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At least 181 records · Page 10Linked to original sources
USGS2026

Growth, movement, and survival of precocial shorebird chicks are constrained by their environment.

Young animals are often less mobile than adults, while also having high energetic demands. They may therefore be more vulnerable to local-scale changes in environmental conditions. In particular, when 1 sex must grow more rapidly than the other to achieve a larger adult size, that sex may experience especially dramatic reductions in growth and survival in the face of suboptimal environmental conditions. In order to investigate the flexibility of individuals in response to local-scale environmental variation during development, we studied the sex-specific growth, movement, and survival of Hudsonian Godwit ( Limosa haemastica ) chicks—a sexually dimorphic, precocial shorebird that breeds in the sub-Arctic and exhibits a male-skewed adult sex ratio. We found that female chicks—which must grow to a larger adult size—reached their maximum growth rates at a later age, but had similar growth rates to males before that and survived equally well to 21 days. We also found that, irrespective of sex, chicks had reduced movement rates when they were young and/or temperatures were cold, and only weakly increased their movement rates when invertebrate abundances remained low across an entire week. Early in life, godwit chicks may therefore be constrained from increasing their foraging efforts by local environmental conditions, forcing females to sustain higher growth rates late in the season past the local resource peak. Such sex-specific vulnerabilities could lead to lower early-life survival and, in turn, skewed adult sex ratios, which have important implications for population dynamics and persistence.

Behavioral Ecology↗
USGS2007

Ground-Water Quality in the Delaware River Basin, New York, 2001 and 2005-2006

The Federal Clean Water Act Amendments of 1977 require that States monitor and report on the quality of ground water and surface water. To satisfy part of these requirements, the U.S. Geological Survey and New York State Department of Environmental Conservation have developed a program in which ground-water quality is assessed in 2 to 3 of New York State's 14 major basins each year. To characterize the quality of ground water in the Delaware River Basin in New York, water samples were collected from December 2005 to February 2006 from 10 wells finished in bedrock. Data from 9 samples collected from wells finished in sand and gravel in July and August 2001 for the National Water Quality Assessment Program also are included. Ground-water samples were collected and processed using standard U.S. Geological Survey procedures. Samples were analyzed for more than 230 properties and compounds, including physical properties, major ions, nutrients, trace elements, radon-222, pesticides and pesticide degradates, volatile organic compounds, and bacteria. Concentrations of most compounds were less than drinking-water standards established by the U.S. Environmental Protection Agency and New York State Department of Health; many of the organic analytes were not detected in any sample. Drinking-water standards that were exceeded at some sites include those for color, turbidity, pH, aluminum, arsenic, iron, manganese, radon-222, and bacteria. pH ranged from 5.6 to 8.3; the pH of nine samples was less than the U.S. Environmental Protection Agency secondary drinking-water standard range of 6.5 to 8.5. Water in the basin is generally soft to moderately hard (hardness 120 milligrams per liter as CaCO3 or less). The cation with the highest median concentration was calcium; the anion with the highest median concentrations was bicarbonate. Nitrate was the predominant nutrient detected but no sample exceeded the 10 mg/L U.S. Environmental Protection Agency maximum contaminant level. The trace elements detected with the highest median concentrations were strontium and iron in unfiltered water and strontium and barium in filtered water. Concentrations of trace elements in several samples exceeded U.S. Environmental Protection Agency secondary drinking-water standards, including aluminum (50-200 micrograms per liter, three wells), arsenic (10 micrograms per liter, one well), iron (300 micrograms per liter, three wells), and manganese (50 micrograms per liter, four wells). The median concentration of radon-222 was 1,580 picoCuries per liter. Radon-222 is not currently regulated, but the U.S. Environmental Protection Agency has proposed a maximum contaminant level of 300 picoCuries per liter along with an alternative maximum contaminant level of 4,000 picoCuries per liter, to be in effect in states that have programs to address radon in indoor air. Concentrations of radon-222 exceeded the proposed maximum contaminant level in all 19 of the samples and exceeded the proposed alternative maximum contaminant level in 1 sample. Eleven pesticides and pesticide degradates were detected in samples from ten wells; all were herbicides or herbicide degradates. Three volatile organic compounds were detected, including disinfection byproducts such as trichloromethane and gasoline components or additives such as methyl tert-butyl ether. No pesticides, pesticide degradates, or volatile organic compounds were detected above established limits. Coliform bacteria were detected in samples from five wells, four of which were finished in sand and gravel; Escherichia coli was not detected in any sample.

Open-File Report↗
USGS2007

Ground-Water Quality in the St. Lawrence River Basin, New York, 2005-06

The Federal Clean Water Act requires that States monitor and report on the quality of ground water and surface water. To satisfy part of these requirements, the U.S. Geological Survey and New York State Department of Environmental Conservation have developed a program in which ground-water quality is assessed in 2 to 3 of New York State's 14 major river basins each year. To characterize the quality of ground water in the St. Lawrence River Basin in northern New York, water samples were collected from 14 domestic and 11 production wells between August 2005 and January 2006. Eight of the wells were finished in sand and gravel and 17 wells were finished in bedrock. Ground-water samples were collected and processed using standard U.S. Geological Survey procedures and were analyzed for 229 constituents and physical properties, including inorganic constituents, nutrients, trace elements, radon-222, pesticides and pesticide degradates, volatile organic compounds, and bacteria. Sixty-six constituents were detected above laboratory reporting levels. Concentrations of most compounds at most sites were within drinking water standards established by the U.S. Environmental Protection Agency and New York State Department of Health, but a few compounds exceeded drinking water standards at some sites. Water in the basin is generally hard to very hard (hardness equal to 121 mg/L as CaCO3 or greater); hardness and alkalinity were generally higher in the St. Lawrence Valley than in the Adirondack Mountains. The cation with the highest median concentration was calcium; the anion with the highest median concentration was bicarbonate. The concentration of chloride in one sample exceeded the 250 milligrams per liter U.S. Environmental Protection Agency Secondary Drinking Water Standard; the concentration of sulfate in one sample also exceeded the 250 milligrams per liter U.S. Environmental Protection Agency Secondary Drinking Water Standard. Nitrate was the predominant nutrient detected but no sample exceeded the 10 mg/L U.S. Environmental Protection Agency Maximum Contaminant Level. The trace elements detected with the highest median concentrations were strontium, barium, and iron. Concentration of trace elements in several samples exceeded U.S. Environmental Protection Agency Secondary Drinking Water Standards, including aluminum (50 micrograms per liter, 4 samples), iron (300 micrograms per liter, 5 samples), and manganese (50 micrograms per liter, 4 samples). The concentration of uranium in one sample from a domestic well finished in crystalline bedrock was three times the U.S. Environmental Protection Agency Maximum Contaminant Level of 30 micrograms per liter. The median concentration of radon-222 was 600 picoCuries per liter, but concentrations as high as 18,800 picoCuries per liter were detected; two wells with high radon concentrations also had high uranium concentrations. Radon-222 is not currently regulated, but the U.S. Environmental Protection Agency has proposed a Maximum Contaminant Level of 300 picoCuries per liter along with an Alternative Maximum Contaminant Level of 4,000 picoCuries per liter, to be in effect in states that have programs to address radon in indoor air. Concentrations of radon-222 exceeded the proposed Maximum Contaminant Level in 60 percent of samples and exceeded the proposed Alternative Maximum Contaminant Level in 8 percent of samples. Six pesticides and pesticide degradates were detected; all were amide or triazine herbicides or degradates. Five volatile organic compounds were detected, including disinfection byproducts such as trichloromethane and gasoline components or additives such as methyl tert-butyl ether. No pesticides, pesticide degradates, or volatile organic compounds were detected above established limits. Coliform bacteria, including Escherichia coli, were detected in three wells finished in carbonate bedrock.

Open-File Report↗
USGS1981

Results of a modeling workshop concerning preservation and protection of wetlands in North Dakota

In a recently signed letter, the Governor of North Dakota and the Assistant Secretary of the Interior for Fish and Wildlife and Parks charged a joint state-federal study group with examination of two separate questions: 1) mitigation for the Garrison Diversion Project; and 2) planning for long-range protection and preservation of fish and wildlife habitat in North Dakota. The cochair for this study group (the Secretary of the Interior's Field Representative, Denver, Colorado, and the Natural Resources Coordinator for North Dakota) further articulated the charge concerning the second of these two questions to include three steps: 1) development of a general plan for preservation and protection of migratory waterfowl and their associated wetland habitat; 2) a comprehensive analysis of alternative strategies, including opportunities and constraints, for achieving the goals articulated in Step 1; and 3) design of a coordinated state-federal public information program to assist in plan implementation. In order to obtain input from a variety of interests, the joint study group initiated step 2 activities with a five-day workshop in Bismarck, N. D.; December 8-12, 1980. The objectives of the workshop were: 1) to identify alternative strategies for preserving and enhancing waterfowl production habitat in North Dakota; 2) to identify opportunities and constraints associated with those alternatives; and 3) to promote communication and understanding of the implications of those alternatives for all affected parties. To achieve these objectives, the workshop utilized a group of concepts and techniques collectively known as Adaptive Environmental Assessment (AEA). Developed by Dr. C. S. Holling and his co-workers at the University of British Columbia, the AEA process involves planners, managers, scientists, and other interested parties in a structures atmosphere whose focus is the construction and examination of a computerized simulation model of the resource system under consideration. The modeling process is used to promote communication, identify pertinent issues, identify key data gaps and uncertainties, direct research efforts to fill those gaps, and explore the possible consequences of various management alternatives. The workshop, which was facilitated by the AEA Group of the U.S. Fish and Wildlife Service (FWS), was attended by approximately 25 invited participants representing a variety of interests concerned with the wetlands protection issue in North Dakota. During the week workshop participants conceptualized and constructed a computerized simulation model incorporating many of the hydrologic, agricultural, and wildlife aspects of the wetlands issue. During the process of constructing this model and examining its behavior, participants identified several interesting alternative strategies that may prove useful in an overall wetland protection program, along with a variety of constraints associated with each. Perhaps the most interesting of these alternatives revolve around the idea that there may be a variety of cases in which water can be retained on the land, with concommitant benefits both for wildlife and flood control, without detriment to agricultural productivity. Examples of this kind of activity include flooding of previously drained Type I wetlands in summer fallow areas, installation of smaller drains in Type I and III wetlands to reduce the rate at which water runs off in the spring, and use of strategically located gates in drainage channels associated with the state highway system to slow runoff and create wetland habitat. Several other alternatives discussed at the workshop are related to the notion of using available, uncommitted water supplied to enhance or create wetlands. Several cases were cited in which more certain water supplies would be useful in increasing waterfowl production or reducing disease problems, especially in dry years. Water for such purposes might come from a variety of current of proposed water development projects, both large and small scale. Finally, the potential for re-establishment of "unsuccessfully" drained (i.e., not consistently usable for agricultural purposes) wetlands was discussed at some length. There are apparently substantial acreages of such wetlands in North Dakota and a program to acquire and rehabilitate them might be of considerable utility. The workshop was thus successful in accomplishing its first two objectives--identification of alternative strategies, opportunities, and constraints. However, it would be naive to suppose that any of the alternatives discussed offers a complete, simple solution to the wetlands issue in North Dakota. The most important result of the workshop may therefore be that which was accomplished relative to the third objective--promotion of communication and understanding. It was gratifying and encouraging to see the spirit of communication and cooperation that developed by the end of the workshop. The fact that representatives of many of the interests concerned with the wetlands issue participated in an open exchange of ideas and information marks an important step forward. We believe that it is imperative that this cooperative attitude be maintained, and that there are a variety of ways in which this might be accomplished. Perhaps the simplest would be a small-scale pilot project and research effort to determine the effects of wetland maintenance on summer fallow areas. Such a research program would provide not only useful information, but an opportunity for many of the affected interests to begin working toward mutually acceptable solutions to the overall wetlands issue.

North Dakota↗
USGS1990

Monitoring long-term effects of offshore oil and gas development along the Southern California outer continental shelf and slope: Background environmental conditions in the Santa Maria Basin

Potential environmental impacts of materials discharged from oil and gas development and production platforms off the coast of southern California (Santa Maria Basin) are being monitored during an ongoing, long-term (fiveyear) field program. The study combines hypothesis testing of platform effects with basic research on the structure and dynamics of the regional ecosystem over a time series encompassing both seasonal and repeated annual scales. Oceanographic features and processes that are being measured focus on the benthos and include biological community indices and species abundances for hard-bottom and soft-bottom (macroinfauna and meiofauna) assemblages; levels and distributions of trace metals and hydrocarbons in bottom sediments, suspended particulates, animal tissues, and pore waters; water currents and otherphysical-oceanographicfeatures; various sedimentological properties (sediment grain size, total organic carbon, shear strength, distribution of mineral types, radioisotope profiles, and degrees of sediment mixing as a result of bioturbation); sediment and pollutant-transport processes; and animal-sediment-pollutant interactions. Synoptic measurement of these different environmental variables over the extended sampling period provides an opportunity to examine long-term variability in the benthic environment with respect to both natural and anthropogenic causes. Efforts to distinguish between natural variability and low-level cumulative impacts of drilling are given special attention. Results obtained during the first two years of sampling provide a basis for beginning to understand environmental processes and relations important in detecting and interpreting any subsequent impacts caused by drilling activities in this complex and productive region of the California outer continental shelf and slope. Background chemical, physical, and biological data generated during this period demonstrate that impacts of discharges from oil and gas operations should be detectable, if they occur, and should be distinguishable from natural environmental variability. Small inputs of barium and petroleum hydrocarbons have been detected and appear to be associated with the minor drilling activities that have occurred in the area thus far, however, these initial inputs have not led to any noticeable biological impacts. These initial results are hopefully of value for two reasons: (1) in providing a summary of basic chemical, physical, and biological features of the benthic environment within the Santa Maria Basin; and (2) in presenting information on research strategies that should be considered in designing studies dealing with similar resource-management problems in other parts of the world.

California↗
USGS2009

Ecosystem effects of environmental flows: Modelling and experimental floods in a dryland river

Successful environmental flow prescriptions require an accurate understanding of the linkages among flow events, geomorphic processes and biotic responses. We describe models and results from experimental flow releases associated with an environmental flow program on the Bill Williams River (BWR), Arizona, in arid to semiarid western U.S.A. Two general approaches for improving knowledge and predictions of ecological responses to environmental flows are: (1) coupling physical system models to ecological responses and (2) clarifying empirical relationships between flow and ecological responses through implementation and monitoring of experimental flow releases. We modelled the BWR physical system using: (1) a reservoir operations model to simulate reservoir releases and reservoir water levels and estimate flow through the river system under a range of scenarios, (2) one- and two-dimensional river hydraulics models to estimate stage-discharge relationships at the whole-river and local scales, respectively, and (3) a groundwater model to estimate surface- and groundwater interactions in a large, alluvial valley on the BWR where surface flow is frequently absent. An example of a coupled, hydrology-ecology model is the Ecosystems Function Model, which we used to link a one-dimensional hydraulic model with riparian tree seedling establishment requirements to produce spatially explicit predictions of seedling recruitment locations in a Geographic Information System. We also quantified the effects of small experimental floods on the differential mortality of native and exotic riparian trees, on beaver dam integrity and distribution, and on the dynamics of differentially flow-adapted benthic macroinvertebrate groups. Results of model applications and experimental flow releases are contributing to adaptive flow management on the BWR and to the development of regional environmental flow standards. General themes that emerged from our work include the importance of response thresholds, which are commonly driven by geomorphic thresholds or mediated by geomorphic processes, and the importance of spatial and temporal variation in the effects of flows on ecosystems, which can result from factors such as longitudinal complexity and ecohydrological feedbacks. ?? Published 2009.

Freshwater Biology↗
USGS2025

Bacterial community diversity and potential eco-physiological roles in toxigenic blooms composed of Microcystis, Aphanizomenon or Planktothrix

Cyanobacterial toxicity, cyanotoxins, and their impact on aquatic ecosystems and human health are well documented. In comparison, less is known about bloom-associated bacterial communities. Co-occurring bacteria can influence bloom development, physiology and collapse, and may also provide a niche for pathogenic bacteria. Existing research focuses on the cyanosphere of Microcystis -dominated blooms, despite the increasing prevalence of filamentous genera ( Aphanizomenon and Planktothrix ). This pilot study aimed to broaden our understanding of the bacterial consortia attached to morphologically distinct cyanobacteria (coccoid and filamentous) dominating phytoplankton communities and to explore their potential roles in amplifying the impacts of cyanobacterial blooms. We investigated four shallow freshwater bodies across three continents and two climate zones: an urban pond in the USA, a dammed reservoir and a natural lake in Poland, and an urban water body in Singapore. Amplicon sequencing (16S rRNA gene) was used to characterize bacterial communities, while shotgun metagenomics identified nitrogen- and phosphorus-cycling genes to infer potential eco-physiological functions. Cyanobacteria dominated bacterioplankton assemblages at all sites (>35.6%), with bloom composition influencing toxigenic profiles. A mixed bloom of Microcystis , Snowella , and Aphanizomenon had the broadest range of cyanotoxin synthetase genes ( mcy E, cyr J, ana F and sxt A). Microcystis blooms correlated with increased Roseomonas , while Planktothrix co-occurred with Flavobacterium – both bacteria likely contribute to nutrient-cycling within blooms and represent potential opportunistic pathogens for aquatic organisms and humans. The Microcystis cyanosphere exhibited the highest number of significant positive correlations with bacteria (19 relations), compared to Planktothrix and Aphanizomenon (11 and 2 relations, respectively). Non-diazotrophic blooms of Microcystis and Planktothrix showed greater abundances of nitrogen – ( ure B, gln A, nar B, and nar HZ) and phosphorus-cycling genes ( pho BHPR and ppk 1), indicating a strong dependence on associated bacteria for nutrient acquisition compared to diazotrophic Aphanizomenon . These findings suggest that Aphanizomenon -dominated blooms may be sustained by simpler microbiomes. Our results provide preliminary evidence of cyanosphere heterogeneity potentially shaped by the dominance or coexistence of three morphologically and eco-physiologically distinct genera of cyanobacteria. A comprehensive knowledge of the taxonomy and functional roles of bloom-associated microbiomes is therefore essential to understand bloom activity, evaluate the environmental threat, and develop effective strategies for prevention and mitigation.

Frontiers in Microbiology↗
USGS2001

Concentration and Detection of Cryptosporidium Oocysts in Surface Water Samples by Method 1622 Using Ultrafiltration and Capsule Filtration

The protozoan parasite Cryptosporidium parvum is known to occur widely in both source and drinking water and has caused waterborne outbreaks of gastroenteritis. To improve monitoring, the U.S. Environmental Protection Agency developed method 1622 for isolation and detection of Cryptosporidium oocysts in water. Method 1622 is performance based and involves filtration, concentration, immunomagnetic separation, fluorescent-antibody staining and 4???,6-diamidino-2-phenylindole (DAPI) counterstaining, and microscopic evaluation. The capsule filter system currently recommended for method 1622 was compared to a hollow-fiber ultrafilter system for primary concentration of C. parvum oocysts in seeded reagent water and untreated surface waters. Samples were otherwise processed according to method 1622. Rates of C. parvum oocyst recovery from seeded 10-liter volumes of reagent water in precision and recovery experiments with filter pairs were 42% (standard deviation [SD], 24%) and 46% (SD, 18%) for hollow-fiber ultrafilters and capsule filters, respectively. Mean oocyst recovery rates in experiments testing both filters on seeded surface water samples were 42% (SD, 27%) and 15% (SD, 12%) for hollow-fiber ultrafilters and capsule filters, respectively. Although C. parvum oocysts were recovered from surface waters by using the approved filter of method 1622, the recovery rates were significantly lower and more variable than those from reagent grade water. In contrast, the disposable hollow-fiber ultrafilter system was compatible with subsequent method 1622 processing steps, and it recovered C. parvum oocysts from seeded surface waters with significantly greater efficiency and reliability than the filter suggested for use in the version of method 1622 tested.

Applied and Environmental Microbiology↗
USGS2016

Salmon redd identification using environmental DNA (eDNA)

Introduction The purpose of this project was to develop a technique to use environmental DNA (eDNA) to distinguish between redds made by Chinook salmon ( Oncorhynchus tshawytscha ) and redds made by Coho salmon ( O. kisutch ) and to distinguish utilized redds from test/abandoned redds or scours that have the appearance of redds. The project had two phases: Phase 1. Develop, test, and optimize a molecular assay for detecting and identifying Coho salmon DNA and differentiating it from Chinook salmon DNA. Phase 2. Demonstrate the efficacy of the technique. Collect and preserve water samples from the interstitial spaces of 10 known redds (as identified by expert observers) of each species and 10 gravel patches that do not include a redd of either species. Collect control samples from the water column adjacent to each redd to establish background eDNA levels. Analyze the samples using the developed molecular assays for Coho salmon (phase I) and Chinook salmon (Laramie and others, 2015). Evaluate whether samples collected from Chinook and Coho redds have significantly higher levels of eDNA of the respective species than background levels (that is, from gravel, water column). Evaluate whether samples collected from the interstitial spaces of gravel patches that are not redds are similar to background eDNA levels. The Sandy River is a large tributary of the Columbia River. The Sandy River meets the Columbia River approximately 23 km upstream of Portland, Oregon. The Sandy River Basin provides overlapping spawning habitat for both Chinook and Coho salmon. Samples provided by Portland Water Bureau for analysis were collected from the Bull Run River, Sixes Creek, Still Creek, Arrah Wanna Side Channel, and Side Channel 18.

Oregon↗
USGS2016

Endocrine-disrupting chemicals and oil and natural gas operations: Potential environmental contamination and recommendations to assess complex environmental mixtures

Background : Hydraulic fracturing technologies, developed over the last 65 years, have only recently been combined with horizontal drilling to unlock oil and gas reserves previously deemed inaccessible. While these technologies have dramatically increased domestic oil and natural gas production, they have also raised concerns for the potential contamination of local water supplies with the approximately 1,000 chemicals used throughout the process, including many known or suspected endocrine-disrupting chemicals. Objectives : We discuss the need for an endocrine component to health assessments for drilling-dense regions in the context of hormonal and anti-hormonal activities for chemicals used. Methods : We discuss the literature on 1) surface and ground water contamination by oil and gas extraction operations, and 2) potential human exposure, particularly in context of the total hormonal and anti-hormonal activities present in surface and ground water from natural and anthropogenic sources, with initial analytical results and critical knowledge gaps discussed. Discussion : In light of the potential for environmental release of oil and gas chemicals that can disrupt hormone receptor systems, we recommend methods for assessing complex hormonally active environmental mixtures. Conclusions : We describe a need for an endocrine-centric component for overall health assessments and provide supporting information that using this may help explain reported adverse health trends as well as help develop recommendations for environmental impact assessments and monitoring programs.

Environmental Health Perspectives↗
USGS2017

Pairing field methods to improve inference in wildlife surveys while accommodating detection covariance

It is common to use multiple field sampling methods when implementing wildlife surveys to compare method efficacy or cost efficiency, integrate distinct pieces of information provided by separate methods, or evaluate method-specific biases and misclassification error. Existing models that combine information from multiple field methods or sampling devices permit rigorous comparison of method-specific detection parameters, enable estimation of additional parameters such as false-positive detection probability, and improve occurrence or abundance estimates, but with the assumption that the separate sampling methods produce detections independently of one another. This assumption is tenuous if methods are paired or deployed in close proximity simultaneously, a common practice that reduces the additional effort required to implement multiple methods and reduces the risk that differences between method-specific detection parameters are confounded by other environmental factors. We develop occupancy and spatial capture–recapture models that permit covariance between the detections produced by different methods, use simulation to compare estimator performance of the new models to models assuming independence, and provide an empirical application based on American marten ( Martes americana ) surveys using paired remote cameras, hair catches, and snow tracking. Simulation results indicate existing models that assume that methods independently detect organisms produce biased parameter estimates and substantially understate estimate uncertainty when this assumption is violated, while our reformulated models are robust to either methodological independence or covariance. Empirical results suggested that remote cameras and snow tracking had comparable probability of detecting present martens, but that snow tracking also produced false-positive marten detections that could potentially substantially bias distribution estimates if not corrected for. Remote cameras detected marten individuals more readily than passive hair catches. Inability to photographically distinguish individual sex did not appear to induce negative bias in camera density estimates; instead, hair catches appeared to produce detection competition between individuals that may have been a source of negative bias. Our model reformulations broaden the range of circumstances in which analyses incorporating multiple sources of information can be robustly used, and our empirical results demonstrate that using multiple field-methods can enhance inferences regarding ecological parameters of interest and improve understanding of how reliably survey methods sample these parameters.

Maine↗
USGS2021

A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity

Community occupancy models estimate species‐specific parameters while sharing information across species by treating parameters as sampled from a common distribution. When communities consist of discrete groups, shrinkage of estimates towards the community mean can mask differences among groups. Infinite mixture models using a Dirichlet process (DP) distribution, in which the number of latent groups is estimated from the data, have been proposed as a solution. In addition to community structure, these models estimate species similarity, which allows testing hypotheses about whether traits drive species response to environmental conditions. We develop a community occupancy model (COM) using a DP distribution to model species‐level parameters. Because clustering algorithms are sensitive to dimensionality and distinctiveness of clusters, we conducted a simulation study to explore performance of the DP‐COM with different dimensions (i.e., different numbers of model parameters with species‐level DP random effects) and under varying cluster differences. Because the DP‐COM is computationally expensive, we compared its estimates to a COM with a normal random species effect. We further applied the DP‐COM model to a bird dataset from Uganda. Estimates of the number of clusters and species cluster identity improved with increasing difference among clusters and increasing dimensions of the DP; but the number of clusters was always overestimated. Estimates of number of sites occupied and species and community level covariate coefficients on occupancy probability were generally unbiased with (near‐) nominal 95% Bayesian Credible Interval coverage. Accuracy of estimates from the normal and the DP‐COM were similar. The DP‐COM clustered 166 bird species into 27 clusters regarding their affiliation with open or woodland habitat and distance to oil wells. Estimates of covariate coefficients were similar between a normal and the DP‐COM. Except sunbirds, species within a family were not more similar in their response to these covariates than the overall community. Given that estimates were consistent between the normal and the DP‐COM, and considering the computational burden for the DP models, we recommend using the DP‐COM only when the analysis focuses on community structure and species similarity, as these quantities can only be obtained under the DP‐COM.

Ecological Applications↗
USGS2022

Life and death in a dynamic environment: Invasive trout, floods, and intraspecific drivers of translocated populations

Understanding the relative strengths of intrinsic and extrinsic factors regulating populations is a long-standing focus of ecology and critical to advancing conservation programs for imperiled species. Conservation could benefit from an increased understanding of factors influencing vital rates (somatic growth, recruitment, survival) in small, translocated populations, which is lacking owing to difficulties in long-term monitoring of rare species. Translocations, here defined as the transfer of wild-captured individuals from source populations to new habitats, are widely used for species conservation, but outcomes are often minimally monitored, and translocations that are monitored often fail. To improve our understanding of how translocated populations respond to environmental variation, we developed and tested hypotheses related to intrinsic (density dependent) and extrinsic (introduced rainbow trout Oncorhynchus mykiss , stream flow and temperature regime) causes of vital rate variation in endangered humpback chub ( Gila cypha ) populations translocated to Colorado River tributaries in the Grand Canyon (GC), USA. Using biannual recapture data from translocated populations over 10 years, we tested hypotheses related to seasonal somatic growth, and recruitment and population growth rates with linear mixed-effects models and temporal symmetry mark–recapture models. We combined data from recaptures and resights of dispersed fish (both physical captures and continuously recorded antenna detections) from throughout GC to test survival hypotheses, while accounting for site fidelity, using joint live-recapture/live-resight models. While recruitment only occurred in one site, which also drove population growth (relative to survival), evidence supported hypotheses related to density dependence in growth, survival, and recruitment, and somatic growth and recruitment were further limited by introduced trout. Mixed-effects models explained between 67% and 86% of the variation in somatic growth, which showed increased growth rates with greater flood-pulse frequency during monsoon season. Monthly survival was 0.56–0.99 and 0.80–0.99 in the two populations, with lower survival during periods of higher intraspecific abundance and low flood frequency. Our results suggest translocations can contribute toward the recovery of large-river fishes, but continued suppression of invasive fishes to enhance recruitment may be required to ensure population resilience. Furthermore, we demonstrate the importance of flooding to population demographics in food-depauperate, dynamic, invaded systems.

Arizona↗
USGS2019

Floodplains provide important amphibian habitat despite multiple ecological threats

Floodplain ponds and wetlands are productive and biodiverse ecosystems, yet they face multiple threats including altered hydrology, land use change, and non‐native species. Protecting and restoring important floodplain ecosystems requires understanding how organisms use these habitats and respond to altered environmental conditions. We developed Bayesian models to evaluate occupancy of six amphibian species across 103 off‐channel aquatic habitats in the Chehalis River floodplain, Washington State, USA. The basin has been altered by changes in land use, reduced river–wetland connections, and the establishment of non‐native American bullfrogs ( Rana catesbeiana = Lithobates catesbeianus ) and centrarchid fishes, all of which we hypothesized could influence native amphibian occupancy. Despite potential threats, the floodplain habitats had relatively high rates of native amphibian occupancy, particularly when compared to studies from non‐floodplain habitats within the species’ native ranges. The biggest challenge for native amphibians appears to be non‐native centrarchid fishes, which strongly reduced occupancy of two native amphibians: the northern red‐legged frog ( Rana aurora ) and the northwestern salamander ( Ambystoma gracile ). Emergent vegetative cover increased occupancy probability for all five native amphibian species, indicating that plant management may offer a strategy to counter the negative effect of centrarchids by providing refuge from predation. We found that temporary and permanent hydroperiod sites supported different species; hence, both should be conserved on the landscape. Lastly, human‐created and natural ponds had similar amphibian occupancy patterns, suggesting that pond construction offers a viable strategy for adding habitats to the floodplain landscape. Overall, floodplain ponds and wetlands provide important amphibian habitat, and we offer management strategies that will bolster amphibian occupancy in an altered floodplain landscape.

Washington↗
USGS2001

Evaluation of USEPA method 1622 for detection of Cryptosporidium oocysts in stream waters

To improve surveillance for Cryptosporidium oocysts in water, the US Environmental Protection Agency developed method 1622, which consists of filtration, concentration, immunomagnetic separation, fluorescent antibody and 4, 6-diamidino-2-phenylindole (DAPI) counter-staining, and microscopic evaluation. Two filters were compared for analysis of 11 stream water samples collected throughout the United States. Replicate 10-L stream water samples (unspiked and spiked with 100–250 oocysts) were tested to evaluate matrix effects. Oocyst recoveries from the stream water samples averaged 22% (standard deviation [SD] = ±17%) with a membrane disk and 12% (SD = ±6%) with a capsule filter. Oocyst recoveries from reagent water precision and recovery samples averaged 39% (SD = ±13%) with a membrane disk and 47% (SD = ±19%) with a capsule filter. These results demonstrate that Cryptosporidium oocysts can be recovered from stream waters using method 1622, but recoveries are lower than those from reagent-grade water. This research also evaluated concentrations of indicator bacteria in the stream water samples. Because few samples were oocyst-positive, relationships between detections of oocysts and concentrations of indicator organisms could not be determined.

Journal - American Water Works Association↗
USGS2017

A practical method for the determination of total selenium in environmental samples using isotope dilution-hydride generation-inductively coupled plasma-mass spectrometry

A safe, practical, and accurate method for the determination of selenium (Se) in range of environmental samples was developed. Small sample masses, 5–20 mg, were amended with 82 Se enriched isotope for the isotope dilution (ID), preceding a multi-step wet digestion with nitric acid (HNO 3 ) and hydrogen peroxide (H 2 O 2 ). Samples were incubated in an autoclave for 3 h at 20 psi and 126°C. Digestates were subsequently reduced with concentrated hydrochloric acid to Se(IV) the most favorable valence for hydride generation (HG). The solutions were then analyzed on an ICP-MS equipped with Flow Injection system (FIAS-400). Polyatomic, isobaric, and background interferences were removed through the use of HG and ID with an 82 Se enriched isotope spike. Recoveries for certified reference materials were determined and averaged 96% for biological tissues (NRCC DOLT3, DOLT4, DORM2, TORT2, and TORT3, and NIST 2976) and 108% for estuarine sediment (NRCC PACS2) with an average coefficient of variation for replicate measurements of ∼ 3.5%. Limit of detection was 0.13 ng Se g −1 dry weight or 0.19 ng Se L −1 . This method can be broadly applied to biological tissues, sediments, suspended particulates, and water samples with minimal modifications making this method highly useful for assessing the ecotoxicology of total Se in aquatic ecosystems.

Limnology and Oceanography: Methods↗
USGS2021

Growth inhibition of the harmful alga Prymnesium parvum by plant-derived products and identification of ellipticine as highly potent allelochemical

Prymnesium parvum is a toxin-producing harmful alga that has caused ecological and economic damage worldwide. Effective methods to control blooms of this species in the field, however, are unavailable. This study examined five natural compounds present in the invasive plant Arundo donax and one synthetic derivative (5,6-dichlorogramine) for their effect on P. parvum growth. All compounds except one inhibited growth in the following order of potency: ellipticine > > 5,6-dichlorogramine > 1 H-indole = 2,4,6-trimethyl-benzonitrile > gramine. Ellipticine was by far the most potent inhibitor, with full algicidal activity at concentrations as low as 0.04 mg L −1 and 3- and 9-day IC 50 values of 0.012 and 0.007 mg L −1 , respectively. A reduction in chlorophyll content and swimming activity and an increase in length and volume (swelling) were documented in algal cells exposed to 0.01–0.02 mg ellipticine L −1 . These results show that ellipticine is among the most potent natural algicides identified to date. The sixth compound tested, oleamide, unexpectedly stimulated algal growth above control levels. Overall, these observations confirm the existence of highly potent anti- P. parvum allelochemicals in giant reed and demonstrate potential for using products derived from this plant in the development of natural, environmentally friendly methods to control harmful algal blooms.

Journal of Applied Phycology↗
USGS2013

Trait contributions to fish community assembly emerge from trophicinteractions in an individual-based model

Community ecology seeks to understand and predict the characteristics of communities that can develop under different environmental conditions, but most theory has been built on analytical models that are limited in the diversity of species traits that can be considered simultaneously. We address that limitation with an individual-based model to simulate assembly of fish communities characterized by life history and trophic interactions with multiple physiological tradeoffs as constraints on species performance. Simulation experiments were carried out to evaluate the distribution of 6 life history and 4 feeding traits along gradients of resource productivity and prey accessibility. These experiments revealed that traits differ greatly in importance for species sorting along the gradients. Body growth rate emerged as a key factor distinguishing community types and defining patterns of community stability and coexistence, followed by egg size and maximum body size. Dominance by fast-growing, relatively large, and fecund species occurred more frequently in cases where functional responses were saturated (i.e. high productivity and/or prey accessibility). Such dominance was associated with large biomass fluctuations and priority effects, which prevented richness from increasing with productivity and may have limited selection on secondary traits, such as spawning strategies and relative size at maturation. Our results illustrate that the distribution of species traits and the consequences for community dynamics are intimately linked and strictly dependent on how the benefits and costs of these traits are balanced across different conditions.

Ecological Modelling↗