Parameterizing the microbial loop: an experiment in reducing model complexity

The structure of the plankton food web in the upper mixed layer has important implications for the export of biogenic material from the euphotic zone. While the action of the microbial loop causes material to be recycled near the surface, activity of the larger zooplankton leads to a significant downward flux of material. The balance between these pathways must be properly represented in climate models to predict carbon export. However, the number of biogeochemical compartments available to represent the food web is limited by the need to couple biogeochemical models with general circulation models. A structurally simple model is therefore sought, with a number of free parameters, which can be constrained by available observations to produce reliable estimates of export.A step towards addressing this aim is described: an attempt is made to emulate the behavior of an 11 compartment model with an explicit microbial loop, using a 4 compartment model. The latter, incorporating a basic microbial loop parameterization, is derived directly from the 'true' model. The results are compared with equivalent results for a 4 compartment model with no representation of the microbial loop. These non-identical twin experiments suggest that export estimates from 4 compartment models are prone to serious biases in regions where the action of the microbial loop is significant. The basic parameterization shows some promise in addressing the problem but a more sophisticated parameterization would be needed to produce reliable estimates. Some recommendations are made for future research

Split-domain calibration of an ecosystem model using satellite ocean colour data

The application of satellite ocean colour data to the calibration of plankton ecosystem models for large geographic domains, over which their ideal parameters cannot be assumed to be invariant, is investigated. A method is presented for seeking the number and geographic scope of parameter sets which allows the best fit to validation data to be achieved. These are independent data not used in the parameter estimation process. The goodness-of-fit of the optimally calibrated model to the validation data is an objective measure of merit for the model, together with its external forcing data. Importantly, this is a statistic which can be used for comparative evaluation of different models. The method makes use of observations from multiple locations, referred to as stations, distributed across the geographic domain. It relies on a technique for finding groups of stations which can be aggregated for parameter estimation purposes with minimal increase in the resulting misfit between model and observations.The results of testing this split-domain calibration method for a simple zero dimensional model, using observations from 30 stations in the North Atlantic, are presented. The stations are divided into separate calibration and validation sets. One year of ocean colour data from each station were used in conjunction with a climatological estimate of the station’s annual nitrate maximum. The results demonstrate the practical utility of the method and imply that an optimal fit of the model to the validation data would be given by two parameter sets. The corresponding division of the North Atlantic domain into two provinces allows a misfit-based cost to be achieved which is 25% lower than that for the single parameter set obtained using all of the calibration stations. In general, parameters are poorly constrained, contributing to a high degree of uncertainty in model output for unobserved variables. This suggests that limited progress towards a definitive model calibration can be made without including other types of observations

A nitrogen-based model of plankton dynamics in the oceanic mixed layer

As a first step toward the development of coupled, basin scale models of ocean circulation and biogeochemical cycling, we present a model of the annual cycles of plankton dynamics and nitrogen cycling in the oceanic mixed layer. The model is easily modified and runs in FORTRAN on a personal computer. In our initial development and exploration of the model\u27s behavior we have concentrated on modeling the annual cycle at Station S near Bermuda using seven compartments (Phytoplankton, Zooplankton, Bacteria, Nitrate, Ammonium, Dissolved organic nitrogen and Detritus). This choice of compartments and the attendant flows (fluxes or intercompartmental exchanges) permits a functional distinction between new and regenerated production. We have examined over 200 different runs and carried out sensitivity analyses. Results of model runs with detrital sinking rates of 1 and 10 meters per day are presented. In these runs, the phytoplankton biomass-specific mortality rate was varied to adjust the annual net primary production (NPP) for the mixed layer to a value equivalent to 45 gC m−2, which was calculated from the literature. Modelled cycles of zooplankton and bacterial stocks, and magnitudes of their annual production which cannot be validated due to sparse observations, are driven by the amplitude of the spring bloom and by changes in foodweb structure. Most, but not all model runs exhibit a spring bloom triggered by the winter depression of zooplankton stocks and the vernal increase in solar irradiance. The bloom is driven by nitrate entrained into the mixed layer during the wintertime deepening of the mixed layer. Following the shoaling of the pycnocline to ca 20 m, nitrate supply is limited to diffusional inputs, nitrate stocks are depleted, and regenerated production exceeds new production. The resulting cycles of new and regenerated production produce an annual cycle of the f-ratio with winter maxima approaching 0.8–0.9 and summer minima reaching ca 0.1–0.2, with annual values averaging 0.7. The model reproduces the Eppley Curve, a hyperbolic relationship of increasing f with increasing primary production. This curve is shown to be the trajectory of the production system in the f-NPP phase plane. These model runs reproduce the annual cycles of areal NPP, and average annual NPP, new production, and particulate N flux values reported in the literature. The model demonstrates that currently accepted values for these annual fluxes can be reconciled only if the f-ratio has a high annual average. At present, the annual average f-ratio is poorly quantified due to severe undersampling in fall and winter. Our model\u27s ecological structure has been successfully incorporated into the Princeton general circulation model for the North Atlantic Ocean

A decade of synthesis and modeling in the US Joint Global Ocean Flux Study

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 53 (2006): 451-458, doi:10.1016/j.dsr2.2006.01.019.A decade long Synthesis and Modeling Project (SMP) was conducted as the final element of the U.S. Joint Global Ocean Flux Study (JGOFS). The SMP goal was to synthesize knowledge gained from field studies into a set of models that reflect our current understanding of the oceanic carbon cycle. Specific, innovative aspects of the project included the close partnership among scientists conducting field, laboratory, remote sensing, and numerical research and the strong emphasis on data management and web-based, public release of models and data products. Several recurrent science themes arose across the SMP effort including: the development of a new generation of ocean ecosystem and biogeochemistry models that include iron limitation, flexible elemental composition, size structure, geochemical functional groups and particle composition; the application of inverse models and data assimilation techniques to marine food-web data; the creation of whole-ocean synthesis products from the JGOFS global CO2 survey and other studies; and the analysis and modeling of ecosystem and biogeochemical responses to climate and CO2 system perturbations on time-scales ranging from seasonal and interannual variability to anthropogenic climate warming and longer.The U.S. JGOFS SMP management effort was supported by grants from the National Science Foundation (NSF/NCAR 97-142 and NSF OCE-0335589)

Spatiotemporal complexity of a ratio-dependent predator-prey system

In this paper, we investigate the emergence of a ratio-dependent predator-prey system with Michaelis-Menten-type functional response and reaction-diffusion. We derive the conditions for Hopf, Turing and Wave bifurcation on a spatial domain. Furthermore, we present a theoretical analysis of evolutionary processes that involves organisms distribution and their interaction of spatially distributed population with local diffusion. The results of numerical simulations reveal that the typical dynamics of population density variation is the formation of isolated groups, i.e., stripelike or spotted or coexistence of both. Our study shows that the spatially extended model has not only more complex dynamic patterns in the space, but also chaos and spiral waves. It may help us better understand the dynamics of an aquatic community in a real marine environment.Comment: 6pages, revtex

An eddy permitting coupled physical-biological model of the North Atlantic. Part I: Sensitivity to advection numerics and mixed layer physics

Physical influences on biological primary production in the North Atlantic are investigated by coupling a four-component pelagic ecosystem model with a high-resolution numerical circulation model. A series of sensitivity experiments demonstrates the important role of an accurate formulation of upper ocean turbulence and advection numerics. The unrealistically large diffusivity implicit in upstream advection approximately doubles primary production when compared with a less diffusive, higher-order, positive-definite advection scheme.This is of particular concern in the equatorial upwelling region where upstream advection leads to a considerable increase of upper ocean nitrate concentrations. Counteracting this effect of unrealistically large implicit diffusion by changes in the biological model could easily lead to misconceptions in the interpretation of ecosystem dynamics. Subgrid-scale diapycnal diffusion strongly controls biological production in the subtropical gyre where winter mixing does not reach the nutricline. The parameterization of vertical viscosity is important mainly in the equatorial region where friction becomes an important agent in the momentum balance

MNS1 variant associated with situs inversus and male infertility

Ciliopathy disorders due to abnormalities of motile cilia encompass a range of autosomal recessive conditions typified by chronic otosinopulmonary disease, infertility, situs abnormalities and hydrocephalus. Using a combination of genome-wide SNP mapping and whole exome sequencing (WES), we investigated the genetic cause of a form of situs inversus (SI) and male infertility present in multiple individuals in an extended Amish family, assuming that an autosomal recessive founder variant was responsible. This identified a single shared (2.34 Mb) region of autozygosity on chromosome 15q21.3 as the likely disease locus, in which we identified a single candidate biallelic frameshift variant in MNS1 [NM_018365.2: c.407_410del; p.(Glu136Glyfs*16)]. Genotyping of multiple family members identified randomisation of the laterality defects in other homozygous individuals, with all wild type or MNS1 c.407_410del heterozygous carriers being unaffected, consistent with an autosomal recessive mode of inheritance. This study identifies an MNS1 variant as a cause of laterality defects and male infertility in humans, mirroring findings in Mns1-deficient mice which also display male infertility and randomisation of left-right asymmetry of internal organs, confirming a crucial role for MNS1 in nodal cilia and sperm flagella formation and function.This article is freely available via Open Access. Click on the Publisher URL to access the full-text

Effect of demographic noise in a phytoplankton-zooplankton model of bloom dynamics

An extension of the Truscott-Brindley model (Bull. Math. Biol. {\bf 56}, 981 (1994)) is derived to account for the effect of demographic fluctuations. In the presence of seasonal forcing, and sufficiently shallow water conditions, the fluctuations induced by the discreteness of the zooplankton component appear sufficient to cause switching between the bloom and no-bloom cycle predicted at the mean-field level by the model.The destabilization persists in the thermodynamic limit of a water basin infinitely extended in the horizontal direction.Comment: 10 pages, 8 figure

Mechanisms controlling primary and new production in a global ecosystem model ? Part I: The role of the large-scale upper mixed layer variability

International audienceA global general circulation model coupled to a simple six-compartment ecosystem model is used to study the extent to which global variability in primary and export production can be realistically predicted on the basis of advanced parameterizations of upper mixed layer physics, without recourse to introducing extra complexity in model biology. The ''K profile parameterization'' (KPP) scheme employed, combined with 6-hourly external forcing, is able to capture short-term periodic and episodic events such as diurnal cycling and storm-induced deepening. The model realistically reproduces various features of global ecosystem dynamics that have been problematic in previous global modelling studies, using a single generic parameter set. The realistic simulation of deep convection in the North Atlantic, and lack of it in the North Pacific and Southern Oceans, leads to good predictions of chlorophyll and primary production in these contrasting areas. Realistic levels of primary production are predicted in the oligotrophic gyres due to high frequency external forcing of the upper mixed layer (accompanying paper Popova et al., 2006) and novel parameterizations of zooplankton excretion. Good agreement is shown between model and observations at various JFOFS time series sites: BATS, KERFIX, Papa and station India. One exception is that the high zooplankton grazing rates required to maintain low chlorophyll in high-nutrient low-chlorophyll and oligotrophic systems lessened agreement between model and data in the northern North Atlantic, where mesozooplankton with lower grazing rates may be dominant. The model is therefore not globally robust in the sense that additional parameterizations were needed to realistically simulate ecosystem dynamics in the North Atlantic. Nevertheless, the work emphasises the need to pay particular attention to the parameterization of mixed layer physics in global ocean ecosystem modelling as a prerequisite to increasing the complexity of ecosystem models

A seasonal three-dimensional ecosystem model of nitrogen cycling in the North Atlantic Euphotic Zone

A seven-component upper ocean ecosystem model of nitrogen cycling calibrated with observations at Bermuda Station “S” has been coupled to a three-dimensional seasonal general circulation model (GCM) of the North Atlantic ocean. The aim of this project is to improve our understanding of the role of upper ocean biological processes in controlling surface chemical distributions, and to develop approaches for assimilating large data sets relevant to this problem. A comparison of model predicted chlorophyll with satellite coastal zone color scanner observations shows that the ecosystem model is capable of responding realistically to a variety of physical forcing environments. Most of the discrepancies identified are due to problems with the GCM model. The new production predicted by the model is equivalent to 2 to 2.8 mol m−2 yr−1 of carbon uptake, or 8 to 12 GtC/yr on a global scale. The southern half of the subtropical gyre is the only major region of the model with almost complete surface nitrate removal (nitrate<0.1 mmol m−3). Despite this, almost the entire model is nitrate limited in the sense that any addition of nitrate supply would go predominantly into photosynthesis. The only exceptions are some coastal upwelling regions and the high latitudes during winter, where nitrate goes as high as ∼10 mmol m−3