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

Nonlocal transport due to Langmuir circulation in a coastal ocean

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 117 (2012): C12007, doi:10.1029/2012JC008340.We present observations and simulations of large-scale velocity structures associated with turbulent boundary layer dynamics of a coastal ocean. Special purpose acoustic Doppler current profiler measurements revealed that such structures were frequently present, in spite of complex coastal environmental conditions. Large eddy simulation results are only consistent with these observations if the Langmuir circulation (LC) effect due to wave-current interaction is included in the model. Thus, model results indicate that the observed large-scale velocity structures are due to LC. Based on these simulations, we examine the shift of energetics and transport from a local regime for purely shear-driven turbulence to a nonlocal regime for turbulence with LC due to coherent large-scale motions that span the whole water column. Without LC, turbulent kinetic energy (TKE) dissipation rates approximately balance TKE shear production, consistent with solid wall boundary layer turbulence. This stands in contrast to the LC case for which the vertical TKE transport plays a dominant role in the TKE balance. Conditional averages argue that large-scale LC coherent velocity structures extract only a small fraction of energy from the wavefield but receive most of their energy input from the Eulerian shear. The analysis of scalar fields and Lagrangian particles demonstrates that the vertical transport is significantly enhanced with LC but that small-scale mixing may be reduced. In the presence of LC, vertical scalar fluxes may be up gradient, violating a common assumption in oceanic boundary layer turbulence parameterizations.This work was supported by the U.S. National Science Foundation (Grant OCE-1130678). CBLAST-Low analysis was supported by the Office of Naval Research under grants N00014-03-1- 0681 and N00014-06-1-0178 to the Woods Hole Oceanographic Institution. Author T.K. received support from Faculty Startup Funds of the School of Marine Science and Policy, University of Delaware.2013-06-1

Response of ocean ecosystems to climate warming

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 18 (2004): GB3003, doi:10.1029/2003GB002134.We examine six different coupled climate model simulations to determine the ocean biological response to climate warming between the beginning of the industrial revolution and 2050. We use vertical velocity, maximum winter mixed layer depth, and sea ice cover to define six biomes. Climate warming leads to a contraction of the highly productive marginal sea ice biome by 42% in the Northern Hemisphere and 17% in the Southern Hemisphere, and leads to an expansion of the low productivity permanently stratified subtropical gyre biome by 4.0% in the Northern Hemisphere and 9.4% in the Southern Hemisphere. In between these, the subpolar gyre biome expands by 16% in the Northern Hemisphere and 7% in the Southern Hemisphere, and the seasonally stratified subtropical gyre contracts by 11% in both hemispheres. The low-latitude (mostly coastal) upwelling biome area changes only modestly. Vertical stratification increases, which would be expected to decrease nutrient supply everywhere, but increase the growing season length in high latitudes. We use satellite ocean color and climatological observations to develop an empirical model for predicting chlorophyll from the physical properties of the global warming simulations. Four features stand out in the response to global warming: (1) a drop in chlorophyll in the North Pacific due primarily to retreat of the marginal sea ice biome, (2) a tendency toward an increase in chlorophyll in the North Atlantic due to a complex combination of factors, (3) an increase in chlorophyll in the Southern Ocean due primarily to the retreat of and changes at the northern boundary of the marginal sea ice zone, and (4) a tendency toward a decrease in chlorophyll adjacent to the Antarctic continent due primarily to freshening within the marginal sea ice zone. We use three different primary production algorithms to estimate the response of primary production to climate warming based on our estimated chlorophyll concentrations. The three algorithms give a global increase in primary production of 0.7% at the low end to 8.1% at the high end, with very large regional differences. The main cause of both the response to warming and the variation between algorithms is the temperature sensitivity of the primary production algorithms. We also show results for the period between the industrial revolution and 2050 and 2090.J. L. Sarmiento and R. Slater were supported by the NOAA Office of Global Programs grant NA56GP0439 to the Carbon Modeling Consortium for model development and by NSF grant OCE00973166 for model and observational interpretations as part of the JGOFS Synthesis and Modeling Project. R. Barber was supported by NSF grant OCE 0136270 as part of the JGOFS Synthesis and Modeling Project. S. Doney and J. Kleypas wish to thank the Community Climate System Model science team and the Climate Simulation Laboratory at NCAR and acknowledge support from NOAA-OGP grant NOAA-NA96GP0360S. Spall is funded through the UK Department for Environment, Food and Rural Affairs contract PECD 7/12/37

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

Underwater Application of Quantitative PCR on an Ocean Mooring

The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions

Modeling the seasonal autochthonous sources of dissolved organic carbon and nitrogen in the upper Chesapeake Bay

In this paper we investigate the seasonal autochthonous sources of dissolved organic carbon (DOC) and nitrogen (DON) in the euphotic zone at a station in the upper Chesapeake Bay using a new mass-based ecosystem model. Important features of the model are: (1) carbon and nitrogen are incorporated by means of a set of fixed and varying C:N ratios; (2) dissolved organic matter (DOM) is separated into labile, semi-labile, and refractory pools for both C and N; (3) the production and consumption of DOM is treated in detail; and (4) seasonal observations of light, temperature, nutrients, and surface layer circulation are used to physically force the model. The model reasonably reproduces the mean observed seasonal concentrations of nutrients, DOM, plankton biomass, and chlorophyll a. The results suggest that estuarine DOM production is intricately tied to the biomass concentration, ratio, and productivity of phytoplankton, zooplankton, viruses, and bacteria. During peak spring productivity phytoplankton exudation and zooplankton sloppy feeding are the most important autochthonous sources of DOM. In the summer when productivity peaks again, autochthonous sources of DOM are more diverse and, in addition to phytoplankton exudation, important ones include viral lysis and the decay of detritus. The potential importance of viral decay as a source of bioavailable DOM from within the bulk DOM pool is also discussed. The results also highlight the importance of some poorly constrained processes and parameters. Some potential improvements and remedies are suggested. Sensitivity studies on selected parameters are also reported and discussed

A vertically resolved model for phytoplankton aggregation

This work presents models of the vertical distribution and flux of phytoplankton aggregates, including changes with time in the distribution of aggregate sizes and sinking speeds. The distribution of sizes is described by two parameters, the mass and number of aggregates, which greatly reduces the computational cost of the models. Simple experiments demonstrate the effects of aggregation on the timing and depth distribution of primary production and export. A more detailed ecological model is applied to sites in the Arabian Sea; it demonstrates that aggregation can be important for deep sedimentation even when its effect on surface concentrations is small, and it presents the difference in timing between settlement of aggregates and fecal pellets

A new vision of ocean biogeochemistry after a decade of the Joint Global Ocean Flux Study (JGOFS)

The Joint Global Ocean Flux Study (JGOFS) has completed a decade of intensive process and time-series studies on the regional and temporal dynamics of biogeochemical processes in five diverse ocean basins. Its field program also included a global survey of dissolved inorganic carbon (DIC) in the ocean, including estimates of the exchange of carbon dioxide (CO2) between the ocean and the atmosphere, in cooperation with the World Ocean Circulation Experiment (WOCE). This report describes the principal achievements of JGOFS in ocean observations, technology development and modelling. The study has produced a comprehensive and high-quality database of measurements of ocean biogeochemical properties. Data on temporal and spatial changes in primary production and CO2 exchange, the dynamics of of marine food webs, and the availability of micronutrients have yielded new insights into what governs ocean productivity, carbon cycling and export into the deep ocean, the set of processes collectively known as the "biological pump." With large-scale, high-quality data sets for the partial pressure of CO2 in surface waters as well for other DIC parameters in the ocean and trace gases in the atmosphere, reliable estimates, maps and simulations of air-sea gas flux, anthropogenic carbon and inorganic carbon export are now available. JGOFS scientists have also obtained new insights into the export flux of particulate and dissolved organic carbon (POC and DOG), the variations that occur in the ratio of elements in organic matter, and the utilization and remineralization of organic matter as it falls through the ocean interior to the sediments. JGOFS scientists have amassed long-term data on temporal variability in the exchange of CO2 between the ocean and atmosphere, ecosystem dynamics, and carbon export in the oligotrophic subtropical gyres. They have documented strong links between these variables and large-scale climate patterns such as the El Nino-Southern Oscillation (ENSO) or the North Atlantic Oscillation (NAO). An increase in the abundance of organisms that fix free nitrogen (N-2) and a shift in nutrient limitation from nitrogen to phosphorus in the subtropical North Pacific provide evidence of the effects of a decade of strong El Ninos on ecosystem structure and nutrient dynamics. High-quality data sets, including ocean-color observations from satellites, have helped modellers make great strides in their ability to simulate the biogeochemical and physical constraints on the ocean carbon cycle and to extend their results from the local to the regional and global scales. Ocean carbon-cycle models, when coupled to atmospheric and terrestrial models, will make it possible in the future to predict ways in which land and ocean ecosystems might respond to changes in climate