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Blog on science on board: instruments, methods & teams’ work

In this section you will find the following articles:

  • “No RESILIENCE without pluri-disciplinarity” by Guerric Barrière
  • “Does the perfect mooring to reveal bio-physical interactions exist?” by Salomé Pellé
  • “How does the CTD work on the RESILIENCE mission?” by Lucas Zaccagnini
  • “Retrospective of the engineering-research alliance on a scientific cruise” by Eugénie Dufour
  • A small organism for man, a big step for science!” by Alycia Valvandrin

No RESILIENCE without pluri-disciplinarity

Guerric Barrière

May, 11th 2022 – Marion Dufresne

Eddies are in the center of the RESILIENCE mission. These complex oceanographic features are mis-understood by the scientific community, especially in the Mozambique channel and across the South African coast. Many scientific teams work on this mission and aim to better understand the eddy life cycle and his influence on biology at different scales. We have all the image of the scientist, alone, in his lab with tubes and chemical solutions. But on an oceanographic mission, it’s different and the RESILIENCE mission shows it perfectly by its multidisciplinary nature and the relationships between the different teams. 10 teams and members of the crew are working together following the same goal.

Let’s see what’s going on in this oceanographical ant farm…

….The physical team is mainly responsible for planning the stations and performing the deployment of the rosette. They collect and analyse the satellite data in real time and identify the most interesting locations for sampling during the daily meetings. Some time before arriving at the station, a trawl net is deployed at the back of the boat to study the micro-nekton. The sampling depth is decided just beforehand thanks to the acoustic profiles provided by the probes under the boat: the EK80 instrument which is using active acoustics for observing distribution of organisms in the water column along the ship’s trajectory. Once at the station, the rosette, a metal frame with Niskin bottles attached, which is equipped with a CTD (conductivity, temperature and density) probe and different sensors (measuring fluorescence, turbidity, currents etc.), is deployed in the water in order to take vertical profiles of the different tracers and to sample the water at different depths. During the RESILIENCE mission, the rosette is also equipped with a device to record acoustic signals laterally, the data collected will be used by the meso-zooplankton and micro-nekton teams. The different depths sampled by the rosette are decided by members of the different scientific teams after analysis of the profiles drawn up during the descent. On the way back up, water samples are taken by the CO2 team, whose data will also be used by the phytoplankton team to determine whether the fluorescence observed can be attributed to new production or just to transport. Other samples are taken to determine the salinity, oxygen and nutrient concentration. The phytoplankton team then takes samples to quantify particulate organic carbon, silica and chlorophyll and the environmental DNA team does the same to determine the composition of the nekton. The fluoroprobe and the phytoplankton net are then put in the water so that the phytoplankton team could study the composition of the communities by discriminating the large groups on a vertical profile and observe the species composition. Finally, a zooplankton net called the ‘multi-net’ is deployed at the back of the boat. This sample organisms at different depths.

Outside of stations, continuous measurements to establish vertical profiles for different tracers are carried out by certain devices such as the MVP (mobile vessel profiler) and the scan-fish. Another device called the geoFISH takes samples from surface water for trace metals team: this sample need to be particulalry “clean” in order to do not distort measurements of trace metals which are in very low concentrations (between 10-12 and 10-9 mol.kg-1). When the boat is in motion, the marine mammals and seabirds teams scans the ocean. In addition, different moorings were deployed during the mission to monitor the continuous evolution of oceanographic parameters at a special place (you can get an overview of the the two mooring deployed during our cruise, the BOMBYX and the WireWalker, in the CV of a machine page or discover the BOMBYX mooring in the following article). Results will then be shared between the teams. Of course, all these operations would not be possible without the help of the crew members and the IFREMER engineering team who are doing a great job despite the complicated conditions.

Let’s finish with a citation of Anne LEBOURGES-DHAUSSY : “I choose team working without hesitation, working alone is not possible in oceanography”. Are you convinced ? See the CV of a machine page for more information on the different instruments used during our mission.

Does the perfect mooring to reveal bio-physical interactions exist?

Salomé Pellé

May, 11th 2022 – Marion Dufresne

After 20 days at sea navigating in the Mozambique channel, the students of the Floating University are now used to life on board. The eddies have ALMOST no secrets for us. During the first leg, we sampled near the French atoll Bassas da India.

Vertical plan of the first hundred meters of the mooring © Physics' Team

This first leg was marked by the deployment of a mooring known as BOMBYX (“BOuée Multimodale pour la Biodiversité et l’océanophYsique”). This technology was originally developed by Hervé Glotin, but this version was adapted by Jean-Luc Fuda and Vincent Rossi. The main objective of this mooring is to record the occurrence and variability of ocean fronts and to link it to the distribution and activities of marine life.

This mooring is composed of a series of instruments attached to a 1 km long steel wire weighted at one end (using old train rails from Marseille, no joke!) to maintain it at the bottom of the ocean. The other end is equipped with floaters to make sure the wire remains taut while staying in the subsurface.

Set of batteries carefully attached to the hydrophone. (c) Floriane Sudre

This mooring is planned to stay in the water and collect data for 6 months, after which the physics’ team will retrieve it. A set of devices are present all along the vertical profile such as ADCPs (Acoustic Doppler Current Profiler) to monitor the horizontal currents in the water column. CTDs (Conductivity, allowing to get the salinity, Temperature and Depth sensors) are attached at different depths to survey salinity and temperature gradients. A fluorimeter also measures seawater fluorescence associated with fronts.

More interestingly, several hydrophones will allow the detection of marine mammals thanks to passive acoustics. This long-term non-invasive technique can give insight on the species visiting these areas and the activities they are exhibiting. In other words, each species emits different sounds which can be modulated depending on their behavior, for example when feeding, breeding, or socializing. At the end, the aim of BOBMYX is to link physical data on the ocean fronts with biological data on megafauna.

This deployment needed a lot of planning as it must remain silent to avoid interference with the hydrophones by creating noise. Moreover, as this technology is completely autonomous, the battery, storage and duty cycle (periodicity of recording) must be carefully set to make sure data can be recorded during half a year.

Deployment of the BOMBYX on the rear deck. © Salomé Pellé

The deployment of this 1 km long mooring took more than 6 hours. It was a tricky operation as they needed to target a specific spot to make sure the depth was exactly the same as scheduled.

Few days after the deployment, the physics team was scared that JASMINE (tropical storm) would detach the mooring. Thankfully this was not the case. An Argos tag is placed near the surface of the mooring for sending signal in case of breakage. Fingers crossed the team will get a lot of exciting data that will help explain the bio-physical interactions occurring in this area.

How does the CTD work on the RESILIENCE mission?

Lucas Zaccagnini

May, 11th 2022 – Marion Dufresne

The CTD is the heart of an oceanographic cruise, and of the work of water hunters, also called oceanographers. But how does it work and what does it involve? First of all, the mission leaders, called PIs (Principal Investigators), have the responsibility (and the power) to determine the location of the station. In our case, an eddy is detected by satellite measurements and the stations are placed at various locations in order to best sample the processes occurring in this structure. Since eddies are mobile, so are the stations. Indeed the position of the stations is continuously adapted to the movements of the eddy which are monitored with satellite images (when available, because they depend on the cloud coverage) or data acquired on board with continuous sampling devices (e.g. thermosalinograph, moving vertical profiler). Once the captain arrives at the station, the crew starts the dynamic positioning. This is a system that allows the boat to stay in the same place during the whole operation, despite waves, current and wind. A computer controlling the two propellers and the bow thruster adjusts the power of these three elements in real time to keep the same GPS position. This ensures that the instruments in the water are not broken and that the measurements are not biased.

What we call “making a CTD” is to put in the water a large probe, the “rosette” (the true name of this device, often renamed “CTD” due to the Conductivity, Temperature and Depth sensors deployed on it). Indeed, this probe is composed of a large metal frame on which are mounted several niskin bottles, the CTD sensors, as well as fluorescence sensors, turbidity sensors and active acoustic instruments to measure currents (the Acoustic Doppler Current Profilers, ADCP). In the case of the RESILIENCE mission, an Acoustic Zooplankton Fish Profiler (analyzing the distribution of micronecton and mesozoplankton with active acoustic techniques) and an Underwater Video Profiler (taking pictures of zooplankton) are added to the rosette to have more complete observations of the organisms in the water column.

Once the rosette has been put in the water, it will be lowered by winch to a certain depth, then during the ascent, several stops will be made at specific depths to close the niskin bottles. The niskin bottles are placed in the water open and are closed at the depths desired by the scientists thanks to the electrocarrier cable that holds the rosette. The different depths are chosen from the descending profiles obtained in real time by the sensors deployed on the rosette (in temperature, salinity, but also fluorescence and turbidity).

Once the rosette is back on deck, the sailors secure it and give the scientists permission to collect water from the niskin bottles. The scribe is a scientist in charge of coordinating the samples, because each team needs a precise volume of water and certain types of samples must be taken first. Water for CO2 and dissolved oxygen measurements must be taken first, because as soon as the water in the bottle comes into contact with the air, the concentration of dissolved gases can change. The faster you take the sample, the more you limit the contamination of the water with dissolved gases. Then comes the sampling for environmental DNA, requiring a mask and gloves in order not to contaminate the water with your own DNA. Samples for the study of phytoplankton are taken last. Once the sampling is completed, the scientific teams start their manipulations to secure their samples or to perform their measurements directly on board. The scientists on CTD watch then rinse the rosette and protect the different sensors.

Retrospective of the engineering-research alliance on a scientific cruise

Eugénie Dufour

May, 11th 2022 – Marion Dufresne

Deployment of the Bombyx. This mooring is equipped with a many instruments, among others a hydrophone, a passive acoustic device working like a microphone that allows to hear and register marine mammal’s vocalization, and a ADCP (“Acoustic Doppler Current Profiler”), a sonar system that measure the current speed thanks to the Doppler effect of particles suspended in the sea water. It will be retrieved in 6 months.  © Salomé Pellé

On the 11th of May, we are on the last leg of the RESILIENCE’s mission, after more than half of the trip. Through all this journey, all the floating university students have participated in many of science shifts, over all the scientists’ teams.

We have thus learned about a lot of new techniques in different sciences such as physics, chemistry, and biology and at the thinner frontier between them. For example, we have discovered the great role of acoustics in biology but also in physics and sailing, which I had no idea before going on this mission! Indeed, acoustics allows to determine the thickness of the water layer, to detect schools of fish or other organisms, to measure the speed of the currents thanks to Doppler’s effect and particle in the sea water, …

Also, engineering make measurements much more automatic facilitating data’s acquisition, such as salinity, depth, temperature, trace metals sampling… In phytoplankton analysis for example, there is an instrument called the fluoroprobe that, thanks to their respective pigment’s fluorescence, can can analyse the proportion of phytoplankton taxonomic groups in the water column, all automated and without microscope observations.

The fluoroprobe (left) and the result that it gives (right) on a vertical profile with the depth on the y-axis and the proportion of the different groups on the x-axis, such as diatoms, chlorophytes (Green algae and cryptophyta) and cyanophytes (blue-green). “Yellow substance” represents the fluorescence of non-photosynthetic particles. In white, the total fluorescence in the vertical profile. © Photos by Guerric Barriere

I’ve been impressed by the resourcefulness of engineer both on the boat, where they always find way to answer to the problems that we (often) encounter with the instruments, and on land, where they imagine a great variety of sophisticated instruments to sample different things, sometime based on the discovery made by researchers.

But even with all these automated measurements, it’s fascinating to see how human mind and manual ability cannot be easily replaced. We had the chance to meet a lot of scientists and crewmates that are passionate of their work and issues that most of human’s being don’t even imagine. For example, Fernando Gomez, taxonomist and researcher in phytoplankton, is facing with many questions on microalgal distribution and activity: how do phytoplankton evolve in oligotrophic waters? Why is there so much symbiosis in those waters? Are every species active at the same time? and what about plankton’s paradox?! Indeed, a lot of symbiosis are observed in oligotrophic water such as places of the Indian Ocean where we’ve been. Nutrients are rare and so cooperation is a way for organisms to survive. For example, ciliates and diatoms can bond together to gain mobility and protect themselves against predator.

Photograph showing the phenomenon of symbiosis between diatoms and ciliates. © Photo by Fernando Gomez, figure legend by Luis Chomienne

In addition, Fernando works on the identification of rare species in the samples collected at sea in order to sequence their DNA. It’s very impressive to see how he twist a glass pipette with a Bunsen burner to then aspirate and isolate organism which are around 20µm.

Another field on which humans cannot be fully replaced (for the moment ?) is the visual observation. Even if some drones and hydrophones are used in megafauna science, either for sampling whale’s blow (with a good dose of hope), either to detect mammal’s vocalisations, human’s eyes are still not replaceable to spot and identify marine mammals or seabirds. It’s difficult to imagine artificial eyes stunned by the unexpected first encounter with a red footed booby starting to follow the ship. Similarly, it’s hard to imagine artificial eyes becoming overexcited by seeing dolphins or tuna surfing beside the boat, enjoying the current’s made by the Marion Dufresne.

A small organism for man, a big step for science!

Alycia Valvandrin

May, 9th 2022 – Marion Dufresne

During the RESILIENCE oceanographic campaign, all organisms are of interest to researchers: from the largest whale to the smallest plankton organisms. Plankton are any living organism that cannot move voluntarily horizontally in the ocean, and whose movement depends on dynamical processes (circulation, waves etc). These plankton organisms are studied by two teams on the Marion Dufresne: the phytoplankton team and the zooplankton team.

Even if these organisms are not visible to the naked eye (except for some zooplankton visible in Figure 1), their importance is no longer in question. Phytoplankton is the basis of the different food webs. Indeed they are primary producers using mineral matter and energy from the sun to create their own organic matter : it’s this organic matter that will be the first to enter the food webs, thus ensuring the survival of all other organisms, whether they are very small like zooplankton, or gigantic like the humpback whale.

Recovered in nets called phytonet and multinet (Figure 3 and 4), the plankton is either analyzed on site (for phytoplankton) or preserved in formaldehyde to be analyzed back on land (for zooplankton).

Fernando Gomez studies the species composition of phytoplankton by observing them under the microscope. Knowing most of the phytoplankton species and their distribution, he can tell if the water layer that was sampled is vertically mixed or not. For example, Triposolenia bicornis is a deep-water phytoplankton species that was found in one sample. As the samples were taken in shallow water, he was able to deduce that if deep water species were found at this level in the water column, it was because this water column had undergone mixing! The presence also of gastropods or polychaetes larvae indicate the presence of the coast not far from here.

In addition to identifying the species present in the samples, allowing to draw conclusions about biocenosis (= a  group of interdependent organisms living and interacting with each other in the same habitat) but also about the physical conditions that it implies, other elements related to plankton can be analysed in the understanding of biological mechanisms. For example, copepod fecal pellets are frequently observed. We can ask ourselves why copepods excrete fecal pellets that will fall into the water column and imply a considerable loss of nutrients? Several hypotheses are now put forward:

  • First, it is possible that excreting its waste as a fecal pellet may ensure that predators are not attracted to the very place where the copepod lives;
  • Second, the membrane where its pellets are created could be a protection against toxic compounds ;
  • Thirdly, releasing a fecal pellet could be an asset when the copepod wants to control its density, such as during vertical migration in the water column. Indeed zooplankton organisms can hardly move actively horizontally, but are known for important vertical migrations, up to several 100 of meters of vertical displacement.

Knowing that the copepod is one of the most abundant animals on the planet, we can at least affirm that this strategy pays off, no matter what the problem is! As you can see, many conclusions can be drawn from plankton, hence their interests by the scientists during this oceanographic cruise!

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