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Don’t Overthink Your Soil Biology

Posted by Andrew McGuire | November 1, 2022

A little learning is a dangerous thing. -Alexander Pope

I am not sure of the causes. Perhaps it’s the demand for soil health information which far surpasses the supply of science-based content? Or maybe the speculation and exaggeration that this high demand produces? The intense focus on soil biology for soil health (Coyne et al. 2022) is surely a factor. And the excitement that comes with learning about the new discoveries in soil microbiology. Whatever it is, the results are clear. First, an over-inflated idea of the size of soil biology benefits. Second, the assumption that our soils have soil biology problems. And finally, to fix the problems, an increased susceptibility to unproven products or practices.

However, learning something about soil biology is far from being able to manage it. And in most cases, the “problems” are not actually problems. A few proven practices will often do.

Roots with microbial presence
How you manage your cropping and tillage largely determines which microbes will thrive in your soil. Photo: McGuire

Perceived soil biology problems

Lack of biodiversity

This is a big one. Anyone following current soil research will soon learn the high value put on soil biodiversity. Given this, it is understandable that farmers or their advisors reach the conclusion that their soil lacks biodiversity. They then try all sorts of things to increase it: compost teas, extracts, 20-species cover crops, or inoculation products.

Here is what you need to know about soil biodiversity. First, diversity itself does nothing (Shade 2017). Rather than being an actual mechanism or cause—think pH, soil structure, disturbance, etc.—biodiversity is only correlated with mechanisms. It is not the cause of soil function, and therefore not so helpful in determining management. Read more here and here.

Even if we assume that diversity is a mechanism, it is unclear what effect it has on soil function in cropped soils (Jacobsen and Hjelmsø, 2014; Nielsen et al., 2011; Pulleman et al., 2022). Although you may see such claims, they are based on artificial manipulation of soil biology by size of organism (Bradford et al. 2002, Wagg et al. 2014, Wagg et al. 2019), in controlled environments, with little discussion of how this represents reduced biodiversity in field soils. In an actual farmland study, higher productivity was related to lower soil biodiversity (Vazquez et al., 2021).

If you are still convinced you need more soil biodiversity, how much more? What nobody can tell you is how much is enough, only the simplistic idea that more is better. In a review of management of soil organisms, Bender et al. (2016) concludes “for the proper functioning of ecosystem processes, a basic toolbox of organisms with certain functional characteristics is necessary, while further increases in soil biodiversity give no direct benefits…” Unless you have evidence to the contrary, assuming you have this basic toolbox of soil microbes is a safe bet.

Lack of microbes

Another perceived problem is that you don’t have enough soil microorganisms. Here, remember that the amount of life in your soil is directly related to the amount of food and habitat available. Increased levels of microbes can be the result of both good and bad practices; from plowing to a rainstorm after a drought, from applying molasses to get a quick but short-lived increase, or from a healthy growing crop giving season-long input of root exudates. And as with biodiversity, higher levels are not necessarily better (Fierer et al. 2021).

A low fungi:bacteria ratio

This is another case of applying ecology to agriculture when the ecology is not sound. In a review of the topic in ecology, Strickland and Rousk (2010) find the results depend on how you do the measurement, and interpretations did not match the ecological theory behind the ratio. Other reviews of the measurement found similar (Wang et al., 2019).

fungi on one side in a ratio with bacteria
With millions of species, the simple F:B ratio may not be very informative. Drawings licensed Adobe Stock.

Soil microbial measurements

There are other perceived problems with soil biology, but you get the point. Most of these “problems” are not problems, and if they were, would not be easily managed. Even the detection of these “problems” is problematic. Many of our measurements of microbial characteristics, including microbial biomass fungal:bacterial ratio, enzyme activities and ratios, mycorrhizal abundance/composition and C and N mineralization rates are not necessarily representative of the actual soil function or are not easily interpreted (Fierer et al. 2021).

“Scientific evidence on the assumed benefits of popular nature-based soil management approaches (increase F:B ratios, restore soil biodiversity and AMF inoculation) for sustainable agricultural production is weak and cannot be generalized.” Pulleman et al. 2022.

As Fierer et al. (2021) conclude, “There is no ‘ideal’ soil microbial community…We should not expect healthy soils to have a single ‘optimal’ community type…”

Microbes are passengers, not drivers

Soil biodiversity, microbial biomass, and F:B ratios all indicate that microbes are passengers, not drivers. Soil microbes are highly sensitive to changes in soil chemical—particularly pH—and physical conditions (Bunemann et al. 2018). Only in specific cases do the microbes drive conditions. Therefore, your management determines what will thrive and what will diminish below measurable levels.

“Biology is only one factor more, not the ‘driver’ of Soil Health.” Coyne et al. 2022.

Rather than practices that give inconsistent results such as compost tea, inoculations, or home brews, might it be better to focus on improving your soil’s physical environment, protect your improvements, and let the microbes do their thing? You are the driver. Where do you want to go?

Focus on carbon inputs and minimizing disturbance

Unless you are missing some necessary organism, which is unlikely, you can get what you need through practices that

  1. build soil habitat and then
  2. protect it.

Much of soil health can be reduced to these two principles. The rest is figuring out the details, and how to do it while making a profit.

Building is about maximizing photosynthesis within your given constraints of climate, markets, and soil type. This provides for both decay—consumption by microbes—and storage as soil organic matter (Janzen et al. 2022). Protecting is about minimizing disturbance.

The practices to do this are not new. I recently watched a webinar on soil biodiversity and sustainable agriculture with four experts from the US and Europe. I kept track of every farming practice they mentioned that had benefits for soil biology. Here is what I heard:

  1. Crop rotation, including cover crops and perennial crops
  2. Manure or compost, and
  3. No-till.

Isn’t there more to it? Apparently not.

diagram of practices and microbes interaction
“To a large and important extent, we assume that the state of soil is a consequence of what is done to it, rather than being an intrinsic property of the system itself.” (Young et al. 2008)

The great soil biology explainer

This brings me to the conclusion that we are in a soil biology explainer, not a revolution. Nearly all the recent research is explaining what is going on in the soil, which has always been going on in the soil. We are not developing many new practices, but rather learning why recommended practices are beneficial. The new knowledge is fascinating and needed, but you don’t need to know it to manage your soil.

Even stuff we thought we had figured out, like the core tenet of regenerative agriculture, that most soil organic matter comes from microbes, is now under scrutiny. “We show that all major methods used to estimate plant versus microbial contributions to SOM have substantial shortcomings” (Whalen et al., 2022).

All this makes me wonder if agriculture neglected soil microbiology for so long because it could? Practices were tested, found beneficial, and then widely used, as with the management of pH, reduced tillage, etc. These gave the desired outcomes. Now we know they also had large effects on soil microbes, but we did not have to understand this to reap the benefits. For the most part, the soil biology you have results from the practices you apply. Soil microbes respond to what is done to the soil. If the results are acceptable, then why worry about the complexity of the soil microbiology?

Wonder at soil biology’s complexity, marvel at its diversity, but don’t overthink its management.


Bender, S.F., C. Wagg, and M.G.A. van der Heijden. 2016. An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability. Trends in Ecology & Evolution 31 (6): 440–452. doi: 10.1016/j.tree.2016.02.016.

Bradford, M.A., T.H. Jones, R.D. Bardgett, H.I. Black, B. Boag, et al. 2002. Impacts of soil faunal community composition on model grassland ecosystems. Science 298 (5593): 615–618.

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.

Coyne, M.S., E.M. Pena-Yewtukhiw, J.H. Grove, A.C. Sant’Anna, and D. Mata-Padrino. 2022. Soil Health – It’s Not All Biology. Soil Security: 100051. doi: 10.1016/j.soisec.2022.100051.

Fierer, N., S.A. Wood, and C.P. Bueno de Mesquita. 2021. How microbes can, and cannot, be used to assess soil health. Soil Biology and Biochemistry 153: 108111. doi: 10.1016/j.soilbio.2020.108111.

Jacobsen, C.S., and M.H. Hjelmsø. 2014. Agricultural soils, pesticides and microbial diversity. Current Opinion in Biotechnology 27: 15–20. doi: 10.1016/j.copbio.2013.09.003.

Janzen, H.H., K.J. van Groenigen, D.S. Powlson, T. Schwinghamer, and J.W. van Groenigen. 2022. Photosynthetic limits on carbon sequestration in croplands. Geoderma 416: 115810. doi: 10.1016/j.geoderma.2022.115810.

Nielsen, U.N., E. Ayres, D.H. Wall, and R.D. Bardgett. 2011. Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity–function relationships. European Journal of Soil Science 62(1): 105–116. doi: 10.1111/j.1365-2389.2010.01314.x.

Pulleman, M.M., W. de Boer, K.E. Giller, and T.W. Kuyper. 2022. Soil biodiversity and nature-mimicry in agriculture; the power of metaphor? Outlook Agric 51(1): 75–90. doi: 10.1177/00307270221080180.

Shade, A. 2017. Diversity is the question, not the answer. ISME J 11(1): 1–6. doi: 10.1038/ismej.2016.118.

Strickland, M.S., and J. Rousk. 2010. Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications. Soil Biology and Biochemistry 42(9): 1385–1395. doi: 10.1016/j.soilbio.2010.05.007.

Vazquez, C., R.G.M. de Goede, M. Rutgers, T.J. de Koeijer, and R.E. Creamer. 2021. Assessing multifunctionality of agricultural soils: Reducing the biodiversity trade-off. European Journal of Soil Science 72(4): 1624–1639. doi: 10.1111/ejss.13019.

Wagg, C., S.F. Bender, F. Widmer, and M.G.A. van der Heijden. 2014. Soil biodiversity and soil community composition determine ecosystem multifunctionality. PNAS 111(14): 5266–5270. doi: 10.1073/pnas.1320054111.

Wagg, C., K. Schlaeppi, S. Banerjee, E.E. Kuramae, and M.G.A. van der Heijden. 2019. Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat Commun 10(1): 4841. doi: 10.1038/s41467-019-12798-y.

Wang, X., W. Zhang, Y. Shao, J. Zhao, L. Zhou, et al. 2019. Fungi to bacteria ratio: Historical misinterpretations and potential implications. Acta Oecologica 95: 1–11. doi: 10.1016/j.actao.2018.10.003.

Whalen, E.D., A.S. Grandy, N.W. Sokol, M. Keiluweit, J. Ernakovich, et al. 2022. Clarifying the evidence for microbial- and plant-derived soil organic matter, and the path towards a more quantitative understanding. Global Change Biology n/a(n/a). doi: 10.1111/gcb.16413.

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.

3 thoughts on "Don’t Overthink Your Soil Biology"

  1. Dr K Pushpa says:

    It’s a wonderful article I have red today. What you are explaining in really need to think. Natural forming practices are the best and solution for the soil health and biological development. In natural farming practices no tillage, multiple cropping system, complete covering of the soil, plants and animals extracts we used to enhance the soil microrganisms in the soil to develop the soil biologically.

  2. Howard Stenn says:

    Thanks for a thoughtful article. I work in the soils/compost industry, and battle specifications calling for adding inoculants and compost tea treatments to perfectly healthy soils all the time. I recently completed a one year evaluation comparing a very expensive biological amendment treatment at a Seattle corporate campus to untreated turf and planting beds, and the treated areas grew/established no better than the control areas. Earthforte Lab (in a blind analyses) evaluated the untreated control areas as healthier. Happy to share results, or the presentation I did for WASLA, if you are interested.

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