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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
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.

13 Responses to 'Does Fertilizer Kill Soil Bacteria?'

  1. 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.

  2. 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.

  3. 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.

  4. tolga erok says:

    very interesting, thank-you for the clear information

  5. Nadav Ziv says:

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

  6. rogerbrook says:

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

  7. 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.

  8. Dan OConnell says:

    Nice article

  9. 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

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