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At least 433 records · Page 24Linked to original sources

USGS2020

High parasite diversity in the amphipod Gammarus lacustris in a subarctic lake

Amphipods are often key species in aquatic food webs due to their functional roles in the ecosystem and as intermediate hosts for trophically transmitted parasites. Amphipods can also host many parasite species, yet few studies address the entire parasite community of a gammarid population, precluding a more dynamic understanding of the food web. We set out to identify and quantify the parasite community of Gammarus lacustris to understand the contributions of the amphipod and its parasites to the Takvatn food web. We identified seven parasite taxa: a direct life cycle gregarine, Rotundula sp., and larval stages of two digenean trematode genera, two cestodes, one nematode, and one acanthocephalan. The larval parasites use either birds or fishes as final hosts. Bird parasites predominated, with trematode Plagiorchis sp. having the highest prevalence (69%) and mean abundance (2.7). Fish parasites were also common, including trematodes Crepidostomum spp., nematode Cystidicola farionis , and cestode Cyathocephalus truncatus (prevalences 13, 6, and 3%, respectively). Five parasites depend entirely on G. lacustris to complete their life cycle. At least 11.4% of the overall parasite diversity in the lake was dependent on G. lacustris , and 16% of the helminth diversity required or used the amphipod in their life cycles. These dependencies reveal that in addition to being a key prey item in subarctic lakes, G. lacustris is also an important host for maintaining parasite diversity in such ecosystems.

Takvatn↗

USGS2016

FishVis, A regional decision support tool for identifying vulnerabilities of riverine habitat and fishes to climate change in the Great Lakes Region

Climate change is expected to alter the distributions and community composition of stream fishes in the Great Lakes region in the 21st century, in part as a result of altered hydrological systems (stream temperature, streamflow, and habitat). Resource managers need information and tools to understand where fish species and stream habitats are expected to change under future conditions. Fish sample collections and environmental variables from multiple sources across the United States Great Lakes Basin were integrated and used to develop empirical models to predict fish species occurrence under present-day climate conditions. Random Forests models were used to predict the probability of occurrence of 13 lotic fish species within each stream reach in the study area. Downscaled climate data from general circulation models were integrated with the fish species occurrence models to project fish species occurrence under future climate conditions. The 13 fish species represented three ecological guilds associated with water temperature (cold, cool, and warm), and the species were distributed in streams across the Great Lakes region. Vulnerability (loss of species) and opportunity (gain of species) scores were calculated for all stream reaches by evaluating changes in fish species occurrence from present-day to future climate conditions. The 13 fish species included 4 cold-water species, 5 cool-water species, and 4 warm-water species. Presently, the 4 cold-water species occupy from 15 percent (55,000 kilometers [km]) to 35 percent (130,000 km) of the total stream length (369,215 km) across the study area; the 5 cool-water species, from 9 percent (33,000 km) to 58 percent (215,000 km); and the 4 warm-water species, from 9 percent (33,000 km) to 38 percent (141,000 km). Fish models linked to projections from 13 downscaled climate models projected that in the mid to late 21st century (2046–65 and 2081–2100, respectively) habitats suitable for all 4 cold-water species and 4 of 5 cool-water species under present-day conditions will decline as much as 86 percent and as little as 33 percent, and habitats suitable for all 4 warm-water species will increase as much as 33 percent and as little as 7 percent. This report documents the approach and data used to predict and project fish species occurrence under present-day and future climate conditions for 13 lotic fish species in the United States Great Lakes Basin. A Web-based decision support mapping application termed “FishVis” was developed to provide a means to integrate, visualize, query, and download the results of these projected climate-driven responses and help inform conservation planning efforts within the region.

Great Lakes Region↗

USGS2026

Short-term estuarine phytoplankton dynamics in response to hurricanes along the Gulf Coast of America: A Variational Autoencoder (VAE) approach with satellite and bio-optical observations

Hurricanes drive diverse estuarine phytoplankton responses and can trigger cascading ecological and physicochemical impacts. Capturing these short-term dynamics requires high spatiotemporal resolution. Here, we applied a globally-applicable coastal ocean color algorithm, Variational Autoencoder (VAE), to Sentinel-2 MSI imagery for chlorophyll- a (Chl- a ) estimation and validated its strong performance across the northern Gulf coast of America (GoA) estuaries, including Galveston Bay (TX), Barataria-Terrebonne Estuary (LA), Apalachicola Estuary (FL) and Tampa Bay (FL). The test set showed strong performance (MAE: 1.44 mg m −3 ; RMSE: 17.7 mg m −3 ; slope: 0.86; median symmetric accuracy: 30.33%). The validated VAE was then applied to 76 Sentinel-2 MSI images to assess phytoplankton biomass responses to hurricanes Harvey (2017), Michael (2018), Ida (2021), Francine (2024), Helene (2024), and Milton (2024) in the GoA estuaries. Results showed that hurricane disturbances on Chl- a typically lasted 3–5 weeks. Estuarine waters west (left) of hurricane tracks showed a rapid decline in Chl- a (∼5 mg m −3 ) due to elevated turbidity from heavy rainfall, and wind-driven flushing in the estuary, followed by a rebound over about two weeks, with Chl- a increasing approximately 10–15 mg m −3 above pre-storm levels. In contrast, right-side waters showed a slower response, likely from oligotrophic seawater intrusion driven by the hurricane's counterclockwise rotation. Post-storm observations showed increased freshwater phytoplankton like chlorophytes and cyanobacteria dominating estuaries, while shelf-waters exhibited elevated dinoflagellates (e.g., Karenia brevis bloom after Hurricane Milton). These results highlight the spatial heterogeneity of hurricane impacts on estuarine phytoplankton dynamics, which may trigger cascading effects on biogeochemical cycling and food webs, potentially prolonging ecosystem recovery.

Alabama, Florida, Louisiana, Mississippi, Texas↗

USGS2000

Primary food resources in the Sacramento-San Joaquin Delta

The Sacramento-San Joaquin River Delta, a complex mosaic of tidal freshwater habitats, is now a focus of ecosystem rehabilitation because of changes in critical functions associated with its geographic location at the landestuary interface. One of these functions is the production, transport, and transformation of organic matter that constitutes the “primary food supply,” that is, the food supply to the base of the food web. Interest in the primary food supply is motivated by evidence for sub-optimal food quantity or quality at trophic levels that support fish recruitment, including primary consumers such as clams, mysids, cladocerans, rotifers, and native copepods. We used the historical data set to examine the magnitudes of the most important organic matter sources for the Delta, the factors underlying their interannual and longer-term variability, and the implications of ecosystem rehabilitation actions for these sources. Here, we present a summary of the first phase of the analysis, including the quantitative importance of different organic matter sources and some of the hydrological controls on their year-to-year variability. The full report of this first phaseincluding data sources, the methods of calculation, and references, is in press elsewhere (Jassby and Cloern forthcoming). The historical data analysis is part of a larger project in which measurements of stable isotopes and biogeochemical markers, and experiments on organic matter biodegradation and zooplankton growth rates, are being used collectively to define the primary food resources and their quality.

California↗

USGS2013

Topobathymetric model of Mobile Bay, Alabama

Topobathymetric Digital Elevation Models (DEMs) are a merged rendering of both topography (land elevation) and bathymetry (water depth) that provides a seamless elevation product useful for inundation mapping, as well as for other earth science applications, such as the development of sediment-transport, sea-level rise, and storm-surge models. This 1/9-arc-second (approximately 3 meters) resolution model of Mobile Bay, Alabama was developed using multiple topographic and bathymetric datasets, collected on different dates. The topographic data were obtained primarily from the U.S. Geological Survey (USGS) National Elevation Dataset (NED) (http://ned.usgs.gov/) at 1/9-arc-second resolution; USGS Experimental Advanced Airborne Research Lidar (EAARL) data (2 meters) (http://pubs.usgs.gov/ds/400/); and topographic lidar data (2 meters) and Compact Hydrographic Airborne Rapid Total Survey (CHARTS) lidar data (2 meters) from the U.S. Army Corps of Engineers (USACE) (http://www.csc.noaa.gov/digitalcoast/data/coastallidar/). Bathymetry was derived from digital soundings obtained from the National Oceanic and Atmospheric Administration’s (NOAA) National Geophysical Data Center (NGDC) (http://www.ngdc.noaa.gov/mgg/geodas/geodas.html) and from water-penetrating lidar sources, such as EAARL and CHARTS. Mobile Bay is ecologically important as it is the fourth largest estuary in the United States. The Mobile and Tensaw Rivers drain into the bay at the northern end with the bay emptying into the Gulf of Mexico at the southern end. Dauphin Island (a barrier island) and the Fort Morgan Peninsula form the mouth of Mobile Bay. Mobile Bay is 31 miles (50 kilometers) long by a maximum width of 24 miles (39 kilometers) with a total area of 413 square miles (1,070 square kilometers). The vertical datum of the Mobile Bay topobathymetric model is the North American Vertical Datum of 1988 (NAVD 88). All the topographic datasets were originally referenced to NAVD 88 and no transformations were made to these input data. The NGDC hydrographic, multibeam, and trackline surveys were transformed from mean low water (MLW) or mean lower low water (MLLW) to NAVD 88 using VDatum (http://vdatum.noaa.gov). VDatum is a tool developed by the National Geodetic Survey (NGS) that performs transformations among tidal, ellipsoid-based, geoid-based, and orthometric datums using calibrated hydrodynamic models. The vertical accuracy of the input topographic data varied depending on the input source. Because the input elevation data were derived primarily from lidar, the vertical accuracy ranges from 6 to 20 centimeters in root mean square error (RMSE). he horizontal datum of the Mobile Bay topobathymetric model is the North American Datum of 1983 (NAD 83), geographic coordinates. All the topographic and bathymetric datasets were originally referenced to NAD 83, and no transformations were made to the input data. The bathymetric surveys were downloaded referenced to NAD 83 geographic, and therefore no horizontal transformations were required. The topbathymetric model of Mobile Bay and detailed metadata can be obtained from the USGS Web sites: http://nationalmap.gov/.

Alabama↗

USGS2017

Can we save large carnivores without losing large carnivore science?

Large carnivores are depicted to shape entire ecosystems through top-down processes. Studies describing these processes are often used to support interventionist wildlife management practices, including carnivore reintroduction or lethal control programs. Unfortunately, there is an increasing tendency to ignore, disregard or devalue fundamental principles of the scientific method when communicating the reliability of current evidence for the ecological roles that large carnivores may play, eroding public confidence in large carnivore science and scientists. Here, we discuss six interrelated issues that currently undermine the reliability of the available literature on the ecological roles of large carnivores: (1) the overall paucity of available data, (2) reliability of carnivore population sampling techniques, (3) general disregard for alternative hypotheses to top-down forcing, (4) lack of applied science studies, (5) frequent use of logical fallacies, and (6) generalisation of results from relatively pristine systems to those substantially altered by humans. We first describe how widespread these issues are, and given this, show, for example, that evidence for the roles of wolves ( Canis lupus ) and dingoes ( Canis lupus dingo ) in initiating trophic cascades is not as strong as is often claimed. Managers and policy makers should exercise caution when relying on this literature to inform wildlife management decisions. We emphasise the value of manipulative experiments and discuss the role of scientific knowledge in the decision-making process. We hope that the issues we raise here prompt deeper consideration of actual evidence, leading towards an improvement in both the rigour and communication of large carnivore science.

Food Webs↗

USGS2020

Direct and indirect effects of a keystone engineer on a shrubland-prairie food web

Keystone engineers are critical drivers of biodiversity throughout ecosystems worldwide. Within the North American Great Plains, the black‐tailed prairie dog is an imperiled ecosystem engineer and keystone species with well‐documented impacts on the flora and fauna of rangeland systems. However, because this species affects ecosystem structure and function in myriad ways (i.e., as a consumer, a prey resource, and a disturbance vector), it is unclear which effects are most impactful for any given prairie dog associate. We applied structural equation models (SEM) to disentangle direct and indirect effects of prairie dogs on multiple trophic levels (vegetation, arthropods, and birds) in the Thunder Basin National Grassland. Arthropods did not show any direct response to prairie dog occupation, but multiple bird species and vegetation parameters were directly affected. Surprisingly, the direct impact of prairie dogs on colony‐associated avifauna (Horned Lark [ Eremophila alpestris ] and Mountain Plover [ Charadrius montanus ]) had greater support than a mediated effect via vegetation structure, indicating that prairie dog disturbance may be greater than the sum of its parts in terms of impacts on localized vegetation structure. Overall, our models point to a combination of direct and indirect impacts of prairie dogs on associated vegetation, arthropods, and avifauna. The variation in these impacts highlights the importance of examining the various impacts of keystone engineers, as well as highlighting the diverse ways that black‐tailed prairie dogs are critical for the conservation of associated species.

Wyoming↗

USGS2026

Nutritional content of phytoplankton communities under ice

The effects of winter environmental conditions on lake ecology can be highly variable. Ice and overlying snow isolate the water below, impeding exchange of materials among water, atmosphere, and the watershed. Even with these limitations, biological communities under the ice can persist, where cold tolerant taxa can be especially abundant. Because many under-ice taxa tend to have a suite of unsaturated lipids that enable them to maintain metabolic function during cold conditions, under-ice biological communities may contain highly nutritious resources for higher level consumers relative to warmer, open-water conditions. To examine the effects of ice presence on under-ice biological productivity and nutritional quality, we aggregated data on under-ice physical, chemical, and biological variables from several existing databases. These data are among the most comprehensive, publicly available environmental and phytoplankton data that can be used to compare under-ice and open-water conditions at the community level. To understand how phytoplankton compositional shifts under ice can precipitate shifts in total algal nutritional content available to consumers relative to open water conditions, we merged characteristic phytoplankton fatty acid profiles with phytoplankton community composition data. Our results suggest that even though photosynthetically active radiation under ice is dramatically reduced by snow cover and opaque ice conditions, algal communities can be highly productive. Furthermore, these under-ice communities tend to be dominated by coldwater taxa, which are associated with elevated essential polyunsaturated fatty acids and reduced saturated fatty acids. Saturated fatty acids tend to be most associated with phytoplankton communities in the summer when cyanobacteria are prevalent, while winter communities tend to be most associated with high polyunsaturated fatty acids. As ice duration and quality continue to shift with increasing temperatures worldwide, phytoplankton assemblages are likely to exhibit altered nutritional profiles that have direct and indirect effects on food webs.

Ecopshere↗

USGS2002

Parasite (Ribeiroia ondatrae) infection linked to amphibian malformations in the western United States

Parasites and pathogens can influence the survivorship, behavior, and very structure of their host species. For example, experimental studies have shown that trematode parasites can cause high frequencies of severe limb malformations in amphibians. In a broad-scale field survey covering parts of California, Oregon, Washington, Idaho, and Montana, we examined relationships between the frequency and types of morphological abnormalities in amphibians and the abundance of trematode parasite infection, pH, concentrations of 61 pesticides, and levels of orthophosphate and total nitrate. We recorded severe malformations at frequencies ranging from 1% to 90% in nine amphibian species from 53 aquatic systems. Infection of larvae by the trematode Ribeiroia ondatrae was associated with, and functionally related to, higher frequencies of amphibian limb malformations than found in uninfected populations (≤5%). Parasites were concentrated around the basal tissue of hind limbs in infected anurans, and malformations associated with infection included skin webbings, supernumerary limbs and digits, and missing or malformed hind limbs. In the absence of Ribeiroia, amphibian populations exhibited low (0-5%) frequencies of abnormalities involving missing digits or distal portions of a hind limb. Species were affected differentially by the parasite, and Ambystoma macrodactylum, Hyla regilla, Rand aurora, R. luteiventris, and Taricha torosa typically exhibited the highest frequencies of abnormalities. None of the water-quality variables measured was associated with malformed amphibians, but aquatic snail hosts (Planorbella spp.) were significant predictors of the presence and abundance of Ribeiroia infection. Morphological comparisons of adult specimens of Ribeiroia collected from different sites and raised in experimental definitive hosts suggested that all samples represented the same species - R. ondatrae. These field results, coupled with experimental research on the effects of Ribeiroia on amphibians, demonstrate that Ribeiroia infection is an important and widespread cause of amphibian limb malformations in the western United States. The relevance of trematode infection to declines of amphibian populations and the influence of habitat modification on the pathology and life cycle of Ribeiroia are emphasized as areas requiring further research.

Ecological Monographs↗

USGS2000

Interim report on the scientific investigations in the Animas River watershed, Colorado to facilitate remediation decisions by the U.S. Bureau of Land Management and the U.S. Forest Service, March 29, 2000 meeting, Denver, Colo.

INTRODUCTION The joint U.S. Department of the Interior and U.S. Department of Agriculture Abandoned Mine Lands Initiative (AMLI) was developed as a collaborative effort between the Federal land management agencies (FLMA, that is the U.S. Bureau of Land Management and the U.S. Forest Service) and the U.S. Geological Survey (USGS) in 1996. The stated goal of the AML Initiative was to develop a strategy for gathering and communicating the scientific information needed to develop effective and cost-efficient remediation of abandoned mines within the framework of a watershed. Four primary objectives of the AMLI are to: 1. Provide the scientific information needed (in the short-term) by the FLMAs to make decisions related to the design and implementation of cleanup actions, 2. Develop a multi-disciplined, multi-division approach that integrates geologic, hydrologic, geochemical and ecological information into a knowledge base for sound decision making, 3. Transfer technologies developed within the scientific programs of the USGS to the field and demonstrate their suitability to solve real, practical problems, and 4. Establish working relationships among involved members of land management and regulatory agencies within the framework of a watershed approach to the cleanup of abandoned mines. Long-term process-based research, including development of analytical tools, is recognized as being critical to the long-term success in remediating watersheds impacted by historical mining activities (AML 5-year plan, http://amli.usgs.gov/amli). In a meeting of Federal agencies (U.S. Bureau of Land Management [BLM], U.S. Bureau of Reclamation [BOR], U.S. National Park Service [NPS], U.S. Forest Service [USFS], the U.S. Environmental Protection Agency [EPA], the U.S. Fish and Wildlife Service [F&WS]), and State agencies (Colorado Division of Public Health and Environment, Colorado Division of Mines and Geology), several watersheds were examined within the state whose water quality was presumed to be impacted by historical mining activities. The Animas River watershed (fig. 1) was selected by the State and Federal agencies as one of two watersheds in the U.S. to be studied in detail by the USGS in the AML Initiative. Beginning in October 1997, each of the four Divisions of the USGS (Water Resources, Geologic, Biological Resources, and National Mapping) initiated a collaborative integrated science study of the watershed. Funds were provided from USGS base funding to each of the four Divisions in response to the priorities set by Congressional action and within the flexibility provided by the budgetary framework funding individual research programs. The AML Initiative provides for a five-year focused scientific effort in the two watersheds with final synthesis of the scientific results from each to be published in 2001. Publications are released on the AML web site on a regular basis (http://amli.usgs.gov/amli). On March 29, 2000, the USGS hosted a meeting for the BLM and USFS to discuss remediation options that were under consideration for the summer of 2000. The purpose of this report is to provide an overview of the scientific rational provided by the USGS to meet objective one above, and to summarize our preliminary interpretations of our data. Additional information from sites on private lands have been collected by the State of Colorado, EPA, and the ARSG. Unfortunately, these data have not been fully supplied to the USGS so our conclusions are based only upon our data. These interpretations provide science-based constraints on possible remediation options to be considered by the FLMA, the State, and local property owners in the Animas River watershed. The report is presented in outline format to facilitate discussion of remediation options at the March 29, 2000 meeting. Not all historical mining sites within the watershed are on public lands. This should not be construed to be a final report of the USGS

Denver↗

USGS2015

Spatial and temporal variation in marine birds in the north Gulf of Alaska: The value of marine bird monitoring within Gulf Watch Alaska

Birds offer useful insights into marine ecosystems. Marine birds are responsive to spatial and temporal variation in the environment, that often originates with fluctuations in oceanographic and climatic drivers and permeates up through food webs to conspicuous top predators such as seabirds (Coyle and Pinchuk 2005, Speckman et al. 2005, Gonzales-Solis et al. 2009, Cushing et al., this report). In that way, marine birds are excellent assimilators, samplers, and indicators of the status of marine environments (Montevecchi 1993, Piatt et al. 2007b, Zador et al. 2013). Marine bird responses to dynamic marine ecosystems can be detected in a variety of metrics, including abundance, distribution, and productivity. For example, in the northern Gulf of Alaska (GOA), decadal-scale variation in oceanographic conditions has been associated with dramatic shifts in prey composition and abundance (Anderson and Piatt 1999). In turn, these shifts were more closely correlated with changes in abundance of fish-eating birds of Prince William Sound (PWS), such as pigeon guillemots (Golet et al. 2002) and marbled and Kittlitz’s murrelets (Kuletz et al. 2011a, 2011b), than in the abundance of species that primarily consume plankton or benthic prey (Agler et al. 1999, Cushing et al., this report). Birds also are responsive to anthropogenic influences in marine environments, including commercial fishing, contamination, introduction of non-native species, coastal development, offshore resource extraction, and vessel traffic. A major anthropogenic perturbation in the northern GOA was the 1989 Exxon Valdez oil spill, in which marine birds suffered high immediate mortality (Piatt and Ford 1996). Additionally, several species showed long-term evidence of declines in the oiled areas of PWS (Lance et al. 2001), as well as impacts to reproductive success years later (Golet et al. 2002). However, the degree of direct impact and vulnerability to chronic injury, which was related to exposure to lingering oil, varied widely among species (see Esler et al., this report). Research and monitoring directed at documenting the timelines and mechanisms of wildlife recovery following the Exxon Valdez oil spill led to an unprecedented understanding of oil spill effects on marine birds, as well as previously unknown information about marine bird ecology in the northern GOA. Quantifying effects of anthropogenic influences requires an understanding of variation in marine bird abundance, distribution, and productivity, in relation to naturally occurring dynamics in marine environments continued marine bird work as part of Gulf Watch Alaska will facilitate this. In addition to their value as indicators of marine conditions and anthropogenic influences, marine birds are protected under the Migratory Bird Treaty Act and are managed by the U.S. Fish and Wildlife Service (USFWS). Marine birds have high societal value from a wide variety of interests (e.g., tourism, bird watching, hunting, mythology), and are an important source of subsistence foods in Alaska (Naves and Braem 2014). Because of the conservation interest in marine birds, as well as their value for indicating the status of marine ecosystems, monitoring of marine birds is an important component of many ocean monitoring programs, including Gulf Watch Alaska.

Alaska↗

USGS2008

Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling.

Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of abundance of rare and patchily distributed species and is particularly appropriate when sampling in all patches is impossible, but a global estimate of abundance is required.

Ecology↗

USGS2023

Pelagic food web interactions in a large invaded ecosystem: Implications for reintroducing a native top predator

A series of species introductions, overexploitation, and habitat modification preceded the extirpation of Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi; LCT), historically the apex predator, from Lake Tahoe, California-Nevada, USA. Studies evaluating limiting factors for LCT emphasise the need to elucidate food web interactions, yet important knowledge gaps regarding trophic interactions among nonnative pelagic fishes and invertebrates remain. We quantified the abundance and consumption demand of planktivores with an emphasis on kokanee ( Oncorhynchus nerka ) and Mysis diluviana . We synthesised this new information with existing information for lake trout ( Salvelinus namaycush ). The seasonal supply of copepods satisfied the consumption demand of kokanee, but only supported low feeding and growth rates. Kokanee relied heavily on Mysis as prey, an unusual result. Mysis exhibited a high degree of herbivory initially followed by heavier consumption on copepods by larger individuals. Consumption demand for Mysis on copepods exceeded that of kokanee during all seasons. Mysis contributed to over 50% of the annual energy budget for lake trout up to 625 mm. Consumption of Mysis by lake trout and kokanee represented a significant source of mortality when compared to the production of Mysis . Predation on kokanee was sustainable, only involved lake trout >625 mm, and was focused on prespawning aggregations. Despite the presence of Mysis -fueled lake trout, kokanee have persisted; a noteworthy pattern when considering the negative responses of kokanee to nonnative lake trout and Mysis observed elsewhere. This pattern suggests that there may still be an effective niche for LCT in the invaded Lake Tahoe ecosystem.

California, Nevada↗

USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California↗

USGS2010

Methylmercury cycling, bioaccumulation, and export from agricultural and non-agricultural wetlands in the Yolo Bypass

This 18-month field study addresses the seasonal and spatial patterns and processes controlling methylmercury (MeHg) production, bioaccumulation, and export from natural and agricultural wetlands of the Yolo Bypass Wildlife Area (YBWA). The data were collected in conjuntion with a Proposition 40 grant from the State Water Resources Control Board in support of the development of Best Management Practices (BMP's) for reducing MeHg loading from agricultural lands in the wetland-dominated Yolo Bypass to the Sacramento-San Joaquin River Delta. The four managemenr-based questions addressed in this study were: 1. Is there a different among agricultural and managfed wetland types in terms of Me Hg dynamic (production, degradation, bioaccumulation, or export)? 2. Does water residence time influence MeHg dynamics? 3. Does the application of sulfate-based fertilizer impact MeHg production rates? 4. Does the presence (or absence) of vegetation influence MeHg production rates? Measurements of MeHg concentrations in sediment, water, and biota (plants, invertebrates, and fish) were made to assess management-level patterns in five wetland types, which included three type of shallowly-flooded agricultural wetlands (white rice, wild rice, and fallow) and two types of managed wetlands (permanently and seasonally flooded). To strengthen our understanding of the processes underlying the seasonal and spatial patterns of MeHg cycling, additional exploratory factors were measured including ancillary sediment and water quality parameters, stable isotope fractionation (oxygen, sulfur, carbon, and nitrogen), photodemethylation rates, and daily-integrated hydrologic budgets. Samples and field data were collected from May 2007 to July 2008, and nearly all sample analyses were completed by September 2008 as per the Quality Assurance Program Plan (QAPP) requirements. Although wetland type was a major factor that drove the study design, within-field hydrology also proved to be an important factor controlling aqueous MeHg and total mercury (THg) concentrations and export. Overall, agricultural wetlands exhibited higher MeHg concentrations in overlying water, sediment, and biota than did managed seasonal and permanent wetlands. This appears to be partly due to higher rates of sediment in microbial production of MeHg on agricultural wetlands during the fall through spring period. Both sulfate- and iron-reducing bacteria have been implicated in the MeHg production process, and both were demonstrably active in all wetlands studied; however, sulfate-reducing bacteria were not stimulated by the addition of sulfate-based fertilizer to agricultural wetlands, suggesting that easily-degraded (labile) organic matter, rather than sulfate, was limiting their activity in these field types. The data suggest that agriculturally-managed soils promoted MeHg production through 1) enhanced microbial activity via higher temperatures and larger pools of labile carbon, and 2) enhanced pools of microbially available inorganic divalent mercury (Hg(II)) resulting from a decrease in reduced-sulfur, solid-phase minerals under oxic or only mildly reducing conditions. MeHg mass balances were assessed by comparing filed-specific MeHg loads for inlets vs. outlet flows. The overall mass balance for MeHg in surface water during the summer irrigation period (June - September 2007) indicated little to no net MeHg export from the six agricultural wetlands taken as a whole. Of the six agricultural wetlands, there was net overall MeHg export from two fields (one fallow and one white rice) during August, and from four of the six fields (one fallow, one white rice, and two wild rice) during September) Over the entire summer irrigation period, two of the fields (one fallow and one wild rive) showed net MeHg export, and the other four fields showed wither net import or no significant change. Rates of measured photomethylation and exchange between sediment and water pools suggest that both processes may be responsible for the lack of MeHg export. Despite significant differences during winter months between fields in surface water concentrations of MeHg, MeHg loads were not calculated in mid-winter because flood waters had overtopped field boundaries and field fidelity could not be established. During the summer 2007 irrigation season, surface water out-flows from agricultural wetlands were 9%-36% of inlet flows, and evaporation rates explained most of this water loss, with infiltration likely accounting for the remainder. Unfiltered aqueous MeHg concentrations increased from <1 ng L -1 in source waters to up to 10 ng L -1 in agricultural wetland drains during the summer irrigation period. Increases in solute concentration caused by evapoconcentration were estimated by determining concentration factors (outflow/inflow) for chloride (a conservative dissolved constituent) and by measuring oxygen isotope ratios ( 18 O/ 16 O, expressed as δ 18 O) in water. Increases in MeHg concentration from inflows-to-outflows exceeded those caused by evapoconcentration on several fields during the summer irrigation season. This was especially true when initial surface water MeHg concentrations were low, as seen in the southern block of fields receiving irrigation water directly from the Toe Drain. The northern block of fields received irrigation water from Greens Lake, which included Toe Drain water plus recirculated drain water from other agricultural fields within the Yolo Bypass and west of the Yolo Bypass; as such, the northern fields showed a smaller percentage increase in MeHg concentration because initial MeHg concentrations in surface water inflows were greater than in inputs to the southern fields. Mercury concentrations in fish were greater in agricultural wetlands white rice and wild rice) than in the two permanently flooded wetlands. Additionally, Hg concentrations in biota showed a general increase from inlets to outlets withing agricultural wetlands, but not within permanent wetlands. This was particular evident in white rice fields where caged western mosquitofish at the outlets had Hg concentrations that were more than 4 times higher than in caged fish held at the inlets. Similar spatial patterns in Hg bioaccumulation in agricultural and permanent wetlands were seen for wild populations of western mosquitofish and Mississippi silversides. In contrast to fish, invertebrates, such as water-boatman (Corixidae) and back swimmers (Notonectidae), had greater Hg concentrations in permanent wetlands than in tempoarirly flooded agricultural wetlands, Fish THg concentrations were weakly correlated with water MeHg,a and not correlated with sediment MeHg. In contrast, invertebrate MeHg concentrations were more strongly correlated with sediment MeHg than with water MeHg concentrations. These results illustrate the complexity of MeHg bioaccumulation through food webs and indicate the importance of simultaneously using multiple biosentinels when monitoring MeHg production and bioaccumulation. Despite high sediment production rates and water concentrations in agricultural wetlands, MeHg export was physically limited by hydrologic export for all wetlands studied. We suggest that load reduction is maximized by limiting water throughout, but that on-site biota exposure is maximized by this loner water residence time. While field-specific hydrologic loads could not be fully quantified during flood conditions in February 2008, we suggest that the primary period of MeHg export from Yolo Bypass Wildlife Area is during those winter flooding periods when overall microbial activity and MeHg production in agricultural soils is fueled by the decomposition of rice straw, and when hydrologic flowthrough is maximal. Local stakeholders participated in two workshops related to this study, demonstrating an interest in understanding factors controlling MeHg production, export, and bioaccumulation. The results of this field study show that permanently flooded, naturally vegetated wetlands are unlikely to a large source of MeHg production within the YBWA, in contrast with agriculturally-managed wetlands. MeHg loading to Toe Drain waters of the Yolo Bypass may be reduced by lowering rated of hydrologic export from agricultural wetlands during the growing season and especially during rice harvest, However, under these water-holding conditions, biota living within agricultural wetlands may thus be exposed to higher MeHg concentrations in surface water, As observed in this study, rapid bioacculumaltion over a 2-month period led to MeHg concentrations in invertebrates and fish more than 6 and 11 times higher, respectively, than proposed TMDL target values to protect wildlife (0.03 ppm ww). The results of this field study, together with the information from YBWA stakeholders, provide a more definitive understanding of how MeHg cycling and bioaccumulation respond to habitat differences and specific management practices. These results directly address 4 core components of CBDA's Mercury Strategy for the Bay-Delta Ecosystem (Wiener et al., 2003a): a) Quantification and evaluation of THg and MeHg sources, b) Quantification of effects of ecosystem restoration on MeHg exposure, c) Assessment of ecological risk, and d) Identification and testing of potential management approaches for reducing MeHg contamination. In addition, the quantitative results reported here assess the effect of current land use practices in the Yolo Bypass MeHg production, bioaccumulation and export, and provide process-based advice towards achieving current goals of the RWQCB-CVR's Sacramento -- San Joaquin Delta Estuary TMDL for Methyl & Total Mercury (Wood et al., 2010b). Further work is necessary to evaluate biotic exposure in the Yolo Bypass Wildlife Area at higher trophic levels (e.g. birds), to quantify winter hydrologic flux of MeHg to the larger Delta ecosystem, and to evaluate rice straw management options to limit labile carbon supplies to surface sediment during winter months. In summary, agricultural management of rice fields -- specifically the periodic flooding and production of easily degraded organic matter -- promotes the production of MeHg beyond rates seen in naturally vegetated wetlands, whether seasonally or permanently flooded., The exported load from MeHg from these agricultural wetlands may be controlled by limiting hydrologic export from fields to enhance on-site MeHg removal processes, but the tradeoff is that this impoundement increases Me Hg exposure to resident organisms.

California↗

USGS2019

Salmon, forage fish, and kelp

Kelp beds are prominent features of northeast Pacific coastlines. They are seasonal in nature, as are the communities that use them. Here, juvenile and adult Chinook salmon ( Oncorhynchus tshawytscha ) – key components of northeast Pacific marine food webs that link plankton and forage fishes to endangered killer whales – have just arrived at the coastal kelp beds (left) and are feeding on the large schools of forage fish such as young‐of‐the‐year herring, which are also migrating in great numbers near the shore. Juvenile herring and smelt will soon move offshore to grow and feed, and finally return as adults to spawn along shorelines. Rapid growth is critical to the survival of young salmon. They quickly learn to work together to herd the small, skittish prey into tight groups. The kelp beds play an important role for both the salmon and their prey, providing refuge for feeding salmon and enhanced prey resources for hungry forage fish, which in turn feed incessantly at the surface of the kelp beds, except when they are disrupted by lightning‐fast attacks by marauding salmon. By October, much of the kelp will be gone, as will the juvenile salmon and forage fish, replaced by their adult congeners (right) that have traveled for years and hundreds of miles to continue the cycle. Globally, kelp forests are in flux. Disturbances, including those induced by climate change, may have serious implications not only for this critical nearshore phase of salmon and forage fish, but also for the future viability of our cold‐water northeast Pacific marine ecosystems.

Frontiers in Ecology and the Environment↗

USGS2018

Trophic pathways supporting Arctic grayling in a small stream on the Arctic Coastal Plain, Alaska

Beaded streams are prominent across the Arctic Coastal Plain (ACP) of Alaska, yet prey flow and food web dynamics supporting fish inhabiting these streams are poorly understood. Arctic grayling ( Thymallus arcticus ) are a widely distributed upper-level consumer on the ACP and migrate into beaded streams to forage during the short 3-month open-water season. We investigated energy pathways and key prey resources that support grayling in a representative beaded stream, Crea Creek. We measured terrestrial invertebrates entering the stream from predominant riparian vegetation types, prey types supporting a range of fish size classes, and how riparian plants and fish size influenced foraging habits. We found that riparian plants influenced the quantity of terrestrial invertebrates entering Crea Creek; however, these differences were not reflected in fish diets. Prey type and size ingested varied with grayling size and season. Small grayling (<15 cm fork length (FL)) consumed mostly aquatic invertebrates early in the summer, and terrestrial invertebrates later in summer, while larger fish (>15 cm FL) foraged most heavily on ninespine stickleback ( Pungitius pungitius ) throughout the summer, indicating that grayling can be insectivorous and piscivorous, depending on size. These findings underscore the potential importance of small streams in Arctic ecosystems as key summer foraging habitats for fish. Understanding trophic pathways supporting stream fishes in these systems will help interpret whether and how petroleum development and climate change may affect energy flow and stream productivity, terrestrial–aquatic linkages and fishes in Arctic ecosystems.

Alaska↗

USGS2024

Establishment of terrestrial mammals on former reservoir beds following large dam removal on the Elwha River, Washington, USA

Terrestrial wildlife species are important yet often overlooked taxa in the recovery of ecosystems following dam removal. Their presence can shape ecosystem recovery, signal restoration of ecosystem function, and influence food web dynamics and nutrient transfer. We used camera traps to examine seasonal use of two former reservoir beds and an upstream reference reach by the mammalian community following the removal of two large dams on the Elwha River, Washington, USA. For certain taxa, we compared current species use to data collected prior to dam removal. Camera traps revealed use by at least fifteen mammal species, including but not limited to American black bear ( Ursus americanus ), Columbian black-tailed deer ( Odocoileus hemionus columbianus ), Roosevelt elk ( Cervus elaphus roosevelti ), puma ( Puma concolor ), coyotes ( Canis latrans ), bobcats ( Lynx rufus ), and snowshoe hares ( Lepus americanus ). Coyotes were found mostly lower in the watershed outside the Olympic National Park boundary, while other species were distributed throughout the restoration area. We did not see major differences in species composition between the restoration areas and the upstream reference reach, though number of detections across study reaches differed for most species. Unlike previous findings, black bears were observed across all seasons in this study, suggesting a shift in seasonal use since dam removal. Full restoration of the terrestrial wildlife community could take decades to unfold, but early patterns demonstrate rapid establishment and use by wildlife on new riparian surfaces that are expected to continue to evolve with restoration of fish and vegetation communities.

Washingotn↗