Open position: Enhancing the LInk between low-and high TROPhic levels in ecosystem models. Application of a size-structured model of unicellular and multicellular plankton coupled to small pelagic fish – Deadline 20 October 2022

A pioneer in ocean science, IFREMER’s cutting-edge research is grounded in sustainable development and open science. Our vision is to advance science, expertise and innovation to:

– Protect and restore the ocean

– Sustainably use marine resources to benefit society

– Create and share ocean data, information & knowledge.

With more than 1,500 personnel spread along the French coastline in more than 20 sites, the Institute explores the 3 great oceans: the Indian, Atlantic and Pacific oceans. A leader in ocean science, IFREMER is managing the French Oceanographic Fleet and its dedicated scientists create ground-breaking technology to push the boundaries of ocean exploration and knowledge, from the abyss to the atmosphere-ocean interface.

Well-established in the international scientific community, our scientists, engineers and technicians are committed to advance knowledge about our planet’s last unexplored frontiers. They provide the science we need for informed decision-making and public policy and they transfer this knowledge and technology to businesses to fulfill public and private needs. Core to our mission is also to strengthen public awareness about the importance of understanding the ocean and its resources, and empowering future generations of leaders through education and outreach national campaigns.

Founded in 1984, IFREMER is a French public organization and its budget approximates 240 million euros. It is operating under the joint authority of the French Ministry for Higher Education, Research and Innovation, the french Ministry of the Sea, the French Ministry for the Ecological and Solidary Transition, and the French Ministry of Agriculture and Food.

General areas of responsibility

DYNECO (Dynamics of Coastal Ecosystems) research unit works on coastal ecosystem evolution in response to natural and anthropic perturbations. It conducts scientific and expert assessment activities in this field aiming to understand, model and predict 1) mater fluxes in the human-land-sea continuum, and 2) spatial and temporal dynamics of the human-habitat-biodiversity interactions. The approaches involve observation, experimentation and modeling.

Within DYNECO, the PELAGOS laboratory focuses on coastal pelagic ecosystems. The laboratory is interested in understanding the biogeochemical fluxes at the interfaces and the dynamics of costal phytoplankton communities, with a special focus on harmful algal blooms. The laboratory brings together chemists, biogeochemists and biologists.

Summary

At global scale, most of the biomass of marine exploited resources and diversity hotspots are found on the coastal areas (Reygondeau, 2019). Moreover, these ecosystems generally contributed to human welfare and socio-economic activities, producing ecosystem services, providing a large part of global primary production and playing a role in climate regulation (Constanza, 1999). However, the preservation of coastal areas is now threatened by global change and human activities (fishing, land and watershed use, eutrophication etc.). Therefore, predicting the trajectories of coastal ecosystem affected by multiple external and internal pressures should consider the whole complex, multi-compartment socio-ecosystem. To do so, an integrated modelling framework of marine ecosystem could be used but requires an alignment and coupling of different existing models for each compartment : hydrodynamics, waves, sediment, biogeochemistry, plankton ecology, fish ecology, halieutic management etc. The MEDIATION project aims to transform integrated modeling methodologies by targeting two questions of major societal interest: how will global change impact the functioning of regional marine ecosystems, and how to assess the effect of environmental preservation measures? To accomplish these tasks, methodological research will be deployed to develop a transversal digital modelling tool designed with a complete modelling chain. Using this tool, future scenarios will be developed with stakeholders that are consistent with practices, in order to inform decision-makers and guide public policies.

In close interaction with the consortium of the MEDIATION project, the PhD candidate will work on the relation between the plankton compartment and small pelagic fish. Indeed, the plankton is a key component of marine ecosystem functioning and the he population dynamics of small pelagic fishes (sardines and anchovies) strongly depends on the quantity and the quality of their planktonic prey. The PhD candidate will develop an ecosystem model extending throughout the full trophic chain from unicellular plankton to fish. A focus will be made on the zooplankton compartment (copepods ranging from 0.2 to 7 mm) to take into account its population dynamics and life-cycle.

An existing mechanistic, trait-based and size-structured model of plankton, the NUM (for ‘Nutrient-Unicellular-Multicellular’) model (Chakraborty et al., 2017 ; Cadier et al., 2020 ; Serra-Pompei et al., 2020) will be used. The model is based on the processes occuring at the cell scale (protists, Andersen and Visser, 2022) or at the organism scale (mesozooplankton, Serra-Pompei et al., 2020). The trait distribution (size, trophic strategies, nutrition mode) is an emergent property of the model. Regarding the small pelagic fish, the PhD candidate will work with the DEB (Dynamic Energy Budget)- IBM (Individual Based Model) for sardines and anchovies. This model gives the abundance, biomass and energetic state of the fish according to their population dynamics (growth, mortality, recruitment and migration) and bottom-up forcing (Bueno-Pardo et al., 2020). It has been used to explain the distribution patterns of  sardines and anchovies together with their physiological state at several spatial and temporal scales (Huret et al., 2010 ; Huret et al., 2019). The DEB-IBM model can be coupled to an hydrodynamical model and a bioegeochemical model. The PhD candidate will design the complete modelling chain using the two model that will be runned in a coupled way (2-ways coupling, Travers et al., 2009). The full integrated model will be used for hindcast and forecast (scenarii) regional simulations of the Bay of Biscay in the context of the MEDIATION project.

In terms of scientific objectives, the expected outcomes of the PhD project should help to fill the gap in ecosystems models and address the inter-compartemnt connection issue by (i) producing more realistic prey seascape for small pelagic fish and (ii) accounting for the resulting feedback loop on LTL dynamics (Daewel et al., 2014, Maar et al., 2014). The application of the model developed by the PhD candidate in the Bay og Biscay is a key action in one of the two demonstrators (MANGA) selected in the MEDIATION project.

You will benefit from the expertise of an interdisciplinary team which will provide you a rich and simulating scientific environment with a large consortium of scientific experts in different complementary fields : coupled CROCO-Sediment-Biogeochemical-Ecology modelling, Bay Of Biscay, in situ surveys, numerical imprivements of the modelling tools etc.

Key words

Plankton/small pelagic fish coupling, traits, size-structured models, mesozooplankton, ontogeny, trophic interactions, individual-based model, Dynamic Energy Budget model, regional modelling, Bay of Biscay

Required Knowledge, skills, and characteristics

  • Master 2 in oceanography/ecology/biogeocgemistry

Required Knowledge, skills, and characteristics

  • We seek for a motivated candidate with solid academic background in marine ecology either/or numerical skills.
  • You must have already developed some skills in programming languages and softwares (Python, Fortran, Matlab, Unix environment, NetCDF files).
  • You must also have intellectual curiosity and an affinity for team working in an interdisciplinary context, but also be comfortable with working in independently.
  • Confidence and ease in giving oral presentations to share your results to a large audience as well as skills in english spoken and writing are also mandatory.

Specific working conditions

  • Based in Plouzané (France) – IFREMER/DYENCO/PELAGOS laboratory
  • You will make several stays in DTU Aqua (Denmark) (collab. Ken H. Andersen)
  • Participation in national/international conferences

Phd is a real opportunity to work on Ifremer’s scientific and technological priority themes. It entitle the holder to a gross monthly salary of 2300 euros for a period of 3 years, which cannot be combined with other scholarships.

How to apply for this position ?

Your application file must include :

  • a curriculum vitae
  • a covering letter
  • a reference letter
  • an academic transcript (Bachelor + Master 1 and first semester Master 2)

Your application must be compiled into 2 PDF files, up to 1.5 MB for each file:

In case of any problem in attaching your documents, please upload your CV on this page (this step is mandatory for your application to be considered) and send all the documents to the thesis supervisor : mathilde.cadier@ifremer.fr

The deadline for applications is October 20, 2022. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject supervisor.

In paralell, please submit your application to the doctoral school : EDSML

Doctoral students’ contracts will start as of January 2nd, 2023, subject to the submission of administrative documents authorizing Ifremer to recruit the doctoral student (certificate of completion of the Master 2 or engineering degree + visa for foreign doctoral students outside the EU).

How to apply for this position

Deadline for applications: 20/10/2022

All applications are processed exclusively via our website. Interested candidates can apply by clicking the “Apply” button. 

For more information about the position, click here.

via IFREMER
Have any news or opportunity in ocean sciences to share? Send it to info_at_nf-pogo-alumni.org