A Problem with Soil Inoculants

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