Should We Be Concerned With Antibiotics in the Soil?


Recently my dad asked me my thoughts on a couple articles he ran across (and how they might apply to growing organic food*): Antibiotic-eating Bug Unearthed in Soil. Followed by Assessing Antibiotic Breakdown in Manure. The first talks about research done on how antibiotics from animal manure breakdown after application onto a farm field, finding one type of bacteria that’s not only resistant, but that can use a particular antibiotic for food. The second article looks at how moisture and air can affect how quickly antibiotics break down in manure piles.

Well, this is a pretty complex issue. I first went through the National Organic Program Standards relating to manure application to fields (section 205.203) and prohibited/allowed substances (sections 205.601 and 205.603 for synthetic substances). The NOP is the definitive federal law on what you can and cannot do to be a certified organic operation as well as put “organic” on any product you sell.

You can read the current NOP Standards here: National Organic Program.

Manure can only be used from a source that does not contain “residues of prohibited substances”. It should be noted that there are some very specific regulation in how to handle fresh manure in terms of temperature and duration of composting, and application to crops for direct human consumption in relation to harvest time. Traditional commodity-driven agriculture has no such regulation. Although it really wouldn’t be wise for a non-organic veggie grower to apply fresh manure to a crop of, say, carrots a couple weeks before harvesting. If people start getting sick off your food it’s a sure bet a food inspector will show up on your farm to track down the source of pathogenic bacteria.

So what are “prohibited substances”? Just because something is manmade doesn’t mean it’s prohibited in organic law, but there are far fewer things that are non-synthetic (ie. from a natural source) and prohibited than synthetic and prohibited. And just because something isn’t specifically stated as prohibited doesn’t mean it’s a good idea to use on an organic farm.

The article he referred me to lists sulfamethazine as the antibiotic being studied. It is not listed under section 205.603, “synthetic substances allowed for use in organic livestock production”. But, the information on this particular antibiotic could be loosely applied to other antibiotics from animals that pass through to the soil. If you keep applying a substance (an antibiotic in this case) to the same population of bacteria over time they will evolve a resistance – as long as a few survive after each application. And this bacteria in particular, a strain of Microbacterium, is not only surviving, but using sulfamethazine as as energy source (ie. food).

But, before we get all excited about antibiotic resistance in this bacteria we should ask if this microbe has any implications for human health or disease. This could be a total non-issue if the microorganism really is very benign to the health of people – or anything else biological for that matter.

Are Soil Bacteria a Concern for Human Health?

Unfortunately, soil can be a source of pathogenic microbes. Probably the 2 most common human diseases that have an environmental source are tetanus (Clostridium tetani) and botulism (Clostridium botulinum). I found a pretty comprehensive article at MedScape on Soil-Related Bacterial and Fungal Infections. Some of the other pathogenic bacteria listed as having an environmental source are:

  • Legionella spp.
  • Anthrax, Bacillus anthracis
  • Campylobacter
  • Escherichia coli 0157:H7
  • Burkholderia pseudomallei

Microbactrium wasn’t listed there. Further research on the web didn’t reveal any connection of this bacteria to human disease conditions.

But, this begs the question: “If this particular species of soil bacteria can evolve a resistance to antibiotics what about other bacteria that naturally are pathogenic?” Only scientific research will be able to tell us about other bacteria, but bacteria in general have been shown to be uniquely adapted to grow many subsequent generations that are able to survive an application of antibiotics. It’s evolution at it’s best.

So, could there be other pathogenic bacteria out there in the soils that are developing an antibiotic resistance? I would say it’s likely.

So What is the Safe Handling of Manure?

Over time antibiotics that pass through an animal will break down. Some will take longer than others. The USDA article cited above shows that the rate at which those substances break down vary depending on water and air content within the manure. Generally, the more moisture AND the more air the faster things will break down.

When you take this into consideration you have to question the efficacy of liquid manure lagoons. There’s a lot of water there, but very little air. So antibiotics will be degrading slower than if they were applied to a field on a regular basis. I would bet that a higher antibiotic concentration could be found in most manure lagoons, whether they’re a CAFO facility or not.

The National Organic Program has specific guidelines for how to compost manure to reduce the risk of pathogenic bacteria surviving and contaminating crops. Fantastic! But, they stop short of prohibiting manure coming from a non-organic source. As a conscientious organic farmer I probably wouldn’t source my manure from a traditional farm anyway, just because I really don’t know what they’ve been feeding their animals.

The Organic Trade Association has a great page on Manure Facts, geared more for the organic consumer. Hopefully good information like that will inform consumers that manure can be managed safely, and is really an essential part of a farming operation that seeks to maintain its soil fertility. Manure has been used for centuries to enrich farming soils, but it’s only in the last century that a connection has been made between animal waste and disease. There are definitely good practices when it comes to managing it.

Which brings us to another serious problem with substances passing through manure and jeopardizing agricultural endeavors:

Killer Compost: When Herbicides Persist Through Manure

Several years ago Mother Earth News started reporting on farms and gardens in the northeast of the US that couldn’t grow any vegetables. The problem was eventually tracked to aminopyralid, a broad-leaf herbicide, being applied to pastures and then consumed by the herbivores there. The manure from these animals was then composted and applied to gardens. And now the problem has cropped all over North America as well as the UK.

Even when the manure was composted for months this herbicide lived on. Applied to gardens and veggie farms it soon became apparent something was wrong when plants grew out in a very stunted way.

Dow Chemical (the manufacturer of aminopyralid) does have a web page warning about not using manure and compost in certain applications: Aminopyralid Stewardship – Forage and Manure Management. My question is if this herbicide is so powerfully persistent why isn’t it banned??


At this point it’s probably a good idea to keep an eye on research concerning soil bacteria and any developing resistance to antibiotics. It’s probably not a huge issue right now, but could potentially become one if antibiotics continued to be applied to farm animals through their routine feeding programs. Antibiotics in feed have become a necessity for animals raised in concentrated, dirty conditions.

However, antibiotic resistance IN animals and humans IS currently a problem. When the animals we raise for food are treated like mere protoplasm to be wrapped in cellophane for the mass market only bad things can come of it. When animals are forced to live in such concentrated conditions antibiotics in the daily feed are necessary to keep them alive. Stuffing them into feedlots and stacking them several feet high in cages to make the most profit is distasteful. Is it really necessary?

This might be inspiring to you as an alternative vision: Joel Salatin on The Sacredness of Food.

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