Swings #5 : Bacteria, the cradle of ocean breathing

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Swings #5 : Bacteria, the cradle of ocean breathing

diatomee bacterie
Photo of phytoplankton (diatom and picoplankton - in green) surrounded by bacteria (in blue) from a seawater sample from the North-Western Mediterranean Sea © Philippe Catala

Bacteria are found everywhere, they colonise our skin, our intestines, our cheeses... only some of them are harmful to our health, and the majority are necessary for our balance and that of the ecosystems. In the ocean, they also have their role to play by "collaborating" with phytoplankton. Part of the SWINGS’ scientific team is studying these unicellular organisms that produce CO2, which are also responsible of the carbon cycle in the ocean.

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By Victoria Lascaux, translated by Elena Masferrer.

In the marine environment, there is an enormous bacterial diversity. In the Southern Ocean, only bacteria adapted to survive and grow in its cold waters are abundant. So, are there specific types of bacteria for each ocean? This is a question that remains unanswered... but it intrigues scientists. Ingrid Obernosterer's team from the Laboratoire d'océanographie microbienne de Banyuls (LOMIC, France) is part of the international BIOGEOSCAPES programme. Among other things, this programme aims to improve our understanding of the microbial communities in the oceans and their metabolic function in relation to trace elements. This programme brings together international scientists determined to explore the world's oceans over several years. On board the Marion Dufresne, SWINGS' scientists, microbial oceanographers, biologists and biochemists, are concerned about the Southern Ocean, as is a poorly studied area.

Inhaling, exhaling: the rhythm of bacteria

Bacteria respire as we do, absorbing oxygen and releasing carbon dioxide (CO2). Conversely, phytoplankton develops thanks to photosynthesis, so they consume carbon dioxide. Determining the balance between absorption and production of CO2, and thus carrying out a carbon balance to describe the ocean's capacity to absorb this atmospheric greenhouse gas, is a major ecological challenge.

Bacterial diversity is linked to phytoplankton communities. Phytoplankton produce organic matter that is consumed by bacteria in the water column. The bacteria produce CO2 and nutrients, a process called remineralisation. The balance of these processes can be influenced by water temperature and iron deficiency.

In order to successfully study these bacteria and carry out the carbon balance, the following questions must be answered: which bacteria are present and what is their respiration rate? What is the primary production due to phytoplankton algae? In order to conduct all the necessary measurements, different techniques are used.

Bacterial diversity

Ingrid Obermosterer
Ingrid Obernosterer in her laboratory aboard the Marion Dufresne © Laurent Godard

« If you look under a microscope, all bacteria look alike, so to study bacterial diversity we must use genomic approaches. »

Ingrid Obernosterer, CNRS researcher LOMIC.

Using molecular biology techniques, the aim is to sequence the genes extracted from the DNA and RNA of the bacterial cell. To carry out this manipulation, bottles are deployed via the rosettes in order to collect as much water as possible. Scientists use cartridges, a sort of filter folded together to concentrate the bacteria and collect enough biomass. To preserve these microbial samples, freezing between -20°C and -80°C is necessary. Back in the laboratory, the genes present in the samples will be determined, an essential step in identifying the diversity of bacteria present at different depths and in different ocean regions.

Characterising the genome of the bacteria is essential, but quantifying their activity is just as important. For this research, a small pellet of a few millimetres in size is fixed to the inner wall of the incubation bottles to measure the bacteria's respiration (O2 consumption) kept in the dark and at a constant temperature.

Colouring to detect algae production

At the same time, colleagues from South Africa and the UK (including Thomas Ryan Keogh) are determining primary production. To do this, they place samples of bottled seawater in incubators on the ship's deck. The incubators are large, one-metre-long cylinders, which are displayed in a bright area of the ship and are fed continuously by surface seawater to reproduce phytoplankton’s natural conditions (solar radiation and water temperature). After 12 or 24 hours of "culture", scientists look at the growth rate of the phytoplankton. They will also add nutrients to certain samples to find out if nitrate, phosphate, iron or, for example, trace metals limit growth. At each new station, the protocol is reproduced. This repetition is important for the scientists, it gives an idea of the state of health of the phytoplankton according to the geographical location. To estimate this primary production, researchers determine the pigment content (such as chlorophyll), an indicator of the biomass of different phytoplankton groups. For this purpose, one litre of seawater is filtered and will then be chemically analysed on land using high-performance liquid chromatography (HPLC).

Thomas Ryan Keogh arranges his water samples in the incubators © Laurent Godard


Another technique and measure are that of nutrient salts. To know the concentration of nitrate, phosphate and silicic acid in seawater, a spectrophotocolorimetric method is used.

A sequence of chemical procedures gives a colourisation of the sample at the end. Depending on the intensity of the colour, it is possible to determine the concentration of the above-mentioned nutrient salts.


Audrey Guéneuguès:  An engineer with an insatiable curiosity

What is your scientific background? 

portrait audrey gueneygues
Audrey Gueneugues © Laurent Godard

In 2004, I was admitted to the Institut national des sciences et techniques de la mer in France. I then worked in various laboratories all over France. Since 2010, I have been a CNRS assistant engineer at the Laboratoire d’océanographie microbienne in Banyuls, France. I am in charge of the clean room, a room where all the air is filtered.

What is your greatest scientific pride?

I am very happy to work in this laboratory and to participate in Stéphane Blain's research on the role of iron in marine environments. I am also proud to have taken part in a mission to the Kerguelen Islands to study the impact of glacier melting on marine environments.

What is your role on board?

My role is to analyse the silicates (nutrient salts) present in seawater samples. These silicates are important because they ensure that the sampling has gone well and that there is no bias in the analyses.

What does a typical day look like?

Every day is different! My role is to prepare the sampling and receive the samples. I must also carry out the analyses and pass them on to the researchers. During the stations, the times when the boat stops to take samples, we can work day and night and we have to look for a time to eat and sleep.

What do you like about this adventure?

This is my seventh time on board the Marion Dufresne, and I still enjoy taking part in these missions. It's an extraordinary adventure: we spend two months with 50 scientists and 50 sailors. It's a real change from the routine of the laboratory. There are also the whales, the albatrosses and the landscapes when you pass near islands that almost nobody knows. There are beautiful starry nights and incredible sunrises. The storms are also very beautiful!

What do you do to escape on board?

There is a small gym and you can play badminton. It helps to keep fit. And then there are funny card games with colleagues.

What books did you bring with you?

The Vernon Subutex trilogy, by Virginie Despentes. We always exchange books with colleagues afterwards.



9 February : The mission continues and intensifies on board the RV Marion Dufresne. Today is the eleventh deployment of the in-situ pumps. The day before, the scientists dressed as astronauts prepared the filters: opening a filter holder, fixing the filter, closing the filter holder and starting again 15 times. Once this choreography was finalised, the particle and seawater filters were installed on the pumps. At 4AM, still asleep, the technical team replaced the batteries and programmed the pumps. The scientists need 2 hours to deploy them at the desired depths. From now on, not a minute to lose, the chronometer is running !


container salle blanche swings
In the filter bubble. Before and after the deployment, Marion Lagarde and Nolwenn Lemaitre meticulously assemble and disassemble the filter holders to collect and cut the filters. At the beginning of the mission, they installed a "bubble" in a laboratory container. It is an area made metal-clean thanks to plastic sheets on the walls and a hood that generates filtered air inside. © Virginie Sanial.


To encourage the whole team, a pancake tour for everyone. Corentin Clerc and Guillaume Barut are becoming pastry chefs, the hardest part is not to make any lumps.


“The pastry is ready, all that remains is to heat the pan”, says Corentin Clerc. © Laurent Godard


12 February : The wind blows and the swell rises to 5-6m. The ship is rocking more than usual, sailors and scientists have to hold on so as not to hit the walls, or colleagues. Easy to say but not easy to do.

« The most complicated in these moments, the shower, the golden rule is "one hand for you, one for the boat" but is it possible to have a third hand for the shower gel? Let's not talk about the water that overflows and sprays the whole bathroom, the slipping is never far away. »

Catherine Jeandel, CNRS researcher, co-chief scientist of SWINGS.

Anecdotes that the team takes the time to tell in their letters to their loved ones. A lack that is becoming more and more apparent.

The mail is being stamped © Laurent Godard


13 February : Between tiredness, bad weather, pancake tasting and the storytelling, the last few days have been busy. Tonight, there is a celebration, Ingrid Obernosterer and Izzy Turnbull's birthdays are the occasion to share a concert orchestrated by the team. Happy birthday girls !

Birthday of Ingrid Obernosterer and Izzy Turnbull © Twitter Swings GS02


To learn more, follow the cruise diary : https://swings.geotraces.org


The Laboratoire d’océanographie microbienne (LOMIC) is a joint research unit of Sorbonne University and the CNRS (UMR 7621) in France.