Soil Microbes – Do You Need To Add Them To The Garden?

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Robert Pavlis

People are starting to understand that microbes (ie microorganisms) are very important to a healthy soil. This knowledge has led to a disturbing trend where people feel the need to add microbes to soil, and manufacturers are responding with an increasing number of products. In this post I will look at the misconceptions behind this trend.

Soil Microbes - do you need to add them to soil?
Soil Microbes – do you need to add them to soil?

Soil Microbes

To start off, let’s define the word microbes. A microbe, also called a microorganism, is a generic term to refer to a wide range of microscopic life which includes things like fungi, algae and bacteria. Algae play a minor role but will not be discussed in this post.

Microorganisms digest organic matter, and in the process they provide nutrients to plants, and improve the structure of the soil. A gardeners job is to increase the number of microbes in the soil, and to provide the food they need to be productive. When this is done properly, plants grow well and soil is improved. There is no question that microbes are important to the gardener, the plants and the soil.

Each gram of soil, which is about the weight of a paperclip, contains anywhere from 100,000 to 1 million living microbes. That is a lot of microbes. Not only are there a lot of them, but there are also many different kinds. The kind of microbes present at any time depends very much on soil conditions such as moisture, temperature, pH, chemicals present, and available food. Even the kinds of plants growing in the soil will have an effect on the type of microbes present. So the microbes under tomato plants will be different from the ones under a zinnia.

Food Science for Gardeners, by Robert Pavlis

How do these microbes get into the soil in the first place? Microbes are very small, and they are everywhere. Animals, insects, air and water move them from place to place.

The bottom line is that your soil contains thousands of different microbes already. If the conditions suit them, they will grow, reproduce and prosper.

You don’t have to add microbes to the soil, because it already has lots of microbes.

What About Poor Soil?

Some people make the argument that poor soil (heavily compacted soil, sand, extremely heavy clay etc) does not have a lot of microbes and therefore there is value in adding more. It is true that poor soil has fewer microbes, both in type and quantity. The soil conditions are such that microbes don’t grow well.

In this case does it make sense to add microbes?

The answer is NO. If you add microbes and the soil conditions are not to their liking, they simply die. If the conditions are acceptable to the microbes you add, they would already be there. Adding microbes to poor soil does not work. You need to first improve the soil, and as this process is taking place more microbes will come.

Sources of Microbes

This section reviews some common sources of microbes, both commercial and home made.

Compost Tea and Manure Tea

I have reviewed this topic in the past in Compost Tea. One of the ascribed benefits of these teas is that they increase the number of microbes in the soil. The problem with compost tea and manure tea is that you have no idea which microbes you are brewing. The home owner has no idea if the microbes are good for the soil or not. It is quite possible that you are brewing up a batch of pathogens that can damage the microbes already in the soil, or your plants, or even yourself. You could be brewing a batch of dangerous E.coli that will make you sick–you just don’t know.

Compost and manure already contain all kinds of microbes. Just add them to the soil as compost or manure and skip the brewing process.

Soil Science for Gardeners book by Robert Pavlis


Mycorrhiza is a type of fungi that is very important for plant growth. Companies have started packaging them and promoting them to consumers. At first they were sold as an additive to soil, but now you can find them added to many soil and soiless products.

Your soil already has mycorrhiza so you don’t need to add them.

There are hundreds and maybe even thousands of different types of mycorrhiza, some of which are very specific to certain varieties of plants. Commercial products, at best, contain 4 types. Many products contain fewer types. You don’t know that the ones in the pail are the ones your plant needs!

Mycorrhiza are fairly sensitive to high temperatures. If the container holding them gets too warm, like sitting on a truck too long, they die. You have no way of knowing that the product you buy actually contains living mycorrhiza. It may just be a very expensive, useless white powder.


Probiotics for soil is the same idea as probiotics for your intestines. They are a combination of microbes that you buy and add to your soil.

How do you know if they are living? You don’t.

Will they live in your soil environment–remember microbes only grow in environments that suit them? You don’t know.

Probiotics for soil is just another way to fleece you of your money.

Keeping Soil Microbes Happy

Your soil already has lots of microbes. Don’t add more using commercial products or compost tea. The secret is to provide the microbes you already have with a home they love. How do you do that? Feed them.

Microbes eat and digest organic matter. Keep adding compost, manure, plant cuttings, wood chip mulch etc, to your soil. Just growing plants in the soil will provide organic matter for microbes to eat. Disturb the soil as little as possible. No rototilling–it destroys microbes. Hoe as little as possible for the same reason. Walk on the soil as little as possible–compaction kills microbes.

Note added January 2015: A comment was made below that made me think about the italicized statements. Does compaction kill microbes? It is something many people say, but is it true? Have I simply fallen into the myth trap and repeated a myth? I think that my statements are not completely true, but the subject is more complicated and needs it’s own post in the future. For now, I do feel confident in saying that compaction is not good for the garden because it destroys soil structure and that the microbe community will be happier without compaction. Rototilling and hoeing also destroys soil structure, and will disrupt fungi in the soil.

Bacteria, the most important microbe, grows very quickly. They can double in number every 20 minutes. If you had only one bacterium and you provided food and other suitable conditions, you would have 250,000 in 10 hours. Who needs to buy them??

You might also be interested in this post about using a microscope to identify microbes: Soil Bacteria – The Myth of Identification and Management.


1) Photo Source: EMSL

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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!

37 thoughts on “Soil Microbes – Do You Need To Add Them To The Garden?”

  1. As always you make some good points about the limits of at home soil microscopy that anyone trying to use it should know, I think you are making another straw-man argument here. Dr. Ingham explicitly states in here soil microscopy videos that are freely available that the goal is not to identify individual species, which she also states is not possible without much more complex processes and equipment. My understanding of her is that she is more suggesting looking at the sample like a forest ecologist would look at any given spot in a forest ecosystem, and one can great insight by doing so without identifying any given species.

    As a forest ecologist that has specialized in the Pacific NW, I could go to a different forest in New Zealand or some other foreign place and be pretty decent at identifying their ecological health simply by looking at its diversity, biomass, and structure. I can tell if I’ve seen 30 different birds, or dozens of different trees, ferns, flowers, etc. If I see predators, or sign thereof, I know something is supporting them. Diverse predators of all shapes and sizes are even better. I can identify predators by their morphological characteristics (skull, footprint, gait) or their scat.

    Similarly, even basic first impressions by a relative novice in soil microscopy (like myself) can be valuable and informative for making decisions as a gardener. For instance, “wow that homemade compost has an abundance of diverse fungi and protozoa compared to the bagged and bought compost we just looked, which had mostly bacteria and fewer humates and aggregates, and even those bacteria were much less numerous.” We can also see the differences in similar factors between soils with differing disturbance histories, and then make decisions with better insight as to where in the soil ecology succession process we are, what we want to avoid doing again, and provide the habitat for what we want to grow below and above ground.

    I appreciate your insights, but I often find your articles deflating straw man arguments that are frustratingly myopic.

  2. My question around this stems from my knowledge of organic gardening/gardeners, not on science, but hopefully someone can fill in my gaps here.

    Apparently, soil that is reused actually becomes better with time. So the first crop harvested in your soil isn’t as good as the 10th crop in your soil. If this is true – and feel free to debate that, would mean that something is different in the soil between grow 1 and grow 20. What would that be? I would think the soil is more “living” with higher microbial counts (and varieties?) as time progresses.

    If the microbes are already all present and can multiply just as effectively (without inoculants) then what is changing in the soil as it ages? Gardeners want to keep their root balls in the soil instead of pulling them in order to keep the rhizosphere microbes present. If the microbes are so easily and quickly replaced, why would one want to keep root balls in? I’m aware of roots following the same path – although I understood the no-till life creates better conditions over time.

    Any thoughts on this?

    • I have mentioned Dr. David Johnson and the Johnson-Su Composting Bio-Reactor before or maybe just his name. He uses the compost he makes to create a slurry to inoculate the seeds he plants with according to him, very good success but am waiting on the research to confirm but this maybe be something we as gardeners and small farmers we have to confirm on our own. There isn’t much money in telling someone how to do something for free. He does have You Tube videos but no book and probably no grant money to do a study or research to confirm. He is a Soil Microbiologist and yes the microbiology is all around us. Nothing is better for the health of the soil than live roots.

      As far as no-till we are trying to sequester carbon to mitigate climate change and by now everybody knows bare soil bleeds carbon. So if you must disturb the soil, do it minimally. Another thing, don’t confuse Soil Organic Matter and compost. Compost is on its way to being som but is still mostly food for the microbes, som is not. It is highly stable and needs either the plants or the environment to act on it to change.

      If you are starting out, please start as Robert suggests with a soil test the first two years and then every 3-5 years depending on production. The first two years will confirm if your practices and methods have you headed in the right direction and how well they are working. Too much compost is not necessarily a good thing according to the first rule of gardening; too much of a good thing can be and usually is a bad thing.

      We are just at the beginning stage of learning the practices and methods of stewarding the soil microbes. Take care of them and feed them properly then the plants should have an environment in which to grow up healthy and productive. The microbes are there or will be soon. I guess I am becoming a gardening cowboy, I knew eventually the hats and boots would be back in style.

        • Robert, you are right, for some reason humus being stable organic matter sticks in my head as som. It is not the learning that is slowing me down but the relearning. I did do some research into the definitions and soil health at the USDA and had an epiphany on the C:N ration as I was researching as to the what, why and when which was a good thing to learn and hopefully understand the importance finally getting it.

    • There are several things that cause this. First when those roots were left decompose it not only left nutrients for the soil but channels for oxygen to move into soil, the same function as worms and strands of fungi. Good soil is porous to allow oxygen. It’s not really about the number of living organisms, it is about the balance. The bacteria attach to roots and eat the plant sugars. Protozoa eat the bacteria and leave behind plant soluble nutrients from their waste. If the protozoa are too abundant they are consumed by nematodes which are eaten by small insects. It’s an entire food web. Given good conditions like adequate oxygen and water over time the soil life will begin to balance, creating better and better conditions for growing. The microbial life in your soil is specific to it’s environment, the PH, the acidity, all factors to what species may be present. It’s just not something that can be imitated.

  3. The Rhizophagy Cycle with Rutgers professor James White

    This is a link to a 2-hour interview, but I’ll just suggest start watching at 1:07:56 and go until 1:10:18. The interview is with a Rutgers prof who’s been researching endophytes for 40 years. The discussion focuses mainly on the rhizophagy cycle. It’s a LONG interview, I know, and would certainly not ask you or anyone to watch it all, in part because the audio quality of the researcher, James White, is not so great, and because he isn’t speaking very fluently! Also, there are places where I think he kind of rambles a bit too long. However, it’s a fascinating interview, which touches on LOTS of things related to microbes.

    • I listened to a bit of it.

      “plants lose the microbes once people mess with them” – that is not true. If it were, scientists would have a hard time studying the microbes.

      Then he goes on to say “if we treat seeds with a lot off Clorox, the seed no longer had microbes on them – true, but what has that got to do with them growing in the ground???

      He then says you should not buy disinfected seeds because it removes the microbes. But those microbes could also be pathogens!

      In the few minutes I listened i did not hear him say that adding bought microbes to soil works. Even if he did, I want to see the published papers.

      • I hope James White didn’t mean that all microbes disappear once people handle the plants. I hope he just meant that many die off!

        As for the Clorox part, the guys discuss that microbes on the surface of the seeds are crucial to strong healthy plants, that don’t need agrochemicals. In other parts of the video, they say that storing seeds in cool, dry places is detrimental to seeds because the microbes that ought to be on the seed during the growing stages aren’t on the seeds.

        As for store-bought microbial products, I’m not promoting them! I saw this video, thought it was really interesting, and wanted to share it with you. I didn’t know how else, so looked for a blog post that was relevant, and this seemed about the most relevant I could find 🙂

  4. Rather than explaining why your entire article was wrong I’ll start with the part you admit you know nothing about. Compaction is bad for soil because it reduces oxygen which anaerobic bacteria growth. What you want is aerobic bacteria which grows in air, a good way to get air deep down is roto tilling. Your happy with any old microbes developing naturally in your garden (nothing wrong) but tea brewers have no idea whats in their tea and the benefits of certain ingredients? Just because you have no idea doeant mean science doesnt 🤣 I’m embarrassed for you tbh

    • Actually science doesn’t either. So far science has only identified something like 20% of the microbes in soil.

      I am not sure what point you are making – nor do you connect the rambling to a fact you are trying to disprove.

      If you think my article is wrong – simple – provide some scientific evidence that it is wrong.

  5. I am curious if using powdered hemp (Industrial type) can be added to both enrich the soil and double as a pesticide for plant growth.

  6. Robert, I had just read an article by a gardening product retailer, discussing soil microbes and beneficial bacteria. That’s why I ended up here… They used many big words and seemed very educated. But, finally, they shot their gun and highly recommended inoculating your soil, once a week, with their products. Okay. Now, the thing that gets me is that whom ever wrote the article, obviously, is educated enough to know that those products were unnecessary, i.e., I think we are not merely dealing with ignorance by misinformation, we are also dealing with calculated, educated scam artists who only want our money. Anyway, I like what you’re doing on Garden Myths, using objectivity to expose these things. Thank you.

    • I think a lot of the marketing is done by people who know better but want to sell stuff. But marketing people rarely have a science degree, and they will just copy what more established products say. In this case the writer just does not know any better.

      If you know the science it is usually easy to pick holes in it, because it is just a string of sciency words with little logic.

      Unfortunately – there are so many of them and only one of me!


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