Agriculture News

April 6, 2020

Risk of E. coli in hydroponic and aquaponic systems may be greater than once thought

aqua-kim Hye-Ji Kim (left), pictured with graduate student Seunghyun Choi, found the presence of E. coli bacteria in aquaponic and hydroponic growing systems, suggesting the bacteria could reach produce consumers. (Agricultural Communication photo/Tom Campbell) Download image

WEST LAFAYETTE, Ind. – A spate of foodborne illnesses in leafy greens and other produce in recent years has sickened consumers and disrupted growers and supply chains. It’s been thought that hydroponic and aquaponic systems could reduce these issues since there is little opportunity for pathogens like E. coli to contaminate the edible parts of plants.

A Purdue University study, however, has found the presence of Shiga toxin-producing E. coli (STEC) – the same bacteria that have made consumers of several produce products ill – in hydroponic and aquaponic growing systems. Hye-Ji Kim, an assistant professor of horticulture and the study’s corresponding author, said the findings suggest growers using these systems should be careful in handling and harvesting to avoid contamination.

“Many people think that there is no chance that E. coli could be present in these systems and that risk of contamination is low,” said Kim, whose results were published in the journal Horticulturae. “Our findings suggest there is some potential for food safety concerns. We’re not saying that these foods are unsafe, but that it’s important to handle these plants properly and carefully.”

aqua-roots Aquaponic and hydroponic growing systems are thought to have little risk of containing bacteria that can sicken produce consumers. After finding E. coli in both types of systems, Hye-Ji Kim suggests growers to use caution to not introduce the bacteria to their operations. (Agricultural Communication photo/Tom Campbell) Download image

The E. coli outbreaks that have occurred in recent years tend to happen in leafy greens and other vegetables grown in irrigated fields. Potential sources could be from E. coli in manure or groundwater that reaches the edible portions of plants, or from those contaminants getting to plants after root damage by wild animals.

Proponents of hydroponic and aquaponic systems suggest their growing methods would reduce or eliminate any risk of contamination. Both soilless systems, hydroponic plants are grown in water and chemical fertilizers or nutrient solutions, and aquaponic systems include the raising of fish, with fish wastewater utilized as water and nutrient source for the plants.

aqua-petri The fish used in aquaponic growing systems may introduce E. coli to water and potentially produce crops, and accidental contamination is possible in hydroponic systems. Hye-Ji Kim and Yi-Ju Wang (pictured) suggest growers take careful steps to ensure that these bacteria don’t reach plants that could sicken consumers. (Agricultural Communication photo/Tom Campbell) Download image

Kim, Yi-Ju Wang, a graduate student in Kim’s lab, and Amanda Deering, a Purdue clinical assistant professor of food science, set up both hydroponic and aquaponic systems for growing lettuce, tomatoes and basil for about two months. The scientists found E. coli in both systems at the time of harvest.

In the aquaponic system, the authors believe the E. coli was introduced by the fish. The bacteria was found in the water, on plant roots and in fish feces.

“Our separate aquaculture system confirmed that fish feces were a major source of contamination with STEC in the aquaponic system,” the authors wrote. “These results indicate that introducing contaminated fish can be a source of foodborne pathogens in aquaponics.”

The presence of E. coli in the hydroponic system, in which fish were not used, suggests that the bacteria was introduced accidentally. Kim believes it could have splashed from a nearby aquaponic system or have been introduced by a visitor who brought it in from outside the greenhouse. Either way, the presence in the system suggests that accidental contamination is a real risk.

E. coli was also found on plant roots in both systems, but the bacteria did not internalize in the plants. In other words, even with the bacteria present in water and on the roots, the edible portions of the plants were still safe to consume.

The key, Kim says, is proper handling to ensure that E. coli or other pathogens don’t make it to the edible parts of plants. Damaged roots would allow bacteria into the plants, potentially making it to edible portions internally. And splashing of water during growing or harvesting could introduce bacteria to the edible portions of the plants.

“The best way to manage these issues is to not touch roots or water throughout production cycles. If you do, you should thoroughly wash your hands before touching the edible parts of the plants,” Kim said. “Proper sanitization of equipment is also important. And acquiring fish that do not contain E. coli would also be beneficial.”

Kim’s lab is continuing to investigate food safety risks in hydroponic and aquaponic systems. Projects include damaging roots and simulating splashes to understand how much contamination can occur.

The Indiana State Department of Agriculture, the U.S. Department of Agriculture’s National Institute of Food and Agriculture, and the Purdue University College of Agriculture funded this research.

Writer: Brian Wallheimer, 765-532-0233,

Source: Hye-Ji Kim, 765-496-0122, 

Note to Journalists: A portrait of one scientist, a picture of another scientist in the lab and a picture of a growing system are available for journalists to use via Google Drive.


The Occurrence of Shiga Toxin-Producing E. coli in Aquaponic and Hydroponic Systems

Yi-Ju Wang1, Amanda J. Deering2 and Hye-Ji Kim1

  1. Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN
  2. Department of Food Science, Purdue University, West Lafayette, IN

Food safety concerns have been raised over vegetables and herbs grown in aquaponics and hydroponics due to the reuse of wastewater and spent nutrient solutions. This study was conducted to determine the occurrence of foodborne pathogens in greenhouse-based aquaponic and hydroponic systems. Fish feces, recirculating water, roots, and the edible portions of lettuce, basil, and tomato were collected at harvest, and microbiological analyses were conducted for the bacterial pathogens Shiga toxin-producing Escherichia coli (STEC), Listeria monocytogenes, and Salmonella spp. Enrichments and selective media were used for the isolation, and presumptive positive colonies were confirmed by PCR. STEC was found in fish feces, in the water of both systems, and on the surface of the roots of lettuce, basil, and tomato regardless of the system. However, contaminated water did not lead to the internalization of STEC into the roots, leaves, and/or fruit of the plants. Meanwhile, L. monocytogenes and Salmonella spp. were not present in any samples examined. Our results demonstrated that there are potential food safety hazards for fresh produce grown in aquaponic and hydroponic production systems.

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