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

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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 damping-off 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.

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Data Availability

The datasets generated and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors are grateful to the laboratory staff and their supervisors for their valuable assistance and reviewing. We especially thank the trainee Fanny Vautrin who helped screen the biocontrol agents.

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  1. S. Massart and M. H. Jijakli contributed equally to this work.

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  1. Laboratory of Integrated and Urban Phytopathology, University of Liège, Gembloux Agro-Bio Tech, Passage des Déportés 2, 5030, Gembloux, Belgium

    G. Stouvenakers, S. Massart & M. H. Jijakli

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All authors contributed to the study conception and design. Material preparation, data collection, and analysis were performed by GS. The first draft of the manuscript was written by GS, and all authors commented on the previous versions of the manuscript. All authors have read and approved the final manuscript.

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Stouvenakers, G., Massart, S. & Jijakli, M.H. First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce. Microb Ecol 86, 1107–1119 (2023). https://doi.org/10.1007/s00248-022-02126-1

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