‘The control of diatom populations by grazing’: Richard Fleming and the first marine ecosystem model

Marine ecosystem models play a central role in the progress of oceanography, and modelling is usually included as a major component in large scientific programmes to complement experimental and observational work. Today’s models often exhibit great complexity in terms of the numbers of variables and processes that are represented, and are frequently embedded in large 3D circulation models. It all seems a far cry from the early beginnings, notably the development of the first ever marine ecosystem model by Richard H. Fleming just over eighty years ago

Ocean carbon sequestration: Particle fragmentation by copepods as a significant unrecognised factor?

Ocean biology helps regulate global climate by fixing atmospheric CO2 and exporting it to deep waters as sinking detrital particles. New observations demonstrate that particle fragmentation is the principal factor controlling the depth to which these particles penetrate the ocean's interior, and hence how long the constituent carbon is sequestered from the atmosphere. The underlying cause is, however, poorly understood. We speculate that small, particle‐associated copepods, which intercept and inadvertently break up sinking particles as they search for attached protistan prey, are the principle agents of fragmentation in the ocean. We explore this idea using a new marine ecosystem model. Results indicate that explicitly representing particle fragmentation by copepods in biogeochemical models offers a step change in our ability to understand the future evolution of biologically‐mediated ocean carbon storage. Our findings highlight the need for improved understanding of the distribution, abundance, ecology and physiology of particle‐associated copepods

Geometric stoichiometry: unifying concepts of animal nutrition to understand how protein-rich diets can be “too much of a good thing”

Understanding the factors that control the growth of heterotrophic organisms is central to predicting food web interactions and biogeochemical cycling within ecosystems. We present a new framework, Geometric Stoichiometry (GS), that unifies the disciplines of Nutritional Geometry (NG) and Ecological Stoichiometry (ES) by extending the equations of ES to incorporate core NG concepts, including macromolecules as currencies and the ability of animals to select foods that balance deficits and excesses of nutrients. The resulting model is used to investigate regulation of consumer growth by dietary protein:carbohydrate ratio. Growth on protein-poor diets is limited by nitrogen. Likewise, we show that growth is also diminished on protein-rich diets and that this can be mechanistically explained by means of a metabolic penalty that arises when animals use protein for energy generation. These penalties, which are incurred when dealing with the costs of producing and excreting toxic nitrogenous waste, have not hitherto been represented in standard ES theory. In order to incorporate GS within ecosystem and biogeochemical models, a new generation of integrated theoretical and experimental studies based on unified concepts of NG and ES is needed, including measurements of food selection, biomass, growth and associated physiology, and involving metabolic penalties

Quantifying the roles of food intake and stored lipid for growth and development throughout the life cycle of a high-latitude copepod, and consequences for ocean carbon sequestration

Copepods are a critical component of ocean ecosystems, providing an important link between phytoplankton and higher trophic levels as well as regulating biogeochemical cycles of carbon (C) and nutrients. Lipid-rich animals overwinter in deep waters where their respiration may sequester a similar quantity of C as that due to sinking detritus. This ‘seasonal lipid pump’ nevertheless remains absent from global biogeochemical models that are used to project future ocean-climate interactions. Here, we make an important step to resolving this omission by investigating the biogeochemical cycling of C and nitrogen (N) by high-latitude copepods using a new individual-based stoichiometric model that includes explicit representation of lipid reserves. Simulations are presented for Calanus finmarchicus throughout its life cycle at Station Mike (66°N, 2°E) in the Norwegian Sea, although the model is applicable to any suitable location and species with a similar life history. Results indicate that growth, development and egg production in surface waters are driven primarily by food intake (quantity) which provides a good stoichiometric match to metabolic requirements. In contrast, the main function of stored lipid is to support overwintering respiration and gonad development with these two processes respectively accounting for 19 and 55% of the lipid accumulated during the previous spring/summer. The animals also catabolise 41% of body protein in order to provide N for the maintenance of structural biomass. In total, each individual copepod sequesters 9.6 μmol C in deep water. If the areal density of animals is 15,000–40,000 m-2, these losses correspond to a sequestration of 1.7–4.6 g C m-2 yr-1. Lipids contribute only 1% of the C used in egg production in the following year. Accumulating extra lipid in spring would potentially increase egg production but our analysis suggests that any such benefit is outweighed by a higher risk of predator mortality. Our work indicates that the seasonal lipid pump may be of similar magnitude to C sequestration via sinking particles in the North Atlantic and highlights the need for improved physiological understanding of lipid use by high-latitude copepods in order to better constrain C fluxes in ocean food-webs and biogeochemical models

Optimal phenology of life history events in Calanus finmarchicus: exit from diapause in relation to interannual variation in spring bloom timing and predation

Respiration of lipids by copepods during diapause (overwintering dormancy) contributes to ocean carbon sequestration via the seasonal lipid pump (SLP). Parameterizing this flux in predictive models requires a mechanistic understanding of how life history adaptation in copepods shapes their timing of exit from diapause. We investigate the optimal phenology of Calanus finmarchicus in the Norwegian Sea using an individual-based model in which diapause exit is represented as a trait characterized by phenotypic mean and variance. Without interannual variability, optimal exit correlated with the onset of the spring phytoplankton bloom and phenotypic variance was of no benefit. In contrast, copepods endured reduced fitness and adopted bet-hedging strategies when exposed to interannual variability in bloom timing and predation: later exit from diapause and phenotypic variance maintained adult numbers in anomalous late-bloom years. Exit nevertheless remained well before the peak of the bloom which is a favorable strategy when low predation early in the year enhances survival of eggs and early developmental stages. Our work highlights the complex interactions between C. finmarchicus and its environment and the need for improved understanding of bet-hedging strategies and the cues of diapause exit to progress the representation of the SLP in global biogeochemical models

Proliferating particle surface area via microbial decay has profound consequences for remineralisation rate: a new approach to modelling the degradation of sinking detritus in the ocean

Sinking detritus particles in the ocean help to regulate global climate by transporting organic carbon into deep waters where it is sequestered from the atmosphere. The rate at which bacteria remineralise detritus influences how deep particles sink and the length-scale of carbon sequestration. Conventional marine biogeochemical models typically represent particles as smooth spheres where remineralisation causes surface area (SA) to progressively shrink over time. In contrast, we propose that particle SA increases during degradation as microbial ectoenzymes cause a roughening of surfaces in a process similar to acid etching on previously smooth glass or metal surfaces. This concept is investigated using a novel model, SAMURAI (Surface Area Modelling Using Rubik As Inspiration), in which the biomass of individual particles is represented as a 3D matrix of cubical sub-units that degrades by progressive removal of sub-units that have faces in contact with the external environment. The model rapidly generates microscale rugosity (roughness) that profoundly increases total SA, giving rise to biomass-specific remineralisation rates that are approximately double those of conventional models. Faster remineralisation means less carbon penetrates the ocean’s interior, diminishing carbon sequestration in deep waters. Results indicate that both SA and microbial remineralisation are highly dynamic, as well as exhibiting large variability associated with particles of different porosities. Our work highlights the need for further studies, both observational and modelling, to investigate particle SA and related microbial dynamics in order to reliably represent the role of ocean biology in global biogeochemical models

Bridging the gap between marine biogeochemical and fisheries sciences; configuring the zooplankton link

Exploring climate and anthropogenic impacts on marine ecosystems requires an understanding of how trophic components interact. However, integrative end-to-end ecosystem studies (experimental and/or modelling) are rare. Experimental investigations often concentrate on a particular group or individual species within a trophic level, while tropho-dynamic field studies typically employ either a bottom-up approach concentrating on the phytoplankton community or a top-down approach concentrating on the fish community. Likewise the emphasis within modelling studies is usually placed upon phytoplankton-dominated biogeochemistry or on aspects of fisheries regulation. In consequence the roles of zooplankton communities (protists and metazoans) linking phytoplankton and fish communities are typically under-represented if not (especially in fisheries models) ignored. Where represented in ecosystem models, zooplankton are usually incorporated in an extremely simplistic fashion, using empirical descriptions merging various interacting physiological functions governing zooplankton growth and development, and thence ignoring physiological feedback mechanisms. Here we demonstrate, within a modelled plankton food-web system, how trophic dynamics are sensitive to small changes in parameter values describing zooplankton vital rates and thus the importance of using appropriate zooplankton descriptors. Through a comprehensive review, we reveal the mismatch between empirical understanding and modelling activities identifying important issues that warrant further experimental and modelling investigation. These include: food selectivity, kinetics of prey consumption and interactions with assimilation and growth, form of voided material, mortality rates at different age-stages relative to prior nutrient history. In particular there is a need for dynamic data series in which predator and prey of known nutrient history are studied interacting under varied pH and temperature regimes

The induction of antibody production by IL-6 is indirectly mediated by IL-21 produced by CD4+ T cells

Interleukin (IL) 6 is a proinflammtory cytokine produced by antigen-presenting cells and nonhematopoietic cells in response to external stimuli. It was initially identified as a B cell growth factor and inducer of plasma cell differentiation in vitro and plays an important role in antibody production and class switching in vivo. However, it is not clear whether IL-6 directly affects B cells or acts through other mechanisms. We show that IL-6 is sufficient and necessary to induce IL-21 production by naive and memory CD4+ T cells upon T cell receptor stimulation. IL-21 production by CD4+ T cells is required for IL-6 to promote B cell antibody production in vitro. Moreover, administration of IL-6 with inactive influenza virus enhances virus-specific antibody production, and importantly, this effect is dependent on IL-21. Thus, IL-6 promotes antibody production by promoting the B cell helper capabilities of CD4+ T cells through increased IL-21 production. IL-6 could therefore be a potential coadjuvant to enhance humoral immunity

Epigenetic Silencing of Spermatocyte-Specific and Neuronal Genes by SUMO Modification of the Transcription Factor Sp3

SUMO modification of transcription factors is linked to repression of transcription. The physiological significance of SUMO attachment to a particular transcriptional regulator, however, is largely unknown. We have employed the ubiquitously expressed murine transcription factor Sp3 to analyze the role of SUMOylation in vivo. We generated mice and mouse embryonic fibroblasts (MEFs) carrying a subtle point mutation in the SUMO attachment sequence of Sp3 (IKEE553D mutation). The E553D mutation impedes SUMOylation of Sp3 at K551 in vivo, without affecting Sp3 protein levels. Expression profiling revealed that spermatocyte-specific genes, such as Dmc1 and Dnahc8, and neuronal genes, including Paqr6, Rims3, and Robo3, are de-repressed in non-testicular and extra-neuronal mouse tissues and in mouse embryonic fibroblasts expressing the SUMOylation-deficient Sp3E553D mutant protein. Chromatin immunoprecipitation experiments show that transcriptional de-repression of these genes is accompanied by the loss of repressive heterochromatic marks such as H3K9 and H4K20 tri-methylation and impaired recruitment of repressive chromatin-modifying enzymes. Finally, analysis of the DNA methylation state of the Dmc1, Paqr6, and Rims3 promoters by bisulfite sequencing revealed that these genes are highly methylated in Sp3wt MEFs but are unmethylated in Sp3E553D MEFs linking SUMOylation of Sp3 to tissue-specific CpG methylation. Our results establish SUMO conjugation to Sp3 as a molecular beacon for the assembly of repression machineries to maintain tissue-specific transcriptional gene silencing