The  PhD student will be based mainly in the DHYSED laboratory of Ifremer’s  DYNECO unit and will also interact with the LEBCO laboratory of the same  unit.
The aim of the DYNECO unit is to study the response of  coastal ecosystems to a number of anthropogenic and natural pressures.  Its research focuses on: i) material flows in the human-land-coastal sea  continuum, ii) the spatial and temporal dynamics of  human-habitat-biodiversity interactions, and iii) ecosystem analysis  methods combining observation, experimentation and modeling.
Within the DYNECO unit:
The  DHYSED laboratory studies hydro-sedimentary processes in interaction  with the biotope and anthropogenic activities at different spatial  scales (i.e. from metropolitan coastlines to estuaries) and temporal  scales (from tidal to multi-decadal).
The LEBCO laboratory is  interested in the diversity and functioning of coastal marine  ecosystems, and more specifically in the responses of species and  communities to natural and anthropogenic pressures.
Summary
You can choose between 3 subjects according to your experience and wishes.
Project  1: Understanding and predicting the causes and the consequences of  seagrass fragmentation in the lagoonal environment of Reunion Island
Seagrasses  form coastal habitats of high ecological value as they are ecosystem  engineers, supporting high levels of biodiversity, improving water  quality, protecting coastlines from erosion, storms and floods, and  trapping carbon. In tropical regions, anthropogenic pressures are very  high, seagrass decline is high and biodiversity is greatly threatened.
On  Reunion Island, seagrass beds are distributed patchily throughout the  lagoon. Seagrass coverage was maintained between 1951 and 2016: although  phases of decline and regeneration occurred, the meadow was highly  resilient. But in 2017, seagrasses began to decline and have almost  disappeared today, suggesting that beyond a certain threshold of  fragmentation, the meadow can no longer regenerate.
The project  aims to analyse the seagrass fragmentation dynamics over decades in a  tropical environment and explore the causes of meadow fragmentation  using an existing time and space seagrass dynamics model coupling a  process-based hydrodynamic-sediment transport model at 10-m resolution  with a probabilistic seagrass growth model. Fragmentation thresholds  beyond which the meadow is no longer resilient could be identified in  this highly anthropogenic tropical system experiencing climate change.  Both an applied and methodological process will be used to better  understand fragmentation processes and their uncertainty in real world  systems, make predictions to provide risk-informed decision support, and  form the toolsets to address many other social, biological, ecological  and complex systems fragmentation processes.
Project  2: Understanding and predicting the natural and anthropogenic causes of  seagrass decline in the lagoonal environment of Reunion Island
As  lagoonal systems are relatively protected from strong currents and  waves, they are suitable areas for seagrass development, however growing  anthropogenic pressures and climate change are causing seagrass  decline. This is the case on Reunion Island where seagrasses have been  disappearing since 2017, well below the cover documented between 1951  and 2016.
The aim of the project is to identify and evaluate the  processes impacting seagrass decline on Reunion Island. The study will  be based on satellite and hyperspectral data and photographic analysis  of the seagrass cover since 1951 combined with identification and  quantification of environmental and anthropogenic processes that could  be linked to the seagrass decline. This dataset will enable different  hypotheses explaining the seagrass dynamics on Reunion Island to be  tested using a modelling approach. The research will involve improving  and modifying an existing time and space seagrass dynamics model which  is a probabilistic seagrass growth model coupled with a process-based  hydrodynamic-sediment transport model.
The work will focus on the  probabilistic seagrass growth model including local processes acting on  the seagrass dynamics such as mechanical destruction from austral and  cyclonic waves, overgrazing by megaherbivores, chemical contaminants,  protection from the coral reef, freshwater resurgences, etc. For this  probabilistic modelling, particular attention will be paid to the  evaluation of thresholds on the different pressures acting on the  seagrass dynamics.
The output of the study will be a conceptual  model describing the seagrass dynamics on Reunion Island highlighting  the processes initiating and maintaining the ongoing decline of  seagrass. This will help to inform the rehabilitation of seagrass beds  in the lagoon.
Project 3: Understanding and  predicting the seagrass dynamics in the lagoonal environment of Reunion  Island to inform seagrass restoration
Seagrasses are  classified as sentinel species because they clearly indicate marine  environmental changes at local, regional and global scales. They are  considered as an indicator of water quality in the Water Framework  Directive and are a bioengineer species monitored in the Marine Strategy  Framework Directive.
Seagrass dynamics are complex, responding to  a range of forcings over different time scales. Therefore, an  integrated ecosystem approach is required to understand the drivers of  seagrass decline and is there is a motivation to develop efficient  models. Our teams have developed a time and space seagrass dynamics  model coupling a process-based hydrodynamic-sediment transport model and  a probabilistic seagrass growth model to simulate the evolution of  seagrasses at regional scale over decades. Such a tool is useful for  local authorities to set up the best management practices to protect  seagrasses.
On Reunion Island, seagrasses are declining at an  alarming rate since 2017 with no clear causes identified. The project  aims to model the effect of management scenarios to prevent the Reunion  Island seagrass decline and to rehabilitate the seagrass in the lagoon  in partnership with local authorities. It also aims to improve existing  indicators for monitoring seagrass habitats and to make proposals for  adapting current monitoring programs in the framework of the various  European directives. This implies identifying and overcoming the limits  of our model: taking into account anthropic pressures (different from  temperature changes and light modifications), integrating a  socio-economic dimension, defining management scenarios, etc. The  developed model will help to discriminate the natural variability from  the variability induced by humans in the seagrass dynamics. This  scientific project will be in partnership with local authorities from  the nature reserve whose mission is to monitor of the state of coastal  ecosystems and which coordinates the various associated monitoring  programs.
Principal activities
You will:
- Refine an existing Dynamic Bayesian Network (DBN) for precise application to the seagrass ecosystem of Reunion Island
- Merge  the DBN model with a coastal hydrodynamics/sediment transport modelling  framework (CROCO-MUSTANG), linking seagrass biology with physical ocean  processes
- Use the integrated model to quantify how local and  global environmental stressors affect seagrass dynamics and try the  hindcast the observed seagrass decline
- Suggest restauration and  conservation management measures with tue use of the developed modelling  framework for seagrass recover in the area.
Profile
- M2 in  ecological modeling or data sciences applied to the environment or  coastal oceanography or modeling in coastal physical oceanography
- Knowledge of hydro-sedimentary and ecological processes structuring the dynamics of coastal ecosystems.
- Interest in interdisciplinarity, particularly between physics and biology
- Good knowledge of machine learning methods (e.g. Bayesian networks or Machine Learning, neural networks)
- Good modeling and programming skills (e.g. Python, R, Fortran, C++).
- Proficiency in Linux environment
- Fluency in English
- Have spent less than 12 months in France the past 3 years.
Specific working conditions
The  person recruited will be hosted by the DHYSED laboratory and will work  in close interaction with the LEBCO laboratory (Coastal Benthic Ecology  Laboratory), and researchers in data science and ecology at the  University of Queensland in Brisbane, Australia. A minimum 6-month stay  at Queensland University of Technology (Brisbane) will be envisaged in  the first part of the thesis to develop the dynamic Bayesian network  describing the spatio-temporal dynamics of seagrass beds in the lagoon  of Reunion Island under different conditions of anthropogenic pressure  and climate change scenarios.
During the course of this work, the PhD student will benefit from:
- international supervision by French and Australian researchers, recognized experts in their field,
- available  and committed supervisors, who will guide them and allow them to  develop their scientific autonomy over the course of 3 years,
- funding to attend international conferences.
PhD  is a real opportunity to work on Ifremer’s scientific and technological  priority themes. It entitles the holder to a gross monthly salary of  2300 euros gross 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 2 Mo for each file.
The  deadline for applications is 27th August, 2024. Nevertheless, we  strongly urge you to let us know as soon as possible of your intention  to apply, by contacting the subject  supervisor: heloise.muller@ifremer.fr
In parallel, please submit your application to the AUFRANDE program:Â https://aufrande.eu/
Doctoral  students’ contracts will start as of January, 2025, 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).
The Institute
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.
For further information about this opportunity click here.