SEARCH · Geology Reports

Results for “Aquatic Ecology”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources

USGS2021

Using expert knowledge to support Endangered Species Act decision‐making for data‐deficient species

Many questions relevant to conservation decision making are characterized by extreme uncertainty due to lack of empirical data and complexity of the underlying ecological processes, leading to a rapid increase in the use of structured protocols to elicit expert knowledge. Published ecological applications often employ a modified Delphi method, where experts provide judgments anonymously and mathematical aggregation techniques are used to combine judgments. The Sheffield Elicitation Framework (SHELF) differs in its behavioral approach to synthesizing individual judgments into a fully specified probability distribution for an unknown quantity. This study demonstrates the remote use of the SHELF protocol for an extinction risk assessment of three subterranean aquatic species petitioned for listing under the US Endangered Species Act. Experts were provided an empirical threat assessment for each known locality using video conferencing and asked for judgments on the probability of population persistence over four generations using online submission forms and R‐shiny apps available through the SHELF package. Despite large uncertainty for all populations, results reveal key differences between species’ risk of extirpation based on spatial variation in dominant threats, local land use and management practices, and microhabitat use. The resulting probability distributions provide decision makers with a full picture of uncertainty that is consistent with the probabilistic nature of risk assessments, and discussions during the behavioral aggregation stage clearly document dominant threats (e.g., development, timber harvest, animal agriculture, and cave visitation) and their interactions with local cave geology and species’ habitat preferences. Our virtual implementation of the SHELF protocol demonstrates the flexibility of this approach for conservation applications operating on budgets and timelines that can limit in‐person meetings of geographically dispersed experts.

Conservation Biology↗

USGS2020

Restoration of rapids habitat in a Great Lakes connecting channel, the St. Marys River, Michigan

Aquatic habitat has been extensively altered throughout the Laurentian Great Lakes to increase navigation connectivity. In particular, the St. Marys River, a Great Lakes connecting channel, lost >50% of its historic rapids habitat over the past century. In 2016, the natural flow was restored to the Little Rapids area of the St. Marys River. The goal of our study was to evaluate physical and ecological responses to the restoration of the Little Rapids area. Extensive habitat and biological data were collected prior to restoration (2013 and 2014), and after restoration (2017 and 2018). Measured parameters included total suspended solids, current velocity, benthic macroinvertebrates, and larval, juvenile, and adult fishes. Total suspended solids stayed low (<4 mg/L) following restoration, with the exception of a single construction‐related event. Pre‐restoration data indicated that all measured velocities were below the target flow rate of 0.24 m/s, whereas 70% of the measured habitat was above the target flow post‐restoration. Abundance and richness of benthic macroinvertebrates were reduced following restoration (>90% reduction). We observed a 45% increase in richness of larval fish 2 years after restoration and a 131% increase in catch per unit effort. For adult fishes, the proportion of individuals with a preference for fast‐moving waters increased from 1.5 to 45% in the restored area, and from 7 to 15% upstream of the restored area; a similar response was observed for lithophilic spawners. The physical and biological conditions of the Little Rapids improved and resembled conditions typical of rapids habitat extent in other areas of the river and other systems.

Michigan↗

USGS2021

Habitat suitability index model improvements

Habitat suitability index (HSI) models were developed for the 2023 Coastal Master Plan to evaluate the potential effects of coastal restoration and protection projects on habitat for key coastal fish, shellfish, and wildlife species. These species included: eastern oyster, brown shrimp, white shrimp, blue crab, crayfish, gulf menhaden, spotted seatrout, largemouth bass, American alligator, gadwall, mottled duck, brown pelican, seaside sparrow, and bald eagle. Most of these species were included in the 2017 Coastal Master Plan analyses, and the HSI models from that effort were refined and improved following the recommendations described in the technical memorandum: 2023 Coastal Master Plan Habitat Suitability Index Model Improvement Recommendations (Sable et al., 2019). In addition to model improvements, HSI models were created for seaside sparrow and bald eagle, both of which are new species for the master plan analyses. For the HSI models that are primarily literature-based, literature reviews were conducted for recent studies that could be used to improve the suitability index (SI) relationships that compose the models. As a result of this review, modifications were made to the salinity-related SIs of the oyster model including: expanding the time period used for salinity effects to spawning; adjusting the range of suitable annual average salinity to be more representative of Louisiana populations; and making oyster’s minimum salinity tolerance temperature dependent. In addition, a new SI was incorporated in the oyster HSI model that accounts for the effects of sediment deposition on oysters. The crayfish HSI model was improved by adjusting the time periods used for the SIs that describe the hydrology required for the crayfish life cycle, and the soil characteristics SI that was part of the 2017 crayfish model was removed because soil conditions do not appear to be limiting for crayfish burrow construction in coastal Louisiana. The other literature-based HSI models from the 2017 Coastal Master Plan, i.e., American alligator, gadwall, mottled duck, and brown pelican, were unchanged, with the exception of a small adjustment made to the suitability of forested wetlands for gadwall. Lastly, a literature-based HSI model was created for seaside sparrow that consists of SIs related to vegetated habitat type, marsh vegetation coverage, and marsh elevation. Statistical-based HSI models were developed for brown shrimp (both small and large juvenile stages), white shrimp (small and large juvenile stages), blue crab (juvenile stage), gulf menhaden (juvenile and adult stages), spotted seatrout (juvenile and adult stages), largemouth bass, and bald eagle. The bald eagle HSI model was developed from a bald eagle nest probability of occurrence model that related nest occurrence from survey data with land cover type. The resulting model showed that combinations of forested wetlands, flotant marsh, and open water habitats were most suitable for nesting bald eagles. The 2023 fish, shrimp, and blue crab HSI models were developed using new approaches for the formulation of the water quality and structural habitat SIs that compose the models. For the 2017 models, the water quality SI was derived using only generalized linear mixed models (GLMMs) to estimate the relationship between salinity, water temperature, and species’ catch. For the 2023 models, however, multiple GLMMs and generalized additive models (GAMMs) were created for each species or life stage. These alternative models were compared and a single model that performed well statistically and was ecologically reasonable was selected for the species’ water quality SI. The structural habitat SI was developed using a meta-analysis of published literature to estimate the relative importance of various estuarine habitats to the fish and shellfish species. The results of this analysis were then used to modify the 2017 structural habitat SI relationship to account for the added habitat value of submerged aquatic vegetation and oyster reefs, which are also important habitats for juvenile fish and shellfish. Similar to the 2017 fish, shrimp, and blue crab models, the water quality and structural habitat SIs were then combined to create the 2023 HSI models. The 2023 Coastal Master Plan HSI models were integrated with the Integrated Compartment Model (and are referred to as ICM-HSIs) and tested using environmental output from the 2017 Coastal Master Plan Future Without Action scenario. The tests showed that, in general, the models produced reasonable representations of species’ habitat distribution. Furthermore, the improvements made to the oyster, crayfish, fish, shrimp, and blue crab HSI models generally yielded more realistic results compared to the 2017 HSI models.

Report↗

USGS2021

Effects of stream intermittency on minnow (Leuciscidae) and darter (Percidae) trophic dynamics in an agricultural watershed

Stream intermittency is predicted to increase where water withdrawals and climate warming are increasing. In regions coupled with high fish diversity, understanding how intermittency influences fish trophic ecology is critical for informing ecosystem function. This study compared fish diets across seasons in perennial and intermittent streams to estimate the immediate and cumulative effects of stream drying on fish foraging patterns. We used gut content analysis to compare the diets of small-bodied, secondary consumer fishes, including two minnow and three darter species found in the lower Flint River Basin of southwestern Georgia, during both the summer (before stream dry-down) and fall (post flow resumption) seasons. Fish communities in perennial streams had greater diet richness compared to fishes in intermittent streams for both seasons. Darter diets were characterised by rheophilic aquatic insects in perennial streams and by benthic crustaceans (copepods, cladocerans and isopods) and predatory aquatic insects in intermittent streams. Minnow diets were typified by freshwater sponges, eggs and organic detritus in intermittent streams and by terrestrial insects and diatoms in perennial streams. Fishes in intermittent streams consumed significantly more benthic crustaceans in the fall (37% increase in proportional volume) compared to preflow cessation conditions in the summer, suggesting these organisms play an important, yet relatively unrecognised role in supporting fish communities in southeastern streams. Our findings enhance our understanding of how stream intermittency influences the trophic dynamics of secondary consumer fishes in an agricultural watershed increasingly affected by water scarcity.

Georgia↗

USGS1992

Use of remote sensing and GIS to identify Flamingo habitat in the Argentine Altiplano

The Argentine altiplano is a remote area which has never been adequately mapped. It is an arid region with harsh climate, little vegetation, sparse population, and an average elevation of over 3,500 feet. Little is known about the large populations of three species of flamingos which nest and feed in the altiplano lakes. In a study funded by the National Geographic Society satellite data (Landsat MSS and TM data) were used to map the location of major water bodies and to analyze the spectral characteristics of the aquatic ecosystems in the altiplano. A comparison of the two images revealed dramatic changes in the size, depth, and spectral reflectance of the lakes utilized by the flamingos.

Altiplano↗

USGS2019

A mosaic of estuarine habitat types with prey resources from multiple environmental strata supports a diversified foraging portfolio for juvenile Chinook salmon

Estuaries provide vital nursery habitat for threatened Chinook salmon (Oncorhynchus tshawytscha) by promoting an ecological portfolio effect, whereby multiple habitat types and environmental strata maximize foraging opportunities for out-migrating salmon by varying the abundance and composition of prey through space and time. To study this portfolio effect, we evaluated the foraging capacity of five estuarine habitat types within the Nisqually River Delta (Puget Sound, Washington, USA). Within each habitat, we sampled invertebrate prey resources from the terrestrial, aquatic, benthic, and epifaunal strata and compared them to juvenile salmon diets from corresponding sampling events. We found that the emergent salt marsh supplied twice as much aquatic prey biomass as any other habitat (720–5523 mg/m3), followed by the mudflat (246–2543 mg/m3) and eelgrass (Zostera marina; 141–2694 mg/m3) habitats. Despite some evidence for selectivity, juvenile salmon diets exhibited substantial compositional overlap, especially when compared to among-habitat differences in available prey resources. Fish that were captured in salt marsh, mudflat, and eelgrass consumed aquatic crustaceans such as mysids, while fish captured upriver in forested and transitional marshes ate a higher proportion of adult and larval insects. The availability and consumption of greater quantities of energy-poor crustaceans in the salt marsh and lower quantities of energy-rich insects upriver highlights a quantity-for-quality tradeoff among estuarine habitats. Our findings indicate that the timing, productivity, and diversity of prey across multiple habitat types and environmental strata determine an estuary’s capacity to support foraging for multiple life history strategies, size classes, and cohorts of juvenile salmon.

Washington↗

USGS2019

Projected urban growth in the Southeastern USA puts small streams at risk

Future land-use development has the potential to profoundly affect the health of aquatic ecosystems in the coming decades. We developed regression models predicting the loss of sensitive fish (R2=0.39) and macroinvertebrate (R2=0.64) taxa as a function of urban and agricultural land uses and applied them to projected urbanization of the rapidly urbanizing Piedmont ecoregion of the southeastern USA for 2030 and 2060. The regression models are based on a 2014 investigation of water quality and ecology of 75 wadeable streams across the region. Based on these projections, stream kilometers experiencing >50% loss of sensitive fish and invertebrate taxa will nearly quadruple to 19,500 and 38,950 km by 2060 (16 and 32% of small stream kilometers in the region), respectively. Uncertainty was assessed using the 20 and 80% probability of urbanization for the land-use projection model and using the 95% confidence intervals for the regression models. Adverse effects on stream health were linked to elevated concentrations of contaminants and nutrients, low dissolved oxygen, and streamflow alteration, all associated with urbanization. The results of this analysis provide a warning of potential risks from future urbanization and perhaps some guidance on how those risks might be mitigated.

PLoS ONE↗

USGS2002

Water quality and aquatic communities of upland wetlands, Cumberland Island National Seashore, Georgia, April 1999 to July 2000

Cumberland Island is the southernmost and largest barrier island along the coast of Georgia. The island contains about 2,500 acres of freshwater wetlands that are located in a variety of physical settings, have a wide range of hydroperiods, and are influenced to varying degrees by surface and ground water, rainwater, and seawater. In 1999-2000, the U.S. Geological Survey, in cooperation with the National Park Service, conducted a water-quality study of Cumberland Island National Seashore to document and interpret the quality of a representative subset of surface- and ground-water resources for management of the seashore's natural resources. As part of this study, historical ground-water, surface-water, and ecological studies conducted on Cumberland Island also were summarized. Surface-water samples from six wetland areas located in the upland area of Cumberland Island were collected quarterly from April 1999 to March 2000 and analyzed for major ions, nutrients, trace elements, and field water-quality constituents including specific conductance, pH, temperature, dissolved oxygen, alkalinity, tannin and lignin, and turbidity. In addition, water temperature and specific conductance were recorded continuously from two wetland areas located near the mean high-tide mark on the Atlantic Ocean beaches from April 1999 to July 2000. Fish and invertebrate communities from six wetlands were sampled during April and December 1999. The microbial quality of the near-shore Atlantic Ocean was assessed in seawater samples collected for 5 consecutive days in April 1999 at five beaches near campgrounds where most recreational water contact occurs. Ground-water samples were collected from the Upper Floridan aquifer in April 1999 and from the surficial aquifer in April 2000 at 11 permanent wells and 4 temporary wells (drive points), and were analyzed for major ions, nutrients, trace elements, and field water-quality constituents (conductivity, pH, temperature, dissolved oxygen, and alkalinity). Fecal-coliform bacteria concentrations were measured, but not detected, in samples collected from two domestic water-supply wells. During the 12-month period from April 1999 to March 2000 when water-quality and aquatic-community samples were collected, rainfall was 12.93 inches below the 30-year average rainfall. Constituent concentrations were highly variable among the different wetlands during the study period. Rainfall and tidal surges associated with tropical storms and hurricanes substantially influenced water quantity and quality, particularly in wetland areas directly influenced by tidal surges. Although surface waters on Cumberland Island are not used as sources of drinking water, exceedances of U.S. Environmental Protection Agency primary and secondary standards for drinking water were noted for comparative purposes. A nitrate concentration of 12 milligrams per liter in one sample from Whitney outflow was the only exceedance of a maximum contaminant level. Secondary standards were exceeded in 26 surface-water samples for the following constituents: pH (10 exceedances), chloride (8), sulfate (5), total dissolved solids (4), iron (2), fluoride (1), and manganese (1). The total-dissolved-solids concentrations and the relative abundance of major ions in surface-water samples collected from wetlands on Cumberland Island provide some insight into potential sources of water and influences on water quality. Major-ion chemistries of water samples from Whitney Lake, Willow Pond, and South End Pond 3 were sodium-chloride dominated, indicating direct influence from rainwater, salt aerosol, or inundation of marine waters. The remaining wetlands sampled had low total-dissolved-solids concentrations and mixed major-ion chemistries--North Cut Pond 2A was magnesium-sodium-chloride-sulfate dominated and Lake Retta and the two beach outflows were sodium-calcium-bicarbonate-chloride dominated. The higher percent calcium and bicarbonate in some wetlands sugg

Georgia↗

USGS2018

An epidemiological model of virus transmission in salmonid fishes of the Columbia River Basin

We have developed a dynamic epidemiological model informed by records of viral presence and genotypes to evaluate potential transmission routes maintaining a viral pathogen in economically and culturally important anadromous fish populations. In the Columbia River Basin, infectious hematopoietic necrosis virus (IHNV) causes severe disease, predominantly in juvenile steelhead trout ( Oncorhynchus mykiss ) and less frequently in Chinook salmon ( O. tshawytscha ). Mortality events following IHNV infection can be devastating for individual hatchery programs. Despite reports of high local mortality and extensive surveillance efforts, there are questions about how viral transmission is maintained. Modeling this system offers important insights into disease transmission in natural aquatic systems, as well as about the data requirements for generating accurate estimates about transmission routes and infection probabilities. We simulated six scenarios in which testing rates and the relative importance of different transmission routes varied. The simulations demonstrated that the model accurately identified routes of transmission and inferred infection probabilities accurately when there was testing of all cohort-sites. When testing records were incomplete, the model accurately inferred which transmission routes exposed particular cohort-sites but generated biased infection probabilities given exposure. After validating the model and generating guidelines for result interpretation, we applied the model to data from 14 annual cohorts (2000–2013) at 24 focal sites in a sub-region of the Columbia River Basin, the lower Columbia River (LCR), to quantify the relative importance of potential transmission routes in this focal sub-region. We demonstrate that exposure to IHNV via the return migration of adult fish is an important route for maintaining IHNV in the LCR sub-region, and the probability of infection following this exposure was relatively high at 0.16. Although only 1% of cohort-sites experienced self-exposure by infected juvenile fish, this transmission route had the greatest probability of infection (0.22). Increased testing and/or determining whether transmission can occur from cohort-sites without testing records (e.g., determining there was no testing record because there were no fish at the cohort-site) are expected to improve inference about infection probabilities. Increased use of secure water supplies and continued use of biosecurity protocols may reduce IHNV transmission from adult fish and juvenile fish within the site, respectively, to juvenile salmonids at hatcheries. Models and conclusions from this study are potentially relevant to understanding the relative importance of transmission routes for other important aquatic pathogens in salmonids, including the agents of bacterial kidney disease and coldwater disease, and the basic approach may be useful for other pathogens and hosts in other geographic regions.

Ecological Modelling↗

USGS2013

Winter feeding, growth and condition of brown trout Salmo trutta in a groundwater-dominated stream

Winter can be a stressful period for stream-dwelling salmonid populations, often resulting in reduced growth and survival. Stream water temperatures have been identified as a primary mechanism driving reductions in fitness during winter. However, groundwater inputs can moderate water temperature and may reduce winter severity. Additionally, seasonal reductions in prey availability may contribute to decreased growth and survival, although few studies have examined food webs supporting salmonids under winter conditions. This study employed diet, stable isotope, and mark-recapture techniques to examine winter (November through March) feeding, growth, and condition of brown trout Salmo trutta in a groundwater-dominated stream (Badger Creek, Minnesota, USA). Growth was greater for fish ≤ 150 mm (mean = 4.1 mg g −1 day −1 ) than for those 151–276 mm (mean = 1.0 mg g −1 day −1 ) during the winter season. Overall condition from early winter to late winter did not vary for fish ≤150 mm (mean relative weight (Wr) = 89.5) and increased for those 151–276 mm (mean Wr = 85.8 early and 89.4 late). Although composition varied both temporally and by individual, brown trout diets were dominated by aquatic invertebrates, primarily Amphipods, Dipterans, and Trichopterans. Stable isotope analysis supported the observations of the dominant prey taxa in stomach contents and indicated the winter food web was supported by a combination of allochthonous inputs and aquatic macrophytes. Brown trout in Badger Creek likely benefited from the thermal regime and increased prey abundance present in this groundwater-dominated stream during winter.

Minnesota↗

USGS2010

Two-dimensional hydrodynamic modeling to quantify effects of peak-flow management on channel morphology and salmon-spawning habitat in the Cedar River, Washington

The Cedar River in Washington State originates on the western slope of the Cascade Range and provides the City of Seattle with most of its drinking water, while also supporting a productive salmon habitat. Water-resource managers require detailed information on how best to manage high-flow releases from Chester Morse Lake, a large reservoir on the Cedar River, during periods of heavy precipitation to minimize flooding, while mitigating negative effects on fish populations. Instream flow-management practices include provisions for adaptive management to promote and maintain healthy aquatic habitat in the river system. The current study is designed to understand the linkages between peak flow characteristics, geomorphic processes, riverine habitat, and biological responses. Specifically, two-dimensional hydrodynamic modeling is used to simulate and quantify the effects of the peak-flow magnitude, duration, and frequency on the channel morphology and salmon-spawning habitat. Two study reaches, representative of the typical geomorphic and ecologic characteristics of the Cedar River, were selected for the modeling. Detailed bathymetric data, collected with a real-time kinematic global positioning system and an acoustic Doppler current profiler, were combined with a LiDAR-derived digital elevation model in the overbank area to develop a computational mesh. The model is used to simulate water velocity, benthic shear stress, flood inundation, and morphologic changes in the gravel-bedded river under the current and alternative flood-release strategies. Simulations of morphologic change and salmon-redd scour by floods of differing magnitude and duration enable water-resource managers to incorporate model simulation results into adaptive management of peak flows in the Cedar River. PDF version of a presentation on hydrodynamic modelling in the Cedar River in Washington state. Presented at the American Geophysical Union Fall Meeting 2010.

Washington↗

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↗

USGS2014

Improving the precision of lake ecosystem metabolism estimates by identifying predictors of model uncertainty

Diel changes in dissolved oxygen are often used to estimate gross primary production (GPP) and ecosystem respiration (ER) in aquatic ecosystems. Despite the widespread use of this approach to understand ecosystem metabolism, we are only beginning to understand the degree and underlying causes of uncertainty for metabolism model parameter estimates. Here, we present a novel approach to improve the precision and accuracy of ecosystem metabolism estimates by identifying physical metrics that indicate when metabolism estimates are highly uncertain. Using datasets from seventeen instrumented GLEON (Global Lake Ecological Observatory Network) lakes, we discovered that many physical characteristics correlated with uncertainty, including PAR (photosynthetically active radiation, 400-700 nm), daily variance in Schmidt stability, and wind speed. Low PAR was a consistent predictor of high variance in GPP model parameters, but also corresponded with low ER model parameter variance. We identified a threshold (30% of clear sky PAR) below which GPP parameter variance increased rapidly and was significantly greater in nearly all lakes compared with variance on days with PAR levels above this threshold. The relationship between daily variance in Schmidt stability and GPP model parameter variance depended on trophic status, whereas daily variance in Schmidt stability was consistently positively related to ER model parameter variance. Wind speeds in the range of ~0.8-3 m s–1 were consistent predictors of high variance for both GPP and ER model parameters, with greater uncertainty in eutrophic lakes. Our findings can be used to reduce ecosystem metabolism model parameter uncertainty and identify potential sources of that uncertainty.

Limnology and Oceanography: Methods↗

USGS2010

Feedbacks between community assembly and habitat selection shape variation in local colonization

1. Non-consumptive effects of predators are increasingly recognized as important drivers of community assembly and structure. Specifically, habitat selection responses to top predators during colonization and oviposition can lead to large differences in aquatic community structure, composition and diversity. 2. These differences among communities due to predators may develop as communities assemble, potentially altering the relative quality of predator vs. predator-free habitats through time. If so, community assembly would be expected to modify the subsequent behavioural responses of colonists to habitats containing top predators. Here, we test this hypothesis by manipulating community assembly and the presence of fish in experimental ponds and measuring their independent and combined effects on patterns of colonization by insects and amphibians. 3. Assembly modified habitat selection of dytscid beetles and hylid frogs by decreasing or even reversing avoidance of pools containing blue-spotted sunfish (Enneacanthus gloriosus). However, not all habitat selection responses to fish depended on assembly history. Hydrophilid beetles and mosquitoes avoided fish while chironomids were attracted to fish pools, regardless of assembly history. 4. Our results show that community assembly causes taxa-dependent feedbacks that can modify avoidance of habitats containing a top predator. Thus, non-consumptive effects of a top predator on community structure change as communities assemble and effects of competitors and other predators combine with the direct effects of top predators to shape colonization. 5. This work reinforces the importance of habitat selection for community assembly in aquatic systems, while illustrating the range of factors that may influence colonization rates and resulting community structure. Directly manipulating communities both during colonization and post-colonization is critical for elucidating how sequential processes interact to shape communities.

Journal of Animal Ecology↗

USGS2017

The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.

Virus Research↗

USGS2025

Disease, environment, and pollution: Understanding drivers behind tumour outbreaks in sea turtles

Various wildlife diseases of the Anthropocene (the Anthropocene currently has no formal status in the Divisions of Geologic Time https://pubs.usgs.gov/fs/2018/3054/fs20183054.pdf , accessed 4 June 2024) have root causes that are found in human-driven environmental disturbances. Fibropapillomatosis of sea turtles is exemplary of a human-exacerbated wildlife disease, and this case study offers an overview of how we applied a One Health approach and interdisciplinary process to better understand its complexity and highlight the interconnections existing between the health of the environment, and of the wildlife and humans living in it. Persistent organic pollutants (POPs) have known detrimental effects on human and wildlife health. Ubiquitous in the environment, these degradation-resistant chemicals have a high bioaccumulation potential. This case study describes the interdisciplinary plan and One Health design implemented to measure the role of harmful pollutants in the occurrence of a marine turtle panzootic fibropapillomatosis (FP). FP is a neoplastic disease that causes the growth of debilitating tumours on soft tissues and internal organs. Disease incidence has been increasing significantly throughout the Anthropocene and the reasons are still uncertain. The pervasive effect of pollution in marine coastal habitats has often been hypothesized as a driver of high disease prevalence but never fully tested. Our project combines disease ecology, marine field biology, and chemical toxicology in the attempt to unravel the intricate dynamics behind FP. We here describe the complex process used to develop a methodology to measure levels of harmful seawater pollutants such as polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and organochlorine pesticides (OCPs) in important sea turtle habitats in Florida. The proposed contaminants are among the top priority harmful pollutants, highly carcinogenic in aquatic animals, and bioaccumulate in sea turtles. Although only providing a description of the methodological process, this case study can help future research to apply similar transdisciplinary studies in the context of wildlife diseases. Understanding the effects of anthropogenic-driven pollution activity on ocean health can clarify its consequences to the health of wildlife and humans living in and around that environment.

One Health Cases↗

USGS2022

Lessons learned from 20 y of monitoring suburban development with distributed stormwater management in Clarksburg, Maryland, USA

Urban development is a well-known stressor for stream ecosystems, presenting a challenge to managers tasked with mitigating its effects. For the past 20 y, streamflow, water quality, geomorphology, and benthic communities were monitored in 5 watersheds in Montgomery County, Maryland, USA. This study presents a synthesis of multiple studies of monitoring efforts in the study area and new analysis of more recent monitoring data to document the primary lessons learned from monitoring. The monitored watersheds include a forested control, an urban control with centralized stormwater management, and 3 suburban treatment watersheds featuring low-impact development and a high density of infiltration-focused stormwater facilities distributed across the watershed. Treatment watersheds were monitored before development, during construction, and after development. Monitoring was initiated to inform adaptive management of stormwater and impervious cover limits within the study area, with a focus on the impacts of distributed stormwater management. Results from our synthesis indicate that distributed stormwater management is advantageous compared with centralized stormwater management in numerous ways. Hydrologic benefits were greater with distributed stormwater infrastructure, demonstrating the ability to mitigate runoff volumes and peak flows and, for small storms, replicate predevelopment conditions. Baseflow temporarily increased during the construction phase in the treatment watersheds. Water-quality benefits were mixed, with declines in baseflow nitrate concentrations but limited changes to nitrate export and increases in specific conductance after development. Substantial topographic changes occurred during construction in the treatment watersheds, including changes within the riparian zone, despite riparian buffer protections. Ecological monitoring indicated that even though index of biotic integrity scores rebounded in some cases, sensitive benthic macroinvertebrate families did not fully recover in the treatment watersheds. Lessons learned from this synthesis highlight the importance of tracking multiple indicators of stream health and considering past land use and that more stormwater facilities distributed across the watershed is beneficial but cannot mitigate the effects of all urban stressors on aquatic ecosystems.

Maryland↗

USGS2005

Hierarchical faunal filters: An approach to assessing effects of habitat and nonnative species on native fishes

Understanding factors related to the occurrence of species across multiple spatial and temporal scales is critical to the conservation and management of native fishes, especially for those species at the edge of their natural distribution. We used the concept of hierarchical faunal filters to provide a framework for investigating the influence of habitat characteristics and normative piscivores on the occurrence of 10 native fishes in streams of the North Platte River watershed in Wyoming. Three faunal filters were developed for each species: (i) large-scale biogeographic, (ii) local abiotic, and (iii) biotic. The large-scale biogeographic filter, composed of elevation and stream-size thresholds, was used to determine the boundaries within which each species might be expected to occur. Then, a local abiotic filter (i.e., habitat associations), developed using binary logistic-regression analysis, estimated the probability of occurrence of each species from features such as maximum depth, substrate composition, submergent aquatic vegetation, woody debris, and channel morphology (e.g., amount of pool habitat). Lastly, a biotic faunal filter was developed using binary logistic regression to estimate the probability of occurrence of each species relative to the abundance of nonnative piscivores in a reach. Conceptualising fish assemblages within a framework of hierarchical faunal filters is simple and logical, helps direct conservation and management activities, and provides important information on the ecology of fishes in the western Great Plains of North America. ?? Blackwell Munksgaard, 2004.

Ecology of Freshwater Fish↗