J. Mar. Sci. Eng., Volume 4, Issue 1 (March 2016) – 28 articles

Ocean Acidification (OA) represents a major field of research and increased efforts are being made to elucidate its repercussions on biota. Species survival is ensured by successful reproduction, which may be threatened under detrimental environmental conditions, such as OA acting in synergy with other climate change related stressors. Achieving successful gametogenesis, fertilization, and the development of larvae into healthy juveniles and adults is crucial for the perpetuation of species and, thus, ecosystems’ functionality. The considerable vulnerability of the abovementioned developmental stages to the adverse conditions that future OA may impose has been shown in many species, including sea urchins which are commonly used due to the feasibility of their maintenance in captivity and the great amount of gametes that a mature adult is able to produce. In the present review, the latest knowledge about the impact of OA on various stages of the life cycle of sea urchins is summarized with remarks on the possible impact of other stressors. The cellular physiology of the gametes before, at fertilization and, at early development, is extensively described with a focus on the complex enzymatic machinery and the intracellular pH (pH_i) and Ca²⁺ homeostasis for their vulnerability when facing adverse conditions such as acidification, temperature variations, or hypoxia. Full article

Several methods of monitoring sediment transport exist and have varying degrees of success depending on the study sites characteristics. Grain Size Trend Analysis (GSTA) is an experimental method based on identifying transport trends from the variation of sediment grain characteristics within a defined study area. The parameters examined when performing GSTA are mean grain size, sorting coefficient and skewness, the most common cases found in field studies being; finer, better sorted and negatively skewed (FB−) or coarser, better sorted and positively skewed (CB+), as most transport trends follow one or the other trend. However, on Rossbeigh beach, Co. Kerry, Ireland, a coarser poorer and more negatively skewed (CP−) trend case gave the most realistic plot of sediment transport trend when compared with sediment transport calculation, bathymetry surveys, hydrodynamic monitoring and morphological modelling. Full article

The backscatter response of a seabed to an incident sonar signal is dependent on the carrier wave frequency: i.e., the seabed is acoustically colourful. Colour is implemented in a prototype three-frequency sidescan sonar system deployed in the Pentland Firth, north Scotland. Sonar amplitude data as a function of frequency are processed to render them an unconfounded effect of the seabed normalized to the response at a reference inclination angle, for colour to be a meaningful property of the seabed. Methods for mapping data at sonar frequencies to optical primary colours for human visualisation are explored. We recommend methods that in our opinion generate colour characteristics harmonious with human vision in which: shadow is white; saturation black; colour shade darkness is proportional to backscatter strength; and shades of red, green and blue are seen in proportion to the backscatter amplitudes of the low-, mid- and high-frequency sonar data. Frequency equalisation is applied to achieve a balance in colour responses in images. The seabed in the survey area is acoustically colourful. Using the “negative BGR” colour mapping method: a weakly backscattering sand dune in the north of the survey area appears as shades of light blue and purple; a strongly backscattering halo of cobbles around the dune appears as shades of hazel brown; a strongly backscattering gravel ridge across the south of the survey area appears as shades of royal blue; and exposed rock as textures ranging in colour from light brown to light blue/green. There is evidence for colour anisotropy (a dependence of colour on the direction of ensonification). Similarities between anthropic colour sonar and the natural sonar of Microchiropteran bats are noted. Bats’ sonar satisfies the information criteria for acoustic colour, and it is hypothesized that it informs a colourfully-perceived world view. Full article

The release of oil into the Gulf of Mexico (GOM) during the Deepwater Horizon event coincided with the white and pink shrimp spawning season. To determine the potential impact on shrimp larvae a series of static acute (24–96 h) toxicity studies with water accommodated fractions (WAFs) of Macondo Canyon (MC) 252 crude oil, the Corexit 9500A dispersant, and chemically enhanced WAFS (CEWAFs) were conducted with nauplii, zoea, mysid, and postlarval Farfantepenaeus duorarum. Median lethal concentrations (LC₅₀) were calculated and behavior responses (swimming, molting, light sensitivity) evaluated. Impacts were life stage dependent with zoea being the most sensitive. Behavioral responses for all stages, except postlarvae, occurred at below LC₅₀ values. Dispersants had the greatest negative impact while WAFs had the least. No short-term effects (survival, growth) were noted for nauplii exposed to sub-lethal CEWAFs 39 days post-exposure. This study points to the importance of evaluating multiple life stages to assess population effects following contaminant exposure and further, that the use of dispersants as a method of oil removal increases oil toxicity. Full article

We study the atmospheric structure in response to the propagation of gravity waves under nonisothermal (nonzero vertical temperature gradient), wind-shear (nonzero vertical zonal/meridional wind speed gradients), and dissipative (nonzero molecular viscosity and thermal conduction) conditions. As an alternative to the “complex wave-frequency” model proposed by Vadas and Fritts, we employ the traditional “complex vertical wave-number” approach to solving an eighth-order complex polynomial dispersion equation. The empirical neutral atmospheric models of NRLMSISE-00 and HWM93 are employed to provide mean-field properties. In response to the propagation of gravity waves, the atmosphere is driven into three sandwich-like layers: the adiabatic layer (0–130 km), the dissipation layer (130–230 km) and the pseudo-adiabatic layer (above 230 km). In the lower layer, (extended-)Hines’ mode or ordinary dissipative wave modes exist, whereas viscous dissipation and thermal conduction fail to exert perceptible influences; in the middle layer, Hines’ mode ceases to exist, and both ordinary and extraordinary dissipative wave modes flourish; in the top layer, only extraordinary wave modes survive, and dissipations affect the real part of the vertical wavenumber ( m r ) substantially; however, they contribute little to the imaginary part, which is the vertical growth rate ( m i ). We also analyze the transition of Hines’ classical mode to ordinary dissipative wave modes, describe both the upward and downward modes of gravity waves and illustrate nonisothermal and wind-shear effects on the propagation of gravity waves of different modes. Full article

Unconventionally-produced crude oils, i.e., Bakken oil and bitumen diluted for transport and known as dilbit, have become prominent components of the North American petroleum industry. Spills of these oils have occurred during transport from production areas to refineries via pipeline, rail, and barge. Some of their physical and chemical properties are distinct and present new challenges in mitigating spill impacts on people and the environment. This paper describes the adaptation of a qualitative risk assessment process to improve spill preparedness and response decisions for these oils when transported in an estuarine area. The application of this collaborative, interdisciplinary process drew upon a literature review, the local knowledge and experience of a broad set of decision makers, practitioners, and technical experts who developed consensus-based recommendations aimed at improving response to spills of these oils. Two emphasized components of this consensus ecological risk assessment (CERA) concerned risks: (1) to human health and safety and (2) from spilled oil and the associated response actions on endangered species. Participants in the process defined levels of concern associated with Bakken and dilbit oils relative to a set of response actions in freshwater, brackish and saltwater habitats and on resources at risk. Full article

Extreme environmental conditions in the deep sea hamper access to protist communities. In combination with the potentially highly diverse species composition, it demands a wide range of methods to be applied at the same time to guarantee a high resolution of quantitative and qualitative studies of deep-sea heterotrophic flagellates (HF). Within this study, we present a possible combination of several culture-independent and culture-dependent methods available for investigating benthic deep-sea HF communities. Besides live-counting and fixation of HF, we refer to cultivation methods and molecular surveys using next generation sequencing. Laboratory ecological experiments under deep-sea conditions (high pressure, low temperature) could allow the approval of the potential deep-sea origin of sampled HF. The combination of different methods offers a unique possibility to receive detailed information on nanofaunal life in the deep sea. Specific fixation techniques to preserve samples directly at the sampling depth must be applied in further studies to reflect the real biodiversity of the largest habitat on earth. Full article

Heterogeneity can boost biodiversity, as well as increase the resilience of an ecosystem to changing environmental conditions; therefore, it is important to understand how topographic heterogeneity in ecosystems is formed. Sandy tidal marshes have a repetitive pattern of higher elevated hummocks surrounded by lower elevated depressions, representing topographic heterogeneity at the scale of a few square meters. The aims of this study were to determine when this topographic heterogeneity forms, how it is structured, and whether it persists during marsh development. The soil topography of marshes consists of coarse-grained sediment formed before marsh vegetation development, with an overlaying fine-grained sediment layer formed after initial marsh development. To gain insight into the formation of topographic heterogeneity, we studied the underlying soil topography of four European sandy marshes, where topographic heterogeneity at a scale of a few square meters was present. The differences in elevation between hummocks and depressions can either be caused by heterogeneity in the coarse-grained sediment or by heterogeneity in the top layer containing the fine-grained sediment. Our results showed that the largest percentage of elevational differences between hummocks and depressions could be attributed to heterogeneity in the underlying coarse-grained substratum. Therefore, we conclude that the patterns in all four marshes were primarily formed before marsh development, before fine-grained sediment was deposited on top of the coarse-grained sediment. However, a smaller percentage of the elevational difference between hummocks and depressions can also be explained by the presence of thicker fine-grained sediment layers on top of hummocks compared with depressions. This implies that marsh accretion rates were higher on hummocks compared with depressions. However, this result was limited to very early stages of marsh development, as marsh accretion rates estimated on marshes ranging between 15- and 120-years-old showed that depressions actually accreted sediments at a significantly faster rate than hummocks. Eventually, the patterns of heterogeneity stabilized and we found similar marsh accretion rates on hummocks and in depressions in the 120-year-old marsh, which resulted in the persistency of these topographic patterns. Full article

Current climate policy and issues of energy security mean wind farms are being built at an increasing rate to meet energy demand. As wind farm development is very likely in the Mediterranean Sea, we provide an assessment of the offshore wind potential and identify expected biological effects of such developments in the region. We break new ground here by identifying potential offshore wind farm (OWF) “hotspots” in the Mediterranean. Using lessons learned in Northern Europe, and small-scale experiments in the Mediterranean, we identify sensitive species and habitats that will likely be influenced by OWFs in both these hotspot areas and at a basin level. This information will be valuable to guide policy governing OWF development and will inform the industry as and when environmental impact assessments are required for the Mediterranean Sea. Full article

Tidal energy is nowadays one of the fastest growing types of marine renewable energy. In particular, Horizontal Axis Tidal Turbines (HATTs) are the most advanced designs and the most appropriate for standardization. This paper presents a review of actual design criteria focusing on the identification of the uncertainties that technology developers need to address during the design process. Key environmental parameters like turbine inflow conditions or predictions of extreme values are still grey areas due to the lack of site measurements and the uncertainty in metocean model predictions. A comparison of turbulence intensity characterization using different tools and at different points in time shows the uncertainty in the prediction of this parameter. Numerical models of HATTs are still quite uncertain, often dependent on experience of the people running them. In the reliability-based calibration of partial safety factors, the uncertainties need to be reflected on the limit state formulation. This paper analyses the different types of uncertainties present in the limit state equation. These uncertainties are assessed in terms of stochastic variables in the limit state equation. In some cases, advantage can be taken from the experience from offshore wind and oil and gas industries. Tidal turbines have a mixture of the uncertainties present in both industries with regard to partial safety factor calibration. Full article

The Laurentian Great Lakes of North America contain approximately 20% of the earth’s fresh water. Smaller lakes, rivers and channels connect the lakes to the St. Lawrence Seaway, creating an interconnected freshwater and marine ecosystem. The largest delta system in the Great Lakes is located in the northeastern portion of Lake St. Clair. This article focuses on the geovisualization of total mercury pollution from sediment samples that were collected in 1970, 1974 and 2001. To assess contamination patterns, dot maps were created and compared with surfaces that were generated using the kriging spatial interpolation technique. Bathymetry data were utilized in geovisualization procedures to develop three-dimensional representations of the contaminant surfaces. Lake St. Clair generally has higher levels of contamination in deeper parts of the lake, in the dredged shipping route through the lake and in proximity to the main outflow channels through the St. Clair delta. Mercury pollution levels were well above the Probable Effect Level in large portions of the lake in both 1970 and 1974. Lower contaminant concentrations were observed in the 2001 data. Lake-wide spatial distributions are discernable using the kriging technique; however, they are much more apparent when they are geovisualized using bathymetry data. Full article

Ports exposed to high energy long wave conditions can experience significantly reduced berth availability, leading to loss of throughput. The Port of Geraldton, located in Western Australia, is an example of such a port. A range of alternatives to mitigate the long wave energy problem at this port have been examined, but each varies significantly in terms of both operational benefit and economic impact. The most technically effective solution may not necessarily yield the largest economic return. In this paper, a discrete event simulation model of port operations is used to assess the cost and benefits of various long wave mitigation approaches. The results showed that mooring configurations involving the use of port-supplied nylon breast lines held under high pre-tension by means of brake winches on the wharf appear to provide among the most favourable economic return for the Port of Geraldton. More effective ship response performance can be achieved through use of pneumatic fenders and shore-based constant tension winches, but at higher cost and slightly less favourable economics. Extending the existing port breakwater provided the least economic return due to its high cost and limited impact on berth long wave energy in the appropriate frequency range. Full article

Inter-annual bar dynamics may vary considerably across sites with very similar environmental settings. In particular, the variability of the bar cycle return period (T_r) may differ by a factor of 3 to 4. To date, data studies are only partially successful in explaining differences in T_r, establishing at best weak correlations to local environmental characteristics. Here, we use a process-based forward model to investigate the non-linear interactions between the hydrodynamic forcing and the morphodynamic profile response for two sites along the Dutch coast (Noordwijk and Egmond) that despite strong similarity in environmental conditions exhibit distinctly different T_r values. Our exploratory modeling enables a consistent investigation of the role of specific parameters at a level of detail that cannot be achieved from observations alone, and provides insights into the mechanisms that govern T_r. The results reveal that the bed slope in the barred zone is the most important parameter governing T_r. As a bar migrates further offshore, a steeper slope results in a stronger relative increase in the water depth above the bar crest which reduces wave breaking and in turn reduces the offshore migration rate. The deceleration of the offshore migration rate as the bar moves to deeper water—the morphodynamic feedback loop—contrasts with the initial enhanced offshore migration behavior of the bar. The initial behavior is determined by the intense wave breaking associated with the steeper profile slope. This explains the counter-intuitive observations at Egmond where T_r is significantly longer than at Noordwijk despite Egmond having the more energetic wave climate which typically reduces T_r. Full article

A comparison was made between the underwater visual acuity of human observers and a high-end stills camera as applied to visual surveys of shallow water coral reefs. The human observers had almost double the visual acuity of the camera, recording a Snellen eye test score of 20/8 at 4.3 m depth against 20/15 for the camera. The human observers had a field of view of 7.8 m (horizontal) by 5.8 m at 4.3 m depth while the camera had a field of view of 4.46 m by 2.98 m, or only one-third of the area observed by the snorkelers. The human observers were therefore able to see a three-times-larger field of view at twice the resolution of the camera. This result comes from the observers actively scanning the scene to put the area of interest in the part of the retina with the greatest resolving power (the fovea), increasing the apparent resolving power of their eyes, against the camera which resolved equally across the image. As a result, in actively identifying targets, humans exceeded the camera, but for more passive observation work they may be closer to the performance of the camera. The implications for autonomous platforms are that to match the human observers for target recognition, platforms will need to operate lower (to increase resolution) and longer (to sample the same area) and so issues such as collision avoidance and navigation will be critical to operationalizing autonomous systems. Full article

Big Hickory Island, located in Lee County along the mixed-energy west Florida coast, experiences high long-term rates of shoreline recession, with much of the erosion concentrated along the central and southern portions of the island. In 2013, approximately 86,300 cubic meters of sand from an adjacent tidal inlet to the north were placed along 457 m to restore the beach and dune system. In an effort to combat erosion, seven concrete king-pile groins with adjustable panels were constructed subsequent to the completion of the beach nourishment. Natural and human-induced dynamics of Big Hickory Island are discussed through analysis of shoreline and morphologic change using historic aerial photographs and topographic and bathymetric field surveys of the recent beach erosion mitigation project. Although much of the long-term anomalously high rates of erosion for the area are related to natural interchanges between the sand resources of the barrier islands and adjacent ebb tidal shoals, additional reduction in sand supply is a result of human-interventions updrift of Big Hickory over the last several decades. The coupled natural and anthropogenic influences are driving the coastal processes toward a different morphodynamic state than would have occurred under natural processes alone. Full article

Within the tropical marine study site of Guánica Bay, Puerto Rico, polychlorinated biphenyls (PCBs) are subjected to coastal and oceanic currents coupled with marine microbial and geochemical processes. To evaluate these processes a hydrodynamic model was developed to simulate the transport of PCBs within nearshore and offshore marine areas of Guánica Bay. Material transport and circulation information from the model were matched with measurements from samples collected from within the bay. These samples, consisting of both intertidal and submerged sediments, were analyzed for physical characteristics (organic carbon, grain size, and mineralogy), microbial characteristics (target bacteria levels and microbial community analyses), presence of PCBs, and PCB-degrading enzymes. Results show that the bay geometry and bathymetry limit the mixing of the extremely high levels of PCBs observed in the eastern portion of the bay. Bay bottom sediments showed the highest levels of PCBs and these sediments were characterized by high organic carbon content and finer grain size. Detectable levels of PCBs were also observed within sediments found along the shore. Microbes from the bay bottom sediments showed a greater relative abundance of microbes from the Chloroflexi, phylum with close phylogenetic associations with known anaerobic PCB-degrading organisms. Based on quantitative PCR measurement of the biphenyl dioxygenase gene, the intertidal sediments showed the greatest potential for aerobic PCB degradation. These results elucidate particular mechanisms of PCB’s fate and transport in coastal, tropical marine environments. Full article

This paper reviews the dynamics of infragravity (long-period) waves over reef systems and the consequences of these waves for operations in ports located behind reefs with particular attention to Western Australia. Swells which originate in the Southern Ocean generate long (infragravity) waves, which propagate to the coast. On the reef edge, the swell waves are largely dissipated, transferring energy to turbulence and heat but also in that process generating long wave energy. The remaining swell waves are dominated by the infragravity waves and propagate towards the mainland and into port basins where they cause moored ship motions with consequences for the operational downtime of the port’s operations. When contemplating solutions to mitigate the impact of the long wave problems, these may be addressed from two sides: from the load side (waves) and the strength side (mooring). The former will be discussed in this paper. Full article

Algae represent a large and diverse group of photosynthetic organisms inhabiting all aquatic habitats. Although the traditional assessment of algal diversity relies mainly on microscopy-based morphological identification, certain limitations exist. In this study, we present a combined molecular and morphological assessment of algal diversity in mudflats from the Savannah River Estuary, Georgia. High diversity of diatoms was documented, and less than 20% of the algal community was physiologically active at the time of collection. From the total genomic DNA extracted from the field samples and lab isolates, 18S rDNA sequences were PCR amplified, cloned, sequenced, identified, and then compared to the taxa identified via microscopy. Only a few of the DNA sequences matched documented taxa, and the abundance of particular algal species was limited to morphological analysis. Surprisingly, upon examination of the remaining lysis buffer from the mechanical lysis step of algal cells, diatom species were left intact even in the presence of a detergent indicating that the diatom species resistant to lysis could be easily underrepresented. Generation of additional algal sequences data, tied to accurate taxonomic identification, is essential to current environmental sequencing projects and potentially would allow faster acquisition of algal community structure within these unique environments. Full article

Modern joint probability methods for estimating storm surge or flood statistics are based on statistical aggregation of many hydrodynamic simulations that can be computationally expensive. Flood risk assessments that consider changing future conditions due to sea level rise or other drivers often require each storm to be run under a range of uncertain scenarios. Evaluating different flood risk mitigation measures, such as levees and floodwalls, in these future scenarios can further increase the computational cost. This study uses the Coastal Louisiana Risk Assessment model (CLARA) to examine tradeoffs between the accuracy of estimated flood depth exceedances and the number and type of storms used to produce the estimates. Inclusion of lower-intensity, higher-frequency storms significantly reduces bias relative to storm suites with a similar number of storms but only containing high-intensity, lower-frequency storms, even when estimating exceedances at very low-frequency return periods. Full article

The present study shows a methodology to carry out a comprehensive study of port agitation and resonance analysis in Geraldton Harbor (Western Australia). The methodology described and applied here extends the short and long wave hindcast outside the harbor and towards the main basin. To perform such an analysis, and as the first stage of the methodology, it is necessary to determine, in detail, both the long and short wave characteristics, through a comprehensive methodology to obtain and to hindcast the full spectral data (short waves + long waves, for frequencies between 0.005 and 1 Hz). Twelve-year spectral hindcast wave data, at a location before the reef, have been modified analytically to include the energy input associated with infragravity waves. A decomposition technique based on the energy balance of the radiation stress of short waves is followed. Predictions for long wave heights and periods at different harbor locations are predicted and validated with data recorded during 2004 to 2009. This new database will ensure an accurate and reliable assessment of long wave hourly data (height, period and currents) in any area within the main basin of the Port of Geraldton, for its present geometry. With this information, two main task will be completed: (1) undertake a forensic diagnosis of the present response of the harbor, identifying those forcing characteristics related to inoperability events; and (2) propose any layout solutions to minimize, change, dissipate/fade/vanish or positively modify the effects of long waves in the harbor, proposing different harbor geometry modifications. The goal is to identify all possible combinations of solutions that would minimize the current inoperability in the harbor. Different pre-designs are assessed in this preliminary study in order to exemplify the potential of the methodology. Full article

The use of passive satellite sensor data in shallow waters is complicated by the combined atmospheric, water, and bottom signals. Accurate determination of water depth is important for monitoring underwater topography and detection of moved sediments and in support of navigation. A Worldview 2 (WV2) image was used to develop high-resolution bathymetric maps (four meters) that were validated using bathymetry from an active sensor Light Detection and Ranging (LiDAR). The influence of atmospheric corrections in depth retrievals was evaluated using the Dark Substract, Fast Line-of-Sight Atmospheric Analysis of Spectral Hypercubes (FLAASH) and the Cloud Shadow Approach (CSA) atmospheric corrections. The CSA combined with a simple band ratio (Band2/Band3) provided the best performance, where it explained 82% of model values. The WV2 depth model was validated at another site within the image, where it successfully retrieved depth values with a coefficient of determination (r²) of 0.90 for all the depth values sampled, and an r² of 0.70, for a depth range to 20 m. The WV2 bands in the visible region were useful for testing different band combinations to derive bathymetry that, when combined with a robust atmospheric correction, provided depth retrievals even in areas with variable bottom composition and near the limits of detection. Full article

The dynamic response of mooring cables for marine structures is scale-dependent, and perfect dynamic similitude between full-scale prototypes and small-scale physical model tests is difficult to achieve. The best possible scaling is here sought by means of a specific set of dimensionless parameters, and the model accuracy is also evaluated by two alternative sets of dimensionless parameters. A special feature of the presented experiment is that a chain was scaled to have correct propagation celerity for longitudinal elastic waves, thus providing perfect geometrical and dynamic scaling in vacuum, which is unique. The scaling error due to incorrect Reynolds number seemed to be of minor importance. The 33 m experimental chain could then be considered a scaled 76 mm stud chain with the length 1240 m, i.e., at the length scale of 1:37.6. Due to the correct elastic scale, the physical model was able to reproduce the effect of snatch loads giving rise to tensional shock waves propagating along the cable. The results from the experiment were used to validate the newly developed cable-dynamics code, MooDy, which utilises a discontinuous Galerkin FEM formulation. The validation of MooDy proved to be successful for the presented experiments. The experimental data is made available here for validation of other numerical codes by publishing digitised time series of two of the experiments. Full article

The sea urchin has long been used as an invertebrate model organism in developmental biology, membrane transport and sperm oocyte interactions, and for the assessment of marine pollution. This review explores the effects of cryopreservation and biobanking in the biology and development of sea urchins, all the way from germaplasm through to juveniles. This review will provide an integral view of the process and all that is known so far about the biology of cryopreserved sea urchins, as well as provide an insight on the applications of the biobanking of these model organisms. Full article

We study the modulation of atmospheric nonisothermality and wind shears on the propagation of seismic tsunami-excited gravity waves by virtue of the vertical wavenumber, m (with its imaginary and real parts, m i and m r , respectively), within a correlated characteristic range of tsunami wave periods in tens of minutes. A generalized dispersion relation of inertio-acoustic-gravity (IAG) waves is obtained by relaxing constraints on Hines’ idealized locally-isothermal, shear-free and rotation-free model to accommodate a realistic atmosphere featured by altitude-dependent nonisothermality (up to 100 K/km) and wind shears (up to 100 m/s per km). The obtained solutions recover all of the known wave modes below the 200-km altitude where dissipative terms are assumed negligible. Results include: (1) nonisothermality and wind shears divide the atmosphere into a sandwich-like structure of five layers within the 200-km altitude in view of the wave growth in amplitudes: Layer I (0–18) km, Layer II (18–87) km, Layer III (87–125) km, Layer IV (125–175) km and Layer V (175–200) km; (2) in Layers I, III and V, the magnitude of m i is smaller than Hines’ imaginary vertical wavenumber ( m i H ), referring to an attenuated growth in the amplitudes of upward propagating waves; on the contrary, in Layers II and IV, the magnitude of m i is larger than that of m i H , providing a pumped growth from Hines’ model; (3) nonisothermality and wind shears enhance m r substantially at an ∼100-km altitude for a tsunami wave period T t s longer than 30 min. While Hines’ model provides that the maximal value of m r 2 is ∼0.05 (1/km 2 ), this magnitude is doubled by the nonisothermal effect and quadrupled by the joint nonisothermal and wind shear effect. The modulations are weaker at altitudes outside 80–140-km heights; (4) nonisothermality and wind shears expand the definition of the observation-defined “damping factor”, β: relative to Hines’ classical wave growth with β = 0 , waves are “damped” from Hines’ result if β > 0 and “pumped” if β < 0 . The polarization of β is determined by the angle θ between the wind velocity and wave vector. Full article

Recent years have seen increased survey and sampling expeditions to the Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyss, driven by commercial interests from contractors in the potential extraction of polymetallic nodules in the region. Part of the International Seabed Authority (ISA) regulatory requirements are that these contractors undertake environmental research expeditions to their CCZ exploration claims following guidelines approved by the ISA Legal and Technical Commission (ISA, 2010). Section 9 (e) of these guidelines instructs contractors to “…collect data on the sea floor communities specifically relating to megafauna, macrofauna, meiofauna, microfauna, nodule fauna and demersal scavengers”. There are a number of methodological challenges to this, including the water depth (4000–5000 m), extremely warm surface waters (~28 °C) compared to bottom water (~1.5 °C) and great distances to ports requiring a large and long seagoing expedition with only a limited number of scientists. Both scientists and regulators have recently realized that a major gap in our knowledge of the region is the fundamental taxonomy of the animals that live there; this is essential to inform our knowledge of the biogeography, natural history and ultimately our stewardship of the region. Recognising this, the ISA is currently sponsoring a series of taxonomic workshops on the CCZ fauna and to assist in this process we present here a series of methodological pipelines for DNA taxonomy (incorporating both molecular and morphological data) of the macrofauna and megafauna from the CCZ benthic habitat in the recent ABYSSLINE cruise program to the UK-1 exploration claim. A major problem on recent CCZ cruises has been the collection of high-quality samples suitable for both morphology and DNA taxonomy, coupled with a workflow that ensures these data are made available. The DNA sequencing techniques themselves are relatively standard, once good samples have been obtained. The key to quality taxonomic work on macrofaunal animals from the tropical abyss is careful extraction of the animals (in cold, filtered seawater), microscopic observation and preservation of live specimens, from a variety of sampling devices by experienced zoologists at sea. Essential to the long-term iterative building of taxonomic knowledge from the CCZ is an “end-to-end” methodology to the taxonomic science that takes into account careful sampling design, at-sea taxonomic identification and fixation, post-cruise laboratory work with both DNA and morphology and finally a careful sample and data management pipeline that results in specimens and data in accessible open museum collections and online repositories. Full article

This research is to facilitate the current understanding of long wave dynamics at coasts and during on-land propagation; experimental and numerical approaches are compared against existing analytical expressions for the long wave run-up. Leading depression sinusoidal waves are chosen to model these dynamics. The experimental study was conducted using a new pump-driven wave generator and the numerical experiments were carried out with a one-dimensional discontinuous Galerkin non-linear shallow water model. The numerical model is able to accurately reproduce the run-up elevation and velocities predicted by the theoretical expressions. Depending on the surf similarity of the generated waves and due to imperfections of the experimental wave generation, riding waves are observed in the experimental results. These artifacts can also be confirmed in the numerical study when the data from the physical experiments is assimilated. Qualitatively, scale effects associated with the experimental setting are discussed. Finally, shoreline velocities, run-up and run-down are determined and shown to largely agree with analytical predictions. Full article

Ports exposed to high energy long wave conditions can experience significantly reduced berth operability. Geraldton is perhaps one of the best known examples. Recent studies to mitigate the problems have concentrated on the reduction of the long waves by extending the breakwater. However, this is quite costly. Various countermeasures related to the mooring configuration are defined and analysed in this paper. The analysed alternatives are use of shore-based mooring lines, installation of softer fenders, a combination of these two, and deployment of Cavotec MoorMaster™ units. These alternatives were compared with the existing mooring configuration and with the option to extend the breakwater. The best improvement (50% increase of threshold long wave height inside the harbour) is reached by installing a combination of pneumatic fenders and constant tension winches set to 30 t, or nylon breast lines on a brake winch with a pretension of 25 t. In this way, the vessel is pulled into the fenders and fender friction prevents excessive surging of the ship along the berth. Full article