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At the moment aquaponic practitioners operating a coupled system are relatively helpless against plant diseases when they occur, especially in the case of root pathogens. No pesticide nor biopesticide is specifically developed for aquaponic use (Rakocy 2007; Rakocy 2012; Somerville et al. 2014; Bittsanszky et al. 2015; Sirakov et al. 2016). In brief, curative methods are still lacking. Only Somerville et al. (2014) list the inorganic compounds that may be used against fungi in aquaponics. In any case, an appropriate diagnostic of the pathogen(s) causing the disease is mandatory in order to identify the target(s) for curative measures. This diagnosis requires good expertise in terms of observation capacity, plant pathogen cycle understanding and analysis of the situation. However, in case of generalist (not specific) symptoms and depending on the degree of accuracy needed, it is often necessary to use laboratory techniques to validate the hypothesis with respect to the causal agent (Lepoivre 2003). Postma et al. (2008) reviewed the different methods to detect plant pathogens in hydroponics, and four groups were identified:
Direct macroscopic and microscopic observation of the pathogen
Isolation of the pathogen
Use of serological methods
Use of molecular methods
Good agricultural practices (GAP) for plant pathogens control are the various actions aiming to limit crop diseases for both yield and quality of produce (FAO 2008). GAP transposable to aquaponics are essentially non-curative physical or cultivation practices that can be divided in preventive measures and water treatment.
Preventive measures have two distinct purposes. The first is to avoid the entry of the pathogen inoculum into the system and the second is to limit (i) plant infection, (ii) development and (iii) spread of the pathogen during the growing period. Preventive measures aiming to avoid the entry of the initial inoculum in the greenhouse are, for example, a fallow period, a specific room for sanitation, room sanitation (e.g. plant debris removal and surface disinfection), specific clothes, certified seeds, a specific room for plant germination and physical barriers (against insect vectors) (Stanghellini and Rasmussen 1994; Jarvis 1992; Albajes et al. 2002; Somerville et al. 2014; Parvatha Reddy 2016). Among the most important practices used for the second type of preventive measures are, the use of resistant plant varieties, tools disinfection, avoidance of plant abiotic stresses, good plant spacing, avoidance of algae development and environmental conditions management. The last measure, i.e. environmental conditions management, means to control all greenhouse parameters in order to avoid or limit diseases by intervening in their biological cycle (ibid.). Generally, in large-scale greenhouse structures, computer software and algorithms are used to calculate the optimal parameters allowing both plant production and disease control. The parameters measured, among others, are temperature (of the air and the nutrient solution), humidity, vapour pressure deficit, wind speed, dew probability, leaf wetness and ventilation (ibid.). The practitioner acts on these parameters by manipulating the heating, the ventilation, the shading, the supplement of lights, the cooling and the fogging (ibid.).
Physical water treatments can be employed to control potential water pathogens. Filtration (pore size less than 10 μm), heat and UV treatments are among the most effective to eliminate pathogens without harmful effects on fish and plant health (Ehret et al. 2001; Hong and Moorman 2005; Postma et al. 2008; Van Os 2009; Timmons and Ebeling 2010). These techniques allow the control of disease outbreaks by decreasing the inoculum, the quantity of pathogens and their proliferation stages in the irrigation system (ibid.). Physical disinfection decreases water pathogens to a certain level depending on the aggressiveness of the treatment. Generally, the target of heat and UV disinfection is the reduction of the initial microorganisms population by 90—99.9% (ibid.). The filtration technique most used is slow filtration because of its reliability and its low cost. The substrates of filtration generally used are sand, rockwool or pozzolana (ibid.). Filtration efficiency is essentially dependent on pore size and flow. To be effective as disinfection treatment, the filtration needs to be achieved with a pore size less than 10 μm and a flow rate of 100 l/msup2/sup/h, even if less binding parameters show satisfactory performances (ibid.). Slow filtration does not eliminate all of the pathogens; more than 90% of the total aerobic bacteria remain in the effluent (ibid.). Nevertheless, it allows a suppression of plant debris, algae, small particles and some soil-borne diseases such as Pythium and Phytophthora (the efficiency is genus dependent). Slow filters do not act only by physical action but also show a microbial suppressive activity, thanks to antagonistic microorganisms, as discussed in Sect. 14.2.3 (Hong and Moorman 2005; Postma et al. 2008; Van Os 2009; Vallance et al. 2010). Heat treatment is very effective against plant pathogens. However it requires temperatures reaching 95 C during at least 10 seconds to suppress all kind of pathogens, viruses included. This practice consumes a lot of energy and imposes water cooling (heat exchanger and transitional tank) before reinjection of the treated water back into the irrigation loop. In addition, it has the disadvantage of killing all microorganisms including the beneficial ones (Hong and Moorman 2005; Postma et al. 2008; Van Os 2009). The last technique and probably the most applied is UV disinfection. 20.8% of EU Aquaponics Hub practitioners use it (Villarroel et al. 2016). UV radiation has a wavelength of 200 to 280 nm. It has a detrimental effect on microorganisms by direct damage of the DNA. Depending on the pathogen and the water turbulence, the energy dose varies between 100 and 250 mJ/cmsup2/sup to be effective (Postma et al. 2008; Van Os 2009).
Physical water treatments eliminate the most of the pathogens from the incoming water but they cannot eradicate the disease when it is already present in the system. Physical water treatment does not cover all the water (especially the standing water zone near the roots), nor the infected plant tissue. For example, UV treatments often fail to suppress Pythium root rot (Sutton et al. 2006). However, if physical water treatment allows a reduction of plant pathogens, theoretically, they also have an effect on nonpathogenic microorganisms potentially acting on disease suppression. In reality, heat and UV treatments create a microbiological vacuum, whereas slow filtration produces a shift in effluent microbiota composition resulting in a higher disease suppression capacity (Postma et al. 2008; Vallance et al. 2010). Despite the fact that UV and heat treatment in hydroponics eliminate more than 90% of microorganisms in the recirculating water, no diminution of the disease suppressiveness was observed. This was probably due to a too low quantity of water treated and a re-contamination of the water after contact with the irrigation system, roots and plant media (ibid.).
Aquaponic water treatment by means of chemicals is limited in continuous application. Ozonation is a technique used in recirculated aquaculture and in hydroponics. Ozone treatment has the advantage to eliminate all pathogens including viruses in certain conditions and to be rapidly decomposed to oxygen (Hong and Moorman 2005; Van Os 2009; Timmons and Ebeling 2010; Gonçalves and Gagnon 2011). However it has several disadvantages. Introducing ozone in raw water can produce by-products oxidants and significant amount of residual oxidants (e.g. brominated compound and haloxy anions that are toxic for fish) that need to be removed, by UV radiation, for example, prior to return to the fish part (reviewed by Gonçalves and Gagnon 2011). Furthermore, ozone treatment is expensive, is irritant for mucous membranes in case of human exposure, needs contact periods of 1 to 30 minutes at a concentration range of 0.1—2.0 mg/L, needs a temporal sump to reduce completely from Osub3/sub to Osub2/sub and can oxidize elements present in the nutrient solution, such as iron chelates, and thus makes them unavailable for plants (Hong and Moorman 2005; Van Os 2009; Timmons and Ebeling 2010; Gonçalves and Gagnon 2011).
In hydroponics, numerous scientific papers review the use of antagonistic microorganisms (i.e. able to inhibit other organisms) to control plant pathogens but until now no research has been carried out for their use in aquaponics. The mode of action of these antagonistic microorganisms is according to Campbell (1989)), Whipps (2001) and Narayanasamy (2013) grouped in:
Competition for nutrients and niches
Induction of diseases resistance in plants
The experiments introducing microorganisms in aquaponic systems have been focused on the increase of nitrification by addition of nitrifying bacteria (Zou et al. 2016) or the use of plant growth promoters (PGPR) such as Azospirillum brasilense and Bacillus spp. to increase plant performance (Mangmang et al. 2014; Mangmang et al. 2015a; Mangmang et al. 2015b; Mangmang et al. 2015c; da Silva Cerozi and Fitzsimmons 2016; Bartelme et al. 2018). There is now an urgent need to work on biocontrol agents (BCA) against plant pathogens in aquaponics with regard to the restricted use of synthetic curative treatments, the high value of the culture and the increase of aquaponic systems in the world. BCA are defined, in this context, as viruses, bacteria and fungi exerting antagonistic effects on plant pathogens (Campbell 1989; Narayanasamy 2013).
Generally, the introduction of a BCA is considered to be easier in soilless systems. In fact, the hydroponic root environment is more accessible than in soil and the microbiota of the substrate is also unbalanced due to a biological vacuum. Furthermore, environmental conditions of the greenhouse can be manipulated to achieve BCA growth needs. Theoretically all these characteristics allow a better introduction, establishment and interaction of the BCA with plants in hydroponics than in soil (Paulitz and Bélanger 2001; Postma et al. 2009; Vallance et al. 2010). However, in practice, the effectiveness of BCA inoculation to control root pathogens can be highly variable in soilless systems (Postma et al. 2008; Vallance et al. 2010; Montagne et al. 2017). One explanation for this is that BCA selection is based on in vitro tests which are not representing real conditions and subsequently a weak adaptation of these microorganisms to the aquatic environment used in hydroponics or aquaponics (Postma et al. 2008; Vallance et al. 2010). To control plant pathogens and more especially those responsible for root rots, a selection and identification of microorganisms involved in aquatic systems which show suppressive activity against plant pathogens is needed. In soilless culture, several antagonistic microorganisms can be picked due to their biological cycle being similar to root pathogens or their ability to grow in aqueous conditions. Such is the case of nonpathogenic Pythium and Fusarium species and bacteria, where Pseudomonas, Bacillus and Lysobacter are the genera most represented in the literature (Paulitz and Bélanger 2001; Khan et al. 2003; Chatterton et al. 2004; Folman et al. 2004; Sutton et al. 2006; Liu et al. 2007; Postma et al. 2008; Postma et al. 2009; Vallance et al. 2010; Sopher and Sutton 2011; Hultberg et al. 2011; Lee and Lee 2015; Martin and Loper 1999; Moruzzi et al. 2017; Thongkamngam and Jaenaksorn 2017). The direct addition of some microbial metabolites such as biosurfactants has also been studied (Stanghellini and Miller 1997; Nielsen et al. 2006; Nielsen et al. 2006). Although some microorganisms are efficient at controlling root pathogens, there are other problems that need to be overcome in order to produce a biopesticide. The main challenges are to determine the means of inoculation, the inoculum density, the product formulation (Montagne et al. 2017), the method for the production of sufficient quantity at low cost and the storage of the formulated product. Ecotoxicological studies on fish and living beneficial microorganisms in the system are also an important point. Another possibility that could be exploited is the use of a complex of antagonistic agents, as observed in suppressive soil techniques (Spadaro and Gullino 2005; Vallance et al. 2010). In fact, microorganisms can work in synergy or with complementary modes of action (ibid.). The addition of amendments could also enhance the BCA potential by acting as prebiotics (see Sect. 14.4).