ISA-Ifremer Postdoctoral Fellowship in Deep-Sea Taxonomy


ISA-Ifremer collaboration in support of the capacity development of a national from a developing State through a postdoctoral fellowship with Ifremer as part of the “Blue Revolution” project


Project: Testing 3D-imaging on meiofauna biodiversity from deep-sea ecosystems targeted for mineral resource exploration




  • The Ocean is the largest living space on the Earth and covers more than 70% of the planet’s surface1,2. Latest estimations suggest that 60-80% of Earth’s biodiversity hides below the surface of the oceans with at least a million species in total. Nonetheless, the vast majority of the seafloor remains to be explored2. Meanwhile, the growing need for marine resources and increasing anthropogenic pressures call for the development of fast and accurate impact assessments on marine ecosystems and life therein3,4. Reliable species identification represents the basis for all ecological, evolutionary, and environmental impact assessments. It is thus crucial for the scientific community to build baseline data sets and catalogues of marine life essential to assess potential changes on marine biodiversity.  
  • Traditionally, taxonomy mainly relies on morphologically identifying characteristics that distinguish one species from another, which is a time-consuming task that requires years of taxonomic expertise. However, the number of taxonomists is in relative decline and the scientific community is battling an uphill struggle against rapid loss of the science of taxonomy5. The introduction of DNA taxonomy6 and metabarcoding7 revitalized taxonomy8 and initiated the development of fast methods using fingerprinting techniques. Nonetheless, effective, and widespread application of these techniques has been hindered primarily by the lack of genetic sequence data in gene repositories. In addition, molecular identities (operational taxonomic units) are in themselves not valuable if they cannot be linked to species identified morphologically and their associated biological and ecological information.
  • Infaunal benthic communities (animals living in the sediments) in the deep seafloor comprise some of the most diverse groups of organisms on the Earth. Due to their high abundance and diversity, widespread distribution, and relatively rapid generation times and metabolic rates9, infaunal benthic organisms have important ecosystem functions, such as nutrient cycling and energy transfer to higher trophic levels and have been identified as important ecological indicators for assessing environmental changes in deep sea ecosystems10,11. However, only a very small amount of this diversity has been described by science, and current knowledge of their biology and ecology is still fragmentary.  Further efforts to develop innovative methods and enhance research capacity to accelerate the progress towards proliferating such data are crucial in advancing the effectiveness and efficiency of impact assessments on deep-sea ecosystems, thereby contributing to informed decision-making based on robust science.


  • The United Nations Convention on the Law of the Sea (UNCLOS) mandates the International Seabed Authority (ISA) to administer the mineral resources and control and organize current exploration activities, as well as future exploitation activities, in the Area for the benefit of mankind as a whole. In parallel, ISA is also mandated to ensure effective protection for the marine environment from potential harmful effects of such activities, as well as to promote and encourage the conduct of marine scientific research in the Area. Especially through the strategic direction 4 (“Promote and encourage marine scientific research in the Area”) of the ISA Strategic Plan for 2019-2023, the members of ISA have established the vision in this regard, which is being implemented according to the High-level Action Plan for 2019-2023. Furthermore, the ISA Action Plan in support of the United Nations Decade of Ocean Science for Sustainable Development has identified six strategic research priorities, which include advancing scientific knowledge of deep-sea ecosystems and potential impacts of activities in the Area, standardizing and innovating methodologies for deep-sea biodiversity assessment, including taxonomic identification and description, as well as strengthening deep-sea scientific capacity of ISA members, in particular developing States.
  • In this regard, ISA has implemented various initiatives to facilitate the development of scientifically robust and coherent methodologies for advancing deep-sea biodiversity assessments for which strong taxonomic basis is key to success. Since 2013, ISA has organized a series of taxonomic standardization workshops, with the latest workshop in September 2020 specifically focusing on identifying strategic approaches for collaboration to advance deep-sea taxonomy. This workshop highlighted that the use of artificial intelligence and machine learning methodologies holds great promise for developing automated routine analyses of biological data, which would support in-situ and ex-situ data acquisition and processing for long-term environmental monitoring and impact assessment. It also emphasized the need to enhance capacity of many institutions and scientists for adequate application of these methodologies at a larger scale.
  • The project “Tara Oceans” recently developed 3D-fluorescence imaging and a computer-based classification tool for fast, high-volume data analysis, which allowed the identification of microbial eukaryotes in plankton studies12 and opened new perspectives for using automatic imaging methods and Artificial Intelligence (AI) for benthic diversity studies. Subsequently, Ifremer has launched the project Blue Revolution to bring together various scientific actors globally to advance this method and develop an automatic tool for the identification of benthic infauna. This will allow a standard acquisition of morphological data for benthic infauna and feed depositories with 3D reconstruction of benthic organisms. Furthermore, one of the core objectives of this project is to train the next generation of taxonomists as leading scientists with expertise in applying smart techniques for species identification.
  • In this context, the ISA secretariat and Ifremer aim to collaborate on developing a 3D-imaging method for diversity assessment of infauna communities in areas where deep-sea mineral resources are found. Under the framework of the Blue Revolution project, a post-doctoral fellowship will be dedicated for testing the 3D-imaging on meiofauna biodiversity, building a reference training dataset, and identifying key species for detecting environmental changes. Upon successful completion of this fellowship, the postdoc will be equipped with modern scientific skills required for conducting deep-sea biodiversity assessments, especially taxonomic identification. The postdoc will also acquire first-hand experience in testing and applying new techniques that will be essential in future marine biodiversity assessments using emerging technologies such as artificial intelligence and machine-learning.


  • The project aims to test a 3D quantitative imagery methodology for diversity assessment of infauna communities found in nodule areas as well as in sediments near active and inactive vent sites. This approach will contribute to generating reference image datasets for developing machine-learning methodologies for species identification. The image data will be complemented with genetic sequences obtained for the same organisms.
  • Samples from French exploration contract areas, one concerning polymetallic nodule resources in the Clarion Clipperton Zone, Central Pacific Ocean, and another concerning polymetallic sulphides in the Mid-Atlantic Ridge, North Atlantic Ocean, are available at the Ifremer collection. The project will focus on meiofauna-sized organisms, which are the most numerous and may be the most diverse metazoan infaunal organisms in nodule areas and in deep-sea sediments in general, and can be used as a proxy for responses of benthic communities to environmental changes. The postdoc will identify the most abundant metazoan meiofauna groups: Nematoda, Copepoda, Kinorhyncha as well as rare taxa. Key species associated with detected environmental changes will be identified.


A draft report will be provided for the review and feedback by the ISA Secretariat, at least one month prior to its finalization, and a final draft report, incorporating the comments from the Secretariat, will be submitted at the end of the project. The final report will include the following:

  • Quantitative biodiversity and functional data of benthic communities;
  • Taxonomic checklist of infauna species found in nodule areas and SMS deposits;
  • List of key species associated with detected environmental changes;  
  • Image and genetic reference library of benthic species; and
  • Outline of two draft manuscripts, with a timeframe for submission in open-access journal (see provisional schedule below)


  • It is expected that this project will significantly contribute to the implementation of the ISA MSR Action Plan in support of UN Decade of Ocean Science, specifically towards strategic research priorities 1 and 2. In particular, the outcomes of this project will provide inputs to advancing knowledge of deep-sea biodiversity and further enabling standardized innovative approaches for deep-sea biodiversity assessments. The project will also contribute to strengthen the deep-sea capacity of ISA members, in particular developing States, thus also contributing to strategic research priority 6. The scientific skills (e.g. taxonomic identification) acquired through this project will be useful for conducting biodiversity assessment in other ocean realms, including deep-sea and marine coastal environments within national jurisdictions.
  • The project report will be made available by the ISA secretariat to relevant ISA organs and stakeholders, including through a side-event to be organized at an ISA meeting, and publication in a scientific journal.


The project will be conducted at Ifremer (Brest, France)[1] through the support provided to a post-doctoral fellowship with 18-month duration. The post-doc will be assisted by the Blue Revolution network of taxonomic experts for species identification and broader team for the different technological developments. Furthermore, the postdoc will be integrated into the Blue Revolution training program, including dedicated workshops/summer schools, special training modules and dedicated e-learning teaching unit.


  • Image-based semi-automated analyses using various devices (digital scanners, ZooSCAN, flow cytometers and microscopes) have been used for plankton research since more than two decades. Few years ago, the TARA team developed a 3D-fluorescence imaging and classification tool for rapid quantitative analysis of microbial organisms in environmental samples. This method entails high-content feature extraction and derivation of quantitative data from images that enables accurate automated taxonomic classification12.
  • Some flow cytometry systems can also sort single individuals after imaging acquisition. Microscopic infauna semi-automated identification is still in its infancy. The FlowCAM system allows the identification and classification of specimens at high taxonomic levels obtaining numbers of individuals comparable to traditional methods13. 3D-fluorescence imaging techniques have been used in a few meiofauna taxonomical studies, but they have not yet been tested for automated species identification14,15.
  • In this project the “Quantitative 3D-imaging” method12 will be adapted for infaunal microscopic benthic communities. Before imaging, faunal samples will be identified at species level and prepared following a multiple step procedure in order to adequately stain the target organisms. The fluorescent dyes developed by Colin et al.12 seem promising in terms of application to diverse eukaryotic organisms. Confocal laser scanning microscopes will be used for high throughput sample imaging. Complementary genetic sequence data will be obtained for representative specimens of identified morphological species. Key species associated with detected environmental changes will be identified both morphologically and genetically.

Provisional schedule

isa-ifremer fellowship schedule


Interested applicants should submit Curriculum Vitae and motivation letter to the ISA Secretariat no later than 30 November 2021 at, considering the following eligibility criteria:

Eligibility criteria

  • National of a developing State Member of ISA
  • Ph.D. degree IN marine biology or ecology or related discipline
  • Background in taxonomy of marine meiofauna (desirable)
  • Skills in microscopy (recommended)
  • Knowledge of deep-sea ecology
  • Proficient in English language (written and spoken)
  • Experience with working in a multidisciplinary team (recommended)

[1] An hybrid modality (remote and in-person training) can be considered depending on the evolution of the pandemic situation at the start of the project.