So far we have learned about the diverse and fascinating microscopic life of the oceans, and we have seen a broad description of what a modeler does exactly. For this third introductory article, we’ll talk about the climate, and how exactly oceanic life interacts with it.

Let’s start with a simple question that shows exactly how important biology is to the ocean. If you had to take a guess, would you say that the amount of salt varies a lot depending on where in the ocean you look? Granted, there must be some variations but my limited experience taught me that ocean tastes pretty much the same no matter where I was. That would mean that the salt concentration doesn’t vary a lot depending on where you swim. And it is indeed true! The amount of salt is roughly the same all over the oceans, between 30 and 40 parts per thousand (meaning that on average, 3.5% of the sea water weight comes from the dissolved salts).

But let’s now look at the amount of nitrate across the globe, by looking at the concentration (in $mmol / m^3$, with $mmol$ being a usual measure of quantity in chemistry):

Source: Copernicus Marine Service Information

Source: Copernicus Marine Service Information

Here, we can see that the concentration of nitrate spans 6 orders of magnitude, going from 1 $mmol$ in 10,000 cubic meters in the poorest regions to almost 100 $mmol$ per cubic meter in the richest, or one million times richer! How come ocean mixing does not level the concentration of nitrate until we have roughly the same amount everywhere like it does for salt?

Well, that’s where biology comes into play. Contrary to salt, nitrate is what oceanographers call a nutrient, meaning that it can be used as a resource by phytoplankton to produce biomass thanks to photosynthesis. In simpler terms, nitrate is food to phytoplankton, whereas salt is not. It is true that ocean mixing should even out the differences, but that process is so slow that it doesn’t have the time to catch up to the biology, hence the stable disparities.

Nitrate is a very important nutrient in the ocean, because it often limits the growth of phytoplankton, but it is not the only one. In general, nitrogen (the main chemical building block of nitrate), iron and phosphate are all crucial to oceanic life, but one is especially important for us humans: carbon. As you probably are aware, studying the carbon cycle, and especially the fate of atmospheric carbon dioxide is a global point of concern right now, and you’ll see that the oceans play a major role in this cycle.

The carbon cycle in the oceans

The oceans take up more than 70% of Earth’s surface, which means that they have a lot of contact with the atmosphere. At every point of contact between the water and the air, physical reactions take place allowing for atmospheric CO2 to dissolve in the oceans and become aqueous.

This process is sometimes dubbed the physical carbon pump. Indeed, no biology is involved at this step, but even so the ocean manages to capture atmospheric CO2 and trap it in dissolved form. You might think “great, climate change is solved, we just need to let the ocean do its job!”, but I wouldn’t celebrate so fast if I were you: even though this pump is very efficient, capturing about half the carbon dioxide released by man, it is the main culprit for ocean acidification, which has dire consequence for marine life.

But back to our pump: how come CO2 dissolves just like that in the ocean? Well, in general we could say that nature hates disparities and tends to even out everything. Just as heat flows from hot things to cold things, if the concentration of carbon in the oceans is lower than that of the atmosphere, carbon will tend to flow from the atmosphere to the oceans. This process is very slow in itself, but the sheer size of the oceans largely compensate for that fact, and that is why the ocean is able to capture so much CO2!

Once the CO2 has entered the oceans, it is available for phytoplankton to perform photosynthesis.

Photosynthesis is the process that fixates CO2 and other nutrients into biomass. So far, we have seen how atmospheric CO2 can be captured by phytoplankton, but its cycle doesn’t end here!

Indeed, phytoplankton are the favorite dish of another group we encountered before, the zooplankton. Zoooplankton feeding on phytoplankton is called grazing, and it allows for the carbon to move up one ladder on what was once called the trophic chain (a fancy term for food chain).

But zooplankton themselves are not the apex predators (they are after all, very very small), and bigger animals can feed on them through predation.

I am not going to lie, the term “bigger animals” does a lot of heavy lifting here, comprising everything from small fishes to blue whales. The ecology of this group is fascinating as you might guess, but for our study it will be sufficient to lump them all together!

All these groups, and especially the bigger animals, then excrete some of the carbon they ingested, and eventually die. These processes create particles, and form the particulate organic matter group.

As the name suggest, organic matter regroups all compounds produced by life, whether dead or alive. An important distinction is to be highlighted here between nutrients and organic matter. Nutrients are always inorganic, and it is photosynthesis that turns them into organic matter ready for consumption. This is the basis of the difference between autotrophs (which we talked about in the first article) which consume inorganic nutrients, and heterotrophs which consume organic nutrients.

These particles of organic matter can then sink to the bottom of the oceans and form the sediments found on the ocean floors.

We typically end the carbon cycle here in oceanography, considering the carbon locked in. Indeed, once settled on the ocean floor, the carbon will not come back into the surface cycle for typically several thousand years.

So there you have it, we have seen how biology manages to trap atmospheric carbon dioxide a long time. This whole process is called the biological pump, and together with the physical pump they form the carbon pump of the oceans. Let’s sum up the whole process:

For a long time, this carbon pathway was thought to be the only relevant path to study for the carbon cycle in the oceans, from the dissolution of atmospheric carbon to the sinking of sediments. And as a first approach, it is enough to understand how carbon can be trapped in the oceans thanks to biology! But as with everything, the whole picture is a little more complicated, and some parts that are missing from the schematics above can be really important (and I’m not only saying that because I focus on those parts in my Ph.D.)

Just as the food chain concept was replaced by the more accurate food web in ecological studies, the biological pump was further complexified in models roughly starting half a century ago with the inclusion of heterotrophic bacteria, which move carbon up the biological pump, effectively recycling nutrients. The interest in this recycling pathway began after a seminal paper by Azam, Fenchel et al. in 1983 coined the specific term stressing the importance of this pathway by calling it the microbial loop.

The microbial loop and the recycling pathway

Let’s go back to our particulate organic matter for a second. I told you very confidently that those particles sank until they reached the sea floors, but what if these particles are too small to sink and just float in the water? Those particles then form a category of their own, which we call dissolved organic matter, and dissolved organic matter is produced through a variety of mechanisms by pretty much everyone in the trophic web and by breaking particulate organic matter down.

I should warn you though, oceanographers are a tricky bunch, and they do not mean dissolved the way you and I mean, like salt is dissolved in sea water. Their definition of dissolved is not chemical (as is the common one) but ‘operational’: they consider anything able to pass through a filter of $0.7~\mu m$ (approximately the hundreth of a hair width) to be dissolved.

This dissolved organic matter is the main resource for the heterotrophic bacteria we studied in our last article. These bacteria can in turn be eaten by zooplankton, thus re-injecting otherwise ‘lost’ carbon into the trophic web, but more interestingly for us they can produce nutrients as a by-product of their respiration. This step is called remineralization.

And this remineralization is very important in the carbon cycle. As I told you earlier, phytoplankton are often limited in nutrients when performing photosynthesis, meaning that recycling them can help phytoplankton populations to grow and change the global carbon cycle in the oceans.

We can now integrate the microbial loop in our global picture of the carbon pump and have a pretty good sense of carbon circulation in the water column (meaning, if we only look at one geographical location from the surface to the ocean floor).


Of course, keep in mind that this is a simplified version of reality. As you now know, modelling requires simplification, and often the question is to know where to stop. Before the paper inventing the term ‘microbial loop’, the action of heterotrophic bacteria was deemed of too little of importance to be put in global model trying to capture the carbon cycle in the oceans, at least as a first step.

The same thing can be said about this representation, and now many studies (including mine!) focus on parts not represented here. For instance, the importance of viruses is thought to be currently underestimated due to the lack of representation in models, and it has only been a few years since people have been trying to actively understand their role in the biogeochemical cycles (and more particularly, the carbon cycle). But that is a story for another time, and many things still need to be discovered about the microbial loop and the interactions between heterotrophic bacteria and dissolved organic matter. Those will be the focus of the next few articles, so stay put!

If you want to go deeper