Simulation of wave propagation over a submerged bar using the VOF method with a two-equation k– turbulence modeling

A two-equation k– turbulence model is used in this paper to simulate the propagation of cnoidal waves over a submerged bar, where the free surface is handled by the volume-of-fluid (VOF) method. Using a VOF partial-cell variable and a donor–acceptor method, the model is capable of treating irregular boundaries, including arbitrary bottom topography and internal obstacles, where the no-slip condition is satisfied. The model also allows the viscous sublayer to be modeled by a wall function approximation implemented in the grid nodes that are immediately adjacent to a wall boundary. The numerical model applied to the propagation of cnoidal waves over a submerged bar can produce results that are in general agreement with some laboratory measurements. Some remarks arising from the comparison between the computational and experimental results are presented.     

The vertical structure of combined wave–current flow

A simple numerical model, based on the Reynolds stress equations and k–ε turbulence closure scheme, is developed for the coastal wave and current bottom boundary layer. The current friction velocity is introduced to account for the effect of currents on waves. The implicit Crank–Nicolson finite difference method discretizes the governing equations. Vertical changing step grids with the constant ratio for two adjacent spatial steps are used together with the equal time steps in the modeling. Vertical profiles of mean current velocity and wave velocity amplitude are obtained. These modeled results are compared with the laboratory experimental data of Van Doorn [1981. Experimental investigation of near bottom velocities in water waves with and without a current. Report M1423, Delft Hydraulics Laboratory, Delft, The Netherlands; 1982. Experimenteel onderzoek naar het snelheidsveld in de turbulente bodemgrenslaag in een oscillerende stroming in een golftunnel. Report M1562, Delft Hydraulics Laboratory, Delft, The Netherlands]. It has been shown that modeled and observed (Van Doorn, T., 1981. Experimental investigation of near bottom velocities in water waves with and without a current. Report M1423, Delft Hydraulics Laboratory, Delft, The Netherlands; 1982. Experimenteel onderzoek naar het snelheidsveld in de turbulente bodemgrenslaag in een oscillerende stroming in een golftunnel. Report M1562, Delft Hydraulics Laboratory, Delft, The Netherlands) mean velocity profiles within the wave and current bottom boundary layer are in better agreement than outside. Modeled and observed (Van Doorn, T., 1981. Experimental investigation of near bottom velocities in water waves with and without a current. Report M1423, Delft Hydraulics Laboratory, Delft, The Netherlands) wave velocity amplitude profiles within the wave and current bottom boundary layer are in better agreement than outside. Modeled wave velocity amplitudes are in good agreement with the laboratory experimental data of Van Doorn [1982. Experimenteel onderzoek naar het snelheidsveld in de turbulente bodemgrenslaag in een oscillerende stroming in een golftunnel. Report M1562, Delft Hydraulics Laboratory, Delft, The Netherlands].     

Effects of 17β-estradiol exposure in the mussel Mytilus galloprovincialis

Mussels Mytilus galloprovincialis were exposed to different concentrations of estradiol (20, 200, and 2000 ng/l) in a semi-static regime (1-day dosing intervals) for up to 7 days in an attempt to see how mussels dealt with exogenous estrogenic compounds. Sex hormone levels were determined in whole tissue. Free-estradiol was only significantly elevated at the highest exposure dose (up to 10-fold). Most of the estradiol was in the tissues as fatty acid esters (>78%), which sharply increased in a dose-dependent manner (from 4 ng/g in controls to 258 ng/g at the high exposure group). In contrast, neither free nor esterified testosterone levels showed significant differences between control and exposure groups. The results suggest the existence of mechanisms that allow mussels to maintain their hormonal status, and the important role that fatty acid esterification may play within those mechanisms. Synthesis and conjugation rates of estradiol were further investigated by measuring the activity of P450 aromatase, and palmitoyl-CoA:estradiol acyltransferase, in digestive gland microsomal fractions. Overall, the study contributes to the better knowledge of molluscan endocrinology, and defines new mechanisms of regulation of free steroid-levels in mussels.     

Variability of organic δC and C/N in the Mersey Estuary, U.K. and its implications for sea-level reconstruction studies

Microfossil analysis (e.g. diatoms, foraminifera and pollen) represents the cornerstone of Holocene relative sea-level (RSL) reconstruction because their distribution in the contemporary inter-tidal zone is principally controlled by ground elevation within the tidal frame. A combination of poor microfossil preservation and a limited range in the sediment record may severely restrict the accuracy of resulting RSL reconstructions. Organic δ¹³C and C/N analysis of inter-tidal sediments have shown some potential as coastal palaeoenvironmental proxies. Here we assess their viability for reconstructing RSL change by examining patterns of organic δ¹³C and C/N values in a modern estuarine environment. δ¹³C and C/N analysis of bulk organic inter-tidal sediments and vegetation, as well as suspended and bedload organic sediments of the Mersey Estuary, U.K., demonstrate that the two main sources of organic carbon to surface saltmarsh sediments (terrestrial vegetation and tidal-derived particulate organic matter) have distinctive δ¹³C and C/N signatures. The resulting relationship between ground elevation within the tidal frame and surface sediment δ¹³C and C/N is unaffected by decompositional changes. The potential of this technique for RSL reconstruction is demonstrated by the analysis of part of an early Holocene sediment core from the Mersey Estuary. Organic δ¹³C and C/N analysis is less time consuming than microfossil analysis and is likely to provide continuous records of RSL change.     

Fitting a predator–prey model to zooplankton time-series data in the Gironde estuary (France): Ecological significance of the parameters

The relationships between the seasonal fluctuations of the copepod Eurytemora affinis and the mysid Neomysis integer were studied from observed data and experimental results, using a predator–prey model in the oligo-mesohaline area of the Gironde estuary. Mean seasonal fluctuations of abundances were derived from long term data series collected from 1978 to 2003 for both species. In situ predator–prey experiments over a seasonal cycle were used to estimate the seasonal variation of the consumption rate of N. integer on E. affinis and to verify the order of magnitude of the biological parameters given by the model.Predator–prey experiments revealed a high seasonal variation in maximum consumption rates with a mean of 56 ± 9 ind. pred⁻¹ d⁻¹. Maximum consumption rates were always higher for adults than for juveniles of Neomysis integer. Recorded selectivities were higher on nauplii than on copepodids + adults of Eurytemora affinis, both for the juveniles and the adults of N. integer. Neomysis integer mainly fed on meroplanktonic larvae, when they were available in higher abundances, than E. affinis in their environment.Spring increases of abundance for Eurytemora affinis copepodids + adults seemed to be mainly controlled by temperature whereas its decreasing abundance in summer was more related to Neomysis integer predation, suggesting that summer fluctuations of E. affinis abundance are probably controlled by mysid predation at summer times. Using a Lotka–Volterra predator–prey model, the seasonal peak of abundance of the mysid N. integer was well reproduced considering a predation on copepodids + adults of E. affinis, and suggested a dependence between mysid and copepod seasonal variations. However, the seasonal peak amplitude could not be explained solely by a predation on copepodids + adults or on nauplii of the copepod. Thus, N. integer is probably dependent on the seasonal fluctuations of the copepod's abundance, complementing its diet with macrophytal detritus during periods of scarce food.     

A spatial ecosystem and populations dynamics model (SEAPODYM) – Modeling of tuna and tuna-like populations

An enhanced version of the spatial ecosystem and population dynamics model SEAPODYM is presented to describe spatial dynamics of tuna and tuna-like species in the Pacific Ocean at monthly resolution over 1° grid-boxes. The simulations are driven by a bio-physical environment predicted from a coupled ocean physical–biogeochemical model. This new version of SEAPODYM includes expanded definitions of habitat indices, movements, and natural mortality based on empirical evidences. A thermal habitat of tuna species is derived from an individual heat budget model. The feeding habitat is computed according to the accessibility of tuna predator cohorts to different vertically migrating and non-migrating micronekton (mid-trophic) functional groups. The spawning habitat is based on temperature and the coincidence of spawning fish with presence or absence of predators and food for larvae. The successful larval recruitment is linked to spawning stock biomass. Larvae drift with currents, while immature and adult tuna can move of their own volition, in addition to being advected by currents. A food requirement index is computed to adjust locally the natural mortality of cohorts based on food demand and accessibility to available forage components. Together these mechanisms induce bottom-up and top-down effects, and intra- (i.e. between cohorts) and inter-species interactions. The model is now fully operational for running multi-species, multi-fisheries simulations, and the structure of the model allows a validation from multiple data sources. An application with two tuna species showing different biological characteristics, skipjack (Katsuwonus pelamis) and bigeye (Thunnus obesus), is presented to illustrate the capacity of the model to capture many important features of spatial dynamics of these two different tuna species in the Pacific Ocean. The actual validation is presented in a companion paper describing the approach to have a rigorous mathematical parameter optimization [Senina, I., Sibert, J., Lehodey, P., 2008. Parameter estimation for basin-scale ecosystem-linked population models of large pelagic predators: application to skipjack tuna. Progress in Oceanography]. Once this evaluation and parameterization is complete, it may be possible to use the model for management of tuna stocks in the context of climate and ecosystem variability, and to investigate potential changes due to anthropogenic activities including global warming and fisheries pressures and management scenarios.     

Humic substances in estuarine soils colonized by Spartina maritima

This study characterizes humic substances (HS) from two soils colonized by Spartina maritima at different physiographical positions in estuarine environments on the north-western coast of the Iberian Peninsula: the Villaviciosa site, a stand close to the main tidal channel, and the Ortigueira site, located in the low salt marsh. Humic and fulvic acids were extracted from the soils and characterized qualitatively by the following spectroscopic techniques: Fourier transform infrared spectroscopy, fluorescence spectroscopy and solid-state ¹³C nuclear magnetic resonance.The characterized HS showed a predominance of low humified compounds with a high proportion of aliphatic components and a low degree of aromaticity. The HS composition differed substantially between sites. In the Villaviciosa soil, the large amount of nonpolar aliphatic components and the very low degree of aromaticity may indicate a significant contribution of marine organic matter and/or microbial material to the HS. However, in the HS from the Ortigueira soil, the higher proportion of polysaccharides together with the presence of lignin-derived compounds may indicate greater inputs of vascular plant material. The δ¹³C isotopic composition of the bulk soils highlights the large input of Spartina maritima debris to the Ortigueira site, whereas in the Villaviciosa site, organic contributions from this C4 vascular plant were not so evident.The results indicate that in these soils colonized by Spartina maritima, physiographical position has an important effect on the composition of soil HS and, therefore, must be considered in the study of organic matter characteristics in such estuarine environments.     

Comparison of the nonlocal transport characteristics of a series of one-dimensional oceanic boundary layer models

Seven one-dimensional oceanic boundary layer models are investigated to assess the possible nonlocal transport characteristics of mass and heat in the upper ocean. The dynamical models have been chosen from the diffusion and bulk types currently in use plus two modifications of the transilient type that have been used extensively for atmospheric work by Stull. The models are forced using wind speed and insolation conditions recorded during a 9-day oceanographic cruise near Bermuda in March 1993 during the decline of the spring bloom. The attenuation of sunlight in the upper ocean is calculated using a full spectral model for downwelling irradiance. The vertical heat transport characteristics are reported and compared. A series of spectral diagnostic tests (Green's function analysis, process spectra, and overall mixing lengths) reveal significant differences in the vertical transport characteristics of the models that are not observed in commonly used diagnostics such as sea surface temperature or mixed layer depth. Age spectra (or modal time since last surface contact) are calculated from Green's functions and reveal how a water mass can be cut off from the surface within a short time period. The large differences in the vertical mixing characteristics of the upper ocean boundary layer models have potential implications on the vertical distributions of short-lived chemical tracers and phytoplankton.     

Size increment of jumbo flying squid Dosidicus gigas mature females in Peruvian waters, 1989–2004

Changes in population structure of the jumbo flying squid Dosidicus gigas in Peruvian waters were studied based on size-at-maturity from 1989 to 2004. From 1989 to 1999, mature squid belonging to the medium-sized group prevailed, but from 2001 on, mature squids were larger. This change is not related to the changes in sea surface temperature and we hypothesized that it was caused by the population increase of mesopelagic fishes as prey.     

Plasma steroid levels in female flounder (Platichthys flesus) after chronic dietary exposure to single polycyclic aromatic hydrocarbons

The chronic effects of polycyclic aromatic hydrocarbons (PAHs) on ovary development, total hepatic lipids and plasma sex- and corticosteroid levels in female flounder (Platichthys flesus) were examined. Sexually mature feral female flounder were exposed via the diet to phenanthrene (0.5, 2.5 or 12.5 nmol/g food) or chrysene (0.4 nmol/g food) for 12 weeks, during the previtellogenic phase of the annual reproductive cycle. PAH exposure did not directly affect germ cell development since no structural and/or developmental differences were observed between control and exposed fish. On the contrary, all treatments resulted in altered plasma steroid levels. The most pronounced effect was the significant decrease in plasma 17β-estradiol to 19±11%, 27±7%, 63±20% and 61±12% in relation to control fish, respectively, in flounders exposed to 12.5, 2.5 or 0.5 nmol phenanthrene/g food and 0.4 nmol chrysene/g food. Impaired ovarian growth was not observed, most likely because experiments were ended before the period of vitellogenesis, even though a non-significant general decline in total hepatic lipids could be observed. Moreover, all exposed flounders, except fish fed with the highest amount of phenanthrene, showed a negative correlation between plasma 17β-estradiol and 17α-hydroxyprogesterone levels (r=−0.46). One possible explanation is that PAH action may be mediated by a specific inhibition of steroidogenic enzymes. These findings provide evidence that selected PAHs are antiestrogenic xenobiotics with the capability to impair female teleost reproductive function.     

Cs2NaMF6(M＝Al,Ga):Cr3+ 络合分子体系局域结构和基态分裂的理论研究

采用双自旋轨道耦合系数模型并结合完全能量矩阵的方法对Cs₂NaMF₆(M=Al, Ga):Cr³⁺ 体系中Cr³⁺ 离子的基态分裂和局域结构进行了研究.通过模拟光谱和EPR谱确定了Cr³⁺ 取代 M³⁺ 形成的两种占位结构的畸变角,发现用双自旋轨道耦合系数模型与单自旋轨道耦合系数模型计算出的畸变角Δθ存在较大的差异.这表     

Day–night and depth differences in haemolymph melatonin of the Norway lobster, Nephrops norvegicus (L.)

Few studies have been conducted to quantify and understand the role of melatonin in invertebrates, and particularly in crustaceans and in deep-sea animals. In this study, we examined day–night differences in haemolymph melatonin of the burrowing decapod crustacean Nephrops norvegicus (L.) during exposure to cycles of monochromatic blue light (480 nm) and darkness cycles of 10 and 0.1 lx. These differential intensity conditions simulate illumination at the depth of the shelf (80–100 m) and of the slope (300–400 m), where these lobster populations are chiefly found in the Western Mediterranean Sea. Our objectives were: (a) to verify the presence of melatonin in the haemolymph of this species using liquid chromatography/tandem mass spectrometry (LC–MS/MS) and fluorescence HPLC (HPLC); and (b) to study the relationship between diel variations in melatonin concentration and locomotor rhythms, in order to examine whether the former influences behaviour. Melatonin was identified in LC–MS/MS by Q1 and Q3 mass peaks at an elution time of 3.7 min, and it was also detected by HPLC. Melatonin concentration was found to be two orders of magnitude higher at 10 lx (4.8±5.3 ng ml⁻¹) than at 0.1 lx (0.06±0.03 ng ml⁻¹). Also, the increase at daytime in 10 lx was absent in 0.1 lx. When the locomotor rhythm of animals exposed to both photoperiod regimes was compared, the diel periodicity was found to be preserved, but the timing of activity shifted from night to day. Extrapolating these data to the field, we interpret our results to mean that locomotor activity preserves its diel character, but not its phase and amplitude, in a bathymetric range where haemolymph melatonin reduces its concentration and rhythmic fluctuation.     

Uptake of atmospheric carbon dioxide in Arctic shelf seas: evaluation of the relative importance of processes that influence pCO2 in water transported over the Bering–Chukchi Sea shelf

The uptake of atmospheric carbon dioxide in the water transported over the Bering–Chukchi shelves has been assessed from the change in carbon-related chemical constituents. The calculated uptake of atmospheric CO₂ from the time that the water enters the Bering Sea shelf until it reaches the northern Chukchi Sea shelf slope (1 year) was estimated to be 86±22 g C m⁻² in the upper 100 m. Combining the average uptake per m³ with a volume flow of 0.83×10⁶ m³ s⁻¹ through the Bering Strait yields a flux of 22×10¹² g C year⁻¹. We have also estimated the relative contribution from cooling, biology, freshening, CaCO₃ dissolution, and denitrification for the modification of the seawater pCO₂ over the shelf. The latter three had negligible impact on pCO₂ compared to biology and cooling. Biology was found to be almost twice as important as cooling for lowering the pCO₂ in the water on the Bering–Chukchi shelves. Those results were compared with earlier surveys made in the Barents Sea, where the uptake of atmospheric CO₂ was about half that estimated in the Bering–Chukchi Seas. Cooling and biology were of nearly equal significance in the Barents Sea in driving the flux of CO₂ into the ocean. The differences between the two regions are discussed. The loss of inorganic carbon due to primary production was estimated from the change in phosphate concentration in the water column. A larger loss of nitrate relative to phosphate compared to the classical ΔN/ΔP ratio of 16 was found. This excess loss was about 30% of the initial nitrate concentration and could possibly be explained by denitrification in the sediment of the Bering and Chukchi Seas.     

Shelf spawning habitat of Emmelichthys nitidus in south-eastern Australia – Implications and suitability for egg-based biomass estimation

The spawning habitat of Emmelichthys nitidus (Emmelichthyidae) in south-eastern Australia is described from vertical ichthyoplankton samples collected along the shelf region off eastern through to south-western Tasmania during peak spawning in October 2005–06. Surveys covered eastern waters in 2005 (38.8–43.5°S), and both eastern and southern waters in 2006 (40.5°S around to 43.5°S off the south-west). Eggs (n = 10,393) and larvae (n = 378) occurred along eastern Tasmania in both years but were rare along southern waters south and westwards of 43.5°S in 2006. Peak egg abundances (1950–2640 per m⁻²) were obtained off north-eastern Tasmania (40.5–41.5°S) between the shelf break and 2.5 nm inshore from the break. Eggs were up to 5-days old, while nearly 95% of larvae were at the early preflexion stage, i.e. close to newly emerged. Average abundances of aged eggs pooled across each survey declined steadily from day-1 to day-5 eggs both in 2005 (97-18) and 2006 (175-34). Moreover, day-1 egg abundances were significantly greater 2.5 nm at either side of the break, including at the break, than in waters ≥5 nm both inshore and offshore from the break. These results, complemented with egg and larval data obtained in shelf waters off New South Wales (NSW; 35.0–37.7°S) in October 2002–03, indicate that the main spawning area of E. nitidus in south-eastern Australia lies between 35.5°S off southern NSW and 43.5°S off south-eastern Tasmania, and that spawning activity declines abruptly south and westwards of 43.5°S around to the south-west coast. In addition, quotient analyses of day-1 egg abundances point to a preferred spawning habitat contained predominantly within a 5 nm corridor along the shelf break, where waters are 125–325 m deep and median temperatures 13.5–14.0 °C. Spawning off eastern Tasmania is timed with the productivity outburst typical of the region during the austral spring, and the temperature increase from the mixing between the southwards advancing, warm East Australian Current and cooler subantarctic water over the shelf. Overall, ichthyoplankton data, coupled with reproductive information from adults trawled off Tasmania, indicate that E. nitidus constitutes a suitable species for the application of the daily egg production method (DEPM) to estimate spawning biomass. This finding, together with evidence in support of a discrete eastern spawning stock extending from southern NSW to southern Tasmania, strengthens the need for DEPM-based biomass estimates of E. nitidus prior to further fishery expansion.     

Geochemical cycling in the Hooghly estuary, India

U–Th decay series isotopes, δ¹⁸O and Si measurements in the river estuarine waters and sediments of the polluted Hooghly estuary as well as the surface waters of the Bay of Bengal, its high salinity end member, are reported. Dissolved Si indicates that there are probably two mixing regimes, dissolved U behaviour is nonconservative and δ¹⁸O behaves conservatively in the overall estuarine region. Isotopes of reactive elements, viz. ²³⁴Th and ²¹⁰Po, are removed from the estuarine waters in <2 days and <1 month, respectively, which is due to high suspended matter (30–301 mg l⁻¹). ²²⁸Ra and ²²⁶Ra are profusely released into the estuarine waters in the low to mid-salinity regions.As expected, the opposite trend is observed in the case of estuarine sediments and suspended matter. Reactive isotopes of Th, ²¹⁰Pb and ²¹⁰Po are enriched, whereas Ra isotopes are depleted with respect to their parent nuclides in the estuarine sediments and suspended matter. ²³²Th/Al ratio appears well suited to study the distribution and mixing of the bed load sediments of the Ganga–Brahmaputra (G–B) and the Hooghly rivers with those from other rivers on the Bay of Bengal floor.     

Grazing experiments and model simulations of the role of zooplankton in Phaeocystis food webs

A combined empirical and modelling study was conducted to further examine the potential importance of grazing by zooplankton in pelagic food webs in which Phaeocystis is a significant or dominant component. Laboratory experiments were designed to measure ingestion of Phaeocystis and other potential prey items which co-occur with Phaeocystis. Grazers included copepods and ciliates, and prey included Phaeocystis colonies and solitary cells, diatoms, ciliates, bacteria, and detritus. These data were expressed in the model currency of nitrogen units, and fit to hyperbolic tangent equations which included minimum prey thresholds. These equations and literature data were used to constrain a food web model whose purpose was to investigate trophic interactions rather than to mimic actual events. Nevertheless, the model output was similar to the general pattern and magnitude of development of Phaeocystis–diatom communities in some environments where they occur, e.g. north Norwegian waters. The model included three forms of nitrogen, three phytoplankton groups, bacteria, two zooplankton groups, and detritus, with detailed flows between compartments. An important component of the model was inclusion of variable prey preferences for zooplankton. The experiments and model simulations suggest several salient conclusions. Phaeocystis globosa colonies were eaten by a medium-sized copepod species, but ingestion appeared to be strongly dependent upon a proper size match between grazer and prey. If not, colonies were eaten little if at all. Phaeocystis solitary cells were ingested rapidly by ciliate microzooplankton, in agreement with prior literature observations. In contrast, detritus was eaten comparatively slowly by both ciliates and copepods. Both types of zooplankton exhibited apparent minimum prey thresholds below which grazing did not occur or was inconsequential. Model simulations implied that transitions between life cycle stages of Phaeocystis may potentially be important to phytoplankton–zooplankton interactions, and that relative rates of ingestion of Phaeocystis by various zooplankton may have significant impacts upon material fluxes through and out of Phaeocystis–diatom ecosystems. Indirect effects of trophic interactions appear to be equally significant as direct effects.     

Sequence model and its application to a Miocene shelf–slope system in the tectonically active Ulleung Basin margin, East Sea (Sea of Japan)

In a broader application of sequence stratigraphic concept to a tectonically active margin setting, this study presents a sequence model that considers all three controls on sequence development (i.e. eustasy, tectonic movement and sediment supply) as independent variables. The model introduces six sequence types (A to F) including type 1 and type 2 sequences defined in the original Exxon scheme. Each sequence shows a variety in number and stacking pattern of its constituent parasequence sets reflecting combined effects of accommodation change and sediment supply. This model is applied to a seismic sequence analysis of the shelf–slope system (middle to upper Miocene) in the southwestern margin of Ulleung Basin which has experienced significant crustal deformation during the Tertiary back-arc opening and subsequent closing of the East Sea (Sea of Japan). The model application delineates four sequence types whose development is closely associated with the tectonic evolution of the Ulleung Basin margin. During the back-arc opening (early to middle Miocene), type A and B sequences were emplaced as a result of steady creation of accommodation space due to a rapid subsidence combined with a tectonic-controlled high to moderate rate of sediment supply. The sequences associated with the extensional tectonism are characterized by active progradation and aggradation without forced regressive phases. In the initiation stage of back-arc closure (middle to late Miocene), subsidence rates were significantly reduced because of a widespread contractional deformation, while subaerial erosion of the uplifted thrust belt resulted in an increase in sedimentation rate. As a result, steady prograding type-E sequences were formed by alternating normal and forced regressions. During the quiescent phase of back-arc closure in the late Miocene, rise-dominant fluctuating relative sea-level change and moderate to low sediment supply gave rise to type-F sequences (similar to type-1 sequences of the Exxon group) reflecting a major control of eustatic sea-level change.