Discussion of “Wave setup and setdown generated by obliquely incident waves” by T.-W. Hsu et al., Coastal Engineering, 53, 865–877, 2006

In the recent paper by Tai-Wen Hsu, John R.-C. Hsu, Wen-Kai Weng, Swun-Kwang Wang, and Shan-Hwei Ou (Coastal Engineering, 53, 865–877, 2006), the authors derived theoretical formulations for calculating the wave setup and setdown induced by obliquely incident waves on a beach. The derivation of an expression for setdown contains errors which would lead to an imbalance in longshore momentum flux outside the surfzone. We correct their derivation and give results in terms of the radiation stress concept in a general case including an oblique wave incidence. We also point out that the correct form of wave setdown is important to describe the zero-net force in the momentum balance outside the surfzone.     

Nutrient flux into an intense deep chlorophyll layer in a mode-water eddy

An intense deep chlorophyll layer in the Sargasso Sea was reported near the center of an anticyclonic mode-water eddy by McGillicuddy et al. [2007. Eddy–wind interactions stimulate extraordinary mid-ocean plankton blooms, Science, accepted]. The high chlorophyll was associated with anomalously high concentrations of diatoms and with a maximum in the vertical profile of ¹⁴C primary productivity. Here we report tracer measurements of the vertical advection and turbulent diffusion of deep-water nutrients into this chlorophyll layer. Tracer released in the chlorophyll layer revealed upward motion relative to isopycnal surfaces of about 0.4 m/d, due to solar heating and mixing. The density surfaces themselves shoaled by about 0.1 m/d. The upward flux of dissolved inorganic nitrogen, averaged over 36 days, was approximately 0.6 mmol/m²/d due to both upwelling and mixing. This flux is about 40% of the basin wide, annually averaged, nitrogen flux required to drive the annual new production in the Sargasso Sea, estimated from the oxygen cycle in the euphotic zone, the oxygen demand below the euphotic zone, and from the ³He excess in the mixed layer. The observed upwelling of the fluid was consistent with theoretical models [Dewar, W.K., Flierl, G.R., 1987. Some effects of wind on rings. Journal of Physical Oceanography 17, 1653–1667; Martin, A.P., Richards, K.J., 2001. Mechanisms for vertical nutrient transport within a North Atlantic mesoscale eddy. Deep-Sea Research II 48, 757–773] in which eddy surface currents cause spatial variations in surface stress. The diapycnal diffusivity at the base of the euphotic zone was 3.5±0.5×10⁻⁵ m²/s. Diapycnal mixing was probably enhanced over more typical values by the series of storms passing over the eddy during the experiment and may have been enhanced further by the trapping of near-inertial waves generated within the eddy.     

Preindustrial, historical, and fertilization simulations using a global ocean carbon model with new parameterizations of iron limitation, calcification, and N2 fixation

The Canadian Model of Ocean Carbon (CMOC) has been developed as part of a global coupled climate carbon model. In a stand-alone integration to preindustrial equilibrium, the model ecosystem and global ocean carbon cycle are in general agreement with estimates based on observations. CMOC reproduces global mean estimates and spatial distributions of various indicators of the strength of the biological pump; the spatial distribution of the air-sea exchange of CO₂ is consistent with present-day estimates. Agreement with the observed distribution of alkalinity is good, consistent with recent estimates of the mean rain ratio that are lower than historic estimates, and with calcification occurring primarily in the lower latitudes. With anthropogenic emissions and climate forcing from a 1850-2000 climate model simulation, anthropogenic CO₂ accumulates at a similar rate and with a similar spatial distribution as estimated from observations. A hypothetical scenario for complete elimination of iron limitation generates maximal rates of uptake of atmospheric CO₂ of less than 1 PgC y⁻¹, or about 11% of 2004 industrial emissions. Even a ‘perfect’ future of sustained fertilization would have a minor impact on atmospheric CO₂ growth. In the long term, the onset of fertilization causes the ocean to take up an additional 77 PgC after several thousand years, compared with about 84 PgC thought to have occurred during the transition into the last glacial maximum due to iron fertilization associated with increased dust deposition.     

A numerical scheme for morphological bed level calculations

The typical equation for bed level change in sediment transport in river, estuary and near shore systems is based on conservation of sediment mass. It is generally a nonlinear conservation equation for bed level. The physics here are similar to shallow water wave equations and gas dynamics equation which will develop shock waves in many circumstances. Many state-of-art morphological models use classical lower order Lax–Wendroff or modified Lax–Wendroff schemes for morphology which are not very stable for long time sediment transport processes simulation. Filtering or artificial diffusion are often added to achieve stability. In this paper, several shock capturing schemes are discussed for simulating bed level change with different accuracy and stability behaviors. The conclusion is in favor of a fifth order Euler-WENO scheme which is introduced to sediment transport simulations here over other schemes. The Euler-WENO scheme is shown to have significant advantages over schemes with artificial viscosity and filtering processes, hence is highly recommended especially for phase-resolving sediment transport models.     

Application of a vanishing, quasi-sigma, vertical coordinate for simulation of high-speed, deep currents over the Sigsbee Escarpment in the Gulf of Mexico

Recent observations over the Sigsbee Escarpment in the Gulf of Mexico have revealed extremely energetic deep currents (near 1 m s⁻¹), which are trapped along the escarpment. Both scientific interest and engineering needs demand dynamical understanding of these extreme events, and can benefit from a numerical model designed to complement observational and theoretical investigations in this region of complicated topography. The primary objective of this study is to develop a modeling methodology capable of simulating these physical processes and apply the model to the Sigsbee Escarpment region. The very steep slope of the Sigsbee Escarpment (0.05–0.1) limits the application of ocean models with traditional terrain-following (sigma) vertical coordinates, which may represent the very complicated topography in the region adequately, can result in large truncation errors during calculation of the horizontal pressure gradient. A new vertical coordinate system, termed a vanishing quasi-sigma coordinate, is implemented in the Navy Coastal Ocean Model for application to the Sigsbee Escarpment region. Vertical coordinate surfaces for this grid have noticeably gentler slopes than a traditional sigma grid, while still following the terrain near the ocean bottom. The new vertical grid is tested with a suite of numerical experiments and compared to a classical sigma-layer model. The numerical error is substantially reduced in the model with the new vertical grid. A one-year, realistic, numerical simulation is performed to simulate strong, deep currents over the Escarpment using a very-high-resolution nested modeling approach. The model results are analyzed to demonstrate that the deep-ocean currents in the simulation replicate the prominent dynamical features of the observed intense currents in the region.     

Adaptations for scavenging by three diverse bathyla species, Eptatretus stouti, Neptunea amianta and Orchomene obtusus

Many deep-sea animals derive part of their nutrition from rare and unpredictable food falls. However, traits that allow organisms inhabiting the sea floor to exploit carrion are poorly understood. We found in laboratory experiments that hagfish (Eptatretus stouti), gastropods (Neptunea amianta) and amphipods (Orchomene obtusus) survived extended periods of starvation, in some cases for more than a year. When exposed to odors emitted from carrion, most individuals of E. stouti and O. obtusus began searching for food within seconds, whereas none responded to the scent of the live prey. In contrast, the slow crawling N. amianta readily consumed carrion but showed no apparent response to any odor solutions tested. Because more motile animals exhibited lower thresholds for response to signal molecules, sensitivity to chemical cues appears related to species mobility. Hagfish were also found to defend carrion from some competitors by releasing slime when feeding. Though varying dramatically in size, morphology, locomotive ability, and phylogeny, these three species all possess traits well suited for a scavenging lifestyle.     

Global detailed gravimetric geoid

A 1 ° × 1 ° global detailed gravimetric geoid has been computed, using a combination of the Goddard Space Flight Center (GSFC) GEM‐8 potential field model and a set of 38,406 1° × 1° mean surface free air anomalies. Numerous short wavelength features are shown in the geoid contour map, e.g., the steep gradients associated with oceanic trenches. Comparison of this geoid with geoceiver derived and astrogeodetic geoid heights in the United States resulted in an r.m.s. difference of about 1.7 m. Comparisons with three GEOS‐3 altimeter derived geoidal profiles revealed that for areas with good surface data coverage, the relative agreement is generally better than 5 m.     

Thioploca spp. sheaths as niches for bacterial and protistan assemblages

Sulfide oxidizing bacterial mats are common in regions of the continental shelves characterized by high primary production and the resultant oxygen minimum zone. These mats are made up of several species of Beggiatoa and/or Thioploca, which oxidize sulfide that is generated in the sediment. Thioploca spp. inhabit a large polysaccharide sheath that encompasses bundles of 1–20 filaments (trichomes), each ranging from 3 to 60 μm in diameter. This sheath has been shown to be a critical component of the autecology of Thioploca. Analysis of Thioploca from cold seeps in Monterey Bay using light and transmission electron microscopy identified new and diverse microbial assemblages associated with interstitial spaces between trichomes, inside the sheath. Small diameter, non‐vacuolate, filamentous prokaryotes were numerous. Amoebae, euglenozoa, ciliates and other protists of unknown affiliation were observed in sheaths. Most of the protists possessed food vacuoles and some protists showed ultrastructural evidence of endosymbionts. These observations suggest that Thioploca sheaths may serve as oases on the sea floor, providing nutritional and detoxification services to previously unrecognized microbial partners.