Description of a flexible and extendable physical–biogeochemical model system for the water column

A modelling system for coupled physical–biogeochemical simulations in the water column is presented here. The physical model component allows for a number of different statistical turbulence closure schemes, ranging from simple algebraic closures to two-equation turbulence models with algebraic second-moment closures. The biogeochemical module consists of models which are based on a number of state variables represented by their ensemble averaged concentrations. Specific biogeochemical models may range from simple NPZ (nutrient–phytoplankton–zooplankton) to complex ecosystem models. Recently developed modified Patankar solvers for ordinary differential equations allow for stable discretisations of the production and destruction terms guaranteeing conservative and non-negative solutions. The increased stability of these new solvers over explicit solvers is demonstrated for a plankton spring bloom simulation. The model system is applied to marine ecosystem dynamics the Northern North Sea and the Central Gotland Sea. Two different biogeochemical models are applied, a conservative nitrogen-based model to the North Sea, and a more complex model including an oxygen equation to the Baltic Sea, allowing for the reproduction of chemical processes under anoxic conditions. For both applications, earlier model results obtained with slightly different model setups could be basically reproduced. It became however clear that the choice for ecosystem model parameters such as maximum phytoplankton growth rates does strongly depend on the physical model parameters (such as turbulence closure models or external forcing).     

Quantitative estimation of the influence of surface thermal fronts over chlorophyll concentration at the Patagonian shelf

Eighteen-year (1985–2002) mean monthly SST Pathfinder data with 9 km spatial resolution have been used to estimate surface gradients by finite differences. Then the seasonal climatological means have been calculated from the intensity of these gradients, and surface thermal fronts present in the Patagonian Continental Shelf (PCS) have been located. Moreover, 6 years (1998–2003) of SeaWiFS data with approximately 4 km spatial resolution have been used to estimate monthly composite images of surface chlorophyll concentration, after which seasonal climatological means distributions have been generated. Both seasonal distributions have been analyzed together and by combining the knowledge of oceanographic processes and phytoplankton responses to light and nutrient availability, regions where the presence of a thermal front affects photosynthetic activity have been identified. Subjective criteria have been applied to define eighteen areas where phytoplankton biomass is influenced by the presence of a thermal front. In these areas, the surface chlorophyll (spatial mean and total), its relationship with the surface chlorophyll of the whole region, and the seasonal evolution of this relationship have been calculated. All frontal areas cover less than 15% of the total surface, but they contribute with over 23% of the phytoplankton annual mean biomass. Considered as a group, during summer they show high chlorophyll values very similar to those in spring. During the cold period, when the water column is vertically mixed in practically the whole of PCS, the influence of physical fronts over the biological production is minimum. The frontal zone image remains clearly defined during summer, when approximately 85% of the area will have a determined mean chlorophyll concentration, while the other 15% has a 2.45 times larger value. While three pattern trends have been identified in the frontal areas, only two of them condition the pattern of the group, due to their horizontal extension.     

Improving the physics of a coupled physical–biogeochemical model of the North Atlantic through data assimilation: Impact on the ecosystem

Several studies on coupled physical–biogeochemical models have shown that major deficiencies in the biogeochemical fields arise from the deficiencies in the physical flow fields. This paper examines the improvement of the physics through data assimilation, and the subsequent impact on the ecosystem response in a coupled model of the North Atlantic. Sea surface temperature and sea surface height data are assimilated with a sequential method based on the SEEK filter adapted to the coupling needs. The model domain covers the Atlantic from 20°S to 70°N at eddy-permitting resolution. The biogeochemical model is a NPZD-DOM model based on the P3ZD formulation. The results of an annual assimilated simulation are compared with an annual free simulation.With assimilation, the representation of the mixed layer depth is significantly improved in mid latitudes, even though the mixed layer depth is generally overestimated compared to the observations. The representation of the mean and variance of the currents is also significantly improved.The nutrient input in the euphotic zone is used to assess the data assimilation impact on the ecosystem. Data assimilation results in a 50% reduction of the input due to vertical mixing in mid-latitudes, and in a four- to six-fold increase of the advective fluxes in mid-latitudes and subtropics. Averaged zonally, the net impact is a threefold increase for the subtropical gyre, and a moderate (20–30%) decrease at mid and high latitudes.Surface chlorophyll concentration increases along the subtropical gyre borders, but little changes are detected at mid and high latitudes. An increase of the primary production appears along the Gulf Stream path, but it represents only 12% on average for mid and high latitudes. In the subtropical gyre centre, primary production is augmented but stays underestimated (20% of observations). These experiments show the benefits of physical data assimilation in coupled physical–biogeochemical applications.     

Carbonate chemistry dynamics and carbon dioxide fluxes across the atmosphere–ice–water interfaces in the Arctic Ocean: Pacific sector of the Arctic

Climatic changes in the Northern Hemisphere have led to remarkable environmental changes in the Arctic Ocean, which is surrounded by permafrost. These changes include significant shrinking of sea-ice cover in summer, increased time between sea-ice break-up and freeze-up, and Arctic surface water freshening and warming associated with melting sea-ice, thawing permafrost, and increased runoff. These changes are commonly attributed to the greenhouse effect resulting from increased atmospheric carbon dioxide (CO₂) concentration and other non-CO₂ radiatively active gases (methane, nitrous oxide). The greenhouse effect should be most pronounced in the Arctic where the largest air CO₂ concentrations and winter–summer variations in the world for a clean background environment were detected. However, the air–land–shelf interaction in the Arctic has a substantial impact on the composition of the overlying atmosphere; as the permafrost thaws, a significant amount of old terrestrial carbon becomes available for biogeochemical cycling and oxidation to CO₂. The Arctic Ocean's role in determining regional CO₂ balance has been ignored, because of its small size (only  4% of the world ocean area) and because its continuous sea-ice cover is considered to impede gaseous exchange with the atmosphere so efficiently that no global climate models include CO₂ exchange over sea-ice. In this paper we show that: (1) the Arctic shelf seas (the Laptev and East-Siberian seas) may become a strong source of atmospheric CO₂ because of oxidation of bio-available eroded terrestrial carbon and river transport; (2) the Chukchi Sea shelf exhibits the strong uptake of atmospheric CO₂; (3) the sea-ice melt ponds and open brine channels form an important spring/summer air CO₂ sink that also must be included in any Arctic regional CO₂ budget. Both the direction and amount of CO₂ transfer between air and sea during open water season may be different from transfer during freezing and thawing, or during winter when CO₂ accumulates beneath Arctic sea-ice; (4) direct measurements beneath the sea ice gave two initial results. First, a drastic pCO₂ decrease from 410 μatm to 288 μatm, which was recorded in February–March beneath the fast ice near Barrow using the SAMI-CO₂ sensor, may reflect increased photosynthetic activity beneath sea-ice just after polar sunrise. Second, new measurements made in summer 2005 beneath the sea ice in the Central Basin show relatively high values of pCO₂ ranging between 425 μatm and 475 μatm, values, which are larger than the mean atmospheric value in the Arctic in summertime. The sources of those high values are supposed to be: high rates of bacterial respiration, import of the Upper Halocline Water (UHW) from the Chukchi Sea (CS) where values of pCO₂ range between 400 and 600 μatm, a contribution from the Lena river plume, or any combination of these sources.     

Parameterization of air–sea gas fluxes at extreme wind speeds

Air–sea flux measurements of O₂ and N₂ obtained during Hurricane Frances in September 2004 [D'Asaro, E. A. and McNeil, C. L., 2006. Measurements of air–sea gas exchange at extreme wind speeds. Journal Marine Systems, this edition.] using air-deployed neutrally buoyant floats reveal the first evidence of a new regime of air–sea gas transfer occurring at wind speeds in excess of 35 m s^− 1. In this regime, plumes of bubbles 1 mm and smaller in size are transported down from near the surface of the ocean to greater depths by vertical turbulent currents with speeds up to 20−30 cm s^− 1. These bubble plumes mostly dissolve before reaching a depth of approximately 20 m as a result of hydrostatic compression. Injection of air into the ocean by this mechanism results in the invasion of gases in proportion to their tropospheric molar gas ratios, and further supersaturation of less soluble gases. A new formulation for air–sea fluxes of weakly soluble gases as a function of wind speed is proposed to extend existing formulations [Woolf, D.K, 1997. Bubbles and their role in gas exchange. In: Liss, P.S., and Duce, R.A., (Eds.), The Sea Surface and Global Change. Cambridge University Press, Cambridge, UK, pp. 173–205.] to span the entire natural range of wind speeds over the open ocean, which includes hurricanes. The new formulation has separate contributions to air–sea gas flux from: 1) non-supersaturating near-surface equilibration processes, which include direct transfer associated with the air–sea interface and ventilation associated with surface wave breaking; 2) partial dissolution of bubbles smaller than 1 mm that mix into the ocean via turbulence; and 3) complete dissolution of bubbles of up to 1 mm in size via subduction of bubble plumes. The model can be simplified by combining “surface equilibration” terms that allow exchange of gases into and out of the ocean, and “gas injection” terms that only allow gas to enter the ocean. The model was tested against the Hurricane Frances data set. Although all the model parameters cannot be determined uniquely, some features are clear. The fluxes due to the surface equilibration terms, estimated both from data and from model inversions, increase rapidly at high wind speed but are still far below those predicted using the cubic parameterization of Wanninkhof and McGillis [Wannikhof, R. and McGillis, W.R., 1999. A cubic relationship between air–sea CO₂ exchange and wind speed. Geophysical Research Letters, 26:1889–1892.] at high wind speed. The fluxes due to gas injection terms increase with wind speed even more rapidly, causing bubble injection to dominate at the highest wind speeds.     

Patterns in diversity and community structure of epipelagic copepods from the Brazil–Malvinas Confluence area, south-western Atlantic

Diversity and structure of epipelagic copepod communities were investigated using 70 zooplankton samples collected from the top 50 m of the Brazil–Malvinas Confluence area between 35° and 55°S. Biogeographic patterns were investigated using multivariate analysis. Biodiversity patterns were examined using different univariate indexes. Representatives of 35 species of copepods from 23 genera and 13 families were found. Two zones were delimited based on their copepod composition, one in the subtropical waters of the Brazil current, and the other in the subantarctic waters of the Malvinas current. Both environments displayed contrasting patterns of biodiversity depending upon which element is measured (regional species richness as well as mean point species richness were significantly higher in the subtropical group of stations, whereas taxonomic distinctness was significantly higher in the subantarctic community). Based on these contrasting results, we suggest the use of both kind of indexes when defining priority areas for conservation.     

The biogeochemical cycling of methane in Ria de Vigo, NW Spain: Sediment processing and sea–air exchange

Methane (CH₄) concentrations were measured in the water column, in sediment porewaters, and in atmospheric air, in the Ría de Vigo, NW Spain, during both the onset (April 2003) and at the end of (September 2004) seasonal upwelling. In addition, CH₄ concentration and stable isotopic signatures (δ¹³CH₄) were measured in porewaters, and sediment methanogenesis and aerobic oxidation of CH₄ were determined in sediment incubations. Surface water column CH₄ (2 m depth) was in the range 3–180 nmol l^− 1 (110–8500% saturation) and followed a generally landward increase but with localised maxima in both the inner and middle Ría. These maxima were consistent with CH₄ inputs from underlying porewaters in which CH₄ concentrations were up to 3 orders of magnitude higher (maximum 350 μmol l^− 1). Surface water CH₄ concentrations were approximately three times higher in September than in April, consistent with a significant benthic CH₄ flux driven by enhanced sediment methanogenesis following the summer productivity maximum. CH₄ and δ¹³CH₄ in sediment porewaters and in incubated sediment slurries (20 °C) revealed significant sediment CH₄ oxidation, with an apparent isotopic fractionation factor (r_c) of  1.004. Using turbulent diffusion models of air–sea exchange we estimate an annual emission of atmospheric CH₄ from the Ría de Vigo of 18–44 × 10⁶ g (1.1–2.7 × 10⁶ mol). This estimate is approximately 1–2 orders of magnitude lower than a previous estimate based on a bubble transport model.     

The shoaling of nutrient-enriched subsurface waters as a mechanism to sustain primary productivity off Central Baja California during El Niño winters

Using CalCOFI data for coastal shallow stations (above 100 m depth), higher than expected nitrate concentrations were detected in near-surface high-temperature waters off of Central Baja California during some El Niño winters. Though recent data are not available for Central Baja California, past El Niño data, though limited, showed nitrate concentrations above 16 μM at temperatures above 16 °C, and nitrate concentrations between 1 and 2 μM at 19 °C, while the previously established relationship of temperature and nitrate for California Current waters predicts nitrate depletion above 14 or 15 °C. The anomalous, high temperature–high nitrate enrichment events documented in Central Baja California were detected as shallow as 9 m and as deep as 73 m, were associated with low-oxygen (between 2 and 4 ml/l) and high-salinity (between 33.8 and 34.3 psu) waters, and occurred during the winter months of an El Niño year. Using recent data for San Diego, CA, similar but weaker enrichment events were detected for the El Niño winter of 1997–1998. The periodic shoaling of a subsurface subtropical water mass of high temperature, high salinity, low oxygen and high nutrients during some El Niño winters is proposed to cause periodic enrichment and to maintain productivity during warming events in this area. Enrichment events were not detected off Ensenada, in Northern Baja California, possibly due to the amplification of the onshore flow during El Niño there, or due to the Ensenada front. The proposed mechanism of periodic enrichment of nutrient-depleted surface waters during some El Niño winters by subsurface waters from the California Undercurrent may explain the following: (1) survival of giant kelp forests at their southern limit in Central Baja California documented during past El Niño events in warm waters, (2) the rapid recovery and high carrying capacity of giant kelp documented after the mass disappearance during El Niño 1997–1998, and (3) the increase in the extent of mesotrophic chlorophyll detected in the area during the 1997–1998 and 1982–1983 El Niño events.     

Time-series analysis of remote-sensed chlorophyll and environmental factors in the Santa Monica–San Pedro Basin off Southern California

The time-series of remote-sensed surface chlorophyll concentration measured by SeaWiFS radiometer from September 1997 to December 2001 and the relevant hydrological and meteorological factors (remote-sensed sea surface temperature, atmospheric precipitation, air temperature and wind stress) in Santa Monica Bay and adjacent waters off southern California were analyzed using wavelet and cross-correlation statistical methods. All parameters exhibited evident seasonal patterns of variation. Wavelet analysis revealed salient long-term variations most evident in air temperature during El Niño 1997–1998 and in wind stress during La Niña 1998–1999. Short-period (<100 days) variations of remote-sensed chlorophyll biomass were mostly typical to spring seasons. Chlorophyll biomass was significantly correlated with air temperature and wind stress: an increase of chlorophyll biomass followed with 5–6-day time lag an increase of wind stress accompanied by a simultaneous decrease of air temperature. The mechanism of these variations was an intensification of phytoplankton growth resulting from the mixing of water column by wind stress and entrainment of nutrients into the euphotic layer.     

Surface chlorophyll in the Black Sea over 1978–1986 derived from satellite and in situ data

Absolute values of chlorophyll a concentration and its spatial and seasonal variations in the Black Sea were assessed by using satellite CZCS and in situ data. Since the satellite CZCS had operated for the 1978–1986 period, CZCS data was used for assessing the past state of the Black Sea just before the onset of drastic changes observed in late 1980s. The approach used for the calculation of the absolute values of chlorophyll a concentration from CZCS data was based on the direct comparison of in situ chlorophyll a data and those of CZCS and by applying the algorithm developed for the transformation of CZCS data into chlorophyll a values. CZCS Level 2 data related with pigment concentration having a spatial resolution of 1 km at nadir were used. The daily Level 3 files were derived by binning Level 2 values into 4-km grid cells and the monthly and seasonal Level 3 files were created by averaging the daily Level 3 files over the corresponding period. In situ chlorophyll a data were obtained by spectrophotometric and fluorometric methods in 15 scientific cruises over the 1978–1986 period. Total number of ship-measured data used for the comparison with those CZCS values was 590.Chlorophyll a concentration (Chl) was derived from CZCS values (C) with regression equations Chl=kC; the coefficient of transformation k was calculated from six different data sets by taking into account distinctions between subregions and seasons. The reasons for difference in the k values have been analyzed.Statistical comparison of the chlorophyll a values measured in situ and those derived from CZCS data was based on log-transformed data and gave the following results: regression SLOPE=0.842, regression INTERCEPT=−0.081, coefficient of determination (R²)=0.806, root–mean–square ERROR=0.195. The mean monthly chlorophyll a distributions derived from CZCS data over 1978–1986 have been constructed and the mean seasonal chlorophyll a values in different regions have been calculated and analyzed. The significant difference in chlorophyll concentration between the western shelf regions and the open part of the Black Sea has been demonstrated, especially in warm season. At almost all seasons, the highest chlorophyll concentration is observed in the western interior shelf region which is under strong influence of Danube. The summer mean chlorophyll concentration in this region is 18 times higher than that in the open parts and about nine times higher than in the eastern shelf region. The greatest seasonal variations are observed in the open part of the Black Sea: chlorophyll concentration in cold season is four to six times higher than in summer and three to five times higher than in April and October. To the contrary, in the western interior shelf regions, the concentration is higher in May–October (about twice than that in November–March). Seasonal variations in the western outer shelf regions are smoothed out as compared with both the western interior shelf and the open regions.     

Atmospheric CO2 measurements and error analysis on seasonal air–sea CO2 fluxes in the Bay of Biscay

Atmospheric molar fraction of CO₂ (xCO₂^atm) measurements obtained on board of ships of opportunity are used to parameterize the seasonal cycle of atmospheric xCO₂ (xCO₂^atm) in three regions of the eastern North Atlantic (Galician and French offshore and Bay of Biscay). Three selection criteria are established to eliminate spurious values and identify xCO₂^atm data representative of atmospheric background values. The filtered data set is fitted to seasonal curve, consisting of an annual trend plus a seasonal cycle. Although the fitted curves are consistent with the seasonal evolution of xCO₂^atm data series from land meteorological stations, only ship-board measurements can report the presence of winter xCO₂^atm minimum on Bay of Biscay. Weekly air–sea CO₂ flux differences (mmol C·m^− 2 day^− 1) produced by the several options of xCO₂^atm usually used (ship-board measurements, data from land meteorological stations and annually averaged values) were calculated in Bay of Biscay throughout 2003. Flux error using fitted seasonal curve relative to on board measurements was minimal, whereas land stations and annual means yielded random (− 0.2 ± 0.3 mmol C·m^− 2·day^− 1) and systematic (− 0.1 ± 0.4 mmol C·m^− 2 day^− 1), respectively. The effect of different available sources of sea level pressure, wind speed and transfer velocity were also evaluated. Wind speed and transfer velocity parameters are found as the most critical choice in the estimate of CO₂ fluxes reaching a flux uncertainty of 7 mmol C·m^− 2·day^− 1 during springtime. The atmospheric pressure shows a notable relative effect during summertime although its influence is quantitatively slight on annual scale (0.3 ± 0.2 mmol C·m^− 2·day^− 1). All results confirms the role of the Bay of Biscay as CO₂ sink for the 2003 with an annual mean CO₂ flux around − 5 ± 5 mmol C m^− 2 day^− 1.     

Characterization of fall–winter upwelling recurrence along the Galician western coast (NW Spain) from 2000 to 2005: Dependence on atmospheric forcing

Upwelling events driving ENACW (Eastern North Atlantic Coastal Water) into the Galician western coast rias had been considered typical spring–summer processes, according to the research developed in this area. However, they can also be observed in fall or winter under northerly winds blowing at shelf. Six different upwelling events were analyzed in the Ria of Pontevedra during the wet season (NDJF) from 2000 to 2005. These events were characterized by means of the zonal Ekman transport (Q_x) at four control points in front of the western rias (locally known as Rias Baixas) and thermohaline variables measured at a fixed station in the main mouth of the Ria of Pontevedra. The duration of the upwelling events ranged from 27 days (during February and March 2002) to 69 days (during November–December 2004 and January 2005). Upwelling events studied in the Ria of Pontevedra from 2000 to 2005 showed the similarity in upwelling features during both seasons (similar wind forcing and upwelled water). Finally, Q_x was correlated with the most representative atmospheric patterns in the Northern Hemisphere (EA, NAO, EA/WR, POL and SCA) from 1966 to 2005. The winter EA pattern has the most influence on Q_x showing an annual evolution with a prevalence of the positive phase from 1976 on. This positive phase is directly correlated with a prevalence of positive values of Q_x which are upwelling unfavorable in the Rias Baixas.     

Distribution of suspended sediment in the coastal sea off the Ganges–Brahmaputra River mouth: observation from TM data

Remote sensing technique was applied to estimate suspended sediment concentration (SSC) and to understand transportation, distribution and deposition of suspended sediment in the estuary and throughout the coastal sea, off the Ganges–Brahmaputra River mouth. During low river discharge period, zone of turbidity maximum is inferred in the estuary near the shore. SSC map shows that maximum SSC reaches 1050 mg/l in this period. Magnitude of SSC is mainly owing to resuspension of the bottom surface sediments induced by tidal currents flowing over shallow water depths. The influence of depth on resuspension is farther revealed from the distribution and magnitude of SSC along the head of Swatch of No Ground (SNG) submarine canyon. During high river discharge period, huge river outflow pushed the salt wedge and flashes away the suspended sediments in the coastal sea off the river mouth. Zone of turbidity maximum is inferred in the coastal water approximately within 5–10 m depth of water, where the maximum SSC reaches 1700 mg/l. In this period, huge fluvial input of the suspended sediments including the resuspended bottom sediments and the particles remaining in suspension for longer period of time since their initial entry control mainly the magnitude of SSC. In the estuary near the shore, seasonal variation in the magnitude of SSC is not evident. In the coastal sea (>5 m water depth), seasonal influence in the magnitude of SSC could be concluded from the discrepancy between SSC values of two different seasons. Transportation and deposition of suspended sediments also experiences seasonal variations. At present, suspended sediments are being accumulated on the shallow shelf (between 5 and 10 m water depth) in low discharge period and on the mid-shelf (between 10 and 75 m water depth) during high discharge period. An empirical (exponential) relationship was found between gradual settle down of suspended sediments in the coastal sea and its lateral distance from the turbidity maximum.     

The influence of different turbulence schemes on modelling primary production in a 1D coupled physical–biological model

A one-dimensional (1D) coupled physical–microbiological model has been applied to a site in the central North Sea. The impact of the choice of the turbulence closure scheme on the modelling the primary production has been investigated.The model was run with four different parameterisations of vertical mixing of heat, momentum and dissolved and suspended matters, using M2 tidal forcing and the hourly mean meteorological forcing of 1989 to reproduce the annual thermal structure and primary production. The four mixing parameterisations are: Level 2 turbulence closure scheme [Mellor, G.L., Yamada, T., 1974. A hierarchy of turbulence closure models for planetary boundary layers. J. Atmos. Sci. 31, 1791–1806; Mellor, G.L., Yamada, T., 1982. Development of a turbulence closure model for geophysical Fluid problems. Rev. Geophys. Space Phys. 20 (4) 851–875] using an explicit numerical scheme [Sharples, J., Tett, P., 1994. Modelling the effect of physical variability on the midwater chlorophyll maximum. J. Mar. Res. 52, 219–238]; a version of the Level 2.5 turbulence closure scheme [Galperin, B., Kantha, L.H., Hassid, S., Rosati, A., 1988. A quasi-equilibrium turbulent energy model for geophysical flows. J. Atmos. Sci. 45, 55–62; Ruddick, K.G., Deleersnijder, E., Luyten, P.J., Ozer, J., 1995. Haline stratification in the rhine/meuse freshwater plume: a 3D model sensitivity analysis. Cont. Shelf Res. 15 (13) 1597–1630] simplified to use an algebraic mixing length by Sharples and Simpson [Sharples, J., Simpson, J.H., 1995. Semidiurnal and longer period stability cycles in the Liverpool Bay region of freshwater influence. Cont. Shelf Res. 15, 295–313], also solved explicitly; the same simplified L2.5 scheme with an implicit numerical solution and modified vertical discretisation scheme [Annan, J.D., 1999. Numerical methods for the solution of the turbulence energy equations in the shelf seas. Int. J. Numer. Methods Fluids 29, 193–206]; and another version of the same scheme (but using a different algebraic mixing length) as described by Xing and Davies [Xing, J., Davies, A.M., 1996a. Application of turbulence energy models to the computation of tidal currents and mixing intensities in the shelf edge regions. J. Phys. Oceanogr. 26, 417–447; Xing, J., Davies, A.M., 1996b. Application of a range of turbulence models to the computation of tidal currents and mixing intensities in shelf edge regions. Cont. Shelf. Res. 16, 517–547; Xing, J., Davies, A.M., 1998. Application of a range of turbulence energy models to the computation of the internal tide. Int. J. Numer. Methods Fluids 26, 1055–1084]. Various model outputs at the sea surface and in depth profiles have been compared with data collected in 1989 as part of the North Sea Project [Huthnance, J.M., 1990. Progress on North Sea Project. NERC News, vol. 12, pp. 25–29, UK]. It is shown that the biological results are extremely sensitive to the small changes in the physical conditions, which arise due to the different turbulence schemes tested. The timing of the spring bloom and the maintenance of the midwater chlorophyll maximum all differ greatly between model runs, and the gross primary production varies by a factor of two from the highest to lowest results. The simplified Level 2.5 scheme, implemented using the numerical methods of Annan [Annan, J.D., 1999. Numerical methods for the solution of the turbulence energy equations in the shelf seas. Int. J. Numer. Methods Fluids 29, 193–206], produces results, which give the best agreement with the available data.     

Seasonal and interannual variation of physical and biological processes during 1994–2001 in the Sea of Japan/East Sea: A three-dimensional physical–biogeochemical modeling study

A Pacific basin-wide physical–biogeochemical model has been used to investigate the seasonal and interannual variation of physical and biological fields with analyses focusing on the Sea of Japan/East Sea (JES). The physical model is based on the Regional Ocean Model System (ROMS), and the biogeochemical model is based on the Carbon, Si(OH)₄, Nitrogen Ecosystem (CoSiNE) model. The coupled ROMS–CoSiNE model is forced with the daily air–sea fluxes derived from the National Centers for Environmental Prediction (NCEP) and the National Center for Atmospheric Research (NCAR) reanalysis for the period of 1994 to 2001, and the model results are used to evaluate climate impact on nutrient transport in Mixed Layer Depth (MLD) and phytoplankton spring bloom dynamics in the JES.The model reproduces several key features of sea surface temperature (SST) and surface currents, which are consistent with the previous modeling and observational results in the JES. The calculated volume transports through the three major straits show that the Korea Strait (KS) dominates the inflow to the JES with 2.46 Sv annually, and the Tsugaru Strait (TS) and the Soya Strait (SS) are major outflows with 1.85 Sv and 0.64 Sv, respectively. Domain-averaged phytoplankton biomass in the JES reaches its spring peak 1.8 mmol N m^− 3 in May and shows a relatively weak autumn increase in November. Strong summer stratification and intense consumption of nitrate by phytoplankton during the spring result in very low nitrate concentration at the upper layer, which limits phytoplankton growth in the JES during the summer. On the other hand, the higher grazer abundance likely contributes to the strong suppression of phytoplankton biomass after the spring bloom in the JES. The model results show strong interannual variability of SST, nutrients, and phytoplankton biomass with sudden changes in 1998, which correspond to large-scale changes of the Pacific Decadal Oscillation (PDO). Regional comparisons of interannual variations in springtime were made for the southern and northern JES. Variations of nutrients and phytoplankton biomass related to the PDO warm/cold phase changes were detected in both the southern and northern JES, and there were regional differences with respect to the mechanisms and timing. During the warm PDO, the nutrients integrated in the MLD increased in the south and decreased in the north in winter. Conversely, during the cold PDO, the nutrients integrated in the MLD decreased in the south and increased in the north. Wind divergence/convergence likely drives the differences in the southern and northern regions when northerly and northwesterly monsoon dominates in winter in the JES. Subjected to the nutrient change, the growth of phytoplankton biomass appears to be limited neither by nutrient nor by light consistently both in the southern and northern regions. Namely, the JES is at the transition zone of the lower trophic-level ecosystem between light-limited and nutrient-limited zones.     

Seasonal study of dissolved CH4, CO2 and N2O in a shallow tidal system of the bay of Cádiz (SW Spain)

During 2004, 10 samplings were performed in order to measure dissolved methane (CH₄), carbon dioxide (CO₂) and nitrous oxide (N₂O) in the surface waters of Río San Pedro, a tidal creek in the salt marsh area of the Bay of Cádiz (SW Spain). The inner partvs of the creek is affected by the inputs coming from an intensive fish farm and the drainage of an extensive salt marsh area.Dissolved CH₄, CO₂ and N₂O concentrations ranged from 11 to 88 nM, 36 to 108 μM and 14 to 50 nM, respectively. Surface waters were in all cases oversaturated with respect to the atmosphere, reaching values of up to 5000% for CH₄, 1240% for CO₂ and 840% for N₂O. Dissolved CH₄, CO₂ and N₂O showed a significant tidal and seasonal variability. Over a tidal cycle, concentrations were always highest during low tide, which points to the influence of the inputs from the fish farm effluent and the drainage of the adjacent salt marsh area, as well as in situ production within the system. Dissolved CH₄, CO₂ and N₂O seasonal patterns were similar and showed maximum concentrations in summer conditions. Using four different parameterizations to calculate the gas transfer coefficients [Liss, P.S. and Merlivat, L., 1986. Air-sea exchange rates: introduction and synthesis. In P. Buat-Ménard (Ed.), The Role of Air-Sea Exchanges in Geochemical Cycling. Reidel, Dordrecht, The Netherlands, p. 113–127.; Clark, J.F., Schlosser, P., Simpson, H.J., Stute, M., Wanninkhof, R., and Ho, D.T., 1995. Relationship between gas transfer velocities and wind speeds in the tidal Hudson River determined by the dual tracer technique. In: B. Jähne and E. Monahan (Eds.), Air-Water Gas Transfer: AEON Verlag and Studio, Hanau, Germany, pp. 785–800.; Carini, S., Weston, N., Hopkinson, G., Tucker, J., Giblin, A. and Vallino, J., 1996. Gas exchanges rates in the Parker River estuary, Massachusetts. Biol. Bull., 191: 333–334.; Kremer, J.N., Reischauer, A. and D'Avanzo, C., 2003. Estuary-specific variation in the air-water gas exchange coefficient for oxygen. Estuaries, 26: 829–836.], the averaged air–water fluxes of CH₄, CO₂ and N₂O from the creek to the atmosphere ranged between 34 and 150 μmol CH₄ m^− 2 day^− 1, 73 and 177 mmol CO₂ m^− 2 day^− 1 and 24 and 62 μmol N₂O m⁻² day⁻¹, respectively.     

Modelling the effects of physical–biological interactions and spatial variability in spawning and nursery areas on transport and retention of sardine Sardinops sagax eggs and larvae in the southern Benguela ecosystem

A particle-tracking individual-based model (IBM) coupled with a 3-D hydrodynamic model was used to investigate how spatial variability in spawning and nursery grounds may influence transport and retention of sardine (Sardinops sagax) eggs and larvae in the southern Benguela ecosystem. A temperature-dependent Bělehrádek development model based on laboratory growth data was used to determine the duration of one egg and two larval stages. Successful transport/retention depended on each particle's stage of development rather than its age. Results show that recruitment could occur in two distinct nursery areas on the west and south coasts of South Africa. Three viable recruitment ‘systems’ were identified: two are retention-based (spawned and retained on the west coast (WC–WC) or the south coast (SC–SC)) and one is transport-based (spawned on the south coast and transported to the west coast (SC–WC)). In the WC–WC system, the vertical distribution of eggs influenced retention; at intermediate depths of spawning (25–50 m) eggs avoided both offshore Ekman drift and deep cold water. In the SC–SC system, the area of spawning was important; > 50% of eggs from the eastern Agulhas Bank (EAB) were retained in the south coast nursery grounds, whereas very few eggs were transported there from west of Cape Agulhas. In the SC–WC system, area of spawning was also important; 40% of the eggs spawned on the western Agulhas Bank (WAB) were transported to the west coast nursery ground. Sardine life history strategy could be divided between two main systems: the west coast system (spawning on the WAB and WC, and recruiting to the WC) and the Agulhas Bank system (spawning on the central and eastern Agulhas Bank, and recruiting to the SC).