Can Alternative Growing Methods Reduce the Risk of E. coli?

Learn more about aquaponics and hydroponics, and the pros and cons of these food production methods.
Can Alternative Growing Methods Reduce the Risk of E. coli?
June 4, 2020

Every year, approximately four million cases of food-borne illness occur in Australia. These food-borne illnesses are caused by microorganisms that contaminate food and when the contaminated food is eaten, it can make people sick. These pathogens can be bacteria, parasites or viruses and they are often transmitted to food through improper food handling. One bacteria in particular — E. coli — has lead to several serious food-borne illness outbreaks in recent years. This has led to questions about how to reduce the risk of contamination with this bacteria in the food system.

What is E. coli and why is it so dangerous?

Escherichia coli (E. coli) is a large group of bacteria that is found in the intestines of people and animals, as well as the environment such as in soil and water. Some E. coli are harmless and are actually good for a healthy human intestinal tract. However, some types of E. coli are dangerous (called pathogenic E. coli) and can cause symptoms such as diarrhoea or even more serious symptoms like hemorrhagic diarrhoea, kidney failure and Thrombotic thrombocytopenic purpura (blood disorder). E. coli can be particularly threatening for those in high-risk groups, such as pregnant women, children, the elderly or people with compromised immune systems.

Pathogenic E. coli can be transmitted through contaminated water, ground beef, unpasteurised dairy products and leafy green produce. When it comes to produce, the exposure often comes as a result from the produce been grown through traditional farming; the produce is contaminated with E. coli through the soil or through a contaminated water source. While safety measure are put in place at farming operations to prevent E. coli contamination, there are many incidences of this bacteria causing food-borne illnesses in Australia and worldwide. Some companies are advocating for alternative methods for growing fresh produce and indicate that these methods prevent E. coli infection in these foods. This has raised questions about whether there truly are safer ways to grow produce that eliminate the risk of E. coli infection.

Is aquaponics or hydroponics a safer option?

A recent study by Purdue University looked into whether aquaponic or hydroponic systems could reduce the risk of E. coli while growing produce. The study looked at a few different pathogens, including E. coli O157:H7, which is one of the more deadly types of the bacteria and commonly associated with food-borne illness outbreaks. It found that there are still risks of E. coli contamination in these systems, despite a growing amount of companies switching to these methods. In contrast, there are many people who are advocating for aquaponics or hydroponics as a safe and effective alternative to growing fresh produce in the ground. Here, we provide the advantages and disadvantages of both systems in order to understand just how effective these systems might be in reducing the risk of pathogenic E. coli infections.


Aquaponics is a type of indoor farming that involves growing produce and raising fish in tanks at the same time. In this system, the fish and the growing produce work in symbiosis: the water the fish live in becomes rich with nutrients which is then used to fertilize the produce, while the produce purifies the water for the fish.

The pros of this system is that it allows for a controlled environment for growing produce. Growers are able to control the water source and the fertiliser is considered all-natural as it comes from fish excrement. Other benefits include the fact that this system uses no soil, which eliminates the risk of contaminating the produce with E. coli from the soil. Advocates for these systems also state that aquaponics help reduce contamination from pathogens as it allows for produce to be grown locally, rather than being imported from other countries with less stringent food safety protocols.

Despite the many advantages to an aquaponics system, the study from Purdue University does bring up some interesting factors. In the study, three aquaponic systems were built in a greenhouse in West Lafayette and were used to grow lettuce, basil and tomatoes. The study was conducted between December 2017 to February 2018; upon the conclusion of the experiment, samples were taken of the roots and the leaves of each plant and then analyzed. Water samples were also taken. The results from the testing showed that there was still a presence of E. coli in the feces from the fish as well as the water.

What is important to note from the study is that researchers were able to verify that the presence of E. coli in the water did not lead to E. coli being detectable in the produce. E. coli was not detectable in the roots or leaves of the lettuce, basil or tomatoes, which means that in this case, the biggest risk of E. coli contamination would come from the splashing of the infected water onto the produce.


Hydroponics is also a type of indoor farming that grows produce without the need for soil. The produce is provided with water and nutrients in order to grow. There are two types of hydroponic techniques: the Nutrient Film Technique and the Neutral Medium Technique. Nutrient Film involves recirculating a water and nutrient mix over the bare root of a plant in a gully. Neutral Medium involves growing produce in a neutral medium, while water supply is provided to the plant through a drip irrigation system.

The benefits of hydroponic systems are similar to that of aquaponic systems. Hydroponics uses less water than traditional farming, allows for faster growing cycles and provides the ability to grow produce year-round. Also, the ability to control the water source and the growing environment, in combination with the fact that no soil is used, means that E. coli contamination can be reduced. 

Purdue University conducted the same testing for hydroponic systems as it did with aquaponic systems. Three hydroponic systems were built in the greenhouse and were used to grow the same types of produce: lettuce, basil and tomatoes. The results from the hydroponic systems were the same as the aquaponic systems. E. coli was detected in the water of the hydroponic systems, however, the researchers indicate that there are a variety of possible reasons for the contamination. The bacteria could have been introduced to the water during set-up, handling or due to incomplete sanitation of all the parts.

Food handling is still essential

By looking at the advantages and disadvantages of these alternative growing systems, it is evident that there is no ‘one-size-fits-all’ solution to reducing the risk of E. coli in the food chain. While traditional farming in open fields has its risks, it also is the most widely used method for producing large swaths of fresh fruits and vegetables. Aquaponics and hydroponics bring a modern and streamlined twist to produce production, but research points to ways that E. coli can still pose contamination risks in these systems.

What is evidently clear is that no matter the method, humans play an essential role in preventing — or increasing — the risk of E. coli contamination in food production. For example, the results of the Purdue University study indicate that E. coli could have been transmitted through human activities such as touching the water, feeding the fish (in aquaponics), sample taking or other methods of cross-contamination such as work shoes. As mentioned above, the study also indicates that proper cleaning methods and sanitation of aquaponic and hydroponic systems is essential to reducing E. coli contamination, thus pointing to the need for proper safety protocols.

Overall, the role humans play in food safety is immense. While steps can be taken to reduce E. coli contamination — such as through using different food production systems — these efforts can be thwarted by improper food safety protocols and food handling procedures. Maintaining food safety and reducing food-borne illness is complex and requires stringent protocols, no matter the method of food production.

Contact the Australian Institute of Food Safety for more information about online food safety training.