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

The Colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant information

<p>Abstract</p> <p>Background</p> <p>To date, there are no clinically reliable predictive markers of response to the current treatment regimens for advanced colorectal cancer. The aim of the current study was to compare and assess the power of transcriptional profiling using a generic microarray and a disease-specific transcriptome-based microarray. We also examined the biological and clinical relevance of the disease-specific transcriptome.</p> <p>Methods</p> <p>DNA microarray profiling was carried out on isogenic sensitive and 5-FU-resistant HCT116 colorectal cancer cell lines using the Affymetrix HG-U133 Plus2.0 array and the Almac Diagnostics Colorectal cancer disease specific Research tool. In addition, DNA microarray profiling was also carried out on pre-treatment metastatic colorectal cancer biopsies using the colorectal cancer disease specific Research tool. The two microarray platforms were compared based on detection of probesets and biological information.</p> <p>Results</p> <p>The results demonstrated that the disease-specific transcriptome-based microarray was able to out-perform the generic genomic-based microarray on a number of levels including detection of transcripts and pathway analysis. In addition, the disease-specific microarray contains a high percentage of antisense transcripts and further analysis demonstrated that a number of these exist in sense:antisense pairs. Comparison between cell line models and metastatic CRC patient biopsies further demonstrated that a number of the identified sense:antisense pairs were also detected in CRC patient biopsies, suggesting potential clinical relevance.</p> <p>Conclusions</p> <p>Analysis from our <it>in vitro </it>and clinical experiments has demonstrated that many transcripts exist in sense:antisense pairs including <it>IGF2BP2</it>, which may have a direct regulatory function in the context of colorectal cancer. While the functional relevance of the antisense transcripts has been established by many studies, their functional role is currently unclear; however, the numbers that have been detected by the disease-specific microarray would suggest that they may be important regulatory transcripts. This study has demonstrated the power of a disease-specific transcriptome-based approach and highlighted the potential novel biologically and clinically relevant information that is gained when using such a methodology.</p

The legacy of Gordon Arthur Riley (1911–1985) and the development of mathematical models in biological oceanography

Gordon Arthur Riley (1911-1985) is remembered for his pioneering work in the development of marine ecosystem models during the mid-20th century. Using models that were necessarily simple because of the limited understanding of plankton physiology at the time, as well as the fact that calculations had to be done by hand, Riley studied the processes that control plankton stocks, production, and nutrient cycling, notably at Georges Bank. His great achievement lay not so much in the simulation of plankton dynamics per se, but rather in bringing to the fore the concept of using modeling as a means of explaining and interpreting the dynamics of marine ecosystems. In this article, we examine Riley's approach and philosophy to ecosystem modeling, which we discuss in context of modern day approaches. In particular, we focus on his landmark paper describing a model study of the dynamics of phytoplankton production on Georges Bank (Riley, 1946: J. Mar. Res., 6, 54-73). After reconstructing the model, we show how Riley created new mathematical characterizations of the environmental dependencies of each process in the phytoplankton equation, and how these relate to modern day formulations. We then reproduce Riley's results and conduct further analyses and sensitivity tests which serve to illustrate Riley's conviction that mathematical models can provide clear, rational explanations for the observed temporal changes in ecosystems. Riley's methods and outlook are discussed in context of the ongoing debate about the merits of complex versus simple marine ecosystem models. Based on our analyses of Riley's model, as well as his own critiques, we argue that although recent decades have seen a proliferation of complex ecosystem models that are intended to reflect our expanded understanding, the doctrines proposed by Riley are no less relevant today. In particular, Riley noted that while increasing model complexity is generally desirable, it can only be done within the confines afforded by observational data and knowledge of the physiology and ecology of key species and their interactions

Remembering John Steele and his models for understanding the structure and function of marine ecosystems

John Steele (1926–2013) is remembered for his ecosystem modelling studies on the role of biological interactions and environment on the structure and function of marine ecosystems, including consequences for fish production and fisheries management. Here, we provide a scientific tribute to Steele focusing on, by means of example, his modelling of plankton predation [Steele and Henderson (1992) The role of predation in plankton models. J. Plankton Res., 14, 157–172] that showed that differences in ecosystem dynamics between the subarctic Pacific and North Atlantic oceans can be explained solely on the basis of zooplankton mortality. The study highlights Steele’s artistry in simplifying the system to a tractable minimal model while paying great attention to the precise functional forms used to parameterize mortality, grazing and other biological processes. The success of this and other works by Steele was in large part due to his effective communication with the rest of the scientific community (especially non-modellers) resulting from his enthusiasm, use of an experiment-like (hypothesis driven) approach to applying his models and by describing simplifications and assumptions in scrupulous detail. We also intend our contribution to remember Steele as the consummate gentleman, notably his humble, behind-the-scenes attitude, his humour and his dedication to enhancing the careers of others

Influence of grazing formulations on the emergent properties of a complex ecosystem model in a global ocean general circulation model

Sensitivity to nonlinear equations may be a characteristic feature of biological models, particularly those that are complex. A complex marine ecosystem model (PlankTOM5.2) that incorporates multiple plankton functional types (PFTs) was embedded in a global ocean general circulation model (OGCM) and its performance assessed for four different formulations of multiple-prey zooplankton functional response: Michaelis–Menten (MM: Holling Type II), Sigmoidal (S: Holling Type III), Blackman (B) and Ivlev (Iv). Predictions of the four simulations were compared for the North Atlantic and North Pacific oceans. Remarkable differences were seen in both spatial extent and magnitude of predicted distributions of PFTs, as well as bulk properties, highlighting how the choice of functional response has a major impact on the resulting ecosystem structure. The range of average concentration of diatoms in surface waters was particularly marked, varying between 0.04 mg m?3 (B and MM) and 0.13 mg m?3 (S) in spring and between 0.01 mg m?3 (B) and 0.07 mg m?3 (S) in autumn. Differences in ecosystem structure affected predicted export flux, which varied by more than 25% among the simulations. Overall, our work highlights that accuracy is required in ecosystem formulation if reliable predictions are to be made when using complex marine ecosystem models embedded in OGCMs and therefore the need for further studies, with appropriate validation, that address structural sensitivity