Taxonomical, ecological and functional exploration of aquaponics microbiota in interaction with lettuce growth

Aquaponics is emerging as an interesting alternative to decrease pressure on planetary resources and to limit the environmental impact of the food production systems. This new technique combines hydroponics i.e. the soilless production of vegetables, with recirculating aquaculture in several types of systems fitted to various environments. Aquaponics, as implemented nowadays, is a fairly novel production system and requires a thorough inquiry of several aspects of its functioning to ensure its viability and reliability. One of these crucial features regards the characterisation of microbial communities and their roles in nutrient cycling. The objective of this thesis is thus to address this huge gap of knowledge regarding microorganisms in aquaponics via the description of the bacterial communities, the study of the potentially plant beneficial functions which could be carried on by the microbiota and their interaction with lettuce growth.
In the first instance, this thesis focuses on the taxonomical description of the bacterial communities which can be found in various aquaponic and aquaculture systems and reports on the evolution of the different communities of one given system over nine weeks, using 16S rRNA gene sequencing. Results show that different systems harboured different microbiota although some common taxa could be found in all samples. It was also observed that within one system each compartment (sump, biofilter, plant roots) hosted specific microbiota and that those communities were relatively stable over time. Indeed, no adaptation period could be noted after the transplantation of seedlings into the system i.e. when the system previously functioning as a recirculating aquaculture system (RAS) was turned into a coupled aquaponic system - which is the main modification that the system underwent during the experiment. No modifications appeared either following the water parameters changes which naturally occur during the functioning of the system. As such it was concluded that the studied bacterial communities were resilient. Eventually, a taxonomic comparison between the lettuce root communities in the aquaponic system with literature regarding soil borne lettuce root communities showed intriguing similarities. This raises new questions regarding the origin of root microorganisms (i.e. seed or system) in aquaponics and its recruitment processes in soilless systems.
However, the use of metabarcoding only provides an overview of the global composition of the communities down to the genus level. Genus identification does not permit to identify specific roles or functions linked with nutrient cycling and plant growth. Consequently, the second part of this thesis focuses directly on the functions present in aquaponics and their potential roles in plant health and care. In this view, 31 bacterial strains were isolated from the sump of the coupled aquaponic system of Gembloux Agro-Bio Tech. Five potentially plant beneficial traits were targeted in these bacteria via the use of in vitro biochemical tests: i) phosphorus and ii) potassium solubilisation and the production of iii) indole acetic acid, iv) siderophores and v) ammonia. Three of the most promising strains were then selected for a series of in vivo trials to assess their impact on lettuce growth in aquaponics. In these trials, three treatments were compared i.e. a mix of the three strains (AHT), one of the strains alone (T) and a control without any inoculation. The AHT bacterial mix treatment provided encouraging results fostering the production of lettuce leaves in light related and nutritive stress conditions while the T strain alone treatment also impacted lettuce growth in stressful conditions albeit in smaller proportions than AHT. An upscaling of the trials would now be required to confirm these observations.
Overall, this thesis provided a first insight into bacterial communities in aquaponics and constitutes a stepping stone for more in depths research on the ecology of bacterial communities in aquaponics and their roles in interaction with crop growth.