A PhD position on "philosophy in marine ecology - Identifying macrophyte holobionts using environmental DNA metabarcoding: importance in biomonitoring and ecosystem management" is open with IFREMER, France.

Mediterranean lagoons are now subjected to multiple local and global anthropic pressures. This results in the modification of the ecosystem structure, functioning and provided services. Understanding the future response of lagoon biological communities is therefore of major interest for defining effective conservation actions to preserve or restore these ecosystems. Metabarcoding is nowadays used as an integrative tool to characterize biodiversity from environmental DNA (eDNA). This tool, commonly used in the marine environment, has not been developed yet for macrophytes even though they play an essential role in the formation of habitats for many species. This thesis project aims to develop methods based on eDNA to assess the diversity of macrophytes and their microbiome, a potential indicator of the host health status. More specifically, the project will focus on (i) evaluating the effectiveness of molecular tools to identify macrophytes, (ii) characterizing the microbiome associated with the macrophytes health status, and (iii) optimizing in situ sampling strategy and eDNA capture tools for macrophyte holobionts in marine environments. Based on experimental and in situ approaches, the development of these methods may allow to anticipate regime shifts of these ecosystems and help implement preventive management measures.

Required Knowledge, skills, and characteristics:

• Master degree in research.
• You will have a strong background in molecular biology (DNA extraction, PCR, Sanger and high throughput sequencing) and data analyses (bioinformatics, R).
• You will be aware of laboratory precautions. Good knowledge in phylogeny, and/or marine/aquatic ecology would be advantageous.
• Highly motivated by the thesis research project, rigorous, dedicated and autonomous.
• Proficient in English.
• Ability and attraction for reading, analyzing and synthesizing scientific publications and results, writing and oral presentations.
• Ability to discuss and interact with internal or external collaborators to Ifremer and MARBEC.

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 3 MB for each file.
• The deadline for applications is April 15th, 2024.