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In Sect. 14.2.3, the suppressiveness of aquaponic systems was suggested. As stated before, the main hypothesis is related to the water recirculation as it is for hydroponic systems. However, a second hypothesis exists and this is linked to the presence of organic matter in the system. Organic matter that could drive a more balanced microbial ecosystem including antagonistic agents which is less suitable for plant pathogens (Rakocy 2012).
In aquaponics, organic matter comes from water supply, uneaten feeds, fish faeces, organic plant substrate, microbial activity, root exudates and plant residues (Waechter-Kristensen et al. 1997; Naylor et al. 1999; Waechter-Kristensen et al. 1999). In such a system, heterotrophic bacteria are organisms able to use organic matter as a carbon and energy source, generally in the form of carbohydrates, amino acids, peptides or lipids (Sharrer et al. 2005; Willey et al. 2008; Whipps 2001). In recirculated aquaculture (RAS), they are mainly localised in the biofilter and consume organic particles trapped in it (Leonard et al. 2000; Leonard et al. 2002). However, another source of organic carbon for heterotrophic bacteria is humic substances present as dissolved organic matter and responsible for the yellow-brownish coloration of the water (Takeda and Kiyono 1990 cited by Leonard et al. 2002; Hirayama et al. 1988). In the soil as well as in hydroponics, humic acids are known to stimulate plant growth and sustain the plant under abiotic stress conditions (Bohme 1999; du Jardin 2015). Proteins in the water can be used by plants as an alternative nitrogen source thus enhancing their growth and pathogen resistance (Adamczyk et al. 2010). In the recirculated water, the abundance of free-living heterotrophic bacteria is correlated with the amount of biologically available organic carbon and carbon-nitrogen ratio (C/N) (Leonard et al. 2000; Leonard et al. 2002; Michaud et al. 2006; Attramadal et al. 2012). In the biofilter, an increase in the C/N ratio increases the abundance of heterotrophic bacteria at the expense of the number of autotrophic bacteria responsible for the nitrification process (Michaud et al. 2006; Michaud et al. 2014). As implied, heterotrophic microorganisms can have a negative impact on the system because they compete with autotrophic bacteria (e.g. nitrifying bacteria) for space and oxygen. Some of them are plant or fish pathogens, or responsible for off-flavour in fish (Chang-Ho 1970; Funck-Jensen and Hockenhull 1983; Jones et al. 1991; Leonard et al. 2002; Nogueira et al. 2002; Michaud et al. 2006; Mukerji 2006; Whipps 2001; Rurangwa and Verdegem 2015). However, heterotrophic microorganisms involved in the system can also be positive (Whipps 2001; Mukerji 2006). Several studies using organic fertilizers or organic soilless media, in hydroponics, have shown interesting effects where the resident microbiota were able to control plant diseases (Montagne et al. 2015). All organic substrates have their own physico-chemical properties. Consequently, the characteristics of the media will influence microbial richness and functions. The choice of a specific plant media could therefore influence the microbial development so as to have a suppressive effect on pathogens (Montagne et al. 2015; Grunert et al. 2016; Montagne et al. 2017). Another possibility of pathogen suppression related to organic carbon is the use of organic amendments in hydroponics (Maher et al. 2008; Vallance et al. 2010). By adding composts in soilless media like it is common use in soil, suppressive effects are expected (Maher et al. 2008). Enhancing or maintaining a specific microorganism such as Pseudomonas population by adding some formulated carbon sources (e.g. nitrapyrin-based product) as reported by Pagliaccia et al. (2007) and Pagliaccia et al. (2008) is another possibility. The emergence of organic soilless culture also highlights the involvement of beneficial microorganisms against plant pathogens supported by the use of organic fertilizers. Fujiwara et al. (2013), Chinta et al. (2014), and Chinta et al. (2015) reported that fertilization with corn steep liquor helps to control Fusarium oxysporum f.sp. lactucae and Botrytis cinerea on lettuces and Fusarium oxysporum f.sp. radicis-lycopersici on tomato plants. And even if hardly advised for aquaponic use, 1 g/L of fish-based soluble fertilizer (Shinohara et al. 2011) suppresses bacterial wilt on tomato caused by Ralstonia solanacearum in hydroponics (Fujiwara et al. 2012).
Finally, though information about the impact of organic matter on plant protection in aquaponics is scarce, the various elements mentioned above show their potential capacity to promote a system-specific and plant pathogen-suppressive microbiota.