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Considerable research has been conducted to characterize heterotrophic and autotrophic bacteria in RAS systems and to better understand their roles in maintaining water quality and cycling of nutrients (for reviews, see Blancheton et al. (2013); Schreier et al. (2010). Non-pathogenic heterotrophs, typically dominated by Alphaproteobacteria and Gammaproteobacteria, tend to thrive in biofilters, and their contributions to transformations of nitrogen are fairly well understood because nitrogen cycling (NC) has been of paramount importance in developing recirculating culture systems (Timmons and Ebeling 2013). It has long been recognized that the bacterial transformation of the ammonia excreted by fish in a RAS system must be matched with excretion rates, because excess ammonia quickly becomes toxic for fish (see Chap. 9). Therefore in freshwater and marine RAS, the functional roles of microbial communities in NC dynamics — nitrification, denitrification, ammonification, anaerobic ammonium oxidation and dissimilatory nitrate reduction — have received considerable research attention and are well described in recent reviews (Rurangwa and Verdegem 2015; Schreier et al. 2010). There are far fewer studies of nitrogen transformations in aquaponics, but a recent review (Wongkiew et al. 2017) provides a summary along with discussion of nitrogen utilization efficiency, which is a prime consideration for plant growth in hydroponics.
After nitrogen, the second most essential macronutrient in aquaponics is phosphorus, which is not a limiting factor for fish that acquire it from feed, but is crucial for plants in hydroponics. However, the forms of phosphate in fish wastes are not immediately bioavailable for plants. Plants must have adequate quantities of inorganic ionic orthophosphate (Hsub2/subPOsub4/subsup-/sup and HPOsub4/subsup2-/sup = Pi) (Becquer et al. 2014), as this is the only bioavailable form for uptake and assimilation. Inorganic phosphate binds to calcium above pH 7.0, so aquaponics system must be careful to maintain pH conditions near pH 7.0. As pH values rise above 7.0, various insoluble forms of calcium phosphate can end up as precipitates in sludge (Becquer et al. 2014; Siebielec et al. 2014). Hence, RAS losses of P are primarily through removal of sludge from the system (Van Rijn 2013). However, somewhere in the aquaponics system, particulate matter must be captured and allowed to mineralize in order to provide sufficient supplies of usable nutrients for crops in the hydroponics unit. The mineralization step will also release other macro- and micronutrients so that there are fewer deficiencies, thus reducing the need for supplementation in the hydroponics compartment. Given that world supplies of phosphate-rich fertilizers are dwindling and supplementation with P is increasingly costly, efforts are being made to maximize the recovery of P from RAS sludge (Goddek et al. 2016b; Monsees et al. 2017).
The bioavailability of macro and micronutrients is currently poorly understood. Previous research (Cerozi and Fitzsimmons 2016a) suggests that the availability of nutrients becomes compromised as pH is reduced below 7.0 and has resulted in coupled hydroponics system for leafy greens being operated around pH 6.0. However, recent research comparing aquaponic conditions and pH 7.0 to hydroponic conditions of pH 5.8 showed no difference in productivity (Anderson et al. 2017a, b). In these studies, hydroponic conditions at pH 7.0 reduced productivity by ~ 22% compared to hydroponic pH 5.8. Initially, the hypothesis was that the differences in productivity could be ascribed to the microbiota of the aquaponic water, but subsequent research dismissed that theory (Wielgosz et al. 2017).
In RAS where C:N ratios increase due to availability of organic matter, denitrifying bacteria, especially Pseudomonas sp., use carbon as an electron donor in anoxic conditions, to produce Nsub2/sub at the expense of nitrate (Schreier et al. 2010; Wongkiew et al. 2017). Biofloc systems are sometimes used to augment feed for fish (Crab et al. 2012; Martínez-Córdova et al. 2015), and biofloc is increasingly being used in aquaponics system, especially in Asia (Feng et al. 2016; Kim et al. 2017; Li et al. 2018). When biofloc is used in aquaponics (da Rocha et al. 2017; Pinho et al. 2017), nutrient cycling becomes even more complex given that DO, temperature and pH influence whether heterotrophic (carbon-utilizing) microbial communities predominate over autotrophic denitrifiers that are capable of reducing sulphide to sulphate (Schreier et al. 2010). Heterotrophs tend to have a higher growth rate than autotrophs in the presence of adequate sources of carbon (Michaud et al. 2009); therefore, manipulating feed type or regimes, or adding an organic carbon source directly, whilst monitoring dissolved oxygen levels, can help keep populations equilibrated whilst still providing hydroponics with N in a usable form (Vilbergsson et al. 2016a).
In hydroponics system, nutrient cycling has been less well-studied since inorganic compounds containing the required balance of nutrients are typically added in order to ensure proper plant growth. However, high nutrient concentrations, especially in humid warm environments such as greenhouses, easily facilitate growth of microbial communities, especially phytopathogens such as fungi (Fusarium) and oomycota (Phytophthora, Pythium sp.), that can quickly sead in circulating water and may result in die-offs (Lee and Lee 2015). Recent efforts to better understand hydroponic rhizobacteria and their beneficial effects in promoting plant growth (but also for inhibiting pathogen proliferation) have utilized various 'omics' techniques to analyse microbial communities and their interactions with root systems (Lee and Lee 2015).
For instance, when probiotic bacteria such as Bacillus, are present, they were shown to enhance P availability and also appear to have an added plant growthpromoting effect in a tilapia-lettuce system (Cerozi and Fitzsimmons 2016b). In aquaponics system, the addition of probiotics to fish feed and RAS water, as well as to the hydroponic water supply, deserves further experimentation, since microbial communities can have multiple modulatory effects on plant physiology. For example, the microbial communities (bacteria, fungi, oomycetes) of four food crops were analysed by metagenomic sequencing when maintained in a constant nutrient film hydroponics system where pH and nutrient concentrations were allowed to fluctuate naturally throughout the plants' life cycles (Sheridan et al. 2017). The authors concluded that treatment with a commercial mixture of plant growth-promoting microbes (PGPMs), in this case bacteria, mycorrhizae and fungi, appeared to confer greater stability and similarities in community composition after 12—14 weeks than in controls. They suggest that this could be attributed to root exudates, which purportedly favour and even control the development of microbial communities appropriate to successive plant developmental stages. Given the known effects of PGPMs in soil-based crop production, and the few studies that are available for soilless systems, further investigation is warranted to determine how to enhance PGPMs and to improve their effects in aquaponics system (Bartelme et al. 2018). If hydroponic cultures are more stable and plant growth is more robust with PGPMs, then the goal should be to characterize microbial communities in aquaponics via metagenomics and correlate them with optimal macro- and micronutrient availability via metabolomics and proteomics.