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Good food safety and ensuring animal welfare are high priorities in gaining public support for aquaponics. One of the most frequent issues raised by food safety experts in relation to aquaponics is the potential risk of contamination with human pathogens when using fish effluent as fertilizer for plants (Chalmers 2004; Schmautz et al. 2017). A recent literature search to determine zoonotic risks in aquaponics concluded that pathogens in contaminated intake water, or pathogens in components of feeds originating with warm-blooded animals, can become associated with fish gut microbiota, which, even if not detrimental to the fish themselves, can potentially be passed up the food chain to humans (Antaki and Jay-Russell 2015). The mechanisms of introduction of pathogens to an aquaponics system are thus of concern, with the likeliest source of faecal coliforms or other pathogenic bacteria stemming from feed inputs to fish. From a biological perspective, there are potential risks of these pathogens proliferating either in biofilters, or, in one-loop systems by introducing airborne pathogens from open plant components back to the fish tanks. Although biosecurity risks are low in the relatively closed environmental space of an aquaponics system — as compared for instance to open pond aquaculture — and are even lower in decoupled aquaponics system wherein portions of the system can be isolated, there is still a perception that fish sludge could be potentially dangerous when applied to plants for human consumption. Escherichia coli (E. coli) is a human enteric pathogen causing foodborne illnesses that has been a key concern regarding the use of animal waste as fertilizer in agriculture or aquaculture, e.g. integrated pig-fish systems (Dang and Dalsgaard 2012). However, it is generally not considered to present a risk in fish-plant aquaponics. For instance, Moriarty et al. (2018) previously demonstrated that UV-radiation treatment can successfully reduce E. coli but also noted that the coliforms detected in the aquaponics system were at background levels and did not proliferate in the fish raceways or in the hydroponically grown lettuce within the experimental system, and thus did not present a health risk. There is limited research on these aspects, but a few preliminary studies have found very low risks of coliform contamination, for instance, by showing no difference in coliform levels from sterilized and non-sterilized RAS water treatments applied to plants (Pantanella et al. 2015). Even though there is a potential risk of internalization of microbes within plant leaves, and thus their transmission to the consumed portions of some edible leafy plants grown in aquaponics, other studies have come to similar conclusions that the risks are minimal of introducing potentially dangerous human pathogens (Elumalai et al. 2017).
However, managing risks, or more importantly managing the perceptions of those risks, remains a high priority for government authorities and aquaponics investors. It is assumed that the quality control of feed inputs and careful handling of fish/fish wastes can limit most of these potential concerns (Fox et al. 2012). Indeed, no known human health incidents have to our knowledge currently been reported in relation to aquaponics system, and this may be a function of the fact that RAS facilities and hydroponic greenhouses typically have good biosecurity measures, including hygiene and quarantine practices that are stringently observed. Recommended microbiological practices for biosecurity have been evaluated for different aquaculture production systems and recommendations formulated into Hazard Analysis Critical Control Points guidelines, an international system for controlling food safety (Orriss and Whitehead 2000). However, there is still a need for better scientific documentation of risks for pathogen transfers to humans, and direct research into management in this area of aquaponics production.
There is existing discipline-specific literature in aquaculture, hydroponics and bioengineering that can help inform and enhance microbial performance in aquaponics. For instance, microbial communities serve a wide range of important functions in fish health, including playing a key role in the digestibility and assimilation of feed, as well as immunodulation, and these functions as well as the role of probiotics in enhancing aquaculture systems are well-reviewed (Akhter et al. 2015). The role of microbes in RAS systems specifically is also well covered, including microbial management of biofilters, as well as research into pathogen control, as well as various techniques to control off-flavours deriving from RAS systems (Rurangwa and Verdegem 2015). Likewise, the microbes in the rhizosphere of plants are important for rooting and plant growth (Dessaux et al. 2016) but also for controlling the spread of pathogens in hydroponic plant production; these areas are well explored in a recent review by Bartelme et al. (2018). However, there is still a very limited understanding of linkages in the microbiome amongst the compartments of aquaponics system, knowledge that is crucial for maximizing productivity and reducing pathogen transfer.
The proliferation of opportunistic pathogens that are dangerous to fish or plant health are important considerations in the economics of aquaponics operations, given that any use of antibiotics or disinfectants can have a potentially detrimental effect on biofilter function, as well as destabilizing microbial relationships in other compartments of the system. Disinfection protocols commonly used in RAS include treating water with ultraviolet light (Elumalai et al. 2017), which, combined with ozone (and usually a combination of both), comprises a first-line abiotic approach to maintaining water quality. Fish eggs/larvae are also often quarantined before being introduced, and any intake water treated, thus reducing direct potential sources of fish pathogen entry to the system.
Incoming water to RAS is also typically allowed to 'mature' in biofilters before being fed into the recirculating system. Experiments, for instance, have shown that inoculating a pre-biofilter with a mixture of nitrifying bacteria, and 'feeding' it with organic matter until bacterial populations match the carrying capacity of the fish tanks, means that the rearing tank water is less likely to be unstable and overtaken by opportunistic bacteria (Attramadal et al. 2016; Rurangwa and Verdegem 2015). However, should pathogens become problematic, the use of high-dose UV, ozone, chemical or antibiotic treatments can sometimes be necessary, although such use is generally disruptive to other compartments of the system, especially the biofilters (Blancheton et al. 2013). Indeed, depending on the dose and location within the system, non-selective treatments for pathogens can actually favour proliferation of opportunists. For instance, high levels of ozone treatment not only kills bacteria, protists and viruses but also oxidizes DOM and affects aggregation of POM, thereby exerting selection pressure on bacterial populations (ibid.).
A detailed discussion of plant pathogens in aquaponics system and their control is included in Chap. 14 and thus is not reiterated here. However, it is worth noting that Bacillus species are routinely used as commercial probiotics in aquaculture, and there is growing evidence that similar Bacillus species are also effective for plants, that are already available in some commercial hydroponics probiotics solutions (Shafi et al. 2017). A recent study has extended such studies on Bacillus to include experimentation in aquaponics system (Cerozi and Fitzsimmons 2016b). The location where the probiotics are introduced — in the fish, plant or biofilters — may be important, but it is not clear from existing work whether the addition of probiotics in the fish component, with potential benefits for the fish, also has better effects on plant growth and health relative to the addition of similar levels of probiotics directly to the hydroponics compartment.
In addition to standard application probiotics, there are a variety of innovative techniques for biocontrol that may in the future become increasingly valuable for reducing the presence and proliferation of harmful microbes. In one recent study, bacterial isolates were selected from an established aquaponics system based on their ability to exert inhibitory effects on both fish and plant fungal pathogens. The goal was to culture these isolates as inocula that could subsequently act as biological controls for diseases within that aquaponics system (Sirakov et al. 2016). For instance, Sirakov et al. demonstrated that a Pseudomonas sp. that they isolated was effective as a biocontrol for the pathogenic fungi Saprolegnia parasitica of fish and Pythium ultimum of plants. The researchers also reported in vitro inhibition of a variety of other bacterial isolates from the different aquaponics compartments, but without testing their in vivo effects. The potential for using such isolates as biological controls is not new, but applications of NGS techniques can now reveal more about interactions of such isolates with each other and with potential pathogens, thus making it possible to optimize the effectiveness of delivery. Use of other 'omics' techniques could help reveal overall community structure and associated metabolic functions, and begin elucidating which organisms and functions are most beneficial. In future, such techniques might allow selection for 'helper strains' within microbial communities, or the identification of exudates that have anti-microbial effects (Massart et al. 2015).