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The parameters for operating aquaponics at a given scale — including water volume, temperature, feed and flow rates, pH, fish and crop ages and densities — all affect the temporal and spatial distribution of the microbial communities that develop within its compartments, for reviews: RAS (Blancheton et al. 2013); hydroponics (Lee and Lee 2015).
In addition to controlling dissolved oxygen, carbon dioxide levels and pH in aquaponics, it is also essential to control the accumulation of solids in the RAS system as fine suspended particles can adhere to gills, cause abrasion and respiratory distress and increase susceptibility to disease (Yildiz et al. 2017). More relevant, the particulate organic matter (POM) must be quickly and effectively removed from RAS systems, or else excessive heterotrophic growth will cause almost all unit processes to fail. RAS feeding rates must be carefully managed to minimize solids loading on the system (e.g. avoid over-feeding and minimize feeding costs). The biophysical properties of feed — particle size, nutrient content, digestibility, sensory appeal, density and settling rate — determine ingestion and assimilation rates, which in turn have an impact on solids build-up and thus water quality. Although water quality is frequently studied in the context of nutrient cycling (see Chap. 9), it is also important to obtain a better understanding of the composition of microbial communities and changes in these based on feed composition, particulate loading and how this influences the growth of heterotrophic and autotrophic bacterial communities.
Various features of RAS system designs have been developed specifically to deal with solids (Timmons and Ebeling 2013); see also review: (Vilbergsson et al. 2016b). For instance, some biofilters function to keep substantial portions of wastes suspended in order to facilitate degradation, whilst others mechanically filter through screens or granular media. Still others rely on sedimentation to simply collect and remove sludge. However, such methods are not particularly effective at recovering nutrients within the sludge and making it bioavailable for plant use. Historically, this sludge has been handled in bioreactors for its methanogenic value or dewatered to be used as fertilizer for soil-based crops, but various newer designs have attempted to improve recovery for use in the hydroponic component. Improving recovery of this sludge is an important area of investigation given that a significant portion of the essential macro- and micronutrients required for plant growth are bound to the particulate organic matter, which, if discarded, is lost from the system. By adding an additional sludge recycling loop to aquaponics system, solid wastes can be converted into dissolved nutrients for reuse by plants rather than being discarded (Goddek et al. 2018). Digesters or remineralizing bioreactors are one way of accomplishing this, however one of the key areas that is currently under-developed includes knowledge of how microbial communities within these sludge digesters can be enhanced (e.g. through addition of microbes) or better utilized (e.g. through better engineered design of linked reactors) to recover nutrients into bioavailable forms for plants. Even though the actual microbial communities within sludge digesters have not been well researched for aquaponics, there is considerable literature on the microbiota of sludge digesters for sewage and animal wastes in agriculture, including fish effluent, that can provide further insight into ideal designs for sludge recovery in aquaponics system. Current research on the incorporation of sludge into aquaponics system involves remineralization in digesters situated between the RAS and hydroponic unit (Goddek et al. 2016a, 2018). Within aerobic or anaerobic bioreactors, environmental conditions that are favourable for waste degradation can effectively break down this sludge into bioavailable nutrients, which can subsequently be delivered to hydroponics system without the presence of soil (Monsees et al. 2017). Many one-loop aquaponics system already include aerobic (Rakocy et al. 2004) and anaerobic (Yogev et al. 2016) digesters to transform nutrients that are trapped in the fish sludge and make them bioavailable for plants. The ability to decouple these has a number of advantages that are further discussed in Chap. 8 and appears to lead to higher growth rates (Goddek and Vermeulen 2018). However, despite the many advances, the actual technology to accomplish this remains challenging. For example, some heterotrophic denitrifying bacteria cultured in anoxic or even aerobic conditions with sludge from RAS will use nitrate as an electron receptor and oxidized carbon sources for energy, while storing excess P as polyphosphate along with divalent metal ions such as Casup+2/sup or Cusup+2/sup. When stressed at alkaline pH, these bacteria degrade polyphosphate and release orthophosphate, which is the necessary form for assimilation of phosphate by plants (Van Rijn et al. 2006). Inserting remineralization bioreactor units, such as those in Goddek et al. (2018), could provide a way to better recover P for hydroponics. Similar methods have, for instance, been used with trout sludge from a RAS that were treated for nitrate and P content in excess of allowable disposal limits (Goddek et al. 2015). However, the microbial communities involved in these processes are sensitive to culture conditions such as C:N ratios, oxygenation, metal ions and pH, so nitrites and other noxious intermediates can accumulate. Despite a vast literature on digesters of various organic wastes, primarily anaerobic for biogas production (Ibrahim et al. 2016), there is far less research on treating RAS wastes (Van Rijn 2013), and in the case of aquaponics system, even less available research about the relationship between nutrient bioavailability and crop growth in hydroponics system (Möller and Müller 2012). At this time, more studies of RAS sludge bioreactors could provide important insights into culture conditions for microbial populations that produce favourable results, for instance, on P recovery, and its introduction into hydroponics units.
One of the current challenges in efforts to assess the recovery of P from sludge arises when comparing trials of anaerobic and aerobic digesters for their efficacy (Goddek et al. 2016b; Monsees et al. 2017). Although both studies used similar sludge composition initially, the results were quite different. In one study (Monsees et al. 2017), measures of various soluble nutrients in aerobic treatments resulted in a 330% increase in P concentration and a 16% decrease in nitrate concentration compared to minor increases in P and a 97% decrease in nitrate in anaerobic treatments. By contrast, results from a similar study (Goddek et al. 2016b) showed that growth of lettuce plants in a hydroponic unit was superior using anaerobic supernatant, even though both anaerobic and aerobic treatments only resulted in slightly better nitrate recovery from anaerobic conditions and almost complete loss of POsub4/sub from both treatments (Goddek et al. 2016b). Obviously, factors such as feed composition and rates, the suspension versus settling of solids, pH (maintained at 7 ± 1 with CaOHsub2/sub in the former and variable 8.2—8.65 in the latter), sampling and fish strains differed in these two studies. Nevertheless, the contrasting results for POsub4/sub and NOsub3/sub indicate the need for further research to optimize nutrient recovery, with the addition of a metagenomics approach to characterize microbial communities so as to better understand their role in these processes.