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Nitrifying and mineralizing bacteria are useful to aquaponic systems, but some other types of bacteria are harmful. One of these harmful groups of bacteria is the sulphate- reducing group. These bacteria are found in anaerobic conditions (no oxygen), where they obtain energy through a redox reaction using sulphur. The problem is that this process produces hydrogen sulphide (H2S), which is extremely toxic to fish. These bacteria are common, found in lakes, saltmarshes and estuaries around the world, and are part of the natural sulphur cycle. These bacteria are responsible for the odour of rotten eggs, and also the grey-black colour of sediments. The problem in aquaponics is when solid wastes accumulate at a faster pace than the heterotrophic bacteria and associated community can effectively process and mineralize them, which can in turn lead to anoxic festering conditions that support these sulphate-reducing bacteria. In high fish density systems, the fish produce so much solid waste that the mechanical filters cannot be cleaned fast enough, which encourages these bacteria to multiply and produce their noxious metabolites. Large aquaponic systems often contain a degassing tank where the hydrogen sulphide can be released safely back to the atmosphere. Degassing is unnecessary in small-scale systems. However, even in small-scale systems, if a foul odor is detected, reminiscent of rotten eggs or raw sewage, it is necessary to take appropriate management action. These bacteria only grow in anoxic conditions, so to prevent them, be sure to supply adequate aeration and increase mechanical filtration to prevent sludge accumulation.
A second group of unwanted bacteria are those responsible for denitrification. These bacteria also live in anaerobic conditions. They convert nitrate, which is the coveted fertilizer for plants, back into atmospheric nitrogen that is unavailable for plants. These bacteria are also common throughout the world, and are important in their own right (see Figure 2.4). However, within aquaponic systems, these bacteria can decrease efficiency by effectively removing the nitrogen fertilizer. This is often a problem with large DWC beds that are inadequately oxygenated. A problem could be suspected when plants show signs of nitrogen deficiencies despite the system being in balance, and when there is a very low nitrate concentration in the water. Investigate possible areas within the DWC canals that are not circulating properly, and further increase aeration with air stones.
Some large aquaponic systems deliberately use denitrification. The feed rate ratio balances the nutrients for the plants but usually results in high nitrate levels. This nitrate can be diluted during water exchanges (suggested in this publication for small-scale systems). Alternatively, controlled denitrification can be encouraged in the mechanical filter. This technique requires careful attention and off-gassing, and is not recommended for small-systems. More information can be found in the section on Further Reading.
A final group of unwanted bacteria are those that cause diseases in plants, fish and humans. These diseases are treated separately in other parts of this publication, with Chapters 6 and 7 discussing plant and fish disease, respectively, and Section 8.6 discussing human safety. Overall, it is important that there are good agricultural practices (GAPs) that mitigate and minimize the risk of bacterial diseases within aquaponic systems. Prevent pathogens from entering the system by: ensuring good worker hygiene; preventing rodents from defecating in the system; keeping wild mammals (and dogs and cats) away from aquaponic systems; avoiding using water that is contaminated; and being aware that any live feed can be a vector for introducing alien micro-organisms into the system. It is especially important not to use rainwater collection from roofs with bird faeces unless the water is treated first. The major risk from warm-blooded animals is the introduction of Escherichia coli, and birds often carry Salmonella spp.; dangerous bacteria can enter the system with animal faeces. Second, after prevention, never let the aquaponic water come into contact with the leaves of the plants. This prevents many plant diseases as well as potential contamination of fish water to human produce, especially if the produce is to be eaten raw. Always wash vegetables before consumption, aquaponic or otherwise. Generally, common sense and cleanliness are the best guards against diseases from aquaponics. Additional sources for aquaponic food safety are provided throughout this publication and in the section on Further Reading.
Source: Food and Agriculture Organization of the United Nations, 2014, Christopher Somerville, Moti Cohen, Edoardo Pantanella, Austin Stankus and Alessandro Lovatelli, Small-scale aquaponic food production, http://www.fao.org/3/a-i4021e.pdf. Reproduced with permission.