Topic of the thesis:
Understanding the resilience of coastal marine ecosystems under global change is a major scientific and societal challenge. Coastal systems are increasingly exposed to multiple stressors, including climate change and shifts in biodiversity, which can alter ecosystem functioning and the services they provide. Central to these dynamics are the trophic links between pelagic primary producers and benthic communities. Changes in phytoplankton communities, the main source of energy entering marine food webs, can cascade to higher trophic levels, affecting the structure, functioning, and stability of benthic ecosystems, including key ecosystem engineers and commercially important shellfish species.
Suspension-feeding bivalves play a pivotal role in this benthic–pelagic coupling. By filtering large volumes of seawater, they transfer organic matter and nutrients from the water column to the seafloor, structuring food webs and regulating water quality. Their ecological importance is matched by their economic value in shellfish production. However, their growth, health, and survival are tightly linked to the availability and quality of phytoplankton resources. Ongoing environmental changes are driving shifts in phytoplankton biomass, species composition, phenology, and biochemical quality, as well as increasing the frequency and distribution of harmful algal blooms (HABs). These changes may profoundly affect trophic interactions and the functioning of benthic communities, yet their impacts on bivalve feeding ecology remain poorly understood under natural conditions.
Bivalves are generally considered omnivorous species, primarily consuming phytoplankton but also relying on alternative sources such as resuspended microphytobenthos. While some phytoplankton taxa (e.g., certain diatoms) are associated with enhanced growth, others, including harmful and/or spiculated diatoms and dinoflagellates, can negatively affect growth. However, current knowledge on their in situ diet is largely based on bulk trophic markers (e.g., stable isotopes, fatty acids), which lack taxonomic resolution and integrate diet over long timescales, limiting our ability to identify specific prey taxa and short-term dietary responses.
This PhD project will apply DNA metabarcoding to characterize the in situ diet of suspension-feeding bivalves with high taxonomic resolution. By analyzing DNA from seawater, bivalve gut contents and faeces, the project will investigate trophic selectivity, short-term dietary variability, and the relationship between phytoplankton availability and bivalve feeding behaviour. Particular attention will be given to dietary shifts in response to harmful or low-quality phytoplankton and their links to physiological responses and toxin accumulation. These data will be complemented with stable isotopes and lipid biomarkers to confirm prey assimilation, identify alternative food sources, and assess nutritional quality. Several species of bivalves (Pacific oyster, variegated scallop, blue mussel) found in various ecosystems in Brittany (the bays of Brest, Morlaix and Mont Saint Michel) are being considered for the project.
An important component of the PhD project will be to analyze long-term dynamics of phytoplankton taxa that are either selected or avoided by bivalves, including harmful or toxic species identified in the in situ monitoring. This will be achieved using time series from the REPHY/PHYTOBS programs, which provide ~20 years of data on phytoplankton diversity and abundance, depending on the site. Statistical analyses will focus on trends, phenological shifts, and changes in the composition and relative abundance of major groups (e.g., diatoms, dinoflagellates), as well as overall biodiversity indices. These analyses will provide critical insights into how long-term changes in phytoplankton communities may influence the feeding, growth, and resilience of bivalves under future climate scenarios.
Overall, this project will combine high-resolution dietary analyses, trophic biomarkers, and long-term ecological data to provide a comprehensive understanding of benthic–pelagic coupling and trophic interactions in coastal ecosystems. It will improve our ability to predict how bivalves and the communities they support respond to ongoing environmental change, supporting both ecosystem management and sustainable shellfish production.
Key words: Trophic ecology; Suspension-feeders; Bivalves; Phytoplankton; Harmful algae
Your mission and activities:
• Participate in field sampling and laboratory-based data acquisition
• Acquire DNA metabarcoding data
• Preparation of samples for lipid, stable isotope and phycotoxin data acquisition
• Bioinformatic and biostatistical data analysis
• Time-series analysis of phytoplankton data
• Manuscript writing and publication of results
• Presentation of results in scientific conferences and project meetings
• Joint supervision of Masters students
Organization of your activities:
• The PhD will be based at the Ifremer unit DYNECO (Plouzané, France), with fieldwork in Brittany and regular visits to the Institut Universitaire Européen de la Mer (IUEM), as well to the Ifremer station in Concarneau
• Molecular laboratory experiments will be conducted at Ifremer (DYNECO)
• Lipids and stable isotopes will be analyzed respectively at the LIPIDOCEAN platform at LEMAR and the PSO platform at IUEM
• Phycotoxins will be analysed at the Ifremer station in Concarneau
• Bioinformatic analysis will be conducted with support from the SeBiMER (Ifremer’s Bioinformatic Service), with access to Ifremer’s computing cluster DATARMOR
• Biostatistics and time series analysis will be conducted on a computer provided by the institute
• Possible interactions with collaborators from the Japan Fisheries Research and Education Agency
Required education:
• Masters degree in the fields of biology, marine ecology, environment or bioinformatics (university or engineering school)
Yours skills, knowledge and experience:
• Interest in trophic ecology, and the functioning of trophic networks on coastal marine environments
• Skills in statistical numerical analysis are required (R, RStudio)
• Experience in the use of molecular tools (DNA extraction, PCR, Illumina library prep) is recommended, but not required
• Experience coding in bash or python is a plus
• Demonstrated written and oral communication skills in French and English
Your qualities:
• Curiosity and spirit of synthesis
• Ability to work in various disciplinary fields
• Team work
• Rigor and organizational skills
• Tenacity and perseverance
Way to apply:
The application must include the following elements in a pdf file:
• a cover letter, explaining why the research topic is of interest to you and why you have the required background and experience for the position
• a curriculum vitae
• a reference letter, ideally from one of the Masters advisors
• an academic transcript (Bachelor + Master 1 and first semester Master 2)
The deadline for applications via this website is May 13, 2026.
We strongly advise contacting the three thesis supervisors as soon as possible with your CV and a message briefly explaining your interest in the topic of the PhD thesis: fabrice.pernet@ifremer.fr, flavia.nunes@ifremer.fr, aline.gangnery@ifremer.fr
In parallel, please submit your application to the doctoral school “Ecole Doctorale Sciences de la Mer et du Littoral”, via the Amethis system:
https://amethis.doctorat.org/amethis-client/prd/consulter/offre/2723
The deadline for applications via the Amethis website is May 17, 2026.
Doctoral student contracts will start as of October 5th, 2026, 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).
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