Not Fabrice

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Fabrice
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  • Article
    Acquired phototrophy in aquatic protists
    (Inter-Research, 2009-11-24) Stoecker, Diane K. ; Johnson, Matthew D. ; de Vargas, Colomban ; Not, Fabrice
    Acquisition of phototrophy is widely distributed in the eukaryotic tree of life and can involve algal endosymbiosis or plastid retention from green or red origins. Species with acquired phototrophy are important components of diversity in aquatic ecosystems, but there are major differences in host and algal taxa involved and in niches of protists with acquired phototrophy in marine and freshwater ecosystems. Organisms that carry out acquired phototrophy are usually mixotrophs, but the degree to which they depend on phototrophy is variable. Evidence suggests that ‘excess carbon’ provided by acquired phototrophy has been important in supporting major evolutionary innovations that are crucial to the current ecological roles of these protists in aquatic ecosystems. Acquired phototrophy occurs primarily among radiolaria, foraminifera, ciliates and dinoflagellates, but is most ecologically important among the first three. Acquired phototrophy in foraminifera and radiolaria is crucial to their contributions to carbonate, silicate, strontium, and carbon flux in subtropical and tropical oceans. Planktonic ciliates with algal kleptoplastids are important in marine and fresh waters, whereas ciliates with green algal endosymbionts are mostly important in freshwaters. The phototrophic ciliate Myrionecta rubra can be a major primary producer in coastal ecosystems. Our knowledge of how acquired phototrophy influences trophic dynamics and biogeochemical cycles is rudimentary; we need to go beyond traditional concepts of ‘plant’ and ‘animal’ functions to progress in our understanding of aquatic microbial ecology. This is a rich area for exploration using a combination of classical and molecular techniques, laboratory and field research, and physiological and ecosystem modeling.
  • Article
    Observational needs supporting marine ecosystems modeling and forecasting: from the global ocean to regional and coastal systems
    (Frontiers Media, 2019-10-15) Capotondi, Antonietta ; Jacox, Michael ; Bowler, Chris ; Kavanaugh, Maria T. ; Lehodey, Patrick ; Barrie, Daniel ; Brodie, Stephanie ; Chaffron, Samuel ; Cheng, Wei ; Dias, Daniela F. ; Eveillard, Damien ; Guidi, Lionel ; Iudicone, Daniele ; Lovenduski, Nicole S. ; Nye, Janet A. ; Ortiz, Ivonne ; Pirhalla, Douglas ; Pozo Buil, Mercedes ; Saba, Vincent S. ; Sheridan, Scott ; Siedlecki, Samantha A. ; Subramanian, Aneesh C. ; de Vargas, Colomban ; Di Lorenzo, Emanuele ; Doney, Scott C. ; Hermann, Albert J. ; Joyce, Terrence M. ; Merrifield, Mark ; Miller, Arthur J. ; Not, Fabrice ; Pesant, Stephane
    Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes involved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.
  • Article
    Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition : incorporation of diverse mixotrophic strategies
    (Elsevier, 2016-01-03) Mitra, Aditee ; Flynn, Kevin J. ; Tillmann, Urban ; Raven, John A. ; Caron, David A. ; Stoecker, Diane K. ; Not, Fabrice ; Hansen, Per J. ; Hallegraeff, Gustaaf M. ; Sanders, Robert W. ; Wilken, Susanne ; McManus, George ; Johnson, Matthew D. ; Pitta, Paraskevi ; Våge, Selina ; Berge, Terje ; Calbet, Albert ; Thingstad, Frede ; Jeong, Hae Jin ; Burkholder, JoAnn M. ; Glibert, Patricia M. ; Graneli, Edna ; Lundgren, Veronica
    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 “microzooplankton”. 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. Accordingly, 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.