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Solubilisation consists of the breaking down of the complex organic molecules composing fish waste and feed leftovers into nutrients in the form of ionic minerals which plants can absorb (Goddek et al. 2015; Somerville et al. 2014). In both aquaculture (Sugita et al. 2005; Turcios and Papenbrock 2014) and aquaponics, solubilisation is conducted mainly by heterotrophic bacteria (van Rijn 2013; Chap. 6) which have not yet been fully identified (Goddek et al. 2015). Some studies have started deciphering the complexity of these bacteria communities (Schmautz et al. 2017). In current aquaculture, the most commonly observed bacteria are Rhizobium sp., Flavobacterium sp., Sphingobacterium sp., Comamonas sp., Acinetobacter sp., Aeromonas sp. and Pseudomonas sp. (Munguia-Fragozo et al. 2015; Sugita et al. 2005). An example of the major role of bacteria in aquaponics could be the transformation of insoluble phytates into phosphorus (P) made available for plant uptake through the production of phytases which are particularly present in γ-proteobacteria (Jorquera et al. 2008). (More research needs to be done in this area). Other nutrients than P can also be trapped as solids and evacuated from the system with the sludge. Efforts are thus being made to remineralise this sludge with UASB-EGSB reactors in order to reinject nutrients into the aquaponic system (Delaide 2017; Goddek et al. 2016; Chap. 10). Furthermore, different minerals are not released at the same rate, depending on the composition of the feed (LetelierGordo et al. 2015), thus leading to more complicated monitoring of their concentration in the aquaponic solution (Seawright et al. 1998).
The main nitrogen source in an aquaponic system is the fish feed and the proteins it contains (Goddek et al. 2015; Ru et al. 2017; Wongkiew et al. 2017; Yildiz et al. 2017). Ideally, 100% of this feed should be eaten by the fish. However, is has been observed that fish only use about 30% of the nitrogen contained in the given feed (Rafiee and Saad 2005). The ingested feed is partly used for assimilation and metabolism (Wongkiew et al. 2017), while the rest is excreted either through the gills or as urine and faeces (Ru et al. 2017). The nitrogen which is excreted through the gills is mainly in the form of ammonia, NHsub3/sub (Wongkiew et al. 2017; Yildiz et al. 2017), while urine and faeces are composed of organic nitrogen (Wongkiew et al. 2017) which is transformed into ammonia by proteases and deaminases (Sugita et al. 2005). In general, the fish excrete nitrogen under the form of TAN, i.e. NHsub3/sub and NHsub4/subsup+/sup. The balance between NHsub3/sub and NHsub4/subsup+/sup depends mostly on the pH and temperature. Ammonia is the major waste produced by fish catabolism of the feed proteins (Yildiz et al. 2017).
Nitrification is a two-step process during which the ammonia NHsub3/sub or ammonium NHsub4/subsup+/sup excreted by the fish is transformed first into nitrite NOsub2/subsup-/sup and then into nitrate NOsub3/subsup-/sup by specific aerobic chemosynthetic autotrophic bacteria. A high availability of dissolved oxygen is required as nitrification consumes oxygen (Carsiotis and Khanna 1989; Madigan and Martinko 2007; Shoda 2014). The first step of this transformation is carried out by ammonia-oxidising bacteria (AOB) such as Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosolobus and Nitrosovibrio. The second step is conducted by nitrite-oxidising bacteria (NOB) such as Nitrobacter, Nitrococcus, Nitrospira and Nitrospina (Rurangwa and Verdegem 2013; Timmons and Ebeling 2013; Wongkiew et al. 2017). Nitrospira is currently deduced to be a complete nitrifier, i.e. to be involved in the production of both nitrite and nitrate (Daims et al. 2015). The same bacteria can be found both in aquaculture and aquaponic systems (Wongkiew et al. 2017). These bacteria are mainly found in biofilms fixed to the media composing the biofilter but can also be observed in the other compartments of the system (Timmons and Ebeling 2013).
Nitrification is of prime importance in aquaponics as ammonia and nitrite are quite toxic for fish: 0.02—0.07 mg/L of ammonia—nitrogen are sufficient to observe damage in warm water fish, and nitrite—nitrogen should be kept under 1 mg/L (Losordo et al. 1998; Timmons and Ebeling 2013). Ammonia affects the central nervous system of the fish (Randall and Tsui 2002; Timmons and Ebeling 2013), while nitrite induces problems with oxygen fixation (Losordo et al. 1998). Nitrate— nitrogen is, however, tolerated by the fish up to 150—300 mg/L (Goddek et al. 2015; Graber and Junge 2009; Yildiz et al. 2017).
Nitrification mostly takes place in biofilters (Losordo et al. 1998; Timmons and Ebeling 2013). Therefore, when starting a system, it is recommended to run the system without fish in order to allow the slowly growing population of nitrifying bacteria to establish (Timmons and Ebeling 2013; Wongkiew et al. 2017). It is also necessary to avoid, as far as possible, the presence of organic matter in the biofilters in order to prevent the growth of highly competitive heterotrophic bacteria (Timmons and Ebeling 2013). Alternatively, commercial mixes of nitrifying bacteria can be added to the system, prior to stocking, to hasten the colonisation process (Kuhn et al. 2010). Nevertheless, small aquaponic systems without biofilter also exist. In these systems, nitrifying bacteria form biofilms of the available surfaces (e.g. hydroponic compartment walls, inert media when using the media bed technique) (Somerville et al. 2014).