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.

Microbe Science for Gardeners Book, 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, 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.

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. Wait till someone explains to them that you can supplement plants with synthetic nutrients add microbes and feed them – all at the same time!

  2. Holy moly after reading the comments. As a new gardener, I appreciate your site as a contrast to all the ‘Gardening Rules’ that abound. It is amusing that people will defend ‘Gardening Rules’ without question as if they were the Ten Commandments.

  3. Robert, it is great to see your writings on this topic of fertilizers and soil microbes. But a bit troubling to see the comments of some who are missing the whole point of your topic. You are spot on with your points. I finished at Cal Poly in 1997, EHS. The study of horticulture science under an “environmental” lens. A woman gasped when I told her I put a little miracle grow on my tomatoes yesterday. “OH heavens, I only go organic” she told me. “Well I do too by and large” I told her. “But I have a three gallon bucket of miracle grow concentrate that I have been trying to use up over the years…left over from a job all the way back to 1997” I continued. That is how long the bucket has lasted–25 years. I could have tried to explain to the woman that, sure, the miracle grow has a higher analysis than organic fertilizers….and that for that reason I use less of it by weight per application–and over time. I could have also painfully explained to the woman that a nitrate ion from a Dr. Earth fertilizer is identical to a nitrate ion from a miracle grow fertilizer. I could have also gone into the fact that I never use pesticides….and then tried to explain things to her regarding CEC, proper fertilizer application practices, microbe-ion relationships, da da da da…..but I had little time yesterday. Thank you for your patience in this blog and debunking of the myths that are abound.

  4. All I know is that “farming” with living soil and dry amendments makes things a lot easier. The soil does all the work for you, and the soil with the microbes allow the plant to take what it needs when they need it. Since I switched from synthetic nutrients to living soil and dry amendments my crop not only became 5 times easier to grow without any deficiencies or toxicities. Never even a yellow leaf. Harvest all improved in quality and quantity by amounts I can’t begin to compare. All of a sudden growing became easy peasy with top shelf harvests.

    • 1) soil is not living – it has life in it.
      2) “soil with the microbes allow the plant to take what it needs when they need it.” – not really. The microbes get their nutrients directly or indirectly from the minerals in soil, or from the organic matter you add – which got its minerals from the soil, not from microbes. Secondly – Almost all soil has microbes – but not all soil has the nutrients that support good yields on crops.

  5. It is sad to see an article like this. There are numerous situation that proves chemical fertilizers kill microbes, further more you have to look at chemical fertilizers applicant in a whole which involves tillage, ripping and monocrop culture.

    • 1) All those examples and yet you were not able to come up with even one?
      2) “tillage, ripping and monocrop culture” – are completely different things and have nothing to do with the effect of fertilizer on microbes.

  6. SMH If synthetics kill microbes then explain why beneficial bacteria are used with synthetics in deep water culture and coco hydroponics? It is true salt build up can kill the micro herd but long before that happens the plant itself dies from it.

  7. Great post and great responses and discussion in the comments. This whole synthetic vs organic, gmo vs non-gmo, etc. drives me nuts as a scientist. Obviously there are pros and cons of each for a variety of different criteria and that’s not what you’re trying to prove here, any attempt at derailing this by adding a “but what about this unrelated thing” is absolutely missing the whole point of the post.

  8. As a retired Extension educator of sustainable Ag, I reflected on your comments of this topic and want to offer some more “Food for Thought”:

    – to state that synthetic and organic fertilizers are chemically equivalent as ultimately “ions” for plant uptake is to ignore the progress in the soil science of the role of the soil food web in facilitating the provision & uptake of nutrients by plant roots. More and more research is highlighting the fact that the biotic interactions at the rhizosphere level can provide nutrients as chelates of nutrient molecules &/ or as soil mineralization products quite efficiently as major sources of soil fertility.
    – I must also call you on your misrepresentation that the use of synthetic fertilizers has not been shown to negatively impact soil life. Research from many sources, eg., Rodale Institute and Soil Association, have reported various measures of greater levels of soil life & biodiversity in organically compared to chemically farmed soils. The loss of soil life consequently reduces the basis of soil fertility described above.
    – This negative “chemical treadmill” then is the cause of current research estimates of overall efficiency of applied synthetic fertilizer to be about or lower than 50% for N, less than 10% for P, and about 40% for K.
    – Finally, I would encourage you to expand your original question about fertilizers to the agroecosystem level. The use of chemical fertilizers is linked to all the management practices of industrial Ag which is documented to produce the following major economic, health, and environmental impacts:

    * They cause dependency on chemical fertilizer companies.
    * Water pollution and disruption of aquatic ecosystems, like in the Gulf of Mexico Dead Zone.
    * Application practices of synthetic fertilizers depletes soil organic matter which leads to soil compaction, loss of water retention, increased erosion, loss of tilth- in other words, loss of “soil health”.
    * Harmful synthetic fertilizers damage human vascular and respiratory systems. Also harmful nitrites from synthetic fertilizers leach into the groundwater, rivers & lakes, and can react w/ hemoglobin in the blood stream to cause methaeglobinaemia.
    * Synthetic fertilizers deplete the soil of nutrients and produce malnourished crops of poor nutritional quality, eg., deficient in iron, zinc, carotene, vitamin C, and protein.
    * Overuse of synthetic fertilizers, eg., N, produce crops more susceptible to pests and, consequently, require increasing amounts of pesticides.

    Thanks for considering my comments, and I look forward to your next entry.

    • 1) I am sure will agree that the plant nutrients released by both synthetic and organic fertilizers are the same. That is not to say there are not other benefits from organic fertilizers.
      2) Rodale Institute is hardly a source of scientific information.
      3) You have expanded my topic by a huge amount. My point with this post is to counter the common argument that synthetic fertilizer is somehow toxic and should not be used simply because they are toxic. Also to emphasize that the nutrients from both sources are identical – something few gardeners understand due to all the misinformation around.

    • Late, but on some of your points,

      “They cause dependency on chemical fertilizer companies.”
      I’m not sure why this is a big deal. In any industrialized country, we already depend on lots of companies. Besides, lots of organic farms also depend on outside inputs like compost or fish fertilizer.

      “Application practices of synthetic fertilizers depletes soil organic matter”
      I’m no farmer so it wouldn’t be surprising to me if typical practices were really like this. But that doesn’t mean it is impossible to farm with synthetic fertilizers and also replenish soil organic content.

      “Synthetic fertilizers deplete the soil of nutrients”
      Growing crops and harvesting them depletes soil of nutrients. If the soil is deficient in certain nutrients following fertilizer application, that’s really the fault of the person failing to select the right quantities of the right fertilizers.

      “Overuse of synthetic fertilizers, eg., N,”
      I don’t see how this is different from organic fertilizers. A huge dose of urine seems like it could do the same thing. Besides, the mere possibility of misusing something doesn’t mean it should be banned.

  9. Time to catch up for the writer of this post. Thank you to cover such an important topic. Look for mixotrophy in this article. You still believe in von Liebig’s simpliciation that was refuted quickly and credibly (and still is) by relevant science
    Then afterwards, you might read:

    • Your first link is a book, not a study.

      The second link looks at soil after 35 years of agriculture using synthetic chemicals. It found microbe populations changed. Not a surprise at all. The problem is that there is no clear cause and effect established. Long term agriculture causes all kinds of issues, the most important is loss of Organic matter. That alone can account for the changing populations. Not to mention things like over fertilization, use of the wrong fertilizers, excessive tilling etc.

      It does not show that applying synthetic fertilizer caused the change.


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