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Nowadays, aquaponic systems are the core of numerous research efforts which aim at better understanding these systems and at responding to new challenges of food production sustainability (Goddek et al. 2015; Villarroel et al. 2016). The cumulated number of publications mentioning "aquaponics" or derived terms in the title went from 12 in early 2008 to 215 in 2018 (January 2018 Scopus database research results). In spite of this increasing number of papers and the large area of study topics they are covering, one critical point is still missing, namely plant pest management (Stouvenakers et al. 2017). According to a survey on EU Aquaponic Hub members, only 40% of practitioners have some notions about pests and plant pest control (Villarroel et al. 2016).
In aquaponics, the diseases might be similar to those found in hydroponic systems under greenhouse structures. Among the most problematic pathogens, in term of spread, are hydrophilic fungi or fungus-like protists which are responsible for root or collar diseases. To consider plant pathogen control in aquaponics, firstly, it is important to differentiate between coupled and decoupled systems. Decoupled systems allow disconnection between water from the fish and crop compartment (see Chap. 8). This separation allows the optimisation and a better control of different parameters (e.g. temperature, mineral or organic composition and pH) in each compartment (Goddek et al. 2016; Monsees et al. 2017). Furthermore, if the water from the crop unit does not come back to the fish part, the application of phytosanitary treatments (e.g. pesticides, biopesticides and chemical disinfection agents) could be allowed here. Coupled systems are built in one loop where water recirculates in all parts of the system (see Chaps. 5 and 7). However, in coupled systems, plant pest control is more difficult due to the both presence of fish and beneficial microorganisms which transform fish sludge into plant nutrients. Their existence limits or excludes the application of already available disinfecting agents and chemical treatments. Furthermore no pesticides or biopesticides have been specifically developed for aquaponics (Rakocy et al. 2006; Rakocy 2012; Somerville et al. 2014; Bittsanszky et al. 2015; Nemethy et al. 2016; Sirakov et al. 2016). Control measures are consequently mainly based on non-curative physical practices (see Sect. 14.3.1) (Nemethy et al. 2016; Stouvenakers et al. 2017).
On the other hand, recent studies highlight that aquaponic plant production offers similar yields when compared to hydroponics although concentrations of mineral plant nutrients are lower in aquaponic water. Furthermore, when aquaponic water is complemented with some minerals to reach hydroponic concentrations of mineral nutritive elements, even better yields can be observed (Pantanella et al. 2010; Pantanella et al. 2015; Delaide et al. 2016; Saha et al. 2016; Anderson et al. 2017; Wielgosz et al. 2017; Goddek and Vermeulen 2018). Moreover, some informal observations from practitioners in aquaponics and two recent scientific studies (Gravel et al. 2015; Sirakov et al. 2016) report the possible presence of beneficial compounds and/or microorganisms in the water that could play a role in biostimulation and/or have antagonistic (i.e. inhibitory) activity against plant pathogens. Biostimulation is defined as the enhancement of plant quality traits and plant tolerance against abiotic stress using any microorganism or substance.
With regard to these aspects, this chapter has two main objectives. The first is to give a review of microorganisms involved in aquaponic systems with a special focus on plant pathogenic and plant beneficial microorganisms. Factors influencing these microorganisms will be also considered (e.g. organic matter). The second is to review available methods and future possibilities in plant diseases control.