By reading the previous three articles, you might have understood that my thesis revolves around modeling the microbial loop (parts of it anyway). This being said, what is the central question I try to answer during my Ph.D.? In other words, why do I study this system?

The answer lies in the works of one of the most famous naturalists of the XIXth century: Charles Darwin, and more precisely in his theory of natural selection. In broad strokes, this theory states that different physiological characteristics (or phenotypes) lead to different chances of surviving and reproducing. If these phenotypes can then be transfered to your offsprings, gradual evolution of the population will occur, eventually leading to the differenciation of species.

Doodling of the Tree of life by Charles Darwin in his On the origin of species.

Doodling of the Tree of life by Charles Darwin in his On the origin of species.

This theory is a key component of my Ph.D., so we’ll try to understand what exactly is at play, and how it is linked to the microbial loop and climate change.

An example of natural selection

Natural selection occurs at many different levels, and we can try to understand the evolution of specific characteristics of the phenotype (or traits) under this framework. Let’s do this with one of the most striking yet simple examples of natural selection: giraffes' necks. Can we try to understand, through our scientific theory of natural selection, how giraffes ended up with such long necks?

In order to do so, let’s first describe as accurately as possible the terms of the theory. According to Darwin, there are three underlying conditions for natural selection to occur:

The trait under study needs to be able to vary. If all individuals in the population share the exact same characteristic, there is no reason to think some will survive longer or have more offsprings.
Many variations can occur in the population, but not all can be transfered to the next generation. For instance, we saw that bacterial growth rate depends on nutrient concentration, which is indeed a variation. But since the variation comes only from external factors, it can’t be passed down to one’s offsprings1. For natural selection to take place, the variations need to be transferable to the next generation.
These heritable variations need to lead to differences in survival and reproduction. If a population has a characteristic that confers it an advantage in a certain environment and passes this advantage down to the next generation, then we can expect this characteristic to outcompete all others eventually, leading to an overall more adapted population.

Let’s now see how our giraffe necks fare under this theory. First of all, we can expect variation in neck length: we can study many other mammals and see that their necks are much shorter. Do the experiment yourself if you have a pet, they should have shorter necks than giraffes2! Then, thanks to advances in the field of genetics, we know that if a giraffe is born with a slightly longer neck due to a random mutation, its offsprings will also have a greater chance to have a longer neck. Finally, are different lengths of necks selected for differently?

Let’s work in incremental stages, and go way back to a time when giraffes had perfectly normal necks.

One day, a new giraffe is born with a slightly longer neck, along with slighlty longer legs.

How does our new giraffe fare in the hard life of the savannah? Well, its longer neck gives it a competitive advantage. Indeed, while all the other giraffes have to compete against one another to eat grass and small leaves from bushes, our new giraffe can simply eat leaves from a tree that are out of reach for the others!

This means that our new giraffe has less struggle, and is overall healthier than its short-necked neighbours. A healthier giraffe lives longer and attracts more mates, leading to more offsprings than the others. The process will repeat and eventually lead to the extinction of the short-neck giraffes due to competition.

But as you can see, our giraffe can’t reach the highest leaves, yet everyone knows that they are the tastiest! Evolution works in slow, incremental changes, which means that one day, yet another mutation can occur, which results in an even longer neck for the mutant.

As you might expect, the same thing happens to the giraffes with the not-so-long-after-all necks that happened to the extinct giraffes. The new population outcompetes them, dooming them to extinction since resources are not infinite.

Where does this process end? Can we expect longer and longer necks on giraffes in the future? Well, at some point having longer necks will prove useless, or even counterproductive. Indeed, for one if the giraffes end up with their face way higher than the trees, giraffes with shorter necks will be at advantage. Having a long neck also comes with a price, as it is more difficult to drink from ponds and increases vulnerability.

We can then expect that giraffes' necks of a certain length will be the most adapted to their environment, with giraffes having slightly longer or shorter necks unable to outcompete our optimal population. This particular length will be called the evolutionary stable strategy for our population of giraffes. As the name suggests, this particular value of neck length is expected to be stable if the environment stays constant.

So there it is, a concrete example of natural selection at work! But I think you’ll agree that we are far from the ocean here, so how do we loop back to the carbon pump?

Bacterial adaptation in the microbial loop

Evolution is a process, and is in fact still happening to this day! Don’t expect giraffes to change much during your lifetime though, as the process is very slow, especially for large organisms. In our example, two steps only were needed to reach the evolutionary stable strategy, but in reality many more steps would be necessary, the whole process spanning hundreds or even thousands of generations of giraffes.

But the smaller the organism and the shorter the generation time, the more chance we have to actually see evolution take place. For instance, heterotrophic bacteria are a good candidate for faster evolution, or adaptation to changing environments. You might have heard of bacterial adaptation as a real concern, as they can evolve to develop antibiotic resistance. The way they develop these resistance is through natural selection, exactly the same way giraffes ended up with long necks.

Even though my Ph. D. focuses on a different type of bacteria, the ones found in the ocean comprising the microbial loop, the same process is at play and we can expect them to evolve and adapt to changing conditions. And the environment is changing in rates never seen before due to climate change. Sea-surface temperature are rising, the ocean is slowly getting more acid and this will ripple through all life in the ocean, inducing a strong pressure to adapt.

But in return, the adapted populations will alter their function in the carbon cycle, thus impacting the environment. My job is to model this eco-evolutionary feedback loop in order to untangle the potential effects climate change and bacterial adaptation will have on the microbial loop and its function.

The eco-evolutionary feedback loop

The eco-evolutionary feedback loop

In particular, adaptation is often overlooked in global reports such as the IPCC, and through my studies I aim to establish whether this is an oversight that needs to be corrected, or if bacterial adaptation has minor effects on the global carbon cycle and can be forgotten in future projections.


In effect, to do so I have to go through the following steps, which I intend to describe in details in the upcoming articles:

  • First, I need to understand how bacteria fit in the carbon pump ecologically (i.e., when no evolution takes place) and what effects they have on the system as a whole. This means designing an ecological model of the microbial loop, integrating it in a broader system of the sea-surface (for now) and evaluating its effect on carbon capture.

  • Then, once I understand the ecological role of heterotrophic bacteria in the carbon cycle a little better, I need to understand which trait is best suited for an evolutionary study. The criteria are simple, yet important: the trait needs to be under strong pressure to adapt, and has to be relevant to the carbon cycle.

This may not seem much, but it can already span a good deal of my Ph.D.! After this is done, several extensions can be explored. First, there is a real need to introduce evolutionary mechanisms in global circulation models used in predicting climate change, and part of my work will focus on that. Then, I also want to study the role of viruses in the microbial loop, as they are thought to be a major actor in biogeochemical cycles. So don’t worry, I think you’ll have plenty to read in the following months!

If you want to go deeper

  • Koonin, E. V. (2011). The logic of chance: the nature and origin of biological evolution. FT press.3

  • Monroe, J. Grey, Markman, David W., BECK, Whitney S., et al. Ecoevolutionary dynamics of carbon cycling in the anthropocene. Trends in ecology & evolution, 2018, vol. 33, no 3, p. 213-225. 10.1016/j.tree.2017.12.006

  1. Though there is more nuance and discussion than we care to go into in this article, the question of heritability of acquired traits is not entirely without basis as often thought. Lamarck’s theory of evolution is often pitted against Darwinian evolution, but they are not mutually exclusive, as the booming field of epigenetics proves. ↩︎

  2. Unless you have a pet giraffe, but if that’s the case please send me a picture! ↩︎

  3. I must be honest, I haven’t had the time to read it yet, but I hear it is very interesting! ↩︎