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At least 1,711 records · Page 95Linked to original sources
USGS2020

Gear comparison study for sampling nekton in Barataria Basin marshes

This project was funded by the Louisiana Trustee Implementation Group (LA TIG) to support decisions related to investments in long-term monitoring. The LA TIG seeks to ensure long-term monitoring informs coastal restoration activities with the goal of sustaining and improving fisheries impacted by the Deepwater Horizon (DWH) Oil Spill. The project objective was to compare nekton catch across an estuarine gradient using different sampling gear with the goal of identifying trade-offs among nekton sampling approaches. To accomplish this objective, Louisiana Department of Wildlife and Fisheries (LDWF), The Water Institute of the Gulf (the Institute), Dynamic Solutions, LLC, Louisiana State University Agricultural Center (LSU AgCenter), and the U.S. Geological Survey (USGS) completed a field gear comparison study from 2018 to 2019. This work compared electrofisher and seine sampling at 12 fixed stations in Barataria Basin using data collected by LDWF. In addition, and in conjunction with LDWF monthly sampling, the same 12 fixed stations were sampled in May 2019 using a throw trap to compare nekton catch and assemblages collected with the throw trap, seine and electrofisher. LDWF has been conducting seine sampling since 1986, and seine data are used by the State of Louisiana to assess juvenile shrimp, crab and fish abundances, sizes and overall assemblages. In 2018, LDWF began conducting electrofisher sampling at 12 Barataria Basin seine stations in order to determine if the two gear types sample similar species and assemblages for potential future replacement of long-term seine sampling with electrofishing. Throw traps were included as they provide density estimates, which are ultimately the desired statistic used in modeling trophic webs, and are used in assessing habitat restoration outcomes. The project compared the nekton catch and assemblages collected using seine, electrofisher, and throw trap data from marsh edge habitats located across the estuarine gradient in Barataria Basin. Specifically, catch per unit effort (CPUE), species richness, species-specific total length (mm) distribution and nekton assemblages were compared between gear types. The first dataset was collected in May 2019 with throw trap (Appendix A), seine (LDWF data), and electrofisher (LDWF data) gear, and the second dataset (collected by LDWF) spanned 14 months of seine and electrofisher monthly sampling occurring from May 2018 through June 2019 at 12 stations in Barataria Basin. Key findings include that gear bias was not evident across the range of water quality conditions (salinity, temperature, o C, dissolved oxygen, mg L-1 , turbidity, NTU; Appendix B: scatter plots) captured during this pilot study, but differences in nekton catch per unit effort (CPUE) and assemblages were evident between gear types. However, those differences largely depended on the parameter examined. For example, the overall CPUE was highest for electrofishing, followed by seine, and then throw trap. When grass shrimp (the most abundant taxon collected) were removed from CPUE, the electrofisher and seine results were similar in CPUE. When CPUE was corrected for gear efficiency and total area sampled, the throw trap had the highest reported density of nekton sampled, followed by electrofisher and seine results. Electrofishing captured the highest number of species, which included more unique species compared to seine or throw trap catches, though all gear types captured at least one unique species. These highlight a need for caution in interpreting assemblage and density data when comparing datasets derived from different sampling methodologies. These key findings can help inform implementation and interpretation of long-term monitoring data in Louisiana as management decisions are made about coastal restoration projects to sustain and improve fisheries. There are trade-offs in selecting gear types for estuarine nekton monitoring of density, abundance, species richness, and assemblages. The table below (Table 1) summarizes some considerations when selecting gear types for long-term monitoring of estuarine nekton. In addition to biological and ecological considerations, other important considerations include cost, the labor required to conduct sampling, logistics, and potential uncertainties related to how effective each gear type is for sampling the wide variety of conditions found across Louisiana’s coastal habitats. For example, although electrofishing may capture higher CPUE, the equipment is more expensive to obtain and maintain compared to the other gear types. Most importantly, this table highlights differences in the nekton assemblages sampled by each gear type; this consideration is critical when designing the goals of a long-term monitoring program as it will inform how the data can be used and interpreted in the future. This report provides caveats, assumptions, and recommendations that can help support the Louisiana Coastal Protection and Restoration Authority (CPRA), LDWF and the LA TIG in comparing data from different gear types, and in making decisions for future monitoring. Findings from this study are limited to the range of water quality conditions occurring during these data collection events; these data and analyses could benefit from sampling across a wider range of water quality conditions, and collection of habitat structure and bottom type data which are not routinely collected but critically influence nekton. Further investigation examining how relative differences detected in key species abundances between gear types might impact ecosystem indicators and energetics in a modeled food web would provide valuable input to understand outputs of the Comprehensive Aquatic System Model for Barataria Basin, including the potential impacts of nekton monitoring decisions on food web models.

Louisiana↗
USGS2014

Causal networks clarify productivity-richness interrelations, bivariate plots do not

Perhaps no other pair of variables in ecology has generated as much discussion as species richness and ecosystem productivity, as illustrated by the reactions by Pierce (2013) and others to Adler et al.'s (2011) report that empirical patterns are weak and inconsistent. Adler et al. (2011) argued we need to move beyond a focus on simplistic bivariate relationships and test mechanistic, multivariate causal hypotheses. We feel the continuing debate over productivity–richness relationships (PRRs) provides a focused context for illustrating the fundamental difficulties of using bivariate relationships to gain scientific understanding. Pierce (2013) disputes Adler et al.'s (2011) conclusion that bivariate productivity–richness relationships (PRRs) are ‘weak and variable’. He argues, instead, that relationships in the Adler et al. data are actually strong and, further, that failure to adhere to the humped-back model (HBM; sensu Grime 1979) threatens scientists' ability to advise conservationists. Here, we show that Pierce's reanalyses are invalid, that statistically significant boundary relations in the Adler et al. data are difficult to detect when proper methods are used and that his advice neither advances scientific understanding nor provides the quantitative forecasts actually needed by decision makers. We begin by examining Grimes' HBM through the lens of causal networks. We first translate the ideas contained in the HBM into a causal diagram, which shows explicitly how multiple processes are hypothesized to control biomass production and richness and their interrelationship. We then evaluate the causal diagram using structural equation modelling and example data from a published study of meadows in Finland. Formal analysis rejects the literal translation of the HBM and reveals additional processes at work. This exercise shows how the practice of abstracting systems as causal networks (i) clarifies possible hypotheses, (ii) permits explicit testing and (iii) provides more powerful and useful predictions. Building on the Finnish meadow example, we contrast the utility of bivariate plots compared with structural equation models for investigating underlying processes. Simulations illustrate the fallibility of bivariate analysis as a means of supporting one theory over another, while models based on causal networks can quantify the sensitivity of diversity patterns to both management and natural constraints. A key piece of Pierce's critique of Adler et al.'s conclusions relies on upper boundary regression which he claims to reveal strong relationships between production and richness in Adler et al.'s original data. We demonstrate that this technique shows strong associations in purely random data and is invalid for Adler et al.'s data because it depends on a uniform data distribution. We instead perform quantile regression on both the site-level summaries of the data and the plot-level data (using mixed-model quantile regression). Using a variety of nonlinear curve-fitting approaches, we were unable to detect a significant humped-shape boundary in the Adler et al. data. We reiterate that the bivariate productivity–richness relationships in Adler et al.'s data are weak and variable. We urge ecologists to consider productivity–richness relationships through the lens of causal networks to advance our understanding beyond bivariate analysis. Further, we emphasize that models based on a causal network conceptualization can also provide more meaningful guidance for conservation management than can a bivariate perspective. Measuring only two variables does not permit the evaluation of complex ideas nor resolve debates about underlying mechanisms.

Functional Ecology↗
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↗
USGS2007

Use of chemical analysis and assays of semipermeable membrane devices extracts to assess the response of bioavailable organic pollutants in streams to urbanization in six metropolitan areas of the United States

Studies to assess the effects of urbanization on stream ecosystems are being conducted as part of the U.S. Geological Survey’s National Water-Quality Assessment (NAWQA) Program. The overall objectives of these studies are to (1) determine how hydrologic, geomorphic, water quality, habitat, and biological characteristics respond to land-use changes associated with urbanization in specific environmental settings, and (2) compare these responses across environmental settings. As part of an integrated assessment, semipermeable membrane devices (SPMDs) were deployed in streams along a gradient of urban land-use intensity in and around Atlanta, Georgia; Raleigh-Durham, North Carolina; and Denver-Fort Collins, Colorado, in 2003; and Dallas-Fort Worth, Texas; Milwaukee-Green Bay, Wisconsin; and Portland, Oregon, in 2004. Sites were selected to avoid point-source discharge and to minimize natural variability within each of the six metropolitan areas. In addition to standard chemical analysis for hydrophobic organic contaminants, three assays were used to address mixtures and potential toxicity: (1) Fluoroscan provides an estimate of the total concentration of polycyclic aromatic hydrocarbons (PAHs); (2) the P450RGS assay indicates the presence and levels of aryl hydrocarbon receptor agonists; and (3) Microtox® measures toxicological effects on photo-luminescent bacteria. Of the 140 compounds targeted or identified by gas chromatography/mass spectrometry analysis in this study, 67 were not detected. In terms of numbers and types of compounds, the following were detected: 2 wood preservatives, 6 insecticides (parent compounds), 5 herbicides, 22 polycyclic aromatic hydrocarbons, 2 dibenzofurans, 4 polychlorinated biphenyls, 7 compounds associated with fragrances or personal care products, 4 steroids associated with wastewater, 5 polydibromated diphenyl ethers (flame retardants), 3 plasticizers, 3 antimicrobials/disinfectants, and 3 detergent metabolites. Of the 73 compounds detected and three assays utilized, 29 were detected in 25 percent or more of the streams and were strongly related to increases in urban intensity (defined as having a Spearman’s rho > 0.5 with percent urban land cover) in at least one of the six metropolitan areas investigated. These 29 endpoints included 16 PAHs, a wood preservative (pentachloroanisole), 2 insecticides (chlorpyrifos and chlordane), 3 herbicides (benfluralin, trifluralin, and dacthal), a synthetic musk (hexahydrohexamethylcyclopentabenzopyran, HHCB), 2 furans (methyldibenzofuran and benzo[b]naphtho[2,3-d]furan), and a flame retardant (BDE 47). In addition, the number of compounds detected and results of the Fluoroscan and P450RGS assays were strongly related to urban intensity. Average water concentrations estimated from SPMDs were compared to screening benchmarks for the protection of human health and aquatic life; of the 14 compounds with available benchmarks, 3 compounds (anthracene, dieldrin, and diazinon) exceeded those levels in one or more streams. Both dieldrin and anthracene exceeded their respective benchmarks in seven streams, and diazinon in only one stream. There were more exceedances in Milwaukee-Green Bay and Raleigh-Durham than in the other metropolitan areas, and there were no exceedances in Dallas-Fort Worth. The six metropolitan areas studied differed in the number and types of endpoints related to urban intensity, probably from a combination of factors governing source strength, transport, and fate of hydrophobic compounds. The number of endpoints strongly related to urban intensity ranged from 3 in Dallas-Fort Worth and Portland to 21 in Raleigh-Durham. High frequencies of detection and strong correlations with urban land cover for pyrogenic PAHs (such as unsubstituted 4-ringed PAHs) in all six metropolitan areas indicate that these compounds are an important component of urbanization, regardless of location. Pentachloroanisole, dibenzofurans, and petrogenic PAHs (alkylated PAHs and heterocyclic dibenzothiophenes) were frequently detected and strongly related to urban intensity in Atlanta, Raleigh-Durham, Milwaukee-Green Bay, and Denver-Fort Collins. Two insecticides were related to urban intensity: chlorpyrifos in Atlanta, Raleigh-Durham, and Dallas-Fort Worth; and chlordane in Raleigh-Durham. Three herbicides were strongly related to urban intensity: trifluralin in Atlanta and Raleigh-Durham; benfluralin in Atlanta, and dacthal in Denver-Fort Collins. The detection frequencies for most wastewater indicator compounds were too low to establish relations with urban intensity. Of the wastewater compounds analyzed, HHCB in Raleigh-Durham and Denver-Fort Collins, and BDE 47 in Denver-Fort Collins and Dallas-Forth Worth, had the strongest relations with urban intensity. In addition to pyrogenic PAHs, levels of aryl hydrocarbon receptor agonists (as measured by the P450RGS assay) were strongly related to increasing urban intensity in all six metropolitan areas. PAHs were the only group of aryl hydrocarbon agonists consistently detected and related with urban intensity in all six metropolitan areas. It is unknown which compounds in the SPMDs caused the increased response in the P450RGS assay because the SPMDs likely contained many aryl hydrocarbon receptor agonists not quantified by chemical analysis. It is clear that bioavailable, aryl hydrocarbon receptor agonists increase in streams with increasing urban intensity in the basin. Potential toxicity mediated by this metabolic pathway should be considered in integrated assessments of the response of aquatic biota to urbanization.

Scientific Investigations Report↗
USGS2008

Mormon cricket control in Utah's west desert - Evaluation of impacts of the pesticide Diflubenzuron on nontarget arthropod communities

Grasshopper and Mormon cricket (Orthoptera) populations periodically build to extremely high numbers and can cause significant economic damage in rangelands and agricultural fields of the Great Plains and Intermountain West. A variety of insecticides have been applied to control population outbreaks, with recent efforts directed at minimizing impacts to nontarget fauna in treated ecosystems. A relatively new insecticide for control of Orthoptera is diflubenzuron, which acts to inhibit chitin production, ultimately causing death during the molt following ingestion of the insecticide. All arthropods, including insects, mites, and crustaceans, use chitin to build their exoskeletons and will die if they are unable to produce it during the next molt. Diflubenzuron is not taxon specific—it affects all arthropods that ingest it, except adult insects, which do not molt. Consequently, application of this pesticide has the potential to significantly reduce not only target populations but all terrestrial and aquatic arthropods within treatment zones. Some research has been done in the Great Plains on the impact of diflubenzuron on nontarget arthropods in the context of grasshopper-control programs, but no work has been done in the Great Basin in Mormon cricket-control areas. This study was instigated in anticipation of the need for extensive control of Orthoptera outbreaks in Utah’s west desert during 2005, and it was designed to sample terrestrial and aquatic arthropod communities in both treated and untreated zones. Three areas were sampled: Grouse Creek, Ibapah, and Vernon. High mortality of Mormon cricket eggs in the wet, cool spring of 2005 restricted the need to control Mormon crickets to Grouse Creek. Diflubenzuron was applied (aerial reduced agent-area treatment) in May 2005. Terrestrial and aquatic arthropod communities were sampled before and after application of diflubenzuron in the Grouse Creek area of northwestern Utah in May and June of 2005. In July 2005, U.S. Geological Survey scientists sampled areas in Ibapah and Vernon that had been treated with diflubenzuron in 2004, along with adjacent untreated areas. Pitfall traps at four treated and four untreated sites were used to collect ground-dwelling terrestrial arthropods. Semiquantitative sweep surveys of aquatic habitats were made before treatment, 2 weeks after treatment, and 4 months after treatment (after leaf fall) at Grouse Creek. One-year post-treatment samples were collected by using the same methods for terrestrial and aquatic arthropods at Ibapah and Vernon in July 2005 (treatments applied in June 2004). More than 124,000 terrestrial arthropods were collected from the three study areas, and more than 200,000 aquatic invertebrates were collected in the aquatic samples. Direct effects of diflubenzuron on aquatic and terrestrial arthropod communities were not apparent in our data from Grouse Creek. The treatment was designed to avoid spraying pesticide on water bodies, and no measurable effects on aquatic communities from either springs or streams were observed, with the exception of the reduction of taxa richness at Vernon (a result confounded by elevational differences in the treatment and nontreatment zones). Some trends indicate diflubenzuron may affect some terrestrial taxa. Ant communities showed some differences, with possible lag effects at Ibapah and Vernon. Forelius was more abundant, while Tapinoma and, perhaps, Formica declined in treated zones in these two study areas. Solenopsis also was more numerous at treated Ibapah sites but varied without pattern at Vernon. Scorpions were abundant at Grouse Creek and Ibapah but rare at Vernon. Numbers did not change during several weeks at Grouse Creek, but at Ibapah, numbers at treated sites were much lower than at untreated sites. The Lygaeidae (in the order Hemiptera) were more abundant in the untreated zones at Ibapah and Vernon, although significantly so only at Ibapah. Lygaeidae were absent from the treated zone at Grouse Creek (before and after treatment) but were present after treatment in the untreated zone. Additional research is recommended to determine more explicitly whether these taxa are sensitive to diflubenzuron applications in the Great Basin.

Utah↗
USGS2012

The FOBIMO (FOraminiferal BIo-MOnitoring) initiative—Towards a standardised protocol for soft-bottom benthic foraminiferal monitoring studies

The European Community Marine Strategy Framework Directive (MSFD) was established to provide guidelines for monitoring the quality of marine ecosystems. Monitoring the status of marine environments is traditionally based on macrofauna surveys, for which standardised methods have been established. Benthic foraminifera are also good indicators of environmental status because of their fast turnover rates, high degree of specialisation, and the preservation of dead assemblages in the fossil record. In spite of the growing interest in foraminiferal bio-monitoring during the last decades, no standardised methodology has been proposed until today. The aim of the FOraminiferal BIo-MOnitoring (FOBIMO) expert workshop, held in June 2011 at Fribourg, Switzerland, which assembled 37 scientists from 24 research groups and 13 countries, was to develop a suite of standard methods. This paper presents the main outcome of the workshop, a list of motivated recommendations with respect to sampling devices, sample storage, treatment, faunal analysis and documentation. Our recommendations fulfil the criteria imposed both by scientific rigour and by the practical limitations of routine studies. Hence, our aim is to standardise methodologies used in bio-monitoring only and not to limit the use of different methods in pure scientific studies. Unless otherwise stated, all recommendations concern living (stained) benthic foraminiferal assemblages. We have chosen to propose two types of recommendations. Mandatory recommendations have to be followed if a study wants to qualify as sound and compatible to the norms. The most important of these recommendations are the interval from 0 to 1 cm below the sediment surface has to be sampled, and an interface corer or box corer that keeps the sediment surface intact is to be used for offshore surveys. A grab sampler must not be deployed in soft sediments. Three replicate samples are to be taken and analysed separately. Samples are to be washed on a 63-μm screen, and the living benthic foraminiferal fauna of the > 125 μm fraction is to be analysed. Splits are to be picked and counted entirely, and all counted foraminifera from at least one replicate per station have to be stored in micropalaeontological slides. Census data, supplementary laboratory data and microslides have to be archived. Advisory recommendations are to sample in autumn, to have a sample size of 50 cm 2 or a tube of 8 cm inner diameter, to use > 70% ethanol as a preservative, rose Bengal at a concentration of 2 grams per litre for staining, and a staining time of at least 14 days. The split size should be defined by a target value of 300 specimens, heavy liquid separation should be avoided, and the 63–125 μm fraction or deeper sediment levels may be considered in some environments. We are convinced that the application of this protocol by a large number of scientists is a necessary first step to a general acceptance of benthic foraminifera as a reliable tool in bio-monitoring studies.

Marine Micropaleontology↗
USGS2015

Estimating sturgeon abundance in the Carolinas using side-scan sonar

Sturgeons (Acipenseridae) are one of the most threatened taxa worldwide, including species in North Carolina and South Carolina. Populations of Atlantic Sturgeon Acipenser oxyrinchus in the Carolinas have been significantly reduced from historical levels by a combination of intense fishing and habitat loss. There is a need for estimates of current abundance, to describe status, and for estimates of historical abundance in order to provide realistic recovery goals. In this study we used N -mixture and distance models with data acquired from side-scan sonar surveys to estimate abundance of sturgeon in six major sturgeon rivers in North Carolina and South Carolina. Estimated abundances of sturgeon greater than 1 m TL in the Carolina distinct population segment (DPS) were 2,031 using the count model and 1,912 via the distance model. The Pee Dee River had the highest overall abundance of any river at 1,944 (count model) or 1,823 (distance model). These estimates do not account for sturgeon less than 1 m TL or occurring in riverine reaches not surveyed or in marine waters. Comparing the two models, the N -mixture model produced similar estimates using less data than the distance model with only a slight reduction of estimated precision.

Marine and Coastal Fisheries: Dynamics, Management↗
USGS2017

Movements of Atlantic Sturgeon of the Gulf of Maine inside and outside the geographically defined Distinct Population Segment

Identification of potential critical habitat, seasonal distributions, and movements within and between river systems is important for protecting the Gulf of Maine (GOM) Distinct Population Segment of Atlantic Sturgeon. To accomplish these objectives, we captured Atlantic Sturgeon in four GOM rivers (Penobscot, Kennebec system, Saco, and Merrimack), and tagged 144 (83.3–217.4 cm TL) internally with uniquely coded acoustic transmitters. Tagged fish were detected between 2006 to 2014 by primary receiver arrays deployed in the four GOM rivers or opportunistically on a secondary group of receivers deployed within the GOM and along the continental shelf. Atlantic Sturgeon tagged in the four rivers were documented at three spawning areas in the Kennebec system in June and July, including one that became accessible in 1999 when the Edwards Dam was removed. After being tagged, the majority (74%) of Atlantic sturgeon were detected in the estuaries of the four GOM rivers, primarily from May through October. Tagged fish spent most of their time in saline water in the Saco River and Merrimack River, moved into brackish water in the Penobscot River, and were found in saline, brackish, and fresh water in the Kennebec system. Approximately 70% of the tagged fish were detected in GOM coastal waters, and aggregated in the Bay of Fundy (May–January), offshore of the Penobscot River (September-February and May), offshore of the Kennebec River (September–February), in Saco Bay and the Scarborough River (July–November), and along the eastern Massachusetts coast between Cape Ann and Cape Cod (April–February). Nine tagged Atlantic sturgeon (7%) left the GOM, three of which moved as far north as Halifax in Canada and six moved as far south as the James River in Virginia. Information from this study will be used to make recommendations to avoid, reduce or mitigate the impacts of in-water projects and on Atlantic sturgeon.

Maine, Massachusetts, New Hampshire↗
USGS2015

Forecasting the effects of fertility control on overabundant ungulates: White-tailed deer in the National Capital Region

Overabundant populations of ungulates have caused environmental degradation and loss of biological diversity in ecosystems throughout the world. Culling or regulated harvest is often used to control overabundant species. These methods are difficult to implement in national parks, other types of conservation reserves, or in residential areas where public hunting may be forbidden by policy. As a result, fertility control has been recommended as a non-lethal alternative for regulating ungulate populations. We evaluate this alternative using white-tailed deer in national parks in the vicinity of Washington, D.C., USA as a model system. Managers seek to reduce densities of white-tailed deer from the current average (50 deer per km 2 ) to decrease harm to native plant communities caused by deer. We present a Bayesian hierarchical model using 13 years of population estimates from 8 national parks in the National Capital Region Network. We offer a novel way to evaluate management actions relative to goals using short term forecasts. Our approach confirms past analyses that fertility control is incapable of rapidly reducing deer abundance. Fertility control can be combined with culling to maintain a population below carrying capacity with a high probability of success. This gives managers confronted with problematic overabundance a framework for implementing management actions with a realistic assessment of uncertainty.

PLoS ONE↗
USGS2013

Rivermouth alteration of agricultural impacts on consumer tissue δ 15 N

Terrestrial agricultural activities strongly influence riverine nitrogen (N) dynamics, which is reflected in the δ 15 N of riverine consumer tissues. However, processes within aquatic ecosystems also influence consumer tissue δ 15 N. As aquatic processes become more important terrestrial inputs may become a weaker predictor of consumer tissue δ 15 N. In a previous study, this terrestrial-consumer tissue δ 15 N connection was very strong at river sites, but was disrupted by processes occurring in rivermouths (the ‘rivermouth effect’). This suggested that watershed indicators of N loading might be accurate in riverine settings, but could be inaccurate when considering N loading to the nearshore of large lakes and oceans. In this study, the rivermouth effect was examined on twenty-five sites spread across the Laurentian Great Lakes. Relationships between agriculture and consumer tissue δ 15 N occurred in both upstream rivers and at the outlets where rivermouths connect to the nearshore zone, but agriculture explained less variation and had a weaker effect at the outlet. These results suggest that rivermouths may sometimes be significant sources or sinks of N, which would cause N loading estimates to the nearshore zone that are typically made at discharge gages further upstream to be inaccurate. Identifying definitively the controls over the rivermouth effect on N loading (and other nutrients) will require integration of biogeochemical and hydrologic models.

Great Lakes↗
USGS2016

Controls on the geochemical evolution of Prairie Pothole Region lakes and wetlands over decadal time scales

One hundred sixty-seven Prairie Pothole lakes, ponds and wetlands (largely lakes) previously analyzed chemically during the late 1960’s and early to mid-1970’s were resampled and reanalyzed in 2011–2012. The two sampling periods differed climatically. The earlier sampling took place during normal to slightly dry conditions, whereas the latter occurred during and immediately following exceptionally wet conditions. As reported previously in Mushet et al. ( 2015 ), the dominant effect was expansion of the area of these lakes and dilution of their major ions. However, within that context, there were significant differences in the evolutionary pathways of major ions. To establish these pathways, we employed the inverse modeling computer code NetpathXL. This code takes the initial and final lake composition and, using mass balance constrained by the composition of diluting waters, and input and output of phases, calculates plausible geochemical evolution pathways. Despite the fact that in most cases major ions decreased, a subset of the lakes had an increase in SO 4 2− . This distinction is significant because SO 4 2− is the dominant anion in a majority of Prairie Pothole Region wetlands and lakes. For lakes with decreasing SO 4 2− , the proportion of original lake water required for mass balance was subordinate to rainwater and/or overland flow. In contrast, lakes with increasing SO 4 2− between the two sampling episodes tended to be dominated by original lake water. This suite of lakes tended to be smaller and have lower initial SO 4 2− concentrations such that inputs of sulfur from dissolution of the minerals gypsum or pyrite had a significant impact on the final sulfur concentration given the lower dilution factors. Thus, our study provides context for how Prairie Pothole Region water bodies evolve geochemically as climate changes. Because wetland geochemistry in turn controls the ecology of these water bodies, this research contributes to the prediction of the impact of climate change on this important complex of ecosystems.

North Dakota↗
USGS2023

Plant water-use strategies predict restoration success across degraded drylands

Plant strategies for coping with water limitation are likely to mediate restoration outcomes in degraded dryland ecosystems. Trade-offs in traits related to water acquisition and use can intensify in more arid environments, making their effects on dryland restoration success even more salient. However, isolating the effects of drought responses from those of other environmental factors, as well as identifying the specific drought resistance traits that influence restoration success, can be difficult. In the present study, we couple a controlled dry-down experiment with a cross-site restoration field trial of out-planted seedlings (RestoreNet) using a suite of dryland herbaceous plant species from the same seed sources. We quantified interspecific variation in physiological responses to drought, specifically reductions in stomatal conductance ( g s ) and stem water potential (SWP), by comparing well-watered control plants to those experiencing decreasing soil moisture. Drought responses of SWP and g s varied independently among species, but both were related to survival in the cross-site restoration field trial when effect sizes were aggregated across all sites. Responses were consistent with acquisitive water-use strategies resulting in greater success, where species with greater declines in SWP or weaker declines in g s under drought had greater survival. The correlation between SWP drought response and survival also intensified in sites with lower accumulated precipitation following restoration. Differences among functional groups revealed two different paths to restoration success: forbs that maintain high g s and narrow safety margins to maximize exploitation of moisture pulses before going into drought dormancy, or C 4 grasses that maintain efficient water uptake in drying soils while risking cavitation. C 3 grass species varied between these two strategies. Synthesis and applications . Taken together, the results of this study and others conducted at RestoreNet sites indicate that while a diversity of physiological responses to drought may exist in dryland plant communities, successfully restoring herbaceous species through out-planting in degraded conditions is likely to be achieved with species that maximize water uptake via one of two strategies, with tolerance of low SWP being particularly important in the most arid settings.

Journal of Applied Ecology↗
USGS2025

Physical habitat is more than a sediment issue: A multi-dimensional habitat assessment indicates new approaches for river management

Degraded physical habitat is a common stressor affecting river ecosystems and typically addressed in the United States (US) through a regulatory focus on sediment. However, a narrow regulatory focus on sediment may overlook other aspects of physical habitat and the processes for its creation, maintenance, and degradation. In addition, there exist few “ready-to-use” regional assessments of the multiple dimensions of physical habitat to better understand continuous patterns of condition and prioritize management efforts across a large spatial scale. In this study, we use rapid habitat monitoring data to train a machine-learning ( i.e., random forest) model to predict twelve physical habitat metrics for nearly 120,000 km of nontidal rivers and streams across the Chesapeake Bay watershed, US. We capture a range of habitat conditions driven by both natural variables and anthropogenic pressures. Covariation among habitat metrics indicated two major dimensions of habitat variation: 1) coarse bed substrate and hydromorphic heterogeneity and 2) bank stability and riparian condition. The model predicted localized changes from 2001 to 2019, and the predicted areas of deterioration roughly balanced improvements across the watershed, indicating little progress towards long-term watershed management goals. To evaluate connections to regulatory and management endpoints, we compared our physical habitat predictions to paired estimates of sediment and flow alteration across the region. Sediment concentrations were greater in reaches with less bank stability and lower riparian quality; however, the relation was weak for coarse bed condition metrics, including embeddedness, which is frequently used for establishing regulatory sediment restrictions. For flow alteration, most habitat metrics had lower scores with altered flow metrics, but metrics of instream habitat heterogeneity and coarse substrate condition were most strongly affected. Increased flashy, high flows negatively affected most metrics, but coarse substrate metrics were also negatively affected by greater low flow severity. This study highlights a potential disconnect between a narrow focus on regulatory sediment targets given the multiple dimensions and responses of physical habitat. A more holistic approach to physical habitat in management interventions – one that considers hydromorphic processes, diversity and variability in microhabitats, and explicit consideration of alterations to both low and high flows – may be warranted. By providing direct estimates of multiple aspects of physical habitat, this model can help support managers in the Chesapeake Bay watershed to better understand the range of habitat conditions, identify high-quality reaches for conservation, and target potential management actions tailored to localized conditions.

Delaware, Maryland, New York, Pennsylvania, Virgin↗
USGS2022

Disentangling direct and indirect effects of extreme events on coastal wetland communities

One of the primary ways in which climate change will impact coastal freshwater wetlands is through changes in the frequency, intensity, timing and distribution of extreme weather events. Disentangling the direct and indirect mechanisms of population- and community-level responses to extreme events is vital to predicting how species composition of coastal wetlands will change under future conditions. We extended static structural equation modelling approaches to incorporate system dynamics in a multi-year multispecies occupancy model to quantify the effects of extreme weather events on a coastal freshwater wetland system. We used data from an 8-year study (2009–2016) on St. Marks National Wildlife Refuge in Florida, USA, to quantify species-specific and community-level changes in amphibian and fish occupancy associated with two flooding events in 2012 and 2013. We examine how physical changes to the landscape, including potential changes in salinity and increased wetland connectivity, may have contributed to or exacerbated the effects of these extreme weather events on the biota of isolated coastal wetlands. We provide evidence that the primary effects of flooding on the amphibian community were through indirect mechanisms via changes in the composition of the sympatric fish community that may have had lethal (i.e. through direct predation) or non-lethal (i.e. through direct or indirect competitive interactions) effects. In addition, we have shown that amphibian species differed in their sensitivity to direct flooding effects and indirect changes in the fish community and wetland-specific conductance, which led to variable responses across the community. These effects led to the overall decline in amphibian species richness from 2009 to 2016, suggesting that wetland-breeding amphibian communities on St. Marks National Wildlife Refuge may not be resilient to predicted changes in coastal disturbance regimes because of climate change. Understanding both direct and indirect effects, as well as species interactions, is important for predicting the effects of a changing climate on individual species, communities and ecosystems.

Journal of Animal Ecology↗
USGS2024

Seasonal drought treatments impact plant and microbial uptake of nitrogen in a mixed shrub grassland on the Colorado Plateau

For many drylands, both long- and short-term drought conditions can accentuate landscape heterogeneity at both temporal (e.g., role of seasonal patterns) and spatial (e.g., patchy plant cover) scales. Furthermore, short-term drought conditions occurring over one season can exacerbate long-term, multidecadal droughts or aridification, by limiting soil water recharge, decreasing plant growth, and altering biogeochemical cycles. Here, we examine how experimentally altered seasonal precipitation regimes in a mixed shrub grassland on the Colorado Plateau impact soil moisture, vegetation, and carbon and nitrogen cycling. The experiment was conducted from 2015 to 2019, during a regional multidecadal drought event, and consisted of three precipitation treatments, which were implemented with removable drought shelters intercepting ~66% of incoming precipitation including: control (ambient precipitation conditions, no shelter), warm season drought (sheltered April–October), and cool season drought (sheltered November–March). To track changes in vegetation, we measured biomass of the dominant shrub, Ephedra viridis , and estimated perennial plant and ground cover in the spring and the fall. Soil moisture dynamics suggested that warm season experimental drought had longer and more consistent drought legacy effects (occurring two out of the four drought cycles) than either cool season drought or ambient conditions, even during the driest years. We also found that E. viridis biomass remained consistent across treatments, while bunchgrass cover declined by 25% by 2019 across all treatments, with the earliest declines noticeable in the warm season drought plots. Extractable dissolved inorganic nitrogen and microbial biomass nitrogen concentrations appeared sensitive to seasonal drought conditions, with dissolved inorganic nitrogen increasing and microbial biomass nitrogen decreasing with reduced soil volumetric water content. Carbon stocks were not sensitive to drought but were greater under E. viridis patches. Additionally, we found that under E. viridis , there was a negative relationship between dissolved inorganic nitrogen and microbial biomass nitrogen, suggesting that drought-induced increases in dissolved inorganic nitrogen may be due to declines in nitrogen uptake from microbes and plants alike. This work suggests that perennial grass plant–soil feedbacks are more vulnerable to both short-term (seasonal) and long-term (multiyear) drought events than shrubs, which can impact the future trajectory of dryland mixed shrub grassland ecosystems as drought frequency and intensity will likely continue to increase with ongoing climate change.

Ecology↗
USGS2014

Impacts of white-tailed deer on red trillium ( Trillium recurvatum ): defining a threshold for deer browsing pressure at the Indiana Dunes National Lakeshore

Overabundant white-tailed deer ( Odocoileus virginianus ) have been a concern for land managers in eastern North America because of their impacts on native forest ecosystems. Managers have sought native plant species to serve as phytoindicators of deer impacts to supplement deer surveys. We analyzed experimental data about red trillium ( Trillium recurvatum ), large flowered trillium ( T. grandiflorum ), nodding trillium ( T. cernuum ), and declined trillium ( T. flexipes ) growth in paired exclosure (fenced) plots and control (unfenced) plots from 2002 to 2010 at the Indiana Dunes National Lakeshore. The latter two species lacked replication, so statistical analysis was not possible. All red trillium plants were surveyed for height-to-leaf, effects of browsing, and presence of flowers. Data from individuals in 2009 demonstrated a sigmoidal relationship between height-to-leaf and probability of flowering. The relationship on moraine soils was shifted to taller plants compared to those on sand substrates, with respectively 50 percent flowering at 18 and 16 cm and 33 percent flowering at 16 and 14 cm height-to-leaf. On a plot basis, the proportion of plants flowering was influenced by height to leaf, duration of protection, and deviation in rainfall. The proportion of plants flowering increased ninefold in exclosures (28 percent) compared to control plots (3 percent) over the 8 years of protection. The mean height-to-leaf was a function of the interaction between treatment and duration, as well as red trillium density. Changes in height-to-leaf in control plots from year to year were significantly influenced by an interaction between change in deer density and change in snowfall depth. There was a significant negative correlation between change in deer density and snowfall depth. Plants in the exclosures increased in height at a rate of 1.5 cm yr −1 whereas control plants decreased in height by 0.9 cm yr −1 . In all, 78 percent of the control plots lacked flowering individuals over the 9 years of study, indicating that red trillium is being negatively affected by deer throughout the East Unit of the park. Of the five deer management zones studied, only one showed pre-impact height-to-leaf and flowering percentages in control plots that then declined after 2005. The results of this study demonstrate that Trillium species growing in the lands of the Indiana Dunes National Lakeshore are being suppressed reproductively by deer browsing. Specifically, we demonstrate, for the first time, the utility of using red trillium ( Trillium recurvatum ) height-to-leaf and percentage of flowering as indicators of the impacts of deer browsing. Application of the recommended thresholds demonstrates their utility in adopting red trillium as a phytoindicator of deer impact. Responses of plants to protection from deer suggest that deer culling might be necessary for 6 or more years for red trillium populations and rare trillium species to recover.

Indiana↗
USGS2019

Projected urban growth in the Southeastern USA puts small streams at risk

Future land-use development has the potential to profoundly affect the health of aquatic ecosystems in the coming decades. We developed regression models predicting the loss of sensitive fish (R2=0.39) and macroinvertebrate (R2=0.64) taxa as a function of urban and agricultural land uses and applied them to projected urbanization of the rapidly urbanizing Piedmont ecoregion of the southeastern USA for 2030 and 2060. The regression models are based on a 2014 investigation of water quality and ecology of 75 wadeable streams across the region. Based on these projections, stream kilometers experiencing >50% loss of sensitive fish and invertebrate taxa will nearly quadruple to 19,500 and 38,950 km by 2060 (16 and 32% of small stream kilometers in the region), respectively. Uncertainty was assessed using the 20 and 80% probability of urbanization for the land-use projection model and using the 95% confidence intervals for the regression models. Adverse effects on stream health were linked to elevated concentrations of contaminants and nutrients, low dissolved oxygen, and streamflow alteration, all associated with urbanization. The results of this analysis provide a warning of potential risks from future urbanization and perhaps some guidance on how those risks might be mitigated.

PLoS ONE↗
USGS2016

The relative contributions of disease and insects in the decline of a long-lived tree: a stochastic demographic model of whitebark pine (Pinus albicaulis)

Pathogens and insect pests have become increasingly important drivers of tree mortality in forested ecosystems. Unfortunately, understanding the relative contributions of multiple mortality agents to the population decline of trees is difficult, because it requires frequent measures of tree survival, growth, and recruitment, as well as the incidence of mortality agents. We present a population model of whitebark pine ( Pinus albicaulis ), a high-elevation tree undergoing rapid decline in western North America. The loss of whitebark pine is thought to be primarily due to an invasive pathogen (white pine blister rust; Cronartium ribicola ) and a native insect (mountain pine beetle; Dendroctonus ponderosae ). We utilized seven plots in Crater Lake National Park (Oregon, USA) where 1220 trees were surveyed for health and the presence of blister rust and beetle activity annually from 2003–2014, except 2008. We constructed size-based projection matrices for nine years and calculated the deterministic growth rate (λ) using an average matrix and the stochastic growth rate (λ s ) by simulation for whitebark pine in our study population. We then assessed the roles of blister rust and beetles by calculating λ and λ s using matrices in which we removed trees with blister rust and, separately, trees with beetles. We also conducted life-table response experiments (LTRE) to determine which demographic changes contributed most to differences in λ between ambient conditions and the two other scenarios. The model suggests that whitebark pine in our plots are currently declining 1.1% per year (λ = 0.9888, λ s = 0.9899). Removing blister rust from the models resulted in almost no increase in growth (λ = 0.9916, λ s = 0.9930), while removing beetles resulted in a larger increase in growth (λ = 1.0028, λ s = 1.0045). The LTRE demonstrated that reductions in stasis of the three largest size classes due to beetles contributed most to the smaller λ in the ambient condition. Our work demonstrates a method for assessing the relative effects of different mortality agents on declining tree populations, and it shows that the effects of insects and pathogens can be markedly different from one another. In our study, beetle activity significantly reduced tree population growth while a pathogen had minimal effect, thus management actions to stabilize our study population will likely need to include reducing beetle activity.

Forest Ecology and Management↗