Thursday, 05 May 2016 18:21

Mystery of the Spring-Smelling Microbes

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Published in Microbial Sciences

HIM buildingThere is an incubator on the top floor of the Harvard Institutes of Medicine building where I work that continuously smells like dirt. And I am not complaining. It’s that refreshing aroma of garden soil, spring rain and deep forest. Everyone in the department can smell it, even halfway down the hall. But why would a medical school smell like the forest? What mysterious molecules float between the walls here and where are they coming from? Not to mention, why do they smell so good, compared with, let’s be honest, the pungent array of odors from the microbial world?

I found the first not-so-subtle clue in the back corner of the incubator: about 20 towering stacks of plates, all Actinobacteria. These cultures were definitely the source of the smell and, I’m proud to say, belonged to two of my Kolter Lab colleagues. On any given day, Gleb and Abigail grow various Streptomyces and Amycolatopsis species in this very spot. They are interested in “Actinos” because these bacteria are some of the most prolific producers of antibiotics in nature. At that point, I was casual in my curiosity. So, I simply admired the highly structured and colorful Actino colonies and went about my day.  

Actino coloniesA few weeks later, far from the incubator, I was again overcome by the smell. This time, it was when I opened a frozen stock of the social bacterium Myxococcus xanthus. Maybe I was a bit delayed to make the connection (blame it on my background in the very different halophilic archaea), but it was not until that moment when the story came together. Actinobacteria and myxobacteria are two of the most characteristic microbial groups within soil. Dirt doesn’t smell like dirt – dirt smells like the microbes that live in dirt.

At last, the molecular identity of this scent was only a Google Scholar search away. I quickly learned that one of the compounds produced by Actinobacteria and myxobacteria in soil (and by some cyanobacteria in water) is called geosmin. Not surprisingly, geosmin translates from Greek as “earth smell.” Chemically, it’s a volatile terpene alcohol, first extracted by Berthelot and André way back in 1891. Genetically, geosmin synthesis pathways have been determined in Streptomyces coelicolor, several myxobacteria and cyanobacteria. And environmentally, remember the earthy smell after a fresh spring rain? We typically sense geosmin within humid air after rainfall, because it is produced alongside spores in these bacteria, which accumulate in the soil during dry-spells.

While it seems the mystery of the spring-smelling incubator has been solved, these microbes and molecules do not fully explain why I was inspired to write this article. Even more intriguing, are the olfaction studies showing that the human nose is exceptionally sensitive to this compound. In fact, at that point in the hallway where the odor first hits me, I may be detecting as little as 0.7 parts of geosmin per billion. No wonder the smell carries so far.

Figure 3 public domain Geosmin StructureOne can’t help but speculate then: of the one trillion different odors that humans perceive, why are we so sensitive to geosmin? Further, from the perspective of evolutionary psychology, there must be some reason that we are attracted rather than repelled by its presence. One popular theory suggests an affinity for geosmin may be deeply rooted among animals, as a way to indirectly locate water or resource-rich ecosystems across arid landscapes via the microbes native to these locations. Imagine, eons in the past, our nomadic ancestors in Africa, and perhaps our pre-human ancestors before them. What is an invigorating yet dispensable attraction to geosmin in the context of modern society, may have once ensured our very survival.

As for the bacteria – what do geosmin-producing species get out of this deal? Well, a ride on the back of a thirsty animal is certainly a pretty good way to disperse spores. In any case, I for one think that each and every microbiology department should have an incubator that smells of these beautiful, and tremendously valuable, medicine-making soil bacteria.

Further Reading

Gerber, N. N., & Lechevalier, H. A. (1965). Geosmin, an Earthy-Smelling Substance Isolated from Actinomycetes. Applied Microbiology, 13(6), 935-938.

Jiang, J., He, X., & Cane, D. E. (2007). Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme. Nat Chem Biol, 3(11), 711-715. doi:10.1038/nchembio.2007.29

Dickschat, J. S., Wenzel, S. C., Bode, H. B., Muller, R., & Schulz, S. (2004). Biosynthesis of volatiles by the myxobacterium Myxococcus xanthus. Chembiochem, 5(6), 778-787. doi:10.1002/cbic.200300813

Last modified on Wednesday, 28 September 2016 15:48
Scott Chimileski

Scott Chimileski is a Research Fellow in Roberto Kolter’s laboratory at Harvard Medical School and a member of the ASM Writer Team. Scott's research is focused on imaging biofilms and other microbial multicellular forms. He is a photographer, coauthor of the book Life at the Edge of Sight: A Photographic Exploration of Microbial World, and is currently spearheading several exhibitions on microbial life at the Harvard Museum of Natural History. You can find him on Twitter @socialmicrobes.