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Does Fertilizer Kill Soil Bacteria?

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.

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 (ref 1), 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.

Adding 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, ref 2, 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.”

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.

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.


  1. Impact of Organic and Inorganic Fertilizers on Microbial Populations;
  2. Ammonia and Urea fertilization – Facts and Myths;$department/deptdocs.nsf/all/faq7758
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Robert Pavlis
Editor of
I live in southern Ontario, Canada, zone 5 and have been gardening a long time. 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!

I hope you find Garden Myths an educational site that helps you understand your garden better.

21 Responses to 'Does Fertilizer Kill Soil Bacteria?'

  1. Rays says:

    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.

  2. deb says:

    Perhaps, but there are other reasons to avoid using these products:

    • 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.

  3. Gavin Anderson says:

    in regards to the study you have a link to, I believe it is flawed. When using plate count method you are growing anaerobic microbes. Plate count methodology is great for assaying human pathogens (what they were created for) however they fail to give a true indication an healthy soils microbial count and/or biomass.

    Also when using plate counts the food source provided to the microbes is extremely limited. They are 000’s of different foods in healthy soil bacteria and fungi use to grow, how can we expect aerobic microbes to grow in anaerobic conditions with limited food source?

    To assess soil life you need to use direct microscopy not plate count methods. Miss information can come from everywhere and I think this case the the study you are referencing.

    Ha, also the organic ferts used consisted of neem cake!!!! a pesticide used to control nematodes. You think that it kills bad nematodes and not the good ones? Its clear the people running the study have know idea about soil microbiology. As someone who understands soil biology would not use neem cake as a fertilizer-pesticide combo

    Who is sending out misinformation?

    “The use of inorganic fertilizers resulted in low organic carbon content, microbial counts and microbial biomass carbon of the soil, although it increased the soil’s NPK level which could be explained by the rates of fertilizers being applied.”

    This statement from the abstract reveals the organic carbon is depleted. This is because the over activity of the bacteria to use up all the nitrogen that was dumped in. The soil has lost humus! We all know how important humus is for soil. Bacteria need 5 carbons for everyone nitrogen so they are going to get those carbons from the humus and organic carbon rather then the plant exudates. I wouldn’t want people thinking all they have to do is correctly manage synthetic ferts and they are in the clear.

    I know this article is focusing about salts not everything else I have mentioned. Thanks for writing it, I have learnt something from it too! 🙂


  4. troysantos says:

    Do you have an idea why people argue that synthetic fertilizers kill microbes? I can understand that, since the plants’ roots can take up the ions right away, the microbes aren’t needed to make these ions available to the plants, and in this way, I can understand that microbes MIGHT die. Though I really can’t say that I can understand WHY EXACTLY they’d die.

    • Microbes don’t die after fertilizer is added. Microbes flourish when nutrients are high – but not too high.

      The main reason people think this is that some groups, like organic gardeners, spread false rumors. These rumors get started because this group is anti-chemical so any chemical is bad, and modern day farming has resulted in a degradation of soil. Fertilizer seems like a good suspect to blame.

    • Chitown says:

      Its probably also a result of people over fertilizing. This article also does mention under ” proper fertilizer application.” with the high concentration on synthetic nutrients its easy to over do it. Its not uncommon for the bottle to suggest using a higher dosage than neccesary. They want you to go through it and come back for more as quickly as possible.

  5. peripeton says:

    The main difference between organic and industrial fertilisers is the impact to the environment during their production. The industrial fertilisers use huge amounts of energy and are usually transported from far away, adding energy waste.

    Organic fertilisers are produced with a lot less energy input and can usually be produced locally. That’s more than enough of a reason to always go organic for me.

    • Very good point. I agree, any time you can NOT buy something you are doing something good for the environment.

      The problem is that some people buy organic material that is also trucked a long way and undergoes processing, ex fish fertilizer and kelp.

  6. Scott Skogerboe says:

    Very interesting take on this subject. Maybe in areas of high rainfall like the eastern portions of North America the case can be made that Salts do not accumulate and have a negative effect on Soil microbes. Sufficient amounts of rainfall do leach salts below the root zone back east. But in the arid parts of the western US (where I live) and elsewhere world wide. Salt accumulation has caused the abandonment of millions of acres. In fact 7.7 sq miles of land is lost to salinization EVERY day. It is costing our society $billions in economic loss every year. It is a serious problem. Yes the salts aren’t all coming from synthetic fertilizers but also come from salty irrigation water which when the water evaporated leaves the salts behind to accumulate. Here is an excellent read on the subject.

    • The reference you gave says “But applying too much water can lead to salinization.” It makes no mention of fertilizers.

      If fertilizers are applied correctly they will only be adding the nutrients plants need. I think these are two different issues.

  7. tolga erok says:

    very interesting, thank-you for the clear information

  8. Nadav Ziv says:

    As always, you have wrote another excellent post. Thank you.

  9. rogerbrook says:

    A good dollop of common sense as usual Robert.
    It really frustrates me how much false information is peddled around in horticulture

  10. Mike Ellison says:

    Excellent article. I too have a background in soil chemistry and own a nursery. I have been saying similar things to the bewilderment of people for years. Thanks for your wisdom.

  11. Dan OConnell says:

    Nice article

  12. Dan OConnell says:

    seems like the main difference between synthetic and organic fertilizers would be mostly rate of release of nutrients. I wasn’t very aware there was such a big controversy over synthetics killing soil bacteria. Nice article