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At least 865 records · Page 48Linked to original sources

USGS2012

Using stable isotopes to test for trophic niche partitioning: a case study with stream salamanders and fish

1.&ensp;Stream salamanders and fish often co-occur even though fish prey on and outcompete salamanders. However, the mechanisms that allow palatable salamanders to coexist with fish are unknown. 2.&ensp;We tested mechanisms in the field that promote coexistence between Idaho giant salamanders ( Dicamptodon aterrimus ) and stream salmonid fishes in headwater streams. Previous research in this system indicated that salamander dispersal did not promote coexistence with fish. We tested the hypothesis that D. aterrimus shift their diet when they occur with fish, facilitating coexistence through local niche partitioning. 3.&ensp;We used nitrogen and carbon stable isotopes to describe the trophic niche of D. aterrimus and fish in three co-occurring populations of salamanders and fish and three populations of salamanders without fish. We used two approaches to quantify trophic niche partitioning with stable isotopes: 95% kernel density estimators and isotopic mixing models. 4.&ensp;We found that salamanders and fish were generalists that consumed aquatic invertebrates primarily, but both species were also cannibalistic and predatory on one another. We also found no support for trophic niche partitioning as a coexistence mechanism because there were no differences in the trophic niche metrics among salamander populations with and without fish. 5.&ensp;Although we did not identify mechanisms that facilitate salamander and fish coexistence, our empirical data and use of novel approaches to describe the trophic niche did yield important insights on the role of predator–prey interactions and cannibalism as alternative coexistence mechanisms. In addition, we found that 95% kernel estimators are a simple and robust method to describe population-level measure of trophic structure.

Freshwater Biology↗

USGS2011

A tree-ring reconstruction of the salinity gradient in the northern estuary of San Francisco Bay

Blue oak tree-ring chronologies correlate highly with winter–spring precipitation totals over California, with Sacramento and San Joaquin river stream flow, and with seasonal variations in the salinity gradient in San Francisco Bay. The convergence of fresh and saline currents can influence turbidity, sediment accumulation, and biological productivity in the estuary. Three selected blue oak chronologies were used to develop a 625-year-long reconstruction of the seasonal salinity gradient, or low salinity zone (LSZ), which provides a unique perspective on the interannual-to-decadal variability of this important estuarine habitat indicator. The reconstruction was calibrated with instrumental LSZ data for the winter–spring season, and explains 73% of the variance in the February–June position of the LSZ from 1956 to 2003. Because this calibration period post-dates the sweeping changes that have occurred to land cover, channel morphology, and natural streamflow regimes in California, the reconstruction provides an idealized estimate for how the LSZ might have fluctuated under the seasonal precipitation variations of the past 625 years, given the modern geometry and bathymetry of the estuary and land cover across the drainage basin. The February–June season integrates precipitation and runoff variability during the cool season, and does not extend into the late-summer dry season when LSZ extremes can negatively affect Sacramento–San Joaquin Delta (Delta) agriculture and some aquatic organisms. However, there is such strong inter-seasonal persistence in the instrumental LSZ data that precipitation totals during the cool season can strongly pre-condition LSZ position in late summer. The 625-year-long reconstruction indicates strong interannual and decadal variability, the frequent recurrence of consecutive 2-year LSZ maxima and minima, large-scale ocean atmospheric forcing, and an interesting asymmetrical influence of warm El Niño–Southern Oscillation (ENSO) events.

California↗

USGS2012

Survival and growth of juvenile Pacific lampreys tagged with passive integrated transponders (PIT) in freshwater and seawater

Tagging methods are needed for both adult and juvenile life stages of Pacific lampreys Lampetra tridentata to better understand their biology and factors contributing to their decline. We developed a safe and efficient technique for tagging juvenile Pacific lampreys with passive integrated transponder (PIT) tags. We tested the short-term survival of PIT-tagged juvenile lampreys in freshwater at four temperatures (9, 12, 15, and 18°C) and their long-term growth and survival in seawater. For both experiments there was little to no tag loss, and juvenile lampreys in freshwater showed high survival at all temperatures at 7 d (95–100%) and 14 d (88–100%) posttagging. Prolonged holding (40 d) resulted in significantly lower survival (28–79%) at warmer temperatures (12–18°C). For juvenile lampreys tagged in freshwater and then transitioned to seawater, survival was 97% for tagged fish until day 94, and at the end of 6 months, survival was about 58% for both tagged and control fish. About half of the tagged and control fish that survived in seawater grew, but there was no difference in growth between the two groups. In freshwater, but not in seawater, most fish that died had an aquatic fungal infection. In both experiments, survival increased with increasing fish length at tagging. Our results indicate that tags similar in size to a 9-mm PIT tag are a feasible option for tagging metamorphosed juvenile lampreys migrating downstream and that when fungal infections are mitigated—as in seawater—long-term (at least 6 months) survival of tagged juvenile lampreys is high.

Transactions of the American Fisheries Society↗

USGS2018

Stable isotope comparison between mantle and foot tissues of two freshwater unionids: Implications for food web studies

Unionid mussels are a key taxon for stable isotope studies of aquatic food webs, often serving as the primary integrator of the pelagic baseline. Past isotope studies with mussels have commonly used either foot tissue or mantle tissue, but no study has yet to quantify the relation of both carbon and nitrogen isotopes between these two tissue sources. This makes it difficult to justify cross-study comparisons when different tissue compartments and different species were used as the basis of food web models. Therefore, we collected foot and mantle tissues from two common mussel species, Amblema plicata and Fusconaia flava , from lotic and lentic sites in the Upper Mississippi and St. Croix rivers (Minnesota/Wisconsin). Paired tissue samples from each individual were analyzed for stable isotopes of nitrogen and carbon. There were strong relations between tissue types for both isotopes between species ( r 2 > 0.93). Paired t -tests indicated that there were statistically significant differences between the tissue sources in some instances, but the difference (0.04–0.21‰) was less than the analytical precision of the mass spectrometer (circa 0.2–0.3‰). We conclude that the isotopic values from these two tissue sources are biologically comparable and recommend that researchers use the tissue source and extraction technique that minimizes stress to the mussels. We also tested for significant differences between species within a site for either isotope or tissue type and found no statistically significant difference between species with the exception of carbon in foot tissue at two sites. The highly correlated isotopic response supports the interchangeable use of both tissue compartments and both species. These findings support comparisons between studies whether the results were based on either of these tissues or the two species studied. Comparability will also simplify sampling designs, save time, and save money for processing samples without diminishing the usefulness of the data.

Minnesota, Wisconsin↗

USGS2014

Long-term growth-increment chronologies reveal diverse influences of climate forcing on freshwater and forest biota in the Pacific Northwest

Analyses of how organisms are likely to respond to a changing climate have focused largely on the direct effects of warming temperatures, though changes in other variables may also be important, particularly the amount and timing of precipitation. Here, we develop a network of eight growth-increment width chronologies for freshwater mussel species in the Pacific Northwest, United States and integrate them with tree-ring data to evaluate how terrestrial and aquatic indicators respond to hydroclimatic variability, including river discharge and precipitation. Annual discharge averaged across water years (October 1–September 30) was highly synchronous among river systems and imparted a coherent pattern among mussel chronologies. The leading principal component of the five longest mussel chronologies (1982–2003; PC1 mussel ) accounted for 47% of the dataset variability and negatively correlated with the leading principal component of river discharge (PC1 discharge ; r = −0.88; P < 0.0001). PC1 mussel and PC1 discharge were closely linked to regional wintertime precipitation patterns across the Pacific Northwest, the season in which the vast majority of annual precipitation arrives. Mussel growth was also indirectly related to tree radial growth, though the nature of the relationships varied across the landscape. Negative correlations occurred in forests where tree growth tends to be limited by drought while positive correlations occurred in forests where tree growth tends to be limited by deep or lingering snowpack. Overall, this diverse assemblage of chronologies illustrates the importance of winter precipitation to terrestrial and freshwater ecosystems and suggests that a complexity of climate responses must be considered when estimating the biological impacts of climate variability and change.

Idaho, Oregon, Washington↗

USGS2024

Global assessment of aquatic Isoëtes species ecology

Isoëtes are iconic but understudied wetland plants, despite having suffered severe losses globally mainly because of alterations in their habitats. We therefore provide the first global ecological assessment of aquatic Isoëtes to identify their environmental requirements and to evaluate if taxonomically related species differ in their ecology. The assessment resulted in an extensive new database on aquatic Isoëtes , ecological niche analyses, and descriptive species accounts. We compiled a global database that includes all known environmental data collected from 1935 to 2023 regarding aquatic Isoëtes. We then evaluated the environmental drivers of 16 species using 2,179 global records. Additionally, we used hypervolume analysis to quantify the ecological niches of the two species with the greatest number of records, finding significant differences and evidence that Isoëtes echinospora occupies a wider ecological niche than Isoëtes lacustris . Fifty-nine species (30% of the c. 200 Isoëtes species known today) were categorised as aquatic and were mainly reported in the Americas and northern Europe. About 38% of the aquatic species are threatened with extinction or are endemic to a small region, according to the International Union for Conservation of Nature's Red List in 2023. Many species were determined to be sensitive to certain water physical and chemical factors, generally preferring oligotrophic conditions such as low total phosphorus, moderate total nitrogen, moderate to low pH, and low conductivity. This analysis includes ecological data in the assessment of rare/threatened aquatic plants globally. This new database and the ecological analyses completed defined the ecological requirements of several species and identified knowledge gaps, which can aid management actions and future research. This paper highlights ecological significance and environmental sensitivities of aquatic Isoëtes . The current level of knowledge is inadequate for a large proportion of known taxa. We affirm the extreme need to support global, collaborative initiatives on which to build future conservation strategies.

Freshwater Biology↗

USGS2015

Effects of elevated water temperature on physiological responses in adult freshwater mussels

Freshwater mussels (order Unionoida) face multiple environmental stressors, which pose serious conservation challenges to this diverse assemblage of aquatic invertebrates. Of these stressors, elevated water temperature from global climate change and other anthropogenic sources may be the most ubiquitous and could be placing many mussel populations dangerously close to their thermal maxima. We tested the hypothesis that elevated water temperatures (20, 25, 30 and 35 °C) adversely affected physiological responses in adults of four North American species of mussels ( Amblema plicata , Elliptio complanata, Fusconaia flava and Lampsilis cardium) in 21-d laboratory tests. Oxygen consumption rates were directly affected by temperature in E. complanata and L. cardium , and indirectly affected by temperature in A. plicata and F. flava . Rates of O 2 consumption were generally positively correlated with water temperature. Ammonium excretion rates varied significantly with temperature in E. complanata and generally increased with temperature. The amount of O 2 consumed relative to nitrogen excreted (O : N ratio), varied significantly with temperature in A. plicata , E. complanata and F. flava . The tissue condition index varied among temperatures and species. These data suggest that elevated temperatures can alter metabolic rates in native mussels and may decrease the amount of energy that is available for key biological processes, such as survival, growth and reproduction.

Freshwater Biology↗

USGS2022

Water-quality trends for a stream draining the Southern Anthracite Field, Pennsylvania

Stream flow, chemical and biological data for the northern part of Swatara Creek, which drains a 112 km 2 area in the Southern Anthracite Field of eastern Pennsylvania, indicate progressive improvement in water quality since 1959, after which most mines in the watershed had been flooded. Drainage from the flooded mines contributes substantially to base flow in Swatara Creek. Beginning in 1995, a variety of treatment systems and surface reclamation were implemented at some of the abandoned mines. At Ravine, Pa., immediately downstream of the mined area, median SO 4 concentration declined from about 150 mg l −1 in 1959 to 75 mg l −1 in 1999 while pH increased from acidic to near-neutral values (medians: c. pH 4 before 1975; c. pH 6 after 1975). Fish populations rebounded from non-existent during 1959–1990 to 21 species identified in 1999. Nevertheless, recent monitoring indicates (1) episodic acidification and elevated concentrations and transport of Fe, Al, Mn, and trace metals during storm flow; (2) elevated concentrations of Fe, Mn, Co, Cu, Pb, Ni, and Zn in streambed sediments relative to unmined areas and to toxicity guidelines for aquatic invertebrates and fish; and (3) elevated concentrations of metals in fish tissue, notably Zn. The metals are ubiquitous in the fine fraction (<0.063 mm) of bed sediment in mining-affected tributaries and the main stem of Swatara Creek. As a result of scour and transport of streambed deposits, concentrations of suspended solids and total metals in the water column are correlated, and those for storm flow typically exceed base flow. Nevertheless, the metals concentrations are poorly correlated with stream flow because concentrations of suspended solids and total metals typically peak prior to peak stream stage. In contrast, SO 4 , specific conductance and pH are inversely correlated with stream flow as a result of dilution of poorly buffered stream water with weakly acidic storm runoff derived mainly from low-pH rainfall. Declines in pH to values approaching 5.0 during storm flow events or declines in redox potential during burial of sediment could result in the remobilization of metals associated with suspended solids and streambed deposits.

Pennsylvania↗

USGS2004

Water-quality, biological, and physical-habitat conditions at fixed sites in the Cook Inlet Basin, Alaska, National Water-Quality Assessment Study Unit, October 1998-September 2001

The Cook Inlet Basin study unit of the U.S. Geological Survey National Water-Quality Assessment Program comprises 39,325 square miles in south-central Alaska. Data were collected at eight fixed sites to provide baseline information in areas where no development has taken place, urbanization or logging have occurred, or the effects of recreation are increasing. Collection of water-quality, biology, and physical-habitat data began in October 1998 and ended in September 2001 (water years 1999-2001). The climate for the water years in the study may be categorized as slightly cool-wet (1999), slightly warm-wet (2000), and significantly warm-dry (2001). Total precipitation was near normal during the study period, and air temperatures ranged from modestly cool in water year 1999 to near normal in 2000, and to notably warm in 2001. Snowmelt runoff dominates the hydrology of streams in the Cook Inlet Basin. Average annual flows at the fixed sites were approximately the same as the long-term average annual flows, with the exception of those in glacier-fed basins, which had above-average flow in water year 2001. Water temperature of all streams studied in the Cook Inlet Basin remained at 0 oC for about 6 months per year, and average annual water temperatures ranged from 3.3 to 6.2 degrees Celsius. Of the water-quality constituents sampled, all concentrations were less than drinking-water standards and only one constituent, the pesticide carbaryl, exceeded aquatic-life standards. Most of the stream waters of the Cook Inlet Basin were classified as calcium bicarbonate, which reflects the underlying geology. Streams in the Cook Inlet Basin draining areas with glaciers, rough mountainous terrain, and poorly developed soils have low concentrations of nitrogen, phosphorus, and dissolved organic carbon compared with concentrations of these same constituents in streams in lowland or urbanized areas. In streams draining relatively low-lying areas, most of the suspended sediment, nutrients, and dissolved organic carbon are transported in the spring from the melting snowpack. The urbanized stream, Chester Creek, had the highest concentrations of calcium, magnesium, chloride, and sodium, most likely because of the application of de-icing materials during the winter. Several volatile organic compounds and pesticides also were detected in samples from this stream. Aquatic communities in the Cook Inlet Basin are naturally different than similar sites in the contiguous United States because of the unique conditions of the northern latitudes where the Cook Inlet Basin is located, such as extreme diurnal cycles and long periods of ice cover. Blue-green algae was the dominant algae found at all sites although in some years green algae was the most dominant algae. Macroinvertebrate communities consist primarily of Diptera (true flies), Ephemeroptera (mayflies), and Plecoptera (stoneflies). Lowland areas have higher abundance of aquatic communities than glacier-fed basins. However, samples from the urbanized stream, Chester Creek, were dominated by oligochaetes, a class of worms. Most of the functional feeding groups were collector-gatherers. The number of taxa for both algae and macroinvertebrates were highest in water year 2001, which may be due to the relative mild winter of 2000?2001 and the above average air temperatures for this water year. The streams in the Cook Inlet Basin typically are low gradient. Bank substrates consist of silt, clay, or sand, and bed substrate consists of coarse gravel or cobbles. Vegetation is primarily shrubs and woodlands with spruce or cottonwood trees. Canopy angles vary with the size of the stream or river and are relatively low at the smaller streams and high at the larger streams. Suitable fish habitat, such as woody debris, pools, cobble substrate, and overhanging vegetation, is found at most sites. Of the human activities occurring in the fixed site basins ? high recreational use, logging, and urbanizat

Scientific Investigations Report↗

USGS2006

Variation in thermal tolerance and routine metabolism among spring- and stream dwelling freshwater sculpins (Teleostei: Cottidae) of the southeastern United States

Evolutionary theory predicts that some aquatic organisms may adapt by directional selection to limiting physical environmental conditions, yet empirical data are conflicting. We sought to test the assumption that sculpins (family Cottidae) inhabiting thermally stable springs of the southeastern United States differ in temperature tolerance and metabolism from populations inhabiting more thermally labile stream habitats. Spring populations of pygmy sculpins ( Cottus pygmaeus ) and Ozark sculpins ( C. hypselurus ) differed interspecifically in thermal tolerance from populations of stream-dwelling mottled ( C. bairdi ) and Tallapoosa sculpins ( C. tallapoosae ), and both stream and spring populations of banded sculpins ( C. carolinae ). No intra- or interspecific differences in thermal tolerance were found among populations of C. bairdi, C. talla poosae , or C. carolinae . Cottus pygmaeus acclimated to 15°C differed intraspecifically in routine metabolism from fish acclimated to 20° and 25°C. Cottus pygmaeus and stream-dwelling C. bairdi and C. carolinae acclimated to temperatures of 20° and 25°C showed no interspecific differences in routine metabolism. Our results suggest that some spring-adapted populations or species may be more stenothermal than stream-dwelling congeners, but a greater understanding of the interactions of other physical and biological factors is required to better explain micro- and macro habitat distributions of eastern North American sculpins.

Ecology of Freshwater Fish↗

USGS2016

Primary sources and toxicity of PAHs in Milwaukee-area streambed sediment

High concentrations of polycyclic aromatic hydrocarbons (PAHs) in streams can be a significant stressor to aquatic organisms. To understand the likely sources and toxicity of PAHs in Milwaukee-area streams, streambed sediment samples from 40 sites and parking lot dust samples from 6 sites were analyzed for 38 parent PAHs and 25 alkylated PAHs. Diagnostic ratios, profile correlations, principal components analysis, source-receptor modeling, and mass fractions analysis were used to identify potential PAH sources to streambed sediment samples, and land-use analysis was used to relate streambed sediment PAH concentrations to different urban-related land uses. On the basis of this multiple lines-of-evidence approach, coal-tar pavement sealant was indicated as the primary source of PAHs in a majority of streambed sediment samples, contributing an estimated 77% of total PAHs to samples, on average. Comparison to the Probable Effect Concentrations and (or) the Equilibrium Partitioning Sediment Benchmark indicates that 78% of stream sediment samples are likely to cause adverse effects to benthic organisms. Laboratory toxicity tests on a 16-sample subset of the streambed sites using the amphipod Hyalella azteca (28-day) and the midge Chironomus dilutus (10-day) measured significant reductions in one or more biological endpoints, including survival, in 75% of samples, with H. azteca more responsive than C. dilutus .

Wisconsin↗

USGS2025

Fish-assemblage and water-quality recovery with declining acidic deposition in Adirondack mountain streams, New York, USA

Long-term records of air-pollutant emissions and atmospheric deposition, as well as water quality in streams of the Adirondack Mountains of New York, USA, indicate that chemical recovery from acidic deposition is progressing. Although Brook Trout Salvelinus fontinalis (Mitchill, 1814) have recently repopulated several lakes, the degree to which fish assemblages and individual species populations have recovered in streams of the region is unknown. The United States Geological Survey sampled acid–base chemistry and fish assemblages at 42 Adirondack region streams (2014–2021), most of which were also sampled in 2 prior periods (primarily 1979–1984 and 1999), to determine the extent and degree of chemical and biological recovery and whether responses could be linked to regional declines in acidic deposition. Between 1990 and 2021, total annual emissions of SO 2 and NO x declined nationwide by 94% and 87%, respectively, and paralleled 88% and 70% decreases in SO 4 2− and NO 3 − concentrations, respectively, in wet deposition in the region. During this interval, mean acid neutralizing capacity increased by 19.9 µeq/L, pH increased by 0.33 units, and inorganic Al (Al i ) decreased by 6.0 µmol/L at one continuously monitored stream, whereas mean acid neutralizing capacity increased by 38.5 µeq/L and mean Al i concentration decreased by ∼3.0 µmol/L during springtime at all 42 Adirondack region streams. Between the 1 st and 3 rd periods, mean fish-assemblage richness, density, and biomass at 40 sites increased by 112%, 236%, and 66%, respectively. Although mean Brook Trout density and biomass did not meaningfully change among periods, their distribution expanded from 20 sites in the strongly impacted sampling period (1979–1984) to 33 sites in the recovery period (2014–2021). Trends in pollutant emissions and deposition, water quality, and fish-assemblage metrics indicate aquatic ecosystems in many Adirondack mountain streams improved markedly following implementation of the 1990 Clean Air Act Amendments and recent N and S allowance-trading and emissions regulations.

New York↗

USGS2024

Secondary contact erodes Pleistocene diversification in a wide-ranging freshwater mussel (Quadrula)

The isolated river drainages of eastern North America serve as a natural laboratory to investigate the roles of allopatry and secondary contact in the evolutionary trajectories of recently diverged lineages. Drainage divides facilitate allopatric speciation, but due to their sensitivity to climatic and geomorphological changes, neighboring rivers frequently coalesce, creating recurrent opportunities of isolation and contact throughout the history of aquatic lineages. The freshwater mussel Quadrula quadrula is widely distributed across isolated rivers of eastern North America and possesses high phenotypic and molecular variation across its range. We integrate sequence data from three genomes, including female- and male-inherited mitochondrial markers and thousands of nuclear encoded SNPs with morphology and geography to illuminate the group's divergence history. Across contemporary isolated rivers, we found continuums of molecular and morphological variation, following a pattern of isolation by distance. In contact zones, hybridization was frequent with no apparent fitness consequences, as advanced hybrids were common. Accordingly, we recognize Q. quadrula as a single cohesive species with subspecific variation ( Q. quadrula rumphiana ). Demographic modeling and divergence dating supported a divergence history characterized by allopatric vicariance followed by secondary contact, likely driven by river rearrangements and Pleistocene glacial cycles. Despite clinal range-wide variation and hybridization in contact zones, the process-based species delimitation tool delimitR, which considers demographic scenarios like secondary contact, supported the delimitation of the maximum number of species tested. As such, when interpreting species delimitation results, we suggest careful consideration of spatial sampling and subsequent geographic patterns of biological variation, particularly for wide-ranging taxa.

eastern North America↗

USGS2012

Time scales of change in chemical and biological parameters after engineered levee breaches adjacent to Upper Klamath and Agency Lakes, Oregon

Eight sampling trips were coordinated after engineered levee breaches hydrologically reconnected both Upper Klamath Lake and Agency Lake, Oregon, to adjacent wetlands. The reconnection, by a series of explosive blasts, was coordinated by The Nature Conservancy to reclaim wetlands that had for approximately seven decades been leveed for crop production. Sets of nonmetallic porewater profilers (U.S. Patent 8,051,727 B1; November 8, 2011; http://www.uspto.gov/web/patents/patog/ week45/OG/html/1372-2/US08051727-20111108.html.) were deployed during these trips in November 2007, June 2008, May 2009, July 2009, May 2010, August 2010, June 2011, and July 2011 (table 1). Deployments temporally spanned the annual cyanophyte bloom of Aphanizomenon flos-aquae and spatially involved three lake and four wetland sites. Spatial and temporal variation in solute benthic flux was determined by the field team, using the profilers, over an approximately 4-year period beginning 3 days after the levee breaches. The highest flux to the water column of dissolved organic carbon (DOC) was detected in the newly flooded wetland, contrasting negative or insignificant DOC fluxes at adjacent lake sites. Over the multiyear study, DOC benthic fluxes dissipated in the reconnected wetlands, converging to values similar to those for established wetlands and to the adjacent lake (table 2). In contrast to DOC, benthic sources of soluble reactive phosphorus, ammonium, dissolved iron and manganese from within the reconnected wetlands were consistently elevated (that is, significant in magnitude relative to riverine and established-wetland sources) indicating a multi-year time scale for certain chemical changes after the levee breaches (table 2). Colonization of the reconnected wetlands by aquatic benthic invertebrates during the study trended toward the assemblages in established wetlands, providing further evidence of a multiyear transition of this area to permanent aquatic habitat (table 3). Both the lake and wetland benthic environments substantively contribute to macro- and micronutrients in the water column. Wetland areas undergoing restoration, and those being used for water storage, function very differently relatively to the established wetland within the Upper Klamath Lake National Wildlife Refuge, adjacent Upper Klamath Lake. Developing long-term management strategies for water quality in the Upper Klamath Basin requires recognition of the multi-year time scales associated with restoring wetlands that provide natural, seasonal ecosystem function and services.

Oregon↗

USGS2023

Redd superimposition mediates the accuracy, precision, and significance of redd counts for cutthroat trout

Redd counts are commonly applied to estimate spawning population size for salmonids and allow for broad spatial and temporal coverage in monitoring efforts. However, the utility of redd counts may be compromised by observation error, particularly with respect to superimposition, where later arriving spawners construct redds overlapping existing redds. Here, we provide a mechanistic evaluation of the effects of superimposition on the error structure and biological significance of redd count data for Yellowstone cutthroat trout ( Oncorhynchus clarkii bouvieri ) spawning within tributaries to the Snake River, Wyoming. We used a Bayesian framework to parse observation error into distinct components and found low detection of redd clusters (i.e., areas of superimposition) was offset by overestimates of the number of redds per cluster, such that observed counts accurately reflected census redd abundance. However, a saturating relationship between redd counts and spawner abundance indicated that counts is best interpreted as effective reproductive effort rather than spawner abundance. Our results provide a mechanistic understanding of redd count data that can be used to assess their application and interpretation for monitoring.

Wyoming↗

USGS2017

Seasonal and diel environmental conditions predict western pond turtle (Emys marmorata) behavior at a perennial and an ephemeral stream in Sequoia National Park, California

Managers making decisions may benefit from a well-informed understanding of a species' population size and trends. Given the cryptic nature and habitat characteristics of the western pond turtle ( Emys marmorata ), however, imperfect detection may be high and population estimates are frequently varied and unreliable. As a case study to investigate this issue, we used temperature dataloggers to examine turtle behavior at 2 long-term monitoring sites with different hydrological characteristics in Sequoia National Park, California, to determine if common stream-survey techniques are consistent with site-specific turtle behavior. Sycamore Creek is an intermittent stream that dries up every summer while the North Fork Kaweah River flows year-round. We found that while turtles spent most of the recorded time in the water (55% in Sycamore Creek and 82% in the North Fork Kaweah River), the timing of traditional surveys only coincided with the turtles' aquatic activity in the North Fork Kaweah River. At Sycamore Creek, turtles were most likely to be in the water at night. In contrast, failure to detect turtles in North Fork Kaweah River is likely owing to the larger size and complexity of the underwater habitat. In both streams, turtles were also more likely to be in the water in the weeks leading up to important changes in hydroperiods. Our findings illustrate the effects that differences in water permanence can have on turtle behavior within the same watershed and how phenotypic plasticity may then affect detection during surveys. Our study highlights the importance of tailoring survey practices to the site-specific behavioral traits of the target species.

California↗

USGS2012

Analysis of host genetic diversity and viral entry as sources of between-host variation in viral load

Little is known about the factors that drive the high levels of between-host variation in pathogen burden that are frequently observed in viral infections. Here, two factors thought to impact viral load variability, host genetic diversity and stochastic processes linked with viral entry into the host, were examined. This work was conducted with the aquatic vertebrate virus, Infectious hematopoietic necrosis virus (IHNV), in its natural host, rainbow trout. It was found that in controlled in vivo infections of IHNV, a suggestive trend of reduced between-fish viral load variation was observed in a clonal population of isogenic trout compared to a genetically diverse population of out-bred trout. However, this trend was not statistically significant for any of the four viral genotypes examined, and high levels of fish-to-fish variation persisted even in the isogenic trout population. A decrease in fish-to-fish viral load variation was also observed in virus injection challenges that bypassed the host entry step, compared to fish exposed to the virus through the natural water-borne immersion route of infection. This trend was significant for three of the four virus genotypes examined and suggests host entry may play a role in viral load variability. However, high levels of viral load variation also remained in the injection challenges. Together, these results indicate that although host genetic diversity and viral entry may play some role in between-fish viral load variation, they are not major factors. Other biological and non-biological parameters that may influence viral load variation are discussed.

Virus Research↗

USGS2015

Benthic response to water quality and biotic pressures in lower south San Francisco Bay, Alviso Slough, and Coyote Creek

Benthic invertebrate communities are monitored because the composition of those communities can effect and be affected by the water quality of an aquatic system. Benthic communities use and sometimes regulate the cycling of essential elements (for example, carbon). Benthic invertebrate taxa may also indicate acutely and chronically stressful environments because they are mostly sessile, accumulate contaminants, and sometimes respond dramatically to oligotrophic as well as eutrophic conditions. Benthic communities can in turn affect water quality by grazing pelagic food resources and increasing the rate of nutrient regeneration through feeding and bioturbating the sediment. South San Francisco Bay is a system dependent on phytoplankton as the base to the food web. Despite abundant nutrients, south San Francisco Bay has had limited phytoplankton production in the last several decades owning to poor light conditions and high grazing losses from the water column by benthic invertebrates. The south San Francisco Bay achieves a balance of biogeochemical conditions in most springs to accommodate a short phytoplankton bloom. This balance has maintained the phytoplankton in south San Francisco Bay at low biomass levels relative to other high-nutrient urban estuaries. The role that benthic invertebrates play in this balance, in these episodic spring events, and in other seasons within the estuary remains of great interest to water-quality and biological resource managers. Our primary objective in this study is to quantify current (2014) benthic-community structure and function in the south San Francisco Bay sloughs and to compare those communities temporally over decadal time scales with a unique long-term dataset. The study area (fig. 1) is inclusive of the area south of the Dumbarton Bridge (DB) including Alviso and Guadalupe Sloughs and Coyote Creek. The following are results highlighted in this report: The benthic communities of Coyote Creek and Alviso, Guadalupe, and Artesian Sloughs were dominated by different organisms but similar functional groups in March, June, and September 2014. Coyote Creek stations (D3 and CC1) had a similar increase in Potamocorbula amurensis biomass followed by a decline in 2014, as was observed annually in the south San Francisco Bay since 1999. The lack of grazing pressure owing to the observed declines in these taxa in 2014 may allow the sloughs to become sources of phytoplankton in spring. Bivalve biomass is elevated in summer and fall relative to the spring and winter except in Artesian Slough, where bivalves did not establish a signifcant presence. Presence of certain species contributes to the prey value of the community to predators. Potamocorbula amurensis is a shallow-burrowing bivalve and hence is easy prey for bottom-feeding predators. In contrast, Macoma petalum is a deposit feeder and can burrow deeper into the substrate than Potamocorbula amurensis , making it harder to be preyed upon. The quantitative importance of such predator-prey relationships on phytoplankton dynamics requires further investigation. There were also more amphipods in the sloughs in March 2014; this group is another potential contributor to the benthic-pelagic biomass balance. There is no observed reason for Artesian Slough to have low bivalve biomass values and high amphipod abundances.

California↗