First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce

Abstract

Aquaponics is defined as a sustainable and integrated system that combines fish aquaculture and hydroponic plant production in the same recirculated water loop. A recent study using high-throughput sequencing (HTS) technologies highlighted that microbial communities from an aquaponic system could control one of the most problematic pathogens in soilless lettuce culture, namely, Pythium aphanidermatum. Therefore, this study aims at isolating the microorganisms responsible for this biocontrol action. Based on the most promising genera identified by HTS, an innovative strategy for isolating and testing original biocontrol agents from aquaponic water was designed to control P. aphanidermatum. Eighty-two bacterial strains and 18 fungal strains were isolated, identified by Sanger sequencing, and screened in vivo to control damping-off of lettuce seeds caused by P. aphanidermatum. Out of these 100 isolates, the eight most efficacious ones were selected and further tested individually to control root rot disease caused by the same pathogen at a later stage of lettuce growth. Strains SHb30 (Sphingobium xenophagum), G2 (Aspergillus flavus), and Chito13 (Mycolicibacterium fortuitum) decreased seed dampingoff at a better rate than a propamocarb fungicide and a Pseudomonas chlororaphis registered biocontrol agent did. In root rot bioassays, lettuce mortality was prevented by applying strains G2 and Chito13, which were at least as efficacious as the fungicide or biopesticide controls. Lettuce disease symptoms and mortality were eradicated by strain SHb30 in the first bioassay, but not in the second one. These results show that aquaponic systems are promising sources of original biocontrol agents, and that HTS-guided strategies could represent interesting approaches to identify new biocontrol agents.

Application of aquaponic microorganisms alone or in consortium as original biocontrol method of lettuce root rots in soilless culture

“…Although as effective as Cf and Cap, combination of G2 with C13 and/or SHb30 (both bacterial strains) did not bring significant additional effect. In relation to Stouvenakers et al (2023), these results showed that antagonistic activity of G2 is reproducible over time. Studies on A. flavus use against P. aphanidermatum are scarce and limited to few papers (Shanmugan and Sakurana Varma, 1999;Stouvenakers et al, 2023), while atoxigenic strains were intensively studied to control aflatoxin in cereal crops (Khan et al, 2021).…”

“…Biocontrol experiment of P. aphanidermatum disease on lettuce seedlings was conducted as described in Stouvenakers et al (2023). Organic pelleted lettuce seeds (Lactuca sativa 'Lucrecia RZ') (Rijk Zwaan, Merksem, Belgium) were sown in 25×25×40 mm rockwool plugs (Grodan B.V., Roermond, The Netherlands).…”

“…The three most effective isolates for controlling P. aphanidermatum on lettuce identified by Stouvenakers et al (2023) were selected for this experiment. Two bacteria and one fungus were used alone or in consortium against the pathogen.…”

“…According to Stouvenakers et al (2023), stock mycelial culture of Pythium aphanidermatum (CBS 132490) was first reactivated on PDA for 3 days at 23°C with a day/night photoperiod of 18h/6h. Then, mycelial plugs of the active growing fungus were grown in Erlenmeyer flasks containing 25 mL of clarified V8 CaCO3 broth (800 mL of distilled water, 200 mL of V8 juice, and 3 g of CaCO3).…”

“…Nevertheless, it was recently highlighted that aquaponics could contain original microorganisms able to control P. aphanidermatum disease (Stouvenakers et al, 2020). From the list of potential antagonistic microorganisms set in it, a selective isolation was undertaken by Stouvenakers et al (2023) and led to 110 isolates. The isolates were then screened to control P. aphanidermatum disease on lettuce.…”