Does Fertilizer Kill Soil Bacteria?

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Robert Pavlis

Read most organic books or blogs and they will tell you that synthetic chemical fertilizers are killing the bacteria and fungi, the microbes, in soil. Dr. Ingham and her Soil Food Web preach this same message. Stop using fertilizers because they kill the bacteria and fungi. My review of Teaming With Microbes found the same message repeated several times.

Does fertilizers really kill bacteria or fungi in soil?

Some people claim that the ‘salts’ in fertilizer do the damage, but anyone making such a claim does not understand what happens to salts in soil. I’ll explain this in more detail below.

Does Fertilizer Kill Soil Bacteria?
Does fertilizer kill bacteria?

Fertilizer Kills Bacteria

Fertilizer provides nutrients like nitrate, ammonium, phosphate, calcium, potassium, sulfur etc. These are all nutrients that plants need to grow. See Fertilizer – Understanding Plant Nutrients for more info.

A lot of organic followers believe that the nutrients from organic sources are some how different from the ones provided by fertilizer. They are NOT! There is no lab in the world that can tell the difference between a nitrate molecule from manure and one from a bag of synthetic fertilizer. Plants can’t tell the difference either, because there is no difference. They don’t care where the nitrate came from.

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A lot of people doubt science and in some advanced areas of investigation science may not be 100% correct. This is not one of these situations. All chemists agree on the above fact and have done so for a long time.

For more on this see my post What is Organic Fertilizer.

Organic material releases the nutrients slowly over many years. Synthetic chemicals release the nutrients as soon as the fertilizer dissolves in water. Is it possible that the quick release of nutrients kills microbes?

Keep in mind that the soil under your fingernail after a day in the garden contains millions if not billions of bacteria. Is it reasonable to think that fertilizer would kill all of them? I don’t think so. Even if the fertilizer killed 99% there would still be billions and billions in every shovel full of soil. And bacteria grow very quickly – as fast as doubling in number every 20 minutes (at least in a lab).

Number of Bacteria After Adding Fertilizer

There have been many studies looking at the number of bacteria in soil after applying fertilizer. In Impact of Organic and Inorganic Fertilizers on Microbial Populations, they looked at both bacteria and fungi populations, and compared untreated soil to (a) soil treated with organic material (manure, rock phosphate, neem cake) and (b) soil treated with synthetic fertilizer. Measurements were done at two different depths.dding synthetic fertilizer resulted in no change in the number of bacteria and an increase in the number of fungi. Organic treatment increased both fungi and bacteria slightly.

Synthetic fertilizer did not kill bacteria in soil and it increased the number of fungi.

Agriculture Canada looked at the effect of ammonia and urea on the microbes in soil over a 10 year study and concluded that “nitrogen applied according to soil test recommendations had minimal long-term detrimental consequences for soil microbes, soil biochemical properties, or soil structure.” (reference no longer available). A review of the long term effects of mineral fertilizers on soil microorganisms concluded that “mineral fertilizer increases microbial biomass in cropping systems”.

The science is quite clear. Fertilizer, when used properly, does not kill microbes.

Microbes Eat Synthetic Fertilizer

Why do fertilizers not kill bacteria? The simple fact is that the nutrients in fertilizer, especially the nitrate, is a nutrient required by bacteria. They eat it! They actually absorb it since they have no mouth, but you get the idea. They also eat the other nutrients; phosphate, potassium, sulfate etc. Bacteria and fungi need these nutrients as much as plants do.

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Once you understand this, it becomes fairly obvious that adding these nutrients to soil will not kill the microbes, unless they are added in very large amounts that prove toxic.

Think of composting. If you add too many browns the composting process goes slowly because there is not enough nitrogen available for the bacteria to eat. Since the bacteria are starving for nitrogen they don’t multiply and composting is slow. Add some nitrogen, either as a fertilizer, or as ‘greens’ which contain higher levels of nitrogen, and the compost pile suddenly heats up. The bacteria now have enough nitrogen to eat, they are active, and they multiply. All of this activity heats up the compost pile.

To better understand composting greens and browns see How to Compost: Browns and Greens.

Fertilizers are Salts and Salts Kill – Don’t They?

You see comments like this all the time; “fertilizers are made up of salts and salts kill bacteria.”

It is true that fertilizers are salts. This is not sodium chloride or table salt. The term ‘salt’ has a different meaning for a chemist. To them, a salt is a compound made up of two or more ions. Table salt is made up of sodium ions and chlorine ions. Ammonium nitrate fertilizer is made up of ammonium ions and nitrate ions, so it is also called a salt.

In dry form the ions come together to form salts. When the salts dissolve in water, the molecules break apart and form ions. When fertilizer salts are spread on the ground the white and gray balls are salt. When it rains, the water dissolves the salt into ions and washes them into the soil. Once they are in the soil they are no longer salts.

Salt will harm bacteria and plant roots if there is direct contact. Due to the large number of microbes in soil, and the small surface area of the fertilizer crystals, this has no significant effect on the microbe populations in soil. Once the salt is dissolved, the ions quickly become diluted as the water moves through the soil layer.

Diluted ions in water do not harm microbes or plant roots. In fact both of their lives depend on the ions being in the water. It is the ions that they absorb – not the salts.

What happens with organic fertilizers like compost and manure? They contain large molecules like protein and carbohydrates. As these are decomposed, they are converted into ions. These ions are the exact same ions that fertilizer produces.

Once commercial fertilizer dissolves in water it is no different than organic fertilizer. Fertilizer does not kill bacteria or fungi.

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Robert Pavlis

I have been gardening my whole life and have a science background. Besides writing and speaking about gardening, I own and operate a 6 acre private garden called Aspen Grove Gardens which now has over 3,000 perennials, grasses, shrubs and trees. Yes--I am a plantaholic!

72 thoughts on “Does Fertilizer Kill Soil Bacteria?”

  1. You missed the whole point. With synthetics nutrients are available immediately for the plant to absorb so the plant doesn’t depend on mycorhizzaes so in return the plant doesnt feed the mycos any glucose cause the plant doesn’t need the mycos to survive. In organic the plant can’t eat organic matter so it depends on mycos to break down the nutrients in to a usable form and in return feeds the mycos glucose which they need to survive. Sure you can use synthetics and mycorhizzaes but your defeating the purpose. You would need to keep adding mycos regularly and also need to feed molasses or a sugar on the regular to feed your mycorhizzaes since the plant is not doing it. Unlike organic where the plant wants the mycos to flourish so the plant feeds the mycos.

    • You missed the whole point! It was never the goal of this article to discuss the various processes going on in the soil. You are describing a completely different article. My goal was
      to look at one main claim that organic gardeners make. Fertilizer does not kill bacteria.

      • Hi Robert. Please hear us out. No offense, but you are the one missing the whole point. You can’t just say that fertilizers don’t kill bacteria and then when we point out that it does kill them in the long run you will then say “Uh I was just trying to show if fertilizers directly kills bacteria or not.” What you are doing is irresponsible journalism which will get people to think that it’s okay to use synthetic fertilizers and you get almost the same benefit with organic fertilizers. I hope you get the point.

        Ask any farmers who uses synthetic fertilizers on their land for a substantial amount of time. They’ll tell you that the soil “dies” after using synthetic fertilizers and you can’t grow crops on it anymore unless you will keep using synthetic fertilizers. It harms the soil, Rob. And that’s what we just all wanted to hear, whether synthetic fertilizer kills the soil in the long run or not.

        • How many of those farmers uses synthetic fertilizer and did not cultivate or run machinery over the land? None.

          How many of those farmers did a test plot that used fertilizer but no cultivation or machinery? I bet none.

          I never said that agricultural practices are not killing bacteria. Cultivation speeds up the reduction of organic matter which means microbes have less food, which means they die out. Machinery running over the land compacts the soil and the reduction of air also harms bacteria.

          Since on farms you can’t separate these destructive forces from the use of fertilizer you can’t use their poor soil quality as a measure of what fertilizer does to bacteria.

          The problem with modern agriculture is the way the land is used – not the fertilizer themselves.

          We are still left with the known fact that the nutrients from organic material are identical to those provided by fertilizer. If one is good for bacteria – so is the other. You can’t reach any other conclusion.

    • Molasses used in compost tea encourages a bloom of bacteria. Fungus can consume glucose, but prefer carbohydrates and other organic carbon sources. Molasses does not contribute to mycorrhiza colonization, but rather roots “opening the door way to colonization”. You’re partially correct. Soils with higher amounts of phosphates results in less root colonization. However, applying phosphates does not “kill” mycorrhiza. After colonization, phosphate applications can be reduced because the plant uses phosphates for efficiently-thanks to mycorrhiza. Relying on phosphorus mineralization by mycorrhiza alone may work well for leafy crops like lettuce, but phosphorus hungry crops will likely become deficient. Believing mycorrhiza can mineralize organic phosphorus alone to keep up with plant growth, is an optimistic belief at best-more likely an uneducated opinion.
      Food for thought. Consider how large of a carbon footprint is created by hauling plant or animal based fertilizers vs concentrated fertilizer. Both of these natural sources are likely derived from conventional agricultural systems too. Check it out: the plant needs certain amounts of nutrients or it becomes deficient. Natural or conventional. Same amount of nutrients are applied. Timing is critical depending on the source. There is also diminishing returns to keep in mind. Over-applying fertilizer will result in waste and pollution. If I didn’t upset you already, this will. Imagine your applying a natural fertilizer, but it doesn’t breakdown to plant available nutrients by the time your crop needs it. Soil pollution. Or your manure applied loses over half of its nitrogen to ammonia. Air pollution. While your conventional neighbor is using nitrogen inhibitors to control the release and reduce pollution. They also applied mycorrhiza before or at planting, or used a mycorrhiza coated seed. Waited fertilizing until mycorrhiza colonized roots during a time when the crop’s demand on phosphates were low. Then on top of that, used drones or technology on the tractor that detect where in the field nutrients were deficient-they can very accurately fertilize. Too complex? They send a leaf tissue analysis to their testing facility during each phase of the crop. Fertilize accurately with virtually no waste. Conventional agricultural uses precision technology. Organic systems have to be careful to resist from fertilizing on intuition. Are conventional farmers as evil as you think?
      Thanks Rob.

  2. Thank you for this article, Robert. You’ve put into clear terms what I’ve suspected for many years. I have gardened strictly organically for over 40 years, 22 of them spent building up organic matter in poor desert soil that is a mix of sand, silt and not much else. I believed what I had always heard, that if you feed the soil Mother Nature will take care of the rest.

    This year I realized that I was pouring a lot of energy, time (and water!) into soil that was naturally deficient due to local alkaline conditions (both soil and water), and no amount of compost or natural amendments would fix it.

    I don’t own a microscope, but even so I can see that my vegetables grown in bottom watered trays using “synthetic” nutrients and potting mix are performing far better than I have ever seen it the dirt. I even tried using half compost and half potting mix, but there was no visible improvement over the commercial potting mix.

    If there is damage to soil microbes, it sure doesn’t show up in the plants! I am using far less water, have zero sign of nutrient deficiencies, and the results are amazing…

    So thanks again for busting this myth, or at least putting a crack in it 😉

    Best, James

  3. Hey Robert

    I don’t know what to think about all you wrote. If salts do not resettle (crystalize) even after dissolving properly in water, how do you explain yourself that the inside of the hoses of my irrigation system once were full of salt crystals? I think same applies to the substrates…They can be full of salts. Thats why alle the professional big scale nurseries in Holland for example work with drain to waiste (30% more than the substrate can uptake at on feed) to flush the settled salts.
    I would like to hear your opinion about this…

    The article was interesting nonetheless….

      • Sorry for not coming back earlier. You mentioned in your answer to my question that ” Salts precipitate when they become insoluble.”

        Thats what i pointed to. They will precipitate all over the substrate and be aggressive in this insoluble condition. So if the beneficial bacteria gets into touch with it, they are affectet negatively.

        Again there really is a reason why the huge nurseries in Holland keep the substrate very wet with 30% drain to waster at every feeding so that the fertilizers never reach that insoluble state and precipitate everywhere in the substrate and become aggressive to beneficial bacteria and the hair roots.

        • Insoluble salts are stable and won’t harm bacteria.

          Nurseries growing in posts don’t really care about the bacteria. They are feeding plants with nutrients directly.

  4. You have either simply misunderstood, or choosen to utterly misrepresent the study you cited. It states clearly that the organically treated field outperformed both the inorganically treated field and the control. The Organic field displayed the highest levels of microbial activity in both bacterial and fungal forms. The inorganically treated field did better than the control but ultimately failed to produce the same microbial outcroppings as the organic field.

    • I don,t believe I made statements about performance, only about micro density.

      Nothing in your statements contradicts the conclusion that microbes were not killed with synthetic fertilizer.

      • Gotta love when someone jumps in with the five dollar words, and completely whiffs on the ball. Good article, thanks for clarifying. I’m using coco coir as a substrate and due to the lack of pre-existing microbial action within, I add fungal and bacterial supplements, along with a near-full spectrum of organic and inorganic fertilizers, carbohydrates, amino acids, B-vitamins, etc. In my mind, it gives the fertility of soil to the excellent properties of coco coir. I would rather err on the side of caution and add the supplements, and find out later that it was a slight waste of money, than not have them to begin with and have the crop suffer. Results are good so far.

        Good stuff with the article, and nice acreage

      • “I don,t believe I made statements about performance, only about micro density.”

        Ok. But then what is the practical use of your conclusion for gardeners if you don’t judge by levels of microbial activity? The sole presence microbacteria is not interesting for the gardener. The interactive exchange of bacteria and the crop/roots is what we aim for. If the bacteria is just present because it survives because its fed with mineral fertilizer, then its of no use to the gardener.

  5. One thing i think should be mentioned is the fact that plants take up nutrients at their own pace and the actual science behind over-fertilization. Fertilizers really high in N, from what i have read, evaporate pretty quickly due to the fact that the form of N you want for plants should actually be in a gaseous form working through symbiosis with nitrogen fixing bacteria that convert the N given off by other soil microbes… but i could be explaining that wrong as I’m not a soil scientist. I think the really ultra organic way is to not use the same principles as conventional agriculture, but to use science to foster a mutually beneficial relationship with soil microbes and the roots of the plant. Higher fertility = higher rate of exchange. the form nitrogen is in with most inorganic fertilizers goes straight to the plant, the microbes don’t have to be there at all! like as with soilless or hydroponics, and it’s pretty much the same fertilizers

    • re:”Fertilizers really high in N, from what i have read, evaporate pretty quickly” – most fertilizer uses nitrate or nitrite salts which would not evaporate. Microbes will over time convert these forms in to atmospheric nitrogen. Urea contains a lot of nitrogen, and it does vaporize into a gas. That it why it should be either buried or watering in. Once in solution it won’t do this.

    • I do the same, but the nutritional requirements of the forest are not exactly the same as what we would feed our garden veggies like tomatoes and peppers.

      • @Sarah Jagenberg: Bingo! Agriculture/gardening (the intentional concentration of certain plants) are cultural innovations. The rules just aren’t the same.

  6. I’d like to know who fertilizers the adult ecosystem of a forest? And who waters it? And how could you defend fertilizers and then admit that they are dangerous when overused? It seems for someone so educated you gave this “horse blinders thought”. It’s not just farms using chem fert, and it’s not just home gardeners. It’s every farm, every home, every business, everyone from landscaping to gardening to growing food you name it. Along with unproper use, you will no matter what get overuse. Did nature not thrive before chemical fertilizers? Did people not eat? Why do natural sources of fertilizers not have such high numbers in NPK, and what about all the other nutriens!!! It doesn’t take a scientist to observe nature and realize that humans are not smarter in any way, and synthetic chemicals will always be abusive and unnecessary in nature. Maybe in human systems where everything is done backwards you can continue to use “science” to defend damage causing practices. Mother Nature has billions of year of practical applicable science, when we observe Mother Nature, we find the truth. And btw if you want to go by scientific experiments, get out there yourself and don’t go test the conditioned soil of farm lands, but instead go run synthetical fert experiments on old forest and then tell me what happens. I love when people as yourself try to set aside the correct science when you never even do any of it yourself. The real truth is we do not need synthetic fertilizers, it is not the way of nature, and because of that it will not lead us to anything good. Be as the earth, humbly, and not by thinking you can manipulate it….

    • Nobody fertilizes the forest, but that has nothing to do with this blog post.

      Re: “how could you defend fertilizers and then admit that they are dangerous when overused? ” – that is basic chemistry. The poison is in the dose. Small amounts of any chemical is safe – large amounts may not be.

      • Mother nature provided the framework, and humans improved it. Did humans survive prior to advanced medicine? Yes. Do they survive longer, and healthier, with advanced medicine? Yes. Will leave extrapolation of the rest to you.

    • You can’t feed the present population by just letting things be, the way it happens in the forest. Everything must be concentrated, that we may all eat. Is this good or nice? Probably not. It is a violation of nature, but it is not reality to ignore that concentration of food plants requires concentration of nutrients. I don’t like it, but that is reality, that is the way things work.

    • “I’d like to know who fertilizers the adult ecosystem of a forest? And who waters it? And how could you defend fertilizers and then admit that they are dangerous when overused?” Are you implying organic ferts cant be over used?

      • 1) Everything is good at the right dose and toxic at high does – even water can kill you.
        2) Yes – organic ferts can be overused and results in toxic conditions.

    • True – overuse will result in pollution. Proper use by homeowners will not cause such a problem. the key is to only use what you need, and only apply the nutrients missing from soil.


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