J. Mar. Sci. Eng., Volume 3, Issue 4 (December 2015) – 20 articles , Pages 1149-1594

Using new large-scale wave-flume experiments we examine the cross-section and planform geometry of wave-formed ripples in coarse sand (median grain size D₅₀ = 430 μm) under high-energy shoaling and plunging random waves. We find that the ripples remain orbital for the full range of encountered conditions, even for wave forcing when in finer sand the ripple length λ_r is known to become independent of the near-bed orbital diameter d_s (anorbital ripples). The proportionality between λ_r and d_s is not constant, but decreases from about 0.55 for d_s / D₅₀ ≈ 1400 to about 0.27 for d_s / D₅₀ ≈ 11 , 500 . Analogously, ripple height η_r increases with d_s, but the constant of proportionally decreases from about 0.08 for d_s / D₅₀ ≈ 1400 to about 0.02 for d_s / D₅₀ > 8000 . In contrast to earlier observations of coarse-grained two-dimensional wave ripples under mild wave conditions, the ripple planform changes with the wave Reynolds number from quasi two-dimensional vortex ripples, through oval mounds with ripples attached from different directions, to strongly subdued hummocky-type features. Finally, we combine our data with existing mild-wave coarse-grain ripple data to develop new equilibrium predictors for ripple length, height and steepness suitable for a wide range of wave conditions and a D₅₀ larger than about 300 μm. Full article

The importance of small-scale seismic events in enclosed water bodies, which can result in large tsunami waves capable of affecting comprehensive damage over small, geographically-confined areas are generally overlooked, although recognizing the occurrence of such events is a necessary element in adequately assessing the risk of natural hazards at specific locations. Here we present evidence for a probable large localized tsunami that occurred within the Bay of La Paz, Baja California Sur, ~1100 year before present (BP), which resulted in the creation of a shelly ridge at an elevation of ~2 m above mean high water (MHW). This ridge consists of a continuous wedge of poorly mixed marine sands and shells ~50 cm in depth deposited along the entire seaward edge of the lake. The marine shells collected from terrestrial environments around the lake include species from a variety of environments, including offshore species with minimum preferred depths of >13 m. The evidence suggests that this material was likely deposited by a tsunami with a runup of 2–3.6 m above MHW, probably associated with the slumping of an island along the tectonically active eastern edge of the bay. Full article

We introduce a model for the dynamics of oil in suspension, appropriate for shallow waters, including the nearshore environment. This model is capable of oil mass conservation and does so by evolving the oil on the sea surface as well as the oil in the subsurface. The shallower portion of the continental shelf poses compounding unique modeling challenges. Many of these relate to the complex nature of advection and dispersion of oil in an environment in which wind, waves, as well as currents all play a role, as does the complex bathymetry and the nearshore geography. In this study we present an overview of the model as well as derive the most fundamental of processes, namely, the shallow water advectiion and dispersion processes. With regard to this basic transport, we superate several fundamental challenges associated with creating a transport model for oil and other buoyant pollutants, capable of capturing the dynamics at the large spatio-temporal scales demanded by environmental and hazard mitigation studies. Some of the strategies are related to dimension reduction and upscaling, and leave discussion of these to companion papers. Here we focus on wave-filtering, ensemble and depth-averaging. Integral to the model is the proposal of an ocean dynamics model that is consistent with the transport. This ocean dynamics model is detailed here. The ocean/oil transport model is applied to a couple of physically-inspired oil-spill problems in demonstrate its specialized capabilities. Full article

The protection of a boat canal at the western entrance of Tangier Island, Virginia, located in the lower Chesapeake Bay, is investigated using different structural alternatives. The existing entrance channel is oriented 45 deg with respect to the local shoreline, and exposed directly to the lower Bay without any protection. The adjacent shoreline has experienced progressive erosion in recent decades by flooding due to severe storms and waves. To protect the western entrance of the channel and shoreline, five different jetty and spur combinations were proposed to reduce wave energy in the lee of jetties. Environmental forces affecting the proposed jettied inlet system are quantified using the Coastal Modeling System, consisting of a spectral wave model and a depth-averaged circulation model with sediment transport calculations. Numerical simulations were conducted for design wave conditions and a 50-year return period tropical storm at the project site. Model results show a low crested jetty of 170-m length connecting to the north shore at a 45-deg angle, and a short south spur of 25-m long, provide adequate wave-reduction benefits among the five proposed alternatives. The model simulation indicates this alternative has the minimum impact on sedimentation around the structured inlet and boat canal. Full article

The Aphia platform is an infrastructure designed to capture taxonomic and related data and information, and includes an online editing environment. The latter allows easy access to experts so they can update the content of the database in a timely fashion. Aphia is the core platform that underpins the World Register of Marine Species (WoRMS) and its more than 80 related global, regional and thematic species databases, but it also allows the storage of non-marine data. The content of Aphia can be consulted online, either by individual users or via machine-to-machine interactions. Aphia uses unique and stable identifiers for each available name in the database through the use of Life Science Identifiers (LSIDs). The system not only allows the storage of accepted and unaccepted names, but it also documents the relationships between names. This makes it a very powerful tool for taxonomic quality control, and also allows the linking of different pieces of information through scientific names, both within the Aphia platform and in relation to externally hosted databases. Through these LSIDs, Aphia has become an important player in the field of (marine) biodiversity informatics, allowing interactions between its own taxonomic data and e.g., biogeographic databases. Some applications in the field of biodiversity informatics encompass the coupling of species traits and taxonomy, as well as the creation of diverse, expert validated data products that can be used by policy makers, for example. Aphia also supplies (part of) its content to other data integrators and the infrastructure can be used to host orphan databases in danger of being lost. Full article

Predicting the effects of anthropogenic CO₂ emissions on coastal ecosystems requires an understanding of the responses of algae, since these are a vital functional component of shallow-water habitats. We investigated microphytobenthic assemblages on rock and sandy habitats along a shallow subtidal pCO₂ gradient near volcanic seeps in the Mediterranean Sea. Field studies of natural pCO₂ gradients help us understand the likely effects of ocean acidification because entire communities are subjected to a realistic suite of environmental stressors such as over-fishing and coastal pollution. Temperature, total alkalinity, salinity, light levels and sediment properties were similar at our study sites. On sand and on rock, benthic diatom abundance and the photosynthetic standing crop of biofilms increased significantly with increasing pCO₂. There were also marked shifts in diatom community composition as pCO₂ levels increased. Cyanobacterial abundance was only elevated at extremely high levels of pCO₂ (>1400 μatm). This is the first demonstration of the tolerance of natural marine benthic microalgae assemblages to elevated CO₂ in an ecosystem subjected to multiple environmental stressors. Our observations indicate that Mediterranean coastal systems will alter as pCO₂ levels continue to rise, with increased photosynthetic standing crop and taxonomic shifts in microalgal assemblages. Full article

A large number of studies have been conducted on organic carbon (OC) variation in mangrove ecosystems. However, few have examined its relationship with soil quality and stratigraphic condition. Mangrove OC characteristics would be explicitly understood if those two parameters were taken into account. The aim of this study was to examine mangrove OC characteristics qualitatively and quantitatively after distinguishing mangrove OC from other OC. Geological survey revealed that the underground of a mangrove ecosystem was composed of three layers: a top layer of mangrove origin and two underlying sublayers of geologic origin. The underlying sublayers were formed from different materials, as shown by X-ray fluorescence analysis. Despite a large thickness exceeding 700 cm in contrast to the 100 cm thickness of the mangrove mud layer, the sublayers had much lower OC stock. Mangrove mud layer formation started from the time of mangrove colonization, which dated back to between 1330 and 1820 ¹⁴C years BP, and OC stock in the mangrove mud layer was more than half of the total OC stock in the underground layers, which had been accumulating since 7200 ¹⁴C years BP. pH and redox potential (Eh) of the surface soils varied depending on vegetation type. In the surface soils, pH correlated to C% (r = −0.66, p < 0.01). C/N ratios varied widely from 3.9 to 34.3, indicating that mangrove OC had various sources. The pH and Eh gradients were important factors affecting the OC stock and the mobility/uptake of chemical elements in the mangrove mud layer. Humic acids extracted from the mangrove mud layer had relatively high aliphatic contents, in contrast with the carboxylic acid rich sublayers, indicating that humification has not yet progressed in mangrove soil. Full article

San Diego, one of the largest ports on the U.S. West Coast and home to the largest U.S. Navy base, is exposed to various local and distant tsunami sources. During the first half of the twentieth century, extensive modifications to the port included but were not limited to dredging, expansion of land near the airport and previous tidal flats, as well as creation of jetties. Using historical nautical charts and available Digital Elevation Models, this study gives an overview of changes to San Diego harbor in the last 150+ years due to human intervention and examines the effects of these changes on tsunamis. Two distant and two local scenarios were selected to demonstrate the impact of modified nearshore topography and bathymetry to incoming tsunamis. Inundation pattern, flow depths, and flooded localities vary greatly from year to year in the four scenarios. Specifically, flooded areas shift from the inner harbor to outer locations. Currents induced by the distant tsunamis intensify with modifications and shift from locations primarily outside the harbor to locations inside. A new characteristic in tsunami dynamics associated with port modifications is the introduction of high current spots. Numerical results also show that the introduction of high currents could threaten navigation, vessels, and facilities at narrow openings and also along the harbor “throat”—therefore, at an increased number of locations. Modifications in the port show that changes could have a negative but also a positive impact through constraint of flooding outside of the harbor and shifting of high currents to locations of minimal impact. The results of this study may be used as a first step toward future harbor design plans to reduce tsunami damages. Full article

One of the main aspects when testing floating offshore platforms is the scaled mooring system, particularly with the increased depths where such platforms are intended. The paper proposes the use of truncated mooring systems to emulate the real mooring system by solving an optimization problem. This approach could be an interesting option when the existing testing facilities do not have enough available space. As part of the development of a new spar platform made of concrete for Floating Offshore Wind Turbines (FOWTs), called Windcrete, a station keeping system with catenary shaped lines was selected. The test facility available for the planned experiments had an important width constraint. Then, an algorithm to optimize the design of the scaled truncated mooring system using different weights of lines was developed. The optimization process adjusts the quasi-static behavior of the scaled mooring system as much as possible to the real mooring system within its expected maximum displacement range, where the catenary line provides the restoring forces by its suspended line length. Full article

Technology Readiness Levels (TRLs) are a widely used metric of technology maturity and risk for marine renewable energy (MRE) devices. To-date, a large number of device concepts have been proposed which have reached the early validation stages of development (TRLs 1–3). Only a handful of mature designs have attained pre-commercial development status following prototype sea trials (TRLs 7–8). In order to navigate through the aptly named “valley of death” (TRLs 4–6) towards commercial realisation, it is necessary for new technologies to be de-risked in terms of component durability and reliability. In this paper the scope of the reliability assessment module of the DTOcean Design Tool is outlined including aspects of Tool integration, data provision and how prediction uncertainties are accounted for. In addition, two case studies are reported of mooring component fatigue testing providing insight into long-term component use and system design for MRE devices. The case studies are used to highlight how test data could be utilised to improve the prediction capabilities of statistical reliability assessment approaches, such as the bottom–up statistical method. Full article

Micronuclei, comet and chromosome alterations assays are the most widely used biomarkers for determining the genotoxic damage in a population exposed to genotoxic chemicals. While chromosome alterations are an excellent biomarker to detect short- and long-term genotoxic effects, the comet assay only measures early biological effects, and furthermore it is unknown whether nuclear abnormalies, such as those measured in the micronucleus test, remain detectable long-term after an acute exposure. In our previous study, an increase in structural chromosome alterations in fishermen involved in the clean-up of the Prestige oil spill, two years after acute exposure, was detected. The aim of this study is to investigate whether, in lymphocytes from peripheral blood, the nuclear abnormalies (micronucleus, nucleoplasmic bridges and nuclear buds) have a similar sensitivity to the chromosome damage analysis for genotoxic detection two years after oil exposure in the same non-smoker individuals and in the same peripheral blood extraction. No significant differences in nuclear abnormalies frequencies between exposed and non-exposed individuals were found (p > 0.05). However, chromosome damage, in the same individuals, was higher in exposed vs. non-exposed individuals, especially for chromosome lesions (p < 0.05). These findings, despite the small sample size, suggest that nuclear abnormalities are probably less-successful biomarkers than are chromosome alterations to evaluate genotoxic effects two or more years after an exposure to oil. Due to the great advantage of micronucleus automatic determination, which allows for a rapid study of hundreds of individuals exposed to genotoxic chemical exposure, further studies are needed to confirm whether this assay is or is not useful in long-term genotoxic studies after the toxic agent is no longer present. Full article

We examine the role of the vegetation cover and the associated hydrological cycle on the deep ocean circulation during the Late Miocene (~10 million years ago). In our simulations, an open Central American gateway and exchange with fresh Pacific waters leads to a weak and shallow thermohaline circulation in the North Atlantic Ocean which is consistent with most other modeling studies for this time period. Here, we estimate the effect of a changed vegetation cover on the ocean general circulation using atmospheric circulation model simulations for the late Miocene climate with 353 ppmv CO₂ level. The Late Miocene land surface cover reduces the albedo, the net evaporation in the North Atlantic catchment is affected and the North Atlantic water becomes more saline leading to a more vigorous North Atlantic Deep Water circulation. These effects reveal potentially important feedbacks between the ocean circulation, the hydrological cycle and the land surface cover for Cenozoic climate evolution. Full article

Highly-dynamic floating bodies such as wave energy convertors require mooring lines with particular mechanical properties; the mooring system must achieve adequate station keeping whilst controlling mooring tensions within acceptable limits. Optimised compliant mooring systems can meet these requirements but where compliance is achieved through system architecture, the complexity of the system increases together with the mooring footprint. This work introduces the “Exeter Tether”, a novel fibre rope mooring tether providing advantages over conventional fibre ropes. The tether concept aims to provide a significantly lower axial stiffness by de-coupling this attribute from the minimum breaking load of the line. A benefit of reduced axial stiffness is the reduction of mooring system stiffness providing a reduction of peak and fatigue loads, without increasing mooring system complexity. Reducing these loads improves system reliability and allows a reduction in mass of both the mooring system and the floating body, thus reducing costs. The principles behind the novel tether design are presented here, along with an outline of eight prototype tether variants. Results from the proof of concept study are given together with preliminary findings from sea trials conducted in Falmouth Bay. Results demonstrate that the Exeter Tether can be configured to achieve a significantly lower axial stiffness than conventional fibre rope and that the stiffness is selectable within limits for a given breaking strength. Strain values greater than 0.35 are achieved at 30% of line breaking strength; this represents more than a threefold increase of the strain achievable with a conventional rope of the same material. The tether was subjected to six months of sea trials to establish any threats to its own reliability and to inform future design enhancements in this respect. Full article

The periodic rise in seawater temperature is one of the main environmental determinants of coral bleaching. However, the direct incidence of these episodic thermal anomalies on coral-associated microbiota and their subsequent effects on coral health are still not completely understood. In this study, we investigated the dynamics of three main microbial communities of the coral holobiont (e.g., Symbiodinium, bacteria and viruses), during an experimental thermal stress (+4 °C) conducted on the scleractinian Fungia repanda. The heat-treatment induced coral bleaching after 11 days and resulted in a final elevation of ca. 9, 130 and 250-fold in the abundance of mucosal viruses, bacteria, and Symbiodinium, respectively. On the contrary, the proportion of actively respiring bacterial cells declined by 95% in heat-stressed corals. The community composition of epibiotic bacteria in healthy corals also greatly differed from bleached ones, which also exhibited much higher production rates of viral epibionts. Overall, our results suggest that the shift in temperature induced a series of microbial changes, including the expulsion and transfer of Symbiodinium cells from the coral polyps to the mucus, the collapse of the physiological state of the native bacterial associates, a substantial alteration in their community structure, and accompanied by the development of a cortege of highly active virulent phages. Finally, this study provides new insights into the environmentally-driven microbial and viral processes responsible for the dislocation of the coral holobiont. Full article

Mental health issues are a significant concern after technological disasters such as the 2010 Gulf Oil Spill; however, there is limited knowledge about the long-term effects of oil spills. The study was part of a larger research effort to improve understanding of the mental and behavioral health effects of the Deepwater Horizon Gulf Oil Spill. Data were collected immediately following the spill and the same individuals were resampled again after the second anniversary (n = 314). The results show that mental health symptoms of depression, serious mental illness and posttraumatic stress have not statistically decreased, and anxiety symptoms were statistically equivalent to immediate symptoms. Results also showed that the greatest effect on anxiety is related to the extent of disruption to participants’ lives, work, family, and social engagement. This study supports lessons learned following the Exxon Valdez spill suggesting that mental health effects are long term and recovery is slow. Elevated symptoms indicate the continued need for mental health services, especially for individuals with high levels of disruption resulting in increased anxiety. Findings also suggest that the longer-term recovery trajectories following the Deepwater Horizon Gulf Oil Spill do not fall within traditional disaster recovery timelines. Full article

Global demand for petroleum keeps increasing while traditional supplies decline. One alternative to the use of conventional crude oils is the utilization of Canadian bitumen. Raw bitumen is a dense, viscous, semi-liquid that is diluted with lighter crude oil to permit its transport through pipelines to terminals where it can then be shipped to global markets. When spilled, it naturally weathers to its original form and becomes dense enough to sink in aquatic systems. This severely limits oil spill recovery and remediation options. Here we report on the application of charred hay as a method for modifying the surface behavior of bitumen in aquatic environments. Waste or surplus hay is abundant in North America. Its surface can easily be modified through charring and/or chemical treatment. We have characterized the modified and charred hay using solid-state NMR, contact angle measurements and infrared spectroscopy. Tests of these materials to treat spilled bitumen in model aquatic systems have been undertaken. Our results indicate that bitumen spills on water will retain their buoyancy for longer periods after treatment with charred hay, or charred hay coated with calcium oxide, improving recovery options. Full article

Domestication is a long and endless process during which animals become, generations after generations, more adapted to both captive conditions and humans. Compared to land animals, domestication of fish species has started recently. This implies that most farmed marine fish species have only changed slightly from their wild counterparts, and production is based partly or completely on wild inputs. In the past decades, global marine fish production has increased tremendously, particularly since the 1990s, to reach more than 2.2 million tons in 2013. Among the 100 marine fish species listed in the FAO’s database in 2013, 35 are no longer produced, and only six have a production higher than 100,000 tons. The top ten farmed marine species accounted for nearly 90% of global production. The future growth and sustainability of mariculture will depend partly on our ability to domesticate (i.e., control the life cycle in captivity) of both currently farmed and new species. Full article

The effect of an ionospheric dynamo electric field on the electron density and total electron content (TEC) perturbations in the F layer (150–600 km altitudes) is investigated at two arbitrarily selected locations (noted as 29° N and 60° N in latitudes) in the presence of seismic tsunami-excited gravity waves propagating in a stratified, nondissipative atmosphere where vertical gradients of atmospheric properties are taken into consideration. Generalized ion momentum and continuity equations are solved, followed by an analysis of the dynamo electric field (E). The E -strength is within several mV/m, determined by the zonal neutral wind and meridional geomagnetic field. It is found that, at the mid-latitude location, n0 e is dominated by the atmospheric meridional wind when E = 0, while it is determined by the zonal wind when E ≠ 0. The perturbed TEC over its unperturbed magnitude lies in around 10% at all altitudes for E = 0, while it keeps the same percentage at most altitudes for E ≠ 0, except a jump to >25% in the F2-peak layer (300–340 km in height). By contrast, at the low-latitude location, the TEC jump is eliminated by the locally enhanced background electron density. Full article

A distinct difference of the earthquake activity in megathrust subduction zones is pointed out, concerning seismic segmentations in the vicinity of Japan—that is, the apparent distribution of earthquake hypocenters characterized by Along-dip Double Segmentation (ADDS) and Along-strike Single Segmentation (ASSS). ADDS is double aligned seismic-segmentation of trench-ward seismic segments along the Japan Trench and island-ward seismic segments along the Pacific coast of the Japan Islands. The 2011 Tohoku-oki megathrust earthquake of Mw9.0 occurred in ADDS. In the meantime, the subduction zone along the Nankai Trough, the western part of Japan, is the source region of a multiple rupture of seismic segments by the 1707 Houei earthquake, the greatest earthquake in the history of Japan. This subduction zone is narrow under the Japan Islands, which is composed of single aligned seismic-segmentation side by side along the Nankai Trough, which is typical of ASSS. Looking at the world seismicity, the 1960 and 2010 Chile megathrusts, for example, occurred in ASSS, whereas the 1952 Kamchatka and the 1964 Alaska megathrusts occurred in ADDS. These megathrusts in ADDS result from the rupture of strong asperity in the trench-ward seismic segments. Since the asperity of earthquakes in ASSS is concentrated in the shallow part of subduction zones and the asperity of frequent earthquakes in ADDS is in deeper parts of the island-ward seismic segments than those of ASSS, there must be a difference in tsunami excitations due to earthquakes in ADDS and ASSS. An analysis was made in detail of tsunami and seismic excitations of earthquakes in the vicinity of Japan. Tsunami heights of ASSS earthquakes are about two times larger than those of ADDS earthquakes with the same value of seismic moment. The reason for this different tsunami excitation is also considered in relation to the seismic segmentations of ADDS and ASSS. Full article

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. Full article