Tag Archives: rhizosphere

It’s not only poop

Today I am going to link again to a post of Todd Wood, and this time it’s about poop. His post is about research that is recently published and explains how fecal transplantation cured in 94% of the reported cases an infection with Clostridium difficile.

Todd wrote in his post that:

Creationist biologist Joe Francis, at the Master’s College in California, has long proposed that God created macro organisms (those you can see) to live in a complex partnership with microorganisms (those you can’t see).  Joe thinks that the relationships between macro and micro are essential to the health of both types of organisms, so without the proper balance of relationships, things can go really wrong.

This study provides an opening to speculation that the cause of a disease not always a question of ‘good’ and ‘bad’ germs is, but in fact depends on the balance of ‘good’ and ‘bad’ germs.

When reading his posts, my attention was drawn to several lectures that I had some time ago. In fact, I remembered that this phenomena is not only illustrated here, but that this is also observed in other organisms.

First of all I want to point out to disease-suppressive soils, which are soils where plants are protected from  particular soil-borne diseases. This protection against those soil-borne diseases occurred only in particular soils, which obviously should have properties that caused this.

Researchers found out that suppressive soils are not suppressive anymore when subjected to pasteurization (which kills all microbes). Second, they found out that suppresiveness can be transplanted (just like the poop), and that non-suppressive soils could become suppressive when 0.1%-10% of the suppressive soil was mixed with the non-suppressive soil. In short, the primary cause of the suppressiveness was caused by microorganisms. Several examples of pathogens which are suppressed by particular kinds of soils are available. Fungal pathogens such as Gaeumannomyces graminis var. tritici, fusarium oxysporum, Phytophthora cinnamoni, and many more were found to be suppressed in certain soils (Haas & Défago, 2005).

I want to emphasize that this idea (proper balance of microorganisms) was already explored at a symposium in 1963 about the ‘Ecology of soil-borne plant pathogens’ (Baker & Snyder, 1665). Researchers then thought that antagonistic microorganisms competed with pathogens, by producing antibiotics.

Further research into disease-suppresive bacteria was also done at the Wageningen university in the Netherlands, and in 2011 an article was published in Science with as goal ‘Deciphering the Rizosphere Microbiome for Disease-Suppressive Bacteria’ (Mendes et al., 2011). What was done as following: They used microarrays to identify bacterial and archaeal community members which grow in the rhizospere of the plants in disease suppressive soils and non-suppressive soils.

What they found is that in suppressive soils not the number of bacterial taxa was the key to deciphering their problem, but that in fact the abundance of those bacterial taxa relative to each other was determining whether a soil was suppressive or not.

The second example that I have is about salmon eggs, which died of a cause of a mysterious origin. And the same thing was observed, that is the imbalance of microbiota in the eggs was causing the suppression of the mysterious disease or not (unpublished).

Let’s come to a conclusion. As Todd Wood pointed out in his post:

Joe and I have long wondered if creationist insights might lead to better treatment of disease, but we were both sort of baffled about how to make microbes fight other microbes.  Well, this is how it’s done, at least for now.

And we can see that this is a widespread phenomena in plants (and more organisms).

In all these examples it is caused by the balance between good and bad.  So the fitness of an organism is in several cases related to his close neighbours and their abundance. Another question is what implications it on the long-term could have for the theory of evolution: Is actually the unit where  natural selection selects on not only the organism itself, but also includes the microbiome?

Actually, I think that Joe is going to love this post too!


Haas, D. & Défago, G. (2005) Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews Microbiology 3, 307-319.
Van Nood et al. (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile.  NEJM DOI: 10.1056/NEJMoa1205037

Mendes, et al. (2011). Deciphering the Rhizosphere Microbiome for Disease-Suppressive BacteriaScience 27 May 2011: 332 (6033), 1097-1100. 2011 

Baker, K. F. & Snyder, W. C. (eds) Ecology of Soil-Borne Plant Pathogens: Prelude to Biological Control (Univ. of California Press, Berkeley, 1965).