With another year of record-breaking warmth just over, the passage of a new climate treaty is definitely timely. But even if these new diplomatic and legislative efforts are successful the planet is ensured some amount of long-term warming—enouigh that around 8% of species are likely to go extinct due to climate change. If the warming is greater than current models project, that number could double.

In all likelihood, though, those numbers are an underestimate, because there are species that no climate scientists are keeping track of. In fact, there are a lot of them, and we may come to miss them quite a bit if they disappear. Who are these guys? Microbes.

There are currently no published studies of how climate change may cause extinction of microbial species. However, there are researchers exploring how warming can alter microbial communities, and their results tend to show that microbial consortia and their functioning are sensitive to climate change.

In experiments at the Harvard Forest, for example, long-term artificial warming led to reductions in both total and active microbial biomass as well as to changes in how the soil community behaved1. Even short-term experiments with just a few months of warming have found reductions in growth and functional diversity as well as evidence for local extinctions2. Interestingly, immigration of new bacteria to those communities was unable to rescue them from these effects, indicating that the ease with which microbes are able to move around may not be enough to prevent negative impacts of climate change.

An alternative way of studying microbial sensitivity is to transplant intact communities to warmer sites. Recent work doing this with grassland soils in China has also shown loss of soil microbial biomass as well as changes in composition and function3. The microbial community was not resistant to warming—it changed—and it wasn’t resilient—it didn’t recover over time through acclimation to the new environment. These results, combined with a significant reduction in diversity, imply that species were lost from the community. These data were not analyzed to test specifically for local extinction events, however, so while it seems like extinctions were likely we cannot know for sure. 

Admittedly it can be pretty hard to study threats to microbes. Most of the species we’ve found have not been documented as anything more than a snippet of a genetic sequence, and there are untold numbers out there for which we don’t even have that. At last count, there were 84 named bacterial phyla (one of the broadest taxonomic groupings), but we have cultured representatives for only 12 of those4. It is very hard to experimentally determine sensitivity to changing conditions for microbes that you can’t isolate and grow. The cultured species that we have in cell line collections or biobanks like ATCC and the German equivalent DSMZ focus almost exclusively on type strains rather than capturing the diversity possible within species—so how much variation there is in sensitivity is even harder to study. On the flip side, keeping track of species in wild communities can be notoriously difficult, particularly with rare taxa, so it may be almost impossible to document a real extinction event with certainty.

“Maybe we don’t need to worry about microbes,” you might think. “They grow all sorts of places. Heck I can’t even keep my house clean, so I’m sure they’ll be fine.” You wouldn’t be the only one to think this. Microbes as a group (which is not actually a single, evolutionarily related group. I’m talking here about bacteria, archaea, and microscopic eukaryotes, i.e. the vast majority of life on earth) have survived all the mass extinctions (arguably causing at least one of them), and they can be found in the most extreme environments on the planet. But it turns out that most of them are extremely specialized5. So as we lose the habitats they are specialized to—climate change is expected to decimate wide swaths of ice sheets, permafrost soils, mangrove forests, and areas above tree line—it is very likely that species that are specific to these habitats will also be lost.

There is at least one group of microbes we can be certain is going to go extinct—all the bugs who are exclusively associated with a species of plant or animal that itself is going to be impacted by climate change. These include the bacteria that make amino acids for insects threatened by shifting phenology, the dinoflagellates that share their photosynthesized sugars with corals dying from ocean acidification, and the nitrogen-fixing bacteria whose legume hosts need cool environments. Host-association is just another form of habitat specialization, and at least 8% of those habitats seem destined for destruction. Even microbes that aren’t necessary for the growth of their hosts will be threatened by losing their partners. Climate change researchers have been calling for a greater inclusion of interactions in models of climate change induced species loss because biotic interactions are an important determinant of species success. Microbe-host interactions are critical for this from the perspective of both parties. 

While inability to disperse or evolve under new conditions is expected to limit microbial taxa much less than larger organisms, it is not really clear how much these factors will protect microbial species. While high mutation rates, horizontal gene transfer, and short generation times can produce fast evolution in microbes, it can still be hard for microbes to adapt. For example, in Richard Lenski’s long term evolution experiment, E. coli was able to evolve the ability to use a new sugar they couldn’t before6. But, the mutation arose in only one of the populations, and the rate of the necessary mutations arising was just once per trillion cell divisions. Furthermore, many microbes are extremely slow growing—with doubling times in the tens of thousands of years. How much evolution could serve to buffer these taxa from climate change remains totally unknown.

Even if microbes can adapt fast enough, entire suites of lifestyles may be lost as the environments that require them disappear. If the great-great-great-great granddaughter of a cell is still around but has evolved a totally new suite of functions, isn’t it fair to say the original “species” has been lost? And in the face of increased variability in climate, the loss of a function like cold tolerance may result in ensured extinction down the line. 

In recorded history, we know of only two microbial species that have gone extinct. Both were driven out intentionally by humans. These events were met with headlines like Rinderpest, Scourge of Cattle, is Vanquished. Today we mourn the passing of the passenger pigeon—to the extent that there are active attempts to bring them back—but not that of smallpox. Continued efforts to extinguish other pathogenic microbes, like polio and malaria, are lauded and given multi-million dollar campaigns. But in the future, the microbes we lose while we weren’t looking may be missed as much as the American Pika and coral reefs. Microbes play critical roles in biogeochemical cycling, plant productivity, human health, and even climate itself. They produce much of the oxygen we breathe. We cannot begin to predict how the earth would function without 16% of them, and this is in no small part because we haven’t even tried. More research is needed into the likely impacts of climate change on microbes, although it may be too late for many already. Thanks to programs like the Earth Microbiome Project, we may at least one day be able to identify what we have lost, but in the absence of efforts to systematically preserve microbial species diversity repopulation efforts will be impossible.


1. Frey, S. D., Drijber, R., Smith, H., & Melillo, J. (2008). Microbial biomass, functional capacity, and community structure after 12 years of soil warming. Soil Biology and Biochemistry40(11), 2904-2907.

2. Lawrence, D., Bell T., & Barraclough T. G. (2016). The effect of immigration on the adaptation of microbial communities to warming. The American Naturalist, 187(2).

3. Liang, Y. et al. (2015). Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. The ISME Journal.

4. Youssef, N. H., Couger, M. B., McCully, A. L., Criado, A. E. G., & Elshahed, M. S. (2015). Assessing the global phylum level diversity within the bacterial domain: A review. Journal of Advanced Research6(3), 269-282.

5. Mariadassou, M., Pichon, S., & Ebert, D. (2015). Microbial ecosystems are dominated by specialist taxa. Ecology Letters18(9), 974-982.

6. Blount, Z. D., Borland, C. Z., & Lenski, R. E. (2008). Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences105(23), 7899-7906.