Buying Soil Probiotics (Microbes) – Are They Beneficial, Effective or Nonsense?

Robert Pavlis

The market is being flooded by new products offering all kinds of soil microbes. Many companies call them “beneficial” and others call them “effective”. Specialty products like mycorrhizal fungi, probiotics and bacteria for degrading lawn thatch are now available. There are even probiotics to speed up your compost pile.

The market is still sorting out the terminology for these products but I see the name probiotics used more. If they are good for your gut, why would they not also be good for your soil?

What do these products really do in the garden and are they worth buying?

Buying Soil Probiotic Microbes - Are They Beneficial, Effective or Nonsense?
Buying Soil Probiotic Microbes – Are They Beneficial, Effective or Nonsense?, credit Youth & Earth

Soil Microbes – A Quick Dive

This section alone could fill a book and in fact it does take up a significant part of my book, Soil Science for Gardeners. Here is a quick summary.

The two key groups of microbes in soil are bacteria and fungi. There is no doubt that these are critical for both soil and plant health and a gardeners job is to grow more microbes in soil. If they do that, they solve all kinds of gardening problems.

Microbe Science for Gardeners Book, by Robert Pavlis

Some facts:

There is no doubt that existing microbes are critical for the garden and that gardeners should take steps to grow more of them, but is there any benefit to adding them from a purchased bottle?

Microbe Populations are Dynamic

Microbes reproduce very fast when conditions suit them, and when conditions are no longer acceptable, they die or go into a state of hibernation, allowing them to wait until conditions improve. Population densities change very rapidly.

The species that are present at any given time are also very dynamic. If soil gets wetter or warmer, new species start to thrive, while others die off. Food sources have a great influence on populations. Most species can digest sugars, but only a few can survive on the lignin in woody plants. Oxygen levels and temperature are also important.

Science is just starting to get a handle on this, so as gardeners we really can’t tell what we have in our garden at any one time. We also have no way of knowing how to manipulate the populations to our advantage because we don’t know when and if it changes.

The fact that manufacturers of products claim to know exactly which microbes you should add to soil is quite surprising and should trigger all kinds of red flags. How can they know this when scientists don’t?

Bacteria grow very quickly when conditions are right
Bacteria grow very quickly when conditions are right, credit: Frontiers for young minds

Soil Microbes Are Always at Capacity

Thanks to Chuck, one of our members in the Garden Fundamental Facebook Group for putting this complex concept into such a simple term.

“Soil microbes are always at capacity.”

What this means is that in any type of soil the microbe population is always at maximum strength. Microbes populate an area so quickly that they are always filling any available space in soil, limited only by the conditions.

In very poor infertile soil, there is limited food so the population is smaller, but it will as large as the resources allow.

Really good fertile soil will have a much higher population, but again it will be at maximum capacity.

You simply won’t find soil where microbes have not grown to their fullest potential.

Soil is always full of microbes
Soil is always full of microbes

What Happens When Microbes are Added to Soil?

They will mostly likely die! A review of this topic concluded that, “Inoculation of soils has already been applied for decades, but it has often yielded inconsistent or disappointing results. This is caused mainly by a commonly observed rapid decline in inoculant population activity following introduction into soil, i.e., a decline of the numbers of inoculant cells and/or a decline of the (average) activity per cell. ”

There are two main reasons for this. The first one is that the space in soil is already occupied by native microbes. In order for the new ones to survive, they have to kill off the existing ones so that there is space and resources for the new ones. You can’t add another person to that phone booth without removing one.

The second reason is one of environment. Microbes are fairly fussy about where they live, what they eat and who their neighbors are. The chances are very good that the soil environment is not suitable for the new microbes, in which case they die. If the soil was suitable, they would already be there.

There is very little evidence that supports the idea that added microbes will prosper and colonize the soil.

What Are Beneficial Microbes?

Most academic discussions just talk about “just” microbes, but manufacturers of products like to use the term “beneficial microbes”. Gardeners seem to like the term too. By definition these are microbes that are beneficial to plants which includes anything that is not a pathogen. Even if a microbe does not help a plant directly, it usually helps indirectly, by providing nutrients to soil, or improving soil structure.

The term beneficial microbes tells the gardener nothing about the contents of a product – it is a marketing term that is used to make the product seem important.

What Are Effective Microbes?

The term Effective Microorganisms (EM) was initiated by Dr. Teruo Higa to describe a combination of about 80 different microbes which were capable of improving the decomposition of organic matter. He developed the idea that the right combination of “positive microbes” would improve any media, including soil. The initial product was called EM-1, which contained three groups of microbes: yeast, photosynthetic bacteria, and lactic acid bacteria.

Since the introduction of EM-1, many other formulations of effective bacteria have been produced by a variety of manufacturers. When you buy a product containing effective microbes, you are buying a combination of microbes that the manufacturer considers important.

Marketing departments and gardeners routinely mix up the terms, beneficial and effective.

What Does the Science Say?

A lot of research has been done in this area and some studies show that bacteria or fungi added to soil improves soil and plant growth, while many others show no effect at all.

The problem with many of these studies is that they don’t design the experiments to separate the contribution of the actual organisms, from the media holding them. I have discussed this before with compost tea. You can’t compare tea containing microbes to water, because we know the tea contains nutrients that help plants grow. To prove the value of the microbes you have to compare compost tea containing live microbes to the same tea containing dead microbes. Almost no studies do that.

Many of the positive studies are lab experiments that are not using native field soil. When field soil is used results tend to be negative. For example, when four commercial products were added to tomatoes growing in field soil containing native populations of microbes, they did not improve plant growth and had limited effect on the native microbe population.

When studies are properly designed, most show no benefit when microbes are added to soil. There are some very specific cases where the addition of identified microbes reduce a specific plant disease. There are also well known inoculants like rhizobium bacteria for legumes. However, the science does not support the general idea that adding microbes to soil will improve soil health.

Quality of Commercial Products

If you buy some soil probiotics you will get a bottle, or package that contains a liquid or powder. A gardener has no way to know what is actually in the material.

Oregon Department of Agriculture has been testing products containing beneficial microbes. “Of the 51 products tested for bacteria, only nine met their guarantees. Of the 14 products tested for Trichoderma, a fungi, none met their guarantees. Of the 17 products containing mycorrhizal fungi, only three met the guarantees made on the product label.” DNA testing showed that in some cases the organism had never been in the product. In other cases the organism was no longer viable.

Remember that probiotics are living organisms. They have to be produced and stored correctly, or the product is worthless.

Probiotics in Agriculture

If probiotics worked, agriculture would be the most important customer for them because agriculture is driven by profit. Any product that can increase yield will be adopted.

A recent discussion, by an industry insider, about the lack of adoption of probiotics in agriculture highlighted two important reasons why they are not used more.

Probiotics are only successful when abiotic soil factors such as texture, pH, temperature, moisture content, and substrate availability are critical assessment to determine if they match the microbes needs. This is difficult for agriculture, but impossible for gardens.

The current science does not support their wide use in agriculture and there is almost no evidence they work in gardens.

Do You Have a Microbe Deficiency?

Companies are telling you that you need to add more microbes. Why not ask the question, “do I have a deficiency?”

How can you measure a deficiency? How can you tell which microbes you have and which ones are deficient?

The short answer is that you can’t find this out. Even labs specializing in this kind of testing can’t identify the microbes you have because scientists have not even named most of them. These labs can give you some general numbers for bacteria activity or fungi populations, but what do you do with this information?

There are no guideline numbers that indicate degrees of healthy soil. No one can test your soil and give you a list of the microbes you are missing.

And yet, manufacturers of these products are quick to tell you that their product will improve your soil. They have no way of knowing this. And you as a gardener have no way to verify that your microbe populations improve after applying the product.

Perhaps the most important point is that you never have a deficiency because microbe populations are always at capacity.

Probiotics Added to Soil

One of the claims by manufacturers is that they are adding large numbers of microbes and that allows them to overpower existing microbes, thereby eliminating pathogens and modifying natural populations.

How many microbes are actually added?

I looked up Plant Probiotics by Micra Culture. It was the first one I found that provided the contents of the product. A 57 g pack is enough to cover 100 sq ft and it contains 20 x 107 bacteria per gram. This adds 108 bacteria/sq ft.

Lower quality soil contains 108 bacteria per teaspoon, or 6 x 1011/cu ft.

That means the product will add 1 bacterium for every 3,000 bacteria already in the top 6 inches of soil, assuming all of the bacteria in the product are still alive. I don’t consider that a “large number!” Remember that bacteria can multiply very quickly. If given extra food, the 3,000 natural bacteria can be 6,000 in 20 minutes. What effect do you think one extra bacterium has on the population? None.

Also note that 1 teaspoon of lower quality soil has 5 times as many bacteria as one pack of this product.

Have Commercial Products Been Tested?

I have researched a dozen different manufacturers to find a scientific study that shows the efficacy of their product. I have contacted manufacturers and asked for their evidence. Most don’t even try to reply. I did get this reply, “This is a bacterial treatment. No information was published.”

I have not found one published scientific paper that shows these commercial products work. Customers have to start demanding this type of evidence before they buy these products.

If you find such studies please post a link to them in the comments below.

Should You Buy Soil Microbes

Although some very specific products may be beneficial for farmers in certain cases, home gardeners should not buy microbes except in rare cases which I will discuss in another post.

Your soil is already saturated with as many microbes as it will support. Any that you add will almost certainly die.

The only thing you can do is take steps to improve your soil health. As the soil gets better, microbe populations increase naturally.

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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!

31 thoughts on “Buying Soil Probiotics (Microbes) – Are They Beneficial, Effective or Nonsense?”

  1. How do you feel about products that contain multiple strains of bacillus that use humic acid as a carrier? Wouldn’t the humic provide the organic matter needed for the microbes to survive and flourish upon application?

    • show me a study that concludes bacillus lives on humic acid?

      Let me expand your point. What happens if you add bacteria along with a food source – would they then live?

      We, yes, until the food runs out. Then you are back to the same starting point.

      Adding compost, for example, along with the microbes in it, gives them a chance to establish themselves in the soil. But if you add sterile compost (ie no microbes) you accomplish a similar end goal. Native microbes will grow in numbers. So it is the compost, not the microbes, that add the value.

      Humic acid is not a natural material found in soil. It is man-made.

  2. It’s totally fine to share your opinion. And you are making some valid points, but please don’t misuse science. Please don’t first refer to science to increase your credibilty, and at the same time question its integrity.
    If you want to refer to the scientific knowledge in this area, why not be objective about it and state the current obstacles and knowledge gaps, while also acknowledging that the majority of scientifically sound studies show a positive effects of microbial additions?
    While some scientific studies have their flaws, most of them get published via a thorough peer-review process where aspects like fertilisation effects are taken into account.
    I understand that you want to help growers and warn them about false promises of available products. I’m with you. But as a scientist myself, I couldn’t leave your misleading reference to science uncommented.

    • “why not be objective about it and state the current obstacles and knowledge gaps” – that was not the goal of this post.
      “the majority of scientifically sound studies show a positive effects of microbial additions” – if that is the case then why not give us some links to these studies?

        • The first link is a meta data study that looks at the use of probiotics (biofertilizers) in Agricultural settings. They looked at the aggregate result of yields and found a 10-20% increase in yield. There conclusion is that “Our results give strong indications that microbial inoculation is more successful in dry regions.” Almost none of the studies were done in North America – most were done in India and middle east.
          – there is no indication of the number of studies that found no increase in yield – just an aggregate average.
          – yield increases in non-dryland conditions were under 10%.
          – there is no indication of the source of the inoculants – they might be commercial products, or laboratory cultures.
          – the study looked at N and P levels but not at other soil improvements
          – no indication of changes in microbe populations in soil
          – higher organic matter levels had lower yields.
          – lower yields with increased irrigation.
          – no indication of soil condition before inoculants were applied

          It does show that some inoculants are useful in agricultural settings, in certain conditions, which was acknowledged in the post. It says nothing about the use of commercial products.
          The problem is trying to take this information and extrapolating it to gardens, which tend to have higher levels of both organic matter and water. It is unlikely that any of the studies were done in garden-like settings. We don’t know if they were done with commercial products that are available to gardeners. The actual microbes involved are grouped into larger categories making it impossible to know which organisms would be the best choice for gardeners.

          The second study is a meta data study looking at the use of biofertilizers for maize. It concluded that, “Yield increases tended to be slightly higher and more variable in greenhouse studies using field soil than in the field” and “We found greater efficacy of Azospirillum spp. and lower efficacy of Bacillus spp. and Enterobacter spp. under field conditions. Surprisingly, biofertilizer strains with confirmed plant-growth-promoting traits such as phosphorus solubilization, nitrogen fixation and phytohormone production in vitro were associated with lower yields in the field than strains not confirmed to possess these traits. These results indicate the need for a novel biofertilizer development framework that integrates information from native soil microbial communities and prioritizes field validation of results.”

          In short it says, there are some cased where there are positive results and some that are not positive – more testing needs to be done.

          The third link is also a meta data study looking at Plant growth promoting rhizobacteria. The search criteria was for “BPGPR and drought and rhizobacteria and drought”. It does conclude that “that PGPR are highly effective for improving plant growth, with a greater effect under drought for above ground traits. ” “The majority of the observations in this meta-analysis were conducted in the greenhouse” – not field studies.

          As mentioned in my post there are some special cases that gardeners might consider. But how do these results relate to gardens that are rarely in drought condition because of access to water?

          A review of plant growth promoting rhizobacteria had this to say, “Under field conditions, other external factors come into play and the ability of soil bacteria to elicit positive effects on plant growth can be impaired and so that the effects of applying specific PGPM can be variable (Nelson, 2004b). The plant rhizosphere is colonized by microorganisms from the soil and the seed. The determinants of soil microorganisms are based on properties such as C and N availability, organic matter content, water availability and pH (Bossio et al., 1998; Drenovsky et al., 2004; Garcia-Pausas and Paterson, 2011) as well as biogeographic patterns including soil type and seasonality (Kristin and Miranda, 2013). Hence it is necessary to develop strategies for effective inoculation methods, so that bacteria of interest gain advantage in colonization efficiency over others. Product quality, compatibility, and stability determine effective colonization and consistent performance of the inoculum under field conditions (Lee et al., 2016).”
          What is clear from this is that there are many variables that affect the efficacy of any product and that these variables have yet to be worked out.

          • Yes, it’s complicated. And I agree that commercial products cannot be trusted blindly. All I am asking is to not ignore the overall conlusion of the current state of scientific knowledge on probiotics, which is: on average, they do provide a significant positive effect on crop yield (some more than others), also in non-drought conditions. As for gardens, I think it is worthwile testing your garden’s state of soil health (surely, Robert can tell you Canadian services that conduct such tests) and, besides other, more important management practices, try out some probiotics, especially if you encounter a disturbed soil or if you are interested in reducing synthetic fertilisers, pesticides and/or irrigation.
            With “try out”, I mean observe if you can actually see a positive effect. The positive effect can be yield increase or maintaining yield while reducing/replacing fertiliser/pesticides, or improved stress tolerance of your crops. And if you do try out probiotics, let us know here!
            At the end of the day it comes down to ones mindset/philsophy: Sustainable gardening doesn’t need much external inputs, but if you are used to quick fixes such as mineral fertilisers and pesticides, why not try solutions that are less damaging to your soil, the ennvironment and your own health.
            Especially for gardens, I highly recommend the use of composts (yes, it’s probiotics too). This way you are introducing a whole community of beneficial microbes, while promoting native ones and improving soil structure and humus levels. If you make compost yourself, it’s free and recycles your kitchen and yard wastes.

          • Happy to be working them out, field scale and at my expense. I think the science of microbes in agriculture/ food/ health is a dynamic emerging study. Science is Always up to a new challenge, or it’s not science.

  3. I’ve sent this article to multiple soil scientists and plant pathologist that I know. Glad articles like this are coming out. Microbes are always at capacity and plants don’t read books.

  4. Soil microbe interaction with plants – is their difference between soils temperate and tropical regions soils. Thanks for educating me about that EM business.

    • Both soil type and temperature can make a difference. I am not sure how much of a difference there is in soil, at a 6″ depth, between temperate and tropical, in summer?

    • Just found Garden Fundametals and this site. I have been excited by the claims of regenerative agriculture that if its practices were adopted worldwide, we could be back to preindustrial levels of carbon, while storing clean groundwater, deacidifying the oceans, making food more nutritious and delicious, and farming cheaper and safer ( Do you agree with that idea? What seems to me to be missing from the “to add microbes or not” discussion are the ways the soil is treated: is it covered? are there commercial chemical inputs? is there minimal disturbance (no till)?

      • “regenerative agriculture that if its practices were adopted worldwide, we could be back to preindustrial levels of carbon, while storing clean groundwater, deacidifying the oceans, making food more nutritious and delicious, and farming cheaper and safer” – pipe dream that is completely unrealistic.

        Not all, but much of the information provided by soilfoodweb is not science based nor is it supported by most scientific groups.

        That does not mean some of the ideas in regenerative agriculture are not valid or useful in certain situations.

  5. In a world awash in soluable fertilizers, and the inherant expense and pollution, what is the harm in the clumsey pursuit of effective innoculation of soils? You can reference Johnson-Su BEAM Reasearch and Bioreactor studies, at New Mexico State University.

    • What is the harm?
      People wasting time and money on products that don’t work.
      Companies polluting the environment and contributing to global warming making useless products.
      Wasting natural resources shipping them all over the world.

      • Just the tip of a very BIG iceberg, I’m sure you probably know.

        I just watched a vid on yt of giant lettuce, squash, watermelon, ect.
        They must have some secrete recipes. Course aquaponics is a completely different animal. But it’s all food for thought. Great info! Thanks

      • I find the clumsey/ infant pursuit of innoculants,to be well worth the expense given the verifiable response documented by David Johnson’s work at Mew Mexico State. Google it, thats free
        The expense and effort wasted in manufacture/distribution and pollution involved in innocculants is pale compared to the clumsey application of fertilizer with it’s inherant waste of the same resources..
        I think there is a lot to learn.

        • You are right! I can’t document it. I find only anecdotal evidence
          Not double blind replicated published and reviewed documentation.
          I am a skeptic myself but I remain intrigued with innoculants.
          As you state in your opening, can you document that soils or any medium are inherantly at mirobial capacity?

  6. I’m confident my soil has all the fungal & bacterial properties necessary for my needs, as my composting regime ensures I have sufficient to add a 2″ layer of organic matter to the surface of my beds every year.
    I’m happy to spend what I’ve saved on worthwhile items, such as decent wines…

    • Who says she is a soil expert? Her followers.

      When someone’s ideas go against those of main stream science that person is not longer an expert. She is popular because it is her business to sell courses and promote her company. That does not make her an expert.

      I have contacted her before, asking her for scientific studies to support some of her ideas – she was unable to do that.

      But if you disagree with anything in this post, please feel free to add links to studies that prove me wrong.

    • 1) Why would anyone test microbial products against fertilizer?
      2) If you are selling such products, you should already have done some testing to show they work. So can you provide links to these studies?


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