Food safety in Aquaponics

We all know that we can grow food in Aquaponics. But my question is how to determine that food in aquaponics is safe.

@ivkinmm, There may be several answers to your questions but with the farms I work with we use internal audits of practices using standards set by Global Gap, Produce GAP, Certified Natural Grown, Best Aquaculture Practices, and USDA Organic depending on the need and size of the farm these ensure that the practices conducted on the farm are in conjunction with food safety standards even if certification, is not desired by the farmers consumers.

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Is there any way to check your crops before this organization. Lets say I have one strawberry plant. I need somehow to check it this one plant. How this checkup can be done ? Express check …

Its more data and documentation than a here you go “tada” sort of thing and they look for intuitive measures you have in place for prevent contamination.

Their biggest concern is food safety and they look for physical, chemical, biological and environmental hazards that could cause a recall or a food safety issue in the public domain.

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The functional solution is to dose your system with LABs at a rate of 1:1000 LABs to system volume twice a month. This eliminates most water pathogen concerns. Just need one of these schools to do it so we can move past this question. Its already being used in the cannabis industry where standards are far far beyond anything in vegetables.


1-s2.0-S0001868620305662-main.pdf (2.7 MB)

If you really want to get to the nuts and bolts of it, here is something to read on the latest detection techniques. I would not get too carried away with the food safety subject, because they have these measures in place and the California greens farmers have an association that literally spoon feeds this process to the farmers and we still keep getting annual lettuce and spinach recalls almost like clock work from California, you dont see GAP declare war on spinach farming do you. It just comes down to who has the biggest voice in the crowd.

Here is a link to the site that talks about this:
California Leafy Green Products Handler Marketing Agreement (LGMA)

Their Resources directory on testing and documentation requirements


I’m currently serving on an advisory board for the Northeast Center to Advance Food Safety, which is developing food safety-specific guidance materials for aquaponic producers. The year-long project just began, so those won’t be out for a little while.

Lactic acid bacteria (LABs) are a part of the natural aquaponic microbiome (Stouvenakers et al. 2020, Sirakov et al. 2016). I don’t think you need to dose your systems, rather use good practices and system design that will encourage a healthy microbiome. At UNH this included rapid solids removal via a mechanical drum screen along with keeping biofilm buildup to a minimum through weekly tank scrubbing. Along with biosecurity, hygiene, regular water quality testing and base additions, this keeps water quality high and carbon accumulation low, increasing the resilience of the natural microbiome. We demonstrated that there was no E. coli, Salmonella, or Listeria in our system after a year of operation. (This was in coupled aquaponics with DWC lettuce as a model crop.) I’ll be publishing this research over the coming year.


Oh you absolutely need to dose them in your system if you want them in a high enough population to act as a prevention. Think of it like spraying bassiana on your plants leaves same kind of preventative dosing. You need to seed your system with other microbes too most peoples systems are badly deficient in microbial diversity its half of there mineral issues they have no microbes to mineralize them. Also by diversifying the Lacto species you get a much wider range of available vitamin B complex which greatly enhances plant growth as well. Its not just naturally found in systems most peoples aquaponic food webs are horribly imbalanced when looked at under the scope. The best way to stay clean is thru good biosecurity. The second best way is thru preventative probiotic dosing that not only benefits you from killing pathogens but accelerates growth of fish and plants 17% increase according to Joe Pates data and as much as a 35% in my testing. While your experiment sounds interesting Im not sure it proves anything. A better test would be like what they did in Hawaii with the intentional introduction of pathogens and then treating them and or seeing what the infection rate is. In cannabis we can’t have any level of anything or it fails. They test every 10 or 20lbs of flower produced depending on the market. They also test our water. We have used it to treat E coli in real world farms that failed testing then passed testing post treatment. Thats a far better example of what works than a system that never had an infection to begin with staying clean. I don’t see what you prove other than that you have good food safety protocols and workers who follow directions. Design and practices don’t fix things once they have gone wrong thats when you need something like LABs dosing to fix things with out messing up your mineralization the way something like a Trichoderma would. I don’t understand this strange fear people have around LABs its cheap and it works it eliminates pathogens and makes both fish and plants grow faster its like not using iron in your aquaponic system level of silly not to use.

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The OP was asking about how to demonstrate the safety of aquaponic produce. That’s a much broader question than what you are discussing about how to deal with a pathogen outbreak if it occurs. I am advocating for a microbiome that is as diverse as possible, which agrees with your point about Lacto diversity, but the way to achieve biodiversity is not necessarily through inoculation (dosing). As I mentioned, I’m talking specifically here about recirculating systems with a liquid plant growth matrix, e.g. deep water culture (DWC) or nutrient film technique (NFT). I don’t claim to have expertise in solid media systems. It has been shown by a couple of different folks that excess organic carbon in aquaponic production water reduces the diversity and number of species of bacteria. In turn, limiting carbon accumulation increases diversity. This helps to prevent the incursion of pathogenic bacteria (of humans, fish, OR plants) due to the resilience of the existing microbiome. It’s not just Lactobacillus that has pathogen-suppressive effects, and several groups of bacteria working together will inherently be more stable and resilient than one genus. Managing the carbon in your system is thus a super important part of reducing the risk of an outbreak, not just of a human pathogen, but in your system itself. UVI-style systems with in-situ solids mineralization lose a ton of nitrogen through denitrification, while the waste serves as a potential reservoir for pathogens.


Inoculation is the only way how else do you expect to get these microbes? They aren’t going to magically appear. Praying doesn’t work for microbes. It is even more important for DWC and NFT as they have a higher chance of pathogens like pythium compared to the more diverse media beds. Excess organic carbon does not reduce diversity it increases it. With out available carbon your microbes cant replicate. When it falls out of range it cuts your microbial replication in half this is another aquaponic myth that is easily proven wrong with a microscope. Aquaponics is not hydro. It doesn’t balance like hydro optimal ratios are way different than hydro its not hyrdro. Inoculating microbes will reduce your TOC not raise it. I get why you misunderstand the issue because its taught so very wrong in aquaponics by most people but this is the future of food safety in aquaponics and hydro there is no sense in fighting it. Its even being used in meat processing facilities now to reduce pathogens a much dirtier environment by far. You right its not just Lactobacillus that has those abilities but that is one any one can buy world wide and replicate with 100% certainty that it is safe and will work as intended. Hoping and wishing your microbes are balanced thru magic in the air is not remotely scientific nor does it help any one fix anything. Lactobacillus is easy to keep isolated due to being anaerobic in milk so you can ensure no pathogens its about food safety after all. I suggest you read Master Chos book to help fill in some of your gaps on the topic. Carbon management is already handled if you have a properly sized filter as far as solids the rest is completely fine and a non issue. Again i understand why your saying what you say but its been taught wrong for years and we need to fix that. Probiotics is the future of food safety not to mention what you can do with organic growth accelerators and organic PGRs.

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Thank you Arvind ! So many useful information.

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happy to be useful !!

Curious about the data that have been gathered re: LABs introduced into the system.
Have there been challenge studies conducted where the baseline microbial ‘pathogen’ (lets use E. coli or Listeria monocytogenes as prospective examples) populations (#/100mL or per mL ) are determined, and then the LABS (known concentrations and volumes are added, presuming the composition of LABS is known at least to genus in the ‘inoculum’) are added. Then 1, 2, 3, 5, 7 days post-addition, the pathogen counts and the LABS counts are determined again.
This is the kind of data that would be instructive, along with the water conditions (pH, temp, DO, NH3, NO3, tds, etc) during the 1-7 days post inoc compared to the pre-inoc.

We have done commercial applications on real world farms but no counts on it only that it was detectable before treatment and not detectable post treatment on systems as large as 60,000 gallons. Thats a pretty good test if you ask me far bigger than most peoples entire farms. The LAB concentrations i can give you the range on its a fairly small range. The dilution rate for treatment was 1:1000 meaning we added one gallon of LABs per 1000 gallons of system volume for any treatments twice a week for 2 weeks. I still have an active culture of the same serum used on all 3 farms and yes I have the range of LAB species that went into the original mix. More LABs species = more variety of vitamin B outputs which also enhances fish and plant growth. I have not done a DNA analysis to see what species remain in the culture currently tho. I dont have time to test for 1,2,3,5,7 days thats to much if some one wants to do that at a university email me we can go over the protocols. What we have proven tho repeatedly is in cannabis grows we can eliminate ecoli 100% of the time so far and still undetectable months later. This is the answer to food safety in aquaponics. Now who wants to replicate it for your paperwork?

And what is LAB when it isn’t an acronym?

LABs or Lactobacillic Acid Bacteria Serum is a fermented solution used around the world for soil farming in many different ways that is made primarily from rice wash, milk, and a microbial inoculant. LABs is used in some form across the world in the Carribean as a 3 - 4 week ferment, in korea as a few day ferment and in africa and other parts of asia in a variety of lengths. Traditionally LABs is taught as a air collected microbial inoculant collected on rice wash and added to milk to ferment it and separate the lactic acid. The combination of yeasts and Lactobacilli break down the plants and provide a rich array of amino acids, Vitamin B complexes and other plant beneficial compounds. The yeast and lactobacilli also love to feed on Ecoli, Salmonella, Listeria, and other illness causing pathogens as well making them the best go to option for maintaining regular system health. They also break down fish waste into more mineralized forms and also eliminate plant pathogens like root rot, septoria, and other root pathogens. You’d be silly not to be using it given all of its benifits.

The vitamin B varieties that LABs produces increases both fish and plant growth rates considerably. You can further improve this by fermenting certain plants with desired growth compounds as well such as with Super LABs or Plant LABs where you ad plants or other natural inputs to further boost your LABs effectiveness.

Think of it as a new option to go next to compost teas in your tool belt. What minerals you can unlock thru AACT will be vastly different than those same inputs in an LABs solution in many cases the LABs solution provides a better break down as it has much less oxygen and can redox much better.

The part you use is the clearer thinner middle layer to a dilution of 1:1000.

Contrary to one wacky person I heard its not from the stomach lining of a cow many lactobacilli are actually from soil or cultured from other sources unrelated to milk entirely.

LABs needs to be used on all commercial farms for food safety sake. Not only does it boost your yields it keeps your system clean at the same time. Probiotics is the food safety of the future not over engineered systems with UV and other things that screw up your nutrients and don’t actually guarantee food safety. We need to use our natural allies instead of trying to sterilize everything all the time it only creates new super bugs.

Here is a great guide to traditional LABs

I prefer to also ad Kefir Grains to my traditional LABs as it ads alot more vitamin B and ferments faster when those are also added post air collection.


Did you also test on Legionella?

Hi Albert. I didn’t use culture-based methods to screen for Legionella. The second part of my study, a metagenomic analysis of water samples from the systems, would have answered the question of whether there were any known pathogens circulating. This work was interrupted by the pandemic; my computer science and genomics collaborators have had to pivot to COVID testing on campus. I’m hoping to finish it eventually, as this information would add a lot of depth and generalizability to what we found.