A SLIP workshop and Annual SLIP meeting for ph.d. students
Søminestationen, 29-31 October 2002
Under the auspices of the research-netwok SLIP (www.fishnet.dk) a workshop on biological-physical interactions in the plankton is organized 29-31 October, 2002.
Purpose
The workshop has a dual purpose:
- To bring (primarily Danish) marine sciences research students together in order to strengthen student networks and to allow students to present their work in a foreign language under relaxed conditions
- To enhance interactions with a French group of scientists working on biological-physical interactions in the plankton
Topic
The distribution and adaptations of planktonic organisms, from vira and bacteria to larval fish, can be understood only in the context of the physical and chemical environment in which they live. Nutrient uptake, motility patterns, feeding and encounter rates, signal transmission and perception are all constrained by often non-intuitive interactions between organism biology and small-scale physical and chemical characteristics of fluid media (e.g. viscosity, fluid motion, and diffusion). On a larger scale, turbulent mixing transports inorganic nutrients to the euphotic zone and together with advection and vertical migratory behaviour redistribute organisms both vertically and horizontally. This workshop focuses on attempts to understand such interactions and their implications to pelagic food web structure (trophic interactions, vertical fluxes, distribution patterns).
Who can participate
Marine sciences ph.d. and masters students and scientists. Priority will be given to students associated the SLIP network, but anyone can apply. There is room for a maximum of 25 participants.
Where and when
The field station of Roskilde University, ‘Søminestationen’, situated at Isefjord near Holbæk, Denmark.
Price
Food and accommodation is covered by SLIP. Travel expenses are covered for SLIP-students.
Application
Applications are mailed to Lilian Andersen () prior to October 4, 2002. Students apply by submitting an abstract of their talk.
Program
There will be about 9 talks by established scientists (see attached list of tentative titles) during the first 1 ½ day. The subsequent 1 ½ day will be allocated to student talks. All students are expected to give 15-min talks on their own research (even if outside the main topic of the workshop).
List of invited talks (preliminary)
- Laurent Seuront:
- Microscale patchiness and biophysical couplings: towards a seascape topography
-
- Laurent Seuront:
Living in a turbulent environment: new insights into the effects of microscale turbulence on zooplankton behavior and trophodynamics
-
- Sami Souissi:
How to make Individual Based Modelling accessible to all ecologists? A demonstration with the new platform MOBIDYC
-
- Sami Souissi:
Consequences of individual behaviour and spatial heterogeneity on the emerging properties at the population scale
-
- Philippe Caparroy:
PASTIS (Pelagic Agents System for Trophic Interactions Studies): A 3D lagrangien tool for modeling realistic small scale interactions between several pelagic entities
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- Uffe H. Thygesen:
- Large-scale approximations of small-scale processes in ecosystems: Motivation, techniques and examples
-
- Thomas Kiørboe:
- Microbial dynamics on marine snow aggregates – the significance of behavior, fluid dynamics, and predator-prey interactions
-
- Andy Visser:
- Behavior, turbulence and patchiness in the plankton (tentative title)
Seuront, Souissi and Caparroy are associated or at the Ecosystem Complexity Research Group, Station Marine de Wimereux, Université des Sciences et technologies de Lille, France
Visser, Thygesen and Kiørboe are at the Danish Institute for Fisheries Research, 2920-Charlottenlund, Denmark
Abstracts of invited talks
Sami Souissi: How to make Individual Based Modelling accessible to all ecologists? A demonstration with the new platform MOBIDYC
The increasing importance of Individual-based modelling (IBM) in population dynamics has led to the greater availability of tools designed to facilitate their creation and use. Yet, these tools are either too general, requiring the extensive knowledge of a computer language, or conversely restricted to very specific applications. Hence, they are of little help to non-computer expert ecologists. In order to build IBM's without hard coding them nor restricting their scope too much, we developed a new platform called MOBIDYC (MOdelling Based on Individuals for the DYnamics of Communities) with a multi-agent architecture. In the literature about multi-agents system (MAS), ‘agents’ are defined as autonomous objects that perceive and react to their environment. Mobidyc is an all-agents architecture focusing on what each agent does than in what it actually is. The advantage of this approach is that all the different elementary tasks individuals do can be grouped into a low number of classes of activities: locate, select, translate, compute, end, and workflow control. This demonstration will show the great potentials of MOBIDYC and also the rapidity of developing and testing IBMs with increasing levels of complexity.
Sami Souissi: Consequences of individual behaviour and spatial heterogeneity on the emerging properties at the population scale
We use the platform MOBIDYC to study the effects of the spatial representation (size of 2D grid) and the individual behaviour (movement of developmental stages, advection,…) on the total abundance of the population. Here a life cycle of a copepod (or any other organism) is represented, then a selective predator can be added easily. These classes of IBMs include a stochastic component (i.e. random walk, probabilistic representation of survival,…), consequently, we need more than one simulation in order to study the patterns of the simulated numbers. We developed with MOBIDYC a tool allowing to start a set of simulations and to save the quantities we wish to analyse. Finally an example of the use of statistical methods for studying the spatio-temporal patterns of simulated numbers will be shown. The use of adequate statistical methods (i.e. multiscaling techniques) can be applied to both real data (from laboratory/mesocosm experiments or from in situ sampling) and simulated data. This allowed us to propose new indices of similitude between ‘real’ and ‘simulated’ patterns of our marine ecosystem, in general very complex.
Philippe Caparroy: PASTIS (Pelagic Agents System for Trophic Interactions Studies): A 3D lagrangien tool for modeling realistic small scale interactions between several
pelagic entities.
Some recent studies have shown the role of copepod behavior (sequences of swimming patterns, attack/escape behaviors), their rheotactic abilities (they detect and react to remote fluid disturbances) and the physical properties of the water at small scales (turbulence, turbidity for visual predators, etc.) on the outcome of predator-prey interactions of planktonic (pelagic) organisms. However, a realistic representation of predator-prey interactions at small scales should include more than a single couple of predator-prey. The inter-individual variability in the patterns of behavior may exist within predators and preys of the same species. Until now, the available models used to study these interactions at small scales cannot represent the complexity of these interactions. PASTIS is build using Object-Oriented computer programming, which allowed to overcome some limits of actually used predation models. In this representation, the interactions between n entities include: i) a deterministic and realistic representation of swimming behavior; ii) a deterministic representation of the predation processes as a succession of conditional discrete temporal events: (encounter, attack, escape, scanning or searching,…) and, iii) a stochastic representation of the pelagic entities motion. We illustrate with different examples the validity of the results obtained with PASTIS and the great potentials of such new approach.
Laurent Seuront: Microscale patchiness and biophysical couplings: towards a seascape topography
In light of the growing awareness of the intermittent nature of both physical and biological patterns and processes in marine sciences, and the emergence of hot topics such as those related to thin layers properties, there is a real need to focus on the existence and the precise nature of couplings between physics and biology at microscale.
In that way, we will first present a new high resolution free-fall instrument developed to simultaneously record shear, temperature, phytoplankton biomass and turbidity, and present some illustrative profiles recorded in tidally mixed coastal waters. Second, considering the demonstrated extremely intermittent nature of the records provided by this instrument, we will introduce some recently developed techniques aimed at characterizing both qualitatively and quantitatively this type of variability. In particular, we will show that the phytoplankton patches present a very specific shape, and a highly structured distribution as a function of both patch intensity and scales. Subsequently, an original (high order) testing procedure aimed at determining the existence and the nature of the coupling between two stochastic processes (e.g. simultaneously recorded profiles of turbulent energy dissipation rates and phytoplankton concentrations, or foraging trajectory of a marine mammal and the spatial distribution of its preys) will be described as well as its advantages when compared with more traditional procedures.
Finally, it is argued that a combination of these two statistical frames could provide a basis to establish a topology of the nature of both the structure of marine ecosystems, and the couplings between physics and biology, as well as between processes associated with different trophic levels (e.g. nutrients and phytoplankton biomass). We will discuss further the potential consequences of our findings on the understanding of marine systems functioning, especially in terms of primary production estimates and zooplankton trophodynamics.
Laurent Seuront: Living in a turbulent environment: new insights into the effects of microscale turbulence on zooplankton behavior and trophodynamics
Microscale turbulence is widely recognized as a major driving force in zooplankton dynamics. In particular, turbulent processes have salient effects on processes such as metabolic rates, encounter rates with preys, grazing, egg production and behavior. More recent results suggest that the swimming abilities of zooplankton can overcome turbulent fluctuations, and that their swimming behavior is highly structured, far from the standard random walk hypothesis.
However, two major limitation related to studies conducted in the laboratory generated turbulence have been raised: (i) the levels of turbulence used are quite often high when compared to the turbulence intensities found in the environment, and (ii) the size of the experimental vessels and/or the design of oscillating grids did not allow the development of an inertial subrange, and then of a realistic turbulence. Here, using turbulence-generating apparatus able to overcome these limitations, we will focus on three major aspects of turbulence effects on zooplankton organisms:
- first, we estimate the capacity of zooplankton organisms to swim against a gradient of turbulence (and then to know whether they can really be regarded as “plankton” organisms or not);
- second, we quantify their swimming behavior in relation with different intensities of turbulence, and different duration of turbulence exposure;
- finally, we quantify zooplankton grazing rates as a function of turbulence quality (i.e. inertial subrange turbulence or non-inertial subrange turbulence), a realistic range of turbulence intensities, food quality and quantity.
The results obtained will be discussed and compared to the theoretical models of predator-prey encounter rates. In particular, using a recent theoretical proposal to include intermittency in predator-prey encounter rates we will show that turbulence intermittency cannot be neglected. Moreover, we will also show that even in low chlorophyll concentration conditions, the effects of turbulence on grazing rates can be totally overcome by the intrinsic biological properties of the phytoplankton populations.
The impact of our results will be finally discussed on the general framework of the effects of turbulent processes on the functioning of marine ecosystems.
Uffe Høgsbro Thygesen: Large-scale approximations of small-scale processes in ecosystems: Motivation, techniques and examples.
A common difficulty in ecosystem modelling is that ecosystems contain dynamics at a wide range of temporal and spatial scales. For instance diffusion is primarily a small-scale process while at larger scales advection becomes dominating. Similarly, the time scales of a bacterium are quite different from those of a whale. In the nomenclature of dynamic systems and their numerical analysis, ecosystems are stiff systems. Despite this, any concrete study must focus on a relatively narrow range of scales, or the conceptual and computational complexity of the models becomes overwhelming. To this end, we must analyse fast sub-processes separately and determine how they affect slower dynamics. In this talk I will survey this problem and some approaches to overcome it, mainly taking from the engineering literature on dynamic systems. Then I will present some novel results regarding diffusion approximations of fast sub-processes. The theoretical material will be illustrated with two examples: Firstly, bacteria performing run/tumble motion in order to locate nutrient-rich regions, while at the same time depleting the ressource. Secondly, the probability of survival of larval fish, based on approximations of the feeding process.
Thomas Kiørboe: Microbial dynamics on marine snow aggregates – the significance of behavior, fluid dynamics, and predator-prey interactions
Microbial communities consisting of bacteria, flagellates and ciliates develop on sinking marine snow aggregates and cause their rapid turnover in the water column. The dynamics of the microbial populations depend on the colonization rate and on the growth and mortality rates of the attached microbial populations. These rates and probabilities, in turn, depend on the motility of the individual microorganisms, their chemosensory capabilities, the fluid dynamic environment of the aggregate, and on complex intra- and inter-specific interactions between the microorganisms (grazing, competition, intra- and inter-specific communication, e.g. through quorum sensing). I use observations of bacterial swimming behavior, flagellate grazing rates, and advection-diffusion and Lotka-Volterra type models to describe the dynamics, and compare predicted with observed development of microbial populations on marine aggregates.
Andy Visser: Behavior, turbulence and patchiness in the plankton (tentative title)