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USGS2018

Mangrove forests in a rapidly changing world: Global change impacts and conservation opportunities along the Gulf of Mexico coast

Mangrove forests are highly-productive intertidal wetlands that support many ecosystem goods and services. In addition to providing fish and wildlife habitat, mangrove forests improve water quality, provide seafood, reduce coastal erosion, supply forest products, support coastal food webs, minimize flooding impacts, and support high rates of carbon sequestration. Despite their tremendous societal value, mangrove forests are threatened by many aspects of global change. Here, we examine the effects of global change on mangrove forests along the Gulf of Mexico coast, which is a valuable region for advancing understanding of global change impacts because the region spans multiple ecologically-relevant abiotic gradients that are representative of other mangrove transition zones across the world. We consider the historical and anticipated future responses of mangrove forests to the following aspects of global change: temperature change, precipitation change, accelerated sea-level rise, tropical cyclone intensification, elevated atmospheric carbon dioxide, eutrophication, invasive non-native species, and land use change. For each global change factor, we provide an initial global perspective but focus primarily on the three countries that border the Gulf of Mexico: United States, Mexico, and Cuba. The interactive effects of global change can have large ecological consequences, and we provide examples that highlight their importance. While some interactions between global change drivers can lead to mangrove mortality and loss, others can lead to mangrove expansion at the expense of other ecosystems. Finally, we discuss strategies for using restoration and conservation to maximize the adaptive capacity of mangrove forests to global change. To ensure that the ecosystem goods and services provided by mangrove forests continue to be available for future generations, there is a pressing need to better protect, manage, and restore mangrove forests as well as the adjacent ecosystems that provide opportunities for adaptation in response to global change.

Estuarine, Coastal and Shelf Science↗

USGS2003

Importance of benthic prey for fishes in coral reef-associated sediments

The importance of open, sandy substrate adjacent to coral reefs as habitat and a food source for fishes has been little studied in most shallow tropical waters in the Pacific, including Hawai'i. In this study, in Hanalei Bay, Hiwai'i, we identified and quantified the major invertebrate fauna (larger than 0.5 mm) in the well-characterized sands adjoining the shallow fringing reefs. Concurrently, we identified the fish species that seemed to make substantial use of these sand habitats, estimated their density there, sampled their gut contents to examine trophic links with the sand habitat, and made other observations and collections to determine the times, locations, and types of activity there. A variety of (mostly small) polychaeres were dominant in the sediments at most sampling stations, along with many small crustaceans (e.g., amphipods, isopods, ostracods, and small shrimps) and fair numbers of mollusks (especially bivalves) and small echinoids. Fish guts examined contained ???77% of the total number of benthic taxa collected, including nearly all those just listed. However, fish consumption was selective, and the larger shrimps, crabs, and small cryptic fishes were dominant in the diets of most of the numerous predator taxa. Diets of benthic-feeding fishes showed relatively low specific overlap. The fish fauna in this area included substrate-indifferent pelagics, species with various degrees of reef relatedness, reef-restricted species, and (at the other extreme) permanent cryptic sand dwellers. Data on occurrence and movements of fishes indicated that a band of sandy substrate several tens of meters wide next to the reef was an active area for fishes, and activity was considerably different at different times of day and for fish of different ages. These results imply an important trophic role for the benthos in these near-reef habitats in support of reef-associated fishes.

Pacific Science↗

USGS2007

Killer whales and marine mammal trends in the North Pacific - A re-examination of evidence for sequential megafauna collapse and the prey-switching hypothesis

Springer et al. (2003) contend that sequential declines occurred in North Pacific populations of harbor and fur seals, Steller sea lions, and sea otters. They hypothesize that these were due to increased predation by killer whales, when industrial whaling's removal of large whales as a supposed primary food source precipitated a prey switch. Using a regional approach, we reexamined whale catch data, killer whale predation observations, and the current biomass and trends of potential prey, and found little support for the prey-switching hypothesis. Large whale biomass in the Bering Sea did not decline as much as suggested by Springer et al., and much of the reduction occurred 50-100 yr ago, well before the declines of pinnipeds and sea otters began; thus, the need to switch prey starting in the 1970s is doubtful. With the sole exception that the sea otter decline followed the decline of pinnipeds, the reported declines were not in fact sequential. Given this, it is unlikely that a sequential megafaunal collapse from whales to sea otters occurred. The spatial and temporal patterns of pinniped and sea otter population trends are more complex than Springer et al. suggest, and are often inconsistent with their hypothesis. Populations remained stable or increased in many areas, despite extensive historical whaling and high killer whale abundance. Furthermore, observed killer whale predation has largely involved pinnipeds and small cetaceans; there is little evidence that large whales were ever a major prey item in high latitudes. Small cetaceans (ignored by Springer et al.) were likely abundant throughout the period. Overall, we suggest that the Springer et al. hypothesis represents a misleading and simplistic view of events and trophic relationships within this complex marine ecosystem. ?? 2007 by the Society for Marine Mammalogy.

Marine Mammal Science↗

USGS2015

Global trends in emerging viral diseases of wildlife origin

Fifty years ago, infectious diseases were rarely considered threats to wildlife populations, and the study of wildlife diseases was largely a neglected endeavor. Furthermore, public health leaders at that time had declared that “it is time to close the book on infectious diseases and the war against pestilence won,” a quote attributed to Dr. William H. Stewart in 1967. There is some debate whether he actually said these words; however, they reflect the widespread belief at that time (Spellberg, 2008). Leap forward to today, and the book on infectious diseases has been dusted off. There is general consensus that the global environment favors the emergence of infectious diseases, and in particular, diseases of wildlife origin (Taylor et al., 2001). Examples of drivers of these infectious diseases include climate and landscape changes, human demographic and behavior changes, global travel and trade, microbial adaptation, and lack of appropriate infrastructure for wildlife disease control and prevention (Daszak et al., 2001). The consequences of these emerging diseases are global and profound with increased burden on the public health system, negative impacts on the global economy and food security, declines and extinctions of wildlife species, and subsequent loss of ecosystem integrity. For example, 35 million people are currently living with HIV infection globally (http://www.who.int/gho/hiv/en); 400 million poultry have been culled since 2003 as a result of efforts to control highly pathogenic H5N1 avian influenza (http://www.fao.org/avianflu/en/index.html), and there are increasing biological and ecological consequences. Examples of health threats to biodiversity include the “spillover” of human diseases to great ape populations (Köndgen et al., 2008), the near-extirpation of the black-footed ferret from canine distemper and sylvatic plague (for a review see Abbott et al., 2012), and threats to Hawaiian forest birds from introduced pathogens such as avian malaria and avian pox (van Riper et al., 1986, 2002). There are also newly discovered pathogens or diseases that have resulted in population declines, and global extinctions of several species. Examples include Batrachochytrium dendrobatidis, which causes a cutaneous fungal infection of amphibians and is linked to declines of amphibians globally (Kriger and Hero, 2009); and recently discovered Pseudogymnoascus (Geomyces) destructans, the etiologic agent of white-nose syndrome (WNS), which has caused precipitous declines of North American bat species (Blehert et al., 2009). Furthermore, there is increasing evidence of the subsequent impacts on human and ecosystem health; for example, increasing risk of exposure to Lyme disease as a consequence of decreased biodiversity (LoGiudice et al., 2003) as well as the economic cost of the loss of bats due to decreased insect control services (Boyles et al., 2011). Figure A12-1 is a timeline of important diseases investigated by the U.S. Geological Survey since the 1970s, which illustrates three factors: 1. The unprecedented emergence of new pathogens and geographic spread of known pathogens since the 1990s; 2. Diseases are increasingly causing large-scale, negative impacts on wildlife populations and spreading over larger geographic areas rather than remaining localized; and 3. Diseases are increasingly of concern for multiple sectors, including public health, agriculture and wildlife management agencies. Of increasing concern are these novel diseases such as WNS as they are hard to anticipate, particularly devastating to human health or wildlife populations, challenging to manage, spread over large geographic areas in short time periods, and may result in ecological ripple effects that are difficult to predict. The following article provides examples of recently emerged viral diseases of wildlife origin. The examples have been selected to illustrate the drivers of emerging viral diseases, both novel pathogens and previously known diseases, the impacts of these diseases, as well as the role of wildlife both as “villains” or reservoirs as well as “victims” of these viral diseases. The article also discusses potential management strategies for emerging viral diseases in wildlife populations and future science directions in wildlife health to prevent, prepare, respond to, and recover from these disease events. Finally, the concept of One Health and its potential role in developing solutions to these issues of mutual concern is discussed.

Conference Paper↗

USGS2016

Nutrient dynamics of the Delta: Effects on primary producers

Increasing clarity of Delta waters, the emergence of harmful algal blooms, the proliferation of aquatic water weeds, and the altered food web of the Delta have brought nutrient dynamics to the forefront. This paper focuses on the sources of nutrients, the transformation and uptake of nutrients, and the links of nutrients to primary producers. The largest loads of nutrients to the Delta come from the Sacramento River with the San Joaquin River seasonally important, especially in the summer. Nutrient concentrations reflect riverine inputs in winter and internal biological processes during periods of lower flow with internal nitrogen losses within the Delta estimated at approximately 30% annually. Light regime, grazing pressure, and nutrient availability influence rates of primary production at different times and locations within the Delta. The roles of the chemical form of dissolved inorganic nitrogen in growth rates of primary producers in the Delta and the structure of the open-water algal community are currently topics of much interest and considerable debate. Harmful algal blooms have been noted since the late 1990s, and the extent of invasive aquatic macrophytes (both submerged and free-floating forms) has increased especially during years of drought. Elevated nutrient loads must be considered in terms of their ability to support this excess biomass. Modern sensor technology and networks are now deployed that make high-frequency measurements of nitrate, ammonium, and phosphate. Data from such instruments allow a much more detailed assessment of the spatial and temporal dynamics of nutrients. Four fruitful directions for future research include utilizing continuous sensor data to estimate rates of primary production and ecosystem respiration, linking hydrodynamic models of the Delta with the transport and fate of dissolved nutrients, studying nutrient dynamics in various habitat types, and exploring the use of stable isotopes to trace the movement and fate of effluent-derived nutrients.

California↗

USGS2021

Is there tree senescence? The fecundity evidence

Despite its importance for forest regeneration, food webs, and human economies, changes in tree fecundity with tree size and age remain largely unknown. The allometric increase with tree diameter assumed in ecological models would substantially overestimate seed contributions from large trees if fecundity eventually declines with size. Current estimates are dominated by overrepresentation of small trees in regression models. We combined global fecundity data, including a substantial representation of large trees. We compared size–fecundity relationships against traditional allometric scaling with diameter and two models based on crown architecture. All allometric models fail to describe the declining rate of increase in fecundity with diameter found for 80% of 597 species in our analysis. The strong evidence of declining fecundity, beyond what can be explained by crown architectural change, is consistent with physiological decline. A downward revision of projected fecundity of large trees can improve the next generation of forest dynamic models.

Proceedings of the National Academy of Sciences↗

USGS2014

Mercury cycling in agricultural and managed wetlands: a synthesis of methylmercury production, hydrologic export, and bioaccumulation from an integrated field study

With seasonal wetting and drying, and high biological productivity, agricultural wetlands (rice paddies) may enhance the conversion of inorganic mercury (Hg(II)) to methylmercury (MeHg), the more toxic, organic form that biomagnifies through food webs. Yet, the net balance of MeHg sources and sinks in seasonal wetland environments is poorly understood because it requires an annual, integrated assessment across biota, sediment, and water components. We examined a suite of wetlands managed for rice crops or wildlife during 2007–2008 in California's Central Valley, in an area affected by Hg contamination from historic mining practices. Hydrologic management of agricultural wetlands for rice, wild rice, or fallowed — drying for field preparation and harvest, and flooding for crop growth and post-harvest rice straw decay — led to pronounced seasonality in sediment and aqueous MeHg concentrations that were up to 95-fold higher than those measured concurrently in adjacent, non-agricultural permanently-flooded and seasonally-flooded wetlands. Flooding promoted microbial MeHg production in surface sediment of all wetlands, but extended water residence time appeared to preferentially enhance MeHg degradation and storage. When incoming MeHg loads were elevated, individual fields often served as a MeHg sink, rather than a source. Slow, horizontal flow of shallow water in the agricultural wetlands led to increased importance of vertical hydrologic fluxes, including evapoconcentration of surface water MeHg and transpiration-driven advection into the root zone, promoting temporary soil storage of MeHg. Although this hydrology limited MeHg export from wetlands, it also increased MeHg exposure to resident fish via greater in situ aqueous MeHg concentrations. Our results suggest that the combined traits of agricultural wetlands — slow-moving shallow water, manipulated flooding and drying, abundant labile plant matter, and management for wildlife — may enhance microbial methylation of Hg(II) and MeHg exposure to local biota, as well as export to downstream habitats during uncontrolled winter-flow events.

California↗

USGS2022

Pesticide exposure of wild bees and honey bees foraging from field border flowers in intensively managed agriculture areas

Bees are critical for food crop pollination, yet their populations are declining as agricultural practices intensify. Pollinator-attractive field border plantings (e.g. hedgerows and forb strips) can increase bee diversity and abundance in agricultural areas, however recent studies suggest these plants may contain pesticides. Pesticide exposure for wild bees in agricultural areas remains largely unknown, however this information is needed to inform agricultural practices and pesticide regulations meant to protect bees. It is important to determine whether border plantings that attract and support pollinators by providing floral resources may also deliver pesticides to them. In this study, we collected various samples for pesticide residue analysis including: multiple species of wild bees, honey bees, flowers from four types of bee-attractive field border plants, and soil. Silicone bands were also utilized as passive aerial samplers of pesticide residues. The five pesticides detected most frequently across all samples were the insecticide bifenthrin, the herbicides thiobencarb, metolaclor, and propanil, and the fungicide fluopyram. We detected the greatest number of parent pesticides in passive aerial samplers (24), followed by soil (21). Pesticides were also detected in field border plant flowers (16), which do not receive direct pesticides applications and many of which were not applied to adjacent field crops. Pesticide concentrations were lower in bees than in flowers but higher in bees than in soils. Pesticide residue per bee (ng/bee) increased with increasing wild bee size, though pesticide concentration (ng/g) did not increase. While honey bees and wild bees contained a similar number and concentration of pesticides overall, pesticide mixtures varied by bee type, and included some mixtures known to cause sublethal effects. The results from this study highlight the benefits of measuring more sample types to capture the total exposome of bees, including a greater range of bee species, as well as the need to consider exposure to pesticides at the landscape level.

California↗

USGS2020

Linkages between temperature, macroinvertebrates, and young-of-year Coho Salmon growth in surface-water and groundwater streams

Ecological resources for fishes in stream food webs shift over space and time, providing a complex template of available resources that can be used for growth. We tracked water temperature in conjunction with young-of-year Coho Salmon size, growth, and diet in 2 streams with contrasting thermal regimes: a groundwater stream with colder temperatures and lower thermal variability all year and a surface-water stream with greater thermal variability and warmer summer temperatures more conducive to young-of-year salmon growth. We hypothesized that fry emergence would occur when rearing conditions are optimal for growth and that, all else being equal, summer fish growth will be greater in the surface-water stream. Previous work on Coho Salmon phenology in these streams showed that peak fry emergence occurred at the same time in early summer in both streams. We measured salmon fry emergence in relation to thermal variability and macroinvertebrate prey availability with subsequent tracking of somatic growth, diet, and body size during the 1 st year of life in both streams. Macroinvertebrate prey availability was highest overall in the colder and thermally-stable groundwater stream than the surface-water stream. Prey availability was particularly high in the thalweg drift during peak fry emergence in the groundwater stream. There was no difference in Coho Salmon diet composition between streams, which included invertebrates from benthic, drift, and riparian habitats. We found no differences in young-of-year Coho Salmon body size, growth, or consumption between streams. Overall, our results suggest that large differences in thermal regimes do not necessarily translate to large differences in young-of-year Coho Salmon size, growth, or diet. Many variables can influence fish growth, and there is not always a direct connection between spatial and temporal dimensions of environmental variability and their cascading effects on young-of-year Coho Salmon growth during the 1 st summer of life.

Freshwater Science↗

USGS2025

Management strategy evaluation to assess trade-offs associated with invasive Blue Catfish fisheries and predation impacts

Objective Many species are intentionally introduced beyond their native range to provide benefits to humans (e.g., food, recreation, or biocontrol). However, introduced species can become invasive and can harm native species, prompting resource managers to explore options to simultaneously conserve native biota and enhance fishing opportunities. Management of Chesapeake Bay Blue Catfish Ictalurus furcatus is complicated because the species supports a renowned trophy fishery and commercial and recreational harvest but also negatively affects native species. Consequently, there is uncertainty and disagreement on how to balance trade-offs associated with varying stakeholder interests. Methods We used a management strategy evaluation to project Blue Catfish population dynamics into the future under different fishery policies to understand whether fishery yield, trophy fishing opportunities, and predation on the economically and ecologically important blue crab Callinectes sapidus could be optimized in the James River, a Chesapeake Bay subestuary. Results Simulated population trajectories indicated that objectives related to maintaining fisheries and conserving prey populations were in conflict. Policies that increased the yield and abundance of trophy-size Blue Catfish (≥100 cm total length) generally increased predation on the blue crab, which supports a valuable fishery. Intense harvest of smaller length-classes and protection of larger Blue Catfish yielded outcomes in which trophy fish abundance increased and blue crab predation declined compared to baseline conditions. However, these outcomes were generally associated with lower Blue Catfish yields after 25 years. There were zero scenarios in which the fishery yield increased and blue crab predation decreased after 25 years. Policies limiting the harvest of small Blue Catfish resulted in large population abundances, suggesting that reducing the abundance of small fish could be important for reducing impacts on native species. Conclusions This study supports the importance of management planning to develop objectives and performance measures based on an improved understanding of trade-offs associated with harvest management for a nonnative fish with economic value.

Virginia↗

USGS2020

A pan-African high-resolution drought index dataset

Droughts in Africa cause severe problems, such as crop failure, food shortages, famine, epidemics and even mass migration. To minimize the effects of drought on water and food security on Africa, a high-resolution drought dataset is essential to establish robust drought hazard probabilities and to assess drought vulnerability considering a multi- and cross-sectional perspective that includes crops, hydrological systems, rangeland and environmental systems. Such assessments are essential for policymakers, their advisors and other stakeholders to respond to the pressing humanitarian issues caused by these environmental hazards. In this study, a high spatial resolution Standardized Precipitation-Evapotranspiration Index (SPEI) drought dataset is presented to support these assessments. We compute historical SPEI data based on Climate Hazards group InfraRed Precipitation with Station data (CHIRPS) precipitation estimates and Global Land Evaporation Amsterdam Model (GLEAM) potential evaporation estimates. The high-resolution SPEI dataset (SPEI-HR) presented here spans from 1981 to 2016 (36 years) with 5 km spatial resolution over the whole of Africa. To facilitate the diagnosis of droughts of different durations, accumulation periods from 1 to 48 months are provided. The quality of the resulting dataset was compared with coarse-resolution SPEI based on Climatic Research Unit (CRU) Time Series (TS) datasets, Normalized Difference Vegetation Index (NDVI) calculated from the Global Inventory Monitoring and Modeling System (GIMMS) project and root zone soil moisture modelled by GLEAM. Agreement found between coarse-resolution SPEI from CRU TS (SPEI-CRU) and the developed SPEI-HR provides confidence in the estimation of temporal and spatial variability of droughts in Africa with SPEI-HR. In addition, agreement of SPEI-HR versus NDVI and root zone soil moisture – with an average correlation coefficient ( R ) of 0.54 and 0.77, respectively – further implies that SPEI-HR can provide valuable information for the study of drought-related processes and societal impacts at sub-basin and district scales in Africa. The dataset is archived in Centre for Environmental Data Analysis (CEDA) via the following link: https://doi.org/10.5285/bbdfd09a04304158b366777eba0d2aeb (Peng et al., 2019a).

Earth System Science Data↗

USGS2022

Assessing per- and polyfluoroalkyl substances (PFAS) in sediments and fishes in a large, urbanized estuary and the potential human health implications

The primary source of chronic exposures to per- and polyfluoroalkyl substances (PFASs) in humans is through the ingestion of contaminated foods and drinking water, with fish and other seafood being a major contributor. Nevertheless, there is scant literature on the dietary exposure to PFASs for the general United States (U.S.) population. The Tampa Bay (Florida, USA) region has the highest population density in the State and communities and their attendant support services are arrayed in an urban to semi-rural continuum from the head of the Bay to the ocean mouth. Tampa Bay supports productive recreational and commercial fisheries, providing a diverse community of species. A variety of potential PFAS sources surround Tampa Bay including airports, industry, wastewater treatment plants, fire-fighting training areas and military installations. The objective of this study is to quantify PFASs in sediment and fishes collected from Tampa Bay to further estimate human health risks from dietary exposures. Sediment ( n = 17) and fish (24 species, n = 140) were collected throughout Tampa Bay in 2020 and 2021 and analyzed for 25 PFAS compounds. Concentrations of PFASs in sediments and edible tissues of fish ranged from 36.8 to 2,990 ng kg -1 (dry weight) and 307 to 33,600 ng kg -1 (wet weight), respectively. Generally, levels were highest in Old Tampa Bay and decreased south towards the Gulf of Mexico. Profiles in both matrices were generally dominated by perfluorooctane sulfonic acid (PFOS) with variations by location. Estimated human health risks from the consumption of contaminated fish collected in Tampa Bay exceeded concentration thresholds for minimum risk levels (MRLs) and tolerable weekly intake (TWIs) values for adults and youths. Additionally, concentrations of PFOS in edible fish tissues of several recreationally important species collected in Tampa Bay exceeded consumption guideline levels established by several governmental agencies. In the current context, the elevated levels of PFAS in Tampa Bay and the exceedances of available thresholds for potential human health risks are a cause for concern and justify a more intensive examination especially for more heavily utilized species, particularly those used in subsistence-level fishing, which, as elsewhere may be significantly under documented.

Florida↗

USGS2021

Mapping out a future for ungulate migrations

Migration of ungulates (hooved mammals) is a fundamental ecological process that promotes abundant herds, whose effects cascade up and down terrestrial food webs. Migratory ungulates provide the prey base that maintains large carnivore and scavenger populations and underpins terrestrial biodiversity (fig. S1). When ungulates move in large aggregations, their hooves, feces, and urine create conditions that facilitate distinct biotic communities. The migrations of ungulates have sustained humans for thousands of years, forming tight cultural links among Indigenous people and local communities. Yet ungulate migrations are disappearing at an alarming rate ( 1 ). Efforts by wildlife managers and conservationists are thwarted by a singular challenge: Most ungulate migrations have never been mapped in sufficient detail to guide effective conservation. Without a strategic and collaborative effort, many of the world's great migrations will continue to be truncated, severed, or lost in the coming decades. Fortunately, a combination of animal tracking datasets, historical records, and local and Indigenous knowledge can form the basis for a global atlas of migrations, designed to support conservation action and policy at local, national, and international levels.

Science↗

USGS2009

Changes in the chemistry of shallow groundwater related to the 2008 injection of CO2 at the ZERT field site, Bozeman, Montana

Approximately 300 kg/day of food-grade CO 2 was injected through a perforated pipe placed horizontally 2–2.3 m deep during July 9–August 7, 2008 at the MSU-ZERT field test to evaluate atmospheric and near-surface monitoring and detection techniques applicable to the subsurface storage and potential leakage of CO 2 . As part of this multidisciplinary research project, 80 samples of water were collected from 10 shallow monitoring wells (1.5 or 3.0 m deep) installed 1–6 m from the injection pipe, at the southwestern end of the slotted section (zone VI), and from two distant monitoring wells. The samples were collected before, during, and following CO 2 injection. The main objective of study was to investigate changes in the concentrations of major, minor, and trace inorganic and organic compounds during and following CO 2 injection. The ultimate goals were (1) to better understand the potential of groundwater quality impacts related to CO 2 leakage from deep storage operations, (2) to develop geochemical tools that could provide early detection of CO 2 intrusion into underground sources of drinking water (USDW), and (3) to test the predictive capabilities of geochemical codes against field data. Field determinations showed rapid and systematic changes in pH (7.0–5.6), alkalinity (400–1,330 mg/l as HCO 3 ), and electrical conductance (600–1,800 μS/cm) following CO 2 injection in samples collected from the 1.5 m-deep wells. Laboratory results show major increases in the concentrations of Ca (90–240 mg/l), Mg (25–70 mg/l), Fe (5–1,200 ppb), and Mn (5–1,400 ppb) following CO 2 injection. These chemical changes could provide early detection of CO 2 leakage into shallow groundwater from deep storage operations. Dissolution of observed carbonate minerals and desorption-ion exchange resulting from lowered pH values following CO 2 injection are the likely geochemical processes responsible for the observed increases in the concentrations of solutes; concentrations generally decreased temporarily following four significant precipitation events. The DOC values obtained are 5 ± 2 mg/l, and the variations do not correlate with CO 2 injection. CO 2 injection, however, is responsible for detection of BTEX (e.g. benzene, 0–0.8 ppb), mobilization of metals, the lowered pH values, and increases in the concentrations of other solutes in groundwater. The trace metal and BTEX concentrations are all significantly below the maximum contaminant levels (MCLs). Sequential leaching of core samples is being carried out to investigate the source of metals and other solutes.

Montana↗

USGS1986

This week?s Citation Classic: 'Stickel, L. F. A comparison of certain methods of measuring ranges of small mammals. J. Mammalogy 35: 1-15, 1954.'

During my first employment as a junior biologist conducting food habits analyses at the Patuxent Research Refuge (now Patuxent Wildlife Research Center) of the US Fish and Wildlife Service, the first station director, Arnold L. Nelson, gave each staff biologist the opportunity to spend a little time conducting field studies on the 2,600-acre research area. These studies were to help in ecological evaluation of the area, but also, no doubt, functioned as a morale builder for biologists daily engaged in difficult, demanding and confining laboratory work. I undertook to measure the population density of small mammals in different habitats. The state-of-the-art methods recommended to me and prevalent in the literature worried me, especially after preliminary field work. Reading the classic, paper by W.H. Burt [Terrioriality and home range concepts as applied to mammals. J. Mammalogy 24:346-352, 1943] was a turning point for me in seeing that knowledge of home-range size was the key to measuring population density. My first papers employed these concepts in field evaluations. However, they could give-only limited attention to the question of how home ranges could be measured. Furthermore, the importance of knowledge of the home range to habitat evaluation and to understanding animal behavior was becoming increasingly apparent. Advocacy of many different methods of measuring home ranges appeared in the literature. It did not seem possible to evaluate them objectively. It occurred to me that artificial populations could be used to help in understanding the mechanisms of measuring home ranges. The effects of random trap-visiting, bias toward central traps, trap-spacing, range shape, and other factors could be considered. So grids of traps were inked onto oversize graph paper, and simulated ranges were cut from plastic to be tossed as randomly as possible on the trap-grids. It was a slow, laborious job. Analysis showed that random captures in artificial populations produced patterns that were similar in many ways to those observed in field studies; the necessity of appropriate trap-spacing in relation to range size became obvious. Some commonly used methods of expressing range size proved to be clearly superior to others. However, the artificial populations could not fully simulate actual populations, where use patterns changed as conditions changed and the ?boundaries? of ranges tended to shift continuously or with time. Progress was made, but problems remained. I suspect that the reasons the paper has been cited frequently rest on the continuing interest in home-range behavior and the continuing difficulty in field evaluations, despite the many advances in observational methodology. The sophisticated techniques that became possible with the use of computers [R.I. Jennrich and F.B. Turner. Measurement of non-circular home range. J. Theor. Biol 23:227-237, 1969] also presented new possibilities for analysis and understanding of home-range characteristics and created a resurgence of interest in home-range behavior and its biological significance.

Current Contents / Agriculture, Biology & Environm↗

USGS2025

Calibration of the Stream Salmonid Simulator (S3) model to estimate annual survival, movement, and food consumption by juvenile Chinook salmon (Oncorhynchus tshawytscha) in the restoration reach of the Trinity River, California, 2006–18

Executive Summary The Trinity River is managed in two sections: (1) from the upper 64-kilometer “restoration reach” downstream from Lewiston Dam to the confluence with the North Fork Trinity River, and (2) the 120-kilometer lower Trinity River downstream from the restoration reach. The Stream Salmonid Simulator (S3) has been previously applied to these reaches and the Klamath River. To estimate fish growth, past S3 calibration efforts in the Trinity and Klamath Rivers used maximum likelihood methods that considered only the abundance of juvenile Chinook salmon ( Oncorhynchus tshawytscha ) passing a fish trap to estimate survival and movement parameters, but not fish consumption. Previous calibrations did not estimate the average proportion of maximum consumption ( C y ) when estimating survival ( S y ) and movement ( M 0 y ) parameters across years ( y ) of data, but because no other information was available in the literature a fixed value of C y =0.66 was assumed. Therefore, the goal of this report is to present an alternative approach that calibrates the S3 model to multivariate data (that is, abundance and size), enabling the estimation of the average proportion of maximum consumption, in conjunction with survival and movement parameters for a particular migration year. We fit the S3 model to individual years of weekly trap abundance estimates and mean fish sizes (fork length) at the Pear Tree Gulch (hereafter referred to as Pear Tree) fish trap representing the restoration reach. We used the Earth Mover’s Distance (EMD) as the objective value to be minimized in parameter optimization. This approach estimated survival, movement, and consumption parameters for each migration year. Because we had information on the abundance of natural and hatchery produced juvenile salmon at the fish traps, we estimated survival and movement for natural and hatchery fish. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile Chinook Salmon. A key theme of the model is that river discharge affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily timeseries of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit drive survival and growth within each habitat unit and movement of fish among habitat units. The physical template of the restoration reach of the Trinity River was classified into 356 meso-habitat units comprised of runs, riffles, and pools. For each habitat unit, we developed a timeseries of daily discharge, water temperature, amount of available spawning habitat, and fry and parr carrying capacity. Capacity time series were constructed using state-of-the-art models of spatially explicit hydrodynamics and quantitative fish habitat relationships developed for the Trinity River. These variables were then used to drive population dynamics such as egg maturation and survival, and in turn, juvenile movement, growth, and survival. We estimated movement, survival, and consumption parameters by calibrating the model to 12 years of weekly juvenile abundance estimates and fish sizes at the Pear Tree fish trap near the downstream end of the restoration reach. We estimated parameters for 12 years that included a wide range of female spawner abundances (1,414–11,494) and water year types (critically dry–extremely wet). We contrast the estimated parameters to the corresponding number of female spawners and the total annual volume of water discharged for the Trinity River (Trinity River Restoration Program; https://www.trrp.net/restoration/flows/summary/ ). The calibration consisted of replicating historical conditions as closely as possible (for example, discharge; temperature; spawner abundance, spawning location and timing, and hatchery releases), and then running the model to predict weekly abundance passing the trap location from each brood year of adults and subsequent migration year of their juvenile progeny. Because density-dependent movement was favored in past evaluations, we estimated S3 parameters based on density-independent survival and density-dependent movement. Likewise, each year’s estimated survival parameter for natural ( S N y ) and hatchery ( S H y ) fish may be interpreted as the mean daily survival probability from emergence or hatchery release to the Pear Tree fish trap. Under density dependence, the estimated movement parameter for natural ( M 0N y ) and hatchery ( M 0H y ) fish represents the intercept of the Beverton-Holt model; the probability of remaining in a habitat at near-zero abundance. We estimated C y by using EMD and incorporating abundance and fish size into model calibration. Average daily proportions of maximum consumption, , across the years were generally high (=0.640; standard deviation (SD) SD=0.176), suggesting that fish were feeding at about two-thirds of expected maximum consumption rates. This average proportion of maximum consumption,is very similar to what has been assumed (=0.66) in previous Trinity and Klamath River S3 calibration and simulation efforts. In 2017, we estimated the lowest C y , suggesting lower average consumption for juvenile salmon in high-discharge water years. When this high discharge year was excluded, there was no apparent trend in C y with annual water volume. Estimates of survival showed little trend over the range in spawner abundances, but a trend towards higher natural and hatchery fish survival with higher annual volumes of water was apparent. Over the 12 years, the average survival of hatchery fish was =0.888 (SD=0.079) and the average survival natural fish was=0.969 (SD=0.01). With respect to fish movement, we estimated higher M 0N y and M 0H y with higher annual volumes of water in the Trinity River. Higher M N0 y or M H0 y suggest greater probability of remaining in a habitat at low fish densities, with potential for density-dependent processes in movement to occur. The highest M 0N y = 0.676 was estimated during brood year 2012, and the overall average for natural fish was =0.276 (SD=0.188) and for hatchery fish was=0.467 (SD=0.235). Under the Beverton-Holt model, as M 0N y or M 0H y approach zero, there is less capacity for change in fish movement as fish density increases. The S3 model was initialized with only the spatiotemporal distribution of spawners, so it performed well at capturing the essential outmigration features that are ultimately governed by rates of growth, movement, and mortality. We used a new optimization method that could accommodate multivariate data on abundance and fish size collected at the Pear Tree fish trap, enabling the calibration of S3 to estimate five parameters for 12 separate years of data. Incorporating weekly fish size data for each year in our parameter optimization process made the estimation of C y possible and represents a step forward in the fitting of the S3 model to fish trap data for the purposes of parameter calibration and the estimation of growth parameters with respect to annual conditions. We identified lack of fit and adding important effects into the S3 model may improve the S3 estimation and simulation of water scenarios. The Trinity River Restoration Program (TRRP) Science Advisory Board recommended that the TRRP focus on developing core elements of a decision support system (DSS; Buffington and others, 2014). Toward that end, the habitat and S3 models described in this report are both core elements of the DSS. The structure of S3 makes it a particularly useful fish production model for the DSS because population dynamics are sensitive to (1) water temperature, (2) daily discharge management, and (3) habitat quality and quantity. Each of these variables are key management parameters under consideration in the TRRP. As such, the S3 model may provide valuable insights into the potentially variable effects of different management decisions on the Trinity River.

California↗

USGS2025

The Grouse & Grazing Project: Effects of cattle grazing on demographic traits of greater sage-grouse

Greater sage-grouse (Centrocercus urophasianus) were once widespread within sagebrush -grassland ecosystems of western North America, but populations have declined since the mid-1960s. Though sage-grouse were not listed as threatened or endangered under the Endangered Species Act (ESA), when examined in 2015, they remain a species of interest and concern. Roughly half of the sage-grouse’s remaining habitat is on federal land, most of it managed by the Bureau of Land Management (BLM) and the U.S. Forest Service (USFS). Livestock grazing is the most extensive land use within sage-grouse habitat and the effects of livestock grazing on sage-grouse are often debated. The extensive decade-long research project summarized in this report was initiated to provide rigorous experimental research to inform the debate regarding the relationship between livestock grazing and sage-grouse. In 2012, the Idaho Grouse & Grazing Project was started with several partners including the University of Idaho, BLM, Idaho Department of Fish and Game (IDFG), and other partners to evaluate the effects of cattle grazing on sage-grouse vital rates. Many additional supporters have provided resources to this research effort including the Public Lands Council, Idaho Cattle Association, Idaho Governor’s Office of Species Conservation, Western Association of Fish & Wildlife Agencies, U.S. Fish and Wildlife Service, USFS, and numerous grazing associations and ranchers in Idaho. This 10-year research project was a scientifically rigorous and replicated experiment, occurring across five study sites in Idaho. This document is intended to provide a summary of the findings of this unprecedented study. Annual reports are available on the project’s website: https://idahogrousegrazing.org and scientific papers are being prepared and submitted to journals. The project focused on the influence of spring cattle grazing on sage-grouse vital rates across five study sites in Idaho including 21 BLM grazing pastures. From 2014-2023, we captured 1,343 grouse, documented the fate of 1,285 nests, and tracked 399 broods. Vegetation was characterized at 4,777 plots and grazing utilization levels were recorded at >30,000 locations. Because insects are an important food source for sage-grouse hens and their chicks, insect biomass and diversity were also examined in this study. We collected arthropods in 12,151 pitfall samples and 6,217 sweep-net samples across 786 plots within our five study sites. At each study site, three or four grazing treatments were implemented after two years of pre-treatment field investigations. These controlled cattle grazing treatments included spring-grazing in even years, spring-grazing in odd years, spring-and-fall grazing in alternating years, and a no grazing (or rested) control. Once grazing treatments were implemented at a study site, we measured sage-grouse demographic traits for 4-8 years post-treatment. Stocking rate (grazing intensity) was assessed across pastures each year and was influenced by vegetation communities, topography, and water sources. Grazed pastures exhibited lower grass cover and height compared to the no grazing pastures, and the extent of this difference varied based on annual precipitation levels. Rested pastures maintained higher grass cover and grass height, but the differences in habitat structure did not consistently translate to differences in sage-grouse demographic traits. Apparent nesting success varied annually and by site, ranging from 24% to 44% over the study period. Like some other studies, results from this research show that successful (i.e., hatched) sage-grouse nests have taller grass heights than failed nests. The average grass height surrounding successful nests in grazed pastures was shorter than that surrounding successful nests in non-grazed (i.e., rested) pastures. It is well documented that grazing reduces grass height, and these observations have led to widely held assumptions that livestock grazing reduces grass height which negatively affects sage-grouse nesting habitat. At the pasture scale, this study has found that sage-grouse nesting success is no greater in pastures that were rested for 4-8 years than those currently or recently grazed. This study gives no indication that removing cattle from pastures affected nesting success. We found some evidence that nest density varied among the grazing treatments, but we did not see compelling evidence of increases in density of nesting hens following cessation of grazing in the no grazing treatments. Brood survival varied by site and year but showed no strong effect of grazing treatment. Climatic conditions, particularly drought in 2021, had a greater effect on brood survival than grazing metrics. We also found no differences in hen survival among the grazing treatments. Results of this study suggest that hens nesting in spring and fall grazed pastures had similar or even slightly higher brood survival than hens in the rested pastures or the spring grazed pastures. Arthropod biomass and species diversity varied among our study sites and the differences between grazed and rested pastures also varied among study sites. Average biomass and diversity of arthropods was higher in the spring grazed pastures on two of three sites examined but higher in the rested pastures on the other site examined. Some taxa of arthropods were more abundant in grazed pastures while other taxa were more abundant in rested pastures. For example, Carabidae (Ground Beetles) and Formicidae (Ants) had higher biomass in grazed pastures, while Tenebrionidae (Darkling Beetles) and Acrididae (Grasshoppers) had higher biomass in non-grazed pastures. Results indicate that grazing effects on arthropod biomass and arthropod diversity are study site-dependent, suggesting a need to better quantify the most important prey taxa for sage-grouse chicks and to better control for other factors that influence arthropod abundance. Based on results of this research, livestock grazing, when properly managed, does not appear to negatively impact sage-grouse nest survival or brood success. This study provides critical insights for land managers balancing livestock production with sage-grouse conservation, supporting adaptive grazing strategies that maintain both economic and ecological objectives.

Idaho↗