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(Click on the following link to listen to an audio version of this blog … The scent of rain
I have written about petrichor and geosmin before. In 2012, I described their earthy-scent rising from our field in Pennsylvania after a rain broke a long dry period, and in 2021, I wrote about standing outside under the eave of our house here in Colorado breathing in their incredible scent while a very rare rainstorm wetted down the parched yards and streets of our neighborhood.
Petrichor comes from a complex array of organic chemicals that have been secreted by plants and soil bacteria onto dry, outside surfaces. The rain stirs up and aerosolizes these chemicals and generates the aesthetically satisfying atmospheric. It is a scent of a cleansing power, a smell of renewal and change. It is a smell of life.
Petrichor had been discussed by scientists since the late 19th Century but was precisely described (and named) by two Australian researchers, I. J. Bear and R. G. Thomas, in 1964. Bear and Thomas later demonstrated that as petrichor builds up in dry soils, it acts to inhibit the germination of seeds. When the rains come and petrichor is released from the soil, this chemical check on seed germination is released. The aroma we smell is the signal for long suppressed plants to begin the growth phase of their life cycles.
Geosmin. Figure by xplus, Wikimedia Commons
The other, “after the rain” scent, geosmin (also known as dimethyl-9-decalol) is the familiar “earth” smell that we perceive during spring soil thaws or after plowing or tilling. Geosmin is synthesized by several types of soil bacteria and fungi, but it is especially the product of a genus of Actinobacteria called Streptomyces. Streptomyces species are very important in breaking down complex and resistant chemicals in the soil and play vital roles in biological decomposition and in the recycling of nutrients in our ecosystems.
Streptomyces also synthesize an incredible array of diverse chemicals that collectively are referred to as “secondary metabolites.” Secondary metabolites often play complex roles in the chemical ecology of an ecosystem, and it is thought that some of the Streptomyces secondary metabolites are extremely important mediators in symbiotic relationships among soil organisms. Some of these secondary metabolites act as chemical defense agents against other bacteria, and a number of these Streptomyces “antibiotics” (including streptomycin, actinomycin, and neomycin) were isolated and identified by Selman Waksman and his students in the 1940’s. These discoveries lead to Waksman’s Nobel Prize in 1952.
Geosmin is concentrated in the spore covers of the Streptomyces bacteria. Human olfactory systems are incredibly sensitive to geosmin and can detect concentrations as low as 400 parts per trillion in the air. Other organisms are also quite sensitive to geosmin. The European glass eel, for example, uses geosmin to find its freshwater breeding grounds! There is also a hypothesis that ancient humans relied on their exquisite sensitivity to geosmin to find fresh, drinking water sources in their dry, savannah habitats!
Streptomyces griseus. Figure by Wiki San Rose. Wikimedia Commons
The specific role of geosmin in the ecology of Streptomyces, though, was, until quite recently, not known. The synthesis of geosmin costs the Streptomyces bacteria valuable energy. What benefit did the bacterium get for this energy expenditure?
Initially, it was thought that geosmin, along with the other secondary metabolites that Streptomyces synthesizes, functions to deter the bacteriophagic predators. Studies, though, have shown that geosmin is not particularly toxic to protists or to animals that eat bacteria. The nematode, Caenorhabditis elegans, for example, shows no negative effects of direct geosmin exposure, but when it is placed into culture dishes with geosmin-producing Streptomyces, it avoids the area occupied by the bacterium. It turns out that C. elegans, like most other nematodes, is poisoned by many of the other chemicals made by Streptomyces, and that the geosmin is an easily detected, non-toxic marker that tells the nematode that toxic Streptomyces are nearby! Geosmin’s notoriously short chemical life span (which makes experimentation with it quite difficult) may also play a role in its function as a warning marker: it will only be present in detectable amounts when living, metabolizing Streptomyces are nearby!
C. elegans. Photo by B. Gladstern,. Wikimedia Commons
Geosmin, then is an aposematic (or “warning”) marker made by Streptomyces. It is functionally similar to the aposematic colorations of poisonous insects (like monarch butterflies). Geosmin as a scent molecule wards off nematodes and many protists just like the colorations of the monarch ward off butterfly-eating birds!
Fruit flies (Drosophila spp.), like nematodes, are repelled by geosmin. They especially avoid any geosmin-rich materials onto which they might lay their eggs. Streptomyces and fruit fly larvae both eat yeasts, and it is thought that the fly’s avoidance of a geosmin-rich substrate is a way to ensure that the food supply for the fruit fly larvae will not be compromised by active Streptomyces competition or contamination.
Collembola (Isotoma habitus). Photo by U. Burkhardt, Wikimedia Commons
Collembola (“springtails”) and mosquitoes, on the other hand, are attracted to geosmin. Collembola actively consume Streptomyces bacteria (they are not affected by the Streptomyces toxins), and follow the geosmin to their bacteria meal. This predation by collembola, though, benefit the Streptomyces by spreading their spores on the bodies and in fecal pellets of the collembola. Mosquito larvae also are unaffected by the Streptomyces toxins and avidly consume the Streptomyces bacteria. It does not seem, though, that the bacteria are benefited by these mosquito larval interactions.
Photo by H. Casselman, Wikimedia Commons
Earthworms and many other soil dwelling invertebrates are also attracted to loci of concentrated geosmin. This attraction may act to recruit soil biota into areas of intense biological decomposition, and, thus, further accelerate and facilitate this vital biogeochemical process. The recruited soil invertebrates may also act to transport and disperse the relatively immobile Streptomyces throughout the soil volume thus increasing the presence and impact of these important bacteria.
So, the rich smell of soil and wetted rocks and concrete may be a harbinger of new plant growth, or it may be a warning against the presence of potential toxins. It may also be a call to sources of fresh water or a guide to find a rich food source. So many possibilities in a single set of chemicals!