Does Fertilizer Kill Soil Bacteria?

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.

Compost Science for Gardeners by Robert Pavlis

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.”

Building Natural Ponds book, by Robert Pavlis

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

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. I’m a soil expert, I’ve spent years studying and have my own fertiliser company. People like to refer to studies, but studies can be bias and contradictory. Soils treated with synthetics contain far less microbial life, regardless of farming practices and the use of pesticides, fungicides, etc.

    Instead of reading and relying on information from others why don’t people take their learning to another level and find out for themselves. Buy a microscope and run strict trials, ensuring a fair test.

    Synthetic fertilisers break the symbiotic relationship between plants and microbial life, creating dependency and a multitude of other problems for crops, plants and on the environment.

    But to stay on point! Synthetic fertilisers used properly kill microbes at an alarming rate. Buy a microscope! They are cheap and see for yourself who is correct. Take your lessons from nature, it’s been around for a while lol.

    • “Instead of reading and relying on information from others why don’t people take their learning to another level and find out for themselves.” – that is precisely what does not work. When people ignore science and go with their observations is is a step backwards to a lower level.

      Synthetic fertilisers used properly kill microbes at an alarming rate.” – lets see some references to support your claim.

  2. Regarding above conversations .what happens when the diluted salts that are placed into the soil as fertilizer then the water evaporates and the salts then become concentrated in the soil returning back into salt form as the plants woukd not be able to consume all the ions present that being so you then have a raw concentrated salt content in the soil not being held by any proces /biology etc apart from when it rains or is watered again ‘re diluting the salts then re evaporating again etc this is one way how the salts damage the soil and roots biology etc now given time I’m sure the biology eventually would process these ion salts but without the biology first controlling the stages of delivery by SKIPPING this step and aplying fertilizers in this way causes damage .now I’m sure that a very very very diluted amount of salt ions would be aceptable on its given ocasion and in the case of HYDROPHONICS it is essential and being used in its proper contexts as the salts/ions are always in diluted form and never concentrate through evaporation etc .there are many aproaches to fertilization and all should be perceived in its proper contexts. But applying synthetic salts into SOIL severely harms both soil and plants. That is just one way it causes harm even ion salts that are extracted from and with natural sources and means can do the same damage if refined and concentrated and removed from their biological contexts .the plication of salts has to be with a biological proces as carrier and in an analogous way the shape has to fit the box or triangle or circle .it has to have the apropriate proces delivered with it as a BUFFER. It’s aplication (salt ion) may have an initial beneficial visual response but the build up of salts over long periods is inevitable if used as a sole source of plant nutrition .I would only use synthetic fertilizer in a hydroponic situation and maybe as a one time dilute aplication with microbiology added to the salt solution prior to its aplication in the field .big subject small but apropriate answer. Thank you.

    • “what happens when the diluted salts that are placed into the soil as fertilizer then the water evaporates and the salts then become concentrated in the soil returning back into salt form” – Then they sit in the soil as a solid until it rains again. As the soil dries, the salt concentration does increase and can damage roots.

      But once they are ions, they also get absorbed to clay and compost particles and when those dry, they don’t reform the salts. Also, ions wash away as water moves down the soil profile, moving out of reach of roots.


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