Antibiotics were first discovered being produced by a soil-borne fungus. We have identified many different antibiotics that are made by plants and fungus, and even synthesized some on our own. Many of the anti-biotics we have developed are not necessarily labeled as such. Many herbicides and pesticides would be examples of an antimicrobial that is applied to agricultural soils. The case for glyphosate is now well established, and others are getting to be better known.

When we consider the widespread use of antibiotics on our soils and in livestock feed we might wonder about the implications for the microbial community in our soils. 

I found this excerpt from Stephen Harrod Buhner1 thought-provoking: 

Once a bacterium develops a method for countering an antibiotic, it systemically begins to pass the knowledge on to other bacteria – not just its offspring – at an extremely rapid rate. Under the pressure of antibiotics, bacteria are interacting with as many other forms and numbers of bacteria as they can. In fact, bacteria are communicating across bacterial species, genus, and family lines, something they were never known to do before the advent of commercial antibiotics. And the first thing they share? Well, it’s resistance information.

Bacteria can share resistance information directly, or simply extrude it from their cells, allowing it to be picked up but later by roving bacteria. They often experiment, combining resistance information from multiple sources in unique ways that increase resistance, generate new resistance pathways, or even stimulate resistance forms that are not yet necessary. Even bacteria in hibernating or moribund states will share whatever information on resistance they have with any bacteria that encounter them. When bacteria take up any encoded information on resistance they weave it into their own dna and this acquired resistance becomes a genetic trait that can be passed on to their descendants forever. As Gaian researchers Williams and Lenton comment…

Microbe transfer between local populations carries genetic information that changes species composition and thus alters the nature of each community’s interaction with its local environment2.

“The nature of each community’s interaction with its local environment” changes. One aspect of that:  as bacteria gain resistance they pass that knowledge on to all forms of bacteria they meet. They are not competing with each other for resources, as standard evolutionary theory predicted, but rather promiscuously cooperating in the sharing of survival information. “More surprisingly,” one research group commented,  “is the apparent movement of genes, such as tetQ and ermB between members of the normal microflora of humans and animals, populations of bacteria that differ in species composition.”3  Anaerobic and aerobic, gram-positive and gram-negative, spirochetes and plasmodial parasites, all are exchanging resistance information. Something that, prior to antibiotic usage, was never known to occur.

And, irritatingly, bacteria are generating resistance to antibiotics we haven’t even thought of yet. For example, after placing a single bacterial species in a nutrient solution containing sublethal doses of a newly-developed and rare antibiotic, researchers found that within a short period of time the bacteria developed resistance to that antibiotic and to twelve other antibiotics that they had never before encountered – some of which were structurally dissimilar to the first. Stuart Levy observes that “it’s almost as if bacteria strategically anticipate the confrontation of other drugs when they resist one.”4

With the growing understanding of how we have compromised our soil biology, we need to consider how we can regenerate that microbiome, add the organisms that have been lost, and recover those that are present but struggling. This is where microbial inoculants, diverse plant species, compost, and compost teas become important tools in agriculture management systems.

1. Buhner, S. H. Plant Intelligence and the Imaginal Realm: Beyond the Doors of Perception into the Dreaming of Earth. (Simon and Schuster, 2014).
2. Williams, H. & Lenton, T. Microbial Gaia: A new model for the evolution of environmental regulation. Gaia Circular, 2007 14–18 (2007).
3. Wax, R. G., Lewis, K., Salyers, A. A. & Taber, H. Bacterial resistance to antimicrobials. (CRC press, 2007).
4. Levy, S. B. The Antibiotic Paradox: How Miracle Drugs Are Destroying the Miracle. (Springer, 2013).