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In this work, an aquaponic cultivation system for Lactuca sativa (L.) and Chicorium intybus (L.) was compared to a hydroponic one, focusing on the main microbial populations related to food safety and their volatile compounds (VOCs), concluding with Spearman correlations among the microbes and VOCs. Different sections of both systems were sampled at the end of the commercial development of the plants. Plants cultivated in aquaponics were in general more contaminated than those from hydroponics, while for the cultivation waters a higher contamination of the hydroponics than aquaponics system was unexpectedly observed. Furthermore, the chicory exhibited higher levels of all microbial groups compared to lettuce grown under the same cultivation system. The results obtained also showed correlations between the distribution of some VOCs and microbial groups in the phyllosphere, while some examples of positive correlations between 2-nonanone (a positive phytostimulant compound) and anaerobic bacilli of the rhizosphere in lettuce were reported. So far, multivariate analysis of VOCs was able to discriminate on the basis of varieties but not on the cultivation systems. In conclusion, the microbial characteristics of the two ecosystems depended both on plant variety and cultivation method but further studies will need to deeply investigate the variables influencing the microbial quality of vegetable foods obtained by aquaponics. On the other hand, the analysis of the VOCs was more related to the microbial community of each plant variety considered, whatever the cultivation system. In precision agriculture, metabolomics may represent an opportunity to study the holobiome and through it the interactions between plants and their microbial populations, to possibly provide for a tool to assess the microbiological quality of vegetable foods obtained by aquaponic systems.

Plant Volatiles of Lettuce and Chicory Cultivated in Aquaponics Are Associated to Their Microbial Community