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  • 1
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    When is a biogeochemical model too complex? Objective model reduction for North Atlantic time-series sites (2013)
    Elsevier
    In:  Progress in Oceanography, 116 . pp. 49-65.
    Details
    Publication Date: 2019-07-30
    Description: Highlights • We objectively identify and remove unconstrained parameters from a marine ecosystem model. • Optimal model complexity is identified using three model selection metrics. • As many as 14 of the model’s 30 parameters can be removed, with no significant reduction in model-data misfit. • Optimal model structures and parameters are different at two different North Atlantic locations. • The specialised structures and parameters at each site may be unsuitable for new environments The degree of structural complexity that should be incorporated in marine biogeochemical models is unclear. We know that the marine ecosystem is complex, and that its observed behaviour is attributable to the interaction of a large number of separate processes, but observations are scarce and often insufficient to constrain more than a small number of model parameters. This issue is addressed using a novel algorithm that systematically removes model processes that are not constrained by observations. The algorithm is applied to a one-dimensional, eight component ecosystem-biogeochemistry model at two North Atlantic time-series sites. Between 11 and 14 of the 30 model parameters can be removed at each site with no significant reduction in the model’s ability to fit upper ocean (0–200 m) biogeochemical tracer and productivity data. The statistically optimal model structures and parameters provide estimates of the most likely state variables and fluxes at each site. Differences in these estimates between the two sites indicate that the optimal models are specialised to both the physical environment and the assimilated observations. At each site the heavily reduced models may thus be suitable for diagnostic purposes but may not be sufficiently complex for more general applications, such as in global ocean general circulation models, or for predicting the response of marine systems to environmental change.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/j.pocean.2013.06.002
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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    Co-existence of distinct Ostreococcus ecotypes at an oceanic front (2017)
    ASLO (Association for the Sciences of Limnology and Oceanography)
    In:  Limnology and Oceanography, 62 (1). pp. 75-88.
    Details
    Publication Date: 2020-02-06
    Description: Western boundary currents support high primary production and carbon export. Here, we performed a survey of photosynthetic picoeukaryotes in the North Pacific Ocean in four transects crossing the Kuroshio Front. Prasinophyte algae comprised 85% of 18S rRNA gene sequences for photosynthetic taxa in the 〈5 μm size fraction. The picoplanktonic (〈2 μm) genera Micromonas and Ostreococcus comprised 30% and 51% of the total photosynthetic 18S rDNA sequences from five stations. Phylogenetic analysis showed that two Ostreococcus ecotypes, until now rarely found to co‐occur, were both present in the majority of samples. Ostreococcus ecotype OI reached 6,830 ± 343 gene copies mL−1, while Ostreococcus ecotype OII reached 50,190 ± 971 gene copies mL−1 based on qPCR analysis of the 18S rRNA gene. These values are higher than in studies of other oceanographic regions by a factor of 10 for OII. The data suggest that meso‐ and finer‐scale physical dynamics had a significant impact on the populations at the front, either by mingling ecotypes from different source regions at fine scales (∼10s km) or by stimulating their growth through vertical nutrient injections. We investigate this hypothesis with an idealized diffusion‐reaction model, and find that only a combination of mixing and positive net growth can explain the observed distributions and overlap of the two Ostreococcus ecotypes. Our field observations support larger‐scale numerical ocean simulations that predict enhanced biodiversity at western boundary current fronts, and suggest a strategy for systematically testing that hypothesis.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1002/lno.10373
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    Marine mixotrophy increases ecological efficiency [Environmental Sciences] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-03-16
    Description: Mixotrophic plankton, which combine the uptake of inorganic resources and the ingestion of living prey, are ubiquitous in marine ecosystems, but their integrated biogeochemical impacts remain unclear. We address this issue by removing the strict distinction between phytoplankton and zooplankton from a global model of the marine plankton food web....
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Effects of dual oxidants on biofilm morphology [Biophysics and Computational Biology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-01-08
    Description: A major theme driving research in biology is the relationship between form and function. In particular, a longstanding goal has been to understand how the evolution of multicellularity conferred fitness advantages. Here we show that biofilms of the bacterium Pseudomonas aeruginosa produce structures that maximize cellular reproduction. Specifically, we develop...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Growth, metabolic partitioning, and the size of microorganisms [Ecology] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-01-12
    Description: Population growth rate is a fundamental ecological and evolutionary characteristic of living organisms, but individuals must balance the metabolism devoted to biosynthesis and reproduction against the maintenance of existing structure and other functionality. Here we present a mathematical model that relates metabolic partitioning to the form of growth. The model captures the observed growth trajectory of single cells and individuals for a variety of species and taxa spanning prokaryotes, unicellular eukaryotes, and small multicellular eukaryotes. Our analysis suggests that the per-unit costs of biosynthesis and maintenance are conserved across prokaryotes and eukaryotes. However, the relative metabolic expenditure on growth and maintenance of whole organisms clearly differentiates taxa: prokaryotes spend an increasing fraction of their entire metabolism on growth with increasing cell size, whereas eukaryotes devote a diminishing fraction. These differences allow us to predict the minimum and maximum size for each taxonomic group, anticipating observed evolutionary life-history transitions. The framework provides energetic insights into taxonomic tradeoffs related to growth and metabolism and constrains traits that are important for size-structured modeling of microbial communities and their ecological and biogeochemical effects.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii [Environmental Sciences] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-02-09
    Description: The marine nitrogen fixing microorganisms (diazotrophs) are a major source of nitrogen to open ocean ecosystems and are predicted to be limited by iron in most marine environments. Here we use global and targeted proteomic analyses on a key unicellular marine diazotroph Crocosphaera watsonii to reveal large scale diel changes in its proteome, including substantial variations in concentrations of iron metalloproteins involved in nitrogen fixation and photosynthesis, as well as nocturnal flavodoxin production. The daily synthesis and degradation of enzymes in coordination with their utilization results in a lowered cellular metalloenzyme inventory that requires ∼40% less iron than if these enzymes were maintained throughout the diel cycle. This strategy is energetically expensive, but appears to serve as an important adaptation for confronting the iron scarcity of the open oceans. A global numerical model of ocean circulation, biogeochemistry and ecosystems suggests that Crocosphaera’s ability to reduce its iron-metalloenzyme inventory provides two advantages: It allows Crocosphaera to inhabit regions lower in iron and allows the same iron supply to support higher Crocosphaera biomass and nitrogen fixation than if they did not have this reduced iron requirement.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Fine scale phytoplankton community structure across the Kuroshio Front (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-11
    Description: Concurrent physical, chemical and biological observations across the Kuroshio Front collected in October 2009 provide a detailed view of the relationship between the physical environment and the phytoplankton community. Depth profiles were taken at stations ~9 km apart along five 70 km transects. With a combination of flow cytometry, microscopy and high-pressure liquid chromatography pigment analysis, we characterized the phytoplankton community structure across the front. The observed phytoplankton community fell into two distinct assemblages, largely separated by the front, but which also reflected patterns in the distribution of Kuroshio and Oyashio water masses shaped by mesoscale lateral mixing. Phytoplankton biomass was elevated where there was a positive vertical flux of nitrate towards the surface, and the frontal circulation drove a lateral transport of nutrients southwards into the subtropical gyre. The observations showed that the phytoplankton respond to forcing on several scales: the phytoplankton community across the front was shaped by a combination of the large scale biogeography of the region, mesoscale mixing of populations and finer scale modification of the light and nutrient environment.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-23
    Description: The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that "Everything is everywhere, but the environment selects", we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Modelling spatial and temporal patterns in size-structured marine plankton communities: top-down and bottom-up controls (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-10
    Description: Idealized equilibrium models have attributed the observed size structure of marine communities to the interactions between nutrient and grazing control. Here, we examine this theory in a more realistic context using a size-structured global ocean food-web model, together with a much simplified version of the same model for which equilibrium solutions are readily obtained. Both models include the same basic assumptions: allometric scaling of physiological traits and size-selective zooplankton grazing. According to the equilibrium model, grazing places a limit on the phytoplankton biomass within each size-class, while the supply rate of essential nutrients limits the number of coexisting size classes, and hence the total biomass, in the system. The global model remains highly consistent with this conceptual view in the large-scale, annual average sense, but reveals more complex behaviour at shorter timescales, when phytoplankton and zooplankton growth may become decoupled. In particular, we show temporal and spatial scale dependence between total phytoplankton biomass and two key ecosystem properties: the zooplankton-to-phytoplankton ratio, and the partitioning of biomass among different size classes.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Size-scaling of macromolecules and chemical energy content in the eukaryotic microalgae (2016)
    Oxford University Press
    Details
    Publication Date: 2016-10-08
    Description: The macromolecular composition and cell size of microalgae can influence their competitive interactions for nutrients and food quality for predators. Here we quantify the cell volume and dry weight based size-scaling of protein, lipid, carbohydrate and chemical energy content of eukaryotic microalgae from data extracted from the scientific literature. Across all the microalgae examined, cell size is an excellent predictor of macromolecular and chemical energy content with size-scaling exponents ranging from 0.8 to 0.93 for cell volume and 0.96 to 1.1 for dry weight. There are second-order taxonomic differences in the size scaling of macromolecular and chemical energy content. Relative to the green algae and dinoflagellates, the diatoms have lower cell volume size-scaling exponents for protein, lipid and chemical energy content due to their larger increase in vacuole volume with increasing cell volume. The dinoflagellates have a lower size-scaling exponent for carbohydrate relative to the diatoms and green algae and the green algae have a relatively high size-scaling exponent for protein as compared to the diatoms. Differences in the size-scaling of macromolecular and chemical energy content across the diatoms, green algae and dinoflagellates appear to reflect fundamental differences in cellular architecture and growth and storage allocation strategies across these microalgal phyla.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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