation products in surface water, ground water, and precipitation in the midwestern United States during the 1990s

Nonpoint-source contamination of water resources from triazine herbicides has been a major water-quality issue during the 1990s in the United States. To address this issue, studies of surface water, ground water, and precipitation have been carried out by the U.S. Geological Survey in the Midwestern United States. Reconnaissance studies of 147 streams were conducted to determine the geographic and seasonal distribution of atrazine, cyanazine, propazine, and simazine. These studies showed that high concentrations of herbicides were flushed from cropland and transported through the stream system as pulses in response to spring and summer rainfall. The studies also revealed the persistence of herbicides and their degradation products in streams. An investigation of 76 reservoirs showed that the occurrence and temporal distribution of herbicides and their degradation products in reservoir outflow could be related to reservoir and drainage-basin characteristics, water and land use, herbicide use, and climate. Significant findings showed that concentrations of atrazine and its degradation products remained elevated all summer and into the fall and that recently applied atrazine mixed with atrazine applied the previous year as water moved through a reservoir. Reconnaissance studies of 303 ground-water wells were completed to determine hydrogeological and seasonal occurrence, concentration, and distribution of herbicides and their degradation products. Samples collected from across the Midwestern United States consistently revealed that triazine herbicide degradation products commonly were found more frequently than their parent herbicide and that ground-water age could be an important factor in explaining variations in herbicide contamination. A final study investigated precipitation in the Midwestern United States, northeast to the Atlantic Ocean, and northward to the Canadian border. It found that the highest herbicide concentrations in precipitation occurred following herbicide application to cropland. Atrazine was detected most often, followed by deethylatrazine, cyanazine, and deisoproplyatrazine. Mass deposition of herbicides by precipitation was greatest in areas where herbicide use was intense and decreased with distance from the Midwest. Findings of the 1990s studies include an improved understanding of the occurrence, persistence, chemistry, and transport of triazine herbicides and their degradation products in the hydrologic environment. A significant increase in knowledge of triazine herbicides and development and improvement of analytical methods were accomplished in the past decade. The results produced are not only significant for the present (2005) but provide an important data set for future use.

Midwest region↗

Snake River Fall Chinook Salmon life history investigations

Predation by nonnative fishes is one factor that has been implicated in the decline of juvenile salmonids in the Pacific Northwest. Impoundment of much of the Snake and Columbia rivers has altered food webs and created habitat favorable for species such as Smallmouth Bass Micropterus dolomieu . Smallmouth Bass are common throughout the Columbia River basin and have become the most abundant predator in lower Snake River reservoirs (Zimmerman and Parker 1995). This is a concern for Snake River Fall Chinook Salmon Oncorhynchus tshawytscha (hereafter, subyearlings) that may be particularly vulnerable due to their relatively small size and because their main-stem rearing habitats often overlap or are in close proximity to habitats used by Smallmouth Bass (Curet 1993; Tabor et al. 1993). Concern over juvenile salmon predation spawned a number of large-scale studies to quantify its effect in the late 1980s, 1990s, and early 2000s (Poe et al. 1991; Rieman et al. 1991; Vigg et al. 1991; Fritts and Pearsons 2004; Naughton et al. 2004). Smallmouth Bass predation represented 9% of total salmon consumption by predatory fishes in John Day Reservoir, Columbia River, from 1983 through 1986 (Rieman et al. 1991). In transitional habitat between the Hanford Reach of the Columbia River and McNary Reservoir, juvenile salmon (presumably subyearlings) were found in 65% of Smallmouth Bass (>200 mm) stomachs and comprised 59% of the diet by weight (Tabor et al. 1993). Within Lower Granite Reservoir on the Snake River, Naughton et al. (2004) showed that monthly consumption (based on weight) ranged from 5% in the upper reaches of the reservoir to 11% in the forebay. However, studies in the Snake River were conducted soon after Endangered Species Act (ESA) listing of Snake River Fall Chinook Salmon (NMFS 1992). During this time, Fall Chinook Salmon abundance was at an historic low, which may explain why consumption rates were relatively low compared to those from studies conducted in the Columbia and Yakima rivers where abundance was higher (e.g., Tabor et al. 1993; Fritts and Pearsons 2004). We speculate that predation on subyearlings by Smallmouth Bass in the Snake River may have increased in recent years for several reasons. Since their ESA listing, recovery measures implemented for Snake River Fall Chinook salmon have resulted in a large increase in the juvenile population (Connor et al. 2013). Considering that subyearlings probably now make up a larger portion of the forage fish population, it is plausible they should make up a large portion of Smallmouth Bass diets. Second, migrating subyearlings delay downstream movement in the transition zones of the Clearwater River and Snake River for varying lengths of time (Tiffan et al. 2010), which increases their exposure and vulnerability to predators. Spatial overlap in locations of Smallmouth Bass and subyearlings that died during migration provides support for this (Tiffan et al. 2010). Finally, the later outmigration of subyearlings from the Clearwater River results in their presence in Lower Granite Reservoir during the warmest summer months when predation rates of Smallmouth Bass should be highest. In 2016, we focused our efforts on Smallmouth Bass predation in Lower Granite Reservoir downstream of the transition zones and the confluence area where we worked during 2012–2015. Similar to past years, our first objective was to quantify Smallmouth Bass consumption rates of subyearlings, determine relative bass abundance, and describe bass diets. In addition, Tiffan et al. (2016a) posited that predation risk to subyearlings may be higher in shoreline habitats that are more suitable for Smallmouth Bass and lower in shoreline habitats that are more suitable for subyearlings. To test this hypothesis, our second objective examines the relationship between Smallmouth Bass predation of subyearlings and habitat suitability.

Idaho, Washington↗

Accounting for site effects in probabilistic seismic hazard analyses of southern California: Overview of the SCEC Phase III Report

This article presents an overview of the Southern California Earthquake Center (SCEC) Phase-III effort to determine the extent to which probabilistic seismic hazard analysis (PSHA) can be improved by accounting for site effects. The contributions made in this endeavor are represented in the various articles that compose this special issue of BSSA. Given the somewhat arbitrary nature of the site-effect distinction, it must be carefully defined in any given context. With respect to PSHA, we define the site effect as the response, relative to an attenuation relationship, averaged over all damaging earthquakes in the region. A diligent effort has been made to identify any attributes that predispose a site to greater or lower levels of shaking. The most detailed maps of Quaternary geology are not found to be helpful; either they are overly detailed in terms of distinguishing different amplification factors or present southern California strong-motion observations are inadequate to reveal their superiority. A map based on the average shear-wave velocity in the upper 30 m, however, is found to delineate significantly different amplification factors. A correlation of amplification with basin depth is also found to be significant, implying up to a factor of two difference between the shallowest and deepest parts of the Los Angeles basin. In fact, for peak acceleration the basin-depth correction is more influential than the 30-m shear-wave velocity. Questions remain, however, as to whether basin depth is a proxy for some other site attribute. In spite of these significant and important site effects, the standard deviation of an attenuation relationship (the prediction error) is not significantly reduced by making such corrections. That is, given the influence of basin-edge-induced waves, subsurface focusing, and scattering in general, any model that attempts to predict ground motion with only a few parameters will have a substantial intrinsic variability. Our best hope for reducing such uncertainties is via waveform modeling based on first principals of physics. Finally, questions remain with respect to the overall reliability of attenuation relationships at large magnitudes and short distances. Current discrepancies between viable models produce up to a factor of 3 difference among predicted 10% in 50-yr exceedance levels, part of which results from the uncertain influence of sediment nonlinearity.

California↗

Overview of the Texas Source Water Assessment Project

The 1996 Amendments to the Safe Drinking Water Act require, for the first time, that each state prepare a source water assessment for all PWS. Previously, Federal regulations focused on sampling and enforcement with emphasis on the quality of delivered water. These Amendments emphasize the importance of protecting the source water. States are required to determine the drinking-water source, the origin of contaminants monitored or the potential contaminants to be monitored, and the intrinsic susceptibility of the source water. Under the amendments to the Act, States must create SWAP Programs. The programs must include an individual source water assessment for each public water system regulated by the State. These assessments will determine whether an individual drinking water source is susceptible to contamination. During 1997?99, TNRCC and USGS staff met as subject-matter working groups to develop an approach to conducting Source Water Susceptibility Assessments (SWSA) and a draft workplan. The draft workplan was then presented to and reviewed by various stakeholder and technical advisory groups. Comments and suggestions from these groups were considered, and a final workplan was produced and presented to the EPA. After EPA approval, work formally began on the Texas SWAP Project. The project has an expected completion date of September 2002. At that time, initial SWSA of all Texas public water supplies should be complete. Ground-water supplies can be considered susceptible if a possible source of contamination (PSOC) exists in the contributing area for the public-supply well field or spring, the contaminant travel time to the well field or spring is short, and the soil zone, vadose zone, and aquifer-matrix materials are unlikely to adequately attenuate the contaminants associated with the PSOC. In addition, particular types of land use/cover within the contributing area may cause the supply to be deemed more susceptible to contamination. Finally, detection of various classes of constituents in water from wells in the vicinity of a public supply well may indicate susceptibility of the public-supply well even though there may be no identifiable PSOC or land use activity. Surface-water supplies are by nature susceptible to contamination from both point and non-point sources. The degree of susceptibility of a PWS to contamination can vary and is a function of the environmental setting, water and wastewater management practices, and land use/cover within a water supply's contributing watershed area. For example, a PWS intake downstream from extensive urban development may be more susceptible to non-point source contamination than a PWS intake downstream from a forested, relatively undeveloped watershed. Surface-water supplies are also susceptible to contamination from point sources, which may include permitted discharges, as well as accidental spills or other introduction of contaminants.

Texas↗

Diatom data from Bradley Lake, Oregon: Downcore analyses

Displaced marine diatoms provide biostratigraphic evidence for tsunami inundation at Bradley Lake, a small freshwater lake on the south-central Oregon coast. During the past 7,200 years, fine-grained lacustrine deposits in the deep axis of the lake were disturbed 17 times by the erosion and emplacement of coarse-grained gyttja and, in some cases, sand. By identifying diatoms in closely spaced core samples, we determined that 13 of the 17 events (termed idisturbance eventsi) record prehistoric tsunamis in Bradley Lake. We consider the evidence strong for 11 events, based on numbers and diversity of marine taxa: De1, De2, De4, De5, De6, De7, De8, De11, De12, De13, and De17. The evidence is less compelling for an additional 2 events (De9 and De10), although tsunami inundation is likely. Finally, we identified 4 events (De3, De14, De15 and De16) in which there were no marine diatoms to support tsunami inundation, although stratigraphic data shows that the lake bottom was disturbed. Freshwater diatoms dominate throughout the Bradley Lake record, showing that the lake has remained a freshwater habitat throughout its existence. However, anomalous occurrences of three species of brackish diatoms (Thalassiosira bramaputrae, Cyclotella meneghiniana, and Mastogloia smithii) may be evidence for short-lived periods of slightly elevated salinities in the lake following De16, De13, De12, De11, De9, De8, and De5. With the exception of De12, increased abundances of one or more of the brackish species is coincident with decreased numbers of freshwater diatoms. A temporary rise in salinity, as evidenced by short-lived increases in abundances of brackish species and decreases in abundances of freshwater species, is consistent with tsunami inundation into the lake.

Oregon↗

Preliminary analysis of clay gouge from a well in the San Andreas fault zone in central California

Drilling into the San Andreas fault zone has begun in central California as part of the U.S.G.S. program of fault zone studies. The purpose of drilling into the fault zone is threefold. First, it will allow recovery of material from depth in order to determine the composition of both solid and fluid phases. Second, it will allow determination of the physical state of the fault zone, that is, the state of stress, pore pressure, and temperature. Finally, it will allow emplacement of instruments at depth in the fault zone for monitoring experiments related to short-term earthquake prediction. In an attempt to drill to the depth of earthquake focii, the initial drill site was chosen at a locale known as Dry Lake Valley (Fig. 1). Although the entire central section of the San Andreas fault is characterized by moderate seismicity and aseismic creep, Dry Lake Valley has particularly shallow earthquakes as well as a fairly high creep rate (18-20 mm/year). Figure 2 is a longitudinal section along the San Andreas fault. The high precision earthquake locations shown are magnitude one or greater events that occurred in 1973-1975 (from W. Ellsworth, pers. comm.). The depth estimates are accurate to about + 0.5 km. It is obvious from the figure that earthquakes in the section of the fault near the well are quite shallow.

California↗

Status and trends of prey fish populations in Lake Michigan, 2008

The Great Lakes Science Center (GLSC) has conducted lake-wide surveys of the fish community in Lake Michigan each fall since 1973 using standard 12-m bottom trawls towed along contour at depths of 9 to 110 m at each of seven index transects. The resulting data on relative abundance, size structure, and condition of individual fishes are used to estimate various population parameters that are in turn used by state and tribal agencies in managing Lake Michigan fish stocks. All seven established index transects of the survey were completed in 2008. The survey provides relative abundance and biomass estimates between the 5-m and 114-m depth contours of the lake (herein, lake-wide) for prey fish populations, as well as burbot, yellow perch, and the introduced dreissenid mussels. Lake-wide biomass of alewives in 2008 was estimated at 8.27 kilotonnes (kt) (1 kt = 1000 metric tons), which was the smallest biomass estimate in the entire time series and 29% lower than the 2007 estimate. Lake-wide biomass of bloater in 2008 was estimated at 3.33 kt, which was the lowest estimate since 1977 and 38% lower than the 2007 estimate. Rainbow smelt lake-wide biomass equaled 0.89 kt, which was only 0.01 kt higher than 2007, which is the lowest estimate in the time series. Deepwater sculpin lake-wide biomass equaled 5.23 kt, which is the fourth straight year of declining biomass. The 2008 estimate is the second smallest in the time series, and 39% lower than the 2007 estimate. Slimy sculpin lake-wide biomass remained relatively high in 2008 (2.75 kt), increasing 25% over 2007. Ninespine stickleback lake-wide biomass equaled only 0.50 kt in 2008, which was 79% lower than the 2007 estimate. The final prey fish, exotic round goby, increased two orders of magnitude between 2007 and 2008, from 0.02 to 4.65 kt. Round gobies now represent 18% of the prey fish biomass. Burbot lake-wide biomass (0.91 kt in 2008) has remained fairly constant since 2002. Numeric density of age-0 yellow perch (i.e., < 100 mm) equaled 0.7 fish per ha, which is indicative of a relatively poor year-class. Lake-wide biomass of dreissenid mussels dropped precipitously in 2008, down to 9.47 kt, and a 96% decline from the 2007 biomass estimate. Overall, the total lake-wide prey fish biomass estimate (sum of alewife, bloater, rainbow smelt, deepwater sculpin, slimy sculpin, round goby, and ninespine stickleback) in 2008 was 25.62 kt, which was the lowest observed since the survey began in 1973.

Lake Michigan↗

Morphometry, gross morphology and available histopathology in North Atlantic right whale (Eubalaena glacialis) mortalities (1970 to 2002)

Fifty-four right whale mortalities have been reported from between Florida, USA and the Canadian Maritimes from 1970 to 2002. Thirty of those animals were examined: 18 adults and juveniles, and 12 calves. Morphometric data are presented such that prediction of body weight is possible if the age, or one or more measurements are known. Calves grew approximately linearly in their first year. Total length and fluke width increased asymptotically to a plateau with age, weight increased linearly with age, weight and snout to blowhole distance increased exponentially with total length, whereas total length was linearly related to fluke width and flipper length. Among the adults and juveniles examined in this study, human interaction appeared to be a major cause of mortality, where in 14/18 necropsies, trauma was a significant finding. In 10/14 of these, the cause of the trauma was presumed to be vessel collision. Entanglement in fishing gear accounted for the remaining four cases. Trauma was also present in 4/12 calves. In the majority of calf mortalities (8/12) the cause of death was not determined. Sharp ship trauma included propeller lacerations inducing multiple, deep lacerations that often incised vital organs including the brain, spinal cord, major airways, vessels and musculature. Blunt ship trauma resulted in major internal bruising and fractures often without any obvious external damage. In at least two cases fatal gear entanglements were extremely protracted: where the entanglements took at least 100 and 163 days respectively to be finally lethal. The sum of these findings show two major needs: (1) that extinction avoidance management strategies focused on reducing trauma to right whales from ship collisions and fishing gear entanglement are highly appropriate and need to be continued and; (2) that as mitigation measures continue to be introduced into shipping and fishing industry practices, there is a strong effort to maximise the diagnostic quality of post-mortem examination of right whale mortalities, to ensure an optimal understanding of resultant trends.

Journal of Cetacean Research and Management↗

Streamflow characteristics of streams in the Helmand Basin, Afghanistan

A majority of the Afghan population lacks adequate and safe supplies of water because of contamination, lack of water-resources management regulation, and lack of basic infrastructure, compounded by periods of drought and seasonal flooding. Characteristics of historical streamflows are needed to assist with efforts to quantify the water resources of the Helmand Basin. The Helmand Basin is the largest river basin in Afghanistan. It comprises the southern half of the country, draining waters from the Sia Koh Mountains in Herat Province to the eastern mountains in Gardez Province (currently known as the Paktia Province) and the Parwan Mountains northwest of Kabul, and finally draining into the unique Sistan depression between Iran and Afghanistan (Favre and Kamal, 2004). The Helmand Basin is a desert environment with rivers fed by melting snow from the high mountains and infrequent storms. Great fluctuations in streamflow, from flood to drought, can occur annually. Knowledge of the magnitude and time distribution of streamflow is needed to quantify water resources and for water management and environmental planning. Agencies responsible for the development and management of Afghanistan's surface-water resources can use this knowledge for making safe, economical, and environmentally sound water-resource planning decisions. To provide the Afghan managers with necessary streamflow information, the U.S. Geological Survey (USGS), in cooperation with the U.S. Agency for International Development (USAID), computed streamflow statistics for data collected at historical gaging stations within the Helmand Basin. The historical gaging stations used are shown in figure 1 and listed in table 1.

Helmand Basin↗