Personal Introduction

My name is Elsa, a geologist from France that enjoys boat rides a bit too much.

I have grown to be sensitive to climate issues from a young age. I remember my mom yelling from across the house telling me to turn the lights off or else polar bears would go extinct. When I look back, I am now sure she was more worried about our electricity bill, but for me, that was the start of my fight against the current climate crisis. But one thing my mom was really concerned about was marine ecosystems, and as a diver she passed that onto me as well.

I jumped on board with an ambitious project called STRESS3D (Evaluating 3D morphometrics changes in calcite shells using a multistressor experimental approach) as a part of my master’s thesis at Lund University. This project directly concerns marine environments and ecosystems, and got me interested right away.

Let me tell you a bit more about it.

Gullmar fjords boat ride

The big picture

Anthropogenic COemissions are responsible for around 60% of global warming and recent climate studies, such as the IPCC 2022 report, aim at quantifying the consequences of its rise (IPCC2022).

We know that the atmospheric CO2 increase is leading to a triple stressor situation in the oceans called the “deadly trio” involving warming, acidification, and deoxygenation of the water. This doesn’t only impact polar bears, but all marine organisms at macro- and micro-scale and have been the principal suspects for the past mass extinctions.

It’s in that context our project ambitiously aims at understanding the impact of these changes (Temperature, O2 and pH) on one group of important calcifying microorganisms, namely foraminifera.

A study conducted at Gullmar fjord, Sweden.

Gullmar Fjords close ups

You can read more about the climate changes report here:

or about the “deadly trio” here: Bijma, J., et al. Climate change and the oceans – What does the future hold? Mar. Pollut. Bull. (2013), 10.1016/j.marpolbul.2013.07.022


Foraminifera (forams) are little known by the general audience and you probably have never even heard of it. But they are quite the star in fields such as paleontology.

Forams are single-celled microorganisms (size ~0.1 to 1 mm) and with ubiquitous widespread occurrence, which makes them some of the most diverse and abundant marine microorganisms. They can be divided into two distinct types, the planktonic forams (living in the water column) and the benthic forams (living in the sediments at/in the sea floor), the latter being the interest of our study.

The species distributions and abundance are strongly controlled by temperature, salinity, oxygen content, pH or food availability. They consequently have a strong response to environmental changes making them the perfect individuals for our experiment.

When deceased, they get fossilized in the sediments which interests many paleontologists, or more adequately called paleo-oceanographers.

Our lucky chosen species are called Ammonia sp., Bulimina marginata, Nonionella sp T1, Nonionellina labradorica and Quiqueloculina sp.

Species Nonionellina labradorica under light microscope
Species Nonionella sp. T1 under light microscope. This species surrounds itself with sediments to thrive
Species Quinqueloculina sp. under epifluorescence microscope
Species Bulimina marginata under epifluorescence microscope

You can read more about foraminifera in the book Modern foraminifera by Barun K. Sen Gupta (2003) chapter 3 (Goldstein, S.T. (1999). Foraminifera: A biological overview. In: Modern Foraminifera. Springer, Dordrecht.





Understanding the response of microorganisms to climate change is challenging to achieve in natural environments because of the difficulty to disentangle different stressors and what causes the responses of the forams.

Therefore, we are experimentally culturing the foraminifera in a dedicated laboratory at the Kristineberg marine research station. 

We expect the organisms to calcify, build new chambers, and hopefully reproduce under experimental assessed conditions. However, we also hypothesize that the calcification will be affected by experimental conditions. 

The little forams are cultured under controlled conditions in aquariums for the expected climate for the year 2100. The latter conditions are designated based on the scenarios listed in the IPCC 2022 climate report for expected future ocean acidification, temperature and deoxygenation.

Afterwards, I and my collaborators will analyze the shell geochemical composition and morphology.

Map of gullmar fjord uploaded by Filipsson et al. 2013

And more practically?



Mid-September 2022 we traveled from Lund to Kristineberg on the Swedish west coast with an international team of dedicated and ambitious foraminiferal scientists (Sweden, USA, France) to reach Gullmar Fjord. One can proudly say it is the only real fjord (as it has a sill in the mouth of the fjord) in Sweden but it is also the most consecutively studied marine area in Sweden which creates an interest for many marine biologists and geologists.

Out in teams, we went sampling for forams close to the shore (mudflat sediment) and out at sea. We used the smaller vessel, R/V Alice, to reach a site where the water depth reaches 50 m. As we are interested in benthic (bottom-dwelling) foraminifera, the sampling consists of getting sediment cores of the sea bottom using both a GEMAX and a box corer (photo).

When back at the station, the sediments had to be sieved to concentrate the sample and a total of almost 5000 foraminifera were hand-picked under the microscope and put in Calcein. It was a lot of work and we had a picking party late in the evening. 

The little Alice.
Some sediment cores from the sea bottom (~50m), about 40cm of sediment matter has been retrieved with the GEMAX corer.
A mud retrieved from the sea bottom with a box-corer, allows us to work with a large amount of sediment.
Isadora and I looking at the cores and scraping some mud off.

The use of calcein

Calcein is a fluorescent compound used to label newly formed chambers of foraminifera. 

If incubated in calcein for several weeks (2-3 weeks, Bernhard et al., 2004), foraminifera will calcify and possibly create new chambers (photo). The new chamber will be marked by a green fluorescence when viewed under an epifluorescence stereoscope.

The use of this compound is to mark the “start” of the experiment. 

When removed from the calcein, forams will keep their fluorescence on that precise chamber but not on the chamber that will further calcify. 

At the very end of the experiment, we will therefore know which chambers calcified before, during and after the input of calcein.

Weighting as precisely as possible the 10mg of the calcein compound powder.
The mixing of the calcein powder with 1L of sea water.
Adding calcein to the petri dishes where forams are chilling.
Result, a new fluorescent chamber has grown on this Ammonia sp. specimen.
in case you didn’t see it…

First experiment of calcein on forams was conducted by Bernhard et al. 2004 (

Setting the experiment

We performed the experiment in two rooms, each regulated at different temperatures.

In the first room the temperature was adjusted on today’s average in situ water temperature in the fjord (~9℃) and has been nominated the cold room.

Within the cold room we displayed;

  1. First aquarium is set to in situ pH level in the fjord of pH 8.1
  2. Second aquarium is set to first water acidification scenario of year 2100 of pH 7.6
  3. Third aquarium is set to second expected water acidification of year 2100 of pH7.4
  4. Fourth is expected water deoxygenation of the year 2100, possibly reaching hypoxic conditions.
  5. Additionally, we tried testing both impacts of de-oxygenation and acidification within one aquarium.

The second room displays the exact same acidification and deoxygenation pattern but regulated to an expected water temperature of the year 2100 reaching ~14℃, nominated the warm room.

Acidification of the oceans occurs when atmospheric CO2 is rising, an observed trend in today’s climate. In our experimental conditions, acidification levels are reached by the use of CO2 bubbling. 

Deoxygenation of the oceans is due to an increase in nutrient and the over-used of the available oxygen to decompose the nutrient surplus, to reproduce that trend experimentally we used nitrogen bubbling.

After having laid forams in each aquariums we let them thrive in their new conditions and fed them every week while making sure that the pH and O2 stayed at the targeted values.

Preparing the petri dishes by removing the calcein and adding sea water to each of them.
Adding silica for copying a somewhat natural environment and adding a mix of algae for feeding.
Adding the petri dishes in each aquariums.
The aquariums were closed with a layer of plastic to maintain hermetic conditions.
pH, salinity and temperature daily check of each aquarium.
Nitrogen gaz bottle (black) for setting hypoxic conditions and CO2 gaz bottle (green) for acidic conditions.

So what happened to them?

After waiting for 2,5 months at the station and checking if our forams were growing in the proper conditions, we finally got to take them out of there. We weren’t sure what to expect when retrieving them, forams could have died massively, dissolved completely or simply be alive and “healthy”.  In order to know we had to incubate them in a compound called Cell Tracker Blue which dyes alive cells in blue. If the forams turn blue under a fluorescent microscope, it means that they were alive at the end of the experiment. Lastly, we unfortunately had to kill and conserve all of them in ethanol (don’t worry forams are exempted of nerves or sensory captors and do not feel a thing). 

We then processed the results in 2 different ways:

  • How many survived, calcified or dissolved?

Live, calcified, and dead forams were all counted under a binocular at the department of Geology in Lund (Sweden) which was a very, very long process. This showed that the harshness of the conditions didn’t allow for many of them to survive the experiment expect for two very lucky species; Ammonia spand Quinquelo sp.

More than lucky, those two species are known to be very adaptative to hydrographic changes and pollution and once again proved theses characteristics in our experiment. 

This is somewhat good news as there is a chance that those microorganisms will be able to thrive in the future climate context.

  • Laser ablation

Laser ablation (or as we call it: LA-MS-ICP) is a complex process that allows the acquisition of foram shells chemical composition. A laser pierces trough foraminiferal chambers, and the resulting dust is analysed for chemical concentration. 

Why do that you’d ask? We want to know how the shell composition is influenced by the environment in which the foram grows and understand how forams chemistry will interact with oceans chemistry in future climatic context. 

To do that, forams chambers must be analyses to understand the evolution of the shell in our aquariums. We expected to see significant change in the chemical composition of the shell after the introduction of the forams in the aquariums. The analyses were conducted on the species with the highest survival rate: Ammonia sp. 

The laser ablation machine, everything happens out of sight
What our Ammonias look like after being pierced by the laser.
Note that we sent a beam trough the last four chamber of the specimen, which calcified in the experimental conditions.