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

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

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

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

An Amish founder variant consolidates disruption of CEP55 as a cause of hydranencephaly and renal dysplasia

This is the author accepted manuscript. The final version is available from Springer Nature via the DOI in this record.The centrosomal protein 55 kDa (CEP55 (OMIM 610000)) plays a fundamental role in cell cycle regulation and cytokinesis. However, the precise role of CEP55 in human embryonic growth and development is yet to be fully defined. Here we identified a novel homozygous founder frameshift variant in CEP55, present at low frequency in the Amish community, in two siblings presenting with a lethal foetal disorder. The features of the condition are reminiscent of a Meckel-like syndrome comprising of Potter sequence, hydranencephaly, and cystic dysplastic kidneys. These findings, considered alongside two recent studies of single families reporting loss of function candidate variants in CEP55, confirm disruption of CEP55 function as a cause of this clinical spectrum and enable us to delineate the cardinal clinical features of this disorder, providing important new insights into early human development.Medical Research CouncilNewlife Foundation for disabled childre

Skill metrics for confronting global upper ocean ecosystem-biogeochemistry models against field and remote sensing data

Author Posting. © Elsevier B.V., 2009. 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 Journal of Marine Systems 76 (2009): 95-112, doi:10.1016/j.jmarsys.2008.05.015.We present a generalized framework for assessing the skill of global upper ocean ecosystem-biogeochemical models against in-situ field data and satellite observations. We illustrate the approach utilizing a multi-decade (1979-2004) hindcast experiment conducted with the Community Climate System Model (CCSM-3) ocean carbon model. The CCSM-3 ocean carbon model incorporates a multi-nutrient, multi-phytoplankton functional group ecosystem module coupled with a carbon, oxygen, nitrogen, phosphorus, silicon, and iron biogeochemistry module embedded in a global, threedimensional ocean general circulation model. The model is forced with physical climate forcing from atmospheric reanalysis and satellite data products and time-varying atmospheric dust deposition. Data-based skill metrics are used to evaluate the simulated time-mean spatial patterns, seasonal cycle amplitude and phase, and subannual to interannual variability. Evaluation data include: sea surface temperature and mixed layer depth; satellite derived surface ocean chlorophyll, primary productivity, phytoplankton growth rate and carbon biomass; large-scale climatologies of surface nutrients, pCO2, and air-sea CO2 and O2 flux; and time-series data from the Joint Global Ocean Flux Study (JGOFS). Where the data is sufficient, we construct quantitative skill metrics using: model-data residuals, time-space correlation, root mean square error, and Taylor diagrams.This work was supported in part by grants from the NSF/ONR National Ocean Partnership Program (N000140210370), the NASA Ocean Biology and Biogeochemistry Program (NNX07AL80G), and the NSF Center for Microbial Oceanography Research and Education (C-MORE)

Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition: Incorporation of Diverse Mixotrophic Strategies

Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic “phytoplankton” and phagotrophic “microzoo-plankton”. However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding,we propose a new functional grouping of planktonic protists in an eco- physiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity,(iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accord- ingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks