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Results for “Case Studies in the Environment”

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

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At least 199 records · Page 11Linked to original sources

USGS1976

Geotechnical description of four Mississippi Delta soil borings

The submerged portion of the Mississippi Delta complex forms an ideal natural laboratory to study the effects of rapid deposition. One of the most obvious of these effects is the mass movements of sediments. Slump and slide signatures, mudflow characteristics, and evidence for creep are all found in abundance on the delta platform. These types of features have been studied by Colemen and Wright (1974) with regard to form and by Garrison (1974) with regard to their spatial distribution. Assembling these authors' findings, it is clear that the entire offshore zone contiguous with the Mississippi River is a myriad of geological action. This situation is indeed stimulating to the sedimentologist, yet it represents a nightmare to the foundation engineer. Emplacing offshore structures in such an environment is a most difficult task, particularly since the high degree of local variability dictates that each case must be handled separately. It is under these circumstances that a marriage between geology and engineering is most fruitful, for determining the relationships between the sedimentological processes and the engineering properties is satisfying to parties from both disciplines. This, then, is the underlying objective of the Mississippi Delta research project. By investigating the instability in a geologic sense, it is hoped that many of the engineering problems will become more soluble and that extrapolation and prediction will become more realistic.

Mississippi Delta↗

USGS2025

Mountain sentinels in a changing world: Review and conservation implications of weather and climate effects on mountain goats (Oreamnos americanus)

Climate change is occurring at an accelerated rate in high-elevation alpine and mountain ecosystems. Cold-adapted, mountain species are at risk due to forecasted change and knowledge is needed to respond to current and future conservation challenges. Mountain goats ( Oreamnos americanus ) are an iconic species of North American mountain cultures and landscapes, and due to specialized adaptations for life in cold, mountainous environments they are particularly sensitive to changes in weather and climate. As sentinels of change in alpine ecosystems, the study of mountain goats offers insight into the ecological effects and conservation challenges associated with climate change in these sensitive and biodiverse environments. Here, we synthesize existing knowledge about how climate change is expected to influence environmental conditions experienced by mountain goats and associated mechanistic changes to behavior, nutritional ecology, demography, health, and interspecific interactions. In many instances, climate change effects are likely to be negative and additive to existing threats (such as human disturbance, hunting, disease, predation) though benefits are expected in some cases. Changes in climate and mountain environments will necessitate re-examination and modification of population monitoring, management, and conservation strategies. Specifically, spatiotemporal (and other) aspects of monitoring and management may need to be adjusted to accommodate emerging and novel conservation challenges. Yet, key data and knowledge gaps remain and should be addressed to advance conservation and decision-making capabilities. For mountain goats and similarly climate-sensitive alpine herbivores, effective conservation will ultimately benefit from collaborations among diverse networks guided by well-planned, strategic visions focused on common ground – namely the resiliency and persistence of culturally and ecologically significant mountain species and the alpine environment they inhabit.

Alaska, Alberta, British Columbia, Idaho, Montana,↗

USGS2009

Landsat mapping of local landscape change: The satellite-era context

To set the stage for a vulnerability analysis, investigators must describe and understand the geographic context, including physical characteristics of the landscape and the political and socioeconomic milieu of the population (Jianchu et al . 2005). Vulnerability studies focus on a particular place, at a specific time through its three dimensions, exposure, sensitivity, and adaptive capacity; therefore, understanding place is essential to analyzing vulnerability. Land-use studies are essential to understanding place because they generalize human activities on the physical landscape. Essentially, land use indicates past human decisions and actions, environmental constraints, and, in some cases, gives insight into subsequent change. Like vulnerability, land use is particular to a place at a certain time, and the analysis of that land use can be used as a baseline for future change and its implications. Vulnerability and land use are linked by the concept of place and are fundamental to contemporary research on human–environment interactions. Although the literature on land use, land-use change, and climate change is extensive, the land-use component of vulnerability is usually conceptualized as a feedback mechanism to climate change: forest cutting releases carbon dioxide, which increases atmospheric carbon dioxide concentrations, which increases radiative forcing, which changes climate, and which ultimately changes land cover and subsequent land use (e.g. DeFries and Bounoua 2004; Jianchu et al . 2005; Salinger et al . 2005; Watson 2005). Moreover, land use is rarely specifically identified as a component of vulnerability.

Book chapter↗

USGS2014

Reconnaissance study of erosion and deposition produced by the flood of August 1955 in Connecticut

A large area in the valley bottoms in Connecticut was inundated by the flood of August 1955. Relative to the total area flooded that part permanently modified by the flow was surprisingly small. Although great in some places, the distribution of these permanent modifications of channel and flood plain was spotty. Erosion of the channel and valley bottom appears to have been most severe in narrow, steep valleys. Environments of deposition were diverse. They appeared to be related to rate and direction of flow, quantity and size of sediments locally available, and in some cases to the presence of vegetation. Most of the coarse sediment deposited in the valley appears to have been derived from local sources such as valley walls and terraces composed of glacial outwash and till and flood plains containing considerable gravel. Fine sand predominated in most of the sediment deposited. Considering the magnitude of the runoff, the quantity of fine sediment transported or deposited by the flood was small. The maximum observed concentration was 473 parts per million in Scantic River at Broad Brook. Newly deposited fine sediments are thin or absent on the flood plains of many valleys which were beneath 20 ft of slow‐moving flood waters. The paucity of deposition in such ideal depositional environments also indicates that the flow did not have a high concentration of fine sediments. A number of boulders five to seven feet in diameter were moved by flood waters in reaches in which smaller gravels were undisturbed. Severe erosion in the uplands was minor. In this reconnaissance we saw little evidence of newly formed gullies and no areas of severe sheet erosion. This was the case in both woodland and pasture land. Large amounts of subsurface flow and relatively unerodible ground are presumed to be responsible for the absence of erosion.

Connecticut↗

USGS2018

Methane in groundwater from a leaking gas well, Piceance Basin, Colorado, USA

Site-specific and regional analysis of time-series hydrologic and geochemical data collected from 15 monitoring wells in the Piceance Basin indicated that a leaking gas well contaminated shallow groundwater with thermogenic methane. The gas well was drilled in 1956 and plugged and abandoned in 1990. Chemical and isotopic data showed the thermogenic methane was not from mixing of gas-rich formation water with shallow groundwater or natural migration of a free-gas phase. Water-level and methane-isotopic data, and video logs from a deep monitoring well, indicated that a shale confining layer ~125 m below the zone of contamination was an effective barrier to upward migration of water and gas. The gas well, located 27 m from the contaminated monitoring well, had ~1000 m of uncemented annular space behind production casing that was the likely pathway through which deep gas migrated into the shallow aquifer. Measurements of soil gas near the gas well showed no evidence of methane emissions from the soil to the atmosphere even though methane concentrations in shallow groundwater (16 to 20 mg/L) were above air-saturation levels. Methane degassing from the water table was likely oxidized in the relatively thick unsaturated zone (~18 m), thus rendering the leak undetectable at land surface. Drilling and plugging records for oil and gas wells in Colorado and proxies for depth to groundwater indicated thousands of oil and gas wells were drilled and plugged in the same timeframe as the implicated gas well, and the majority of those wells were in areas with relatively large depths to groundwater. This study represents one of the few detailed subsurface investigations of methane leakage from a plugged and abandoned gas well. As such, it could provide a useful template for prioritizing and assessing potentially leaking wells, particularly in cases where the leakage does not manifest itself at land surface.

Colorado↗

USGS2018

Geomorphometry in landscape ecology: Issues of scale, physiography, and application

Topographic measures are frequently used in a variety of landscape ecology applications, in their simplest form as elevation, slope, and aspect, but increasingly more complex measures are being employed. We explore terrain metric similarity with changes in scale, both grain and extent, and examine how selecting the best measures is sensitive to changes in application. There are three types of topographic measures: 1) those that relate to orientation for approximating solar input, 2) those that capture variability in terrain configuration, and 3) those that provide metrics about landform features. Many biodiversity hotspots and predators have been found to coincide with areas of complexity, yet most complexity measures cannot differentiate between terrain steepness and uneven and broken terrain. Currently characterizing terrain in landscape-level analyses can be challenging, especially at coarser spatial resolutions but developing methods that improve landscape-level assessments include multivariate approaches and the use of neighborhood statistics. Some measures are sensitive to the spatial grain of calculation, the physiography of the landscape, and the scale of application. We show which measures have the potential to be multi-collinear, and illustrate with a case study how the selection of the best measures can change depending on the question at hand using mountain lion (Puma concolor) occurrence data. The case study showed a combination of infrequently employed metrics, such as view-shed analysis and focal statistics, outperform more commonly employed singular metrics. The use of focal statistics as a measure of topographic complexity shows promise for improving how mountain lions use terrain features.

Environment and Ecology Research↗

USGS2014

Late Holocene vegetation, climate, and land-use impacts on carbon dynamics in the Florida Everglades

Tropical and subtropical peatlands are considered a significant carbon sink. The Florida Everglades includes 6000-km 2 of peat-accumulating wetland; however, detailed carbon dynamics from different environments within the Everglades have not been extensively studied or compared. Here we present carbon accumulation rates from 13 cores and 4 different environments, including sawgrass ridges and sloughs, tree islands, and marl prairies, whose hydroperiods and vegetation communities differ. We find that the lowest rates of C accumulation occur in sloughs in the southern Everglades. The highest rates are found where hydroperiods are generally shorter, including near-tails of tree islands and drier ridges. Long-term average rates of 100 to >200 g C m −2 yr −1 are as high, and in some cases, higher than rates recorded from the tropics and 10–20 times higher than boreal averages. C accumulation rates were impacted by both the Medieval Climate Anomaly and the Little Ice Age, but the largest impacts to C accumulation rates over the Holocene record have been the anthropogenic changes associated with expansion of agriculture and construction of canals and levees to control movement of surface water. Water management practices in the 20th century have altered the natural hydroperiods and fire regimes of the Everglades. The Florida Everglades as a whole has acted as a significant carbon sink over the mid- to late-Holocene, but reduction of the spatial extent of the original wetland area, as well as the alteration of natural hydrology in the late 19th and 20th centuries, have significantly reduced the carbon sink capacity of this subtropical wetland.

Florida↗

USGS2003

Mobility of authigenic rhenium, silver, and selenium during postdepositional oxidation in marine sediments

Sedimentary records of redox-sensitive trace elements hold significant potential as indicators of paleoceanographic environmental conditions. Records of Re can reveal the intensity of past reducing conditions in sediments at the time of deposition, whereas records of Ag may record the magnitude of past diatom fluxes to the seafloor. Confidence in paleoenvironmental reconstruction from records of either metal, however, requires it to have experienced negligible redistribution since deposition. This study examines diagenetic rearrangements of Re and Ag that occur in response to exposure to bottom-water O 2 in environments of low sedimentation rate, including Madeira Abyssal Plain turbidites and eastern Mediterranean basin sapropels. Authigenic Re was remobilized quantitatively by oxidation but poorly retained by the underlying sediments. All records are consistent with previous work demonstrating that only a limited reimmobilization of Re occurs preferentially in C org -rich, reducing sediments. Silver was also mobilized quantitatively by oxidation, but it was subsequently immobilized more efficiently in all cases as sharp peaks immediately into anoxic conditions below active oxidation fronts, and these peaks remain immobile in anoxic conditions during long-term burial. Comparison of Ag, S, and Se records from various cores suggests that Ag is likely to have been immobilized as a selenide, a mechanism previously proposed for Hg in similar situations (Mercone et al., 1999) . Coexisting narrow peaks of Ag and Hg with Se offer a means of assessing whether oxidative burndown has ever occurred at the top of C org - and sulfide-rich sedimentary units. Although these results suggest that caution must be used when inferring paleoenvironmental information from records of Ag and Re in cores with low sediment accumulation rates (<5 cm ka −1 ), they should not affect the promise that authigenic Ag and Re records hold for paleoenvironmental reconstruction in sediments with higher accumulation rates and where anoxic conditions have been maintained continuously.

Geochimica et Cosmochimica Acta↗

USGS2009

The Ozark Highlands

The Ozark Highlands include diverse topographic, geologic, soil, and hydrologic conditions that support a broad range of habitat types. The landscape features rugged uplands - some peaks higher than 2,500 feet above sea level - with exposed rock and varying soil depths and includes extensive areas of karst terrain. The Highlands are characterized by extreme biological diversity and high endemism (uniqueness of species). Vegetation communities are dominated by open oak-hickory and shortleaf pine woodlands and forests. Included in this vegetation matrix is an assemblage of various types of fens, forests, wetlands, fluvial features, and carbonate and siliceous glades. An ever-growing human population in the Ozark Highlands has become very dependent on reservoirs constructed on major rivers in the region and, in some cases, groundwater for household and public water supply. Because of human population growth in the Highlands and increases in industrial and agricultural activities, not only is adequate water quantity an issue, but maintaining good water quality is also a challenge. Point and nonpoint sources of excessive nutrients are an issue. U.S. Geological Survey (USGS) partnership programs to monitor water quality and develop simulation tools to help stakeholders better understand strategies to protect the quality of water and the environment are extremely important. The USGS collects relevant data, conducts interpretive studies, and develops simulation tools to help stakeholders understand resource availability and sustainability issues. Stakeholders dependent on these resources are interested in and benefit greatly from evolving these simulation tools (models) into decision support systems that can be used for adaptive management of water and ecological resources. The interaction of unique and high-quality biological and hydrologic resources and the effects of stresses from human activities can be evaluated best by using a multidisciplinary approach that the USGS can provide. Information varying from defining baseline resource conditions to developing simulation models will help resource managers and users understand the human impact on resource sustainability. Varied expertise and experience in biological and water-resources activities across the entire Highlands make the USGS a valued collaborator in studies of Ozark ecosystems, streams, reservoirs, and groundwater. A large part of future success will depend on the involvement and active participation of key partners.

Fact Sheet↗

USGS2017

Ecology and space: A case study in mapping harmful invasive species

The establishment and invasion of non-native plant species have the ability to alter the composition of native species and functioning of ecological systems with financial costs resulting from mitigation and loss of ecological services. Spatially documenting invasions has applications for management and theory, but the utility of maps is challenged by availability and uncertainty of data, and the reliability of extrapolating mapped data in time and space. The extent and resolution of projections also impact the ability to inform invasive species science and management. Early invasive species maps were coarse-grained representations that underscored the phenomena, but had limited capacity to direct management aside from development of watch lists for priorities for prevention and containment. Integrating mapped data sets with fine-resolution environmental variables in the context of species-distribution models allows a description of species-environment relationships and an understanding of how, why, and where invasions may occur. As with maps, the extent and resolution of models impact the resulting insight. Models of cheatgrass ( Bromus tectorum ) across a variety of spatial scales and grain result in divergent species-environment relationships. New data can improve models and efficiently direct further inventories. Mapping can target areas of greater model uncertainty or the bounds of modeled distribution to efficiently refine models and maps. This iterative process results in dynamic, living maps capable of describing the ongoing process of species invasions.

Book chapter↗

USGS2001

HAZUS 99 estimated annualized earthquake losses for the United States

Recent earthquakes around the world show a pattern of steadily increasing damages and losses. The increases are due primarily to two factors: 1) significant growth in urban areas that are prone to earthquakes; and 2) the vulnerability of the older building stock, even buildings that were constructed within the past twenty years. In the United States, earthquake risk has grown substantially with development, while the earthquake hazard has remained relatively constant. To understand the hazard, we study earthquake characteristics and locales in which they occur. To understand risk, we must include characteristics of the built environment in the locales where earthquakes occur, and we must assess potential damages to the built environment and the people who use it. That is a complex undertaking and one this study intends to advance. It is important to estimate the varying degrees of seismic risk throughout the United States because we need that understanding in order to make informed decisions on mitigation policies, priorities, strategies and funding levels—in both the public and private sectors. We can reduce earthquake losses to older buildings by rehabilitating them, and we can reduce earthquake losses in new buildings by applying seismic codes to their design and construction. However, decisions to spend money on either of those solutions require evidence of risk. In the absence of a nationally accepted criterion and methodology for comparing seismic risk across regions, a consensus on optimal mitigation approaches has been difficult to reach. We are all aware of regions with high hazard and high risk, such as Los Angeles, but there is growing recognition that some regions with low seismic hazard actually have high seismic risk, as is the case in New York City and Boston. This risk results, in part, from concentrations of buildings and infrastructure built without use of seismic codes or provisions. Additionally, mitigation policies and practices in the public and private sectors may not have been adopted because a community’s earthquake risk was not clearly demonstrated, and neither was the value of mitigation measures in reducing that risk. The low hazard/high risk problem exists in a number of areas in the U.S., where the infrequency of damaging earthquakes has been interpreted, wrongly, as lack of risk. While earth scientists work to increase knowledge about the hazard throughout the United States, structural engineers and other professionals work to enumerate the many factors that comprise risk. This study is one result of that endeavor. It is based on loss estimates generated by Hazards U.S. (HAZUS), a Geographic Information System (GIS)- based earthquake loss estimation tool, developed by the Federal Emergency Management Agency (FEMA) in cooperation with the National Institute of Building Sciences (NIBS). The HAZUS tool provides an approach to quantifying future earthquake losses that is national in scope, uniform in application, and comprehensive in its coverage of the built environment.

Report↗

USGS2018

Implementation of MOVE.1, censored MOVE.1, and piecewise MOVE.1 low-flow regressions with applications at partial-record streamgaging stations in New Jersey

The U.S. Geological Survey (USGS) uses Maintenance of Variance Extension Type 1 (MOVE.1) regression to transfer streamflows measured at long-term continuous-record streamgaging stations to partial-record (PR) streamgaging stations where intermittent base-flow measurements are available. MOVE.1 regression is used widely throughout the hydrologic community to extend historic low flows and low-flow statistics at continuous-record streamgaging stations to streamgaging stations that have access to only a partial record of low flows. The method correlates base-flow measurements at PR streamgaging stations with daily mean streamflows measured at index stations that exhibit similar streamflow characteristics. Following changes in the computing platform for storing, processing, retrieving, and publishing National Water Information System (NWIS) hydrologic data, legacy Statistical Analysis System (SAS) code developed by the USGS to implement the MOVE.1 regression was no longer suitable for reading and processing NWIS streamflow data. To migrate the MOVE.1 program so that it could continue to read streamflow data using the new hydrologic data platform, the SAS code was re-written in R, an open source programming language and software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing. The work described in this report was performed in a study conducted by USGS in cooperation with the New Jersey Department of Environmental Protection. During migration from SAS to R, graphical and tabular output generated by the R script was compared to output produced by the legacy SAS code to ensure that equations used to perform the MOVE.1 regression remained the same. An option to perform censored MOVE.1 regression was added to extend the MOVE.1 methodology to cases where one or more measured continuous-record or PR streamgaging station flows are zero valued. In addition to permitting censored regression, the new R script includes an option to perform piecewise MOVE.1 regression when the relation between PR station and index station low flows varies significantly across the range of index station streamflows. Together with traditional MOVE.1 regression, censored, and piecewise MOVE.1 regression methods implemented by the R script offer less biased estimates than ordinary least squares regression for the annual 7-day 10-year and other low-flow statistics at PR stations for a range of base-flow conditions. The R script is used to implement the MOVE.1 regression methods across a variety of computing platforms.

New Jersey↗

USGS2025

Blueprints for riverine cod nest boxes draw from multiple design considerations

Designing aquatic nest boxes is rarely afforded detailed scientific account. Here we provide some historical context for nest boxes used in production of large-bodied fishes of the Australian freshwater cod genus Maccullochella . Our experience with eastern freshwater cod is used as a case study to: (a) convey aspects of the complexity of the nest box design process and to (b) demonstrate the importance of visual literacy in project communication across the variety of contributors to the eco-design process. Specifically, we describe a new, two-variant, triangular nest box design for application in rivers and modifications to a standard stainless steel nest box for hatchery-pond-based spawning of eastern freshwater cod M. ikei . We designed the boxes to test adult preference for single versus double entrance/exits to cavities in hatchery and field environments. An important consideration specific to hatchery production is harvesting demersal, adhesive eggs prior to hatching to minimise fungal infection of eggs and physical loss of larvae, in addition to providing critical first feeding of larvae. In contrast, field nest box design incorporated multiple factors and associated trade-offs related to both internal and external design, ranging from manufacturer capability, material types, cost, transportability, hydrological performance, biodegradability, retrievability, as well as biological and ecological function. Only preliminary findings from field nest box deployments are provided here, and we focus primarily on elements of visual language in the form of conceptual drawings, sketches and final schematics which have been central to our process. We emphasise the benefit of harnessing input from multiple fields of expertise and documenting and testing designs of nest boxes for cavity nesting fishes, under both controlled hatchery and more complex field conditions.

Aquaculture, Fish and Fisheries↗

USGS2019

Imaging spectroscopy for the detection, assessment and monitoring of natural and anthropogenic hazards

Natural and anthropogenic hazards have the potential to impact all aspects of society including its economy and the environment. Diagnostic data to inform decision-making are critical for hazard management whether for emergency response, routine monitoring or assessments of potential risks. Imaging spectroscopy (IS) has unique contributions to make via the ability to provide some key quantitative diagnostic information. In this paper, we examine a selection of key case histories representing the state of the art to gain an insight into the achievements and perspectives in the use of visible to shortwave infrared IS for the detection, assessment and monitoring of a selection of significant natural and anthropogenic hazards. The selected key case studies examined provide compelling evidence for the use of the IS technology and its ability to contribute diagnostic information currently unattainable from operational spaceborne Earth observation systems. User requirements for the applications were also evaluated. The evaluation showed that the projected launch of spaceborne IS sensors in the near-, mid and long term future, together with the increasing availability, quality and moderate cost of off the shelf sensors, the possibilities to couple unmanned autonomous systems with miniaturized sensors, should be able to meet these requirements. The challenges and opportunities for the scientific community in the future when such data become available will then be ensuring consistency between data from different sensors, developing techniques to efficiently handle, process, integrate and deliver the large volumes of data, and most importantly translating the data to information that meets specific needs of the user community in a form that can be digested/understood by them. The latter is especially important to transforming the technology from a scientific to an operational tool. Additionally, the information must be independently validated using current trusted practices and uncertainties quantified before IS derived measurement can be integrated into operational monitoring services.

Colorado↗

USGS2019

Phylogeography and evolution of infectious hematopoietic necrosis virus in China

Infectious hematopoietic necrosis virus (IHNV) is a well-known rhabdoviral pathogen of salmonid fish. In this study, a comprehensive analysis of 40 IHNV viruses isolated from thirteen fish farms in nine geographically dispersed Chinese provinces during 2012 to 2017 is presented. Identity of nucleotide and amino acid sequences among all the complete glycoprotein (G) genes from Chinese isolates was 98.0–100% and 96.7–100%, respectively. Coalescent phylogenetic analyses revealed that all the Chinese IHN virus characterized in this study were in a monophyletic clade that had a most recent common ancestor with the J Nagano (JN) subgroup within the J genogroup of IHNV. Within the Chinese IHNV clade isolates obtained over successive years from the same salmon fish farm clustered in strongly supported subclades, suggesting maintenance and diversification of virus over time within individual farms. There was also evidence for regional virus transmission within provinces, and some cases of longer distance transmission between distant provinces, such as Gansu and Yunnan. The data demonstrated that IHNV has evolved into a new subgroup in salmon farm environments in China, and IHNV isolates are undergoing molecular evolution within fish farms. We suggest that Chinese IHNV comprises a separate JC subgroup within the J genogroup of IHNV.

Molecular Phylogenetics and Evolution↗

USGS2026

Guide and data requirements for submission of mineral deposit mineral chemistry data in the Critical Minerals in Ores - Mineral Chemistry (CMiO-MIN) database

The Critical Minerals in Ores - Mineral Chemistry (CMiO-MIN) database (Hawkins et al., 2026) is designed to capture ore and ore-related mineral compositional data from critical mineral-bearing deposits across the globe. Samples included within this database must be well-characterised and come from localities that have been sufficiently studied to have a reasonable constraint on their deposit type and environment of formation. As such, only samples analysed by modern geochemical methods, and with certain minimum metadata attribution, can be accepted. Data that is submitted to the CMiO-MIN database will also be published via the Geoscience Australia Portal (portal.ga.gov.au) and Critical Minerals Mapping Initiative Portal (www.criticalminerals.org). The CMiO-MIN database is a companion database for the Critical Minerals in Ores (CMiO) database (Champion et al., 2021) that was first published in 2021. This guide draws heavily from the submission guide for CMiO (Case et al., 2024) to ensure similar processes for each database. For more information about the CMiO database please refer Champion et al. (2021) and Case et al. (2024; 2025).

Report↗

USGS2022

Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.

Estuaries and Coasts↗

USGS2008

Biomedical and veterinary science can increase our understanding of coral disease

A balanced approach to coral disease investigation is critical for understanding the global decline of corals. Such an approach should involve the proper use of biomedical concepts, tools, and terminology to address confusion and promote clarity in the coral disease literature. Investigating disease in corals should follow a logical series of steps including identification of disease, systematic morphologic descriptions of lesions at the gross and cellular levels, measurement of health indices, and experiments to understand disease pathogenesis and the complex interactions between host, pathogen, and the environment. This model for disease investigation is widely accepted in the medical, veterinary and invertebrate pathology disciplines. We present standard biomedical rationale behind the detection, description, and naming of diseases and offer examples of the application of Koch's postulates to elucidate the etiology of some infectious diseases. Basic epidemiologic concepts are introduced to help investigators think systematically about the cause(s) of complex diseases. A major goal of disease investigation in corals and other organisms is to gather data that will enable the establishment of standardized case definitions to distinguish among diseases. Concepts and facts amassed from empirical studies over the centuries by medical and veterinary pathologists have standardized disease investigation and are invaluable to coral researchers because of the robust comparisons they enable; examples of these are given throughout this paper. Arguments over whether coral diseases are caused by primary versus opportunistic pathogens reflect the lack of data available to prove or refute such hypotheses and emphasize the need for coral disease investigations that focus on: characterizing the normal microbiota and physiology of the healthy host; defining ecological interactions within the microbial community associated with the host; and investigating host immunity, host-agent interactions, pathology, pathogenesis, and factors that promote the pathogenicity of the causative agent(s) of disease.

Journal of Experimental Marine Biology and Ecology↗