SEARCH · USGS Science

Results for “Environmental Biology of Fishes”

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 379 records · Page 21Linked to original sources

USGS2026

Assessment of the fish tumors or other deformities beneficial use impairment and associated risks at two Lake Michigan Areas of Concern

The U.S. Great Lakes Areas of Concern (AOCs) have been designated due to significant environmental degradation, with multiple Beneficial Use Impairments (BUIs) requiring remediation before delisting. The “fish tumors or other deformities” BUI remains at the Sheboygan River and the Lower Green Bay and Fox River AOCs, necessitating evaluation in white sucker ( Catostomus commersonii ), a sentinel species. This study documented the prevalence of skin and liver neoplastic and preneoplastic lesions at these AOCs, assessed temporal trends at the Sheboygan River AOC from 2012 to 2021, and investigated potential risk factors influencing liver neoplasm development using histological and molecular approaches. Histopathological analyses revealed that skin neoplasms were present in 15.5% of fish from the Green Bay AOC and 21.5% from the Sheboygan River AOC, while liver neoplasms were detected in 7.0% and 6.0% of fish, respectively. At the Sheboygan River AOC, the prevalence of skin tumors declined from 32.6% in 2012 to 21.5% in 2021, and liver tumor prevalence decreased from 8.3% in 2012 to 6.0% in 2021. Hepatic transcript analyses identified significant expression of genes associated with contaminant exposure, oxidative stress, and immune response, suggesting ongoing exposure to environmental stressors. The presence of white sucker hepatitis B-like virus (WSHBV) in hepatocytes was confirmed, though no direct correlation between viral transcript abundance and neoplastic lesions was found. Findings indicate tumor prevalence has declined over time, however rates remain elevated compared to previous reference site assessments. The study underscores the potential multifactorial nature of carcinogenesis in wild fish populations, involving both chemical and biological stressors.

Lake Michigan↗

USGS2021

Mixed evidence for biotic homogenization of southern Appalachian fish communities

Anthropogenic impacts on the landscape can drive biotic homogenization, whereby distinct biological communities become more similar to one another over time. Land-use change in the Southern Appalachian region is expected to result in homogenization of the highly diverse freshwater fish communities as in-stream habitat alterations favor widespread cosmopolitan species at the expense of more narrowly distributed highland endemic species. We compiled four datasets spanning 25 years to (1) evaluate the effects of environmental factors on relative abundance and richness of highland endemic vs. cosmopolitan species in this region and (2) test for taxonomic homogenization, measured as a change in beta diversity over time. We found that several environmental factors differentially affected highland endemic and cosmopolitan species, with the proportion of forested land cover in a watershed most strongly predicting higher relative abundance and richness of highland endemic species. Our analysis of beta diversity change, however, shows mixed evidence of taxonomic homogenization, depending on how common species are weighted. Shifts in community composition, with or without homogenization, may warrant attention in biodiversity conservation planning.

Georgia, North Carolina↗

USGS2020

Physical and chemical stressors on algal, invertebrate, and fish communities in 14 Milwaukee area streams, 2004–2013

In 2004, the U.S. Geological Survey (USGS) began sampling 14 wadable streams in urban or urbanizing watersheds near Milwaukee, Wisconsin. The overall goal of the study is to assess the health of the aquatic communities in the Milwaukee Metropolitan Sewerage District planning area to inform current and future watershed management. In addition to collection of biological data on aquatic communities, physical and chemical data were also collected to evaluate effects of potential environmental stressors on the aquatic communities. This fact sheet summarizes the primary results of the study from 2004 to 2013. Detailed information is described in Scudder Eikenberry and others (2020a), and all data are available in Scudder Eikenberry and others (2020b; https://doi.org/10.5066/P9FWMODL ).

Wisconsin↗

USGS2011

Selective uptake and biological consequences of environmentally relevant antidepressant pharmaceutical exposures on male fathead minnows

Antidepressant pharmaceuticals have been reported in wastewater effluent at the nanogram to low microgram-per-liter range, and include bupropion (BUP), fluoxetine (FLX), sertraline (SER), and venlafaxine (VEN). To assess the effects of antidepressants on reproductive anatomy, physiology, and behavior, adult male fathead minnows ( Pimeplwles promelas ) were exposed for 21 days either to a single concentration of the antidepressants FLX, SER, VEN, or BUP, or to an antidepressant mixture. The data demonstrated that exposure to VEN (305 ng/L and 1104 ng/L) and SER (5.2 ng/L) resulted in mortality. Anatomical alterations were noted within the testes of fish exposed to SER and FLX, both modulators of the neurotransmitter serotonin. Additionally, FLX at 28 ng/L induced vitellogenin in male fish—a common endpoint for estrogenic endocrine disruption. Significant alterations in male secondary sex characteristics were noted with single exposures. Effects of single compound exposures neither carried over, nor became additive in the antidepressant mixtures, and reproductive behavior was not affected. Analysis of brain tissues from the exposed fish suggested increased uptake of FLX, SER and BUP and minimal uptake of VEN when compared to exposure water concentrations. Furthermore, the only metabolite detected consistently in the brain tissues was norfluoxetine. Similar trends of uptake by brain tissue were observed when fish were exposed to antidepressant mixtures. The present study demonstrates that anatomy and physiology, but not reproductive behavior, can be disrupted by exposure to environmental concentrations of some antidepressants. The observation that antidepressant uptake into fish tissues is selective may have consequences on assessing the mode-of-action and effects of these compounds in future studies.

Aquatic Toxicology↗

USGS2004

Water-quality and biological conditions in the Lower Boise River, Ada and Canyon Counties, Idaho, 1994-2002

The water quality and biotic integrity of the lower Boise River between Lucky Peak Dam and the river's mouth near Parma, Idaho, have been affected by agricultural land and water use, wastewater treatment facility discharge, urbanization, reservoir operations, and river channel alteration. The U.S. Geological Survey (USGS) and cooperators have studied water-quality and biological aspects of the lower Boise River in the past to address water-quality concerns and issues brought forth by the Clean Water Act of 1977. Past and present issues include preservation of beneficial uses of the river for fisheries, recreation, and irrigation; and maintenance of high-quality water for domestic and agricultural uses. Evaluation of the data collected from 1994 to 2002 by the USGS revealed increases in constituent concentrations in the lower Boise in a downstream direction. Median suspended sediment concentrations from Diversion Dam (downstream from Lucky Peak Dam) to Parma increased more than 11 times, nitrogen concentrations increased more than 8 times, phosphorus concentrations increased more than 7 times, and fecal coliform concentrations increased more than 400 times. Chlorophyll-a concentrations, used as an indicator of nutrient input and the potential for nuisance algal growth, also increased in a downstream direction; median concentrations were highest at the Middleton and Parma sites. There were no discernible temporal trends in nutrients, sediment, or bacteria concentrations over the 8-year study. The State of Idaho?s temperature standards to protect coldwater biota and salmonid spawning were exceeded most frequently at Middleton and Parma. Suspended sediment concentrations exceeded criteria proposed by Idaho Department of Environmental Quality most frequently at Parma and at all but three tributaries. Total nitrogen concentrations at Glenwood, Middleton, and Parma exceeded national background levels; median flow-adjusted total nitrogen concentrations at Middleton and Parma were higher than those in undeveloped basins sampled nationwide by the USGS. Total phosphorus concentrations at Glenwood, Middleton, and Parma also exceeded those in undeveloped basins. Macroinvertebrate and fish communities were used to evaluate the long-term integration of water-quality contaminants and loss of habitat in the lower Boise. Biological integrity of the macroinvertebrate population was assessed with the attributes (metrics) of Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness and metrics used in the Idaho River Macroinvertebrate Index (RMI): taxa richness; EPT richness; percent dominant taxon; percent Elmidae (riffle beetles); and percent predators. Average EPT was about 10, and RMI scores were frequently below 16, which indicated intermediate or poor water quality. The number of EPT taxa and RMI scores for the lower Boise were half those for least-impacted streams in Idaho. The fine sediment bioassessment index (FSBI) was used to evaluate macroinvertebrate sediment tolerance. The FSBI scores were lower than those for a site upstream in the Boise River Basin near Twin Springs, a site not impacted by urbanization and agriculture, which indicated that the lower Boise macroinvertebrate population may be impacted by fine sediment. Macroinvertebrate functional feeding groups and percent tolerant species, mainly at Middleton and Parma, were typical of those in areas of degraded water quality and habitat. The biological integrity of the fish population was evaluated using the Idaho River Fish Index (RFI), which consists of the 10 metrics: number of coldwater native species, percent sculpin, percent coldwater species, percent sensitive native individuals, percent tolerant individuals, number of nonindigenous species, number of coldwater fish captured per minute of electrofishing, percent of fish with deformities (eroded fins, lesions, or tumors), number of trout age classes, and percent carp. RFI scores for lower Boise sites indicated a d

Scientific Investigations Report↗

USGS1982

Physical, Hydrological, and Biological Characteristics of the Loxahatchee River Estuary, Florida

The Loxahatchee River estuary empties into the Atlantic Ocean at Jupiter Inlet in southeastern Florida. Although relatively small, the estuary is important for its esthetic value and for its sport fishing, boating, recreation, tourism, and prime residential development. In recent years, the condition of the estuary has become of concern to many citizens and agencies of the State. In response to this concern, the U.S. Geological Survey planned and carried out an in-depth environmental investigation. The events that led to the investigation and the objectives of the investigation are outlined in a recent U.S. Geological Survey report by McPherson and Sabanskas (WRI 80-1109).

Water-Resources Investigations Report↗

USGS1989

Streamside habitats in southern forested wetlands: Their role and implications for management

The value of streamside forests to fish and wildlife and the influence of forest management on their value have been recognized in a general sense for decades. However, in today’s climate of increasing environmental regulation and intensive forest management, there is need for more detailed understanding of the value of streamside forests to fish and wildlife. Dickson and Huntley (1987:38) described the problem well when they wrote that “quantitative data on the effects of riparian zones on wildlife populations are insufficient to enable wildlife managers to justify the retention of riparian zones in land-use plans on a biological and economical basis.” Due in large part to the passage of water pollution control legislation, as well as legislation mandating multiple-use management in our national forests, progress is being made. During the last l&15 years, a great deal of research has been directed at understanding the value and appropriate management of the riparian zone (Brouha and Parsons 1985). The vast majority of research on riparian habitats has been conducted in western forests and/or narrow zones in otherwise upland areas. Also, much of the work done in southern forested wetlands has applied to entire floodplain forests. In this paper, we review the literature on streamside habitats within southern forested wetlands and, for reasons described in the next section, we make a distinction between streamside forests and floodplain (or riparian) forests. We also discuss in less detail the value of streamside habitats within other southern forest types, such as pine or mixed pine-hardwood.

General Technical Report↗

USGS1994

Characterization of ecological risks at the Milltown Reservoir-Clark Fork River Sediments Superfund Site, Montana

A comprehensive field and laboratory approach to the ecological risk assessment for the Milltown Reservoir-Clark Fork River Sediments Site, a Superfund site in the Rocky Mountains of Montana, has been described in the preceding reports of this series. The risk assessment addresses concerns over the ecological impacts of upstream releases of mining wastes to fisheries of the upper Clark Fork River (CFR) and the benthic and terrestrial habitats further downstream in Milltown Reservoir. The risk characterization component of the process integrated results from a triad of information sources: (a) chemistry studies of environmental media to identify and quantify exposures of terrestrial and aquatic organisms to site-related contaminants; (b) ecological or population studies of terrestrial vegetation, birds, benthic communities, and fish; and (c) in situ and laboratory toxicity studies with terrestrial and aquatic invertebrates and plants, small mammals, amphibians, and fish exposed to contaminated surface water, sediments, wetland soils, and food sources. Trophic transfer studies were performed on waterfowl, mammals, and predatory birds using field measurement data on metals concentrations in environmental media and lower trophic food sources. Studies with sediment exposures were incorporated into the Sediment Quality Triad approach to evaluate risks to benthic ecology. Overall results of the wetland and terrestrial studies suggested that acute adverse biological effects were largely absent from the wetland; however, adverse effects to reproductive, growth, and physiological end points of various terrestrial and aquatic species were related to metals exposures in more highly contaminated depositional areas. Feeding studies with contaminated diet collected from the upper CFR indicated that trout are at high risk from elevated metals concentrations in surface water, sediment, and aquatic invertebrates. Integration of chemical analyses with toxicological and ecological evaluations of metal effects on the wetland and fishery has provided an important foundation for environmental decisions at this site.

Montana↗

USGS2022

Round Goby captured in a North American estuary: Status and implications in the Hudson River, New York

Round Goby Neogobius melanostomus , a nonnative fish species to North America, has been rapidly expanding through the connected waterways of the Laurentian Great Lakes. Herein, we document the eastward and southern expansion of Round Goby into the Hudson River, New York, an iconic coastal estuary that drains to Long Island Sound and the Atlantic seaboard. In summer and early fall 2021, routine fish monitoring conducted by the New York State Department of Environmental Conservation documented a population of Round Goby in the tidal portion of the Hudson River. Over the course of monitoring in 2021, personnel collected 112 Round Goby between Albany, New York, and Poughkeepsie, New York, with the southernmost collection occurring approximately 140 km downstream of invasion front as reported in 2020 within the New York State Canal System. Although Round Goby previously colonized large rivers and streams in the Great Lakes watershed, there is little information about the invasion success and ecological impacts of Round Goby in estuarine environments in North America. We discuss the distribution and biological characteristics of the Hudson River Round Goby population as well as the potential ecological implications and areas of future research and monitoring for this range expansion.

New York↗

USGS1986

Biomonitors of stream quality on agricultural areas: fish versus invertebrates

Although the utility of using either fish or benthic invertebrates as biomonitors of stream quality has been clearly shown, there is little comparative information on the usefulness of the groups in any particular situation. We compared fish to invertebrate assemblages in their ability to reflect habitat quality of sediment-impacted streams in agricultural regions of northeast Missouri, USA. Habitat quality was measured by a combination of substrate composition, riparian type, buffer strip width, and land use. Invertebrates were more sensitive to habitat differences when structural measurements, species diversity and ordination, were used. Incorporating ecological measurements, by using the Index of Biological Integrity, increased the information obtained from the fish assemblage. The differential response of the two groups was attributed to the more direct impact of sediments on invertebrate life requisites; the impact of sedimentation on fish is considered more indirect and complex, affecting feeding and reproductive mechanisms.

Environmental Management↗

USGS2010

Assessment of ecological conditions and potential effects of water produced from coalbed natural gas development on biological communities in streams of the Powder River structural basin, Wyoming and Montana, 2005-08

Ongoing development of coalbed natural gas in the Powder River structural basin in Wyoming and Montana led to formation of an interagency task group to address concerns about the effects of the resulting production water on biological communities in streams of the area. The interagency task group developed a monitoring plan and conducted sampling of macroinvertebrate, algal, and fish communities at 47 sites during 2005-08 to document current ecological conditions and determine existing and potential effects of water produced from coalbed natural gas development on biological communities. Macroinvertebrate, algal, and fish community composition varied between drainage basins, among sites within drainage basins, and by year. Macroinvertebrate communities of the main-stem Tongue River were characterized by higher taxa richness and higher abundance of Ephemeroptera, for example, compared to macroinvertebrate communities in plains tributaries of the Tongue River and the main-stem Powder River. Fish communities of the Tongue River were characterized by higher taxa richness and abundance of introduced species compared to the Powder River where native species were dominant. Macroinvertebrate community metric values from sites in the middle reach of the main-stem Powder River, from below Willow Creek to below Crazy Woman Creek, differed from metric values in the upper and lower reaches of the Powder River. Metrics indicative of communitywide differences included measures of taxa richness, relative abundance, feeding mode, and tolerance. Some of the variation in the macroinvertebrate communities could be explained by variation in environmental variables, including physical (turbidity, embeddedness, bed substrate size, and streamflow) and chemical (alkalinity and specific conductance) variables. Of these environmental variables, alkalinity was the best indicator of coalbed natural gas development because of the sodiumbicarbonate signature of the production water. Algal samples from the main-stem Powder River generally confirmed the pattern observed in the macroinvertebrate communities. Algal communities at sites in the middle reach of the Powder River commonly were characterized by dominance by a single taxon and by low biovolume of algae compared to other sites. In contrast to the macroinvertebrate and algal communities, species richness of fish communities was highest in the middle reach of the Powder River. Although a few significant differences in fish metrics were determined along the main-stem Powder River, the differences did not correspond to the pattern observed for the macroinvertebrate and algae communities. Differences in biological communities were noted between years, potentially due to the effects of drought. Macroinvertebrate community metrics, such as Diptera taxa richness, were significantly different in the severe drought year of 2006 from metric values in 2005 and 2007-08. Waterquality data collected during the study indicated that, with few exceptions, water-quality constituents generally did not exceed State or Federal acute and chronic criteria for the protection of aquatic life.

Scientific Investigations Report↗

USGS2025

Targeted quantitation of 6ppd-quinone in fish tissue samples with liquid chromatography-tandem mass spectrometry

The tire additive transformation product N -(1,3-dimethylbutyl)- N’ -phenyl- p -phenylenediamine-quinone (6PPD-quinone) has recently garnered global attention due to its acute toxicity to some salmonids, such as coho salmon ( Oncorhynchus kisutch ), and its ubiquitous presence in urban stormwater systems. In the present study, we developed and compared the extraction efficiency of two sample preparation methodologies for quantification of 6PPD-quinone among two fish tissue sample types that included fillet of smallmouth bass ( Micropterus dolomieu ) and whole-body samples of O. kisutch fry subjected to in vivo exposure tests with 6PPD-quinone. The two sample preparation methods tested included an accelerated solvent extraction (ASE) approach and a sonication extraction approach. Both sample preparation methods included identical purification steps for the crude sample extracts with enhanced matrix removal cartridges. The purified sample extracts were subjected to targeted analysis of 6PPD-quinone using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The results showed that extractions made with the reported ASE method demonstrated significantly higher absolute recovery (80–96%) of the extracted internal standard, [ 13 C 6 ]-6PPD-quinone, than sonication-based extractions (74–80%) in both fish tissue sample types. The proposed ASE method shows acceptable limits of quantification (0.37–0.67 ng g −1 ), linearity (R 2 > 0.996), and repeatability (RSD ≤ 9%). This work advances research capabilities for investigations on the toxicokinetic processes of 6PPD-quinone in biological samples.

Environmental Toxicology and Chemistry↗

USGS2012

Patterns of metal composition and biological condition and their association in male common carp across an environmental contaminant gradient in Lake Mead National Recreation Area, Nevada and Arizona, USA

There is a contaminant gradient in Lake Mead National Recreation Area (LMNRA) that is partly driven by municipal and industrial runoff and wastewater inputs via Las Vegas Wash (LVW). Adult male common carp ( Cyprinus carpio ; 10 fish/site) were collected from LVW, Las Vegas Bay (receiving LVW flow), Overton Arm (OA, upstream reference), and Willow Beach (WB, downstream) in March 2008. Discriminant function analysis was used to describe differences in metal concentrations and biological condition of fish collected from the four study sites, and canonical correlation analysis was used to evaluate the association between metal and biological traits. Metal concentrations were determined in whole-body extracts. Of 63 metals screened, those initially used in the statistical analysis were Ag, As, Ba, Cd, Co, Fe, Hg, Pb, Se, Zn. Biological variables analyzed included total length (TL), Fulton's condition factor, gonadosomatic index (GSI), hematocrit (Hct), and plasma estradiol-17β and 11-ketotestosterone (11kt) concentrations. Analysis of metal composition and biological condition both yielded strong discrimination of fish by site (respective canonical model, p < 0.0001). Compared to OA, pairwise Mahalanobis distances between group means were WB < LVB < LVW for metal concentrations and LVB < WB < LVW for biological traits. Respective primary drivers for these separations were Ag, As, Ba, Hg, Pb, Se and Zn; and TL, GSI, 11kt, and Hct. Canonical correlation analysis using the latter variable sets showed they are significantly associated ( p < 0.0003); with As, Ba, Hg, and Zn, and TL, 11kt, and Hct being the primary contributors to the association. In conclusion, male carp collected along a contaminant gradient in LMNRA have distinct, collection site-dependent metal and morpho-physiological profiles that are significantly associated with each other. These associations suggest that fish health and reproductive condition (as measured by the biological variables evaluated in this study) are influenced by levels of certain metals in the Lake Mead environment.

Nevada↗

USGS2010

Effects of urbanization on stream ecosystems along an agriculture-to-urban land-use gradient, Milwaukee to Green Bay, Wisconsin, 2003-2004

In 2003 and 2004, 30 streams near Milwaukee and Green Bay, Wisconsin, were part of a national study by the U.S. Geological Survey to assess urbanization effects on physical, chemical, and biological characteristics along an agriculture-to-urban land-use gradient. A geographic information system was used to characterize natural landscape features that define the environmental setting and the degree of urbanization within each stream watershed. A combination of land cover, socioeconomic, and infrastructure variables were integrated into a multi-metric urban intensity index, scaled from 0 to 100, and assigned to each stream site to identify a gradient of urbanization within relatively homogeneous environmental settings. The 35 variables used to develop the final urban intensity index characterized the degree of urbanization and included road infrastructure (road area and road traffic index), 100-meter riparian land cover (percentage of impervious surface, shrubland, and agriculture), watershed land cover (percentage of impervious surface, developed/urban land, shrubland, and agriculture), and 26 socioeconomic variables (U.S. Census Bureau, 2001). Characteristics examined as part of this study included: habitat, hydrology, stream temperature, water chemistry (chloride, sulfate, nutrients, dissolved and particulate organic and inorganic carbon, pesticides, and suspended sediment), benthic algae, benthic invertebrates, and fish. Semipermeable membrane devices (SPMDs) were used to assess the potential for bioconcentration of hydrophobic organic contaminants (specifically polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and organochlorine and pyrethroid insecticides) in biological membranes, such as the gills of fish. Physical habitat measurements reflective of channel enlargement, including bankfull channel size and bank erosion, increased with increasing urbanization within the watershed. In this study, percentage of riffles and streambed substrate size were more strongly related to local geologic setting, slope, watershed topography, and river-engineering practices than to urbanization. Historical local river-engineering features such as channelization, bank stabilization, and grade controls may have confounded relations among habitat characteristics and urbanization. A number of hydrologic-condition metrics (including flashiness and duration of high flow during pre- or post-ice periods) showed strong relations to the urban intensity index. Hydrologic-condition metrics cannot be used alone to predict habitat or geomorphic change. Chloride and SPMD measures of potential toxicity and polycyclic aromatic hydrocarbon concentrations showed the strongest positive correlations to urbanization including increases in road infrastructure, percentage of impervious surface in the watershed, urban land cover, and land-distribution related to urban land cover. This suggests that automobiles and the infrastructure required to support automobiles are a significant source of these compounds in this study area. Chloride in spring and summer showed a significant positive correlation with the urban intensity index; concentrations increased with increasing road infrastructure, urban land cover, and a number of landscape variables related to urbanization. Spring concentrations of sulfate, prometon, and diazinon correlated to fewer urban characteristics than chloride, including increases in road infrastructure, percentage of impervious surface, and urban land cover. Changes in biological communities correlated to the urban intensity index or individual urban-associated variables. Decreased percentages of pollution-sensitive diatoms and diatoms requiring high dissolved-oxygen saturation correlated to increases in the percentage of developed urban land, total impervious surface, stream flashiness, population density, road-area density, and decreases in the percentage of wetland in the watershed. Invertebrate taxa richness and Coleop

Scientific Investigations Report↗

USGS1983

Accumulation, sublethal effects, and safe concentration of a refined oil as evaluated with cutthroat trout

Cutthroat trout ( Salmo clarki ) were exposed for 90 days in the laboratory to a refined oil collected from the North Platte River at a seepage site below the American Oil Company refinery at Casper, Wyoming. Fish were exposed to five concentrations and a control, and seven biological responses (survival, growth, gill pathology, liver pathology, caudal fin erosion, caudal fin pathology and swimming performance) were correlated with water concentration and tissue accumulation of petroleum hydrocarbons. Fish in the highest water concentration, 183 μ g/L total oil, accumulated tissue concentrations of 4.6 μ g/g total naphthalenes and responded adversely to all seven biological measurements. Cutthroat trout in the lowest water concentration, 24 μ g/L total oil, had a mean tissue concentration of 1.2 μ g/g total naphthalenes, but their response was similar to that of the control fish to all seven biological responses. Fish exposed to 39 μ g/L water concentration accumulated tissue concentrations of 2.7 μ g/g and responded negatively to 2 of the 7 biological measurements. Therefore, the maximum safe limit for this oil and cutthroat trout is between 24 and 39 μ g/L.

Archives of Environmental Contamination and Toxico↗

USGS2020

Nanopore amplicon sequencing reveals molecular convergence and local adaptation of rhodopsin in Great Lakes salmonids

Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus ) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle and MinION. We sequenced five visual opsin genes for individuals of C. artedi , C. hoyi , C. kiyi , and C. zenithicus. Comparisons revealed species-specific differences in a key spectral tuning amino acid in rhodopsin (Tyr261Phe substitution), suggesting local adaptation of C. kiyi to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

Lake Superior↗

USGS2005

GIS compilation of data collected from the Pulley Ridge Deep Coral Reef region

Pulley Ridge is a chain of drowned barrier islands that extends almost 200 km in 60-90 m water depths (Fig. 1). This drowned ridge is located on the Florida Platform in the southeastern Gulf of Mexico about 250 km west of Cape Sable, Florida (Jarrett and others, 2005). These islands formed during the early Holocene marine transgression approximately 12,000 - 14,000 years before present, and were then submerged by sea level rise and preserved near the outer edge of the Florida Platform. The southern portion of Pulley Ridge is the focus of this study. This area hosts zooxanthellate scleractinian corals, green, red and brown macro algae, and a mix of deep and typically shallow-water tropical fishes. This largely photosynthetic community is unique in that it thrives with less than 5% of the light typically associated with shallow-water reefs with similar fauna. Several factors help to account for the existence of this unique deep-water community. First, the underlying drowned barrier islands provide both elevated topography and lithified substrate for the establishment of the hardbottom community. Second, the region is commonly bathed by the Loop Current, which brings relatively clear and warm water to this area. Third, the ridge's position on the continental shelf places it within the thermocline which provides nutrients to the reef during upwelling (Halley and others, 2003). The USGS has made two proposals to resource managers for the designation of marine protected areas based on the geophysical and photographic data in this report. The proposals describe areas that may require some regulatory protection of marine life utilizing the sea floor (Fig. 1). The first proposal is that the area of greatest hermatypic coral cover (Fig. 1) is considered for future management actions and designated a Habitat Area of Particular Concern (HAPC) by the Gulf of Mexico Fishery Management Council. HAPCs are identified on the basis of habitat level considerations: The importance of the ecological function provided by the habitat. The extent to which the habitat is sensitive to human-induced environmental degradation. Whether and to what extent development activities are or will be stressing the habitat. The rarity of the habitat type. The second proposed area is for Coral Essential Fish Habitat (CEFH, Fig. 1). CEFHs are defined as "those waters and substrate necessary to corals for spawning, breeding, feeding, or growth to maturity." The following definitions are provided for clarification: waters is defined as "aquatic areas and their associated physical, chemical, and biological properties that are used by corals" substrate means "sediment, hard bottom, structures underlying the waters, and associated biological communities" necessary means "the habitat required to support a sustainable population and the managed species' contribution to a healthy ecosystem" spawning,breeding, feeding, or growth to maturity covers the full life cycle of a species. The CEFH shown in Figure 1 is the greatest coral cover in the region as determined by the bottom photo and video transects acquired during this study. This report presents the geophysical and photographic data that were collected to describe the surficial and shallow subsurface geologic framework of the area where these deep-water corals are known to occur. The data types include multibeam bathymetry, sidescan-sonar imagery, images of high-resolution seismic-reflection profiles, and bottom photographs. In addition, the tracklines for the seismic data, locations of bottom photographs and camera drifts, and tracklines along which submersible and remotely operated vehicle (ROV) observations were made are contained in the GIS files accompanying this report. Unfortunately, video footage from the camera drifts, submersible, and ROV cruises is not available on this DVD due to the quantity of data. The bottom photograph data set has been previously published (Cross and others, 2004), however it is included in this publication in an effort to integrate the varying data sets in one location. This integration is accomplished through the GIS data included on this DVD.

Florida↗

USGS2006

Forecasting selenium discharges to the San Francisco Bay-Delta Estuary: Ecological effects of a proposed San Luis Drain extension

Selenium discharges to the San Francisco Bay-Delta Estuary (Bay-Delta) could change significantly if federal and state agencies (1) approve an extension of the San Luis Drain to convey agricultural drainage from the western San Joaquin Valley to the North Bay (Suisun Bay, Carquinez Strait, and San Pablo Bay); (2) allow changes in flow patterns of the lower San Joaquin River and Bay-Delta while using an existing portion of the San Luis Drain to convey agricultural drainage to a tributary of the San Joaquin River; or (3) revise selenium criteria for the protection of aquatic life or issue criteria for the protection of wildlife. Understanding the biotransfer of selenium is essential to evaluating effects of selenium on Bay-Delta ecosystems. Confusion about selenium threats to fish and wildlife stem from (1) monitoring programs that do not address specific protocols necessary for an element that bioaccumulates; and (2) failure to consider the full complexity of the processes that result in selenium toxicity. Past studies show that predators are more at risk from selenium contamination than their prey, making it difficult to use traditional methods to predict risk from environmental concentrations alone. This report presents an approach to conceptualize and model the fate and effects of selenium under various load scenarios from the San Joaquin Valley. For each potential load, progressive forecasts show resulting (1) water-column concentration; (2) speciation; (3) transformation to particulate form; (4) particulate concentration; (5) bioaccumulation by invertebrates; (6) trophic transfer to predators; and (7) effects on those predators. Enough is known to establish a first-order understanding of relevant conditions, biological response, and ecological risks should selenium be discharged directly into the North Bay through a conveyance such as a proposed extension of the San Luis Drain. The approach presented here, the Bay-Delta selenium model, determines the mass, fate, and effects of selenium released to the Bay-Delta through use of (1) historical land-use, drainage, alluvial-fill, and runoff databases; (2) existing knowledge concerning biogeochemical reactions and physiological parameters of selenium (e.g., speciation, partitioning between dissolved and particulate forms, and bivalve assimilation efficiency); and (3) site-specific data mainly from 1986 to 1996 for clams and bottom-feeding fish and birds. Selenium load scenarios consider effluents from North Bay oil refineries and discharges of agricultural drainage from the San Joaquin Valley to enable calculation of (a) a composite freshwater endmember selenium concentration at the head of the estuary; and (b) a selenium concentration at a selected seawater location (Carquinez Strait) as a foundation for modeling. Analysis of selenium effects also takes into account the mode of conveyance for agricultural drainage (i.e., the San Luis Drain or San Joaquin River); and flows of the Sacramento River and San Joaquin River on a seasonal or monthly basis. Load scenarios for San Joaquin Valley mirror predictions made since 1955 of a worsening salt (and by inference, selenium) build-up exacerbated by an arid climate and massive irrigation. The reservoir of selenium in the San Joaquin Valley is sufficient to provide loading at an annual rate of approximately 42,500 pounds of selenium to a Bay-Delta disposal point for 63 to 304 years at the lower range of projections presented here, even if influx of selenium from the California Coast Ranges could be curtailed. Disposal of wastewaters on an annual basis outside of the San Joaquin Valley may slow the degradation of valley resources, but drainage alone cannot alleviate the salt and selenium build-up in the San Joaquin Valley, at least within a century. Load scenarios also show the different proportions of selenium loading to the Bay-Delta. Oil refinery loads from 1986 to 1992 ranged from 8.5 to 20 pounds of selenium per day; with treatment and cleanup, loads decreased to 3.0 pounds of selenium per day in 1999. In contrast, San Joaquin Valley agricultural drainage loads disposed of in a San Luis Drain extension could range from 45 to 117 pounds of selenium per day across a set of historical and future conditions. Components of this valley-wide load include five source subareas (i.e., Grassland, Westlands, Tulare, Kern, and Northern) defined by water and drainage management. Loads vary per subarea mainly because of proximity of the subarea to geologic sources of selenium and irrigation history. Loads from the Sacramento River, depending on flow conditions, range from 0.8 to 10 pounds of selenium per day. Loads from the San Joaquin River vary depending on restoration and flow conditions, which are considered. A consistent picture of ecological risk emerges under modeled selenium discharges from a proposed San Luis Drain extension. The threat to the estuary is greatest during low flow seasons and critically dry years. Where selenium undergoes reactions typical of low flow or longer residence time, highly problematic bioaccumulation in prey (food) is forecast. Surf scoter, greater and lesser scaup, and white sturgeon appear to be most at risk because these Bay-Delta predators feed on deposit and filter-feeding bivalves. Recent findings add Sacramento splittail and Dungeness crab to that list. During the low flow season of critically dry years, forecasted selenium concentrations in water, particulate matter, prey (diet), and predator tissue exceed guidelines with a high certainty of producing adverse effects under the most likely load scenario from a proposed San Luis Drain extension. High flows afford some protection under certain conditions in modeled San Joaquin River scenarios. However, meeting a combined goal of releasing a specific load during maximum flows and keeping selenium concentrations in the river below a certain objective to protect against bioaccumulation may not always be attainable. Management of the San Joaquin River on a constant concentration basis also could create problematic bioaccumulation during a wet year, especially during the low flow season, because high flows translate to high loads that are not always offset by seasonal river inflows. Prior to refinery cleanup, selenium contamination was sufficient to threaten reproduction in key species within the Bay-Delta ecosystems and human health advisories were posted based on selenium concentrations in tissues of diving ducks. During this time, selenium concentrations in the Bay-Delta were well below the most stringent recommended water quality criterion [1 microgram per liter (1 µg/L)]. Enhanced biogeochemical transformations to bioavailable particulate selenium and efficient bioaccumulation by bivalves characterized the system. If these biogeochemical conditions continue to prevail and agricultural selenium sources replace or exceed refinery sources, ecological forecasts suggest the risk of adverse effects will be difficult to eliminate under an out-of-valley resolution to the selenium problem. The Bay-Delta selenium model presented here is a systematic approach for conducting forecasts of the ecological effects from selenium on aquatic food webs. It is a new tool that links and models the major processes leading from loads through consumer organisms to predators. It also is a feasible approach for site-specific analysis and could provide a framework for developing new protective selenium foodweb guidelines and predator criteria. Model components that help ensure understanding ecosystems and the basis of environmental protection are (1) contaminant concentrations and speciation in sources, such as particulate material, that most influence bioavailability; (2) bioaccumulation models that calculate concentrations in diet, specifically in bivalves of the Bay-Delta that act as sensitive indicators of selenium contamination; (3) food-web type that determines what animals are threatened and when; and (4) multiple media concentrations (water, particulate material, and tissue of prey and predators) that, in-combination, determine risk or hazard.

California↗