Category Archives: Sampling

Welcome to the cave…. (by Alex)

Welcome to the cave (or wet lab), home to a special group of people known as team SFES (sample, filter, eat & sleep), complete with sterile gloves, wellington boots (rubber boots/sailing boots for the internationals), many bottles of seawater and filtering rigs.

Home to Lisa, Alex, Bruno, Amélie and Federica

Home to Lisa, Alex, Bruno, Amélie and Federica

The day starts off with a refreshing early morning at 5am to…. you’ve guessed it, sample the mesocosms. Next on the agenda is filtering for ~ 8 hours, this sometimes has a bit of a cave disco vibe to it with flashing head torches, questionable music taste and wonderfully poor singing.
As the sun starts to dip we emerge from the cave in search of food and a nice pillow to rest our heads. After a few weeks of eating out in Villefranche, we could probably write a paper on how to confuse the waiter by ordering in 4 languages.
Time for bed and alarm set for 04:15am.

Cave Paintings by Alex, Anastasia and Laure

Cave Paintings by Alex, Anastasia and Laure

All you need is…(2)

The song says ‘All you need is love‘ in mesocosms experiment we’ll say ‘All you need is GLOVES’!! When we are sampling some of the parameters need to be protected from us. That maybe sound strange but we are a source of contamination because of our skin and hairs. To measure some of the nutrients (ammonium, nitrate, nitrite, phosphate, …) as well as metals. So, the best way we could sample would be cover from head to toe and change every day… but not very doable as we have to wear sailing clothes!

To minimize the contamination, we have few things to do. First of all is to wear gloves but also avoid to touch our hair or skin (not very easy when we want to itch or to blow its nose!). The boxes have to be rinsed every day and even on the cubis, the back of the box with the sampler has to be rinsed into seawater before placing the sampler on it…. All a clean process taught by Cécile and Justine the two “clean room’s” scientists.

When Cécile and Justine aren’t dressed with nice sailing clothes they are with white labcoat, ‘charlotte’ to avoid contamination with hairs and overshoes…all this to avoid contamination. Justine, is measuring nano-nutrients which are the elements used by phytoplankton to growth but very easy to contaminate. She already explained her part during the previous experiment.

Mesocosms by night….

In our experiment, there is a type of people who work by night: it’s the 5am sampling team. We explained you why we have to do it in a previous post.

Here are some of the pictures we took while it wasn’t raining during a dark beautiful night! and there is more pictures in the Gallery.

A mesocosms being sampled by night...even more mysterious what's inside..

A mesocosms being sampled by night…even more mysterious what’s inside..

A night team in action...

A night team (Lisa and Mauro in case you didn’t recognise them 😉 ) in action…

But the best it’s always the sunrise. A little sunlight’s moment before we hole up in our laboratories…

The best moment of the day: after 1hour of sampling in the dark (and under the rain most of the time), sunrise! We can admire the sun light effect at the forefront.

The best moment of the day: after 1hour of sampling in the dark (and under the rain most of the time), sunrise! We can admire the sun light effect at the forefront.

Nice square meter, three boxes, one sampler and one boat hook…


Justine, Bruno and Angela are finishing to prepare the boxes for the sampling and the samplers are ready to use!

Here is our material list when we have to sample. We already talked about the ‘cubis’ which are 9m2 platforms with 80cm freeboard from which we do all our sampling. Except microlayer and atmosphere exchange, the samples are taken along the 12m depth of the water column using a ‘sampler’. Actually it’s like a big syringe with a plunger moving as long as we go down to the mesocosm. Each run is 5 liters of water and most of the time we have to do 3 runs (‘cast’ in Mesocosms Vocabulary). Once the ‘sampler’ is back at the surface, one person of the team use the hook to bring the sampler on the side of the mesocosm and with a nice mouvement the sampler as to be on a box without touching the cubi (to avoid contamination). Not always easy because relatively heavy and even harder when there is swell or wind!!

Content of one box for 8.30am sampling: 3 bottles for organic matter; 1 for carbon isotope; 1 for nutrients; 1 for pigments and 3 small flasks for carbonate chemistry.

Content of one box for 8.30am sampling: 3 bottles for organic matter; 1 for carbon isotope; 1 for nutrients; 1 for pigments and 3 small flasks for carbonate chemistry.

Once the sampler is secured, we can start to pour the water from the ‘sampler’ to the multiple different sub-bottles. Some of them have to be rinsed other not; some need to be filled without bubbles (create air-water exchange which bias the analysis) … took us few sampling to find the best way to fulfill each of the parameters! For each mesocosm we have a box containing all the bottles. So, 1 box for the ‘sampler’; 3 boxes for the bottles to fill (4 for the team who is doing the outside sampling) and one kook: doesn’t leave lot of space for the 2 people on the cubis!

Anastasia and Samir sampling at 8:30am

Anastasia and Samir sampling at 8:30am

The wind keeps blowing

The bad weather conditions continue and forces the different teams to stay on the labs or their rooms. Specially the wind has not been on our side. Yesterday the sampling that was suppose to take place at 8:30 was delayed until 12:30 and today`s is completely cancelled. In the morning we could hear the wind blowing strong and making things fly away in Nice. Up to 26 kts are expected, and this is sufficient to create waves that are difficult to handle during sampling.

Weather 2013-03-06 at 5.33.21 PM

Map of the wind forecast from:

Security of all participants comes first, and nobody wants to fall in the waters of 12 – 13°C

So far, the panorama for tomorrow looks very different and we expect to have the normal  early morning and 8:30 samplings.

Trace elements at sea’s skin (by Alina)

Most of the people when studying ocean are sampling into the water column. However before entering into the oceans a skin have to be crossed. The few micrometers separating the water column and atmosphere is called microlayer and many interesting process occur. Alina explain us how to sample the microlayer and analyze trace metals (metals elements with very low concentration).

Sampling the Microlayer:

Microlayer sampling system during an experiment in 2011.

Microlayer sampling system during an experiment in 2011.

I have devised a new sampling method to get microlayer samples for trace metals.  The sampler is a quartz tube that is dipped vertically into the water; then slowly raised out of the water vertically. The water that drips off the tube is, in theory, the microlayer and is collected into a funnel that is connected to a receiving bottle.  Normally sampling the microlayer is done on calm days with little to no wind and waves.On Friday March 1 however, we had a treat and it was windy! It is good to get days where we think there is no microlayer (or it is well mixed) to compare to the calm days. The surface team had a fun roaster coaster ride on the cubi and earned the title of only team to sample that day!

Microlayer team sampling on the cubis during a very windy day (we had to cancel the other sampling)

Microlayer team sampling on the cubis during a very windy day (we had to cancel the other sampling)

After Collection Analysis:

The real fun begins for me after I leave this campaign…well, not really, but the bulk of sample analysis for me will be done in the labs on Florida State University’s campus and also at the National High Magnetic Field Lab, located down the street from campus.  So for those of you that are jealous of my afternoons off, don’t be because once I go home I will have 12 hour days for a few weeks.  Ever wonder how to analyze trace elements in nMolar concentration in seawater? Well, you have come to the right person! I have spent the better part (or worse depending on my mood that day) of the last 3 years learning techniques to determine the concentrations of trace elements in the dissolved and particulate phases of the water column.

Seawater extraction column

Seawater extraction column

The dissolved phase, for me, is what passes through a 0.4 μm pore sized filter.  I look at 10 elements, iron (Fe) being the most important as it is a major minor nutrient for marine critters.  The concentrations typically found in the dissolved phase are nMolar to pMolar in oligotrophic environments for Fe and the other elements I study (I have them all listed on my information page).  My research group uses an inductively-coupled plasma-mass spectrometer (ICP-MS) to determine the concentrations.  Now, anyone who has worked around an ICP-MS knows that sending straight seawater through it is a very bad idea. All the salts in seawater cause many issues and your data would not be reliable, if you manage to get any before your front end clogs up.  In order to get around the problem, my research group uses extraction columns which remove the metals from the seawater (Milne et al., 2010).  The column has resin inside that acts as a binding site for the metals.  The metals will adhere to the resin while the rest of the salts will pass through into waste when you get the pH of the sample right (something that takes a lot of practice).  Nitric acid (1.0 Molar) is then sent over the column that elutes the metals and sends them to a small collection vial.  The extraction process also concentrates the metals about 10 times, which makes it easier to analyze them on the ICP-MS.  This process (I left out a couple of steps for simplicity sake) takes 9 minutes per sample.  40 samples per day are about my limit as I must sit with the system the entire time.  The whole process is done in a Class-100 clean lab and I wear my little pastry chef outfit (hairnet, lab coat, gloves, clean lab shoes) to keep things as clean as possible.  The extracted samples are then ready to analyze on the ICP-MS.  Sounds like fun, right?

Me in my clean lab back in Florida

Me in my clean lab back in Florida

The particulate phase is a quicker and an easier process.  I save all my filters that my samples went through.  The filters are simply digested in order to get the total metal concentrations on the particles.  The digestion potion is a lovely combination of concentrated nitric, hydrochloric, and hydrofluoric acids (yum!) that dissolves the particle minerals.  They are then dried down, re-suspended in 0.34 Molar (2%) HNO3 and analyzed on the ICP-MS.  So, if I don’t die from digesting ~200 filters, I will be able to share the metal particulate concentrations.

Lots to do when I get home and not a lot of time to do it as I’m working on writing my Master’s thesis for an October 2013 defense and a publication on my microlayer sampler!  Good thing we didn’t sample today or tomorrow, maybe I can be productive?

Videoprofiling in the mesocosms

This year, we take the opportunity to be in Villefranche to use an instrument that has been developed at the Laboratoire d’Océanographie: the Underwater Vision Profiler.

The Underwater Vision Profiler 5 (UVP5;, Picheral et al 2010) is an underwater intelligent camera developed by the Laboratoire d’Oceanographie de Villefranche-sur-mer to quantify the vertical distribution of macroscopic particles and zooplankton from 100 µm up to few millimeters in size. The smaller size limit is fixed by the optical resolution of the camera, whereas the larger size limit is determined by the volume of water illuminated per image. The UVP5 is compact (30 kg in air) and can operates as a stand-alone instrument with an independent power supply. Images are recorded at a frequency up to 6 Hz and analyzed on board by a dedicated software. Finally, Zooprocess (, Gorsky et al. 2010) is used to extract the the largest zooplanktons from the images and sort them into groups.

UVP view from underwater ( Picture: D.Luquet (OOV))

UVP view from underwater (
Picture: D.Luquet (OOV))


Gorsky, G., Ohman, M.D., Picheral, M., Gasparini, S., Stemmann, L., Romagnan, J.B., Cawood, A., Pesant, S., Garcia-Comas, C., Prejger, F., 2010. Digital zooplankton image analysis using the ZooScan integrated system. J. Plankton Res. 32, 285-303.
Picheral, M., Guidi, L., Stemmann, L., Karl, D.M., Iddaoud, G., Gorsky, G., 2010. The Underwater Vision Profiler 5: An advanced instrument for high spatial resolution studies of particle size spectra and zooplankton. Limnol. Oceanogr. Meth. 8, 462–473.

Laid up for one day

When the wind come into the bay ....

When the wind come into the bay ….

For the 8th day of the experimental period we have been obliged to stay on land due to bad weather condition. The wind from North-East enter the Bay since this morning and it’s too dangerous to go sampling on our ‘cubis’. These platforms are 80cm above sea level so, when there is 50cm of short waves it make everything more complicated!!. So today was a ‘day off’. Well, not for everyone.

Actually at 6.30am, Alex and Laure (the incubation team) have been able to bring back the incubations and so, work on their samples. The incubations are bottles containing water sampled into the mesocosms the day before and kept for 24hours to measure process such as Primary Production (amount of biomass produced by microorganisms per day) or nitrogen fixation (see Lisa post). Other processes are measured by the early morning team (Mauro, Aggeliki) but don’t need to go back in situ.

Microlayer sampling similar to "roller coaster" this day!

Microlayer sampling similar to “roller coaster” this day!

It wasn’t a day off neither for the 8am team who had time to sample before the weather get worst!

We all hope that tomorrow we are going to be able to sample in good conditions!!

All you need is…(1) (by Anastasia)

So, yes, it’s true, another mesocosm experiment is on the go! Kind of harder this time, if you consider the cold, the wind, the amount of analyses being done, and… the local boats that transfer tourists back and forth from the cruise ship several times! Just to provoke us that they are on holidays!

Passenger ferry entering into the bay and soon followed by boats transfer passenger doing waves and taunting us by being in holidays!!

Passenger ferry entering into the bay and soon followed by boats transfer passenger doing waves and taunting us by being in holidays!!

Cold is undoubtedly the worst enemy, not only during the sampling process, but also in general, as people during wintertime need more energy (more food, more sleep… or is it only my feeling??). Energy is flying away from our bodies a bit more easily this time in Villefranche and, after only a few days of work, exhaustion is apparent! However, this is just the ‘not-so-nice’ part of the experiment. The major part is an exciting event with new and old members participating, a lot of memories and many happy and funny moments. Exploring the city in the search for dinner (as the restaurant nearby is closed, which actually didn’t disappoint us too much…let’s be honest!) as well as in the search for super markets, which are all far far away from the port!

It’s a unique experience after all that for sure gets better day by day. People are now settled down in their labs and things are more convenient than at the beginning, when a slight panic feeling overcame many of us (hm was it me?). Just joking. Positive thinking is all we need! And love (don’t forget about it even when sampling!), as the song says…

How days are passing (by Angela)

As it was said, it`s been 4 days of sampling, until now with no major complications; only the weather and few inconveniences (loosing a hook and having to replace it by a peddle, one buoy to close to allow the cubi pass through -which the divers fixed this immediately-, and the autosampler coming only half full) this are minor things that the team have outcome fast and safe. When samples arrive from the 8:30am sampling, all the bottles for the 10:00am team are ready and the team waiting. The boat just change passengers and goes back to the mesocosms. Most of us had already experienced and get into the sampling routine and its rhythm which makes things easier. The fact that Lisa runs from her Lab. to prepare tea to those coming from sampling when is very cold also helps a lot!

After sampling, scientist disappear in their labs and the pumps start its melody. On this days, however, it`s very probable that a heavy rain would be listen even stronger.

Weather forecast for tomorrow isn`t very nice; rain, cold, some wind…. we will see.