PostDoc position: Meiofauna imaging for biodiversity studies – Deadline 27 August 2024

The postdoctoral fellow will be based in the Deep Sea Laboratory of Ifremer’s BEEP unit (Biology and Ecology of deEP Sea ecosystems) located on the campus of the Ifremer Bretagne center.

Deep-sea marine ecosystems reveal a high level of biological diversity linked to the variability of benthic environments. The biodiversity and dynamics of these ecosystems in their natural state are still poorly understood. Despite our partial and superficial exploration of this vast realm, we know that all marine habitats, including the deepest trenches, experience direct or indirect human impacts.

In this context the BEEP Unit develops research projects to acquire knowledge about the biodiversity and functioning of these ecosystems in order to support the development of a sustainable environmental management and propose solutions for the responsible use of the deep-sea natural resources.

Benthic meiofaunal communities (sediment-dwelling animals) include some of the most diverse groups of organisms on Earth, so it’s not surprising that only a small proportion of this diversity has been described by science, and that our knowledge of their biology and ecology is still very fragmentary.

Inside the Deep Sea Lab, the position to be filled is part of the MEIODYSSEA project, coordinated by the BEEP Unit, which aims to leverage cutting-edge technology and innovative tools, to overcome the meiofauna taxonomic bottleneck, forging a swift and dependable benchmark for meiofauna identification. This will culminate in the description of an estimated 125 to 200 new species. By implementing this standard across thousands of samples spanning diverse marine ecosystems and depth zones, MEIODYSSEA aims to redefine our approach to seafloor exploration and substantially bridge the knowledge gap about marine meiofauna diversity, ecology, and evolutionary history, which will facilitate conservation of vulnerable marine ecosystems.

In this context you will be working in a team composed of experts in meiofauna taxonomy, engineers in microscopy and imagery data, and technicians in biology.

General areas of responsibility

Meiofauna is a collective name for a diverse assemblage of eukaryotic organisms dominating the benthic environment, including small animals and protists operationally defined based on the standardized mesh size of sieves with 1000 μm and 32 μm as upper and lower limits, respectively (Zeppilli et al. 2015; 2018). Meiofauna vitally contributes to ecosystem processes and functions and has been used successfully as ecological indicators and sentinels for ecosystem health (Zeppilli et al. 2015). In the meiofauna community, the number of undescribed species is staggering. In some ecosystems, such as the deep sea, the number of undescribed species can reach up to 90%. Even in the best-studied areas, the number of undescribed species can reach 40%, emphasizing that the marine meiofauna census is far from complete (Curini-Galletti et al. 2012).

In this context, you will be in charge of studying meiofauna of coastal benthic samples from the TREC expedition and of deep-sea samples from the EDEN and BICOSE3 cruises (Clarion-Clipperton Zone (CCZ) polymetallic nodules and seafloor massive sulfides (SMS) deposits). You will be in charge of sample processing to ecology analyses of these contrasting area using the innovative pipeline for meiofauna study developed by the MEIODYSSEA project. According to complementary data of each sampling (metabarcoding, environmental), you will explore the role of meiofauna in ecosystems and the repartition of undescribed specimens.

Unknown species will be explored deeply for taxonomic description and its role in ecosystems.

Principal activities

• You will process meiofauna taxa in a unique high throughput analysis pipeline including sample separation by density (ludox), automated sorting of meiofauna with flow cytometry imaging, automated imaging of meiofauna using motorized microscope.
• You will process flow cytometry data and flow imaging data (image annotation / extraction of morphometry / biomass / functional traits) to explore the power of low resolution / large scale biodiversity study on benthic ecosystems.
• You will process and annotate high-resolution imaging data (from motorized microscope and focus stacking acquisition) using artificial intelligence tools in development.
• All imaging data will be used in the context of ecology studies (linking barcoding data and environmental data) to evaluate anthropogenic impact in shallow water benthic communities (TREC) and mining threat in deep sea environment (polymetallic nodules and SMS deposits).
• The discovery of new species is expected during the contract. Thus, description of new specimen will be achieved with high-resolution image acquisition (3D imaging with partners of the project). You will be in charge of high-resolution imaging development to support taxonomical description of new species. You will contribute to species description, with MEIODYSSEA associated partners, based on barcoding, transcriptomic and proteomic analyses.
• All the results will be valorized in international conference, publication and outreach events.

Collaborative work environment

• Internal: BEEP unit and Ifremer’s DYNECO unit (study of coastal ecosystems)
• External: MEIODYSSEA project partners (Jamstec, Senckenberg, Naturalis), TREC Expedition partners

Profile

Required education and experience 

• PhD in (marine) biology (BAC+8) – ( obtained 3 years ago maximum)

Required knowledge, skills and characteristics

Knowledge, skills and abilities

• Laboratory best practices
• Knowledge in microscopy and image processing
• Knowledge in annotation software or web applications (e.g., EcoTaxa, BIIGLE)
• Proficiency in ecology (biodiversity analyses)
• Skills in taxonomy, initial experience in the field of meiofauna, or plankton, would be appreciated
• Writing skills

Personal human qualities

• Good team-working skills
• Interest in collaborative projects (international partners)
• Interest in innovative techniques
• Training capability (student internships)
• Autonomy
• Initiative

Specific working conditions

• Full-time position
• Temporary contract of 18 months

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.

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.