Food Safety and E. coli in Aquaponic and Hydroponic Systems

This document is The Aquaponics Association’s response to a recent publication on E. coli in Aquaponic and Hydroponic systems.

PDF Version: Food Safety and E. Coli in Aquaponic and Hydroponic Systems

April 27, 2020

By Tawnya Sawyer; Nick Savidov, PhD; George Pate; and Marc Laberge 

Overview of the Study

On April 6, 2020, Purdue Agriculture News published a story about a study related to the contamination risk of Shiga toxin-producing E. coli (STEC) in Aquaponic and Hydroponic production. The full study was published in MDPI Journal Horticulturae in January 2020.

Researchers conducted the study from December 2017 through February 2018. The Study consisted of side-by-side aquaponic and hydroponic systems in a controlled environment lab growing lettuce, basil, and tomatoes with tilapia. The purpose of the study was to identify the food safety risks associated with soilless systems. The study indicates that both the aquaponic and hydroponic systems contained Shiga toxin-producing E. coli (STEC) at the time of sampling. It did not find the presence of Listeria spp., or Salmonella spp. 

The authors contend that the aquaponic system and specifically the fish feces were likely the sources of E. coli. However, we believe that there is no evidence to prove that this was the actual source of contamination since the authors admit traceback was not performed, and there were several other possible introductions.

The pathogen was present in the water and on the root system of the plants. The researchers did not detect it in the edible portion of the plants. However, if the water is positive for a contaminant, and it accidentally splashes onto the edible portion of the crop throughout its life, or during harvest, this could still result in a food safety concern.

History of E. coli in Soil-less growing systems 

Until now, researchers have only discovered environmental E. coli in soilless growing systems. It is essential to note that there are hundreds of types of non-fecal coliform bacteria in the air, water, soil, as well as the fecal coliform bacteria represented mostly by E.coli in the waste of all mammals, humans, and some birds. A vast majority of these coliforms are perfectly harmless.

The E. coli found in this Study — Shiga toxin-producing O157:H7 — historically has been associated with warm-blooded mammals, more specifically bovine fed corn in feedlots (Lim JY et al. 2007), as well as swine and turkeys. Further research must be performed to prove that cold-blooded, non-mammal aquatic species such as tilapia can harbor this strain of pathogenic E. coli. A wide group of studies, university professors and industry professionals currently refute the possibility that tilapia can harbor this strain. The lack of evidence detailing the ability of aquatic animals to harbor E. coli makes the fish contaminated with this specific strain of bacteria very rare and suspect.

Many foodborne illnesses from fresh produce such as romaine lettuces, green onions, herbs, and sprouts, are traced back to the soil; the irrigation water used in these crops (Solomon et al. 2002); the seed stock; or poor sanitation in handling facilities.

There are a wide variety of community and commercial aquaponic and hydroponic growing facilities that routinely perform pathogen testing and have not identified this pathogen present. If it was present, traceback procedures would be followed to identify and remove the source, as well as any necessary food safety precautions and recalls performed.

Our Position

The Aquaponic Association and its members agree that food safety and proper handling practices are critical to commercializing our industry and the safety of our customers. One thing that the study points out is that a contaminant can occur in a soilless system, which creates a potential food safety concern. We agree on this; however, we have numerous concerns with the procedures and statements made in the publication.

We have reached out to the professional investigator on this study Hye-Ji Kim to get answers to essential questions that the study publication does not adequately address. There are significant gaps and questions with the study.

 Concerns About the Study Findings and Publication 

Lack of Traceability

The study group is unsure how the pathogen was introduced into the two systems. They admit that no traceback was performed to identify the source of contamination. They speculate both in the study and in their email response that this pathogen was:

1) Accidentally introduced

2) That it is from the fish feces in the aquaponics system that splashed into the hydroponic system through the open top of the fish tank during feeding,

3) that it was from contaminated fish stock (which were provided by the Purdue Animal Sciences Research and Education Center)

4) That it was human contamination from visitors or operator handling issues.

A traceback was not conducted as it was not within the scope of the study (Kim personal communications). We disagree; the discovery of O157:H7 strain in the university greenhouse with the suspicion of fish being contaminated should have resulted in immediate action in order to track down the source of contamination and prevent infection of the university students and staff. Outside of a University setting, traceback would have been mandatory in a commercial facility. It is questionable that the University did not perform these procedures because it was “out of the scope of the study”.

Questioning Fish Feces as the Source of Contamination

Blaming fish feces as the contaminating source seems incredibly misleading when so many other options exist, and no traceback proved that as the source. The contents of the fish intestines were tested for the presence of E. coli, and none was found (Kim personal communications). It seems that if the fish does not have STEC E. coli inside its gut, then it is more likely the fish feces being positive would be related to the contaminated water that the feces was floating in.

In wild fish species, levels of E. coli appear to follow trends similar to ambient water and sediment concentrations; as concentrations in their environments rise, so do concentrations within the fish (Guillen et al., 2010).

Furthermore, it seems very suspect that a two-month-old system in a controlled environment lab could have been so quickly contaminated. It is well-known that E.coli cannot survive in a biologically-active environment, such as an anaerobic digester or aquaponic system (T.Gao et al., 2011). E. coli are outcompeted by other microorganisms, which adapted to survive in the environment outside animal guts much better than E. coli. Thus, E. coli O157:H7, which is specially adapted to live in cattle guts, will inevitably be replaced by other microorganisms.

As for the hydroponic system showing positive results, this also seems suspect if the nutrients were synthetic, as there would be very little chance for the E. coli to survive without a biological host or continuous contamination source being present. An accidental exposure in the hydroponic system would have become diluted over time, or the pathogen died off to the point that they would have been undetectable. The fact is the organic matter in hydroponics is virtually absent and, therefore, provides a poor environment for E. coli growth and propagation (Dankwa, 2019). Therefore. one would need a continuous source, not an accidental one (like splashing), in order to maintain the E. coli population in hydroponics.

Since both systems were contaminated, we suggest that there is a more likely common pathogen source that the researchers did not correctly identify and remove. The source of contamination could be from source water, filtering system, repurposed equipment, airborne in the greenhouse or HVAC system, human vector, lab equipment, the seed stock, nutrients, or other inputs.

The Purdue Animal Research and Education Center, where the researchers sourced the fish, is an operation that also has swine, cattle, and poultry production. Research suggests that pathogenic E. coli can travel 180 m through airborne exposure (Berry et al., 2015). Airborne exposure poses a more significant risk to controlled environments as pathogens can persist in the HVAC system (Riggio et al., 2019). STEC has the potential to live in dust particles for up to 42 weeks, which can act as a possible vector of contamination if there is a continuous source. Therefore, even a slight possibility of the pathogenic Shiga-producing O157:H7 strain of E. coli transfer from the Animal Research and Education Center resulting in the uncontrolled cross-contamination of other research labs and facilities certified below Biosafety level 2 not designed to work with the pathogenic bacteria would raise a serious concern about the existing safety practices (Boston University).

Lack of 3rd Party or Peer University Test Verification

It has also been recognized that there is a high frequency of false-positive signals in a real-time PCR-based “Plus/Minus” assay (Nowrouzian FL, et al., 2009). Hence the possibility that the PCR verification method may have resulted in inaccurate results. The pathogen was not verified by a 3rd party lab to be actual STEC E.coli O157:H7. Only positive or negative results were obtained for this study.

We recommend several other universities and third-party labs to run samples and validate the results. However, no samples have been provided, which may be impossible to obtain based on the study being conducted in early 2018. Without this verification, there are questions about the possibility of false-positives due to the presence of environmental E.coli, fecal coliforms, or a wide variety of other bacteria commonly found in nutrient-rich environments (Konstantinidis et al., 2011).

Impact of Sterilization

The study conclusion suggests that sterilization efforts are critical. “Our results indicated that contamination with bacterial pathogens could likely be reduced in aquaponic and hydroponic systems if the entire systems were thoroughly sanitized before each use and pathogen-free fish were used for the operation.” This statement is inaccurate and could be detrimental to proper food safety practices. As the microflora of the system develops, it creates an environment that can suppress phytopathogens (Bartelme et al., 2018) and other zoonotic pathogens as a result of antibiotic compounds released by beneficial bacteria (Compant et al., 2005). In Recirculating Aquaculture Systems (RAS), some microbial communities take over 15 years to develop (Bartelme et al., 2017), resulting in greater stability over time.

Many papers support this hypothesis with regards to probiotics in wastewater treatment, aquaculture, and hydroponics. Microbial community analysis also depicts a greater microbial diversity in aquaponics over decoupled or aquaculture systems (Eck et al., 2019), indicating a more significant potential for suppression of pathogens in coupled aquaponic systems over RAS or decoupled aquaponic system. No pathogens were discovered in a mature coupled aquaponics system during 18 years of continuous research in Canada since 2002 (Savidov, personal communications).

These findings support the argument that more biologically mature systems are less likely to develop pathogens and that periodic sanitation should not be done outside of initial start-up unless a zoonotic pathogen (Henderson 2008), is detected. If a pathogen is found, producers should follow proper sanitation and recall procedures.


Overall, this and other research into food safety are ongoing, and new information becomes available continuously to help shape the best practices for proper greenhouse management. As the Aquaponic Association, we hope to provide the most accurate and reliable resources for this purpose. At the same time, we hope to reduce the possibility of studies like this creating unnecessary fear, or unsubstantiated claims that could harm the growth of the aquaponic (and hydroponic) industry. When a document like this is published, it will be quoted by the media, and referenced in other studies as if it is an absolute. Other research must be performed to validate or negate this study’s outcomes.

Our findings conclude that while there is a low chance of the persistence of a pathogen in properly designed aquaponic and hydroponic systems, there is still a potential concern. No agricultural system is immune to this. Compared to soil production, soil-less crops grown in a controlled environment are far less likely to become infected pathogens from mammals, birds and other creatures which are difficult to prevent in field crop production. Human contamination or poor handling practices are of significant concern (Pattillo et al., 2015). The best way to avoid risk is to adhere to food safety guidelines set forth by the USDA, GlobalGAPs, the Aquaponic Association, and other accredited organizations.



Bartelme, R.P., McLellan, S.L., Newton, R.J., 2017. Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira. Front. Microbiol. 8.

Bartelme, R.P., Oyserman, B.O., Blom, J.E., Sepulveda-Villet, O.J., Newton, R.J., 2018. Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics. Front. Microbiol. 9, 8.

Berry, E.D., Wells, J.E., Bono, J.L., Woodbury, B.L., Kalchayanand, N., Norman, K.N., Suslow, T.V., López-Velasco, G., Millner, P.D., 2015. Effect of Proximity to a Cattle Feedlot on Escherichia coli O157:H7 Contamination of Leafy Greens and Evaluation of the Potential for Airborne Transmission. Appl. Environ. Microbiol. 81, 1101–1110.

Compant, S., Duffy, B., Nowak, J., Clément, C., Barka, E.A., 2005. Use of Plant Growth-Promoting Bacteria for Biocontrol of Plant Diseases: Principles, Mechanisms of Action, and Future Prospects. Appl. Environ. Microbiol. 71, 4951–4959.

Dankwa, A.S., 2019. Safety  Assessment of Hydroponic Closed System 127.

Eck, M., Sare, A., Massart, S., Schmautz, Z., Junge, R., Smits, T., Jijakli, M., 2019. Exploring Bacterial Communities in Aquaponic Systems. Water 11, 260.

Guillen, Wrast, Environmental Institute of Houston, 2010, Fishes as Sources of E. coli Bacteria in Warm Water Streams,

Henderson, H., 2008. Direct and indirect zoonotic transmission of Shiga toxin–producing Escherichia coli. J. Am. Vet. Med. Assoc. 232, 848–859.

Konstantinidis, Chengwei Luo, 2011. Georgia Tech Institute, Environmental E. coli: New way to classify E. coli bacteria and test for fecal contamination,

Lim JY et al., Escherichia coli O157:H7 colonization at the rectoanal junction of long-duration culture-positive cattle. Appl Environ Microbiol. 2007;73:1380–1382

Boston University Agent Sheet E.coli EHEC or STEC) (

Nowrouzian FL1, Adlerberth I, Wold AE., 2009 High frequency of false-positive signals in a real-time PCR-based “Plus/Minus” assay.

Riggio, G., Jones, S., Gibson, K., 2019. Risk of Human Pathogen Internalization in Leafy Vegetables During Lab-Scale Hydroponic Cultivation. Horticulturae 5, 25.

Solomon et al., Effect of Irrigation Method on Transmission to and Persistence

of Escherichia coli O157:H7 on Lettuce Journal of Food Protection, Vol. 65, No. 4, 2002, Pages 673–676

  1. Gao*, T. Haine,  A. Chen,  Y. Tong, and X. Li, 2011, 7 logs of toxic strain of E coli  were removed by mesophilic AD process while ~ 5 logs increase of the strain were seen in water control with the same condition for 7 days

Pattillo*, Shaw, Currey, Xie, Rosentrater, 2015, Aquaponics Food Safety and Human Health,


2019 Aquaponics Food Safety Statement

The Aquaponics Association presents the 2019 Aquaponics Food Safety Statement, signed by over 130 organizations, including 98 from the U.S. This statement explains the food safety credentials of produce grown in aquaponic systems.

PDF version: 2019 Aquaponics Food Safety Statement

December 9, 2019
Aquaponics Food Safety Statement

Established Science Confirms Aquaponic Fish and Produce are Food Safe

Aquaponics is a food production method integrating fish and plants in a closed, soil-less system. This symbiotic relationship mimics the biological cycles found in nature. Aquaponics has been used as a farming technique for thousands of years and is now seeing large-scale viability to feed a growing global population.

Benefits of aquaponics include dramatically less water use; no toxic chemical fertilizers or pesticides; no agriculture discharge to air, water or soil; and less food miles when systems are located near consumers where there is no arable soil.

Aquaponics has consistently proven to be a safe method to grow fresh, healthy fish, fruits, and vegetables in any environment. Governments and food safety certifiers must utilize the most current, accurate information to make food safety decisions about aquaponics at this time when our food systems adapt to a growing population and environmental concerns.

Food Safety Certification for Aquaponics

For years, commercial aquaponic farms have obtained food safety certification from certifying bodies such as Global GAP, USDA Harmonized GAP, Primus GFS, and the SQF Food Safety Program. Many aquaponic farms are also certified USDA Organic. These certifying bodies have found aquaponics to be a food safe method for fish, fruits, and vegetables. As far back as 2003, researchers found aquaponic fish and produce to be consistently food safe (Rakocy, 2003; Chalmers, 2004).  Aquaponic fish and produce continue to be sold commercially across North America following all appropriate food safety guidelines.

Recent Certification Changes Based on Unfounded Concerns

Recently, Canada GAP, a food safety certifier, announced that it will phase out certification of aquaponic operations in 2020, citing concerns about the potential for leafy greens to uptake contaminants found in aquaponic water.

Correspondence with Canada GAP leadership revealed that the decision to revoke aquaponics certification eligibility was based on research and literature surveys related to the uptake of pharmaceutical and pathogenic contaminants in hydroponic systems. However, these concerns are unfounded based on the established evidence.

First, the Canada GAP decision assumes that aquaponic growers use pharmaceuticals to treat fish, and that these pharmaceuticals would be taken up by plants causing a food safety risk.

In fact, pharmaceuticals are not compatible with aquaponics. Aquaponics represents an ecosystem heavily dependent on a healthy microorganism community (Rinehart, 2019; Aquaponics Association, 2018). The pharmaceuticals and antibiotics referenced by Canada GAP would damage the beneficial microorganisms required for aquaponics to function properly.

Second, the CanadaGAP decision misrepresents the risk of pathogenic contamination. Aquaponic produce – like all produce – is not immune to pathogenic contamination. However, aquaponics is in fact one of the safest agriculture methods against pathogenic risk. Most pathogenic contamination in our modern agriculture system stems from bird droppings, animal infestation, and agriculture ditch or contaminated water sources. In contrast, commercial aquaponic systems are “closed-loop” and usually operated in controlled environments like greenhouses. Almost all operations use filtered municipal or well water and monitor everything that enters and leaves the system.

Aquaponics and Food Safety

If practiced appropriately, aquaponics can be one of the safest methods of food production. The healthy microbes required for aquaponics serve as biological control agents against pathogenic bacteria. (Fox, 2012) The healthy biological activity of an aquaponic system competitively inhibits human pathogens, making their chances for survival minimal. This is, in effect, nature’s immune system working to keep our food safe, rather than synthetic chemicals.

The Government of Alberta, Canada ran extensive food safety tests in aquaponics from 2002 to 2010 at the Crop Diversification Centre South (CDC South) and observed no human pathogenic contamination during this entire eight-year period (Savidov, 2019, Results available upon request). As a result of this study, the pilot-scale aquaponic operation at CDC South was certified as a food safe operation in compliance with Canada GAP standards in May 2011 (GFTC OFFS Certification, May 26, 2011). Similar studies conducted by University of Hawaii in 2012 in a commercial aquaponic farm revealed the same results. (Tamaru, 2012)

Current aquaponic farms must be able to continuously prove their food safety. The U.S. Food Safety Modernization Act requires farms to be able to demonstrate appropriate mitigation of potential sources of pathogenic contamination as well as water testing that validates waters shared with plants are free from contamination by zoonotic organisms. So, if there is a food safety concern in aquaponics, food safety certifiers will find and document it.


The recent certification decision from Canada GAP has already set back commercial aquaponic operations in Canada and has the potential to influence other food safety certifiers or create unfounded consumer concerns. At a time when we need more sustainable methods to grow our food, it is essential to work on greater commercial-government collaboration and scientific validation to ensure fact-based food safety standards.

In order to expand the benefits of aquaponics, we need a vibrant commercial sector. And for commercial aquaponics to succeed, we need reliable food safety certification standards based on established science.

Consumers can feel secure knowing that when they purchase aquaponic fish and produce, they are getting fresh food grown in one of the safest, most sustainable methods possible.


The Aquaponics Association, along with the undersigned entities


Gardens on Air – A Local Farm, Inc.
Southern Organics

AONE Aquaponics
Fresh Farm Aquaponics
Go Fish Farm
SchoolGrown Aquaponics
Seouchae Natural Farming
Shwava, Inc.
University of California, Davis

The Aquaponic Source
Bountyhaus School Farms
Colorado Aquaponics
Dahlia Campus for Health and Wellness Aquaponic Farm
Ecoponex Systems International LLC
Emerge Aquaponics
Flourish Farms @ The GrowHaus
Grand Valley Greens, LLC
GroFresh Farms 365
Northsider Farms LLC

Marine Bait Wholesale

Aquaponics AI

The Aquaponics Doctors, Inc.
Aquaponic Lynx LLC
The Family Farm
GreenView Aquaponics, LLC
Sahib Aquaponics
Traders Hill Farm

FM Aquaponic Farm
Georgia Aquaponic Produce LLC
TRC Aquaponics
Ula Farms

Friendly Aquaponics, LLC


Central Illinois Aquaponics

Janelle Hager, Kentucky State University
K&L Organics
Purple Thumb Farms
West KY Aquaponics

Small Scale Aquaponics

Aquaponics Academy
Lesley University
O’Maley Innovation Middle School

Anne Arundel Community College
Greenway Farms, LLC


Menagerie Greens Inc.

North Carolina
Grace Goodness Aquaponics Farm, LLC
100 Gardens

New Hampshire
University of New Hampshire

New York
iGrow News
Oko Farms

New Mexico
Desert Verde Farm
Growing the Greens
High Desert Aquaponics
Howling Coyote Farms
Lettuce, Etc. LLC
Project Urban Greenhouse
Sanctuary at ABQ
Santa Fe Community College

Berean Aquaponic Farms and Organics LLC
CHCA Eagle Farms
Wildest Farms
Williams Dairy Farms

Freedom FFA
Greener Grounds LLC

Alternative Youth Activity
Ingenuity Innovation Center
Live Local Organic
Triskelee Farm

Aquaponics at State High
Yehudah Enterprises LLC

Puerto Rico
Fusion Farms
Granja Ecologica Pescavida

Rhode Island
The Cascadia Bay Company

Great Head LLC

BioDiverse Technologies LLC
BnE Enterprises
East Texas Aquaponics, LLC
Gentlesoll Farm
HannaLeigh Farm
K&E Texan Landscaping
King’s Farm
Tarleton State University, Aquaponics Hydrotron
West Texas Organic Gardening

Aquaponics Olio
Wasatch High School

Grace Aquaponics
INMED Partnerships for Children
Return to Roots Farm

The Mill ART Garden, LLP

The Farm Plan
Impact Horizon, Co.
Life Tastes Good LLC
Northwest Aquaponics LLC
Wind River Produce

Washington, DC
Anacostia Aquaponics DC LLC
P.R. Harris Food Hub


New South Wales
Wirralee Pastoral
Solum Farm


Chhuyang – Aquaponics in Bhutan


Rio Grande do Norte
Habitat Marte

Santa Catarina
Pedra Viva Aquicultura 


Via Pontica Foundation


Agro Resiliency Kit (ARK) Ltd.
Fresh Flavor Ltd
Lethbridge College
W.G. Guzman Technical Services

British Colombia
Garden City Aquaponics Inc.
Green Oasis Foods Ltd.
Pontus Water Lentils Ltd.

Aquatic Growers
University of Guelph
Power From Within Clean Energy Society

ML Aquaponics Inc

Yukon Territory
North Star Agriculture


Central Laboratory for Aquaculture Research


Vegetal Grow Development


Prof Brahma Singh Horticulture Foundation, New Delhi

Blue’s and Green’s
Spacos Innovations Private Limited


Grow Up 


Negeri Sembilan
BNS Aquafresh Farming


University of Abuja


Nueva Ecija
Central Luzon State University

Metro Manila, NCR
IanTim Aquaponics Farm


True Spirit Lda


Sectors 2 & 4
Bucharest Association of Romanian Aquaponics Society




Ucad Dakar


Aquaponics Singapore 

Brian Filipowich, Aquaponics Association
Juli Ogden, The Farm Plan
Dr. Nick Savidov, Lethbridge College
Tawnya Sawyer, The Aquaponic Source
Dr. R. Charlie Shultz, Santa Fe Community College
Meg Stout, Independent

Brian Filipowich




Chalmers, 2004. Aquaponics and Food Safety. Retrieved from

Filipowich, Schramm, Pyle, Savage, Delanoy, Hager, Beuerlein. 2018. Aquaponic Systems Utilize the Soil Food Web to Grow Healthy Crops. Aquaponics Association.

Fox, Tamaru, Hollyer, Castro, Fonseca, Jay-Russell, Low. A Preliminary Study of Microbial Water Quality Related to Food Safety in Recirculating Aquaponic Fish and Vegetable Production Systems. Publication of the College of Tropical Agriculture and Human Resources, the Department of Molecular Biosciences and Bioengineering, University of Hawaii, February 1, 2012.

Rakocy, J.E., Shultz, R.C., Bailey, D.S. and Thoman, E.S.  (2003). Aquaponic production of tilapia and basil:  comparing a batch and staggered cropping system.  South Pacific Soilless Culture Conference. Palmerston North, New Zealand.

Rinehart, Lee. Aquaponics – Multitrophic Systems, 2019. ATTRA Sustainable Agriculture. National Center for Appropriate Technology.

Tamaru, Fox, Hollyer, Castro, Low, 2012. Testing for Water Borne Pathogens at an Aquaponic Farm. Publication of the College of Tropical Agriculture and Human Resources, the Department of Molecular Biosciences and Bioengineering, University of Hawaii, February 1, 2012.

The Amazing Microbiology of Aquaponics

As our nation prepares to pass the once-every-5-year Farm Bill, let’s remember that aquaponic systems have been shown to have the same – if not more – quantity and diversity of rich microbiology as organic soil.

Check out our Aquaponics Food Web Report: Aquaponics food web aug 2018

Whether as a consumer, grower, policy-maker, or business owner, we all make decisions that affect
where and how our food is produced.

As we shape our new food system, one critical consideration is whether we retain access to high quality
fresh fruits and vegetables, particularly those grown sustainably. We must assess whether new growing methods like aquaponics can deliver fruits and vegetables grown from seed with the same symbiotic biological processes used by plants since the dawn of time.

Our report shows that aquaponic systems feature a vibrant, thriving community of happy little micro-critters!