SEARCH · Search USGS

Results for “Ecology of Freshwater Fish”

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.

1,663 records · Page 4Linked to original sources

USGS2026

Birds, breakpoints, and baselines: How citizen science data can reveal ecological boundaries in Kenya’s Upper Tana watershed

Tropical watersheds are increasingly threatened by climate change, land-use conversion, and resource extraction, yet conventional biodiversity monitoring in these systems is often spatially and temporally limited. Citizen science offers a complementary approach, enabling biodiversity data collection over large areas that can supplement professional scientific surveys. We analyzed 10 years (2012–2022) of Upper Tana Watershed bird data from the Kenya Bird Map project, covering 114 pentads (9 × 9 km) within a 17,000 km 2 watershed to assess patterns of bird community composition and distribution across this watershed and to also evaluate the effects of environmental variables, seasonality, and sampling effort to help inform improvements in future citizen science projects. Citizen (or community) scientists recorded 575 species (>50% of Kenya’s total avifauna) in 74 families. Asymptotic species accumulation indicates that most probable species present in the watershed were detected. Threshold indicator taxa analysis revealed distinct ecological boundaries along elevation (∼1,500 m), precipitation (∼1,100 mm), and mean temperature (∼19°C) gradients, corresponding to a turnover from xeric savanna to mesic montane forest assemblages. Notably, bird communities showed little seasonal differentiation between wet and dry periods, consistent with dominance by resident year-round species. Data limitations including uneven survey distribution and frequency, absence of abundance metrics, and coarse representation of local environmental conditions that likely reduced our ability to detect fine-scale species–habitat relationships. Addressing these gaps through spatially balanced sampling at greater resolution, greater survey frequency in underrepresented areas, and improved capture of habitat metrics could strengthen the use of citizen-science bird data for watershed bioassessment. Our findings demonstrate that structured citizen-science initiatives can identify ecological boundaries and inform adaptive management of tropical socio-ecological systems under rapid environmental change.

Upper Tana watershed↗

USGS2024

Earthquake effects surveyed during the nineteenth century as ecological features of Chinookan tidelands

Lasting effects of a Cascadia earthquake in 1700 were documented during surveys of Chinookan tidelands near the mouth of the Columbia River between 1805 and 1868. The effects resemble estuarine consequences, near Anchorage, of the 1964 Alaska earthquake: fatal drowning of subsided meadows and forests by post-earthquake tides, rebirth of marshes and forests through post-earthquake sedimentation, and uplift. Chinookan remains of killed forests were recorded by James Graham Cooper, John J. Lowell, and Cleveland Rockwell. Cooper, attached to a railroad survey and the Smithsonian Institution, wrote of redcedar stumps and trunks standing dead in tidal marshes of Shoalwater (now Willapa) Bay. Two such snags served as bearing trees for Lowell as he platted a Shoalwater Bay township under contract with the General Land Office. Rockwell, of the US Coast Survey, flecked landward edges of tidal flats west of Astoria with symbols that evoke remains of a bygone spruce forest. The Lewis and Clark Expedition, while in that area in 1805–1806, mapped and puzzled over tideland vegetation that post-1700 succession helps explain.

Alaska, British Columbia, California, Oregon, Wash↗

USGS2025

Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host

Symbiodiniaceae-associated microbiota strongly influence cnidarian symbioses. We systematically reduced the bacterial and fungal communities associated with Symbiodiniaceae to study potential effects on the cnidarian holobiont Exaiptasia diaphana (Aiptasia). Clonal anemones were inoculated with xenic Breviolum minutum (SSB01) and microbiome-manipulated cultures after antibacterial or antifungal treatment. The asexual reproduction of pedal laceration allowed for three generations of clonal aposymbiotic Aiptasia to be utilised in this study, from the initial adult generation (G0), to the first (G1), and second (G2) generation. We inoculated small and large G1 Aiptasia with SSB01 algae and monitored onset of symbiosis, rate of algal proliferation, and holobiont characteristics. Sequencing the 16S and 18S rRNA gene regions identified significant differences in the bacterial and fungal communities of the G0 and G1 generations, alongside differences between the size classes of small and large G1 anemones. The microbiome of larger G1 individuals was distinct to the smaller G1 anemones, suggesting a microbiome maturation process. Control Breviolum minutum cultures exhibited a significantly greater proliferation rate in large G1 anemones when compared to antibacterial or antifungal treated cultures, whereas the opposite trend was documented in the small G1 anemones. Although no differences were observed between algal photochemical parameters, or the growth and polyp activity of G1 juveniles, we observed a significant influence in the production of G2 clones between treatments. Overall, we provide strong ecological implications of manipulating Symbiodiniaceae microbiome, not for the algae themselves, but for the maturation of the host Aiptasia, as well as for the cnidarian holobiont over multiple generations.

The ISME Journal↗

USGS2026

Wind River subbasin restoration: Annual report of U.S. Geological Survey activities January 2024 through December 2024

We sampled juvenile wild Oncorhynchus mykiss (Steelhead Trout) in headwater streams of the Wind River, Washington, to characterize population attributes and investigate life-history metrics, particularly migratory patterns, and early life-stage survival. Additionally, this sampling provides an index of abundance of non-native Brook Trout Salvelinus confluentus . We used passive integrated transponder (PIT) tagging and a series of instream PIT-tag interrogation systems (PTISs) to track juveniles and adults. The Wind River subbasin is considered a wild Steelhead refuge by Washington Department of Fish and Wildlife (WDFW). No hatchery Steelhead Trout have been released in the Wind River subbasin since 1997, and hatchery adults are estimated at less than one percent of spawners in most years. Over 25 years of Steelhead Trout status and trend monitoring and research in the subbasin is contributing to understanding of population response to numerous restoration actions in the subbasin, including removal of Hemlock Dam from Trout Creek in 2009, which had an inadequate adult ladder and contributed to increased water temperatures, to near lethal levels for salmonids. Data from our study, and companion work by WDFW, are contributing to the Columbia Basin Fish and Wildlife Program (2009) Research, Monitoring, and Evaluation (RM&E) Strategy of Fish Population Status Monitoring. Specifically, this work addresses the sub-strategies of 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and Uncertainties Research regarding differing life histories of a wild Steelhead Trout population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer and fall 2024, we PIT-tagged 2,075 Steelhead Trout parr (age-0 and age-1), in the Trout Creek and upper Wind River watersheds. Age-0 and age-1 parr were at high abundance due to strong spawner numbers in 2023 and 2024 (Estimate of 932 in 2023; and a moderate number of spawners in 2024 though an estimate is not available at this time; 24-year median = 619; Charlie Cochran, WDFW Fish Biologist, personal commun., 2025). An additional 100 parr (age-0 and age-2 or older) were tagged to provide fish for estimating detection efficiencies at PTISs. Steelhead Trout parr were recaptured and detected through repeat headwater sampling, smolt trapping, instream PTISs and Columbia River mainstem PIT-tag detection. We maintained and upgraded six instream PTISs to detect PIT-tagged Steelhead Trout parr, smolts, and adults, providing data for population assessments, and life-cycle research. Detection data from PIT-tagged adult Steelhead Trout at our four primary PTISs allow assessment of adult escapement to tributary watersheds within the Wind River subbasin. Most adult Steelhead detected were tagged by WDFW at an adult trap in the lower Wind River and some as smolts at screw traps. Adult Steelhead Trout detection efficiency estimates at our primary PTIS in Trout Creek have been greater than 99 percent during eight of the past ten years and have exceeded 97% at our primary PTIS in the Wind River during nine of the past ten years. Adult escapement estimates to tributary watersheds are helping evaluate the efficacy of the 2009 removal of Hemlock Dam from rkm 2.0 of Trout Creek. Detections at the instream PTISs have shown trends of age-0 and age-1 Steelhead Trout parr emigration from natal areas during summer and fall, in addition to the expected movement of parr and smolts in spring. Our data suggest that most fish from a cohort that migrate downstream will do so at age-1 for additional rearing in the subbasin. We have estimated that from 15% to 56% of parr tagged as age-0 fish in headwater areas make downstream migrations at age-1 for additional rearing (median = 29%). We have estimated that from 1% to 27% of Steelhead Trout parr, tagged as age-1 fish, make downstream migrations during fall (median = 3.5%): this is especially pronounced in the upper Wind River portion of the watershed (median 10%). These findings raise questions about parr rearing habitat and whether migrations are density- or habitat-quality driven, and answers to such questions are long-term goals of this study as active and passive habitat restoration occurs. Repeat sampling at sites in the subbasin within and between years has enabled assessment of juvenile Steelhead Trout growth patterns. Growth rates (relative change in weight) of age-0 PIT-tagged parr during summer have been similar across the subbasin, though slightly lower in the Trout Creek watershed (Trout Creek sites, 0.57 - 1.25%/day, Wind River sites = 0.94 – 2.48%/day). Summer growth rates have been lower for age-1 parr in the Trout Creek watershed than the upper Wind River watershed (Trout Creek sites, = 0.03 - 0.14%/day, Wind River sites = 0.05 – 0.19%/day). Yearly relative growth was similar across the subbasin for both age-0 and age-1 tagged parr. During 2024 range of mean daily relative change in weight from the previous year for age-0 tagged fish was: Trout Creek sites = 0.96 – 1.41%/day, Wind River sites = 0.80 – 1.30 %/day; and for age1 tagged fish was: Trout Creek sites = 0.37 - 0.50 %/day, Wind River sites = no age-1 tagged recaptures. Non-native Brook Trout are present in the subbasin, chiefly the Trout Creek watershed. Mean percent-of-catch that is Brook Trout, at four sample sites in Trout Creek, has declined from the period 1998 – 2003 to the period 2011 – 2024 (range of decrease = 19 - 82%). Percent-of-catch (of 64 samples, 52 < 10%; 3 > 20%) and number of Brook Trout at the Trout Creek sites from 2011 through 2024, though variable, have generally declined. Habitat restoration evaluation efforts are critical to ensure efficient use of money and resources but require long-term monitoring of population metrics. Detailed viable salmonid population and life-history data, such as that provided by PIT-tagging and instream PTIS networks inform fisheries policy and management and enable assessment of long-term effects of habitat restoration actions such as the removal of Hemlock Dam on Trout Creek and proposed major instream habitat restoration in the upper Wind River.

Washington↗

USGS1999

Characterization of selected biological, chemical, and physical conditions at fixed sites in the Upper Colorado River Basin, Colorado, 1995-98

Biological community samples were collected at 15 sites in the Upper Colorado River Basin (UCOL) in Colorado as part of the National Water-Quality Assessment (NAWQA) Program. Sites sampled in two physiographic provinces, the Southern Rocky Mountains and the Colorado Plateau, represented agriculture, mining, urban and recreation, and mixed land uses and background conditions. Nine measures of water quality, which include information on nutrients, specific conductance (a surrogate for salinity), trace elements in streambed sediment, pesticides in fish tissue, fish communities, and macroinvertebrate richness and composition and stream habitat were used for comparisons among sites within the two physiographic provinces. Sampling sites from three other NAWQA study units—the Rio Grande Valley, the South Platte River Basin, and the Upper Snake River Basin study units—were categorized on the basis of land use and stream size in order to develop a larger data set for comparison to sites in the UCOL. Three categories of land use—forested (includes mining, urban and recreation, and background), agriculture, and mixed—were used for comparison to the UCOL fixed sites. Results indicated that all sites other than the Colorado River below Baker Gulch (a background site) showed some water-quality characteristics to be significantly affected. Results indicated that the concentrations of cadmium and zinc in streambed sediment at mining land-use sites in the Southern Rocky Mountains physiographic province generally were orders of magnitude higher than streambed-sediment concentrations at the background site. Streambed-sediment concentrations at mining land-use sites in the UCOL were greater than the 75 th percentile of concentrations from sites in the three other NAWQA study units. Fish communities and habitat conditions were degraded at mining land-use sites compared to the background site. Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness and the percentage of EPT were lower at mining land-use sites than at the background site and were less than the 50 th percentile of those for sites from the three other NAWQA study units. Nutrient concentrations at urban and recreation sites in the Southern Rocky Mountain physiographic province generally were greater than concentrations at the background site and generally were between the 25 th and 90 th percentile of concentrations for sites from the three other NAWQA study units. Habitat conditions and fish communities at urban and recreation sites were slightly degraded compared to the background site. EPT richness and the percentage of EPT were lower at urban and recreation sites than at the background site and were between the 25 th and 75 th percentile of those for sites from the three other NAWQA study units. The percentage of Chironomidae, which may be indicative of pollutant-tolerant organisms, was higher at urban and recreation sites than at the background site. Mixed land-use sites in the Southern Rocky Mountains physiographic province had similar nutrient concentrations and similar cadmium and zinc streambed-sediment concentrations. Fish-community degradation index values were very different among the three mixed land-use sites in the Southern Rocky Mountains physiographic province. Larger percentages of omnivores and anomalies such as lesions and deformities at two mixed land-use sites resulted in higher degradation values of the fish community. Agriculture land-use sites had higher concentrations of nutrients and selenium than the background site in the Colorado Plateau physiographic province. Concentrations of p,p '-DDE in fish tissue at agriculture sites were higher than the 75 th percentile of concentrations for sites from the three other NAWQA study units. Fish communities had degradation values near the 75 th percentile for agriculture sites. The percentage of EPT was low at agriculture sites when compared to the background site. Two mixed land-use sites in the Colorado Plateau physiographic province had similar concentrations of nutrients, selenium, and p,p '-DDE, and similar EPT richness and composition. These two sites were located downstream from agricultural and urban activities. Some water-quality measures at these two sites indicated degradation compared to a mixed land-use site upstream from most of the agriculture and urban activities in the Colorado Plateau physiographic province.

Colorado↗

USGS2025

U.S. Geological Survey science strategy to address white-nose syndrome and bat health in 2025–2029

Since its discovery in 2006, the fungal disease known as white-nose syndrome (WNS) has killed millions of bats. Of the 47 bat species native to the conterminous United States, Alaska, Hawaii, and Canada, 12 have been affected by WNS, including 3 endangered species and 1 proposed endangered species. WNS has also been detected in 40 States and 9 Canadian Provinces. U.S. Geological Survey (USGS) scientists have been critical in identifying the causal fungus for WNS ( Pseudogymnoascus destructans [Pd]), characterizing the effects of WNS, and tracking the spread of Pd in many bat populations in North America. The mission of the USGS WNS and Bat Health Science Team is to deliver integrated science in order to build resiliency into free-ranging bat populations through more effective WNS management, build capacity for bat health science, and enhance bat health information sharing across USGS science centers and cooperative research units as well as with stakeholders. The USGS can play an important role in supporting regional and national capacity building by providing resources and guidance to local, State, and Tribal management entities and by providing tools to enhance disease management. The USGS Ecosystems Mission Area’s Biological Threats and Invasive Species Research Program is the lead Federal program for free-ranging wildlife disease research and surveillance. As of 2024, guided by the science priorities set by the WNS Steering Committee, USGS scientists are engaged in a nationwide response to WNS. This work is done in close coordination with our partners at the U.S. Fish and Wildlife Service, National Park Service, Bureau of Land Management, U.S. Forest Service of the U.S. Department of Agriculture, U.S. Department of Defense, as well as State and Tribal agencies. In addition to conducting WNS research, the USGS is mapping the spread of WNS and coordinating the North American Bat Monitoring Program (NABat) to understand how WNS and other stressors affect the status and trends of native bats across their range. The USGS is supporting the national WNS response through four science goals: (1) provide situational awareness on the health of bat populations; (2) conduct ecological studies of bats along the gradient of disease vulnerability; (3) contribute actionable science to enhance the resiliency of bat populations; and (4) implement an adaptive, holistic approach to bat health.

Circular↗

USGS2025

Unlocking ecological insights from sub-seasonal visible-to-shortwave infrared imaging spectroscopy: The SHIFT campaign

We stand at the threshold of a transformative era in Earth observation, marked by space-borne visible-to-shortwave infrared (VSWIR) imaging spectrometers that promise consistent global observations of ecosystem function, phenology, and inter- and intra-annual change. However, the full value of repeat spectroscopy, the information embedded within different temporal scales, and the reliability of existing algorithms across diverse ecosystem types and vegetation phenophases have remained elusive due to the absence of suitable sub-seasonal spectroscopy data. In response, the Surface Biology and Geology (SBG) High-Frequency Time Series (SHIFT) campaign was initiated during late February 2022 in Santa Barbara County, California. SHIFT, designed to support NASA's SBG mission, addressed mission scoping, scientific advancement, applications development, and community building. This ambitious endeavor included weekly Airborne Visible InfraRed Imaging Spectrometer-Next Generation (AVIRIS-NG) imagery acquisitions for 13 weeks (spanning February 24 to May 29, 2022), accompanied by coordinated terrestrial vegetation and coastal aquatic data collection. We describe the rich datasets collected and illustrate how the complex sub-seasonal patterns of change can be linked to biological science and applications, surpassing insights from multispectral observations. Leveraging open-source processing methods and cloud-based analysis tools, the SHIFT campaign showcases the readiness of the scientific community to harness ecological insights from remotely sensed hyperspectral time series. We provide an overview of SHIFT's goals, data collections, preliminary results, and the collaborative efforts of early career scientists committed to unlocking the transformative potential of high-frequency time series data from space-borne VSWIR imaging spectrometers.

Ecosphere↗

USGS2024

Editorial: From cold seeps to hydrothermal vents: Geology, chemistry, microbiology, and ecology in marine and coastal environments

This Research Topic compiles contemporary studies on cold seeps, hydrothermal vents, mud volcanoes, and related seafloor features that are associated with focused fluid emissions and the transfer of carbon, other chemical species, and sometimes heat from the geosphere to the ocean. Because these features sometimes tap fluids and gas originating kilometers below the seafloor, they provide an important window into deep processes that are otherwise inaccessible to scientists. At the shallow portion of their journey, migrating fluids nearing the seafloor contribute to a range of unique biological, physical, and chemical processes within the sediments themselves and at the sediment-water interface. Seafloor fluid emissions play a critical role in global biogeochemical cycles, ocean chemistry, and possibly even climate change. Seafloor leakage points often emit hydrocarbon gases (especially methane and CO 2 ) and are sometimes the loci for deposition of seafloor minerals that have economic value. A burgeoning area of research focuses on natural products generated at these features, seeking compounds with potential pharmaceutical or other applications. Multidisciplinary studies have become routine for characterization of seafloor fluid emission sites, attesting to the inseparability of geologic, physical, chemical, and biological processes in these settings. It is increasingly common for researchers to combine in a single research cruise: subbottom imaging and seafloor mapping; porewater and water column geochemistry and gas sampling; sediment retrieval for lithologic, biostratigraphic, and solid phase analyses; and studies of benthic and subseafloor communities at the microbial to macrofaunal scales. This multidisciplinary approach has the advantage of ensuring the spatial and temporal coincidence of surveys and samples, an important factor at highly dynamic seafloor fluid emission sites. In addition, researchers often use remotely operated vehicles (ROVs), autonomous underwater vehicles (AUVs), or human-occupied vehicles (HOVs) to record video of the seafloor, compile photomosaics, collect targeted samples, and survey with high-resolution geophysical near-seafloor systems, providing a degree of detail about seafloor fluid emission sites that is unprecedented compared to most areas of the deep ocean. While rarer, long-term cabled observatories or shorter-term deployments of portable observatories are also used at some loci for seafloor fluid flux and are particularly helpful for capturing temporal variations at these dynamic features. Here we summarize the Research Topic’s contribution to multidisciplinary seafloor emission studies in the categories of cold seeps, mud volcanoes, and hydrothermal vents. Figure 1 shows the geographic distribution of the studies in this Research Topic and key features referred to in this Introduction.

Frontiers in Earth Science↗

USGS2026

King Rails in southeastern Arkansas are majority resident

King Rails ( Rallus elegans ), a declining species of secretive marsh bird, have a mixed migratory strategy, with some individuals migrating and some being year-round residents. Determining the distribution of migratory versus resident King Rails is critical to guiding habitat management and assessing risks to populations. We examined the migratory status of adult King Rails at the Choctaw West Wildlife Management Area in southeastern Arkansas, the only known site in Arkansas with multiple breeding pairs. Of the 23 adult King Rails we tagged in 2022 and 2023, two birds migrated away from the local area, one in each year. One migrated 145 km, and the other 450 km. Our findings suggest that the line between the migratory and resident range of Arkansas King Rails could be north of our site.

Arkansas↗

USGS2024

Interactive effects of salinity and hydrology on radial growth of bald cypress (Taxodium distichum (L.) Rich.) in coastal Louisiana, USA

Tidal freshwater forests are usually located at or above the level of mean high water. Some Louisiana coastal forests are below mean high water, especially bald cypress ( Taxodium distichum (L.) Rich.) forests because flooding has increased due to the combined effects of global sea level rise and local subsidence. In addition, constructed channels from the coast inland act as conduits for saltwater. As a result, saltwater intrusion affects the productivity of Louisiana’s coastal bald cypress forests. To study the long-term effects of hydrology and salinity on the health of these systems, we fitted dendrometer bands on selected trees to record basal area increment as a measure of growth in permanent forest productivity plots established within six bald cypress stands. Three stands were in freshwater sites with low salinity rooting zone groundwater (0.1–1.3 ppt), while the other three had higher salinity rooting zone groundwater (0.2–4.9 ppt). Water level was logged continuously, and salinity was measured monthly to quarterly on the surface and in groundwater wells. Higher groundwater salinity levels were related to decreased bald cypress radial growth, while higher freshwater flooding increased radial growth. With these data, coastal managers can model rates of bald cypress forest change as a function of salinity and flooding.

Louisiana↗

USGS2026

Estimation of parental abundance using hierarchical Bayesian modeling with data augmentation

Pedigree-based estimation methods leverage the fact that each offspring in a cohort is genotypically “marked” by its parents and represent a recent and promising toolset for estimating population dynamics. This includes pedigree accumulation estimators that model the “accumulation” of inferred unique parents within a given cohort to estimate parental abundance. Unlike close-kin mark-recapture approaches, which rely on intercohort comparisons, pedigree accumulation modeling can be completed solely using intracohort samples. This is particularly advantageous for semelparous species, where intercohort pairs are impossible and adult life stages can be difficult to sample without affecting their likelihood of successfully reproducing. Previous work has evaluated a range of estimators for such datasets, concluding that the non-parametric Chao estimator provides the most accurate and precise estimates for feasible levels of sampling effort. We used simulated data to evaluate an alternative estimator based on hierarchical modeling and data augmentation in a Bayesian framework. Results indicate that estimates from the hierarchical Bayesian estimator had comparable accuracy and better precision than both the previously tested Chao1 estimator and the improved iChao formulation across a range of sample sizes and sex ratios. Furthermore, the Bayesian estimator was far more robust to simulated errors in pedigree reconstruction, especially the presence of false negatives. Hierarchical Bayesian pedigree accumulation models can also provide additional insight into underlying reproductive ecology through their use of an explicit observation process, allowing for the incorporation or estimation of species- and population-specific reproductive dynamics. More broadly, the parametric nature of these models offers opportunities to efficiently pool information among datasets as well as to propagate uncertainty within more complex models.

Ecology and Evolution↗

USGS2026

Family life is critical for migration and survival in a long-lived social bird

Extended parental care is common among birds and particularly well known among long-lived migratory species. Yet, factors influencing the duration of parental care are poorly understood, and empirical evidence for the functional importance of family life for offspring development is scarce. Using unique tracking and genetic data of 55 adult and juvenile migratory Bewick’s swans, among which 18 parent-offspring pairs and 13 sibling pairs, we quantify variation in family bond duration and identify the cause and consequences of their dissolution. Families generally broke up during the second half of the first northward migration of the offspring, when offspring were nearly one year old. Earlier separation occurred on the wintering grounds in response to disturbance ( n = 10 juveniles) and led to delayed migration and, critically, lower survival (40 vs. 86%). Our results provide rare empirical evidence that family bonds, as a pathway for social learning, are not just important, but vital to the migration and survival of young family-living birds.

Behavioral Ecology and Sociobiology↗

USGS2026

Creation of aerial camera system boresight installations in Bangor, Maine; Monroe, Louisiana; and Bassville Park, Florida

Aerial camera systems rely on boresights for defining internal and external metrics. The U.S. Fish and Wildlife Service’s Migratory Bird Surveys Branch required boresights to calibrate their camera systems for creating georeferenced imagery that can then be used in geographic information systems. The U.S. Geological Survey created high-accuracy boresight installations in Bangor, Maine, in July 2024; Monroe, Louisiana, in September 2024; and Bassville Park, Florida, in January 2025 to provide this metric-defining capacity to the U.S. Fish and Wildlife Service. This U.S. Geological Survey Data Report details the methods and results of the boresight installation process and provides camera operators with the data needed to use each of the installations.

Florida, Louisiana, Maine↗

USGS2012

Development of vegetation based soil quality indices for mineralized terrane in arid and semi-arid regions

Soil quality indices (SQIs) are often management driven and attempt to describe key relationships between above- and below-ground parameters. In terrestrial systems, indices that were initially developed and modified for agroecosystems have been applied to non-agricultural systems in increasing number. We develop an SQI in arid and semi-arid ecosystems of the Western US impacted by different types of geologic mineralization using the relationship between vegetation community parameters and soil abiotic and biotic properties. We analyze these relations in soils associated with three different mineralization types: podiform chromite, Cu/Mo porphyry, and acid-sulfate gold vein systems at four different sites in California and Nevada. Soil samples were collected from undisturbed soils in both mineralized and nearby unmineralized substrates as well as from waste rock and tailings. Aboveground net primary productivity (ANPP), canopy cover and shrub density were measured for the vegetative communities. Minimum data sets were developed based on correlations between the soil and vegetation parameters, refined using principal components analysis, scored using non-linear functions, and combined into an overall SQI. The indices are comprised of one or two microbial parameters and three to six abiotic parameters, the latter consisting of nutrients and metals. Given the preliminary development of this approach, the parameters and combinations to arrive at an SQI for a given site cannot at this time be correlated or compared with that of another site. This SQI approach provides a means of quantifying disturbed ecosystem recovery resulting from mining, and could be applied to other disturbances in a way that readily distills the information for potential use by land managers. However, severely disturbed areas with little to no aboveground biomass, such as unreclaimed tailings, have likely crossed an ecological threshold that precludes the use of this type of monitoring tool.

California↗

USGS2025

Assessment of channel morphology, hydraulics, and bedload transport along the Siletz River, western Oregon

Significant Findings Chinook salmon ( Oncorhynchus tshawytscha ) and Pacific lamprey ( Entosphenus tridentatus ) are native, anadromous fish species in the Siletz River Basin, western Oregon, that face many threats to their survival in freshwater and the ocean. The Confederated Tribes of Siletz Indians of Oregon seek to mitigate freshwater threats to Chinook salmon and Pacific lamprey, where possible, with habitat conservation and restoration efforts. This study was conducted to assist the Confederated Tribes of Siletz Indians of Oregon in documenting and understanding the hydrogeomorphic processes shaping present-day habitat conditions and assessing future habitat implications for Chinook salmon and Pacific lamprey along the main-stem Siletz River. As such, this study focused on understanding geomorphic processes and patterns of channel change, including lateral and vertical adjustments in channel position and changes in bed-material sediment (sands, gravels, and cobbles that mantle the channel bed), which collectively determine overall patterns of channel morphology and fluvial habitats. Objective One was to evaluate lateral changes in channel position, vertical changes in bed elevation, and longitudinal patterns in bed-material particle size along the Siletz River using detailed channel maps developed from aerial photographs collected from 1939 to 2016, long-term records of stage and discharge collected by the U.S. Geological Survey (USGS) near the City of Siletz, and sediment particle size data. Objective Two was to assess hydraulic conditions using one- and two-dimensional hydraulic models and transport capacity of bed-material sediment using bedload transport models and sediment particle size data for a range of discharge conditions. Objective Three was to identify potential burrowing habitat for lamprey larvae (PBH) along the Siletz River network and provide insights in local factors influencing PBH along the main-stem Siletz River. The overall findings are synthesized to describe habitat implications for Chinook salmon and Pacific lamprey under present-day and future conditions. Results of Objective One, an evaluation of changes in channel position and bed elevations and longitudinal patterns in bed-material particle size along the Siletz River, include the following From 1939 to 2016, channel planform and the mapped area of gravel bars did not change considerably along the 97.2-kilometers (km) of Siletz River between Elk Creek and Millport Slough, except for in short sections generally less than 1 km long. This inherent lateral channel stability results from the resistant bedrock and terraces that bound most of the channel and limit lateral changes in channel position. Intermittent sections along the study reach where the active channel widened at channel bends displayed noticeable planform changes and increases in mapped bar area. From water year (WY; a 12-month period from October 1 through September 30 and named for the year in which it ends) 1906 to 2021, changes in the stage-discharge relation interpreted as rising and lowering channel bed levels were observed at the USGS streamgage 14305500 (Siletz River at Siletz, OR) in response to floods (such as high flows in February 1996 and January 2002 that exceeded 0.1 and 0.667 annual exceedance probabilities [AEP] events, respectively). However, the rating curve representing the stage-discharge relation did not change in response to high-magnitude floods between 2007 and 2021. Along the approximately 54-km of the Siletz River between Moonshine Park and the Bulls Bag area, surficial particle distributions varied considerably between sampling sites in response to changes in channel width and gradient, sediment inputs from tributaries, and basin geology. Despite this variability, median particle sizes tended to decrease in size in the downstream direction over the 54 km. Results of Objective Two, an evaluation of hydraulic and bedload transport conditions along the Siletz River, include the following The most substantial increases in maximum and mean water velocity and bedload sediment transport capacity occurred at events between the 0.995 and 0.50 AEPs. Events of these magnitudes occur approximately every 1–2 years. Smaller events (0.995 AEP) are generally contained by the banks of the main channel, whereas larger events (0.50 AEP) generally spill over the banks and inundate high-elevation bar and low-elevation floodplain surfaces. Multiple smaller floods within a WY that exceed the 0.995 and 0.50 AEPs (such as in WY 1996) can transport as much or more bed-material sediment than a single, higher magnitude event (such as the maximum event recorded in WY 2000 with an estimated AEP of around 0.002). Bedload transport capacity generally exceeds sediment supply (greater than 2 millimeters [mm]) for most of the study area from Wildcat Creek to the City of Siletz as evidenced by substantial in-channel bedrock. Despite overall conditions of limited sediment supply, transport capacity still varies considerably within and between years with discharge magnitude and spatially in relation to local hydraulics imposed by bedrock, channel morphology, and human infrastructure (such as bridges). Results of Objective Three, an analysis of PBH for lamprey larvae, include the following About 28 percent of the Siletz River network meets the mean annual suspended sediment loads and channel slope criteria for PBH. Along the main-stem Siletz River, in-channel bedrock outcrops and high transport capacity are expected to further constrain PBH. Together, these results suggest that most of the Siletz River between Wildcat Creek and the City of Siletz has had only modest vertical and lateral change between the 1930s and 2010s because of the bedrock in and along the main channel and the river’s relatively high transport capacity relative to bed-material sediment supply. However, localized sections of the Siletz River where the active channel widens, particularly at channel bends, exhibited some change in channel planform and the locations and area of gravel bars. In the future, moderate increases in autumn-winter discharge may not result in substantial changes in coarse gravel bars along the Siletz River but may result in selective transport of finer bed-material sediment (gravel, sands, and silts) that provide spawning habitats for Chinook salmon and Pacific lamprey and burrowing habitats for lamprey larvae. Assuming no substantial changes in bed-material sediment supply, increased bedload transport capacity may cause frequent entrainment of lamprey larvae that are burrowed in coarse sand deposits, suspension and downstream transport of salmon eggs incubating in gravels, and reductions in the areas of spawning gravels for Chinook salmon and Pacific lamprey. Exact implications of current and future discharge conditions for these species along the Siletz River depends on many factors, including sediment supply, local hydraulics, and the timing of flood events relative to fish life stages.

Oregon↗

USGS2024

Beyond the wedge: Impact of tidal streams on salinization of groundwater in a coastal aquifer stressed by pumping and sea-level rise

Saltwater intrusion (SWI) is a well-studied phenomenon that threatens the freshwater supplies of coastal communities around the world. The development and advancement of numerical models has led to improved assessment of the risk of salinization. However, these studies often fail to include the impact of surface waters as potential sources of aquifer salinity and how they may impact SWI. Based on field-collected data, we developed a regional, variable-density groundwater model using SEAWAT for east Dover, Delaware. In this location, major users of groundwater from the surficial aquifer are the City of Dover and irrigation for agriculture. Our model includes salinized marshland and tidal streams, along with irrigation and municipal pumping wells. Model scenarios were run for 100 years and included changes in pumping rates and sea-level rise (SLR). We examined how these drivers of SWI affect the extent and location of salinization in the surficial aquifer by evaluating differences in chloride concentration near surface waters and the subsurface freshwater-saltwater interface. We found the presence of the marsh inverts the typical freshwater-saltwater wedge interface and that the edge of the interface did not migrate farther inland. Additionally, we found that tidal streams are the dominant pathways of SWI at our site with salinization from streams being exacerbated by SLR. Our results also show that spatial distribution of pumping affects both the magnitude and extent of salinization, with an increase in concentrated pumping leading to more intensive salinization than a more widely distributed increase of the same total pumping volume.

Delaware↗

USGS2026

Re-examining the growing degree day minimum for grass carp spawning initiation in Lake Erie: Have we missed the mark?

Understanding the timing of life history processes of invasive fish species, such as adult aggregations during spawning, allows natural resource managers to optimize targeted population control efforts. Temperature-based estimates of the timing of spawning initiation for grass carp ( Ctenopharyngodon idella ) exist from its native range, but have not previously been developed for grass carp reproduction in its invaded range in the Laurentian Great Lakes of North America. We accounted for differences among methods across studies and calculated cumulative growing degree days (GDD) for the dates of grass carp egg capture in Lake Erie tributaries (Sandusky, Maumee, and Huron rivers) during 2015–2024 and compared these values to the existing GDD base 15°C requirement estimate from the native range (633 GDD–15°C). The earliest egg detection in Lake Erie (Sandusky River) was 19 GDD–15°C or 361 GDD–5°C (latest egg detection was 2285 GDD–5°C from the Sandusky River), indicating that spawning was initiated up to 25 days earlier than would be predicted by the native range GDD. Moreover, spawning in Lake Erie tributaries occurred earlier than predicted for 58% of spawning events examined based on the native range GDD. The GDD values for spawning initiation in Lake Erie tributaries can be used to refine the timing of control efforts targeting pre-spawn and spawning adult fish, inform the timing of egg sampling, and provide linkages to existing early life stage models to infer the length of the growing season available for age-0 fish to reassess tributary suitability.

Lake Erie, Maumee, River, Sandusky river↗

USGS2025

Towards mobile wind measurements using joust configured ultrasonic anemometer for applications in gas flux quantification

Small uncrewed aerial systems (sUASs) can be used to quantify emissions of greenhouse and other gases, providing flexibility in quantifying these emissions from a multitude of sources, including oil and gas infrastructure, volcano plumes, wildfire emissions, and natural sources. However, sUAS-based emission estimates are sensitive to the accuracy of wind speed and direction measurements. In this study, we examined how filtering and correcting sUAS-based wind measurements affects data accuracy by comparing data from a miniature ultrasonic anemometer mounted on a sUAS in a joust configuration to highly accurate wind data taken from a nearby eddy covariance flux tower (aka the Tower). These corrections had a small effect on wind speed error, but reduced wind direction errors from 50° to >120° to 20–30°. A concurrent experiment examining the amount of error due to the sUAS and the Tower not being co-located showed that the impact of this separation was 0.16–0.21 ms − 1 "> ms − 1 , a small influence on wind speed errors. Lower wind speed errors were correlated with lower turbulence intensity and higher relative wind speeds. There were also some loose trends in diminished wind direction errors at higher relative wind speeds. Therefore, to improve the quality of sUAS-based wind measurements, our study suggested that flight planning consider optimizing conditions that can lower turbulence intensity and maximize relative wind speeds as well as include post-flight corrections.

Alaska↗