Aquaculture is undergoing rapid development worldwide, but the sustainability of
aquaculture systems is more and more questioned in view of the many changes taking place
(climate, animal welfare, antibiotic resistance, etc.). The mobilisation of agroecological
principles in fish production is increasingly recommended, particularly with a goal of exploiting biodiversity (i.e. planed and associated biodiversity) within farming systems. Such approaches remain to be explored in artificial systems such as Recirculated Aquaculture Systems (RAS). At the same time, integrated animal health management is highly recommended (no pesticides or antibiotics). The functioning of RAS is highly dependent on the equilibrium between the various biological communities present, particularly fish (polyculture) and microbial communities (ex: biofilter, associated biodiversity), and in some cases plant community (in the case of aquaponics).
Fish show a very high biological diversity in their morpho-anatomical organization, particularly
in their digestive tract, due to the existence of very varied diets (herbivorous, omnivorous and
carnivorous species). These characteristics influence the microbiota present in the digestive
tract of fish and could therefore affect the microbial communities present in the RAS. The
microorganisms present in the RAS inputs (water, food, material, farmer …) could also
influence the microbial communities. In parallel, the production of mucus (bactericidal
properties) on the skin of fish is more or less abundant according to species and could also
influence the microbial communities. Within the framework of an experimental approach that will be based on the equipment of the Aquaculture Experimental Platform (PEA) of the AFPA research unit (structure affiliated with the European AQUAEXCEL network and labelled LUE INFRA+), the objectives of the thesis will be (i) to characterize the effects of fish diversity (monoculture vs. polyculture) and microbial inputs in closed circuits on fixed and circulating microbial diversity within the framework of a dynamic approach, and (ii) to test the hypothesis that biomanipulation of the fish compartment (species association) allows for regulation of microbial communities in closed circuits. The impact on microbial communities related to the purification capacity of fish effluents and the prevention of the emergence of fish pathologies will be analysed, as well as the permissiveness of the systems.
Expected skills: The candidate should be motivated, autonomous and have a solid experience
in microbiology (Pasteurian microbiology) and molecular biology (New Generation
Sequencing, qPCR, metabarcoding). Complemental knowledge in biostatisctics, fish
immunology and physiology would be a great advantage. The applicant should be able to
write, read and speak fluently in English, and will to train for a degree in animal
experimentation. A stay of several months in a foreign English-speaking laboratory will be
strongly encouraged.
Keywords: Fish diversity, microbial ecology, transfers of microbial communities, agro-ecology,
biocontrol, aquaculture, antibiotic resistance
Applications: Files (CV + motivation letter + 2 personal references) must be sent by 31/05/22
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