Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Challenge”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 811 records · Page 45Linked to original sources
USGS2012

A two-phase sampling design for increasing detections of rare species in occupancy surveys

1. Occupancy estimation is a commonly used tool in ecological studies owing to the ease at which data can be collected and the large spatial extent that can be covered. One major obstacle to using an occupancy-based approach is the complications associated with designing and implementing an efficient survey. These logistical challenges become magnified when working with rare species when effort can be wasted in areas with none or very few individuals. 2. Here, we develop a two-phase sampling approach that mitigates these problems by using a design that places more effort in areas with higher predicted probability of occurrence. We compare our new sampling design to traditional single-season occupancy estimation under a range of conditions and population characteristics. We develop an intuitive measure of predictive error to compare the two approaches and use simulations to assess the relative accuracy of each approach. 3. Our two-phase approach exhibited lower predictive error rates compared to the traditional single-season approach in highly spatially correlated environments. The difference was greatest when detection probability was high (0·75) regardless of the habitat or sample size. When the true occupancy rate was below 0·4 (0·05-0·4), we found that allocating 25% of the sample to the first phase resulted in the lowest error rates. 4. In the majority of scenarios, the two-phase approach showed lower error rates compared to the traditional single-season approach suggesting our new approach is fairly robust to a broad range of conditions and design factors and merits use under a wide variety of settings. 5. Synthesis and applications. Conservation and management of rare species are a challenging task facing natural resource managers. It is critical for studies involving rare species to efficiently allocate effort and resources as they are usually of a finite nature. We believe our approach provides a framework for optimal allocation of effort while maximizing the information content of the data in an attempt to provide the highest conservation value per unit of effort.

Methods in Ecology and Evolution↗
USGS2015

Efficacy of an extract from garlic, Allium sativum, against infection with the furunculosis bacterium, Aeromonas salmonicida, in rainbow trout, Oncorhynchus mykiss

Juvenile rainbow trout, Oncorhynchus mykiss , were fed diets containing 0, 0.5, 1.0, and 2.0% of a garlic extract, challenged with a modified 50% lethal dose of Aeromonas salmonicida and monitored for 28 d. There were significant increases in survival of trout fed 0.5 and 1.0% garlic extract as compared to the control and 2.0% garlic extract groups. A target animal safety study was performed at varying increments using the target dose of 0.5% garlic extract at 0× (0% garlic extract), 1× (0.5% garlic extract), 3× (1.5% garlic extract), and 5× (2.5% garlic extract) for 3× (6 wk) the duration of the original study. There was a significant increase in the level of circulating lymphocytes and a significant decrease in the level of circulating monocytes. The latter correlated to an increased level of pigment-containing macrophage centers within the renal tissue as garlic extract dosing increased, denoting a potential deleterious inflammatory effect as macrophage infiltration became severe at the highest dose. These studies suggest that feeding low-dose (0.5% or 1.0%) garlic extract improves survivability in rainbow trout when challenged with A. salmonicida and appears safe; however, higher levels do not appear to be effective and may cause deleterious effects on health.

Journal of the World Aquaculture Society↗
USGS2019

Looking to the Future: Key points for sustainable management of Northern Great Plains grasslands

The grasslands of the northern Great Plains region of North America are considered endangered ecosystems and priority conservation areas yet have great ecological and economic importance. Grasslands in the northern Great Plains (referred to as NGP from this point) are no longer self-regulating adaptive systems. The challenges to these grasslands are widespread and serious (e.g., climate change, invasive species, fragmentation, altered disturbance regimes, and anthropogenic chemical loads). Because the challenges facing the region are dynamic, complex, and persistent, a paradigm shift in how we approach restoration and management of the grasslands in the northern Great Plains is imperative. The goal of this paper is to highlight 4 key points for land managers and restoration practitioners to consider when planning management or restoration actions. First, we discuss the appropriateness of using historical fidelity as a restoration or management target because of changing climate, widespread pervasiveness of invasive species, the high level of fragmentation, and altered disturbance regimes. Second, we highlight ecosystem resilience and long-term population persistence as alternative targets. Third, because the NGP is so heavily impacted with anthropogenic chemical loading, we discuss the risks of ecological traps and extinction debt. Finally, we highlight the importance of using adaptive management and having patience during restoration and management. Consideration of these 4 points will help management and restoration of grasslands move toward a more successful and sustainable future. Although we specifically focus on the northern Great Plains of North America, these same issues and considerations apply to grasslands globally as well as many other ecosystems.

Restoration Ecology↗
USGS2023

A recruitment niche framework for improving seed-based restoration

As larger tracts of land experience degradation, seed-based restoration (SBR) will be a primary tool to reestablish vegetation and ecosystem function. SBR has advanced in terms of technical and technological approaches, yet plant recruitment remains a major barrier in some systems, notably drylands. There is an unmet opportunity to test science-based approaches to seed mix design and application, based not only on diversity or local provenance, but on the unique recruitment strategies of species. We lay out a framework that uses a quantitative representation of species' recruitment niches to match them to targeted goals (e.g. drought or invasion resistance) and methods (e.g. precision tools and technologies) in SBR. We first describe how to quantify the recruitment niche with seed and seedling traits tied to observed recruitment responses to environmental factors. We then show how a quantified recruitment niche framework can serve as the foundation to address three major restoration challenges: (1) designing forward-looking seed mixes that increase resilience to future climate and disturbance, (2) accounting for natural recovery in SBR planning, and (3) applying precision seeding practices to maximize restoration success. Finally, we demonstrate these ideas with existing data and discuss key challenges to adoption in SBR practice. While the ideas in this framework are based in ecological theory, they will require substantial testing and refinement by scientists engaged in SBR efforts. If this framework is integrated into research agendas, we believe it has the potential to unify and advance diverse elements of seed-based restoration ecology and improve restoration outcomes.

Restoration Ecology↗
USGS2019

Injection-induced earthquakes

Earthquakes in unusual locations have become an important topic of discussion in both North America and Europe, owing to the concern that industrial activity could cause damaging earthquakes. It has long been understood that earthquakes can be induced by impoundment of reservoirs, surface and underground mining, withdrawal of fluids and gas from the subsurface, and injection of fluids into underground formations. Injection-induced earthquakes have, in particular, become a focus of discussion as the application of hydraulic fracturing to tight shale formations is enabling the production of oil and gas from previously unproductive formations. Earthquakes can be induced as part of the process to stimulate the production from tight shale formations, or by disposal of wastewater associated with stimulation and production. Here, I review recent seismic activity that may be associated with industrial activity, with a focus on the disposal of wastewater by injection in deep wells; assess the scientific understanding of induced earthquakes; and discuss the key scientific challenges to be met for assessing this hazard.

Science↗
USGS2021

Disruption of the Francisella noatunensis orientalis pdpA gene results in virulence attenuation and protection in zebrafish

Several Francisella spp. including F. noatunensis are regarded as important emerging pathogens of wild and farmed fish. However, very few studies have investigated the virulence factors that allow these bacterial species to be pathogenic in fish. The Francisella Pathogenicity Island (FPI) is a well-described, gene-dense region encoding major virulence factors for the genus Francisella. PdpA is a member of the pathogenicity determining protein genes encoded by the FPI that are implicated in the ability of the mammalian pathogen, F. tularensis , to escape and replicate in infected host cells. Using a sacB suicide approach, we generated pdpA knockouts to address the role of PdpA as a virulence factor for F. noatunensis . Because polarity can be an issue in gene-dense regions, we generated two different marker-based mutants in opposing polarity ( Fno Δ pdpA1 and Δ pdpA2 ). Both mutants were attenuated (p<0.0001) in zebrafish challenges and displayed impaired intracellular replication (p<0.05) and cytotoxicity (p<0.05), all of which could be restored to wild-type (WT) levels by complementation for Fno Δ pdpA 1. Importantly, differences were found for bacterial burden and induction of acute phase and pro-inflammatory genes for Fno Δ pdpA 1 and Δ pdpA 2 compared to WT during acute infection. In addition, neither mutant resulted in significant histopathological changes. Finally, immunization with Fno Δ pdpA1 led to protection (p<0.012) against an acute lethal-dose 40 challenge with WT Fno in the zebrafish model of infection. Taken together, this study further demonstrates physiological similarities within the genus Francisella relative to their phylogenetic relationships and the utility of zebrafish for addressing virulence factors for the genus.

Infection and Immunity↗
USGS2009

Sediment regime constraints on river restoration - An example from the lower Missouri river

Dammed rivers are subject to changes in their flow, water-quality, and sediment regimes. Each of these changes may contribute to diminished aquatic habitat quality and quantity. Of the three factors, an altered sediment regime is a particularly unyielding challenge on many dammed rivers. The magnitude of the challenge is illustrated on the Lower Missouri River, where the largest water storage system in North America has decreased the downriver suspended-sediment load to 0.2%–17% of pre-dam loads. In response to the altered sediment regime, the Lower Missouri River channel has incised as much as 3.5 m just downstream of Gavins Point Dam, although the bed has been stable to slightly aggrading at other locations farther downstream. Effects of channel engineering and commercial dredging are superimposed on the broad-scale adjustments to the altered sediment regime. The altered sediment regime and geomorphic adjustments constrain restoration and management opportunities. Incision and aggradation limit some objectives of flow-regime management: In incising river segments, ecologically desirable reconnection of the floodplain requires discharges that are beyond operational limits, whereas in aggrading river segments, small spring pulses may inundate or saturate low-lying farmlands. Lack of sediment in the incising river segment downstream of Gavins Point Dam also limits sustainable restoration of sand-bar habitat for bird species listed under the Endangered Species Act. Creation of new shallow-water habitat for native fishes involves taking sediment out of floodplain storage and reintroducing most or all of it to the river, raising concerns about increased sediment, nutrient, and contaminant loads. Calculations indicate that effects of individual restoration projects are small relative to background loads, but cumulative effects may depend on sequence and locations of projects. An understanding of current and historical sediment fluxes, and how they vary along the river, provides a quantitative basis for defining management constraints and identifying opportunities.

Special Paper of the Geological Society of America↗
USGS2010

Geological mapping goes 3-D in response to societal needs

The transition to 3-D mapping has been made possible by technological advances in digital cartography, GIS, data storage, analysis, and visualization. Despite various challenges, technological advancements facilitated a gradual transition from 2-D maps to 2.5-D draped maps to 3-D geological mapping, supported by digital spatial and relational databases that can be interrogated horizontally or vertically and viewed interactively. Challenges associated with data collection, human resources, and information management are daunting due to their resource and training requirements. The exchange of strategies at the workshops has highlighted the use of basin analysis to develop a process-based predictive knowledge framework that facilitates data integration. Three-dimensional geological information meets a public demand that fills in the blanks left by conventional 2-D mapping. Two-dimensional mapping will, however, remain the standard method for extensive areas of complex geology, particularly where deformed igneous and metamorphic rocks defy attempts at 3-D depiction.

GSA Today↗
USGS2022

Invertibility aware integration of static and time-series data: An application to lake temperature modeling

Accurate predictions of water temperature are the foundation for many decisions and regulations, with direct impacts on water quality, fishery yields, and power production. Building accurate broad-scale models for lake temperature prediction remains challenging in practice due to the variability in the data distribution across different lake systems monitored by static and time-series data. In this paper, to tackle the above challenges, we propose a novel machine learning based approach for integrating static and time-series data in deep recurrent models, which we call Invertibility-Aware-Long Short-Term Memory(IA-LSTM), and demonstrate its effectiveness in predicting lake temperature. Our proposed method integrates components of the Invertible Network and LSTM to better predict temperature profiles (forward modeling) and infer the static features (i.e., inverse modeling) that can eventually enhance the prediction when static variables are missing. We evaluate our method on predicting the temperature profile of 450 lakes in the Midwestern U.S. and report relative improvement of 4% to capture data heterogeneity and simultaneously outperform baseline predictions by 12% when static features are unavailable.

Conference Paper↗
USGS2018

Estimating disperser abundance using open population models that incorporate data from continuous detection PIT arrays

Autonomous passive integrated transponder (PIT) tag antenna systems continuously detect individually marked organisms at one or more fixed points over long time periods. Estimating abundance using data from autonomous antennae can be challenging, because these systems do not detect unmarked individuals. Here we pair PIT antennae data from a tributary with mark-recapture sampling data in a mainstem river to estimate the number of fish moving from the mainstem to the tributary. We then use our model to estimate abundance of non-native rainbow trout Oncorhynchus mykiss that move from the Colorado River to the Little Colorado River (LCR), the latter of which is important spawning and rearing habitat for federally-endangered humpback chub Gila cypha. We estimate 226 rainbow trout (95% CI: 127-370) entered the LCR from October 2013-April 2014. We discuss the challenges of incorporating detections from autonomous PIT antenna systems into mark-recapture population models, particularly in regards to using information about spatial location to estimate movement and detection probabilities.

Colorado River↗
USGS2019

Size-specific apparent survival rate estimates of white sharks using mark-recapture models

For species that exist at low abundance or are otherwise difficult to study, it is challenging to estimate vital rates such as survival and fecundity and common to assume that survival rates are constant across ages and sexes. Population assessments based on overly simplistic vital rates can lead to erroneous conclusions. We estimated sex and length-based annual apparent survival rates for white sharks (Carcharodon carcharias). We found evidence that annual apparent survival differed over ontogeny in a system with competitive foraging aggregations, from 0.63 (SE = 0.08) for newly recruiting sub-adults to 0.95 (SE = 0.02) for the largest sharks. Our results reveal a potential challenge to ontogenetic recruitment in a long-lived, highly mobile top marine predator, as survival rates for sub-adult white sharks may be lower than previously assumed. Alternatively, younger and competitively inferior individuals may be forced to permanently emigrate from primary foraging sites. This study provides new methodology for estimating apparent survival as a function of diverse covariates by capture-recapture study including when sex assignment is uncertain.

California↗
USGS2022

Incorporating antenna detections into abundance estimates of fish

Autonomous passive integrated transponder (PIT) tag antennas are commonly used to detect fish marked with PIT tags but cannot detect unmarked fish, creating challenges for abundance estimation. Here we describe an approach to estimate abundance from paired physical capture and antenna detection data in closed and open mark-recapture models. Additionally, for open models, we develop an approach that incorporates uncertainty in fish size, because fish size changes through time (as fish grow bigger) but is unknown if fish are not physically captured (e.g., only detected on antennas). Incorporation of size uncertainty allows for estimation of size-specific abundances and demonstrates a generally useful method for obtaining state-specific abundances estimates under state uncertainty. Simulation studies comparing models with and without antenna detections illustrate that the benefit of our approach increases as a larger proportion of the population is marked. When applied to two field data sets, our approach to incorporating antenna detections reduced uncertainty in abundance substantially. We conclude that PIT antennas hold great potential for improving abundance estimation, despite the challenges they present.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2022

Combining fixed-location count data and movement data to estimate abundance of a lake sturgeon spawning run

Estimating abundance of migrating fishes is challenging. While sonars can be deployed continuously, improper assumptions about unidirectional migration and complete spatial coverage can lead to inaccurate estimates. To address these challenges, we present a framework for combining fixed-location count data from a dual-frequency identification sonar (DIDSON) with movement data from acoustic telemetry to estimate spawning run abundance of lake sturgeon ( Acipenser fulvescens ). Acoustic telemetry data were used to estimate the probability of observing a lake sturgeon on the DIDSON and to determine the probability that a lake sturgeon passing the DIDSON site had passed the site previously during the season. Combining probabilities with DIDSON counts, using a Bayesian integrated model, we estimated the following abundances: 99 (42–215 credible interval, CI) in 2017, 131 (82–248 CI) in 2018, and 92 (47–184 CI) in 2019. Adding movement data generated better inferences on count data by incorporating fish behavior (e.g., multiple migrations in a single season) and its uncertainty into abundance estimates. This framework can be applied to count and movement data to estimate abundance of spawning runs of other migratory fishes in riverine systems.

Vermont↗
USGS1974

Comparison of protection in rainbow trout (Salmo gairdneri) inoculated with and fed Hagerman redmouth bacterins

Rainbow trout ( Salmo gairdneri ) fed 1.0 mg Hagerman redmouth bacterin per fish for 2 wk had no detectable specific, circulating, agglutinating antibody. In fish given a single subcutaneous inoculation of 1.0 mg of bacterin per fish, antibody was present from 3 wk later until 3 mo later, when the final sample was taken. Median lethal doses at various intervals after the bacterins were administered indicated that the inoculated fish could withstand a greater challenge by subcutaneous inoculation of the virulent bacteria than the orally immunized fish. The fish fed the vaccine lost their protection within 6 wk, whereas the inoculated fish had high levels of protection through 3 mo. The degree of protection was also confirmed by a "natural" exposure challenge.

Journal of the Fisheries Research Board of Canada↗
USGS2015

Conservation paleobiology: Leveraging knowledge of the past to inform conservation and restoration

Humans now play a major role in altering Earth and its biota. Finding ways to ameliorate human impacts on biodiversity and to sustain and restore the ecosystem services on which we depend is a grand scientific and societal challenge. Conservation paleobiology is an emerging discipline that uses geohistorical data to meet these challenges by developing and testing models of how biota respond to environmental stressors. Here we ( a ) describe how the discipline has already provided insights about biotic responses to key environmental stressors, ( b ) outline research aimed at disentangling the effects of multiple stressors, ( c ) provide examples of deliverables for managers and policy makers, and ( d ) identify methodological advances in geohistorical analysis that will foster the next major breakthroughs in conservation outcomes. We highlight cases for which exclusive reliance on observations of living biota may lead researchers to erroneous conclusions about the nature and magnitude of biotic change, vulnerability, and resilience.

Annual Review of Earth and Planetary Sciences↗
USGS2017

Ecosystem services from transborder migratory species: Implications for conservation governance

This article discusses the conservation challenges of volant migratory transborder species and conservation governance primarily in North America. Many migratory species provide ecosystem service benefits to society. For example, insectivorous bats prey on crop pests and reduce the need for pesticides; birds and insects pollinate food plants; and birds afford recreational opportunities to hunters and birdwatchers. Migration is driven by the seasonal availability of resources; as resources in one area become seasonally scarce, individuals move to locations where resources have become seasonally abundant. The separation of the annual lifecycle means that species management and governance is often fractured across international borders. Because migratory species depend on habitat in different locations, their ability to provide ecosystem services in one area depends on the spatial subsidies, or support, provided by habitat and ecological processes in other areas. This creates telecouplings, or interconnections across geographic space, of areas such that impacts to the habitat of a migratory species in one location will affect the benefits enjoyed by people in other locations. Information about telecoupling and spatial subsidies can be used to craft new governance arrangements such as Payment for Ecosystem Services programs that target specific stakeholder groups and locations. We illustrate these challenges and opportunities with three North American case studies: the Duck Stamp Program, Mexican free-tailed bats ( Tadarida brasiliensis mexicana ), and monarch butterflies ( Danaus plexippus ).

Annual Review of Environment and Resources↗
USGS2024

Methods for quantifying interactions between groundwater and surface water

Driven by the need for integrated management of groundwater (GW) and surface water (SW), quantification of GW–SW interactions and associated contaminant transport has become increasingly important. This is due to their substantial impact on water quantity and quality. In this review, we provide an overview of the methods developed over the past several decades to investigate GW–SW interactions. These methods include geophysical, hydrometric, and tracer techniques, as well as various modeling approaches. Different methods reveal valuable information on GW–SW interactions at different scales with their respective advantages and limitations. Interpreting data from these techniques can be challenging due to factors like scale effects, heterogeneous hydrogeological conditions, sediment variability, and complex spatiotemporal connections between GW and SW. To facilitate the selection of appropriate methods for specific sites, we discuss the strengths, weaknesses, and challenges of each technique, and we offer perspectives on knowledge gaps in the current science.

Annual Review of Environment and Resources↗
USGS2012

Optimal egg size in a suboptimal environment: reproductive ecology of female Sonora mud turtles (Kinosternon sonoriense) in central Arizona, USA

We studied the reproductive ecology of female Sonora mud turtles (Kinosternon sonoriense) at Montezuma Well, a chemically-challenging natural wetland in central Arizona, USA. Females matured between 115.5 and 125 mm carapace length (CL) and 36-54% produced eggs each year. Eggs were detected in X-radiographs from 23 April-28 September (2007-2008) and the highest proportion (56%) of adult females with eggs occurred in June and July. Clutch frequency was rarely more than once per year. Clutch size was weakly correlated with body size, ranged from 1-8 (mean = 4.96) and did not differ significantly between years. X-ray egg width ranged from 17.8-21.7 mm (mean 19.4 mm) and varied more among clutches than within. Mean X-ray egg width of a clutch did not vary significantly with CL of females, although X-ray pelvic aperture width increased with CL. We observed no evidence of a morphological constraint on egg width. In addition, greater variation in clutch size, relative to egg width, suggests that egg size is optimized in this hydrologically stable but chemically-challenging habitat. We suggest that the diversity of architectures exhibited by the turtle pelvis, and their associated lack of correspondence to taxonomic or behavioral groupings, explains some of the variation observed in egg size of turtles.

Arizona↗