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This chapter aimed to give a first report of plant pathogens occurring in aquaponics, reviewing actual methods and future possibilities to control them. Each strategy has advantages and disadvantages and must be thoroughly designed to fit each case. However, at this time, curative methods in coupled aquaponic systems are still limited and new perspectives of control must be found. Fortunately, suppressiveness in terms of aquaponic systems could be considered, as already observed in hydroponics (e.g. in plant media, water, and slow filters). In addition, the presence of organic matter in the system is an encouraging factor when compared to soilless culture systems making use of organic fertilisers, organic plant media or organic amendments.
For the future, it seems important to investigate this suppressive action followed by identification and characterization of the responsible microbes or microbe consortia. Based on the results, several strategies could be envisaged to enhance the capacity of plants to resist pathogens. The first is biological control by conservation, which means favouring beneficial microorganisms by manipulating and managing water composition (e.g. C/N ratio, nutrients and gases) and parameters (e.g. pH and temperature). But identification of these influencing factors needs to be realized first. This management of autotrophic and heterotrophic bacteria is also of key importance to sustain good nitrification and keep healthy fish. The second strategy is augmentative biological control by additional release of beneficial microorganisms already present in the system in large numbers (inundative method) or in small numbers but repeated in time (inoculation method). But prior identification and multiplication of an aquaponic BCA should be achieved. The third strategy is importation, i.e. introducing a new microorganism normally not present into the system. In this case, selection of a microorganism adapted and safe for aquaponic environment is needed. For the two last strategies, the site of inoculation in the system must be considered depending on the aim desired. Sites where microbial activity could be enhanced are the recirculated water, the rhizosphere (plant media included), the biofilter (such as in slow sand filters where BCA addition is already tested) and the phyllosphere (i.e. aerial plant part). Whatever the strategy, the ultimate goal should be to lead the microbial communities to provide a stable, ecologically balanced microbial environment allowing good production of both plant and fish.
To conclude, following the requirements of integrated plant pest management (IPM) is a necessity to correctly manage the system and avoid development and spread of plant diseases (Bittsanszky et al. 2015; Nemethy et al. 2016). The principle of IPM is to apply chemical pesticides or other agents as a last resort when economic injury level is reached. Consequently, control of pathogens will need to be firstly based on physical and biological methods (described above), their combination and an efficient detection and monitoring of the disease (European Parliament 2009).