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USGS2024

Improved efficient physics-based computational modeling of regional wave-driven coastal flooding for reef-lined coastlines

Coastal flooding affects low-lying communities worldwide and is expected to increase with climate change, especially along reef-lined coasts, where wave-driven flooding is particularly prevalent. However, current regional modeling approaches are either insufficient or too computationally expensive to accurately assess risks in these complex environments. This study introduces and validates an improved computationally efficient and physics-based approach to compute dynamic wave-driven regional flooding on reef-lined coasts. We coupled a simplified-physics flood model (SFINCS) with a one-dimensional wave transformation model (XBeach-1D). To assess the performance of the proposed approach, we compared its results with results from a fully resolving two-dimensional wave transformation model (XBeach-2D). We applied this approach for a range of storms and sea-level rise scenarios for two contrasting reef-lined coastal geomorphologies: one low relief area and one high relief area. Our findings reveal that SFINCS coupled with XBeach-1D generates flood extents comparable to those produced by XBeach-2D, with a hit rate of 92%. However, this method tends to underpredict the flood extent of weaker, high-frequency storms and overpredict stronger, low-frequency storms. Across scenarios, our approach overpredicted the mean flood water depth, with a positive bias of 7 cm and root mean square difference of 15 cm. Offering approximately 100 times greater computational efficiency than its two-dimensional XBeach counterpart, this flood modeling technique is recommended for wave-driven flood modeling in scenarios with high computational demands, such as modeling numerous scenarios or undertaking detailed regional-scale modeling.

Journal of Marine Science & Engineering↗

USGS2024

Characterization of the structural–stratigraphic and reservoir controls on the occurrence of gas hydrates in the Eileen Gas Hydrate Trend, Alaska North Slope

One of the most studied permafrost-associated gas hydrate accumulations in Arctic Alaska is the Eileen Gas Hydrate Trend. This study provides a detailed re-examination of the Eileen Gas Hydrate Trend with a focus on the gas hydrate accumulation in the western part of the Prudhoe Bay Unit. This integrated analysis of downhole well log data and published geophysical data has provided new insight on structural, stratigraphic, and reservoir controls on the occurrence of gas hydrates in the Eileen Gas Hydrate Trend. This study revealed the relatively complex nature of the gas hydrate occurrences in the Eileen Gas Hydrate Trend, with gas hydrates present in a series of coarsening upward, laterally pervasive, mostly fine-grained sand beds exhibiting high gas hydrate saturations. Most of the gas hydrate-bearing reservoirs in the Eileen Gas Hydrate Trend are laterally segmented into distinct northwest- to southeast-trending fault blocks, occur in a combination of structural–stratigraphic traps, and are only partially hydrate filled with distinct down-dip water contacts. These findings suggest that the traditional parts of a petroleum system (i.e., reservoir, gas source, gas migration, and geologic timing of the system formation) also control the occurrence of gas hydrates in the Eileen Gas Hydrate Trend.

Alaska↗

USGS2022

Geologic framework, anthropogenic impacts, and hydrodynamics contribute to variable sediment availability and shoreface morphology at the Rockaway Peninsula, NY

Recent field and modeling studies have shown that barrier island resiliency is sensitive to sediment fluxes from the shoreface, making it important to evaluate how shoreface sediment availability varies in coastal systems. To do this, we assessed shoreface geology and morphology along the Rockaway Peninsula, NY, USA. We find that spatial variability in shoreface volume is influenced by sediment accommodation above the Holocene-Pleistocene (H-P) contact, historical barrier island evolution, and natural and engineered morphologic features, suggesting that simply identifying the H-P boundary may not be adequate for defining the shoreface reservoir. Further, sediment flux from the lower shoreface to the beach may be reduced by geologically limited cross-shore sediment distribution and shoreface steepening mediated by human modifications to the shoreline. Finally, the geologic limit of the shoreface is often shallower than a wave-based estimate of shoreface extent, implying that the geologic shoreface extent at our study site can be mobilized over short time scales (years-decades) and that the wave-based shoreface extent may be inaccurate when estimating shoreline response to sea-level rise. Our results demonstrate that the combination of hydrodynamics, humans, and geology on shoreface sediment fluxes impact how barrier islands respond to future changes in sediment supply and climate.

New York↗

USGS2022

The potential of wave energy conversion to mitigate coastal erosion from hurricanes

Wave energy conversion technologies have recently attracted more attention as part of global efforts to replace fossil fuels with renewable energy resources. While ocean waves can provide renewable energy, they can also be destructive to coastal areas that are often densely populated and vulnerable to coastal erosion. There have been a variety of efforts to mitigate the impacts of wave- and storm-induced erosion; however, they are either temporary solutions or approaches that are not able to adapt to a changing climate. This study explores a green and sustainable approach to mitigating coastal erosion from hurricanes through wave energy conversion. A barrier island, Dauphin Island, off the coast of Alabama, is used as a test case. The potential use of wave energy converter farms to mitigate erosion due to hurricane storm surges while simultaneously generating renewable energy is explored through simulations that are forced with storm data using the XBeach model. It is shown that wave farms can impact coastal morphodynamics and have the potential to reduce dune and beach erosion, predominantly in the western portion of the island. The capacity of wave farms to influence coastal morphodynamics varies with the storm intensity.

Alabama↗

USGS2022

Shoaling wave shape estimates from field observations and derived bedload sediment rates

The shoaling transformation from generally linear deep-water waves to asymmetric shallow-water waves modifies wave shapes and causes near-bed orbital velocities to become asymmetrical, contributing to net sediment transport. In this work, we used two methods to estimate the asymmetric wave shape from data at three sites. The first method converted wave measurements made at the surface to idealized near-bottom wave-orbital velocities using a set of empirical equations: the “parameterized” waveforms. The second method involved direct measurements of velocities and pressure made near the seabed: the “direct” waveforms. Estimates from the two methods were well correlated at all three sites (Pearson’s correlation coefficient greater than 0.85). Both methods were used to drive bedload-transport calculations that accounted for asymmetric waves, and the results were compared with a traditional excess-stress formulation and field estimates of bedload transport derived from ripple migration rates based on sonar imagery. The cumulative bedload transport from the parameterized waveform was 25% greater than the direct waveform, mainly because the parameterized waveform did not account for negative skewness. Calculated transport rates were comparable to rates estimated from ripple migration except during the largest event, when calculated rates were as much as 100 times greater, which occurred during high period waves.

Florida, Massachusetts, New York↗

USGS2022

A numerical study of geomorphic and oceanographic controls on wave-driven runup on fringing reefs with shore-normal channels

Many populated, tropical coastlines fronted by fringing coral reefs are exposed to wave-driven marine flooding that is exacerbated by sea-level rise. Most fringing coral reef are not alongshore uniform, but bisected by shore-normal channels; however, little is known about the influence of such channels on alongshore variations on runup and flooding of the adjacent coastline. We con-ducted a parametric study using the numeric model XBeach that demonstrates that a shore-normal channel results in substantial alongshore variations in waves, wave-driven water levels, and the resulting runup. Depending on the geometry and forcing, runup is greater either on the coastline adjacent to the channel terminus or at locations near the alongshore extent of the channel. The impact of channels on runup increases for higher incident waves, lower incident wave steepness, wider channels, a narrower reef, and shorter channel spacing. Alongshore varia-tion of infragravity waves is predominantly responsible for large-scale variations in runup out-side the channel, whereas setup, sea-swell waves, and very-low frequency waves mainly increase runup inside the channel. These results provide insight into which coastal locations adjacent to shore-normal channels are most vulnerable to high runup events, using only widely available data such as reef geometry and offshore wave conditions.

Journal of Marine Science and Engineering↗

USGS2022

Categorizing active marine acoustic sources based on their potential to affect marine animals

Marine acoustic sources are widely used for geophysical imaging, oceanographic sensing, and communicating with and tracking objects or robotic vehicles in the water column. Under the U.S. Marine Mammal Protection Act and similar regulations in several other countries, the impact of controlled acoustic sources is assessed based on whether the sound levels received by marine mammals meet the criteria for harassment that causes certain behavioral responses. This study describes quantitative factors beyond received sound levels that could be used to assess how marine species are affected by many commonly deployed marine acoustic sources, including airguns, high-resolution geophysical sources (e.g., multibeam echosounders, sidescan sonars, subbottom profilers, boomers, and sparkers), oceanographic instrumentation (e.g., acoustic doppler current profilers, split-beam fisheries sonars), and communication/tracking sources (e.g., acoustic releases and locators, navigational transponders). Using physical criteria about the sources, such as source level, transmission frequency, directionality, beamwidth, and pulse repetition rate, we divide marine acoustic sources into four tiers that could inform regulatory evaluation. Tier 1 refers to high-energy airgun surveys with a total volume larger than 1500 in 3 (24.5 L) or arrays with more than 12 airguns, while Tier 2 covers the remaining low/intermediate energy airgun surveys. Tier 4 includes most high-resolution geophysical, oceanographic, and communication/tracking sources, which are considered unlikely to result in incidental take of marine mammals and therefore termed de minimis . Tier 3 covers most non-airgun seismic sources, which either have characteristics that do not meet the de minimis category (e.g., some sparkers) or could not be fully evaluated here (e.g., bubble guns, some boomers). We also consider the simultaneous use of multiple acoustic sources, discuss marine mammal field observations that are consistent with the de minimis designation for some acoustic sources, and suggest how to evaluate acoustic sources that are not explicitly considered here.

Journal of Marine Science and Engineering↗

USGS2024

Photogrammetry of the deep seafloor from archived unmanned submersible exploration dives

Large amounts of video images have been collected for decades by scientific and governmental organizations in deep (>1000 m) water using manned and unmanned submersibles and towed cameras. The collected images were analyzed individually or were mosaiced in small areas with great effort. Here, we provide a workflow for utilizing modern photogrammetry to construct virtual geological outcrops hundreds or thousands of meters in length from these archived video images. The photogrammetry further allows quantitative measurements of these outcrops, which were previously unavailable. Although photogrammetry had been carried out in recent years in the deep sea, it had been limited to small areas with pre-defined overlapping dive paths. Here, we propose a workflow for constructing virtual outcrops from archived exploration dives, which addresses the complicating factors posed by single non-linear and variable-speed vehicle paths. These factors include poor navigation, variable lighting, differential color attenuation due to variable distance from the seafloor, and variable camera orientation with respect to the vehicle. In particular, the lack of accurate navigation necessitates reliance on image quality and the establishment of pseudo-ground-control points to build the photogrammetry model. Our workflow offers an inexpensive method for analyzing deep-sea geological environments from existing video images, particularly when coupled with rock samples.

Journal of Marine Science and Engineering↗

USGS2024

Model sensitivity analysis for coastal morphodynamics: Investigating sediment parameters and bed composition in Delft3D

Numerical simulation of sediment transport and subsequent morphological evolution rely on accurate parameterizations of sediment characteristics. However, these data are often not available or are spatially and/or temporally limited. This study approaches the problem of limited sediment grain-size data with a series of simulations assessing model sensitivity to sediment parameters and initial bed composition configurations in Delft3D, leading to improved modeling practices. A previously validated Delft3D sediment transport and morphology model for Dauphin Island, Alabama, USA, is used as the benchmark case. A method for the generation of representative sediment grain sizes and their spatially varying distributions is presented via end-member analysis of in situ surficial sediment samples. Derived sediment classes and their spatial distributions are applied to two sensitivity case simulations with increasing bed composition complexity. First, multiple sediment classes are applied in a single fully mixed layer, regardless of sediment type. Second, multiple sediment classes are applied in a thin, fully mixed transport layer with underlayers containing only the non-cohesive sediment classes below. Simulations were carried out in a probabilistic, Delft3D MorMerge configuration to capture long-term morphology change for 10 years. We found there is sensitivity to the inclusion of additional sediment classes and sediment distribution made evident in bed level and morphology change. Inclusion of highly mobile fine sediments altered model results in each sensitivity case. The model was also found to be sensitive to initial bed composition in terms of bed level and morphology change, with notable differences between sensitivity cases on decadal timescales, indicating an armoring effect in the second sensitivity case, which used the transport and underlayer bed configuration. The results of this study offer guidance for numerical modelers concerned with sediment behavior in coastal and estuarine environments.

Alabama↗

USGS2026

The USGS Rotating X-ray Computed Tomography (RXCT) Coral-Core Archive: Scope, access, and standardization

We announce the U.S. Geological Survey (USGS) Rotating X-ray Computed Tomography (RXCT) Coral-Core Archive, a digital resource derived from ~400 coral reef cores curated at the USGS Pacific and St. Petersburg Coastal and Marine Science Centers. The archive de-livers calibrated 3-D image volumes that enable reproducible values of skeletal density, linear extension, and calcification from decadal-to-centennials scale records of coral growth and bioerosion. Cross-study comparability within the archive is supported by a unified RXCT workflow that minimizes imaging artifacts. This includes rejecting im-age-intensity–density regressions with r² < 0.95, back-calculating standard densities to verify a ±10% target precision, and confirming that band-averaged density values fall within published species- and site-specific ranges. Given global coral-reef decline and the rarity of physical archives, we release data under FAIR (Findable, Accessible, Interopera-ble, Reusable) principles. Calibrated imagery and scan metadata are distributed through CoralCache/CoralCT for analysis (DeCarlo et al., 2025), while core locations and collection metadata are published through the USGS Geologic Core and Sample Database (DOI: 10.5066/F7319TR3) with links to CT slice imagery in a USGS ScienceBase repository (DOI: 10.5066/P139Y9H4). This archive provides a powerful dataset for evaluating environ-mental controls on coral growth, establishing restoration baselines, and improving coastal-hazard assessments in the face of global coral-reef declines.

American Somoa, Guam, Florida, Hawaii, U.S. Virgin↗

USGS2014

Advances in a distributed approach for ocean model data interoperability

An infrastructure for earth science data is emerging across the globe based on common data models and web services. As we evolve from custom file formats and web sites to standards-based web services and tools, data is becoming easier to distribute, find and retrieve, leaving more time for science. We describe recent advances that make it easier for ocean model providers to share their data, and for users to search, access, analyze and visualize ocean data using MATLAB® and Python®. These include a technique for modelers to create aggregated, Climate and Forecast (CF) metadata convention datasets from collections of non-standard Network Common Data Form (NetCDF) output files, the capability to remotely access data from CF-1.6-compliant NetCDF files using the Open Geospatial Consortium (OGC) Sensor Observation Service (SOS), a metadata standard for unstructured grid model output (UGRID), and tools that utilize both CF and UGRID standards to allow interoperable data search, browse and access. We use examples from the U.S. Integrated Ocean Observing System (IOOS®) Coastal and Ocean Modeling Testbed, a project in which modelers using both structured and unstructured grid model output needed to share their results, to compare their results with other models, and to compare models with observed data. The same techniques used here for ocean modeling output can be applied to atmospheric and climate model output, remote sensing data, digital terrain and bathymetric data.

Journal of Marine Science and Engineering↗

USGS2014

Model behavior and sensitivity in an application of the cohesive bed component of the community sediment transport modeling system for the York River estuary, VA, USA

The Community Sediment Transport Modeling System (CSTMS) cohesive bed sub-model that accounts for erosion, deposition, consolidation, and swelling was implemented in a three-dimensional domain to represent the York River estuary, Virginia. The objectives of this paper are to (1) describe the application of the three-dimensional hydrodynamic York Cohesive Bed Model, (2) compare calculations to observations, and (3) investigate sensitivities of the cohesive bed sub-model to user-defined parameters. Model results for summer 2007 showed good agreement with tidal-phase averaged estimates of sediment concentration, bed stress, and current velocity derived from Acoustic Doppler Velocimeter (ADV) field measurements. An important step in implementing the cohesive bed model was specification of both the initial and equilibrium critical shear stress profiles, in addition to choosing other parameters like the consolidation and swelling timescales. This model promises to be a useful tool for investigating the fundamental controls on bed erodibility and settling velocity in the York River, a classical muddy estuary, provided that appropriate data exists to inform the choice of model parameters.

Virginia↗

USGS2015

Application of a coupled vegetation competition and groundwater simulation model to study effects of sea level rise and storm surges on coastal vegetation

Global climate change poses challenges to areas such as low-lying coastal zones, where sea level rise (SLR) and storm-surge overwash events can have long-term effects on vegetation and on soil and groundwater salinities, posing risks of habitat loss critical to native species. An early warning system is urgently needed to predict and prepare for the consequences of these climate-related impacts on both the short-term dynamics of salinity in the soil and groundwater and the long-term effects on vegetation. For this purpose, the U.S. Geological Survey’s spatially explicit model of vegetation community dynamics along coastal salinity gradients (MANHAM) is integrated into the USGS groundwater model (SUTRA) to create a coupled hydrology–salinity–vegetation model, MANTRA. In MANTRA, the uptake of water by plants is modeled as a fluid mass sink term. Groundwater salinity, water saturation and vegetation biomass determine the water available for plant transpiration. Formulations and assumptions used in the coupled model are presented. MANTRA is calibrated with salinity data and vegetation pattern for a coastal area of Florida Everglades vulnerable to storm surges. A possible regime shift at that site is investigated by simulating the vegetation responses to climate variability and disturbances, including SLR and storm surges based on empirical information.

Journal of Marine Science and Engineering↗

USGS2016

Gene transcript profiling in sea otters post-Exxon Valdez oil spill: A tool for marine ecosystem health assessment

Using a panel of genes stimulated by oil exposure in a laboratory study, we evaluated gene transcription in blood leukocytes sampled from sea otters captured from 2006–2012 in western Prince William Sound (WPWS), Alaska, 17–23 years after the 1989 Exxon Valdez oil spill (EVOS). We compared WPWS sea otters to reference populations (not affected by the EVOS) from the Alaska Peninsula (2009), Katmai National Park and Preserve (2009), Clam Lagoon at Adak Island (2012), Kodiak Island (2005) and captive sea otters in aquaria. Statistically, sea otter gene transcript profiles separated into three distinct clusters: Cluster 1, Kodiak and WPWS 2006–2008 (higher relative transcription); Cluster 2, Clam Lagoon and WPWS 2010–2012 (lower relative transcription); and Cluster 3, Alaska Peninsula, Katmai and captive sea otters (intermediate relative transcription). The lower transcription of the aryl hydrocarbon receptor (AHR), an established biomarker for hydrocarbon exposure, in WPWS 2010–2012 compared to earlier samples from WPWS is consistent with declining hydrocarbon exposure, but the pattern of overall low levels of transcription seen in WPWS 2010–2012 could be related to other factors, such as food limitation, pathogens or injury, and may indicate an inability to mount effective responses to stressors. Decreased transcriptional response across the entire gene panel precludes the evaluation of whether or not individual sea otters show signs of exposure to lingering oil. However, related studies on sea otter demographics indicate that by 2012, the sea otter population in WPWS had recovered, which indicates diminishing oil exposure.

Alaska↗

USGS2016

Dynamic reusable workflows for ocean science

Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog search and data access make it now possible to create catalog-driven workflows that automate — end-to-end — data search, analysis and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS) which automates the skill-assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC) Catalog Service for the Web (CSW), then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS) for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enters the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased use of dynamic notebooks across the geoscience domains.

Journal of Marine Science and Engineering↗

USGS2018

Projected 21st century coastal flooding in the Southern California Bight. Part 1: Development of the third generation CoSMoS model

Due to the effects of climate change over the course of the next century, the combination of rising sea levels, severe storms, and coastal change will threaten the sustainability of coastal communities, development, and ecosystems as we know them today. To clearly identify coastal vulnerabilities and develop appropriate adaptation strategies due to projected increased levels of coastal flooding and erosion, coastal managers need local-scale hazards projections using the best available climate and coastal science. In collaboration with leading scientists world-wide, the USGS designed the Coastal Storm Modeling System (CoSMoS) to assess the coastal impacts of climate change for the California coast, including the combination of sea-level rise, storms, and coastal change. In this project, we directly address the needs of coastal resource managers in Southern California by integrating a vast range of global climate change projections in a thorough and comprehensive numerical modeling framework. In Part 1 of a two-part submission on CoSMoS, methods and the latest improvements are discussed, and an example of hazard projections is presented.

Journal of Marine Science and Engineering↗

USGS2018

Sediment transport model including short-lived radioisotopes: Model description and idealized test cases

Geochronologies derived from sediment cores in coastal locations are often used to infer event bed characteristics such as deposit thicknesses and accumulation rates. Such studies commonly use naturally occurring, short-lived radioisotopes, such as Beryllium-7 ( 7 Be) and Thorium-234 ( 234 Th), to study depositional and post-depositional processes. These radioisotope activities, however, are not generally represented in sediment transport models that characterize coastal flood and storm deposition with grain size patterns and deposit thicknesses. We modified the Community Sediment Transport Modeling System (CSTMS) to account for reactive tracers and used this capability to represent the behavior of these short-lived radioisotopes on the sediment bed. This paper describes the model and presents results from a set of idealized, one-dimensional (vertical) test cases. The model configuration represented fluvial deposition followed by periods of episodic storm resuspension. Sensitivity tests explored the influence on seabed radioisotope profiles by the intensities of bioturbation and wave resuspension and the thickness of fluvial deposits. The intensity of biodiffusion affected the persistence of fluvial event beds as evidenced by 7 Be. Both resuspension and biodiffusion increased the modeled seabed inventory of 234 Th. A thick fluvial deposit increased the seabed inventory of 7 Be and 234 Th but mixing over time greatly reduced the difference in inventory of 234 Th in fluvial deposits of different thicknesses.

Journal of Marine Science and Engineering↗

USGS2018

Storm surge propagation and flooding in small tidal rivers during events of mixed coastal and fluvial influence

The highly urbanized estuary of San Francisco Bay is an excellent example of a location susceptible to flooding from both coastal and fluvial influences. As part of developing a forecast model that integrates fluvial and oceanic drivers, a case study of the Napa River and its interactions with the San Francisco Bay was performed. For this application we utilize Delft3D-FM, a hydrodynamic model that computes conservation of mass and momentum on a flexible mesh grid, to calculate water levels that account for tidal forcing, storm surge generated by wind and pressure fields, and river flows. We simulated storms with realistic atmospheric pressure, river discharge, and tidal forcing to represent a realistic joint fluvial and coastal storm event. Storm conditions were applied to both a realistic field-scale Napa river drainage as well as an idealized geometry. With these scenarios, we determine how the extent, level, and duration of flooding is dependent on these atmospheric and hydrologic parameters. Unsurprisingly, the model indicates that maximal water levels will occur in a tidal river when high tides, storm surge, and large fluvial discharge events are coincident. Model results also show that large tidal amplitudes diminish storm surge propagation upstream and that phasing between peak fluvial discharges and high tide is important for predicting when and where the highest water levels will occur. The interactions between tides, river discharge, and storm surge are not simple, indicating the need for more integrated flood forecasting models in the future.

California↗