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USGS2014

Monitoring fish distributions along electrofishing segments

Electrofishing is widely used to monitor fish species composition and relative abundance in streams and lakes. According to standard protocols, multiple segments are selected in a body of water to monitor population relative abundance as the ratio of total catch to total sampling effort. The standard protocol provides an assessment of fish distribution at a macrohabitat scale among segments, but not within segments. An ancillary protocol was developed for assessing fish distribution at a finer scale within electrofishing segments. The ancillary protocol was used to estimate spacing, dispersion, and association of two species along shore segments in two local reservoirs. The added information provided by the ancillary protocol may be useful for assessing fish distribution relative to fish of the same species, to fish of different species, and to environmental or habitat characteristics.

Mississippi↗

USGS2011

Fish and land use influence Gammarus lacustris and Hyalella azteca (Amphipoda) densities in large wetlands across the upper Midwest

Gammarus lacustris and Hyalella azteca (hereafter G. lacustris and H. azteca , respectively) are important components of secondary production in wetlands and shallow lakes of the upper Midwest, USA. Within the past 50 years, amphipod densities have decreased while occurrences of fish and intensity of agricultural land use have increased markedly across this landscape. We investigated influences of fish, sedimentation, and submerged aquatic vegetation (SAV) on densities of G. lacustris and H. azteca in semipermanent and permanent wetlands and shallow lakes ( n = 283) throughout seven eco-physiographic regions of Iowa, Minnesota, and North Dakota during 2004–2005. G. lacustris and H. azteca densities were positively correlated with densities of SAV ( P < 0.001 and P < 0.001, respectively). Both species were negatively correlated with densities of large fish (non-Cyprinidae; P = 0.01 and P = 0.013, respectively) and with high densities of fathead minnows ( Pimephales promelas ; P < 0.001 and P = 0.033, respectively). H. azteca densities also were negatively correlated with densities of small fish (e.g., other minnows [Cyprinidae] and sticklebacks [Gasterosteidae]; P = 0.048) and common carp ( Cyprinus spp.; P = 0.022). G. lacustris densities were negatively correlated with high levels of suspended solids (an index for sedimentation; P < 0.001). H. azteca densities were positively correlated with the width of upland-vegetation buffers ( P = 0.004). Our results indicate that sedimentation and fish reduce amphipod densities and may contribute to the current low densities of amphipods in the upper Midwest. Thus, removing/excluding fish, and providing a thick buffer of upland vegetation around wetlands may help restore amphipod densities and wetland and water quality within this landscape.

Iowa, Minnesota, North Dakota↗

USGS2019

Individual based modelling of fish migration in a 2-D river system: Model description and case study

Context: Diadromous fish populations in the Pacific Northwest face challenges along their migratory routes from declining habitat quality, harvest, and barriers to longitudinal connectivity. These stressors complicate the prioritization of proposed management actions intended to improve conditions for migratory fishes including anadromous salmon and trout. Objectives: We describe a multi-scale hybrid mechanistic–probabilistic simulation model linking migration corridor conditions to fish fitness outcomes. We demonstrate the model’s utility using a case study of salmon and steelhead adults in the Columbia River migration corridor exposed to spatially- and temporally-varying stressors. Methods: The migration corridor simulation model is based on a behavioral decision tree that governs individual interactions with the environment, and an energetic submodel that estimates the hourly costs of migration. Emergent properties of the migration corridor simulation model include passage time, energy use, and survival. Results: We observed that the simulated fish’s initial energy density, the migration corridor temperatures they experienced, and their history of behavioral thermoregulation were the primary determinants of their fitness outcomes. Insights gained from use of the model might be exploited to identify management interventions that increase successful migration outcomes. Conclusions: This paper describes new methods that extend the suite of tools available to aquatic biologists and conservation practitioners. We have developed a 2-dimensional spatially-explicit behavioral and physiological model and illustrated how it can be used to simulate fish migration within a river system. Our model can be used to evaluate trade-offs between behavioral thermoregulation and fish fitness at population scales.

Landscape Ecology↗

USGS2024

Evaluation of a carbon dioxide fish barrier through numerical modelling

The Chicago Area Waterway System (CAWS) is a potential route for the migration of aquatic invasive species from the Mississippi River Basin into the Great Lakes. Electric dispersal barriers were installed in the Chicago Sanitary Ship Canal, within CAWS, to prevent invasive fish from reaching the Great Lakes. Despite the high efficiency of these barriers, occasional maintenance events create a vulnerability that fish can exploit to access the Great Lakes. This study aimed to assess the feasibility of a carbon dioxide (CO 2 ) infusion system to deter fish during the maintenance of the electric barriers. An algebraic slip mixture model was implemented in the OpenFOAM solver to represent the underwater CO 2 bubble plume and predict the concentration of dissolved CO 2 in the canal. Simulations under three canal flowrates and two sparger systems were conducted assuming a constant gas flowrate. Numerical results indicate that, for all simulated conditions, the CO 2 concentration is not fully mixed creating passageways that invasive fish could potentially use to migrate upstream. Injecting 4-mm bubbles induces two large-scale recirculations that are expected to synergistically improve fish avoidance. On the other hand, injection of 20 μ "> μ m bubbles results on almost immediate dissolution with minimal effect on the flow pattern. To improve effectiveness, a gas pulse system was proposed and numerically evaluated. Based on the simulations, this system not only extends the operation of the CO 2 barrier but also increases efficiency creating CO 2 gradients that can promote a more responsive behaviour from fish. Moreover, the pulse concept mitigates potential effect of elevated CO 2 downstream from the treated area.

Illinois↗

USGS2011

Interrelationships between fish tissue mercury concentrations and water quality for South Dakota natural lakes and impoundments

The purpose of this study was to determine whether water quality parameters commonly associated with primary productivity may be used to predict the susceptibility of a specific water body to exceed proposed fish consumption advisory limitation of 0.3 mg kg −1 . South Dakota currently has nine lakes and impoundments that exceed fish tissue mercury advisory limits of 1.0 mg kg −1 total mercury, far exceeding US Environmental Protection Agency and Food and Drug Administration 0.3 mg kg −1 consumption criteria. Previous studies suggest that increased aquatic productivity may mitigate the effects of biological production and subsequent uptake of methyl mercury through bio-dilution; however, it is uncertain whether these trends may exist within highly alkaline and highly productive aquatic conditions common to South Dakota lakes and impoundments. Water quality parameters and fish tissue mercury data for northern pike and walleye were collected and assessed using existing South Dakota Department of Environment and Natural Resources and Game Fish and Parks data. The data was initially screened using both parametric linear regression and non-parametric Mann–Whitney rank sum comparisons and further assessed using binary logistic regression and stepwise logistic regression methodology. Three separate phosphorus measurements (total, total dissolved, and Trophic State Index) and pH were determined to significantly correlate with increased mercury concentrations for the northern pike-in-impoundments model. However, phosphorus surprisingly was not a strong predictor for the remaining scenarios modeled. For the northern pike-in-natural lakes models, alkalinity was the most significant water quality parameter predicting increased mercury concentrations. Mercury concentrations for the walleye-in-natural lakes models were further influenced by pH and alkalinity. The water quality and fish tissue mercury interrelationships determined within this study suggest aquatic productivity, and consequential eutrophication processes appear to be reasonable indicators of fish tissue mercury susceptibility for aquatic conditions common to South Dakota and highlight the continuing need to minimize eutrophication through effective watershed management strategies.

South Dakota↗

USGS2015

Tidal management sffects sub-adult fish assemblages in impounded South Carolina Marshes

In coastal South Carolina, most impounded marshes are managed for waterfowl; fewer are managed for fishes. Tidal control is central to each strategy but raises concerns that nursery function could be impaired. This research examined the assemblage composition of fishes during early-life stages. We sampled two impoundments of each management type monthly in 2008 and 2009. We used light traps to collect 61,527 sub-adult fish representing 21 species and 16 families and push nets to collect 12,670 sub-adult fish representing 13 species and 11 families. The effective number of species detected at larval stage in “fish” impoundments (summer mean = 2.52 ± 0.20, winter mean = 2.02 ± 0.66) was greater than in “waterfowl” impoundments (summer mean = 1.27 ± 0.14, winter mean = 1.06 ± 0.09); CI = 90 %. Species richness did not differ between management types, but hierarchical linear models predicted differences in assemblage composition. These findings underscore the importance of frequent water exchange for maintaining diverse assemblages of early-life-stage fishes in marsh impoundments.

South Carolina↗

USGS2023

Etiology of a fish kill, Including the endangered Tidewater Goby (Eucyclogobius newberryi), in a northeastern pacific coastal lagoon

Ecological disturbances such as fish kills can negatively impact ecosystem processes in coastal lagoons. To gain an understanding of factors causing fish kills, we examined conditions associated with a summertime fish kill in a northeastern Pacific coastal lagoon (Rodeo Lagoon, CA, USA). Examination of available data indicated the fish kill was likely caused by hypoxia involving the following etiology: (1) strong onshore winds (up to 12 m/s) mixed a stratified water column, (2) water column mixing transported nutrients from near the bed into the photic zone, (3) increased nutrient concentrations in the photic zone (> 200%) together with high solar irradiance fueled a phytoplankton bloom, (4) death and decomposition of phytoplankton (72% decrease in abundance) contributed to biological oxygen demand that led to (5) hypoxic conditions (as low as 0.6 mg/L) that caused the fish kill. The event resulted in the death of an estimated 3677 Tidewater Goby ( Eucyclogobius newberryi ), a species listed as endangered under the US Endangered Species Act, and numerous (but not enumerated) Threespine Stickleback ( Gasterosteus aculeatus ), unidentified sculpins (Cottidae), and macroinvertebrates (primarily Amphipoda). The processes contributing to the event are likely re-occurring phenomena responsible for observed periodic fish kills. Coastal lagoons with limited freshwater inflows and connection to the Pacific Ocean may retain nutrients and be susceptible to similar events.

California↗

USGS1983

Inbreeding in fish populations used for aquaculture

The theoretical causes of inbreeding depression are reviewed. Studies to measure depression at a series of inbreeding levels in rainbow trout populations using the method of inbred-outbred half-sib families are discussed. While the actual depression estimates varied widely between populations and inbreeding levels, significant levels of depression were found in many hatchery, field, and brood stock performance traits after only one generation of brother-sister mating. Especially susceptible to inbreeding depression, were measures of growth based upon attained fish weight at a given age in each test situation examined: 147 day weight (0.0 to 19.1%), 364 day weight (6.2 to 62.8%), weight after 6 months in fishing pond (−4.6 to 25.4%), weight after 12 months in fishing pond (13.0 to 29.1%), 2-year male weight (11.3 to 55.3%), and 2-year female weight (10.2 to 57.0%). Other hatchery performance traits that showed inbreeding depression were: egg hatch-ability (−0.2 to 53.1%), fry survival (0.4 to 8.2%), feed conversion efficiency (5.0 to 9.0%), fish length at 2-years of age (4.7 to 36.9%), and egg mass produced at 2-years (12.1 to 57.0%). Field performance traits that yielded inbreeding depression were percent recovery of fish stocked (−2.5 to 41.1%) and biomass index (16.2 to 47.7%). Literature on the effects of inbreeding in fish populations is reviewed and the breeding approaches for controlling the rate of inbreeding accumulation in brood stock populations are outlined and discussed.

Aquaculture↗

USGS1991

Metal bioavailability and toxicity to fish in low-alkalinity lakes: A critical review

Fish in low-alkalinity lakes having pH of 6·0–6·5 or less often have higher body or tissue burdens of mercury, cadmium, and lead than do fish in nearby lakes with higher pH. The greater bioaccumulation of these metals in such waters seems to result partly from the greater aqueous abundances of biologically available forms (CH 3 Hg + , Cd 2+ , and Pb 2+ ) at low pH. In addition, the low concentrations of aqueous calcium in low-alkalinity lakes increase the permeability of biological membranes to these metals, which in fish may cause greater uptake from both water and food. Fish exposed to aqueous inorganic aluminum in the laboratory and field accumulate the metal in and on the epithelial cells of the gills; however, there is little accumulation of aluminum in the blood or internal organs. In low-pH water, both sublethal and lethal toxicity of aluminum has been clearly demonstrated in both laboratory and field studies at environmental concentrations. In contrast, recently measured aqueous concentrations of total mercury, methylmercury, cadmium, and lead in low-alkalinity lakes are much lower than the aqueous concentrations known to cause acute or chronic toxicity in fish, although the vast majority of toxicological research has involved waters with much higher ionic strength than that in low-alkalinity lakes. Additional work with fish is needed to better assess (1) the toxicity of aqueous metals in low-alkalinity waters, and (2) the toxicological significance of dietary methylmercury and cadmium.

Environmental Pollution↗

USGS2012

Freshwater to seawater transitions in migratory fishes

The transition from freshwater to seawater is integral to the life history of many fishes. Diverse migratory fishes express anadromous, catadromous, and amphidromous life histories, while others make incomplete transits between freshwater and seawater. The physiological mechanisms of osmoregulation are widely conserved among phylogenetically diverse species. Diadromous fishes moving between freshwater and seawater develop osmoregulatory mechanisms for different environmental salinities. Freshwater to seawater transition involves hormonally mediated changes in gill ionocytes and the transport proteins associated with hypoosmoregulation, increased seawater ingestion and water absorption in the intestine, and reduced urinary water losses. Fishes attain salinity tolerance through early development, gradual acclimation, or environmentally or developmentally cued adaptations. This chapter describes adaptations in diverse taxa and the effects of salinity on growth. Identifying common strategies in diadromous fishes moving between freshwater and seawater will reveal the ecological and physiological basis for maintaining homeostasis in different salinities, and inform efforts to conserve and manage migratory euryhaline fishes.

Book chapter↗

USGS2005

Threats, conservation strategies, and prognosis for suckers (Catostomidae) in North America: insights from regional case studies of a diverse family of non-game fishes

Catostomid fishes are a diverse family of 76+ freshwater species that are distributed across North America in many different habitats. This group of fish is facing a variety of impacts and conservation issues that are somewhat unique relative to more economically valuable and heavily managed fish species. Here, we present a brief series of case studies to highlight the threats such as migration barriers, flow regulation, environmental contamination, habitat degradation, exploitation and impacts from introduced (non-native) species that are facing catostomids in different regions. Collectively, the case studies reveal that individual species usually are not threatened by a single, isolated factor. Instead, species in general face numerous stressors that threaten multiple stages of their life history. Several factors have retarded sucker conservation including widespread inabilities of field workers to distinguish some species, lack of basic natural history and ecological knowledge of life history, and the misconception that suckers are tolerant of degraded conditions and are of little social or ecological value. Without a specific constituent group lobbying for conservation of non-game fishes, all such species, including members of the catostomid family, will continue to face serious risks because of neglect, ignorance, and misunderstanding. We suggest that conservation strategies should incorporate research and education/outreach components. Other conservation strategies that would be effective for protecting suckers include freshwater protected areas for critical habitat, restoration of degraded habitat, and design of catostomid-friendly fish bypass facilities. We believe that the plight of the catostomids is representative of the threats facing many other non-game freshwater fishes with diverse life-history strategies globally.

Biological Conservation↗

USGS2019

Igneous rocks in the Fish Creek Mountains and environs, Battle Mountain area, north-central Nevada: A microcosm of Cenozoic igneous activity in the northern Great Basin, Basin and Range Province, USA

The Great Basin of the western United States, the northern component of the Basin and Range Province, is a region of Cenozoic lithospheric extension with multiple periods and types of igneous activity. The composition and volume of Cenozoic magmas reflect a complex interaction between mantle-derived magmas and highly diverse crust, where both mantle sources and magmatic processes were modulated by tectonic environment. The Fish Creek Mountains in north-central Nevada underwent multiple igneous events ranging from ca. 40 Ma to 1 Ma that span all of the complex Cenozoic tectono-magmatic episodes of the Great Basin. The Fish Creek Mountains, therefore, is an ideal location to evaluate the different sources and processes involved in magma generation. Many plutons were emplaced in the region between about 40 and 38 Ma, several of which host base and precious metal deposits. Between 36 and 33 Ma, lava fields and calderas of the 37–19 Ma Ignimbrite Flare-up were emplaced. Both these and the preceding plutons resulted from southwestward rollback of the Farallon plate beneath North America during by far the most voluminous phase of Cenozoic magmatism. The lavas range from rare basalt and basaltic andesite to andesite, dacite, and rhyolite, have continental arc-like incompatible element patterns, and high initial 87 Sr/ 86 Sr and low εNd that require a metasomatized lithospheric mantle source combined with minor crustal component. Ignimbrites of the 34.4 Ma Cove Mine (trachydacite to rhyolite) and 34.0 Ma Caetano calderas (rhyolite to high-silica rhyolite) are abundantly porphyritic, include hydrous phases, were largely derived from partial melts of crustal rocks, but likely include 20–30% of a mantle-derived component. Igneous activity ceased in the region as the rollback-arc migrated to the southwest, but at 24.9 Ma a new caldera formed in the southern Fish Creek Mountains that was filled by ignimbrites of the Fish Creek Mountains Tuff. Intracaldera rhyolite ignimbrites range from aphyric, pumice-rich deposits at the base to progressively more quartz-feldspar phyric ignimbrites at higher levels; all flow units lack hydrous phases. No contemporaneous mafic or intermediate igneous activity accompanied caldera formation, but initial 87 Sr/ 86 Sr values in the Fish Creek Mountains tuffs are lower than in the Caetano Tuff, suggesting a greater mantle contribution to the 24.9 Ma ignimbrites. After another hiatus in igneous activity, the region was intruded and overlain by basalt to rhyolite dykes and lavas of the northern Nevada rift between 16.8 and 15.1 Ma. The primarily tholeiitic igneous suite is of the same age, chemistry, and isotopic composition as the Grande Ronde Formation of the Columbia River flood basalts, and evolved members (trachydacite and rhyolite) are crustally contaminated. The youngest northern Nevada rift lava is an alkali olivine basalt with isotopic affinity to basalts of the eastern Snake River Plain. After 10 Ma of quiescence, the region was locally covered by mafic lava flows with high-alumina olivine tholeiite compositions, represented by the 5.4 Ma Pumpernickel Valley flows. Their mid-ocean ridge-like incompatible element compositions indicate a depleted mantle source for the lavas, but radiogenic isotopic compositions indicate that the lavas of this region include a significant contribution from a mafic to ultramafic, high- 87 Sr/ 86 Sr source. The final igneous event in the Fish Creek Mountains region, the 4.0 to 1.0 Ma Buffalo Valley volcanic field, includes flows and spatter cones of transitional to alkalic basalt that are divided into two geochemical groups with identical isotopic compositions. They represent variable, low percent partial melts of the asthenosphere at different depths, yielding different rare earth element characteristics. Similar to the Lunar Crater volcanic field, the Buffalo Valley rocks represent a rare case where the lithosphere in the central Great Basin is now thin enough to allow melting of the underlying asthenosphere. Cenozoic magmatism in the northern Great Basin exhibits several transitions in magma sources and tectonic setting with time. Magmatism began as pre-extension, subduction-related, primarily lithospherically-derived magmas emplaced on/in tectonically-thickened crust. The onset of extension was partially driven by impingement of the Yellowstone plume that resulted in emplacement of rift-related volcanic and intrusive rocks in the northern Nevada rift, followed by the eruption of extension-related HAOT lavas along the northwest margin of the Great Basin. Finally, lithospheric thinning allowed for partial melting of the asthenosphere and eruption of alkaline basaltic lavas.

Nevada↗

USGS2017

A computational fluid dynamics modeling study of guide walls for downstream fish passage

A partial-depth, impermeable guidance structure (or guide wall) for downstream fish passage is typically constructed as a series of panels attached to a floating boom and anchored across a water body (e.g. river channel, reservoir, or power canal). The downstream terminus of the wall is generally located nearby to a fish bypass structure. If guidance is successful, the fish will avoid entrainment in a dangerous intake structure (i.e. turbine intakes) while passing from the headpond to the tailwater of a hydroelectric facility through a safer passage route (i.e. the bypass). The goal of this study is to determine the combination of guide wall design parameters that will most likely increase the chance of surface-oriented fish being successfully guided to the bypass. To evaluate the flow field immediately upstream of a guide wall, a parameterized computational fluid dynamics model of an idealized power canal was constructed in © ANSYS Fluent v 14.5 (ANSYS Inc., 2012). The design parameters investigated were the angle and depth of the guide wall and the average approach velocity in the power canal. Results call attention to the importance of the downward to sweeping flow ratio and demonstrate how a change in guide wall depth and angle can affect this important hydraulic cue to out-migrating fish. The key findings indicate that a guide wall set at a small angle (15° is the minimum in this study) and deep enough such that sweeping flow dominant conditions prevail within the expected vertical distribution of fish approaching the structure will produce hydraulic conditions that are more likely to result in effective passage.

Ecological Engineering↗

USGS2007

Quantifying tolerance indicator values for common stream fish species of the United States

The classification of fish species tolerance to environmental disturbance is often used as a means to assess ecosystem conditions. Its use, however, may be problematic because the approach to tolerance classification is based on subjective judgment. We analyzed fish and physicochemical data from 773 stream sites collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program to calculate tolerance indicator values for 10 physicochemical variables using weighted averaging. Tolerance indicator values (TIVs) for ammonia, chloride, dissolved oxygen, nitrite plus nitrate, pH, phosphorus, specific conductance, sulfate, suspended sediment, and water temperature were calculated for 105 common fish species of the United States. Tolerance indicator values for specific conductance and sulfate were correlated (rho = 0.87), and thus, fish species may be co-tolerant to these water-quality variables. We integrated TIVs for each species into an overall tolerance classification for comparisons with judgment-based tolerance classifications. Principal components analysis indicated that the distinction between tolerant and intolerant classifications was determined largely by tolerance to suspended sediment, specific conductance, chloride, and total phosphorus. Factors such as water temperature, dissolved oxygen, and pH may not be as important in distinguishing between tolerant and intolerant classifications, but may help to segregate species classified as moderate. Empirically derived tolerance classifications were 58.8% in agreement with judgment-derived tolerance classifications. Canonical discriminant analysis revealed that few TIVs, primarily chloride, could discriminate among judgment-derived tolerance classifications of tolerant, moderate, and intolerant. To our knowledge, this is the first empirically based understanding of fish species tolerance for stream fishes in the United States.

Ecological Indicators↗

USGS2019

Temporal variability in stream fish assemblage metrics and implications for long-term monitoring

High natural variability in the condition of fish communities in headwater streams complicates detection of long-term responses to changes in water quality. As a result, little is known about the impacts and recovery of fishes from acid deposition in streams of New York. Twenty-one fish metrics from annual electrofishing surveys at 13 streams sites in the Catskill and Adirondack mountains were assessed to quantify temporal variability and identify effective monitoring strategies for detecting change in headwater stream fish assemblages. Metrics included the density and biomass of Brook Trout populations and entire fish communities using length-, area-, and effort-based standardization techniques. Linear mixed models were used to estimate changes in coefficients of variation (CV) for different classes of metrics and standardization techniques, and a simulation-based power analysis was conducted to assess differences in statistical power for each metric with various sampling designs. Metric CV varied significantly as a result of standardization technique and whether metrics were calculated for the entire community or Brook Trout only. The sampling effort necessary to detect a 30% change with power of 0.80 was strongly correlated with CV (R 2 = 0.77). The number of sampling events at the 13 sites needed to detect this change ranged from 1 to >60, suggesting metric selection can strongly affect statistical power and the resources necessary to detect change. Thus, metric selection is a complex decision that must consider study objectives and biological relevance, in addition to natural variability and statistical power. However, adequate statistical power was achieved at relatively small sample sizes using certain metrics, indicating that fish communities in headwater streams can be a valuable component of long-term assessments of acidification impacts and recovery.

New York↗

USGS2022

Evaluating acid-aluminum stress in streams of the Northeastern U.S. at watershed, fish community and physiological scales

In spite of overall improvements in air and water quality, biological stress from low pH and high concentrations of inorganic aluminum continue to impact fish and fish habitat in northeastern North America, with independent and interactive effects on individuals, populations and communities. Integrative indicators can therefore be useful in monitoring both impact and recovery across multiple scales. Using coupled water chemistry (pH, conductivity, and base cation and inorganic aluminum concentration), geographic (site elevation and watershed area) and biological (fish diversity, fish abundance, gill aluminum concentration and gill physiology) data, we developed an integrated indicator of acid aluminum stress across the White and Green mountains in central New England, USA. As has been established in a number of previous studies, preliminary analysis clearly indicated that across all sites, inorganic aluminum concentration was consistently greatest during the spring season. Structural Equation modelling (SEM) revealed that toxic conditions (concurrent low pH and high concentrations of inorganic aluminum) were well summarized with an integrated toxicity score, related to both base cation concentrations and elevation, with sites at higher elevations more likely to experience toxic conditions as well as low base cation concentrations. As hypothesized, fish diversity and abundance were negatively related to toxicity score. In spite of considerable variation among individuals, gill aluminum was positively related to toxicity score for both Atlantic salmon and brook trout. Observed elevated gill aluminum levels associated with reduced gill metabolic activity in Atlantic salmon smolts from impacted systems likely result in impaired osmoregulatory function and seawater tolerance. Overall, our results suggest that the integrated toxicity score metric is strongly associated with a syndrome of physiological stress, reduced abundance, and low species diversity for stream fishes in New England and can likely serve as a reliable indicator of continued impairment or recovery of acid-aluminum vulnerable systems in this ecoregion.

New Hampshire, Vermont↗

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↗

USGS2014

Mercury bioaccumulation in estuarine wetland fishes: Evaluating habitats and risk to coastal wildlife

Estuaries are globally important areas for methylmercury bioaccumulation because of high methylmercury production rates and use by fish and wildlife. We measured total mercury (THg) concentrations in ten fish species from 32 wetland and open bay sites in San Francisco Bay Estuary (2005–2008). Fish THg concentrations (μg/g dry weight ± standard error) differed by up to 7.4× among estuary habitats. Concentrations were lowest in open bay (0.17 ± 0.02) and tidal wetlands (0.42 ± 0.02), and highest in managed seasonal saline wetlands (1.27 ± 0.05) and decommissioned high salinity salt ponds (1.14 ± 0.07). Mercury also differed among fishes, with Mississippi silversides (0.87 ± 0.03) having the highest and longjaw mudsuckers (0.37 ± 0.01) the lowest concentrations. Overall, 26% and 12% of fish exceeded toxicity benchmarks for fish (0.20 μg/g wet weight) and piscivorous bird (0.30 μg/g wet weight) health, respectively. Our results suggest that despite managed wetlands' limited abundance within estuaries, they may be disproportionately important habitats of Hg risk to coastal wildlife.

California↗