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A major food safety concern with aquaponics is the cultivation of vegetable crops in water containing fish excreta and other organic matter, including fish and plant particulate residuals. Pathogenic bacteria can enter the system via water, animal faeces, plant seedlings, tools or humans. The major risk from warm-blooded animals is the introduction of Escherichia coli, while birds can carry Salmonella spp. (FAO 2014). E. coli O157:H7, Salmonella spp., and Listeria monocytogenes are the main foodborne pathogens that can be found in recirculating water system and which have been shown to survive in these conditions. Faecal contamination of aquaponic systems has mostly been detected when a poor quality water source was used or when faecal inputs from domestic animals or wildlife were possible (Fox et al. 2012). Despite previously published reports indicating internalization2 of human foodborne pathogens such as E. coli O157:H7 and Salmonella in vegetables, the study done by Moriarty et al. (2018) did not provide evidence for bacterial internalization. Internalization may be a phenomenon only seen in specific circumstances such as very high bacterial concentration and plant injury (especially when roots are damaged) that increase the probability for the occurrence of bacterial internalization.

2 Bacteria enter through natural openings in the plant surface and/or through sites of biological or physical damage, or bacteria are pulled into the internal tissues along with water ([Deering et al. 2012)](

In addition, fish from non-reliable sources can introduce foodborne viruses and disease (e.g. Vibrio spp.) that are not commonly associated with fruits and vegetables (Fox et al. 2012). Parasites such as Cryptosporidium and Girdia lamblia can also be introduced in the water itself, so the source of water used in aquaponics is very important for the safety of the food produce (Ljubojević et al. 2017). The main route of bacterial contamination of produce is from water depositing bacteria on the surface.

Conditions in aquaponic systems (warm, wet, low-oxygen environments with high organic material) favour foodborne pathogens that are also hazardous to fish and plants. The presence of sediment appears to be one of the primary factors influencing pathogen persistence (Aquaponics Association 2015). Therefore, aquaponic producers should not allow these conditions to develop in their systems for technological as well as for food safety reasons. Studies with foodborne pathogens in fish suggest that if exposed, fish can carry foodborne pathogens for a short period. When they are in a tank with good aeration and solids removal, pathogen survival in fish is very low. When fish are in a tank with sediment accumulation and poor aeration, however, pathogens persist in the fish much longer and at higher levels (Aquaponics Association 2015).

Most fish do not contain significant levels of human disease-causing hazards. If fish are thermally treated before consumption, any contamination is usually quickly eliminated (Lee et al. 2015). However, special care is needed if the fish will be eaten raw (e.g. sushi, carpaccio, or ceviche). Leafy greens and other raw vegetables are also high risk products: 13.9% of the foodborne outbreaks in the EU are caused by fruits and vegetables (EFSA & ECDC 2017). Leafy greens are a high-risk crop because they:

  • are frequently eaten raw

  • grow close to the surface

  • have a very high surface area for their mass

Leafy greens tend to deliver a much higher dose of pathogens per serving than any other type of produce if they are contaminated (Aquaponics Association 2015). Herbs, like basil or mint, tend to have a lower risk because smaller quantities of these plants are eaten compared to lettuce (Lee et al. 2015). A study by Barnhart et al. (2015) demonstrated no significant difference between contamination of unpacked smooth-textured leafy greens at grocery stores grown using aquaponics, hydroponics, and soil cultivation.

Chemical and toxin contamination is a concern as well. However, the controlled environment in aquaponic facilities may make these hazards less likely compared to other forms of agricultural production. The aquaponic producer has to be aware that any chemical product used with plants could affect the fish, and any product used with the fish could affect the plants and consumers. The potential public health consequences of physical hazard contamination in primary production appear to be relatively uncommon.

To eliminate or reduce the risks to acceptable levels, aquaponic producers should implement preventive measures such as GAP (Good Agricultural Practice) and GHP (Good Hygiene Practice). A hazard analysis and critical control point (HACCP) systemic preventive approach should also be implemented as an upgrade of GAP and GHP (Figure 1).


Figure 1: GAP and GHP as important prerequisites of the HACCP, constituting ¾ and ¼ respectively of preventive approach to food safety

Copyright © Partners of the [email protected] Project. [email protected] is an Erasmus+ Strategic Partnership in Higher Education (2017-2020) led by the University of Greenwich, in collaboration with the Zurich University of Applied Sciences (Switzerland), the Technical University of Madrid (Spain), the University of Ljubljana and the Biotechnical Centre Naklo (Slovenia).

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