Fine-Tuning with Soil Health; Soilborne Disease?

Healthy soils produce healthy crops, right? Nope. Although it would seem the very definition of soil health, this popular thinking does not match what plant pathologists find (Janvier et al., 2007). It’s not true.

You can have a soil that is healthy in all other ways and still have problems with soilborne disease. But then, one may ask, is it really healthy? We can define away the dilemma – if you have soilborne disease problems, you don’t have a healthy soil—but then we may never have healthy soil. Instead of the soft thinking of catch phrases, let’s look at the hard reality.

Macro photo of disease hyphae on soil
Can soil health eliminate soilborne disease?

Soil health reduces disease potential

First, the easy part. So far as it improves soil structure, drainage and aeration, and reduces compaction, soil health also reduces the potential for soilborne disease incidence and severity. This is the environment corner of the plant disease triangle.

Figure of the disease triangle and soil health
Disease triangle. Soil health can reduce the potential for soilborne disease by improving a soil’s physical properties.

Soil health and soilborne disease suppression

What “healthy soils produce healthy crops” is really getting at is soilborne disease suppression. Rather than just reducing the potential for disease, suppression acts against the actual pathogens in the soil. It is the soil version of immunity; pathogens can be present in the soil but plants don’t get disease. It is the Mega-Millions jackpot-win of soilborne disease control, something often pursued but rarely achieved.

General suppression is related to soil health

Plant pathologists identify two types of soilborne disease suppression, general and specific (Schlatter et al., 2017). General suppression is related to higher populations and activity of the general microbe population, so it is related to soil health. The good news is that general suppression is broad spectrum. The bad news is that it does not completely suppress every pathogen in all conditions.

Although general suppression can be achieved through improved soil health, research results are inconsistent because of the many factors involved: pathogen, the soil type, crop, and climate. Soil health may improve general disease suppression but does not produce completely the immunity to diseases implied in “healthy soils produce healthy crops.”

Figure of the disease triangle and soil health
Disease triangle. Soil health may or may not suppress soilborne diseases.

Specific suppression is not related to soil health

The Jackpot-Win of disease suppression is called specific suppression. Unlike general suppression, it is linked to the activity of a smaller number of specific microbes. And it is complete suppression, but only of one pathogen. Unfortunately, the properties that make soils suppressive are specific to each soilborne disease; a soil that suppresses one disease in one crop will not suppress another soilborne disease in another crop. It’s like immunity to measles but not to the common cold. The best-known examples of specific disease suppressive soils are for take-all in wheat, Rhizoctonia bare patch, also in wheat, and common scab in potatoes (Schlatter et al. 2017).

How to get specific disease suppression

Since it is complete suppression, it would be useful to achieve specific disease suppression when and where we want it. Here is how you get it for potatoes: grow nothing but potatoes for 20+ years on the same soil (Lorang et al. 1989; Menzies, 1959). The same can be done for wheat (Cook, 2003). We’ve found that thee best examples we have of specific disease suppression are the result of long-term monocropping.

Researchers have studied disease suppressive soils, hoping to identify how they suppress disease so as to come up with non-monocropping methods of attaining them, but with little success. The mechanisms are complicated. One research team identified 17 distinct microbes involved in one instance of specific suppression of Rhizoctonia (Mendes et al., 2011).

As it is clear that 20 years of potato production will result in poor soil health (in the absence of other interventions, Hills et al., 2018), we can see that we may have a disease suppressive soil, but not soil health.

A few other observations of specific suppression:

  • A break in the mono-cropping that creates suppression will often break the suppression (with take-all suppression but not with Rhizoc, Schlatter et al., 2017).
  • Composts with specific qualities can sometimes promote disease suppression (Hoitink et al., 1997)
  • Green manures can also sometimes promote disease suppression (Abawi and Widmer 2000; McGuire 2003; Wiggins and Kinkel, 2005)
  • Soil biodiversity does not guarantee disease suppressiveness (Hossain et al. 2021)

Practices vs. soil health for disease suppression

So, going broke monocropping is not a practical option. Nor is achieving soil health a complete solution: “No soil health management practice consistently suppresses disease.” (Soilborne Plant Pathogen Fact Sheet, 2021). The big lever here is crop rotation, not soil health. It is the traditional practice used to avoid soilborne disease problems in annual cropping. As with nutrients and water, soil health is fine tuning for soilborne disease.

Venn diagram of soil health and soilborne disease with general suppression in the overlap
Think of soil health as a separate issue from soilborne disease suppression. You can have soil health without disease suppression, or disease suppression without soil health.

Given all this, we should consider suppressive soils and healthy soils as two different things (Figure 3), especially when we consider multiple crops and diseases in a rotation. And abandon the “healthy soils produce healthy plants” thinking. It does not describe reality, which is much more complex.

Table of disease factors
Table 1. Soil health can reduce soilborne disease incidence across a broad spectrum of pathogens by changing the physical environment, while specific disease suppression can eliminate incidence of one disease through changes in the biological environment.


Abawi, G.S., and T.L. Widmer. 2000. Impact of soil health management practices on soilborne pathogens, nematodes and root diseases of vegetable crops. Applied Soil Ecology 15(1): 37–47.

Cook, J. 2003. Take-all of wheat. Physiological and Molecular Plant Pathology 62(2): 73–86. doi: 10.1016/S0885-5765(03)00042-0.

Hills, K., H. Collins, G. Yorgey, A.M. McGuire, and C. Kruger. 2018. Safeguarding Potato Cropping Systems in the Pacific Northwest Through Improved Soil Health. WSU CSANR.

Hoitink, H.A.J., A.G. Stone, and D.Y. Han. 1997. Suppression of plant diseases by composts. HortScience : a publication of the American Society for Horticultural Science 32(2): 184–187.

Hossain, Z., M. Hubbard, Y. Gan, and L.D. Bainard. 2021. Root rot alters the root-associated microbiome of field pea in commercial crop production systems. Plant Soil 460(1): 593–607. doi: 10.1007/s11104-020-04779-8.

Janvier, C., F. Villeneuve, C. Alabouvette, V. Edel-Hermann, T. Mateille, et al. 2007. Soil health through soil disease suppression: Which strategy from descriptors to indicators? Soil Biology and Biochemistry 39(1): 1–23.

Lorang, J.M., N.A. Anderson, F.I. Lauer, and D.K. Wildung. 1989. Disease decline in a Minnesota potato scab plot. Am. Potato J 66: 531.

McGuire, A.M. 2003. Mustard Green Manures Replace Fumigant and Improve Infiltration in Potato Cropping System. Crop management. doi: 10.1094/CM-2003-0822-01-RS.

Mendes, R., M. Kruijt, I. de Bruijn, E. Dekkers, M. van der Voort, et al. 2011. Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria. Science 332(6033): 1097–1100. doi: 10.1126/science.1203980.

Menzies, J.D. 1959. Occurrence and transfer of a biological factor in soil that suppresses potato scab. Phytopathology 49: 648–652.

Schlatter, D., L. Kinkel, L. Thomashow, D. Weller, and T. Paulitz. 2017. Disease Suppressive Soils: New Insights from the Soil Microbiome. Phytopathology® 107(11): 1284–1297. doi: 10.1094/PHYTO-03-17-0111-RVW.

Soil Health Institute. 2021. Soilborne Plant Pathogen Fact Sheet. Soil Health Institute.

Wiggins, B.E., and L.L. Kinkel. 2005. Green manures and crop sequences influence alfalfa root rot and pathogen inhibitory activity among soil-borne streptomycetes. Plant and soil 268(1–2): 271–283.


This paper is a great example of the difficulty of suppressing soilborne pathogens by soil health methods. Of the 11 treatments, which included cover crop monocultures and mixes, compost, and other organic amendments, only a combination of treatments suppressed Pythium. Nothing worked on Rhizoctonia. Open access.

Kurm, V., J. Visser, M. Schilder, E. Nijhuis, J. Postma, et al. 2023. Soil Suppressiveness Against Pythium ultimum and Rhizoctonia solani in Two Land Management Systems and Eleven Soil Health Treatments. Microb Ecol. doi: 10.1007/s00248-023-02215-9.


4 comments on "Fine-Tuning with Soil Health; Soilborne Disease?"
  1. Healthy soils producing healthy plants is a promotional phrase based on general fact relating to worthy efforts. Identifying limitations to the that premise is highly important (especially for soil health proponents), and this article is appreciated. Indeed, potato producers (here in Maine but no doubt everywhere) are rightly on guard for unintended pathogen consequences of otherwise desirable soil health improvements (or any other promoted practice or amendment). It’s incumbent upon those of us working to reduce runoff/erosion etc via what are now known as soil health practices to aggressively evaluate such things – because they can both undermine our efforts and can harm farming enterprises. I am happy to say that there is a lot of effort to do just that at least in my neck of the woods.

  2. Great article, thank you for it!
    The way I see it, healthy soil\field is like a healthy body, in the essence of disease suppression.
    We can maintain a healthy lifestyle, which will suppress a lot of naturally existing diseases floating around us, but when we have symptoms we check it up and take medicine.
    The same is with the field. If the soil is healthy, we don’t have to worry about diseases spreading like fire all around the field, as the soil will suppress them to a certain level. Combining healthy soils with field scans using technology to detect localized disease outbreaks can be a sustainable solution (precision agriculture).
    This will allow for the development of hybrids that aim to produce more and with higher quality, instead of focusing mostly on disease-resistant hybrids.
    Of course, some soil ‘vaccines’ can be developed to eliminate more specific diseases.
    In my opinion, healthy soil with precision agriculture practices is the solution.

  3. […] not reduce the soilborne diseases important there. Soil health is not soilborne pest suppression (see article on this). Conversely, the disease reducing system did not affect any of the chosen soil health […]

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