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At least 595 records · Page 33Linked to original sources

USGS2020

A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels

Resource managers may be hesitant to make decisions based on environmental (e)DNA results alone since eDNA is an indirect method of species detection. One way to reduce the uncertainty of eDNA is to identify laboratory‐based protocols that ensure repeatable and reproducible results. We conducted a double‐blind round‐robin analysis of probe‐based assays for DNA of dreissenid ( Dreissena spp.) mussels, which are prolific aquatic invaders that can cause significant economic and ecological impacts. DNA extract from water samples spiked with known amounts of dreissenid DNA and from water samples collected from waters with and without dreissenids were analyzed by four independent research laboratories. We used results to calculate detection repeatability within laboratories and assays, detection reproducibility among laboratories and assays, and estimated dreissenid DNA copy number precision and accuracy. Laboratory and assay repeatability and reproducibility of detection results were high, 91% and 92%, respectively. The estimated copy numbers were neither precise nor accurate for samples spiked with <773 gene copies. These results suggest that eDNA surveillance of dreissenid mussels, using the protocols evaluated herein, can generate reliable detection data for decision‐making. However, managers should be cautious about using the quantitative information often associated with eDNA detections, especially when DNA is at lower abundance. Our results provide strong support that eDNA has the potential to provide repeatable and reproducible evidence under varying laboratory conditions and for different sample water chemistries. This is reassuring since the demand for eDNA surveillance is widespread and number of laboratories that process eDNA samples is growing steadily.

California, Montana, Nevada, New York, Oregon, Was↗

USGS2014

Ecological consequences of the expansion of N 2 -fixing plants in cold biomes

Research in warm-climate biomes has shown that invasion by symbiotic dinitrogen (N 2 )-fixing plants can transform ecosystems in ways analogous to the transformations observed as a consequence of anthropogenic, atmospheric nitrogen (N) deposition: declines in biodiversity, soil acidification, and alterations to carbon and nutrient cycling, including increased N losses through nitrate leaching and emissions of the powerful greenhouse gas nitrous oxide (N 2 O). Here, we used literature review and case study approaches to assess the evidence for similar transformations in cold-climate ecosystems of the boreal, subarctic and upper montane-temperate life zones. Our assessment focuses on the plant genera Lupinus and Alnus , which have become invasive largely as a consequence of deliberate introductions and/or reduced land management. These cold biomes are commonly located in remote areas with low anthropogenic N inputs, and the environmental impacts of N 2 -fixer invasion appear to be as severe as those from anthropogenic N deposition in highly N polluted areas. Hence, inputs of N from N 2 fixation can affect ecosystems as dramatically or even more strongly than N inputs from atmospheric deposition, and biomes in cold climates represent no exception with regard to the risk of being invaded by N 2 -fixing species. In particular, the cold biomes studied here show both a strong potential to be transformed by N 2 -fixing plants and a rapid subsequent saturation in the ecosystem’s capacity to retain N. Therefore, analogous to increases in N deposition, N 2 -fixing plant invasions must be deemed significant threats to biodiversity and to environmental quality.

Oecologia↗

USGS2025

Speciation genomics in the tiger whiptail lizards ( Aspidoscelis tigris complex)

The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of high-quality reference genomes for most non-model species limits our understanding of the impact of this process for many taxonomic groups. This restricts the range of insights that genomic tools can provide for conservation biologists, who often hope to employ genomic datasets to accurately identify historically isolated lineages to protect and to predict their evolutionary fate in the face of environmental change. Tiger whiptail lizards ( Aspidoscelis tigris complex) are an abundant and important ecological component of ecosystems across the southwestern United States. In this study, we assembled and annotated a chromosome-level reference genome for A. t. stejnegeri from coastal California. We then used this reference genome to reconstruct patterns of speciation and admixture within the larger species complex, finding evidence that gene flow is widespread both geographically and across the genome.

northern Mexico, southwestern United States↗

USGS2004

Evaluation of Water Quality for Two St. Johns River Tributaries Receiving Septic Tank Effluent, Duval County, Florida

Tributary streamflow to the St. Johns River in Duval County is thought to be affected by septic tank leachate from residential areas adjacent to these tributaries. Water managers and the city of Jacksonville have committed to infrastructure improvements as part of a management plan to address the impairment of tributary water quality. In order to provide data to evaluate the effects of future remedial activities in selected tributaries, major ion and nutrient concentrations, fecal coliform concentrations, detection of wastewater compounds, and tracking of bacterial sources were used to document septic tank influences on the water quality of selected tributaries. The tributaries Fishing Creek and South Big Fishweir Creek were selected because they drain subdivisions identified as high priority locations for septic tank phase-out projects: the Pernecia and Murray Hill B subdivisions, respectively. Population, housing (number of residences), and septic tank densities for the Murray Hill B subdivision are greater than those for the Pernecia subdivision. Water-quality samples collected in the study basins indicate influences from ground water and septic tanks. Estimated concentrations of total nitrogen ranged from 0.33 to 2.86 milligrams per liter (mg/L), and ranged from less than laboratory reporting limit (0.02 mg/L) to 0.64 mg/L for total phosphorus. Major ion concentrations met the State of Florida Class III surface-water standards; total nitrogen and total phosphorus concentrations exceeded the U.S. Environmental Protection Agency Ecoregion XII nutrient criteria for rivers and streams 49 and 96 percent of the time, respectively. Organic wastewater compounds detected at study sites were categorized as detergents, antioxidants and flame retardants, manufactured polycarbonate resins, industrial solvents, and mosquito repellent. The most commonly detected compound was para-nonylphenol, a breakdown product of detergent. Results of wastewater sampling give evidence that stream water in the study basins is affected by septic tank effluent. Fecal coliform bacteria concentrations were measured on a monthly basis; of 115 samples, 63 percent exceeded the State of Florida fecal coliform bacteria standard for Class III surface waters of 800 colonies per 100 milliliters of water on any 1 day. Fecal coliform bacteria concentrations ranged from less than 20 colonies per 100 milliliters of sample to greater than or equal to 160,000 colonies per 100 milliliters of sample. Antibiotic resistance patterns of fecal coliform bacteria were used to identify the sources of fecal coliform bacteria. Significant sources of fecal coliform bacteria included wild animals, dogs, and humans. A majority of the fecal coliform bacteria were classified to be from human sources. Because the primary source of fecal coliform bacteria is from human sources, and most likely septic tank effluent, management of human sources may substantially improve microbiological water quality in both the Fishing Creek and South Branch Big Fishweir Creek basins.

Water-Resources Investigations Report↗

USGS2022

Environmental monitoring for invasive fungal pathogens of ʽŌhiʽa (Metrosideros polymorpha) on the Island of Hawaiʽi

The invasive rust Austropuccina psidii was detected in the Hawaiian Islands in 2005 and has become widely established throughout the archipelago in both native and introduced species of Myrtaceae. Initial predictions about the impacts of the fungus on native ʽōhiʽa lehua ( Metrosideros polymorpha ), a keystone native tree, have not materialized, but there is ongoing concern that introductions of new genotypes of the fungus could lead to widespread mortality with catastrophic effects on native ecosystems. By contrast, two recently emergent Ascomycete pathogens, Ceratocystis lukuohia ( Ceratocystis wilt of ‘ōhi‘a) and C. huliohia ( Ceratocystis canker of ‘ōhi‘a), collectively known to cause Rapid ʽŌhiʽa Death (ROD), are causing significant mortality in native forests on Hawaiʻi and Kauaʻi Islands, but pathways of spread are still incompletely understood. We used a network of passive environmental samplers for collecting windblown urediniospores of Austropuccina to evaluate the effectiveness of environmental monitoring to detect seasonal and landscape-scale differences in airborne propagules of this rust on Hawai`i Island. The samplers were also used to determine if windborn ambrosia beetle frass or spores of Ceratocystis can spread long distances. We found frequent detections and regional and seasonal differences in numbers of samplers that were positive for urediniospores of Austropuccinia , but little evidence of long-distance airborne dispersal of the ROD-causing fungi. The simple, inexpensive platform for sampling airborne fungal spores that we used may have value as a monitoring tool for detecting spread of airborne fungal pathogens, evaluating habitats for suitability for restoration efforts, and for detecting new pathogen introductions, particularly new Austropuccinia genotypes both in Hawaiʻi and other parts of the world.

Hawaii↗

USGS2026

Understanding the links between functional performance and environment in cold desert ecosystems through the flagship biocrust forming moss Syntrichia caninervis

Background and aims Biocrust communities shape the soil surface in drylands, regulating important ecosystem properties. Despite this, few works address key functional attributes in these poikilohydric photosynthetic communities, including the length of metabolic activity in the field and its relationship with microclimate. We aim to disentangle the links between functional performance of a keystone biocrust species and environment in drylands, in order to better understand ecosystem functioning and services provided to the soil by these organisms. Methods We developed a 23 months monitoring experiment using very high resolution measurements of chlorophyll a fluorescence and microclimate in the field, comparing habitats with soils of different particle size composition and microclimatic conditions for the flagship biocrust moss Syntrichia caninervis on the Colorado Plateau, Utah, USA. Results While growing in soils of different composition did not impair the functional performance of the species, the sun/shade plasticity did affect key physiological attributes. Our results quantified a strategy based on avoidance of the most extreme environmental conditions, where metabolic activity only occur during 19.9% of the total time monitored. Relative humidity was the best microclimatic predictor of metabolic activity, and the annual length of metabolically active periods showed strong convergences with other drylands of the world. Conclusions These results collectively suggest a strong control of the environment over the ecosystem services provided by biocrusts. Our results include evidence for an improved understanding of the plasticity of S. caninervis to its variety of habitats, and its response to potential threats under different climate change scenarios.

Utah↗

USGS2023

Density-dependent processes and population dynamics of native sculpin in a mountain river

Understanding the processes governing population dynamics is important for effective conservation and environmental management. Disentangling the relative role of density-dependent versus density-independent processes on population dynamics is often made difficult by the inability to control for abiotic or biotic factors, but long-term datasets are invaluable in this pursuit. We used a 14-year dataset from the Logan River, Utah, to assess long-term trends in abundance and evidence of density-dependent and density-independent effects on population dynamics of Paiute sculpin ( Cottus beldingii ) across six sites. Additionally, we evaluated the feeding ecology of sculpin over 4 years. Sculpin densities generally increased from upstream to downstream, and the annual per capita rate of increase was negatively and significantly correlated with sculpin density at four of six sites. We observed a negative relationship between total gut content and sculpin density but did not observe a negative relationship between relative condition and density. Sculpin displayed a generalist feeding strategy, and interannual differences in diet composition appeared to be influenced by interannual differences in flow, particularly years with higher magnitude flow. The observed spatial patterns in sculpin abundance throughout the watershed matched those of invasive brown trout ( Salmo trutta ), the top piscivore in the Logan River, and likely represent affinities for the suite of ecological conditions associated with downstream sections of the Logan River. Our results suggest that sculpin populations are regulated largely by density-dependent processes and match those from other studies on sculpin population dynamics including a range of species and habitats that differ vastly in abiotic conditions.

Ecology of Freshwater Fish↗

USGS2010

Breakpoint analysis and relations of nutrient and turbidity stressor variables to macroinvertebrate integrity in streams in the Crawford-Mammoth Cave Uplands Ecoregion, Kentucky, for the development of nutrient criteria

To assist Kentucky in refining numeric nutrient criteria in the Pennyroyal Bioregion, the U.S. Geological Survey and the Kentucky Division of Water collected and analyzed water chemistry, turbidity, and biological-community data from 22 streams throughout the Crawford-Mammoth Cave Upland ecoregion (U.S. Environmental Protection Agency Level IV Ecoregion, 71a) within the Pennyroyal Bioregion from September 2007 to May 2008. Statistically significant and ecologically relevant relations among the stressor (total phosphorus, total nitrogen, and turbidity) variables and response (macroinvertebrate-community attributes) variables and the breakpoint values of biological-community attributes and metrics in response to changes in stressor variables were determined. Thirteen of 18 macroinvertebrate attributes were significantly and ecologically correlated (p-value < 0.10) with at least one nutrient measure. Total number of individuals, Ephemeroptera-Plecoptera-Trichoptera richness, and average tolerance value were macroinvertebrate measures that most strongly correlated with the concentrations of nutrients. Comparison of the average macroinvertebrate-breakpoint value for the median concentration of total phosphorus (TP, 0.033 mg/L) and for median concentration of total nitrogen (TN, 1.1 mg/L) to Dodds' trophic classification for TP and TN indicates streams in the Crawford-Mammoth Cave Uplands ecoregion within the Pennyroyal Bioregion would be classified as mesotrophic-eutrophic. The biological breakpoint relations with median concentrations of TP in this study were similar to the U.S. Environmental Protection Agency proposed numeric TP criteria (0.037 mg/L), but were 1.5 times higher than the proposed numeric criteria for concentrations of TN (0.69 mg/L). No sites were impacted adversely using median turbidity values based on a 25 Formazin nephelometric turbidity unit biological threshold. The breakpoints determined in this study, in addition to Dodds' trophic classifications, were used as multiple lines of evidence to show changes in macroinvertebrate community and attributes based on exposure to nutrients.

Kentucky↗

USGS2015

Effects of the environmental estrogenic contaminants bisphenol A and 17α-ethinyl estradiol on sexual development and adult behaviors in aquatic wildlife species

Endocrine disrupting chemicals ( EDCs ), including the mass-produced component of plastics, bisphenol A (BPA) are widely prevalent in aquatic and terrestrial habitats. Many aquatic species, such as fish, amphibians, aquatic reptiles and mammals, are exposed daily to high concentrations of BPA and ethinyl estradiol (EE2), estrogen in birth control pills. In this review, we will predominantly focus on BPA and EE2, well-described estrogenic EDCs. First, the evidence that BPA and EE2 are detectable in almost all bodies of water will be discussed. We will consider how BPA affects sexual and neural development in these species, as these effects have been the best characterized across taxa. For instance, such chemicals have been in many cases reported to cause sex-reversal of males to females. Even if these chemicals do not overtly alter the gonadal sex, there are indications that several EDCs might demasculinize male-specific behaviors that are essential for attracting a mate. In so doing, these chemicals may reduce the likelihood that these males reproduce. If exposed males do reproduce, the concern is that they will then be passing on compromised genetic fitness to their offspring and transmitting potential transgenerational effects through their sperm epigenome . We will thus consider how diverse epigenetic changes might be a unifying mechanism of how BPA and EE2 disrupt several processes across species. Such changes might also serve as universal species diagnostic biomarkers of BPA and other EDCs exposure. Lastly, the evidence that estrogenic EDCs-induced effects in aquatic species might translate to humans will be considered.

General and Comparative Endocrinology↗

USGS1974

Relations of the brown pelican to certain environmental pollutants

Nearly all brown pelican eggs collected from 13 colonies in South Carolina, Florida, and California in 1969 and from 17 colonies in South Carolina and Florida in 1970 exhibited eggshell thinning. Of the 100 eggs analyzed for residues of pollutants, all eggs contained measurable quantities of DDE; most eggs contained measurable quantities of p,p'-DDD, p,p'-DDT, dieldrin, or PCB's (polychlorinated biphenyls). All eggs contained measurable quantities of mercury. DDE appears to have been responsible for virtually all the eggshell thinning. There is strong evidence that DDE played a major role in lowered reproductive success in South Carolina and California, and this pollutant appears to be intimately related to the population decline in South Carolina. Other pollutants, particularly dieldrin, may have had deleterious effect on reproductive success in South Carolina. Carcasses of pelicans collected by shooting in Florida and South Carolina in 1970 varied in residue load according to age and geographic location. Birds under 1 year of age contained smaller quantities of residues than did birds I year or older.

Pesticides Monitoring Journal↗

USGS2005

Hydrogeology and trichloroethene contamination in the sea-level aquifer beneath the Logistics Center, Fort Lewis, Washington

The U.S. Army disposed of waste trichloroethene (TCE) and other materials in the East Gate Disposal Yard near the Logistics Center on Fort Lewis, Washington, from the 1940s to the early 1970s. As a result, ground water contaminated with primarily TCE extends more than 3 miles downgradient from the East Gate Disposal Yard. The site is underlain by a complex and heterogeneous sequence of glacial and non-glacial deposits that have been broadly categorized into an upper and a lower aquifer (the latter referred to as the sea-level aquifer). TCE contamination was detected in both aquifers. This report describes an investigation by the U.S. Geological Survey (USGS) of the source, migration, and attenuation of TCE in the sea-level aquifer. A refined conceptual model for ground-water flow and contaminant migration into and through the sea-level aquifer was developed in large part from interpretation of environmental tracer data. The tracers used included stable isotopes of oxygen (18O), hydrogen (2H), and carbon (13C); the radioactive hydrogen isotope tritium (3H); common ions and redox-related analytes; chlorofluorocarbons; and sulfur hexafluoride. Tracer and TCE concentrations were determined for samples collected by the USGS from 37 wells and two surface-water sites in American Lake during 1999-2000. Ground-water levels were measured by the USGS in more than 40 wells during 2000-01, and were combined with measurements by the U.S. Army and others to create potentiometric-surface maps. Localized ground-water flow features were identified that are of particular relevance to the migration of TCE in the study area. A ridge of ground water beneath American Lake diverts the flow of TCE-contaminated ground water in the sea-level aquifer to the west around the southern end of the lake. Tracer data provided clear evidence that American Lake is a significant source of recharge to the sea-level aquifer that has created that ridge of ground water. High ground-water altitudes at locations north and northeast of the Logistics Center combined with the ridge beneath American Lake prevent TCE contaminated water beneath the Logistics Center from migrating toward municipal water-supply wells northeast of the site. The 1999-2000 TCE concentrations measured by the USGS at older wells screened in the sea-level aquifer were similar to those measured since 1995, but the known downgradient extent of the TCE contamination expanded nearly 2 miles after the Army installed and sampled new wells during 2003-04. Concentrations of TCE in the sea-level aquifer were consistently highest in the upper part of the aquifer throughout the plume, although TCE has spread throughout much of the thickness of the aquifer in the downgradient portions of the plume. Environmental tracer data indicated that the primary pathway for contaminant migration into the sea-level aquifer is through the previously identified confining unit window, an area where the predominately fine-grained confining unit is relatively coarse grained and more permeable. Other less substantial pathways for contaminant migration also were identified near the East Gate Disposal Yard and the I-5 pump-and-treat facilities. Those areas are near active pumping wells and ground-water reintroduction facilities, but there is no evidence that the contaminant migration was caused or enhanced by those activities. Within the sea-level aquifer, TCE concentrations continue to migrate westward in the flow field strongly influenced by ground-water recharge from American Lake. Historical data are not available to definitively determine if the 5-?g/L leading edge of the current TCE plume is stable or if it is still moving downgradient. However, an evaluation of the available data combined with TCE traveltime estimates indicates that the peak TCE concentrations in the sea-level aquifer may have not yet reached the wells near the currently defined leading edge of the plume. Hypothetically, the 5-?g/L leading edge

Scientific Investigations Report↗

USGS2023

Linked foraging and bioenergetics modeling may inform fish parasite infection dynamics

The parasitic copepod Salmincola californiensis infects Pacific salmon and trout ( Oncorhynchus spp.) and often reaches high prevalence and intensity in reservoirs compared to stream systems. Recent research indicates that temperature plays a fundamental role in copepod development and fish susceptibility. Here, we expand a linked foraging and bioenergetics model to simulate infection risk. Based on juvenile salmon vertical migration patterns, we add estimates of copepod generations produced and thermal strata metrics that appear associated with copepodid aggregations and increased infection. Severe damage on hosts may be caused by the infectious copepodid, a life-stage not readily visible and thus not detectable using traditional fish screenings. We discuss model limitations, opportunities for future research, and the potential for inclusion of copepod expansion equations to existing linked bioenergetics models or observed behaviors of salmonids in other lentic systems. We demonstrate that using a temperature sensitive model framework that includes copepod infection dynamics is useful in interpreting other lines of evidence, such as fish mortality estimates. Collectively, our work provides a testable framework for future comparisons of infection potential and demonstrates how bioenergetics models may be useful in understanding host–parasite interactions.

Environmental Biology of Fishes↗

USGS2006

The legacy of leaded gasoline in bottom sediment of small rural reservoirs

The historical and ongoing lead (Pb) contamination caused by the 20th-century use of leaded gasoline was investigated by an analysis of bottom sediment in eight small rural reservoirs in eastern Kansas, USA. For the reservoirs that were completed before or during the period of maximum Pb emissions from vehicles (i.e., the 1940s through the early 1980s) and that had a major highway in the basin, increased Pb concentrations reflected the pattern of historical leaded gasoline use. For at least some of these reservoirs, residual Pb is still being delivered from the basins. There was no evidence of increased Pb deposition for the reservoirs completed after the period of peak Pb emissions and (or) located in relatively remote areas with little or no highway traffic. Results indicated that several factors affected the magnitude and variability of Pb concentrations in reservoir sediment including traffic volume, reservoir age, and basin size. The increased Pb concentrations at four reservoirs exceeded the U.S. Environmental Protection Agency threshold-effects level (30.2 mg kg-1) and frequently exceeded a consensus-based threshold-effects concentration (35.8 mg kg-1) for possible adverse biological effects. For two reservoirs it was estimated that it will take at least 20 to 70 yr for Pb in the newly deposited sediment to return to baseline (pre-1920s) concentrations (30 mg kg-1) following the phase out of leaded gasoline. The buried sediment with elevated Pb concentrations may pose a future environmental concern if the reservoirs are dredged, the dams are removed, or the dams fail. ?? ASA, CSSA, SSSA.

Journal of Environmental Quality↗

USGS1998

Experimental investigations regarding the use of sand as an inhibitor of air convection in deep seismic boreholes

Tilt has been the nemesis of horizontal long period seismology since its inception. Modern horizontal long period seismometers with their long natural periods are incredibly sensitive to tilt. They can sense tilts smaller than 10 -11 radians. To most readers, this is just a very very small number, so we will begin with an example, which should help to illustrate just how small 10 -11 radians is. Suppose we have an absolutely rigid rod which is approximately 4170 kilometers long; this just happens to be the Rand McNally map scaled crow flight distance between Los Angeles and Boston. Tilting this rod 10 -11 radians corresponds to raising one end of the rod 0.0000417 meters. Alas, this is just another very very small number! However, this corresponds to slipping a little less than one third a sheet of ordinary copying paper under one end of this perfectly rigid rod. To clarify, we mean, take a sheet of paper just like the paper this report is printed on and split it a little less than one third in the thickness direction, then put it under the end of the 4170 kilometer long rod! This will tilt the rod 10 -11 radians. Real world seismometers are nowhere near the length of this rod. A KS-54000 is about two meters long. Tilting a rod only two meters long 10~n radians corresponds to moving one end of this rod a mere 0.00000000002 meters or 0.02 millimicrons. As one of the authors old math teachers used to say, "That's PDS" (PDS = Pretty Damn Small). Unfortunately, the long period seismologist does not have the luxury of ignoring PDS numbers when it suits him as the mathematician frequently does. He must live in the real world in which tilts this small create severe contamination of long period seismic data. At periods longer than 20 seconds, tilt noise contaminates the long period data from all instruments installed on or near the earth's surface. Many years of experimentation revealed that installing the sensors at depth in deep mines drastically reduced the level of tilt noise in long period data. However, low levels of tilt noise persisted even at great depth; this noise was caused by air convection in the vault in which the sensors were installed. Over the years, methods were developed to control the air motion with mechanical barriers (boxes) around the sensors and by stratifying (creating a situation in which the air temperature increases with height) the air in the vault near the seismometer. These methods decreased tilt noise in deep mines to very low levels. However, deep mines, that are economically and environmentally suitable and accessible to seismology, are not plentiful and are not evenly distributed over the earth's surface. Therefore, the borehole deployable Teledyne Geotech KS-36000 and later the KS-54000 sensor systems were developed to fulfill the need for instruments that could be installed at depth wherever high quality long period data was desired. Early in the development program, it became evident to the Teledyne Geotech personnel that air convection within the borehole was going to be a significant problem in KS deployments. Experimental and theoretical investigations conducted by Teledyne Geotech (see Douze and Sherwin, 1975, and Sherwin and Cook, 1976) produced a list of recommended installation procedures for reducing the effects of air convection. These procedures consisted of wrapping the sensor in a relatively thin layer of foam insulation, filling the free space volume in the vicinity of the centralizer-bail assembly with foam insulation, and the installation of styrofoam hole plugs immediately above the cable strain relief assembly at the top of the sensor package and at the top of the borehole. This technology has performed quite satisfactorily for over 20 years but evidence of tilt noise in the system output has persisted throughout the KS deployment program (the evidence was that the horizontal components were usually noisier than the vertical components) even in deep boreholes. Some deep borehole sites have been plagued by quite high levels of horizontal noise. Therefore, there has been a definite need for a new technique for controlling low level tilt noise in deep boreholes and the use of sand has been under consideration for several years. Figure 1 contains conceptual illustrations of both the conventional holelock installed KS sensor system and the same sensor installed in sand. This figure demonstrates the major differences between the two installation methods. The curved arrows in the borehole on the left in the figure denote possible air convection cells which are believed to be the source of tilt noise in some of the conventional installations. This air motion is eliminated in a sand installation by filling most of the free air volume surrounding the seismometer with sand as shown in the right hand portion of the figure. The sand actually performs two functions; it prevents air motion and provides a remarkably ridgid clamping of the seismometer in the borehole. This report presents the results of quantitative experimental investigations into the effectiveness of controlling low level air convection in seismic borehole installations with sand. The main body of the experimental effort consisted of installing two KS-540001 sensor systems in closely spaced shallow boreholes, allowing the sensors to reach equilibrium operation, and then pouring sand into both boreholes to observe any changes caused by pouring sand into the holes. The hypothesis of the experiment was that the sand would fill up the entire free air volume between the sensor package and the borehole walls thereby preventing movement of the air in the vicinity of the sensor package. The validity of this hypothesis had been qualitatively proven by earlier experiments at ASL and by the sand installations at the IRIS/ASL stations ANMO in 1995 and COLA in 1996. This experiment documents the degree of improved noise levels to be expected if KS instruments are installed in sand instead of in the conventional manner.

Open-File Report↗

USGS2000

Tumor prevalence and biomarkers in brown bullheads (Ameiurus nebulosus) from the tidal Potomac River watershed [poster]

Associations between contaminant exposure and liver and skin tumor prevalence were evaluated in brown bullheads (Ameiurus nebulosus) from the tidal Potomac River watershed. Thirty bullheads (>260 mm) were collected from (1) Quantico embayment, near a Superfund site which released organochlorine contaminants; (2) Neabsco Creek, a tributary with petroleum inputs from runoff and marinas; and (3) Anacostia River (spring and fall), an urban tributary designated as a Chesapeake Bay Region of Concern, contaminated with PCBs, PAHs, and organochlorine pesticides. Fish were collected from the Tuckahoe River, as a reference. Cytochrome P450 activity, bile PAH metabolites, and muscle organochlorine pesticide/PCB concentrations were measured in randomly-selected individuals and sediment contaminants were analyzed. We found statistically significant differences in liver tumor prevalences: Anacostia (spring)-50%, Anacostia (fall)-60%, Neabsco-17%, Quantico-7%, Tuckahoe-10%. Skin tumor prevalences were significantly different: Anacostia (spring)-37%, Anacostia (fall)-10%, Neabsco-3%, Quantico-3%, Tuckahoe-0%. Tumor prevalence in Anacostia bullheads warrants concern and was similar to those at highly contaminated sites in the Great Lakes. There was evidence of higher PAH exposure in Anacostia fish but a cause-effect linkage cannot be established. Fish tumor surveys, with histopathological examination of internal and external organs, are recommended for monitoring the status of Regions of Concern.

Society of Environmental Toxicology and Chemistry,↗

USGS2009

Ecological Requirements for Pallid Sturgeon Reproduction and Recruitment in the Lower Missouri River: A Research Synthesis 2005-08

This report provides a synthesis of results obtained between 2005 and 2008 from the Comprehensive Sturgeon Research Program, an interagency collaboration between the U.S. Geological Survey, Nebraska Game and Parks Commission, U.S. Fish and Wildlife Service, and the U.S. Army Corps of Engineers' Missouri River Recovery - Integrated Science Program. The goal of the Comprehensive Sturgeon Research Program is to improve fundamental understanding of reproductive ecology of the pallid sturgeon with the intent that improved understanding will inform river and species management decisions. Specific objectives include: *Determining movement, habitat-use, and reproductive behavior of pallid sturgeon; *Understanding reproductive physiology of pallid sturgeon and relations to environmental conditions; *Determining origin, transport, and fate of drifting pallid sturgeon larvae, and evaluating bottlenecks for recruitment of early life stages; *Quantifying availability and dynamics of aquatic habitats needed by pallid sturgeon for all life stages; and *Managing databases, integrating understanding, and publishing relevant information into the public domain. Management actions to increase reproductive success and survival of pallid sturgeon in the Lower Missouri River have been focused on flow regime, channel morphology, and propagation. Integration of 2005-08 Comprehensive Sturgeon Research Program research provides insight into linkages among flow regime, re-engineered channel morphology, and pallid sturgeon reproduction and survival. The research approach of the Comprehensive Sturgeon Research Program integrates opportunistic field studies, field-based experiments, and controlled laboratory studies. The field study plan is designed to explore the role of flow regime and associated environmental cues using two complementary approaches. An upstream-downstream approach compares sturgeon reproductive behavior between an upstream section of the Lower Missouri River with highly altered flow regime to a downstream section that maintains much of its pre-regulation flow variability. The upstream section also has the potential for an experimental approach to compare reproductive behavior in years with pulsed flow modifications ('spring rises') to years without. The reproductive cycle of the female sturgeon requires several years to progress through gonadal development, oocyte maturation, and spawning. Converging lines of evidence support the hypothesis that maturation and readiness to spawn in female sturgeon is cued many months before spawning. Information on reproductive readiness of shovelnose sturgeon indicates that sturgeon at different locations along the Lower Missouri River between St. Louis and Gavins Point Dam are all responding to the same early cue. Although not a perfect surrogate, the more abundant shovelnose sturgeon is morphologically, physiologically, and genetically similar to pallid sturgeon, and thereby provides a useful comparative model for the rarer species. Day length is the likely candidate to define a temporal spawning window. Within the spawning window, one or more additional, short-term, and specific cues may serve to signal ovulation and release of gametes. Of three potential spawning cues - water temperature, water discharge, and day of year - water temperature is the most likely proximate cue because of the fundamental physiological role temperature plays in sturgeon embryo development and survival, and the sensitivity of many fish hormones to temperature change. It also is possible that neither temperature nor discharge is cueing spawning; instead, reproductive behavior may result from the biological clock advancing an individual fish's readiness to spawn day after day through the spawning period until the right moment, independent of local environmental conditions. Separation of the individual effects of discharge events, water temperature, and other possible factors, such as proximity to male

Scientific Investigations Report↗

USGS2005

Occurrence of fecal-indicator bacteria and protocols for identification of fecal-contamination sources in selected reaches of the West Branch Brandywine Creek, Chester County, Pennsylvania

The presence of fecal-indicator bacteria indicates the potential presence of pathogens originating from the fecal matter of warm-blooded animals. These pathogens are responsible for numerous human diseases ranging from common diarrhea to meningitis and polio. The detection of fecal-indicator bacteria and interpretation of the resultant data are, therefore, of great importance to water-resource managers. Current (2005) techniques used to assess fecal contamination within the fluvial environment primarily assess samples collected from the water column, either as grab samples or as depth- and (or) width-integrated samples. However, current research indicates approximately 99 percent of all bacteria within nature exist as attached, or sessile, bacteria. Because of this condition, most current techniques for the detection of fecal contamination, which utilize bacteria, assess only about 1 percent of the total bacteria within the fluvial system and are, therefore, problematic. Evaluation of the environmental factors affecting the occurrence and distribution of bacteria within the fluvial system, as well as the evaluation and modification of alternative approaches that effectively quantify the larger population of sessile bacteria within fluvial sediments, will present water-resource managers with more effective tools to assess, prevent, and (or) eliminate sources of fecal contamination within pristine and impaired watersheds. Two stream reaches on the West Branch Brandywine Creek in the Coatesville, Pa., region were studied between September 2002 and August 2003. The effects of sediment particle size, climatic conditions, aquatic growth, environmental chemistry, impervious surfaces, sediment and soil filtration, and dams on observed bacteria concentrations were evaluated. Alternative approaches were assessed to better detect geographic sources of fecal contamination including the use of turbidity as a surrogate for bacteria, the modification and implementation of sandbag bacteria samplers, and the use of optical brighteners. For the purposes of this report, sources of bacteria were defined as geographic locations where elevated concentrations of bacteria are observed within, or expected to enter, the main branch of the West Branch Brandywine Creek. Biologic sources (for example, waterfowl) were noted where applicable; however, no specific study of biologic sources (such as bacterial source tracking) was conducted. Data indicated that specific bacterial populations within fluvial sediments could be related to specific particle-size ranges. This relation is likely the result of the reduced porosity and permeability associated with finer sediments and the ability of specific bacteria to tolerate particular environments. Escherichia coli (E. coli) showed a higher median concentration (2,160 colonies per gram of saturated sediment) in the 0.125 to 0.5-millimeter size range of natural sediments than in other ranges, and enterococcus bacteria showed a higher median concentration (61,830 colonies per gram of saturated sediment) in the 0.062 to 0.25-millimeter size range of natural sediments than in other ranges. There were insufficient data to assess the particle-size relation to fecal coliform bacteria and (or) fecal streptococcus bacteria. Climatic conditions were shown to affect bacteria concentrations in both the water column and fluvial sediments. Drought conditions in 2002 resulted in lower overall bacteria concentrations than the more typically wet year of 2003. E. coli concentrations in fluvial sediment along the Coatesville study reach in 2002 had a median concentration of 92 colonies per gram of saturated sediment; in 2003, the median concentration had risen to 4,752 colonies per gram of saturated sediment. Symbiotic relations between bacteria and aquatic growth were likely responsible for increased bacteria concentrations observed within an impoundment area on the Coatesville study reach. This reach showed evidence of elevated aquatic growth and sharp increases in E. coli concentrations from upstream to downstream through the impoundment area in both 2002 and 2003. In 2003, E. coli concentrations within the waters column increased from 940 colonies per 100 milliliters upstream to 6,000 colonies per 100 milliliters at the dam crest. Given that these bacteria likely resulted from natural bacterial regrowth, the use of E. coli as an indicator of fecal contamination was severely impaired. Variable environmental conditions along the West Branch Brandywine Creek made the common field-chemical parameters of specific conductance, temperature, pH, and dissolved oxygen ineffective and (or) impossible to use for the determination of inputs of fecal contamination. Extreme variations in chemical gradients commonly were related to the urban/industrial signature of the watershed. For example, during base-flow sampling in 2002, specific-conductance values exceeding 1,000 microsiemens per centimeter observed in effluent from a local steel mill. This effluent raised the specific conductance within the West Branch Brandywine from just above 200 microsiemens per centimeter upstream from the outfall to just below 500 microsiemens per centimeter downstream from the outfall. These chemical gradients also, likely, had an effect on the initial colonization of bacteria, the formation of biofilms, and the persistence of certain types of bacteria along the study reach. Data collected in 2003 indicated that nutrients increased during both base-flow and stormflow conditions along the Coatesville study reach. For example, during base-flow sampling in 2003, 20 pounds of phosphorus was shown to enter the West Branch Brandywine Creek along the Coatesville study reach. The largest contributors to this base-flow nutrient load were likely two wastewater-treatment facilities adjacent to the study reach. During stormflow sampling in 2003, 480 pounds of phosphorus was shown to enter the West Branch Brandywine Creek along the Coatesville study reach. Data, along with other research, indicated the largest contributor to this stormflow nutrient load was likely remobilized sediment originating from a large dam impoundment. These elevated nutrient concentrations were considered sufficient to promote accelerated aquatic growth along the reach. Data collected in 2003 showed that wastewater constituents entered the West Branch Brandywine Creek largely from urban storm-sewer systems. Samples from the primary storm sewer for the city of Coatesville had detections for 20 of 69 wastewater constituents. These constituents included both strong and weak indicators of fecal contamination and generally indicated the storm-sewer system along the Coatesville study reach was a likely source of fecal-indicator bacteria and fecal contamination under base-flow conditions. By comparison, 5 constituents were detected in samples from the upstream end of the reach, and 10 constituents were detected in samples from the downstream end of the reach. During stormflow, numbers of detections were similar along the entire length of the study reach-five in samples from the upstream end, eight in samples from the center of the reach, and seven in samples from the downstream end of the reach. These data indicate that point sources (such as culverts and pipes, septic systems, and wastewater-treatment facilities) are not likely the origin of bacteria contamination during stormflow. The bacteria concentrations observed during stormflow events probably result from remobilized sessile bacteria stored within fluvial sediments. In this case, these bacteria should not be considered indicators of current fecal contamination. Impervious surfaces were found to increase bacteria concentrations along the West Branch Brandywine Creek because contaminated runoff from impervious areas generally flows into, and is concentrated within, the confines of the local storm-sewer system. During 2002, storm-sewer outfalls draining impervious areas were associated with all major locations of elevated bacterial concentrations (greater than 1,200 colonies per gram of saturated sediment) in fluvial sediments. During 2003, wetter conditions and overall bacteria concentrations higher than in 2002 resulted in point sources of bacterial contamination becoming less pronounced; however, the storm-sewer system, draining adjacent impervious areas, was still observed to be the primary source of bacteria along the reach. Where stormwater and (or) other runoff from these areas was allowed to infiltrate and (or) flow through wetland and riparian buffers, bacteria concentrations were not observed to be elevated above background levels commonly observed throughout similar areas of the same reach. Two run-of-the-river dams along the Coatesville study reach were evaluated for their effects on observed bacterial concentrations. These dams were shown to have greater or lesser effects on bacterial concentrations depending on the size of the structure and the capacity of the structure to impede flows. The smaller upstream dam had an approximate height of 3 feet and showed little observed effect on measured turbidity values; these data indicated that the dam did not effectively impede the flow of water or sediment within the West Branch Brandywine Creek. Consequently, this small dam did not show any observed effect on bacterial concentrations either upstream or downstream of the structure. The larger dam, near the middle of the reach, had an approximate height of 20 feet and showed greater effects on both turbidity and bacteria concentrations. The capacity of the larger dam to impede flows, combined with nutrients entering the reach, resulted in increased biologic activity throughout the impoundment area. Within this larger impoundment, enterococcus bacteria populations were observed to decrease sharply and E. coli bacteria populations were observed to increase sharply as flow approached the dam crest. All bacteria levels were then observed to drop to background levels, in both the water column and fluvial sediment, immediately downstream from the dam crest. Additional study is required to determine the cause for this rapid die off. Turbidity was assessed as a potential surrogate for E. coli bacteria. Regression analysis indicated higher turbidity levels usually can indicate higher concentrations of bacteria (R2 = 0.67), but the relation was too sporadic on the West Branch Brandywine Creek to use turbidity as a surrogate for estimated bacteria concentrations. Evaluation of data from individual base-flow and stormflow events resulted in variable and generally poor statistical relations between E. coli bacteria and turbidity (R2 values ranged from 0.02 to 0.94). Sandbag samplers were used in 2003 to determine their suitability for the assessment of fecal contamination. Sandbag samplers rely on the ability of bacteria to attach to surfaces and use the larger sessile bacteria populations instead of the more commonly used planktonic bacteria populations. E. coli bacteria concentrations observed in the sandbag samplers, after 1 week in place, were similar to those found within natural sediments collected concurrently. Enterococcus bacteria concentrations within the same sandbag samplers were not similar, and were generally lower, than those observed within the natural sediments. This discrepancy was likely because sand within the samplers was sieved to a size that was likely too coarse for enterococcus bacteria to persist. Optical-brightener samplers were installed along with each sandbag sampler. Optical brighteners are additives used in common household detergents; therefore, detection of optical brighteners, along with elevated fecal-indicator bacteria concentrations, strongly indicates a link to humans. Positive results for optical brighteners were detected only at the outfalls of two sewage-treatment facilities; because of treatment of the effluent from these facilities, these samples did not have elevated bacteria concentrations. The lack of additional positive results was largely because this method is not sensitive to low concentrations of optical brighteners.

Pennsylvania↗

USGS2004

Temporal and geographic variation in survival of juvenile black brant

First-year survival has important implications for the structure and growth of populations. We examined variation in seasonal survival of first-year Pacific Black Brant ( Branta bernicla nigricans ) marked late in summer in Alaska at two brood-rearing areas on the Yukon-Kuskokwim Delta (Tutakoke and Kokechik) and one area on the Arctic Coastal Plain to provide insight into the magnitude and timing of mortality during fall migration. First-year survival was lower in early fall (15 July-1 October), when birds fledged from brood-rearing areas and migrated to their primary fall staging area at Izembek Lagoon, Alaska, than during late fall and early winter (1 October-15 February), when birds made a long-distance transoceanic flight (>5000 km) to wintering areas in Baja California, Mexico. When compared to other years, monthly survival during early fall was 20-24% lower in 1992, the year of latest hatch dates and slowest growth of goslings. There was strong evidence to indicate that survival varied geographically within the early fall period. Monthly survival estimates during early fall were lowest for birds from Tutakoke, highest for birds from the Arctic Coastal Plain, and intermediate at Kokechik. Our findings revealed that most juvenile mortality occurred during the first 2 months following banding, and variation in juvenile survival during this period was likely influenced significantly by environmental parameters and habitat conditions on the breeding grounds. Monthly survival estimates during the subsequent 4 months were similar across geographic areas, and long-distance migration was likely the most important contributor to juvenile mortality during this period.

Alaska↗