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USGS2009

Summary of surface-water quality data from the Illinois River Basin in Northeast Oklahoma, 1970-2007

The quality of streams in the Illinois River Basin of northeastern Oklahoma is potentially threatened by increased quantities of wastes discharged from increasing human populations, grazing of about 160,000 cattle, and confined animal feeding operations raising about 20 million chickens. Increasing numbers of humans and livestock in the basin contribute nutrients and bacteria to surface water and groundwater, causing greater than the typical concentrations of those constituents for this region. Consequences of increasing contributions of these substances can include increased algal growth (eutrophication) in streams and lakes; impairment of habitat for native aquatic animals, including desirable game fish species; impairment of drinking-water quality by sediments, turbidity, taste-and-odor causing chemicals, toxic algal compounds, and bacteria; and reduction in the aesthetic quality of the streams. The U.S. Geological Survey, in cooperation with the Oklahoma Scenic Rivers Commission, prepared this report to summarize the surface-water-quality data collected by the U.S. Geological Survey at five long-term surface-water-quality monitoring sites. The data summarized include major ions, nutrients, sediment, and fecal-indicator bacteria from the Illinois River Basin in Oklahoma for 1970 through 2007. General water chemistry, concentrations of nitrogen and phosphorus compounds, chlorophyll-a (an indicator of algal biomass), fecal-indicator bacteria counts, and sediment concentrations were similar among the five long-term monitoring sites in the Illinois River Basin in northeast Oklahoma. Most water samples were phosphorus-limited, meaning that they contained a smaller proportion of phosphorus, relative to nitrogen, than typically occurs in algal tissues. Greater degrees of nitrogen limitation occurred at three of the five sites which were sampled back to the 1970s, probably due to use of detergents containing greater concentrations of phosphorus than in subsequent periods. Concentrations of nitrogen, phosphorus, and sediment, and counts of bacteria generally increased with streamflow at the five sites, probably due to runoff from the land surface and re-suspension of streambed sediments. Phosphorus concentrations typically exceeded the Oklahoma standard of 0.037 milligrams per liter for Scenic Rivers. Concentrations of chlorophyll-a in phytoplankton in water samples collected at the five sites were not well correlated with streamflow, nor to concentrations of the nutrients nitrogen and phosphorus, probably because much of the algae growing in these streams are periphyton attached to streambed cobbles and other debris, rather than phytoplankton in the water column. Sediment concentrations correlated with phosphorus concentrations in water samples collected at the sites, probably due to sorption of phosphorus to soil particles and streambed sediments and runoff of soils and animal wastes at the land surface and resuspension of streambed sediments and phosphorus during wet, high-flow periods. Fecal coliform bacteria counts at the five sites sometimes exceeded the Oklahoma Primary Body Contact Standard of 400 colonies per 100 milliliters when streamflows were greater than 1000 cubic feet per second. Ultimately, Lake Tenkiller, an important ecological and economic resource for the region, receives the compounds that runoff the land surface or seep to local streams from groundwater in the basin. Because of eutrophication from increased nutrient loading, Lake Tenkiller is listed for impairment by diminished dissolved oxygen concentrations, phosphorus, and chlorophyll-a by the State of Oklahoma in evaluation of surface-water quality required by section 303d of the Clean Water Act. Stored phosphorus in soils and streambed and lakebed sediments may continue to provide phosphorus to local streams and lakes for decades to come. Steps are being made to reduce local sources of phosphorus, including upgrades in capacity and effective

Arkansas, Oklahoma↗

USGS2013

Factors influencing detection of eDNA from a stream-dwelling amphibian

Environmental DNA (eDNA) methods for detecting and estimating abundance of aquatic species are emerging rapidly, but little is known about how processes such as secretion rate, environmental degradation, and time since colonization or extirpation from a given site affect eDNA measurements. Using stream-dwelling salamanders and quantitative PCR (qPCR) analysis, we conducted three experiments to assess eDNA: (i) production rate; (ii) persistence time under different temperature and light conditions; and (iii) detectability and concentration through time following experimental introduction and removal of salamanders into previously unoccupied streams. We found that 44–50 g individuals held in aquaria produced 77 ng eDNA/h for 2 h, after which production either slowed considerably or began to equilibrate with degradation. eDNA in both full-sun and shaded treatments degraded exponentially to <1% of the original concentration after 3 days. eDNA was no longer detectable in full-sun samples after 8 days, whereas eDNA was detected in 20% of shaded samples after 11 days and 100% of refrigerated control samples after 18 days. When translocated into unoccupied streams, salamanders were detectable after 6 h, but only when densities were relatively high (0.2481 individuals/m 2 ) and when samples were collected within 5 m of the animals. Concentrations of eDNA detected were very low and increased steadily from 6–24 h after introduction, reaching 0.0022 ng/L. Within 1 h of removing salamanders from the stream, eDNA was no longer detectable. These results suggest that eDNA detectability and concentration depend on production rates of individuals, environmental conditions, density of animals, and their residence time.

Molecular Ecology Resources↗

USGS2015

A food web modeling analysis of a Midwestern, USA eutrophic lake dominated by non-native Common Carp and Zebra Mussels

Food web modeling is recognized as fundamental to understanding the complexities of aquatic systems. Ecopath is the most common mass-balance model used to represent food webs and quantify trophic interactions among groups. We constructed annual Ecopath models for four consecutive years during the first half-decade of a zebra mussel invasion in shallow, eutrophic Clear Lake, Iowa, USA, to evaluate changes in relative biomass and total system consumption among food web groups, evaluate food web impacts of non-native common carp and zebra mussels on food web groups, and to interpret food web impacts in light of on-going lake restoration. Total living biomass increased each year of the study; the majority of the increase due to a doubling in planktonic blue green algae, but several other taxa also increased including a more than two-order of magnitude increase in zebra mussels. Common carp accounted for the largest percentage of total fish biomass throughout the study even with on-going harvest. Chironomids, common carp, and zebra mussels were the top-three ranking consumer groups. Non-native common carp and zebra mussels accounted for an average of 42% of the total system consumption. Despite the relatively high biomass densities of common carp and zebra mussel, food web impacts was minimal due to excessive benthic and primary production in this eutrophic system. Consumption occurring via benthic pathways dominated system consumption in Clear Lake throughout our study, supporting the argument that benthic food webs are significant in shallow, eutrophic lake ecosystems and must be considered if ecosystem-level understanding is to be obtained.

Iowa↗

USGS2021

Mapping climate change vulnerability of aquatic-riparian ecosystems using decision-relevant indicators

Climate change has and is projected to continue to alter historical regimes of temperature, precipitation, and hydrology. To assess the vulnerability of climate change from a land management perspective and spatially identify where the most extreme changes are anticipated to occur, we worked in collaboration with land managers to develop a climate change vulnerability map for the midwestern United States with a focus on riparian systems. The map is intended for use by regional administrators to help them work across various program areas (e.g. fisheries, endangered species) to prioritize locations needing support for adaptation planning. The tool can also be utilized locally by managers to better understand the effects that projected climate scenarios have on the hydrology of management units as they develop adaptation strategies. The vulnerability map is watershed-based (360 watershed units within the region) and combines 15 climate change indicators that were selected by U.S. Fish and Wildlife Service natural resource managers based upon known and anticipated effects to species and habitats. The projected change in each of these indicators from the historical period (1986–2005) to the future period (2040–2059) was aggregated into a composite score for each watershed. Landscape-scale metrics reflective of a watershed’s adaptive capacity were combined with the climate change indicators to produce a vulnerability score. We found sub-regional variation in vulnerability to climate change with the greatest vulnerability in Iowa, central Illinois, and northwest Ohio. Greater vulnerability was seen in the higher greenhouse gas concentration scenario, Representative Concentration Pathway (RCP) 8.5 compared to the lower greenhouse gas concentration scenario RCP 4.5, when looking at the mean of the five downscaled climate models used in this study. By quantifying and mapping climate change vulnerability, natural resource managers can better understand the degree of vulnerability for individual watersheds and identify areas of prioritization in regional and local planning efforts.

Iowa, Illinois, Indiana, Michigan, Minnesota, Miss↗

USGS2023

Less is more: Less herbicide does more when biological control is present in Pontederia crassipes

An experiment along with simulation modeling was applied to study the combinations of herbicide treatment and biological control that best limit invasive water hyacinth ( Pontederia crassipes , formerly Eichhornia crassipes ) in freshwater aquatic systems. The experiment consisted of 14 different treatments of P. crassipes in 1.67 m 2 outdoor tank mesocosms. Seven treatments were with and seven were without insect biological control agents, Neochetina eichhorniae . In both of the sets of seven treatments, there was one no-herbicide treatment, a one-time full-strength herbicide treatment with 40 %, 80 % and 100 % coverage of the P. crassipes , and a one-time half-strength herbicide treatment with 40 %, 80 %, and 100 % surface area coverage. An overarching hypothesis was that leaving part of a tank unsprayed, providing habitat for the maintenance of biological control agents, would optimize control. Data from the experiment, measured on five days over the 167-day period, were used to calibrate a difference equation model of P. crassipes with and without the biological control agent. The model was then used to project longer term dynamics of the system. The model predicted that an initial one-time herbicide treatment, combined with application of the biocontrol agent at 80 % areal coverage, could maintain P. crassipes at levels lower than the carrying capacity of the plant's biomass over the long term, though not enough that N. eichhorniae would be considered, by itself, a highly effective control. However, the results suggest that a combination of biocontrol with 80 % spraying coverage every 600 days or so would be an effective integrated biocontrol strategy for maintaining decreased P. crassipes biomass at low levels over the long term.

Ecological Modelling↗

USGS2004

Implications of hydrologic variability on the succession of plants in Great Lakes wetlands

Primary succession of plant communities directed toward a climax is not a typical occurrence in wetlands because these ecological systems are inherently dependent on hydrology, and temporal hydrologic variability often causes reversals or setbacks in succession. Wetlands of the Great Lakes provide good examples for demonstrating the implications of hydrology in driving successional processes and for illustrating potential misinterpretations of apparent successional sequences. Most Great Lakes coastal wetlands follow cyclic patterns in which emergent communities are reduced in area or eliminated by high lake levels and then regenerated from the seed bank during low lake levels. Thus, succession never proceeds for long. Wetlands also develop in ridge and swale terrains in many large embayments of the Great Lakes. These formations contain sequences of wetlands of similar origin but different age that can be several thousand years old, with older wetlands always further from the lake. Analyses of plant communities across a sequence of wetlands at the south end of Lake Michigan showed an apparent successional pattern from submersed to floating to emergent plants as water depth decreased with wetland age. However, paleoecological analyses showed that the observed vegetation changes were driven largely by disturbances associated with increased human settlement in the area. Climate-induced hydrologic changes were also shown to have greater effects on plant-community change than autogenic processes. Other terms, such as zonation, maturation, fluctuations, continuum concept, functional guilds, centrifugal organization, pulse stability, and hump-back models provide additional means of describing organization and changes in vegetation; some of them overlap with succession in describing vegetation processes in Great Lakes wetlands, but each must be used in the proper context with regard to short- and long-term hydrologic variability.

Aquatic Ecosystem Health & Management↗

USGS2019

Does incorporating gear selectivity during macroscale investigations of fish growth reduce size-selective sampling bias in parameter estimates?

Understanding of fish growth, the spatial variability in individual growth, and the potential drivers of such variability is a fundamental component of many ecological investigations. However, sampling gears are always size-selective, and this selectivity can result in biased parameter estimates that can lead to, for example, biased stock assessments that use growth estimates. Using seven flathead catfish ( Pylodictis olivaris ) populations from across the USA as an example, we investigated to what degree the incorporation of gear selectivity in growth models reduces size-selective bias in the estimation of growth parameters during macroscale investigations of fish growth. We developed a series of simulation scenarios by combining different sampling methods to obtain fish samples and different gear selectivity assumptions to estimate parameters. Results showed that the efficacy of incorporating gear selectivity in growth models to reduce size-selective sampling bias during macroscale investigations depends on multiple factors, including ( i ) the size distribution of small and large fish in the sample (which is a function of sampling methods), and ( ii ) consistency of sampling methods across populations. Incorporation of gear selectivity may reduce bias when data are lacking for large fish and when sampling methods are inconsistent across populations. Demographics of the sampled populations and the growth parameter of interest can also affect the utility of directly incorporating gear selectivity into growth models. Because multiple factors can influence the efficacy of incorporating gear selectivity into growth models, the decision to do so likely needs to be made on a case-by-case basis. This study extends the existing gear selectivity research by focusing on macroscale fish growth investigations across multiple populations and provides guidance on how to handle gear selectivity assumptions during such investigations.

Canadian Journal Fisheries and Aquatic Sciences↗

USGS2020

Climate change vulnerability assessment for Pacific Lamprey in rivers of the Western United States

Pacific Lamprey (Entosphenus tridentatus) are a native anadromous species that, like salmon, historically returned to spawn in large numbers in watersheds along the west coast of the United States (U.S.). Lamprey play a vital role in river ecosystems and are one of the oldest vertebrates that have persisted over time likely influencing the evolution of many aquatic species. Pacific Lamprey have declined in abundance and are restricted in distribution throughout Washington, Oregon, Idaho and California. A key uncertainty influencing Pacific Lamprey status is the impact of climate change. We modified the NatureServe Climate Change Vulnerability Index (CCVI) to accommodate climate predictions from the International Panel on Climate Change. Using downscaled information, we characterized changes in 15 rivers occupied by Pacific Lamprey in the western U.S. We evaluated this risk under Representative Concentration Pathways (RCP) 4.5 and 8.5 for two time periods (mid-century 2040–2069 and end-century 2070–2099). The CCVI scores generally increased when going from RCP 4.5 to RCP 8.5 in three Global Climate Models for both mid-century and end-century, which our analyses forecasts degraded stream temperature and hydrologic conditions under increasing greenhouse gas emissions. The geographically assessed results suggest that climate change impacts to Pacific Lamprey vulnerability are magnified in highly altered rivers. If we continue to observe greenhouse gas emission levels associated with the RCP 8.5, Pacific Lamprey will be at greater risk to climate change impacts. In order to mitigate the risk from climate change toward the end of the century, additional actions will need to be prioritized to rapidly reduce the impact of these threats such as increasing flow, creating backwater habitat, restoring riparian vegetation and reducing stream disturbances. The findings revealed the patterns of vulnerability for Pacific Lamprey across their U.S. range are informative for prioritizing river restoration actions when paired with regional implementation plans.

California, Washington, Oregon, Idaho↗

USGS2006

Denitrification across landscapes and waterscapes: A synthesis

Denitrification is a critical process regulating the removal of bioavailable nitrogen (N) from natural and human-altered systems. While it has been extensively studied in terrestrial, freshwater, and marine systems, there has been limited communication among denitrification scientists working in these individual systems. Here, we compare rates of denitrification and controlling factors across a range of ecosystem types. We suggest that terrestrial, freshwater, and marine systems in which denitrification occurs can be organized along a continuum ranging from (1) those in which nitrification and denitrification are tightly coupled in space and time to (2) those in which nitrate production and denitrification are relatively decoupled. In aquatic ecosystems, N inputs influence denitrification rates whereas hydrology and geomorphology influence the proportion of N inputs that are denitrified. Relationships between denitrification and water residence time and N load are remarkably similar across lakes, river reaches, estuaries, and continental shelves. Spatially distributed global models of denitrification suggest that continental shelf sediments account for the largest portion (44%) of total global denitrification, followed by terrestrial soils (22%) and oceanic oxygen minimum zones (OMZs; 14%). Freshwater systems (groundwater, lakes, rivers) account for about 20% and estuaries 1% of total global denitrification. Denitrification of land-based N sources is distributed somewhat differently. Within watersheds, the amount of land-based N denitrified is generally highest in terrestrial soils, with progressively smaller amounts denitrified in groundwater, rivers, lakes and reservoirs, and estuaries. A number of regional exceptions to this general trend of decreasing denitrification in a downstream direction exist, including significant denitrification in continental shelves of N from terrestrial sources. Though terrestrial soils and groundwater are responsible for much denitrification at the watershed scale, per-area denitrification rates in soils and groundwater (kg N·km −2 ·yr −1 ) are, on average, approximately one-tenth the per-area rates of denitrification in lakes, rivers, estuaries, continental shelves, or OMZs. A number of potential approaches to increase denitrification on the landscape, and thus decrease N export to sensitive coastal systems exist. However, these have not generally been widely tested for their effectiveness at scales required to significantly reduce N export at the whole watershed scale.

Ecological Applications↗

USGS2021

Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms

Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population-level genetic diversity and estimates of the number of genetic contributors in a sample. Using a panel of microsatellite loci, we evaluated intraspecific genetic diversity in the round goby (Neogobius melanostomus) using eDNA samples from experimental mesocosms. First, we tested the similarity between eDNA and individual tissue-based estimates of allele frequencies. Subsequently, we used a likelihood-based DNA mixture framework to estimate the number of unique genetic contributors in mesocosm eDNA samples and in simulated mixtures of alleles. Allele frequencies from eDNA accurately reflected allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples under controlled conditions. DNA mixture analyses were able to estimate the number of genetic contributors from eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low-frequency alleles. This study is the first to document the application of eDNA and multiple amplicon-based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in mesocosms. With proper validation, this approach has the potential to advance non-invasive survey methods to characterize populations and broadens the application of eDNA methodologies to inform population-level management objectives.

New York↗

USGS2018

Assessing historical and projected carbon balance of Alaska: A synthesis of results and policy/management implications

We summarize the results of a recent interagency assessment of land carbon dynamics in Alaska, in which carbon dynamics were estimated for all major terrestrial and aquatic ecosystems for the historical period (1950–2009) and a projection period (2010–2099). Between 1950 and 2009, upland and wetland (i.e., terrestrial) ecosystems of the state gained 0.4 Tg C/yr (0.1% of net primary production, NPP), resulting in a cumulative greenhouse gas radiative forcing of 1.68 × 10 −3 W/m 2 . The change in carbon storage is spatially variable with the region of the Northwest Boreal Landscape Conservation Cooperative (LCC) losing carbon because of fire disturbance. The combined carbon transport via various pathways through inland aquatic ecosystems of Alaska was estimated to be 41.3 Tg C/yr (17% of terrestrial NPP). During the projection period (2010–2099), carbon storage of terrestrial ecosystems of Alaska was projected to increase (22.5–70.0 Tg C/yr), primarily because of NPP increases of 10–30% associated with responses to rising atmospheric CO 2 , increased nitrogen cycling, and longer growing seasons. Although carbon emissions to the atmosphere from wildfire and wetland CH 4 were projected to increase for all of the climate projections, the increases in NPP more than compensated for those losses at the statewide level. Carbon dynamics of terrestrial ecosystems continue to warm the climate for four of the six future projections and cool the climate for only one of the projections. The attribution analyses we conducted indicated that the response of NPP in terrestrial ecosystems to rising atmospheric CO 2 (~5% per 100 ppmv CO 2 ) saturates as CO 2 increases (between approximately +150 and +450 ppmv among projections). This response, along with the expectation that permafrost thaw would be much greater and release large quantities of permafrost carbon after 2100, suggests that projected carbon gains in terrestrial ecosystems of Alaska may not be sustained. From a national perspective, inclusion of all of Alaska in greenhouse gas inventory reports would ensure better accounting of the overall greenhouse gas balance of the nation and provide a foundation for considering mitigation activities in areas that are accessible enough to support substantive deployment.

Alaska↗

USGS2020

Effects of stormwater runoff from selected bridge decks on conditions of water, sediment, and biological quality in receiving waters in South Carolina, 2013 to 2018

The U.S. Geological Survey, in cooperation with the South Carolina Department of Transportation, investigated the effects of stormwater runoff from bridge decks on stream water quality conditions in South Carolina. The investigation assessed 5 bridges in 3 physiographic provinces in South Carolina (Piedmont, Upper Coastal Plain, and Lower Coast Plain) that had a range of bridge, traffic, and hydrologic characteristics. The five selected South Carolina bridge sites (coincident with U.S. Geological Survey stations) and corresponding highways were Lynches River at Effingham (station 02132000; U.S. Highway 52), North Fork Edisto River at Orangeburg (station 02173500; U.S. Highway 301), Turkey Creek above Huger (station 02172035; South Carolina Highway 41), South Fork Edisto River near Denmark (station 02173000; U.S. Highway 321), and Fishing Creek at Highway 5 below York (station 021473415; South Carolina Highway 5). Bridge decks at the selected sites used open chutes, scuppers, and downspouts to drain stormwater directly into the receiving water at evenly spaced intervals. Stream water, sediment, and biological samples were collected and analyzed for a variety of constituents to evaluate the stream conditions for this study. Five to six stream samples were collected at transects upstream and downstream from each selected bridge site using the equal-width-increment technique during observable stormwater runoff. Routine samples of the receiving waters were collected 12 to 14 times at the upstream transect during nonstorm conditions. Samples were analyzed for physical properties, suspended sediment, nutrients, major ions, trace metals, polycyclic aromatic hydrocarbons, and Escherichia coli . Bridge-deck sediment and streambed sediment at upstream and downstream transects were collected once at each bridge site and analyzed for metals and semivolatile organic compounds that include polycyclic aromatic hydrocarbons. Benthic macroinvertebrate community surveys were conducted once using Hester-Dendy multiplate artificial substrate samplers deployed at multiple upstream and downstream transects concurrently. Statistical analysis of the water-quality data determined that stormwater runoff from bridges did not significantly degrade physical properties, nor nutrient, trace-metal, Escherichia coli , and suspended-sediment concentrations at the selected sites beyond the variability at the upstream transect (no bridge influence) during the study period. During storm sampling at the bridge sites, water-quality conditions were statistically similar upstream and downstream from each bridge, except for greater turbidity, total nitrogen, and total organic nitrogen plus ammonia concentrations found downstream from the bridge site on Fishing Creek; higher total chromium concentrations detected downstream from the bridge site on Turkey Creek; and increased Escherichia coli concentrations found downstream from the bridge site on the North Fork Edisto River. Total recoverable lead, cadmium, and copper concentrations were the only trace metals that periodically exceeded the South Carolina Department of Health and Environmental Control freshwater aquatic-life criteria at some bridge sites (lead, copper, and cadmium in Turkey Creek; cadmium and lead in Fishing Creek; lead in the South Fork Edisto River and Lynches River), but the exceedances occurred more frequently during routine sampling upstream from the bridge sites than during storm sampling at upstream and downstream transects. In general, stormwater runoff from the bridge decks did not seem to be the major source of metal enrichment in receiving waters during the study period. North Fork and South Fork Edisto Rivers and Turkey Creek had only one storm sample that exceeded South Carolina Department of Health and Environmental Control recreational criterion for Escherichia coli at both the upstream and downstream locations, while Fishing Creek had more frequent exceedances. Polycyclic aromatic hydrocarbons were detected infrequently in the stream samples. In general, sediment trace-metal concentrations were below the threshold and probable effect concentration at all bridge sites, except for the chromium concentration (45.1 milligrams per kilogram) detected upstream from the bridge site on Fishing Creek that exceeded the threshold effect concentration of 43.4 milligrams per kilogram. Based on enrichment ratios less than 1.5, bridge-deck runoff did not seem to be affecting trace-metal accumulation in the streambed sediment downstream from the bridge sites, except for lead at the bridge site on the Lynches River and manganese at the bridge site on Fishing Creek. Individual polycyclic aromatic compound concentrations and the sum of 18 compounds did not exceed any threshold and probable effect concentrations, indicating polycyclic aromatic hydrocarbon concentrations in the streambed sediment at downstream and upstream transects were not likely to affect the health of benthic macroinvertebrate communities. Although the cumulative polycyclic aromatic hydrocarbon concentrations in downstream sediment at the sites on Turkey and Fishing Creeks were well below the threshold effect concentration of 1,610 micrograms per kilogram, the 3- to 100-fold increase in downstream concentrations indicated a strong probability of a bridge-deck runoff source. Overall, benthic macroinvertebrate community health downstream from the bridge sites did not seem to be affected by bridge-deck runoff based on several multivariate analyses that indicated statistically similar benthic macroinvertebrate communities at upstream and downstream transects. Of the five bridge sites in this study, the site on Turkey Creek seemed to have the least healthy benthic macroinvertebrate communities because of the lowest Ephemeroptera, Plecoptera, and Trichoptera spp. (mayflies, stoneflies, and caddisflies, respectively) taxa, species richness, and diversity; and the highest biotic indices, indicative of poorer ecological health, at upstream and downstream transects. This ecological finding was not unexpected because of seasonal periods of negligible flow when dissolved-oxygen concentrations fell below 4 milligrams per liter during the study period. Of the five bridge sites in this study, the site on the South Fork Edisto River seemed to have healthier benthic macroinvertebrate communities because of the greater mean Ephemeroptera, Plecoptera, and Trichoptera spp. taxa; and lower mean biotic indices at upstream and downstream transects.

Scientific Investigations Report↗

USGS1991

Diurnal photosynthesis cycle in CAM and non-CAM seasonal pool aquatic macrophytes

Seasonal pools undergo marked diurnal changes in pH, free carbon dioxide, and oxygen levels. Previous studies showed that Isoetes howellii utilized crassulacean acid metabolism (CAM) photosynthesis as a means of assimilating carbon at night when ambient carbon dioxide levels are high. However, much of the pool flora is not CAM. We hypothesized that coexistence under extreme carbon—limiting conditions would select for other photosynthetic characteristics in these non—CAM species. Quantitative carbon uptake measurements wee made in the field on the CAM Isoetes howellii and the non—CAM Eleocharis acicularis, Downingia bella, and Plagiobothrys undulatus. Despite wide phylogenetic separation, thee species are structurally convergent in that they all produce aquatic stage with an isoetid growth form. They are functionally similar in that none appear to utilize bicarbonate, and all are carbon limited through much of the day, as indicated by a marked midday depression in carbon uptake that last through the afternoon. All four species were capable of carbon fixation at night, although only in Isoetes howellii was this accompanied by an overnight accumulation of acid. It was estimated that dark fixation in I. howelli contributed up to 40% of its total carbon gain under submerged conditions, but was <1% under aerial conditions. The role of dark fixation in the other three, non—CAM, species is unknown. Short—term (1 s) steady—term (1 s) steady—state 1 4 C tracer studies in the laboratory revealed that, under submerged conditions in the light, all species assimilated carbon into the C 3 photosynthetic product phosphoglycerate (PGA) and the C 4 photosynthetic products of malate, citrate, and aspartate. The proportion of label fixed into C 4 organic acids was greatest in E. acicularis. The ratio of RuBP carboxylase/PEP carboxylase was broadly similar in all species, ranging from 8.8 to 11.5. When the pools dried down and the plants became aerial, photosynthetic rates increased and a midday depression such as occurred under submergence was not observed. Carbon fixation in the dark became negligible, and the RuBP carboxylase/PEP carboxylase ratio increased. Seasonal changes in biomass showed I. howellii and E. acicularis dominated the pools early in the season, and the biomass of the other two species increased later when the pools dried. The latter species, D. bella and P. undulatus, also had higher rates of photosynthesis under aerial conditions.

Ecology↗

USGS2014

Latitudinal and photic effects on diel foraging and predation risk in freshwater pelagic ecosystems

1. Clark & Levy ( American Naturalist , 131 , 1988, 271–290) described an antipredation window for smaller planktivorous fish during crepuscular periods when light permits feeding on zooplankton, but limits visual detection by piscivores. Yet, how the window is influenced by the interaction between light regime, turbidity and cloud cover over a broad latitudinal gradi- ent remains unexplored. 2. We evaluated how latitudinal and seasonal shifts in diel light regimes alter the foraging- risk environment for visually feeding planktivores and piscivores across a natural range of turbidities and cloud covers. Pairing a model of aquatic visual feeding with a model of sun and moon illuminance, we estimated foraging rates of an idealized planktivore and piscivore over depth and time across factorial combinations of latitude (0 – 70 ° ), turbidity (0 1 – 5 NTU) and cloud cover (clear to overcast skies) during the summer solstice and autumnal equinox. We evaluated the foraging-risk environment based on changes in the magnitude, duration and peak timing of the antipredation window. 3. The model scenarios generated up to 10-fold shifts in magnitude, 24-fold shifts in duration and 5 5-h shifts in timing of the peak antipredation window. The size of the window increased with latitude. This pattern was strongest during the solstice. In clear water at low turbidity (0 1 – 0 5 NTU), peaks in the magnitude and duration of the window formed at 57 – 60 ° latitude, before falling to near zero as surface waters became saturated with light under a midnight sun and clear skies at latitudes near 70 ° . Overcast dampened the midnight sun enough to allow larger windows to form in clear water at high latitudes. Conversely, at turbidities ≥ 2 NTU, greater reductions in the visual range of piscivores than planktivores created a window for long periods at high latitudes. Latitudinal dependencies were essentially lost during the equinox, indicating a progressive compression of the window from early summer into autumn. 4. Model results show that diel-seasonal foraging and predation risk in freshwater pelagic ecosystems changes considerably with latitude, turbidity and cloud cover. These changes alter the structure of pelagic predator – prey interactions, and in turn, the broader role of pelagic consumers in habitat coupling in lakes.

Journal of Animal Ecology↗

USGS2015

Accounting for groundwater in stream fish thermal habitat responses to climate change

Forecasting climate change effects on aquatic fauna and their habitat requires an understanding of how water temperature responds to changing air temperature (i.e., thermal sensitivity). Previous efforts to forecast climate effects on brook trout habitat have generally assumed uniform air-water temperature relationships over large areas that cannot account for groundwater inputs and other processes that operate at finer spatial scales. We developed regression models that accounted for groundwater influences on thermal sensitivity from measured air-water temperature relationships within forested watersheds in eastern North America (Shenandoah National Park, USA, 78 sites in 9 watersheds). We used these reach-scale models to forecast climate change effects on stream temperature and brook trout thermal habitat, and compared our results to previous forecasts based upon large-scale models. Observed stream temperatures were generally less sensitive to air temperature than previously assumed, and we attribute this to the moderating effect of shallow groundwater inputs. Predicted groundwater temperatures from air-water regression models corresponded well to observed groundwater temperatures elsewhere in the study area. Predictions of brook trout future habitat loss derived from our fine-grained models were far less pessimistic than those from prior models developed at coarser spatial resolutions. However, our models also revealed spatial variation in thermal sensitivity within and among catchments resulting in a patchy distribution of thermally suitable habitat. Habitat fragmentation due to thermal barriers therefore may have an increasingly important role for trout population viability in headwater streams. Our results demonstrate that simple adjustments to air-water temperature regression models can provide a powerful and cost-effective approach for predicting future stream temperatures while accounting for effects of groundwater.

Virginia↗

USGS2018

An analytical framework for estimating aquatic species density from environmental DNA

Environmental DNA (eDNA) analysis of water samples is on the brink of becoming a standard monitoring method for aquatic species. This method has improved detection rates over conventional survey methods and thus has demonstrated effectiveness for estimation of site occupancy and species distribution. The frontier of eDNA applications, however, is to infer species density. Building upon previous studies, we present and assess a modeling approach that aims at inferring animal density from eDNA. The modeling combines eDNA and animal count data from a subset of sites to estimate species density (and associated uncertainties) at other sites where only eDNA data are available. As a proof of concept, we first perform a cross-validation study using experimental data on carp in mesocosms. In these data, fish densities are known without error, which allows us to test the performance of the method with known data. We then evaluate the model using field data from a study on a stream salamander species to assess the potential of this method to work in natural settings, where density can never be known with absolute certainty. Two alternative distributions (Normal and Negative Binomial) to model variability in eDNA concentration data are assessed. Assessment based on the proof of concept data (carp) revealed that the Negative Binomial model provided much more accurate estimates than the model based on a Normal distribution, likely because eDNA data tend to be overdispersed. Greater imprecision was found when we applied the method to the field data, but the Negative Binomial model still provided useful density estimates. We call for further model development in this direction, as well as further research targeted at sampling design optimization. It will be important to assess these approaches on a broad range of study systems.

Ecology and Evolution↗

USGS2015

Variations in water temperature and implications for trout populations in the Upper Schoharie Creek and West Kill, New York, USA

Water temperature is a key component of aquatic ecosystems because it plays a pivotal role in determining the suitability of stream and river habitat to most freshwater fish species. Continuous temperature loggers and airborne thermal infrared (TIR) remote sensing were used to assess temporal and spatial temperature patterns on the Upper Schoharie Creek and West Kill in the Catskill Mountains, New York, USA. Specific objectives were to characterize (1) contemporary thermal conditions, (2) temporal and spatial variations in stressful water temperatures, and (3) the availability of thermal refuges. In-stream loggers collected data from October 2010 to October 2012 and showed summer water temperatures exceeded the 1-day and 7-day thermal tolerance limits for trout survival at five of the seven study sites during both summers. Results of the 7 August 2012 TIR indicated there was little thermal refuge at the time of the flight. About 690,170 m 2 of water surface area were mapped on the Upper Schoharie, yet only 0.009% (59 m 2 ) was more than 1.0 °C below the median water surface temperature (BMT) at the thalweg and no areas were more than 2.0 °C BMT. On the West Kill, 79,098 m 2 were mapped and 0.085% (67 m 2 ) and 0.018% (14 m 2 ) were BMT by 1 and 2 °C, respectively. These results indicate that summer temperatures in the majority of the study area are stressful for trout and may adversely affect growth and survival. Validation studies are needed to confirm the expectation that resident trout are in poor condition or absent from the downstream portion of the study area during warm-water periods.

New York↗

USGS2007

A gap analysis and comprehensive conservation strategy for riverine ecosystems of Missouri

North America harbors an astounding proportion of the world's freshwater species, but it is facing a freshwater biodiversity crisis. A first step to slowing the loss of biodiversity involves identifying gaps in existing efforts to conserve biodiversity and prioritizing opportunities to fill these gaps. In this monograph we detail two separate, but complementary, conservation planning efforts - a Gap Analysis (GAP) and a State Wildlife Action Plan (WAP) - for Missouri that address this first step. The goal of the Missouri Aquatic GAP Project was to identify riverine ecosystems, habitats, and species not adequately represented (i.e., gaps) within existing conservation lands. The goal of the freshwater component of the Missouri Wildlife Action Plan was to identify and map a set of conservation-opportunity areas (COAs) that holistically represent all riverine ecosystems, habitats, and species in Missouri. Since conservation planning is a geographical exercise, both efforts utilized geographic information systems (GIS). Four principal GIS data sets were used in each planning effort: (1) a hierarchical riverine ecosystem classification, (2) predicted species distributions, (3) public ownership/stewardship, and (4) a human-threat index. Results of the gap analyses are not encouraging. Forty five, mostly rare, threatened, or endangered, species are not represented in lands set aside for conserving biodiversity. Results also illustrate the fragmented nature of conservation lands, which are mainly situated in the uplands and fail to provide connectivity among riverine habitats. Furthermore, many conservation lands are severely threatened by an array of human disturbances. In contrast, results of the WAP provide hope that relatively intact riverine ecosystems still exist. A total of 158 COAs, representing &sim;6% of the total kilometers of stream in Missouri, were selected for the WAP. This illustrates that a wide spectrum of biodiversity can be represented within a small portion of the total resource base, but the area of conservation concern is often much larger. Identifying priority riverscapes for conservation is an important first step toward effective biodiversity conservation. Yet, achieving the ultimate goal of conserving biodiversity will require vigilance on the part of all responsible parties, with particular attention to addressing and coordinating the many remaining logistical tasks.

Missouri↗