Ph-D student position
A Ph-D position (a four-year contract) funded by the French National Research Institute for Agriculture, Food and the Environment (INRAE) and Special Research Fund (FSR; University of Namur) is available at the University of Lorraine (Vandœuvre-lès-Nancy, France) in the Research Unit Animal and Animal Product Functionality (UR AFPA; team Domestication in Inland Aquaculture). The Ph-D student will work on the development of conceptual and experimental approaches to design new polyculture systems, a Project of International Research Partnership (2020-2024) between UR AFPA and Research Unit in Environmental and Evolutionary Biology (URBE, University of Namur). Several stays in Belgium will be necessary for the Ph-D.

Application should include: (i) a cover letter, (ii) curriculum vitae, and (iii) the contact details of three reference persons. This should be sent as a single pdf at marielle.thomas@univ-lorraine.fr and thomas.lecocq@univ-lorraine.fr

Contact
Thomas LECOCQ and Marielle THOMAS, Research Unit Animal and Animal Product Functionality (UR AFPA), Domestication in Inland Aquaculture (DAC), Université de Lorraine, Faculté des Sciences et Technologies, Boulevard des Aiguillettes BP 70239, F-54506 Vandœuvre-lès-Nancy, FRANCE, Tel: +33 3 72 74 56 96.

Working environments
The Domestication in Inland Aquaculture team works on the sustainable development of aquaculture. Our works aims at fostering the fish production diversification thanks to new species domestication and new approaches (polyculture). We study (i) the domestication consequences on fish biology and (ii) the domestication process through interspecific and intraspecific comparative approaches in order to improve the fish domestication. The team has all facilities for molecular and physiological analyses as well as fish bioassays (i.e. experimental platform in aquaculture, a part of the European network AQUAEXCEL since 2015; see https://www.urafpa.fr/index.php/plateforme/technique/4).
The Research Unit in Environmental and Evolutionary Biology (URBE) studies aquatic organisms and environments, at all integration levels, from molecules to ecosystems. Rather than focusing on specific molecular and cellular approaches of life, URBE investigates of biochemistry, physiology, evolution, and ecology.

Research background
The Ph-D subject is part of the research work done at Domestication in Inland Aquaculture team since 2013 in which agro-ecological concepts are applied on fish farming to improve the tomorrow’s aquaculture (1,2). In agro-(eco)systems, biodiversity – in a broad sense – contributes to the production of ecosystem services or to strengthening the resilience of systems to climatic or economic hazards. Nevertheless, these biodiversity-agriculture relationships have been studied mainly in terrestrial systems but much less in aquatic agro-systems. In this context, biodiversity will be considered not only from a taxonomic point of view, but also according to a functional approach, i.e. through the study of the functional traits of species (3) and their interrelationships. The rearing of several fish species in the same farming system may allow an optimal use of resources (trophic, spatial or temporal) and/or lead to species-specific effects (mutualism, commensalism) (4,5). For instance, the relevance of polyculture approaches has been demonstrated in the case of fish species that produce mucus with antifungal, antibacterial and cytotoxic properties that can improve the health status and survival rate of other species (6). Such functional modalities need to be further studied and such work can be carried out in an original way in Recirculated Aquaculture Systems (RAS), which refers to the land sparing option. This production system was selected by URAFPA and URBE at the beginning of the work on the domestication of Percidae. The thesis work will thus focus on the research of polyculture scenarios involving one or two species of percidae (Perca fluviatilis and/or Sander lucioperca) for application in RAS.
The Ph-D student will investigate how combination of several fish species that are compatible (i.e. sharing the ecological niche with minimal or no detrimental interactions and competition for resources) and complementary (i.e. exploitation of different resources and/or commensal or mutualistic interactions) can improve the efficiency, resilience, and sustainability of Percidae aquaculture (i.e. European perch and pikeperch). This will require to overcome several scientific challenges:
1. Considering all possible fish species combinations among all freshwater taxa cannot be achieved through bioassays which are time- and money-consuming but also potential unethical if detrimental interactions happen during the experiment. This calls for the development of in silico approaches, which are reasonably more appropriate from a scientific, ethical, and practical point of view. The first scientific challenge is therefore to develop a robust prospective method, based on the functional and ecological traits of fish, to build multi-species scenarios before any experimentation. For this step, the Ph-D student will develop a prospective in silico method to assess the degree of compatibility and complementarity between fish species, based on approaches combining fish functional traits and the environment specificities. Datasets will be mined from fish functional databases such as TOFF developed by URAFPA (Traits OF Fish [7]; https://toff-project.univ-lorraine.fr). We will investigate correlations between functional traits of fish (Percidae and other species) and ecological niche occupancy traits, and carry out exploratory multivariate analyses (PCA, nMDS, CAH) or calculate similarity indices by constructing distance matrices. The prospective method aims at defining a decision model based on a scoring system (degree of compatibility and complementarity between species).
2. A second challenge is to improve our understanding of the complexity of biological processes within agro-systems, which contain a deliberately increased biodiversity. This task consists of experimentally validating the prospective approach with a multi-scale and multi-criteria evaluation strategy that can be generalized in various agronomic contexts. Then, the Ph-D student will perform an experimental validation at the Aquaculture Platform of URAFPA, using comparative approaches of mono- and polyculture. An evaluation at different scales (species, population, community, and rearing system) will be developed using multiple biological (zootechnical, physiological and behavioral variables) and environmental criteria to which other parameters may be added. A premium will be placed on the evaluation of fish welfare. In this respect, we will also seek to clarify the role of the level of domestication of Percidae on interspecific relations and the welfare of fish reared in closed circuits.

Ph-D objectives
On the basis of prospective functional ecology approaches and experimental studies, the Ph-D student will investigate ichthyodiversity in order to define the contribution of polyculture to the efficiency, resilience and sustainability of fish production systems. This will require to define which traits (e.g. morphology, physiology, behavior, phenology) must be considered and how to analyze them in order to establish new polyculture scenarios (i.e. specific fish combinations in a particular farming system). Based on these traits, it will be necessary to define the criteria and methods used to select promising scenarios, before testing them experimentally and then considering their implementation in real farming conditions.
All analyses will take place at the University of Lorraine and University of Namur. At the end of her/his Ph-D thesis, the candidate will have developed high skills in integrative analyses and fish experiment designing required for the next steps of her/his researcher career.

Ph-D student profile
We are looking for highly motivated person with a MSc in a related discipline (e.g., zoology, evolutionary biology, ecology). The project includes physiological and behavioral analyses, such that experience with or affinity to these analyses is required as well as skills in statistics and knowledge of or the willingness to learn R-language. Experimental works in the lab also involves fish stock management and development of experimental designs. The candidate is expected to (i) search, read, and understand scientific literature in English, (ii) have team skills along with a sense of responsibility, and (iii) develop, quickly, excellent skills in statistical data analysis and scientific writing in English.

References
1. Dumont B., Fortun-Lamothe L., Jouven M., Thomas M., Tichit M., 2013. Prospects from agroecology and industrial ecology for animal production in the 21th century. Animal, 7: 1028-1043.
2. Dumont B., Puillet L., Savietto D., Aubin J., Ingrand S., Niderkorn V., Thomas M., 2020. Incorporating diversity into animal production systems to strengthen their efficiency, robustness and resilience. Frontiers in Sustainable Food Systems, 4:109.
3. Violle C, Navas M-L, Vile D, Kazakou E, Fortunel C, Hummel I, et al, 2007. Let the concept of trait be functional! Oikos, 116: 882–892.
4. Thomas M., Pasquet A., Aubin J., Nahon S., Lecocq T., 2021. When more is more: taking advantage of species diversity to move toward a sustainable aquaculture. Biological Reviews, 96, 767-784.
5. Thomas M., Lecocq T., Abregal C., Nahon S., Aubin J., Jaeger C., Wilfart A., Schaeffer L., Ledoré Y, Puillet L., Pasquet A., 2020. The effects of polyculture on behaviour and production of pikeperch in recirculation systems. Aquaculture Reports, 17, 100333.
6. Tendencia EA, Fermin AC, dela Peña MR, Choresca CH. Effect of Epinephelus coioides, Chanos chanos, and GIFT tilapia in polyculture with Penaeus monodon on the growth of the luminous bacteria Vibrio harveyi. Aquaculture. 2006;253: 48–56.
7. Lecocq T., Benard A., Pasquet A., Nahon S., Ducret A., Dupont-Marin K., Lang I., Thomas M., 2019. TOFF, a database of traits of fish to promote advances in fish aquaculture. Scientific Data, 6(1), 301.

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