| Summary: | The study of microorganisms in aquaponics is an important topic which requires more research before exploiting the full potential of beneficial microorganisms. In this experiment, we focused on the evolution over time of the bacterial communities in four compartments of an aquaponic system i.e., the sump, the biofilter, the lettuce rhizoplane and lettuce root. We studied these communities over the course of a lettuce growth cycle via regular sampling and sequencing of the 16S rRNA gene of the collected bacteria. We also followed the physicochemical parameters of the aquaponic water throughout the experiment. Results show that a different community could be found in each compartment and that all four communities were stable throughout time and resilient to naturally occurring water parameter changes which characterize functioning aquaponic systems. Furthermore, the communities of the sump and biofilter also seem stable over the years as the predominant taxa (<i>Luteolibacter</i>, <i>Flavobacterium</i>, <i>Nitrospira</i>) observed in our study are similar to the ones previously reported for this aquaponic system. Finally, our results provide proof for similarities between aquaponic and soil borne lettuce root communities (gammaproteobacteria, <i>Flavobacterium</i>, <i>Pseudomonadaceae</i>, <i>Sphingomonadaceae)</i> thus showing that aquaponics can be similar to soil production in terms of microbial life.
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