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A Problem with Soil Inoculants

Posted by Andrew McGuire | November 22, 2022
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As I wrote in my last post, the focus and excitement around soil biology leads many to believe that they have a soil biology problem. To fix this perceived problem, some recommend trying various types of soil amendments or inoculants to enhance the soil’s microbial community. This includes compost, manure, and their extracts and teas. There is a problem with this strategy though; the microbes at home in manure, compost, or in their extracts, tend to die off in the soil. They don’t adapt well to the soil’s habitats and don’t compete well with native microbes.

It’s ecological

This basic problem really should have been recognized earlier if those promoting these “natural” solutions had been thinking ecologically.

“Everything is everywhere, but the environment selects.”

Ecologist Lourens Gerhard Marinus Baas Becking said this back in 1934 (Wit and Bouvier, 2006). By it, he meant that 1) microbes–bacteria, fungi, etc.–are so widely distributed that any of them could be anywhere, and 2) the environment they find themselves in determines whether they thrive or just hang on, perhaps below the level we can detect.

Soil microbes are super sensitive to changes in their micro-environments (Bunemann et al. 2018). Each specific environment or niche will support a unique combination of microbes with unique population levels. This rich diversity of micro-habitats promotes the microbial diversity we see in soils (Young et al. 2008). However, it also presents an obstacle to inoculation efforts.

A bacterium or fungi, raised in a carbon-rich, wet, and warm compost or manure, is going to find the cooler, dryer, less carbon-rich conditions of the soil quite hostile. And then there are the natives.

Drawing of the environment selecting microbes for the conditions
The environmental conditions determine who thrives.

Native microbes eat invaders

Besides the hostile territory, a well-adapted community of native microbes awaits the inoculation newcomers. The natives have numbers on their side and are entrenched in their favored habitats. Ecologically, the invading microbes don’t have a chance.

Schlatter et al. (2022) looked at bacteria and fungi (2023) in fresh liquid dairy manure. 60 days after manure application, they found less than 5% of the manure bacteria surviving in the soil. Manure-borne fungi also died off rapidly. Even when applied to sterilized soil, “the soil environment selects”: the manure-borne bacteria and fungi died off quickly. The authors conclude, “soils appear to provide a strong barrier against invasion of manure-borne fungi [and bacteria].”

Lion behind a small dog
Native soil microbes are better adapted to their conditions than microbes produced in other environments. The latter become food for the former. Licensed Adobe Stock.

Another study, this time using solid cattle manure, found the same; bacteria and fungi in the manure did not survive long when released into hostile soil (Semenov et al., 2021).

This result, that microbes produced in a non-soil environment die off when applied to the soil, applies to manure and compost, and also extracts and teas of either. Therefore, any beneficial effects of these amendments are probably tied to other parts of the amendments rather than their biology. With manure and compost, it’s the carbon resources and nutrients (Schlatter et al. 2022). With extracts and teas, it is nutrients, phytohormones or other non-biological components (Pant et al. 2012). And the effect of all those non-native microbes dying.


Does this apply to foliar applications of extracts and teas? The microbial niche on a plant leaf would seem to be even more different from the tea brewer, compost, or manure than that of the soil. So yes, I think it applies. However, there are non-biological components that could have benefits, even perhaps stimulating the existing leaf biology or promoting plant health directly.

Tractor spraying a soybean field
Will the microbes in foliar applications fare better than those applied to the soil? “The environment selects” would still seem to apply. Licensed Adobe Stock.

Build your soil, it will select your microbes

Contrary to Baas Becking, not everything is everywhere. In fact, microbes may be completely absent from some soils in Antarctica (Dragone et al., 2021). However, the tenet remains instructive with a little adjustment: the redundancy of soil microbes in terms of function makes it likely that whatever you need in your soil is there. The environment, which you determine through your management, selects what will thrive.


Bünemann, E.K., G. Bongiorno, Z. Bai, R.E. Creamer, G. De Deyn, et al. 2018. Soil quality – A critical review. Soil Biology and Biochemistry 120: 105–125. doi: 10.1016/j.soilbio.2018.01.030.

Dragone, N.B., M.A. Diaz, I.D. Hogg, W.B. Lyons, W.A. Jackson, et al. 2021. Exploring the Boundaries of Microbial Habitability in Soil. Journal of Geophysical Research: Biogeosciences 126(6): e2020JG006052. doi: 10.1029/2020JG006052.

Kim, M.J., C.K. Shim, Y.K. Kim, S.J. Hong, J.H. Park, et al. 2015. Effect of Aerated Compost Tea on the Growth Promotion of Lettuce, Soybean, and Sweet Corn in Organic Cultivation. Plant Pathol J 31(3): 259–268. doi: 10.5423/PPJ.OA.02.2015.0024.

Pant, A.P., T.J. Radovich, N.V. Hue, and R.E. Paull. 2012. Biochemical properties of compost tea associated with compost quality and effects on pak choi growth. Scientia horticulturae 148: 138–146.

Schlatter, D.C., J.D. Gamble, S. Castle, J. Rogers, and M. Wilson. 2022. Abiotic and biotic filters determine the response of soil bacterial communities to manure amendment. Applied Soil Ecology 180: 104618. doi: 10.1016/j.apsoil.2022.104618.

Schlatter, D.C., J.D. Gamble, S. Castle, J. Rogers, and M. Wilson. 2023. Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment. Applied and Environmental Microbiology 0(0): e01931-22. doi: 10.1128/aem.01931-22.

Semenov, M.V., G.S. Krasnov, V.M. Semenov, N. Ksenofontova, N.B. Zinyakova, et al. 2021. Does fresh farmyard manure introduce surviving microbes into soil or activate soil-borne microbiota? Journal of Environmental Management 294: 113018. doi: 10.1016/j.jenvman.2021.113018.

Wit, R.D., and T. Bouvier. 2006. ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environmental Microbiology 8(4): 755–758. doi: 10.1111/j.1462-2920.2006.01017.x.

Young, I.M., J.W. Crawford, N. Nunan, W. Otten, and A. Spiers. 2008. Microbial Distribution in Soils: Physics and Scaling. Advances in Agronomy. Academic Press. p. 81–121

12 thoughts on "A Problem with Soil Inoculants"

  1. Andrew McGuire says:

    I wonder if inoculants would be more consistent if they took the 4Rs strategy from nutrient management?

    The Right product, one for a specific purpose,
    applied at the Right rate, enough to be effective,
    at the Right time, when a specific purpose is most beneficial,
    and at the Right location, a specific location rather than the bulk soil.

    Even if microbes don’t survive long, the right one or mix, at the right time and place could be be beneficial even if they don’t survive long.

  2. I have been working with Biostimulants/Probiotics sense 1985. The first thing I observed was a dramatic increase in insect resistance. The products I have been using are by Humagro. It starts with a Micro carbon with about 100 nutrients and vitamins attached. This feeds existing microbes and takes them from being couch potatoes to being NFL players as far as doing their job of making nutrients more available to the plants, and thus healthier plants that are more insect resident and a better quality end product. Unfortunately in the 1990s when GMO products came out the idea of healthy plants was through under the bus and I had to go into hiding. We grow and market Probiotly Grown Popcorn. What kept me going was the compliments from my customers despite sharp criticism from Universities. Now those critics want me to give them Thousands of $ to ketch up of on what I have been doing. Thank You for the article.

  3. timatto son says:

    Great blog. Question: goal seems to be “increasing soil health. how do you know when you have “enough soil health”?

    1. Andrew McGuire says:

      Great question. I’ll answer with another blog post,

  4. Heath Gimmestad says:

    Thanks Andy:
    I have been trying different bugs in a jug for many years. To date never have really found anything that seems to make an overall positive impact. I would agree the only applications that may move the biological needle are foliar applications. My new model is to feed the existing soil biology we have and not to try and add new biology to the existing system. I think feeding the existing biology is the direction to go. You (Andy) are/were the person to convince me this is the answer. I heard you say it during one of your many presentations.

    1. Andrew McGuire says:

      Hi Heath. Sorry for the late response, our comment notifications are not coming to me so I just saw this. Thanks for the comments. See my comment about the 4Rs above as a possible way for some (?) inoculants to work better.

  5. Kris Butcher says:

    The final paragraph is a great place to begin. In regards to the 4R’s mentioned above, it would be valuable to understand and apply that to modern fertility practices and products. Those 4 principles are mentioned often, it seems though that a true understanding of what our so called conventional fertilizer and crop protection products are doing in our soils may be hamstringing any efforts to actually build soils.

    As a historically “conventional” farmer I am ever increasingly feeling misled by the mainstream crop protection and academic industries. Whether it is my ignorance or theirs, what is being preached seems to be leading us down a treacherous road. I hope this to not be true and that those with the greatest reach will take a heartfelt look at the true design of the system and begin to use their voice to help us understand how to identify and integrate both biological and conventional approaches when applicable.

    1. Andrew McGuire says:

      Kris, thanks for the comment. From what I have seen in research results, fertilizers are not a problem unless you are trying to allow biological nutrient supply channels to work. The problem there is that they do work in low-nutrient environments, but the rates at which they supply nutrients is too low for modern crop production.
      On the crop protection side, the effects seem to be very specific between a product and organisms in the soil. There are always tradeoffs.

  6. Bryant Mason says:

    Are you familiar with the work of Dr. David Johnson and the Johnson-Su bioreactor? They’re quite popular with growers. If so, what would you attribute the crop response to?

    1. Andrew McGuire says:

      Yes, I know some about the Johson-Su composting. However, I have not seen any peer reviewed results published on the benefits of the compost. And compost can definitely have benefits not related to the microbes actually in the compost.

  7. Oliver Knox says:

    Loved the article. Supports much of what I’ve seen and taught since the mid 90s. Would welcome an opportunity to talk further or work up ideas in this space, if you (and I) every had the time. Perhaps ironically, I still find myself working with inoculants 30 years on. I’ve seen some incredible things, but think there are other ways to deliver what our farmers want and soils need.
    Please keep pushing the science and sense over the beliefs and bull.
    Yours, Oliver

    1. Andrew McGuire says:

      Oliver, thank you for the comments. I would bet that we are better at using inoculants now than we were 30 years ago, but they are not an easy fix.

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