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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↗

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↗

USGS1999

The evolutionary history of steelhead ( Oncorhynchus mykiss ) along the US Pacific Coast: Developing a conservation strategy using genetic diversity

Changes in genetic variation across a species range may indicate patterns of population structure resulting from past ecological and demographic events that are otherwise difficult to infer and thus provide insight into evolutionary development. Genetic data is used, drawn from 11 microsatellite loci amplified from anadromous steelhead ( Oncorhynchus mykiss ) sampled throughout its range in the eastern Pacific Ocean, to explore population structure at the southern edge in California. Steelhead populations in this region represent less than 10% of their reported historic abundance and survive in very small populations found in fragmented habitats. Genetic data derived from three independent molecular systems (allozymes, mtDNA, and microsatellites) have shown that the southernmost populations are characterized by a relatively high genetic diversity. Two hypothetical models supporting genetic population substructure such as observed were considered: (1) range expansion with founder-flush effects and subsequent population decline; (2) a second Pleistocene radiation from the Gulf of California. Using genetic and climatic data, a second Pleistocene refugium contributing to a southern ecotone seems more feasible. These data support strong conservation measures based on genetic diversity be developed to ensure the survival of this uniquely diverse gene pool.

ICES Journal of Marine Science↗

USGS2000

Photographic evaluation of the impacts of bottom fishing on benthic epifauna

The gravel sediment habitat on the northern edge of Georges Bank (East coast of North America) is an important nursery area for juvenile fish, and the site of a productive scallop fishery. During two cruises to this area in 1994 we made photographic transects at sites of varying depths that experience varying degrees of disturbance from otter trawling and scallop dredging. Differences between sites were quantified by analyzing videos and still photographs of the sea bottom. Videos were analyzed for sediment types and organism abundance. In the still photos, the percentages of the bottom covered by bushy, plant-like organisms and colonial worm tubes (Filograna implexa) were determined, as was the presence/absence of encrusting bryozoa. Non-colonial organisms were also identified as specifically as possible and sediment type was quantified. Significant differences between disturbed and undisturbed areas were found for the variables measured in the still photos; colonial epifaunal species were conspicuously less abundant at disturbed sites. Results from the videos and still photos were generally consistent although less detail was visible in the videos. Emergent colonial epifauna provide a complex habitat for shrimp, polychaetes, brittle stars and small fish at undisturbed sites. Bottom fishing removes this epifauna, thereby reducing the complexity and species diversity of the benthic community. (C) 2000 International Council for the Exploration of the Sea.

Georges Bank↗

USGS1975

Location of the non-tidal current null zone in northern San Francisco Bay

Variations in Sacramento-San Joaquin River discharge into northern San Francisco Bay causes shifts in location of the bottom density current null zone. At a river flow of 2000 m 3 /s this null zone is approximately 20 km from the seaward end of the estuary, whereas at a river flow of 100 m 3 /s it is 80 km from the seaward end; the corresponding distances of salinity penetration are approximately 40 and 90 km from the seaward end. Seaward of the null zone, during low (summer) river discharge conditions, the inward-flowing bottom density current appears typically strong (5–15 cm/s) relative to the outward-flowing river current (river discharge per unit cross-channel area) of <2 cm/s. Landward from this null zone the average river current increases with decreasing cross-channel area. This circulation implies that during the summer water within the null zone has the longest average advective replacement time relative to water seaward or landward of the null zone.

California↗

USGS1978

Numerical simulation of dissolved silica in the San Fancisco Bay

A two-dimensional (vertical) steady-state numerical model that simulates water circulation and dissolved-silica distributions is applied to northern San Francisco Bay. The model (1) describes the strong influence of river inflow on estuarine circulation and, in turn, on the biologically modulated silica concentration, and (2) shows how rates of silica uptake relate to silica supply and mixing rates in modifying a conservative behavior. Longitudinal silica distributions influenced by biological uptake (assuming both vertically uniform and vertically decreasing uptake situations) show that uptake rates of 1 to 10 μg-at. l −1 day −1 are sufficient to depress silica concentrations at river inflows of 100–400 m 3 s −1 , respectively, and that the higher rates appear ineffective at inflows above 400 m 3 s −1 . The simulations further indicate that higher silica utilization in the null zone is not essential to depress silica concentrations strongly there. Advective water-replacement times at river inflows of 400, 200 and 100 m 3 s −1 are computed to be less than 25, 45 and 75 days, respectively, for a 120-km estuary-river system.

California↗

USGS2006

Submarine geology of Hana Ridge and Haleakala Volcano's northeast flank, Maui

We present a morphostructural analysis of the submarine portions of Haleakala Volcano and environs, based upon a 4-year program of geophysical surveys and submersible explorations of the underwater flanks of Hawaiian volcanoes that was conducted by numerous academic and governmental research organizations in Japan and the U.S. and funded primarily by the Japan Agency for Marine–Earth Science and Technology. A resulting reconnaissance geologic map features the 135-km-long Hana Ridge, the 3000 km 2 Hana slump on the volcano's northeast flank, and island-surrounding terraces that are the submerged parts of volcanic shields. Hana Ridge below 2000 m water depth exhibits the lobate morphology typical of the subaqueously erupted parts of Hawaiian rift zones, with some important distinctions: namely, subparallel crestlines, which we propose result from the down-rift migration of offsets in the dike intrusion zone, and an amphitheater at its distal toe, where a submarine landslide has embayed the ridge tip. Deformation of Haleakala's northeast flank is limited to that part identified as the Hana slump, which lies downslope from the volcano's submerged shield, indicating that flank mobility is also limited in plan, inconsistent with hypothesized volcanic spreading driven by rift-zone dilation. The leading edge of the slump has transverse basins and ridges that resemble the thrust ramps of accretionary prisms, and we present a model to describe the slump's development that emphasizes the role of coastally generated fragmental basalt on gravitational instability of Haleakala's northeast flank and that may be broadly applicable to other ocean-island slumps.

Hawai'i↗

USGS2014

A systematic approach towards the identification and protection of vulnerable marine ecosystems

The United Nations General Assembly in 2006 and 2009 adopted resolutions that call for the identification and protection of vulnerable marine ecosystems (VMEs) from significant adverse impacts of bottom fishing. While general criteria have been produced, there are no guidelines or protocols that elaborate on the process from initial identification through to the protection of VMEs. Here, based upon an expert review of existing practices, a 10-step framework is proposed: (1) Comparatively assess potential VME indicator taxa and habitats in a region; (2) determine VME thresholds; (3) consider areas already known for their ecological importance; (4) compile information on the distributions of likely VME taxa and habitats, as well as related environmental data; (5) develop predictive distribution models for VME indicator taxa and habitats; (6) compile known or likely fishing impacts; (7) produce a predicted VME naturalness distribution (areas of low cumulative impacts); (8) identify areas of higher value to user groups; (9) conduct management strategy evaluations to produce trade-off scenarios; (10) review and re-iterate, until spatial management scenarios are developed that fulfil international obligations and regional conservation and management objectives. To date, regional progress has been piecemeal and incremental. The proposed 10-step framework combines these various experiences into a systematic approach.

Marine Science↗

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↗

USGS2016

Regional monitoring programs in the United States: Synthesis of four case studies from Pacific, Atlantic, and Gulf Coasts

Water quality monitoring is a cornerstone of environmental protection and ambient monitoring provides managers with the critical data they need to take informed action. Unlike site-specific monitoring that is at the heart of regulatory permit compliance, regional monitoring can provide an integrated, holistic view of the environment, allowing managers to obtain a more complete picture of natural variability and cumulative impacts, and more effectively prioritize management actions. By reviewing four long-standing regional monitoring programs that cover portions of all three coasts in the United States – Chesapeake Bay, Tampa Bay, Southern California Bight, and San Francisco Bay – important insights can be gleaned about the benefits that regional monitoring provides to managers. These insights include the underlying reasons that make regional monitoring programs successful, the challenges to maintain relevance and viability in the face of ever-changing technology, competing demands and shifting management priorities. The lessons learned can help other managers achieve similar successes as they seek to establish and reinvigorate their own monitoring programs.

California, Delaware, Florida, Maryland, New Jerse↗

USGS2016

Chesapeake Bay recovery and factors affecting trends: Long-termmonitoring, indicators, and insights

Monitoring the outcome of restoration efforts is the only way to identify the status of a recovery and the most effective management strategies. In this paper, we discuss Chesapeake Bay and watershed recovery and factors influencing water quality trends. For over 30 years, the Chesapeake Bay Program Partnership’s long-term tidal and watershed water quality monitoring networks have measured physical, chemical and biological parameters throughout the bay and its surrounding watershed underpinning an adaptive management process to drive ecosystem recovery. There are many natural and anthropogenic factors operating and interacting to affect the watershed and bay water quality recovery responses to management actions. Across habitats and indicators, the bay and its watershed continue to express a diverse spatial and temporal fabric of multiscale conditions, stressors and trends that show a range of health conditions and impairment s , as well as evidence of progress and degradation. Recurrent independent reviews of the monitoring program have driven a culture of continued adaptation of the monitoring networks to reflect ever evolving management information needs. The adherence to bay and watershed-wide consistent monitoring protocols provides monitoring data supporting analyses and development of scientific syntheses that underpin indicator and model development, regulatory assessments, targeting of management actions, evaluation of management effectiveness, and directing of priorities and policies.

Delaware, Maryland, Virginia↗

USGS2019

Life history, genetics, range expansion and new frontiers of the lionfish (Pterois volitans, Perciformes: Pteroidae) in Latin America

Pterois volitans (lionfish) is a midsize predatory fish commonly found in waters of the western Pacific and Indian Ocean. The species was first documented in Dania Beach, Florida (northwestern Caribbean) in 1985. Since that time the species has expanded its range rapidly to the Northwestern Atlantic Ocean, Gulf of Mexico, and Caribbean Sea. Since its introduction P. volitans has changed community structure and biodiversity of Caribbean reef communities and other coastal tropical ecosystems. Continuous introductions (accidental or intentional), limited natural predators, naïve-range prey behavior, high predation rates on competitors, continuous reproduction, and an extended period of larval dispersal have been the keys for successful invasion and rapid range extension of P. volitans . This invasion has become so severe that it has been recognized as one of the world’s top conservation issues. Here, we review the life history, behavior, and historical and contemporary genetic patterns that facilitate expansion and the colonization process. A greater understanding of lionfish biology, ecology, and the changes related to its present condition as a super-invader could improve current and future management strategies and new detection and response methodologies. We also examine new invasion frontiers that this species has the potential to colonize such as the eastern Pacific. This information will provide managers, the scientific community, and the civil society better tools for eradication, control and management of future invasions of this and other invasive species.

Caribbean Sea, Latin America↗

USGS2021

Stable isotopes used to infer trophic position of green turtles (Chelonia mydas) from Dry Tortugas National Park, Gulf of Mexico, United States

Evaluating resource use patterns for imperiled species is critical for understanding what supports their populations. Here we established stable isotope ( δ 13 "> δ13 C, δ 15 "> δ15 N) values for the endangered green sea turtle ( Chelonia mydas ) population found within the boundaries of Dry Tortugas National Park (DRTO), south Florida, USA. There is little gene flow between turtles sampled at DRTO and in other rookeries in Florida, underscoring the need to study this distinct population. Between 2008 and 2015 we collected multiple sample types (skin [homogenized epidermis/dermis], whole blood, red blood cells, plasma, carapace) from 151 unique green turtles, including 43 nesting females and 108 in-water captures; some individuals were resampled multiple times across years to evaluate consistency of isotope signatures. Isotopic ratios ranged from -27.3 to -5.4 for δ 13 "> δ 13 C and 3.7 to 10.6 for δ 15 "> δ 15 N. Using linear mixed models, we evaluated covariates (sample type, turtle size and year) that best explained the isotope patterns observed in turtle tissues. Predictions from the top model for δ 13 "> δ 13 C indicated a slight decrease over time and for δ 15 "> δ 15 N a slight increase in the middle sampling years (2010–2012); results indicated that turtle size appeared to be the driver behind the range in δ 13 "> δ 13 C and δ 15 "> δ 15 N observed in turtle skin. We found a pattern in stable carbon isotope values that are indicative of an ontogenetic change from an omnivorous diet in smaller turtles to a seagrass-based diet in larger turtles. When we compared the stable carbon and nitrogen isotope values of the samples collected from turtles with that of seagrasses found in DRTO, we found that turtles > 65 cm SCL had similar stable carbon isotope values to the seagrass species present. Results of this study suggest stable isotope analysis coupled with data for available resources can be useful for tracking and detecting future changes in green turtle resource shifts in DRTO.

Florida↗

USGS2023

Satellite tracking reveals use of Biscayne National Park by sea turtles tagged in multiple locations

Although historical observations date back to the 1800’s, there is little information on sea turtle occupancy within Biscayne National Park (BNP). The park is located along the Florida reef tract and is dominated by the Gulfstream, which acts as a corridor for many marine animals. Here we used satellite telemetry to determine areas of use in BNP for two species of imperiled sea turtles, loggerhead ( Caretta caretta ) and green ( Chelonia mydas ) turtles. We included data for turtles tagged between 2009–2021 at sites both within park waters and in five locations outside the park boundary; individuals were captured both in the water and on land. We tagged 60 individuals (female, n = "> = 48; male, n = "> = 3; immature, n = "> = 9); loggerheads (n = "> = 33) ranged in size from 66.2 to 109.9 cm CCL (curved carapace length) and green turtles (n = "> = 27) ranged in size from 39.1 to 111.9 cm CCL. We used behavioral switching state-space modeling (SSM) to obtain daily predicted positions for each turtle, classified turtle behavior within the park as either foraging, migration, or both foraging and migration, and summarized high-use areas for each species across all months of the year. Turtles used park waters year-round, with concentrated use of deeper waters during seasonal migrations. Across all 60 turtles, 21 spent their tracking time foraging within BNP boundaries and 30 used the park as part of their migratory pathway; five turtles used the park for both foraging and migration, and the remaining four had SSM points very close to the park. Loggerhead migration occurred from February through November, whereas green turtle migration was concentrated in August. Both turtle species exhibited high overlap (i.e., usage) with seagrass habitat. These findings are relevant as managers consider strategies to minimize anthropogenic impacts to resident and migratory sea turtles using park waters.

Florida↗

USGS2024

Long-term trends in abundance and potential drivers for eight species of coastal birds in the U.S. South Atlantic

The U.S. South Atlantic coastal region is used by many marine birds for foraging, reproduction, and migration. We developed standardized indices of relative abundance from long–term (1980–2016), semi-structured monitoring data (eBird) for eight species: Brown Pelican ( Pelecanus occidentalis ), Double-Crested Cormorant ( Nannopterum auritum ), White Ibis ( Eudocimus albus ), Wood Stork ( Mycteria americana ), Piping Plover ( Charadrius melodus ), American Oystercatcher ( Haematopus palliatus ), Clapper Rail ( Rallus crepitans ), and Northern Gannet ( Morus bassanus ). Following a period of stable or declining abundance from the 1980s through the 1990s, most species have shown stable or slightly upward trends through the late 2000s; Brown Pelican and Piping Plover have shown some evidence of recent declines. Species–specific correlations between abundance indices developed from presence/absence data and those developed from count data were positive for all species and ranged from 0.53 to 0.86. Dynamic factor analysis identified common trends in abundance among several species, in particular, Brown Pelican, Double–Crested Cormorant, and White Ibis. Model performance was improved with inclusion of an indicator of sea level rise, but not forage fish abundance or temperature, indicating habitat availability mediated by changing water levels may explain some of the underlying abundance trends. Our results provide baseline information on long–term trends for several important coastal birds that can help inform research, monitoring and conservation efforts in the U.S. South Atlantic region.

Florida, Georgia, North Carolina, South Carolina↗

USGS2007

Constancy of the relation between floc size and density in San Francisco Bay

The size and density of fine-sediment aggregates, or flocs, govern their transport and depositional properties. While the mass and volume concentrations of flocs can be measured directly or by optical methods, they must be determined simultaneously to gain an accurate density measurement. Results are presented from a tidal cycle study in San Francisco Bay, where mass concentration was determined directly, and volume concentration was measured in 32 logarithmically spaced size bins by laser-diffraction methods. The relation between floc size and density is investigated assuming a constant primary particle size and fractal floc dimension. This relation is validated with measurements from several sites throughout San Francisco Bay. The constancy of this relation implies a uniform primary particle size throughout the Bay, as well as uniform aggregation/disaggregation mechanisms (which modify fractal dimension). The exception to the relation is identified during near-bed measurements, when adverted flocs mix with recently resuspended flocs from the bed, which typically have a higher fractal dimension than suspended flocs. The constant relation for suspended flocs simplifies monitoring and numerical modeling of suspended sediment in San Francisco Bay.

California↗

USGS2007

Sensitivity of estuarine turbidity maximum to settling velocity, tidal mixing, and sediment supply

Estuarine turbidity maximum, numerical modeling, settling velocity, stratification The spatial and temporal distribution of suspended material in an Estuarine Turbidity Maxima (ETM) is primarily controlled by particle settling velocity, tidal mixing, shear-stress thresholds for resuspension, and sediment supply. We vary these parameters in numerical experiments of an idealized two-dimensional (x-z) estuary to demonstrate their affects on the development and retention of particles in an ETM. Parameters varied are the settling velocity (0.01, 0.1, and 0.5 mm/s), tidal amplitude (0.4 m 12 hour tide and 0.3 to 0.6 m 14 day spring neap cycle), and sediment availability (spatial supply limited or unlimited; and temporal supply as a riverine pulse during spring vs. neap tide). Results identify that particles with a low settling velocity are advected out of the estuary and particles with a high settling velocity provide little material transport to an ETM. Particles with an intermediate settling velocity develop an ETM with the greatest amount of material retained. For an unlimited supply of sediment the ETM and limit of salt intrusion co-vary during the spring neap cycle. The ETM migrates landward of the salt intrusion during spring tides and seaward during neap tides. For limited sediment supply the ETM does not respond as an erodible pool of sediment that advects landward and seaward with the salt front. The ETM is maintained seaward of the salt intrusion and controlled by the locus of sediment convergence in the bed. For temporal variability of sediment supplied from a riverine pulse, the ETM traps more sediment if the pulse encounters the salt intrusion at neap tides than during spring tides. ?? 2007 Elsevier B.V. All rights reserved.

Proceedings in Marine Science↗