Aquaponics as future urban food production systems: phytopathological challenges and opportunities thanks to aquaponic microbiota characterization and original biocontrol agent isolation

Aquaponics is a sustainable way to produce simultaneously fish and plants, notably in urban areas. In such system, plant disease control is problematic because sanitary treatments can be toxic for fish. However, aquaponics could naturally contain microorganisms with suppressive activity against plant pathogens. Aquaponic microbial composition in the lettuce rhizosphere was studied for this activity. The high-throughput sequencing analyses highlighted numerous microorganisms that were potentially disease suppressive, including Methyloversatilis, Sphingobium, Hydrogenophaga, Catenaria, Burkholderiaceae, and Aspergillaceae taxa. After selective isolation and an in vivo screening step, three strains excelled in the biocontrol of diseases caused by P. aphanidermatum on lettuce seeds and seedlings grew in hydroponics conditions. They were SHb30 (Sphingobium xenophagum), G2 (Aspergillus flavus) and Chito13 (Mycolicibacterium fortuitum). Their combinations were also efficient in controlling lettuce root rot disease caused by the same pathogen. This study showed that aquaponics is an interesting source of original biocontrol agents that could be used in soilless conditions to improve plant health and then urban food supply.