Representing phytoplankton aggregates in biogeochemical models

We show how to represent changes in the distribution of size and sinking speed of marine particles by a two-parameter model. In contrast to fully size-resolved models, this representation holds promise for constructing ocean biogeochemical models with detailed spatial resolution and seasonally varying sinking speed. We treat the mass and number of particles as separate state variables, each obeying its own conservation law. Average size and sinking speed of particles change as particles aggregate or the largest particles sink out. The distribution of particle sizes is assumed to follow a power law, whose exponent changes as a function of average particle size. Compared to biogeochemical models with constant particle sinking speed, our approach imposes a modest increase in computational cost and produces important effects like more rapid sinking immediately following a phytoplankton bloom. Compared to models that use hundreds of size classes to represent the detailed evolution of particle size distribution, our approach offers a major reduction in computational cost, while maintaining realistic behaviour like the sudden onset of significant aggregation when particles are sufficiently abundant.     

A four-dimensional validation of a coupled physical–biological model of the Arabian Sea

In this paper, we use a coupled biological/physical model to synthesize and understand observations taken during the US JGOFS Arabian Sea Process Study (ASPS). Its physical component is a variable-density, -layer model; its biological component consists of a set of advective–diffusive equations in each layer that determine nitrogen concentrations in four compartments, namely, nutrients, phytoplankton, zooplankton, and detritus. Solutions are compared to time series and cruise sections from the ASPS data set, including observations of mixed-layer thickness, chlorophyll concentrations, inorganic nitrogen concentrations, particulate nitrogen export flux, zooplankton biomass, and primary production. Through these comparisons, we adjust model parameters to obtain a “best-fit” main-run solution, identify key biological and physical processes, and assess model strengths and weaknesses.Substantial improvements in the model/data comparison are obtained by: (1) adjusting the turbulence-production coefficients in the mixed-layer model to thin the mixed layer; (2) increasing the detrital sinking and remineralization rates to improve the timing and amplitude of the model's export flux; and (3) introducing a parameterization of particle aggregation to lower phytoplankton concentrations in coastal upwelling regions.With these adjustments, the model captures many key aspects of the observed physical and biogeochemical variability in offshore waters, including the near-surface DIN and phytoplankton P concentrations, mesozooplankton biomass, and primary production. Nevertheless, there are still significant model/data discrepancies of P for most of the cruises. Most of them can be attributed to forcing or process errors in the physical model: inaccurate mixed-layer thicknesses, lack of mesoscale eddies and filaments, and differences in the timing and spatial extent of coastal upwelling. Relatively few are clearly related to the simplicity of the biological model, the model's overestimation of coastal P being the most obvious example. Overall, we conclude that future efforts to improve biogeochemical models of the Arabian Sea should focus on improving their physical component, ensuring that it represents the ocean's physical state as closely as possible. We believe that this conclusion applies to coupled biogeochemical modeling efforts in other regions as well.     

Vertical Nutrient Distributions in the Western North Pacific Ocean: Simple Model for Estimating Nutrient Upwelling, Export Flux and Consumption Rates

A one-dimensional, steady-state model has been developed to understand the factors controlling vertical distributions of nutrients such as nitrate and phosphate in the western North Pacific water columns. The model includes simple physics and some biogeochemical processes. Nutrients are supplied by upwelling of nutrient-rich deep waters with a constant upwelling velocity and nutrient regeneration due to decomposition of sinking particulate matter; the latter is expressed by an exponential-type export flux. Nutrients are consumed in the water column due to uptake by marine organisms, represented by a first-order substrate kinetics. The consumption rate constant is given as an exponential function of depth. The model has been applied to a data set of WOCE (World Ocean Circulation Experiment) P9 one-time measurements observed in the western North Pacific. The calculated curves fit well to observed vertical nutrient profiles from 100 m depth to over 2,500 m depth at 35 stations from 19°N to 33°30′ N along 137°E with correlation factors of greater than 0.998. A modified model, including a correction term representing a depth-dependent upwelling velocity, can reproduce observed vertical nutrient profiles at 32 stations from 5°N to 18°30′ N along 137°E with correlation factors greater than 0.993. The results support the hypothesis that most of the vertical nutrient profiles in the western North Pacific are controlled by particle export flux, consumption rate, remineralization rate and upwelling velocity. This revised version was published online in July 2006 with corrections to the Cover Date.     

An unrealistic high-salinity tongue simulated in the tropical Atlantic: another example illustrating the need for a more careful treatment of vertical discretizations in OGCMs

An unrealistically high-salinity maximum is found to develop in a high-resolution model of the north and equatorial Atlantic below the shallow halocline in the Gulf of Guinea. The spurious water mass with salinities too high by as much as 1 psu is formed when the vertical advection is treated by the standard central-differencing advection scheme. The problem is considerably reduced either by increasing the vertical resolution of the numerical grid, or by switching to a higher-order upwind-weighted scheme for vertical advection. This note stresses the need for a careful consideration of vertical discretization even in typical high-resolution ocean general circulation models (OGCMs). Particular attention is needed for studying heat and salt budgets or transports of biogeochemical tracers.     

Natural air–sea flux of CO2 in simulations of the NASA-GISS climate model: Sensitivity to the physical ocean model formulation

Results from twin control simulations of the preindustrial CO₂ gas exchange (natural flux of CO₂) between the ocean and the atmosphere are presented here using the NASA-GISS climate model, in which the same atmospheric component (modelE2) is coupled to two different ocean models, the Russell ocean model and HYCOM. Both incarnations of the GISS climate model are also coupled to the same ocean biogeochemistry module (NOBM) which estimates prognostic distributions for biotic and abiotic fields that influence the air–sea flux of CO₂. Model intercomparison is carried out at equilibrium conditions and model differences are contrasted with biases from present day climatologies. Although the models agree on the spatial patterns of the air–sea flux of CO₂, they disagree on the strength of the North Atlantic and Southern Ocean sinks mainly because of kinematic (winds) and chemistry (pCO₂) differences rather than thermodynamic (SST) ones. Biology/chemistry dissimilarities in the models stem from the different parameterizations of advective and diffusive processes, such as overturning, mixing and horizontal tracer advection and to a lesser degree from parameterizations of biogeochemical processes such as gravitational settling and sinking. The global meridional overturning circulation illustrates much of the different behavior of the biological pump in the two models, together with differences in mixed layer depth which are responsible for different SST, DIC and nutrient distributions in the two models and consequently different atmospheric feedbacks (in the wind, net heat and freshwater fluxes into the ocean).     

Beneath the surface: Characteristics of oceanic ecosystems under weak mixing conditions – A theoretical investigation

This study considers an important biome in aquatic environments, the subsurface ecosystem that evolves under low mixing conditions, from a theoretical point of view. Employing a conceptual model that involves phytoplankton, a limiting nutrient and sinking detritus, we use a set of key characteristics (thickness, depth, biomass amplitude/productivity) to qualitatively and quantitatively describe subsurface biomass maximum layers (SBMLs) of phytoplankton. These SBMLs are defined by the existence of two community compensation depths in the water column, which confine the layer of net community production; their depth coincides with the upper nutricline. Analysing the results of a large ensemble of simulations with a one-dimensional numerical model, we explore the parameter dependencies to obtain fundamental steady-state relationships that connect primary production, mortality and grazing, remineralization, vertical diffusion and detrital sinking. As a main result, we find that we can distinguish between factors that determine the vertically integrated primary production and others that affect only depth and shape (thickness and biomass amplitude) of this subsurface production layer. A simple relationship is derived analytically, which can be used to estimate the steady-state primary productivity in the subsurface oligotrophic ocean. The fundamental nature of the results provides further insight into the dynamics of these “hidden” ecosystems and their role in marine nutrient cycling.     

Local remineralization patterns in the mesopelagic zone of the Eastern North Atlantic, off the NW Iberian Peninsula

The short-time-scale variability of the remineralization patterns in the domain of Eastern North Atlantic Central Waters (ENACW) off the NW Iberian Peninsula is studied based on biogeochemical data (oxygen, nutrient salts, total alkalinity, pH, dissolved organic matter and fluorescence of dissolved humic substances) collected weekly between May 2001 and April 2002. The temporal variability of inorganic variables points to an intensification of remineralization during the summer and autumn, with an increase of nutrients, total inorganic carbon and fluorescence and a decrease of oxygen. During the subsequent winter mixing, there is a biogeochemical reset of the system, with lower nutrients, total inorganic carbon and fluorescence and higher oxygen. In contrast to inorganic variables, the levels of dissolved organic matter in the ENACW seem to respond to short-term events probably associated with fast sinking particles, where solubilisation of organic matter prevails over remineralization. Applying a previously published stoichiometric model, we observed a vertical fractionation of organic-matter remineralization. Although there is a preferential remineralization of proteins and P compounds in the entire domain of ENACW, the percentage was higher in the upper ENACW (σ<27.10 kg/m³) than in the lower; the percentage of N and P compounds in the oxidised organic matter was >80% for the upper ENACW and 63% for the lower. Likewise, the redissolution of calcareous structures contributes about 6% and 13% to the carbon regenerated in the upper and lower layers of ENACW, respectively.     

Thorium-234 as a tracer of spatial,temporal and vertical variability in particle flux in the North Pacific

An extensive ²³⁴Th data set was collected at two sites in the North Pacific: ALOHA, an oligotrophic site near Hawaii, and K2, a mesotrophic HNLC site in the NW Pacific as part of the VERTIGO (VERtical Transport In the Global Ocean) study. Total ²³⁴Th:²³⁸U activity ratios near 1.0 indicated low particle fluxes at ALOHA, while ²³⁴Th:²³⁸U ～0.6 in the euphotic zone at K2 indicated higher particle export. However, spatial variability was large at both sites—even greater than seasonal variability as reported in prior studies. This variability in space and time confounds the use of single profiles of ²³⁴Th for sediment trap calibration purposes. At K2, there was a decrease in export flux and increase in ²³⁴Th activities over time associated with the declining phase of a summer diatom bloom, which required the use of non-steady state models for flux predictions. This variability in space and time confounds the use of single profiles of ²³⁴Th for sediment trap calibration purposes. High vertical resolution profiles show narrow layers (20–30 m) of excess ²³⁴Th below the deep chlorophyll maximum at K2 associated with particle remineralization resulting in a decrease in flux at depth that may be missed with standard sampling for ²³⁴Th and/or with sediment traps. Also, the application of ²³⁴Th as POC flux tracer relies on accurate sampling of particulate POC/²³⁴Th ratios and here the ratio is similar on sinking particles and mid-sized particles collected by in-situ filtration (>10–50 μm at ALOHA and >5–350 μm at K2). To further address variability in particle fluxes at K2, a simple model of the drawdown of ²³⁴Th and nutrients is used to demonstrate that while coupled during export, their ratios in the water column will vary with time and depth after export. Overall these ²³⁴Th data provide a detailed view into particle flux and remineralization in the North Pacific over time and space scales that are varying over days to weeks, and 10's–100's km at a resolution that is difficult to obtain with other methods.     

A Comparison of Simulated Particle Fluxes Using NEMURO and Other Ecosystem Models in the Western North Pacific

JGOFS has revealed the importance of marine biological activity to the global carbon cycle. Ecological models are valuable tools for improving our understanding of biogeochemical cycles. Through a series of workshops, the North Pacific Marine Science Organization (PICES) developed NEMURO (North Pacific Ecosystem Model Understanding Regional Oceanography) a model, specifically designed to simulate the lower trophic ecosystem in the North Pacific Ocean. Its ability to simulate vertical fluxes generated by biological activities has not yet been validated. Here compare NEMURO with several other lower trophic level models of the northern North Pacific. The different ecosystem models are each embedded in a common three-dimensional physical model, and the simulated vertical flux of POM and the biomass of phytoplankton are compared. The models compared are: (1) NEMURO, (2) the Kishi and Nakata Model (Kishi et al., 1981), (3) KKYS (Kawamiya et al., 1995, 2000a, 2000b), and (4) the Denman model (Denman and Peña, 2002). With simple NPZD models, it is difficult to describe the production of POM (Particulate Organic Matter) and hence the simulations of vertical flux are poor. However, if the parameters are properly defined, the primary production can be well reproduced, even though none of models we used here includes iron limitation effects. On the whole, NEMURO gave a satisfactory simulation of the vertical flux of POM in the northern North Pacific.     

Effect of coagulation on a model planktonic food web

Observations have shown that aggregates (“marine snow”) are an important fraction of the organic matter vertical flux in the ocean. There has been a separation in biological models describing this flux, with coagulation models focused on phytoplankton blooms for which particle concentrations are high and grazing is low and neglectable and with plankton models focused on food web interactions neglecting coagulation dynamics. This separation has partly resulted from the difficulty in describing the interactions among the multiple particle sources using a coagulation model for a food web. New approaches for describing particle dynamics now make it possible to do so. The present study examines the effect of combining the food web model of Fasham et al. (1990. Journal of Marine Research 34, 591–639) with a coagulation dynamics model and applying the combined model to describe the annual cycle of an oligotrophic plankton system. As part of the model formulation, the coagulation kernels had to be altered to include both the case of fractal particles interacting and the case of smaller particles being faster settling. Results show that coagulation can have an important effect on particle flux even in the low particle concentration oligotrophic environment by increasing average particle settling speed and by increasing the ratio of maximum to minimum daily vertical flux over the course of a yearly cycle. As part of this, coagulation forms large, rapidly sinking particles. Grazing and the accompanying formation of fecal pellets can compete with coagulation for particles, but the fecal pellets can also participate in the formation of large aggregates. Among the variables that can influence export rates are phytoplankton size and concentration as well as depth of the surface mixed layer. The results provide evidence for the importance of coagulation processes in enhancing particle export even in central ocean regions.     

A generalized coordinate ocean model and a comparison of the bottom boundary layer dynamics in terrain-following and in z-level grids

Sensitivity studies with a new generalized coordinate ocean model are performed in order to compare the behavior of bottom boundary layers (BBLs) when terrain-following (sigma or combined sigma and z-level) or z-level vertical grids are used, but most other numerical aspects remain unchanged. The model uses a second-order turbulence closure scheme that provides surface and BBL mixing and results in a quite realistic climatology and deep water masses after 100 year simulations with a coarse resolution (1° × 1°) basin-scale terrain-following grid. However, with the same turbulence scheme but using a z-level grid, the model was unable to produce dense water masses in the deep ocean. The latter is a known problem for coarse resolution z-level models, unless they include highly empirical BBL schemes.A set of dense water overflow experiments with high-resolution grids (10 and 2.5 km) are used to investigate the influence of model parameters such as horizontal diffusivity, vertical mixing, horizontal resolution, and vertical resolution on the simulation of bottom layers for the different coordinate systems. Increasing horizontal diffusivity causes a thinner BBL and a bottom plume that extends further downslope in a sigma grid, but causes a thicker BBL and limited downslope plume extension in a z-level grid. A major difference in the behavior of the BBL in the two grids is due to the larger vertical mixing generated by the turbulence scheme over the step-like topography in the z-level grid, compared to a smaller vertical mixing and a more stably stratified BBL in the sigma grid. Therefore, the dense plume is able to maintain its water mass better and penetrates farther downslope in the sigma grid than in the z-level grid. Increasing horizontal and vertical resolution in the z-level grid converges the results toward those obtained by a much coarser resolution sigma coordinate grid, but some differences remain due to the basic differences in the mixing process in the BBL.     

Amino acid and hexosamine composition and flux of sinking particulate matter in the equatorial Pacific at 175°E longitude

Sinking matter collected by sediment traps, which were deployed in the equatorial Pacific Ocean at 175°E for about 11 months during 1992–1993, were analyzed for their flux and labile components in terms of amino acids and hexosamines. The samples provided a temporal resolution of 15 days and were collected from 1357 (shallow trap) and 4363 m (deep trap) depths where sea floor depth was 4880 m. Particle flux along with major components (carbonate, organic matter, biogenic opal and lithogenic material) and amino acid parameters showed distinct temporal variations, which were more pronounced in the shallow trap relative to deep trap. A coupling between the fluxes in the shallow and deep traps was more evident during the period of maximum particle flux, which seems to be connected with the short reappearance of non-El Niño conditions in equatorial Pacific during the 1991–1993 El Niño event. The biogeochemical indicators C/N, Asp/Bala, Glu/Gaba, Bala+Gaba mol%, THAA-C% and THAA-N% implied that the increase in sinking flux was associated with upwelling and enhanced surface production. Degradation of sinking particulate organic matter between the shallow and deep traps was also evident. Occasionally higher mass and major component fluxes in the deep trap relative to the shallow trap are attributed to contribution of resuspended particulates from sea floor (nepheloid layer) or to laterally advected particulates from nearby areas. Carbonate and opal composition of the sinking flux showed a predominance of calcareous plankton; however, Asp/Gly mol ratio and Ser+Thr mol% indicated enhanced occurrence of diatoms during the periods of higher flux.     

Sensitivity of 234Th export to physical processes in the central equatorial Pacific

We determined the sensitivity of the calculated sinking flux of ²³⁴Th in the central equatorial Pacific to physical processes and scavenging mechanisms by imposing a meridional and vertical advection and diffusion field on a simple dissolved and particulate ²³⁴Th cycle. We used the model to estimate the efficiency with which the ²³⁴Th deficiency relative to ²³⁸U reflected the predicted sinking flux of ²³⁴Th on particles and compared our results with ²³⁴Th data taken during the JGOFS-EqPac 1992 Survey II Cruise. ²³⁴Th deficiencies near the equator were strongly affected by both vertical advection and horizontal diffusion. The model ²³⁴Th deficiency at the equator underestimated the model ²³⁴Th sinking flux by 144% in neglecting advection and diffusion in the presence of strong upwelling at the equator. The model ²³⁴Th deficiency at the equator corrected for advection overestimated the sinking flux of ²³⁴Th by 33% in neglecting horizontal diffusion. Analysis of the scavenging mechanism suggests that, during situations of export governed by rapidly sinking particles, ²³⁴Th-based estimates of particle export are only half as sensitive to advection compared to situations of export governed by slowly sinking particles. Given that results using the mechanism of slowly sinking particles compare better with the observed ²³⁴Th deficiency and calculated meridional ²³⁴Th fluxes at the equator than the mechanism of rapidly sinking particles, we consider the mechanism of slowly sinking particle more appropriate for this region. In agreement with previous studies based on observed ²³⁴Th gradients, this study supports the incorporation of vertical advection terms in the ²³⁴Th balance to estimate particulate carbon export at the equator but suggests that this method may have overestimated the sinking flux at the equator during EqPac Survey II by 0–63% due to the role of horizontal diffusion.     

Roles of Biogeochemical Processes in the Oceanic Carbon Cycle Described with a Simple Coupled Physical-Biogeochemical Model

To evaluate the contribution of biogeochemical processes to the oceanic carbon cycle and to calculate the ratio of calcium carbonate to organic carbon downward export, we have incorporated biological and alkalinity pumps in the yoked high-latitude exchange/interior diffusion-advection (YOLDA) model. The biogeochemical processes are represented by four parameters. The values of the parameters are tuned so that the model can reproduce the observed phosphate and alkalinity distributions in each oceanic region. The sensitivity of the model to the biogeochemical parameters shows that biological production rates in the euphotic zone and decomposition depths of particulate matters significantly influence horizontal and vertical distributions of biogeochemical substances. The modeled vertical fluxes of particulate organic phosphorus and calcium carbonate are converted to vertical carbon fluxes by the biological pump and the alkalinity pump, respectively. The downward carbon flux from the surface layer to the deep layer in the entire region is estimated to be 3.36 PgC/yr, which consists of 2.93 PgC/yr from the biological pump and 0.43 PgC/yr from the alkalinity pump, which is consistent with previous studies. The modeled rain ratio is higher with depth and higher in the Pacific and Indian Oceans than in the Atlantic Ocean. The global rain ratio at the surface layer is calculated to be 0.14 to 0.15. This value lies between the lower and higher ends of the previous estimates, which range widely from 0.05 to 0.25. This study indicates that the rain ratio is unlikely to be higher than 0.15, at least in the surface waters.     

Understanding the export of biogenic particles in oceanic waters: Is there consensus?

We examine progress towards a global view of oceanic export of particulate organic carbon (POC) and other nutrient elements (P, N, Si) from the surface (upper 100 m), through the subsurface, to the deep sea (>1000 m), focusing on syntheses published since 1999 and on the Joint Global Ocean Flux Study. Food-web structure is important, and surface and subsurface processes contribute similarly to determine the fraction of net primary production (NPP) reaching the deep sea. NPP by large cells generally favours high surface export of POC. Preferential remineralization of P and N (versus C) with depth is common, as is regional variation in subsurface POC flux attenuation.The role of mineral fluxes is complex. Annual mean fluxes of POC and minerals are correlated in global deep sediment trap records, but causality and the relative importance of different minerals depends on the assumptions made. Time-series observations at single sites can oppose the geographic trends, and their large seasonal variability in the contribution of POC to total flux is at odds with mechanistic models for POC transport by minerals. Despite generally positive correlations between biogenic carbonate and POC fluxes, the overall role of carbonate export is to decrease the transfer of carbon dioxide from the atmosphere to the ocean. Both autotrophs and heterotrophs produce minerals, and progress in separating these contributions is required for the deconvolution of mineral ballast and food-web effects.Many recent models suggest global surface POC export of ∼10 GTC/yr, despite widely varying biological complexity. This limits the usefulness of their prediction of ecosystem and carbon cycle responses to global change. Progress requires better observations for model validation, and more efforts to relate the models to the observed complexity, rather than to overly simplified global syntheses. We advocate more time-series stations targeting under-studied biogeochemical regions, development of automated in situ tools for study of the subsurface ocean, and increased emphasis on combining ecological and biogeochemical methods.     

High resolution profiles of vertical particulate organic matter export off Cape Blanc,Mauritania: Degradation processes and ballasting effects

Vertical carbon fluxes between the surface and 2500 m depth were estimated from in situ profiles of particle size distributions and abundances me/asured off Cape Blanc (Mauritania) related to deep ocean sediment traps. Vertical mass fluxes off Cape Blanc were significantly higher than recent global estimates in the open ocean. The aggregates off Cape Blanc contained high amounts of ballast material due to the presence of coccoliths and fine-grained dust from the Sahara desert, leading to a dominance of small and fast-settling aggregates. The largest changes in vertical fluxes were observed in the surface waters (<250 m), and, thus, showing this site to be the most important zone for aggregate formation and degradation. The degradation length scale (L), i.e. the fractional degradation of aggregates per meter settled, was estimated from vertical fluxes derived from the particle size distribution through the water column. This was compared with fractional remineralization rate of aggregates per meter settled derived from direct ship-board measurements of sinking velocity and small-scale O₂ fluxes to aggregates measured by micro-sensors. Microbial respiration by attached bacteria alone could not explain the degradation of organic matter in the upper ocean. Instead, flux feeding from zooplankton organisms was indicated as the dominant degradation process of aggregated carbon in the surface ocean. Below the surface ocean, microbes became more important for the degradation as zooplankton was rare at these depths.     

Modeling vertical motion at ocean fronts: Are nonhydrostatic effects relevant at submesoscales?

Through a suite of three-dimensional, high-resolution numerical modeling experiments, we examine the role of nonhydrostatic effects on O(1 km) submesoscale processes at ocean fronts, with particular focus on the vertical velocity field. Several differences between nonhydrostatic and hydrostatic models are pointed out using a framework that enables precise comparison, but it is difficult to identify categorical differences between the model solutions at the grid resolutions afforded. The instantaneous vertical velocity structure is sensitive to the model choice and, even more so, to grid resolution, but the average vertical flux is similar in both hydrostatic and nonhydrostatic cases.When a frontal region with horizontal density gradients is perturbed by wind, a profusion of submesoscale, O(1 km), secondary circulation features develops in the upper 50 m. Narrow, elongated cells of intense up- and down-welling are found to occur close to the surface, overlying broader regions of weaker up- and down-welling associated with the mesoscale meanders of the baroclinically unstable front. The submesoscale down-welling is considerably stronger than up-welling and is concentrated in 1–2 km width filaments within which velocities can attain magnitudes as high as 200 m day⁻¹. The submesoscale features are found to be robust at horizontal grid resolutions varying between 1 and 0.25 km and exist even in the hydrostatic model. Submesoscale circulation is difficult to observe or resolve in coarser resolution circulation models, but is likely to play a significant role in the exchange of energy and properties between the surface ocean and thermocline. Possible mechanisms for the generation of these features are investigated in a follow-on paper.     

Does planktonic community structure determine downward particulate organic carbon flux in different oceanic provinces?

A previous study based on data from a NE Atlantic site provided evidence, using an existing foodweb/vertical-flux modelling approach, that the size-structure of the phytoplankton community — rather than primary production — can be the dominant control on downward particulate organic carbon (POC) flux. In order to assess whether taking community structure into account can also provide more reliable estimates of downward POC flux in other oceanic provinces, epipelagic observations (mainly size-fractionated primary production, biomass, community structure data and heterotrophic bacterial production) and POC flux data from deep-moored sediment traps were collated from the six different ocean regions for which suitable data are available. At each site the epipelagic data were used in conjunction with two standard versions of the foodweb/vertical-flux model (one permits direct sinking of large ungrazed algae out of surface waters, the other does not) and published empirical depth/POCflux algorithms to predict the POC flux to the deep ocean. Predictions were also made using published primary-production/POC-flux algorithms, and the two sets of predictions were compared to the deep-ocean POC flux measurements. While the version of the foodweb/ vertical-flux model permitting the direct sinking of ungrazed algae provided the most reliable predictor of POC flux for five of the six sites, no conventional algorithm provided comparable predictions for more than two sites. The reliability of these predictions is discussed in the context of recent modelling studies that explore the extent to which flow fields in the water column overlying deep-moored sediment traps confound attempts to relate particle flux measurements to observations of surface-water processes. The present study suggests that the sinking of ungrazed large cells, probably diatoms, may be the key determinant of the magnitude of the downward POC flux in a variety of ocean regions. Planned ocean-observing programmes may provide sufficient epipelagic data to allow this approach to be used to improve the accuracy of basin-scale estimates of downward POC flux and hence reduce the uncertainty of the magnitude of this flux within the oceanic carbon budget.     

A coupled 1-D biological/physical model of the northeast subarctic Pacific Ocean with iron limitation

The recent NE subarctic Pacific study of the Canadian JGOFS project was designed primarily to address why phytoplankton biomass and production at Ocean Station Papa (OSP: 50°N, 145°W) are not as high as the nitrate concentrations could potentially support. To examine the possible role of iron (Fe) limitation in concert with microzooplankton grazing and physical supply of nitrate, we have coupled a four-compartment Nitrogen–Phytoplankton–Zooplankton–Detritus planktonic ecosystem model with a 60-layer (each 2 m thick) one-dimensional mixed-layer model (Mellor–Yamada level 2.5), driven by annual forcing characteristic of OSP. Both the physical and ecological models are forced with the same annual heat budget, mean phytoplankton concentration was tuned with the equilibrium solution of the model, and the zooplankton parameter values were chosen to be representative of microzooplankton. Modelled sea surface temperature ranged between 6 (fixed – late winter) and 13–14°C, depending on the distribution and amount of phytoplankton and detritus calculated by the model. Simulations with Fe limitation reducing the maximum specific growth rate of phytoplankton (for Fe-replete conditions) by a factor of ∼3 best reproduced the annual cycle of surface layer nitrate, although the resulting annual f-ratio calculated from the fluxes into and out of the nitrogen compartment was marginally higher than recent estimates of f-ratio based on observations at OSP. The best simulations with Fe limitation agreed with observations of the annual cycle of surface nitrate concentration, the f-ratio, particulate nitrogen concentration in the euphotic layer, the export production, and the remineralization depth scale for sinking detritus, to within ∼50%, probably within the range of observational uncertainty and/or seasonal and interannual variability. Possible modifications include separating the detrital pool into suspended and sinking organic matter, decreasing the rate of remineralization with increasing depth, and examining the supply of nitrate to the surface layer by means of horizontal advection. The observational basis required to formulate these processes is marginal at present.     

A study of overflow simulations using MPAS-Ocean: Vertical grids,resolution, and viscosity

MPAS-Ocean is used to simulate an idealized, density-driven overflow using the dynamics of overflow mixing and entrainment (DOME) setup. Numerical simulations are carried out using three of the vertical coordinate types available in MPAS-Ocean, including z-star with partial bottom cells, z-star with full cells, and sigma coordinates. The results are first benchmarked against other models, including the MITgcm’s z-coordinate model and HIM’s isopycnal coordinate model, which are used to set the base case used for this work. A full parameter study is presented that looks at how sensitive overflow simulations are to vertical grid type, resolution, and viscosity. Horizontal resolutions with 50 km grid cells are under-resolved and produce poor results, regardless of other parameter settings. Vertical grids ranging in thickness from 15 m to 120 m were tested. A horizontal resolution of 10 km and a vertical resolution of 60 m are sufficient to resolve the mesoscale dynamics of the DOME configuration, which mimics real-world overflow parameters. Mixing and final buoyancy are least sensitive to horizontal viscosity, but strongly sensitive to vertical viscosity. This suggests that vertical viscosity could be adjusted in overflow water formation regions to influence mixing and product water characteristics. Lastly, the study shows that sigma coordinates produce much less mixing than z-type coordinates, resulting in heavier plumes that go further down slope. Sigma coordinates are less sensitive to changes in resolution but as sensitive to vertical viscosity compared to z-coordinates.