The PUF Herald ✒

Read stories in category : education information innovation internship professors project research students teaching visufront

DISCo night

Through this PUF-sponsored project we have been able to study the orientation of fish larvae during the day and relate it to physical forcings such the position of the sun in the sky. It is already pretty crazy to think that those cm-sized organisms are able to detect the position of the sun from underwater and orient with respect to it. However, fish larvae are known to settle on the coast at night, not during the day. So while the sun would be a useful cue for large scale navigation in the ocean, they have to use some other cue to settle at night.

But studying behaviour at night is, of course, more challenging than during the day. Only a handful studies have tackled the question and always used traps or lab experimental settings, never in situ observations. We set out to change this and observe larvae in the DISC at night. To do so, we needed a way to see without being seen. Because light wavelengths in the red color range are quickly absorbed in water, most sea creatures do not "see" the reds. We went even beyond red and used infra-red LEDs to light up the DISC observation area, just to be sure we would not disturb the organisms. But infra-red is basically heat and the LEDs heat up very much during prolonged use, which makes them difficult to attach to a transparent plastic instrument. Furthermore, while CCD sensors on digital cameras record infra-red just fine, these wavelengths are problematic for picture quality in normal-life applications and all lenses include an infra-red filter to block them out. So it took over a year of development with Bellamare to get to a working system, comprised of very bright infra-red LEDs (to shine through red-absorbing water) potted in custom aluminium and epoxy housings, a large Lithium battery pack to power them for a few hours, a modified GoPro camera with a customised lens, etc. The result is below: a nice, focused image, captured in complete darkness!

Disc Night

Thanks to the new extension of the project (as explained in the previous post), we could plan the first in situ observations of fish larvae at night, offshore Miami. The "DISCo night" team was lead by Professor Claire Paris and comprised Captain Evan D'Alessandro, Craig Raffenberg and Alessandro Cresci (Pr Paris' students), and Pr Jean-Olivier Irisson, from UPMC. Between July 29th and August 5th, we caught many larvae of the bicolor Damselfish (Stegastes partitus) and deployed the DISC for four nights to observe their behaviour. Instead of the usual time-lapse pictures, we captured video to get a better understanding of their behaviour. In turn, this required some non-negligible changes to discr, the software written to analyse DISC data. A few bad weather days in the middle of the week allowed to prototype those changes.

Disc Miami Disc Miami Disc Miami Disc Miami Disc Miami Disc Miami Disc Miami Disc Miami Disc Miami Disc Miami Disc Miami

The bad weather days and the abundance of larvae were also an incentive to test the new lab-based experimental setup of Pr Paris, at RSMAS. Her wet lab is equipped with a cylindrical aquarium large enough to fit the DISC (and a PhD student, if needed), light-insulating curtains, and an array of lighting systems allowing to simulate full daylight, select some wavelengths, or use wavelengths invisible to humans such as UV or infra-red. Damselfish larvae were observed in the DISC, while it was rotating in this setup, during the day (using simulated daylight) and at night (using infra-red). The goal of these first experiments is to determine if larvae still orient indoors, which would suggest that this behaviour is somewhat ingrained and not conditioned by external stimuli. Now we need to analyse the data!

Disc Miami Disc Miami Disc Miami

— · —

It ain't over 'til it's over

This project should have been over for a while now but, as the title of this post (and Lenny Kravitz) says, things are never really over. Thanks to careful spending (and a few cancellations…) we actually had funds remaining on the US side. And thanks to the open minds and great support of the PUF project managers, we are allowed to use them, as per a second no-cost extension of the project!


We would like to take this opportunity to deeply thank the managing officers of the PUF program. The financial support of the PUF has been extremely useful and, almost as importantly, enjoyable to use.

The project started late because it took forever to sign the contracts thanks to the heaviness and slowness of the administrative systems of both universities. This was almost painless for the project itself because we were easily granted a no-cost extension every year, to account for the delay in the activities of the project.

On the research side, when the shipping company vastly underestimated the cost of shipping ISIIS to France and we had to reallocate funds in the first year to cover part of these expenses, they understood it was out of our hands and supported us. When we lost a DISC instrument at sea during the second year and had to quickly turn around and order another one with funds that were supposed to be dedicated to a sound recording system (and therefore postpone that part of the project), they accepted that this decision was making the best out of a bad situation. Finally, when we shifted focus from the influence of sound on the orientation of fish larvae to the observation of their orientation at night, because given the evolution of the field in the ~3 years since we wrote the initial proposal, this seemed like a more topical question, they trusted our decision.

On the educational side also, things changed quite a bit along the course of the project. The number of French students ready to leave for a second year of Masters was less than we expected, so we opened this opportunity to first year students. The number of US students who wanted to travel to France to take a multivariate statistics class was more than we could handle, so we had the professors travel to the US instead. In all cases, we accounted for these changes in the yearly reports, explained them and they were understood.

In an era when most funding agencies almost require you to get three quotes and a PO to buy a pencil, working with project managers who understand the inherent uncertainty associated with doing something new, be it in research or education, who are supportive and understanding, is extremely refreshing. And in the end, science wins, because we, as researchers and professors, can focus on advancing the field, on building new things, on creating new ways to train students instead of becoming accountants and form-fillers. So, once again, we thank the PUF very, very much for their support and we hope we made the best out of it.

— · —

Lagrangian modelling with the CMS in Villefranche

In what will probably be the last mobility event of this 3-years PUF program, Claire Paris, the coordinator of the US part of this project, came to France to teach a class on the Lagrangian modelling of marine larvae, in the numerical modelling class of Villefranche-sur-mer. She taught this class last year for the first time (at exactly the same date, on Dec 11th!) and the class was again well received. Knowing the level of experience of the students allowed to better focus the computer lab exercices of the afternoon. During the class, the students were able to learn about the intricacies of the Connectivity Modelling System first hand, from the mouth of its creator! During the lab that we co-taught, students built a simple advection-diffusion model in a idealised current field before analysing the results of real CMS simulations that were run for them before the class. Altogether, this made for a rich and diverse experience. Here is a picture of the group of students in Villefranche together with myself, Jean-Olivier Irisson, or Simon Ramondenc, a PhD student from Villefranche who co-tutored the lab part, (far left) and Claire Paris (far right).

Claire Lagrangian Class 1 Claire Lagrangian Class 1

— · —

Robin Faillettaz is a doctor!

After Jessica in Miami, last week, it was now Robin Faillettaz' turn to defend his PhD thesis, in Villefranche-sur-Mer. His thesis work was an integral part of this PUF project: the VISUFRONT cruise (using ISIIS and UVP) in 2013, the behavioural experiments and the joint efforts for image analysis in 2014, and now his defense, in 2015. His work dealt with the distribution and behaviour of fish larvae, in response to their physical and chemical environment.

His jury was composed of two reviewers: Howard Browman, from the IMR in Norway, and Paolo Guidetti, from the University of Nice; one president: Eric Thiebaut, from UPMC, Marine Station of Roscoff; one examiner: Claire Paris, from RSMAS, University of Miami –the co-supervisor of this project– (Ana Sabatés, from the CSIC in Barcelona, was also supposed to be here but could not attend because of a personal matter); and his two advisors: Philippe Koubbi and myself. After 45 mins (precisely!) of presentation and over two hours of questions and discussion, the jury declared his thesis worthy of the grade of doctor and his overall presentation "exceptional".

Congratulations to Robin, who I was very happy to supervise for the last three years. This project is a success in a great part because of his hard work. Below are a few pictures, before, during and after the defense!

Robin PhD Robin PhD Robin PhD Robin PhD

— · —

Jessica Luo is a doctor!

Jessica Luo was a RSMAS PhD student under the supervision of Bob Cowen, the original coordinator of this PUF program at RSMAS (before he moved to Oregon State University). She is not a student anymore now but a doctor, after brilliantly defending her dissertation on Oct 30th, at RSMAS!

She studied gelatinous zooplankton (i.e. jellies) using the data and images collected by the In Situ Ichthyoplankton Imaging System (ISIIS). During her PhD, she also came to Villefranche for a class and learn image analysis tools, she participated in the VISUFRONT cruise funded by this PUF project, collaborated with Robin Faillettaz (a PhD student at OOV who will also defend soon) and myself. I was very happy to be part of her PhD thesis committee, to be present at her defense, and to be co-author on one of her dissertation papers. From what I saw in her manuscript, there are many more to come.

Jessica also invested a lot of time in the planktonportal project, a collaborative science website where enthusiasts can help identify plankton on ISIIS images. As a nice gift to Jessica, yshish (the very active volunteer moderator of that project) organised a contest to reach 1,000,000 plankton identifications on the project. That incredible milestone was met (and even exceeded) by the time Jessica defended. Big shoutout to the planktonportal community!

For the next year, Jessica will continue to work with Bob Cowen and Su Sponaugle in Oregon, which will give her the opportunity to publish all the good science she presented us and to do further research with plankton images and data, in tandem with us in Villefranche.

Jessica Defense Jessica Defense

— · —

Fish larvae orientation, between Miami and Villefranche

This week was my last trip to Miami as part of this PUF program. It was full of new ideas and events (as the other posts on this blog indicate) and also familiar: I got to meet again with old friends and collaborators at RSMAS and I spent the week with Pr Claire Paris, the coordinator of the PUF program for RSMAS.

We discussed our respective works on fish larvae orientation and the Drifting In Situ Chamber, the instrument she pioneered and which we now both use. I had the opportunity to present the research done with that instrument in Villefranche through a seminar titled "Mediterranean fish larvae: orienteering champions". We discussed both old data (which will soon turn into new papers!) and the developments of the instrument, in particular for the work of her numerous PhD students: Matt Foretich who works on olfaction (and whose thesis committee I sit on), Alessandro Cresci who works on magnetic orientation (and who recently came to Villefranche for a class), and Romain Chaput (pictured below) who will work on group orientation, who did his Master's degree internship with Pr Paris through this PUF program and now starts a PhD with her. Romain and Claire asked me to also be part of his committee and I gladly accepted. Not only do I enjoy working with Claire but I have also been particularly interested in the question of the dynamics of groups of fish since some work we did together on that topic a few years ago (which got submitted for publication this very week!)

So overall, another very enjoyable week, full of work and promises. The last as part of this PUF program but hopefully (surely!) not the last in this fruitful partnership.

Slides Irisson 1 Slides Irisson 1 Slides Irisson 1 Romain Starts Thesis

— · —

An exciting time for plankton imaging

Teams at OOV and RSMAS (and now OSU) have been working with instruments that allow us to take images of planktonic animals in situ: the Underwater Video Profiler (UVP) at OOV and the In Situ Ichthyoplankton Imaging System (ISIIS) at RSMAS/OSU. Half of the research done through this PUF project was built on those instruments, coupling them for the VISUFRONT cruise during the first year of the project. We worked on analysing the images and data recorded by these instruments since then.

My coming to RSMAS this week was an occasion to discuss plankton imaging again, two years later, with Bob Cowen. It was a long, interesting and fruitful discussion. It seems we are at a tipping point for plankton imaging. On the RSMAS/OSU side, ISIIS has now been used in several projects and multiple scientific papers have been and are being written. An automated image processing and segmenting routine is operational and fast. The collaborative website for plankton identification generates a steady stream of human-validated identifications for images taken by ISIIS. The kaggle Data Science Bowl competition spurred several promising algorithms for automated image classification. On the OOV side, the UVP is being miniaturised to be included in autonomous underwater instruments and collect more data in more places. A web application for semi-automated, collaborative image classification by scientists has been developed and is ready for UVP and ISIIS images. Dr Ben Graham, one of the authors of a winning algorithms of the kaggle competition will be coming to OOV to discuss including his work as the classification backend of this application. And, on both sides of the Atlantic, the instruments and associated tools are becoming standard enough to be considered by environment monitoring programs.

So overall, the times are exciting and full of opportunities for all the teams involved in this PUF program!

— · —

Marine connectivity talks

Hi everyone!

I am Katell Guizien, a CNRS researcher, and I work in one of the three marine stations of UPMC, in Banyuls-sur-Mer. Connectivity is a central part of my research line on the conditions for persistence of benthic invertebrates populations. Having a project to transpose in the Caribbean sea the methodology I developed for populations in the Gulf of Lions, a region of the Mediterranean sea, I grabbed this unique opportunity offered by the PUF project to visit Claire Paris in RSMAS. I went to Miami in July for a very short but intense week!

Claire and I spent many hours every day confronting our approaches and thoughts about marine connectivity, applied to Caribbean fish and Mediterranean benthic invertebrates, respectively! We exchanged about hydrodynamical models resolution, experimental methodology to study larval motility behaviour and discovered how convergent our experiences were. We need to share our views about connectivity. The week was also very positive to establish new connections with atmospherical modellers and planting seeds for a sabbatical stay at RSMAS to develop the Caribbean project! I ended my week there by giving a seminar about Biodiversity conservation and larval dispersal, illustrated on the Gulf of Lions test case.

— · —

My summer class in Villefranche, an enriching experience

My name is Alessandro Cresci and currently I am a graduate student at the RSMAS, University of Miami, advised by Dr. Claire Paris. Thank to the exchange program with the UMPC I was able to attend the summer class in multivariate statistics in Villefranche, with Dr. J-O Irisson, Dr. S-D Ayata and Dr. S.Gasparini.

I am personally very grateful for this enriching and extremely helpful experience.

My research is focused on the study of the orienting abilities of marine fish larvae, and in particular on the magnetic sense. Before joining the class, I could conduct experiments in Norway at the marine station of Austevoll in order to collect data about the orientation of the post-larval glass eels in their natural environment utilizing the DISC (Drifting In Situ Chamber) technology. The class in multivariate statistics allowed me to improve my knowledge on the analytical techniques, which provided me of new tools for exploring my data, and relate the behavior of my eels to many environmental parameters. Moreover, the class has a full module dedicated to the statistical analysis by the software R. This gave me the possibility to successfully utilize R in the analysis on my DISC data and to highlight new, unknown aspects of the behavior of the glass eels.

This summer class has been of great utility for my research and I was able to submit a manuscript to Nature Communications.

I would recommend to everybody to make this great experience of study in the unique colors of the Mediterranean Sea.

alessandro alessandro alessandro

— · —

Baby-sitter for fish larvae: patience and astonishment

I was looking for an internship in oceanography and I was lucky to be involved in this project during one full-on month. Initially, it was planned that I would observe larvae in the DISC at night, to push the fish larvae behaviour research started last year further. Unfortunately, the infrared light system was not ready yet, so I ended up DISCing during the day (too bad, I had to sleep at night!). This allowed to verify whether the results found last year were robust. Fifty Chromis chromis larvae were tested in the DISC; 30 were observed the same day (a new record for the largest number of observations in one day!) with perfect experimental conditions (and sighting of an ocean sunfish!).

I also measured the swimming speed of Diplodus annularis in a swimming chamber. I can say that during two days, I was the only person being cold whereas the outside temperature was 30°C or more. The 33 Diplodus annularis swam between 5 cm/s and 25 cm/s. The next step was extracting lipids from the fish muscle in order to know if the individual speed was related to the body condition of the individual. The final results from this will come next year.

My internship was a great opportunity to learn about fish larvae and why they should be studied. I am very grateful to Jean-Olivier Irisson and Robin Faillettaz for their trust, their patience and their knowledge. I have shared great moments with them.

Julie's internship Julie's internship Julie's internship Julie's internship Julie's internship

— · —

DISCing again!

Last year's research goal was to observe the orientation and swimming behaviour of fish larvae in the Mediterranean Sea, for the first time. We concluded that the species we observed had significant oriented swimming abilities which could influence their trajectory in the ocean. They are not just transported by currents. These findings are now written in two scientific articles, one in press and another one under review.

This year, we are DISC'ing (and swimming) again! Thanks to the help of Julie Lafaye who came here for a one month internship, we measured the swimming speeds of Diplodus annularis and observed the orientation behaviour of Chromis chromis. The first goal is to check the repeatability of the results we found last year. But we also noticed important differences between individuals, in the same species. Some larvae would only swim at 5 cm/s while others would reach 25 cm/s. This year's goal is therefore to try to understand the source of these differences. For this purpose, we preserve the fish in a way that will allow us to measure their fat reserves, their symmetry, their body mass index, etc. All those indexes could be correlated with differences in individual performance.

Because we want to assess individual differences, with lots of inter-individual variations, we need a large number of observations to conclude so the exploitation of this data will continue over a few months at least. But thanks to Julie's efficiency we are on to a good start!

The DISC's camera captured many pictures of Chromis larvae but also a few more "artistic" ones. And no, Julie is not sticking her tongue out on the last picture; that's the waterproof paper label for the fish under study that she is holding in her mouth!

DISC Julie DISC Julie DISC Julie

— · —

Disseminating the DISC technology

The Drifting In Situ Chamber (DISC) is the instrument invented by Claire Paris (RSMAS) to study the orientation behaviour of marine larvae. The software dedicated to the analysis of this data was developed by Jean-Olivier Irisson (OOV). So this is really a collaborative endeavour. This technology has been used in Florida, Australia, Israël and even Norway. Now a new instrument has been purchased by colleagues in Corsica. Sylvia Agostini and her student, Amélie Rossi, came to Villefranche to learn the deployment and data analysis techniques. Those were two very full days, starting with the assembly of the instrument, calibration of the electronics, a few deployments at sea and the full data analysis procedure.

Now we cannot wait to see if Mediterranean fish larvae orientate the same way in Corsica and here, because the species are the same, the locations are close but the land-sea position is reversed (land to the North here, land to the South in Corsica). We will know next year!

Sylvia in Villefranche Sylvia in Villefranche Sylvia in Villefranche

— · —

The end of an awesome adventure

A page is turned, not without stress and effort but such a beautiful page! I have completed my 3 courses with success and learned so much about ecology and biology of coral, management of fisheries and physical oceanography! During my internship, I learned how to sample and take care of coral in aquaria as well as many lab techniques (DNAS extraction, qPCR, PCR, blasting, cell counting) to try to understand a small part to the exiting secret of the coral/Symbiodinium symbiosis. (I focused on the comparison of two technics to estimate the Symbiodinium density)

I would like to thank a lot the PUF program which gave me this opportunity, Mr. Irisson and Mrs. Paris who fought and never gave up with the administrative process, all professors for their help and the Baker’s team for its welcoming attitude. Special thanks go to Dr. Andrew Baker for hosting me in his lab and for his help and kindness, Ana Palacio for all that she taught me, gladly and with passion, and to Grace Snyder for her help with lab work and for the best key lime pie of the world!

Someone said “The real voyage of discovery consists not in seeking new landscapes but in having new eyes.”

My eyes are filled of experiences

My brain of new knowledge

And my heart of new people.

Here are a few of them: the Baker team! Also: one of my babies sampled, a scientist's cocktail (one step in the DNA extraction process) and a few others pictures that are going to stay in my mind.

M-O End 1 M-O End 1 M-O End 1 M-O End 1 M-O End 1 M-O End 1 M-O End 1

— · —

Miami after few months

I left Miami yesterday and I feel I will come back over there as soon as possible. In January Dr Claire Paris welcomed me in her lab and team and gave me the wonderful opportunity to develop my own research project. I chose to study the impact of the coral diversity on the fish larvae dispersion and recruitment. I arrived in the lab and was immediately integrated in the team.

Together we developed lab experiments, modified a model, and organized field sampling. Our results are above all expectations. We found that larvae are more attracted by high diversity reefs and showed that this preference coupled with orientation behavior could change the dispersion and settling location of fish larvae.

Last week I sent my master thesis and realized how much work was done during these 6 months and how much my co-workers helped me. From advice on setting up lab experiments, to driving the boat during field work, they helped me on everything. Today I would like to tell them thank you. In Miami I have found very nice people, team mates and friends (also called the French mafia at the RSMAS). Matt, Cedric, Andy, Erica, David and Ana, without you I don't know if would have been able to go in the field, to do the model, to deal with the administration, and to always feel motivated.

They also take on their time to make me travel in Florida, to visit Miami, to go to parties (not sure this last point was boring for them). I discovered the RSMAS, and I was happy to see a big university (or department) working on various fields of marine sciences. It is always interesting to talk with everybody and it opened my mind on so many subjects completely new for me. This place is also very well furnished in nice scientific equipments and full of opportunities to develop projects.

To do this internship at the RSMAS was something very important for me. I had the chance to work with very good professors and researchers to learn more on corals, statistics and of course modeling. Now, thank to the experience I acquired, I feel more comfortable about doing a PhD and I really hope to do it with the same team!

Here is a picture of a late stag larvae (very, very late ;) ) and a plot of a simulation of dispersal of larvae over Florida reefs using the Connectivity Modelling System.

Romain End 1 Romain End 1

— · —

The end of the Nurse sharks modeling experience

All good things come to an end, and so my master internship has reached its own. I think I can proudly say to have taken advantage the most from this opportunity. From a scientific point of view it has been surely an astonishing adventure. I entered the mysterious world of Bayesian statistics and I wandered among new charming analysis methods and statistical concepts until now completely obscure to me. I got to thanks my supervisor, Dr. 'Beth' Babcock to have let me in, and to have found the patience to explain me this world and its rules. It has been a pleasure to work with her and to spend time together discussing about the conceptualization of the model. To reflect and exchanges ideas about the various sharks' probabilities helped me personally grow on this field and to fully understand the Bayesian modelling dynamics. Furthermore, I'm truly enthusiastic of my results: I'm looking forward to present them in few weeks to the Pierre and Marie Curie University commission as my master thesis. With surprise, I discovered at the last minute that my hierarchical model was not too complex only for me, but even for my computer! It took two weeks to run, but I was completely satisfied with the output. We finally demonstrated the decrease of the nurse shark population in Glover's Reef Marine Reserve, and the need for new management efforts.

Aside from my project I also had the opportunity to work in a highly specialized center as RSMAS, of the University of Miami, in contact with great minds and pillars of oceanographic science. It's useless to say how motivating this kind of environment can be.

I wish to express my sincere gratitude to the Partner University Fund (PUF), which gave me the possibility to cross the ocean to join this astonishing laboratory. I'd like to specially thank Dr. Irisson, who saved me several times during the bureaucracy procedure and believed on the possibility of this exchange even in the hardest moments, but also Dr. Paris, who kindly welcomed me on the Rosenstiel School of Marine and Atmospheric Science. And finally, last but not least, I'd like to particularly thanks the French crew of RSMAS, among which there were other PUF students, who allowed me to not forget France, and my lovely roommate Camille, who suffered several personal modeling crisis which were entirely part of the scientific process.

Here are a few pictures relating my semester here: a huge egret in face of the RSMAS laboratory, profiting of the sunset after a long day of work; me and Camille, at the Miami Open, watching our first real tennis match; the fantastic RSMAS oceanographic ship; rays near the surface (not exactly nurse sharks but Elasmobranch at least); and my laptop, abandoning me after a week of model-running!

Camille End of Internship Camille End of Internship Camille End of Internship Camille End of Internship Camille End of Internship

— · —

A semester of coral science

My semester in Miami is ending and I just realize how the time has flown. I have completed the three courses with success and I have learned a lot but particularly about coral research. The most interesting part was my internship where I was able to work on an ongoing research project focused on the potentially recovery of a Caribbean coral species following a bleaching event. I also had the opportunity to join the Ph.D students during sampling times. I had the chance to be with two great Ph.D students who teach me a lot in the lab and thanks to them I am more convinced than ever about my professional project. Overall, this abroad program in RSMAS was a good occasion to meet people and learn more about coral science, and I am obviously glad of this experience!

Here are a few pictures relating my experiences: the tanks for experiments in the hatchery, me coring corals for another OEM student's project, the tools to measure lipid content of coral samples, the start of a coral sampling day and a Lab picture!

Camille End of Internship Camille End of Internship Camille End of Internship Camille End of Internship Camille End of Internship

— · —

Back in Miami to analyse the "tiny" VISUFRONT dataset with a novel method

Time has been running since my last stay in RSMAS last year… oh no, wait, that was already two years ago! Going back to this lab was a real pleasure. I met the a new member of the Paris Lab, Romain Chaput, who was doing his master's thesis with Claire Paris – supported by PUF. I gave him a hand to sample fish larvae at night and joined the party to pose for the shooting of the Paris’s Lab crew; that was a lot of fun! Because we were both French and had quite similar names we earned the title of "French baguettes"… I was also there just in time to bid farewell to Erica Staaterman, whom I met when she came in Villefranche and then when I was in Miami. She defended her PhD (successfully!) right before I left. Finally, my stay was also the opportunity to discuss about the future, once my PhD (and this PUF project) will be over.

I quickly felt at home there, which put me in good conditions to go deep into the analysis of the VISUFRONT dataset. During the cruise back in 2013, we followed two sampling strategies: first, a "traditional" cross-front transect and, second, a lagrangian approach by continuously sampling a water mass that we tracked with drifters for 36h. Here, I focused on the second part. The objective of my stay was to generate a realistic current field based on the physical data collected during the cruise and to simulate particles inside it with the CMS, the biophysical model developed by Claire B. Paris.

CTD (measuring hydrological variables) and ADCP (measuring currents) sensors were deployed along with "surface" and "deep" drifters during the cruise. You may not remember our older posts, but we had quite a few issues during the cruise, in particular with the GPS. And yes, you guessed it, ADCP data require accurate GPS positioning. Therefore, processing these ADCP data was a cumbersome endeavour, which was made finally successful thanks to the help of L. Prieur (OOV) and C. Heyndrickx (DT INSU, CNRS). We made it! And once we got the physical data processed and ready to use, we included them in an "Objective Analysis", a powerful analysis parametrized with the observed trajectories of the drifters, which provided a comprehensive description of the water mass. Then, we used this newly generated current field with the CMS, to track particles within this water mass. The purpose will be to check if the patches of organisms observed during cruise were simply passively drifting or not. We now have information on larval fish behaviour, so we suspect that at least fish larvae will not be passively drifting. Identifying which behaviour are necessary simulate to match their observed trajectories would provide very interesting data regarding larval fish behaviour and dispersal in the ocean, but this is still a work in progress for now. More to come in the next years !

Here are a few pictures from the Paris Lab shoot, Erica's defense, the view from my office spot in RSMAS (yes I was still focused on the code seen on my screen below), the final ADCP field (after three weeks of hard work!) and the final simulation with ship track in black, actual drifters in white and simulated drifters in shades of blue; we still underestimate actual drift a little but it is much better than what we started from!

robin miami 1 robin miami 2 robin miami 3 robin miami 4 robin miami 5

— · —

Analyses Multivariées, the RSMAS edition

As part of this PUF sponsored exchange, students at RSMAS can come to OOV to take classes. In the past two years, one class in particular attracted many RSMAS students: a three weeks intensive course about multivariate statistics. So many students were interested in fact that the funds allocated to student exchange would not have sufficed to cover their travel. In addition, there was not enough room at OOV to host UPMC and RSMAS students at the same time. So we chose to bring the class to them!

After a bit of an administrative struggle, the class was set up at RSMAS, thanks to the sustained efforts of Elizabeth Babcock. And the three professors, Sakina-Dorothée Ayata, Stéphane Gasparini and myself, Jean-Olivier Irisson, travelled to give lectures and supervise labs for two weeks, from March 2nd to March 13th. The topics covered what we usually teach in France: an introduction to the statistical programming language R and statistical GUI software, ordination methods (PCA, CA, MCA, MDS, etc.), clustering methods (hierarchical clustering, k-means, LDA, etc.), and some multivariate data series techniques. Equipped with that knowledge, the students then had a few days to work on a small dataset and presented us their results through a video-conference earlier this week.

From our point of view, the class was a success. The room was very full, with PhD students but also post-doc, and even RSMAS faculty attending. Our "students" were more advanced than the Masters student we usually teach the class to and that prompted a deeper description of the various techniques (plus, some students actually finished the labs!). But now, we are waiting for the feedback from the students to know how the class was received!

Multivariate data analysis is a field of statistics that has a long tradition in France. Some of the techniques we teach have been developed by french researchers (correspondence analysis for example), some even by researchers working in Villefranche (turning points methods for the analysis of data series)! The class itself has a long history and has been taught by various professors over the years in Villefranche. We feel it has matured into something "special"; we are very proud to be teaching it and, now, to bring it overseas. Together with Elizabeth Babcock, we will try to continue offering it after the end of the project. Funding for education-only initiatives, such as this, is even harder to come by than research funding but we keep our hopes up for now!

Here are a few pictures of Sakina warning students about the misuses of PCA, the three professors in a typical Miami setting, and Stéphane and Elizabeth with some of the students at the end of the class.

Ame2 2 Ame2 3 Ame2 4 Ame2 5

— · —

The 'PUF' people

Because of several parallel projects, many people involved in this PUF program were in Miami for a few days. This was a perfect opportunity to take a group picture, which we happily did by lining up on RSMAS' dock. On the picture are a few students of the statistics class currently taught at RSMAS by OOV professors, RSMAS and UPMC professors involved in classes over the three years of the project, UPMC master students currently doing an internship at RSMAS, RSMAS professors supervising these internships, RSMAS PhD students contributing to the research projects or having participated in classes over the last two years, etc. Many more could not be there and were very much missed but it was already a pleasure to see so many people gathered in the same place for a little while.

After the picture, we all shared a drink at the wetlab, RSMAS' in house bar, to chat and exchange impressions. In particular it was a rare opportunity for the three project coordinators (from left to right on the picture: Jean-Olivier Irisson, Amy Clement, and Claire Paris) to actually talk rather than email each other! Students and professors took a couple hours out of their busy schedule to share ideas, regarding science… or not. A great time!

Puf People 1 Puf People 2 Puf People 3 Puf People 4

— · —

My semester/expedition/adventure in Miami

After multiple administrative setbacks, I finally arrived in Miami… with a bronchitis! So now, I know exactly why health insurance is mandatory (160$ for a consult and 60$ for antibiotics).

The PUF program gave me the opportunity to spend the 2d semester of my first year of masters at RSMAS. I chose 3 classes :

  • Coral Reef Biology, Ecology, And Conservation
  • Management And Conservation Of Marine Ecosystems
  • The Physical Environment of Marine Organisms

The two first are completely new for me and the third is easier thanks to theoretical knowledge acquired at UPMC last semester. The three courses are really interesting, with small groups of student, which allow us to discuss easily with teachers.

I was lucky to get a spot in Dr. Andrew Baker's laboratory. Dr Baker's team is absolutely great! They are all enthusiastic, friendly and patient with my imperfect english! I will work with Ana Palacio on the impact of different type of nutrient on the density of zooxanthellae (symbiodinium, the symbiotic algae of most of coral) because some recent studies have shown that high zooxanthellae densities in the coral host drive an increased sensitivity to coral bleaching. We will start soon… if we manage to find non-sick people to collect coral colonies!

Daily life in Miami is incredible for the weather and tropical fauna! You should be careful when you drive, do not crush a big iguana on the parking!

PS : I had never seen so many different kinds of cheddar! (the photo only shows a small part..)

To be continued !

marine-oceane1 marine-oceane2 marine-oceane3 marine-oceane4 marine-oceane5

— · —

A semester in Miami

To follow my second semester at the Rosenstiel School of Marine and Atmospheric Science is a great opportunity and thanks to the PUF program and Dr. Irisson I'm finally able to start this adventure.

I have chosen three classes; "Coral reef biology ecology and conservation" by Dr. Baker, "Management and conservation of marine ecosystems" by Dr. Die and "Physical environment of marine organisms" lead by Dr. Bakun and I can say it is a real chance and honor to have class with Dr. Andrew Bakun. These classes and teachers are very interesting and the fact that there are few students attending these classes allows more focused and interactive discussions.

In the meantime I have started to work on my internship. I am part of Chris Langdon's Lab and my proposed study is using essential physiological measurements to etablish differential bleaching responses of an endemic coral species (Orbicella faveolata). Sampled colonies of this species are collected at Horseshoe reef, following the coral bleaching event caused by sustained high sea surface temperature over the 2014 summer months in the Florida Keys.

I really feel integrated in the team, PhD students are really nice and they are always available to help me through my research.

Daily life in Miami is great, I live in Key Biscayne with another Italian OEM student and everyday we get to the RSMAS by bike; the view on Biscayne Bay is day by day more beautiful. And what a pleasure to lunch at the beach-front cafeteria where we have already seen manatees!

I am glad to be here, in less than a month I have learnt so much and we're only at the beginning!

camille1 camille2 camille3 camille4

— · —

Modeling nurse sharks

Conservation and fisheries management: can they coexist? They may appear really similar to an outsider eye but currently they are two strongly separated research fields, to the point that even the vocabulary differs!

Thanks to the PUF project I have the opportunity to start an internship for my second year of MSc with one of the first researcher to combine these two aspects together: Dr. Elizabeth Babcock of the Rosenstiel School of Marine and Atmospheric Sciences (RSMAS). It has just been few weeks that I am working on it but the internship has already a charming project.

The aim of my research is to understand the protective potential of a marine protected area (MPA) on reef sharks. I am using data from Glover's Reef atoll, an MPA from Belize, a country where sharks are heavily fished and I will work on the nurse shark species (Ginglymostoma cirratum). It has been 14 years that nurse sharks are conventionally tagged in this region, and I will analyze and model this big dataset through Bayesian modeling. I will later use also acoustic telemetry data to estimate the probability of detection of these individuals and hence better assess their population status.

At the moment I am still struggling with programming codes but being here, at RSMAS, is already an incredible experience. I am working in contact with the best oceanographic researchers of the world, and no better words come to my mind to describe this internship other than an inspiring and truly motivating experience to start my future career.

I am sorry I cannot show you any shark picture but here some photos of my exciting R life, and some landscapes of the breathtaking center of RSMAS, on Virginia Key!

Greta1 Greta2 Greta3

— · —

ASLO meeting in Granada

In biological oceanography, the meetings of the American Society for Limnology and Oceanography (ASLO) are important yearly milestones. Some results of this PUF project were already presented through a poster at the Ocean Sciences Meeting 2014, co-organised by ASLO. This year, the ASLO meeting in Granada was the opportunity to present results of the first and second year of the project, through two oral presentations in the sessions Biological Connectivity and its Importance Within the Context of Global Change and Plankton Ecology - Zooplankton. The talks were about the interaction between behaviour of fish larvae and physical forcings and about the fine-scale distribution of zooplankton across a mesocale front. Both talks were presented in front of a large audience and generated interesting questions and discussions (photos of the two talks below).

Of course, scientific meetings are also great occasions to meet colleagues and generate new ideas (especially around a glass of wine and delicious tapas in Granada!). Discussions started around the themes of the two talks (connectivity and in situ imaging of the ocean). In particular, we met with Katell Guizien of the Ocean Observatory of Banyuls, UPMC, the chairwoman of a connectivity session, who should be visiting Claire Paris at RSMAS in the near future to talk about bio-physical modelling. Interesting points were made regarding automated recognition of organisms in images by ISIIS or UVP users from all over the world.

So, overall a very interesting and stimulating meeting; let's meet again in New Orleans in 2016!

Aslo Robin 1 Aslo Robin 2 Aslo Jo

— · —

Miami, fish larvae and corals

I arrived in Miami a month ago. The town is as Cuban as American. Two different cultures and languages co-exist, two landscapes with high buildings and rainforest gardens. I enjoy to travel each day through the city with my bike (thank you Matt for this useful gift). The RSMAS is located on Virginia key, in front of Miami and the most amazing view to the town is from my office.

I am here to do my Master 2 internship. Under the direction of Dr Claire Paris (RSMAS), and the co-supervision of Dr Jean-Olivier Irisson (OOV), I will study the fish larval recruitment.

Fish larvae are driven by currents but they need to settle in precise places: the coral reefs. To find these small places lost in the immensity of the ocean, larvae could follow environmental cues. And when you are looking for coral reefs, it seems natural to follow cues given by corals. This is what we are looking: Is the coral diversity a key factor for fish larval settlement ?

Why is that important ? Because successful settlement drives a part of the distribution of fish species in an area. Know abilities of larvae to recruit in specific places will allow us to have a better understanding of fish assemblages.

To study this exciting subject I will have the chance to work in the new Marine Technology & Life Sciences Seawater Complex, where Dr Claire Paris has her office and two laboratories. This building, and the RSMAS campus, have plenty of advantages: new labs and equipments to perform experiments, resting rooms with tea and coffee, nice boats for field surveys, a good restaurant with a beautiful view… but above all amazing teammates.

Here a view from my office window and my new work friend…

romain1 romain2

— · —

Lagrangian modelling class by Claire Paris

A modelling class given as part of the Oceanography Masters degree in Villefranche has traditionally had a lot of success with students. This was the case again this year with many students picking it as their lass class of the semester. In the past, RSMAS students took the class, Arthur Mariano came to teach physical Lagrangian modelling and data analysis, David Die came to teach fisheries modelling. This year, Claire Paris came to give a class and a lab about Lagrangian models for connectivity studies. She presented the details of the Connectivity Modelling System developed in her lab over the last 10 years. Dealing with the amount of data such models typically produce proved challenging within a 3 hours lab… and learning that was an important take-home message for students.

Claire also took advantage of her stay to present another application of this model, to predict the fate of oil spilled by the Deepwater Horizon blowout, as part of a lab seminar. Focusing on the physical and chemical parameters of the model allowed highlighting its versatility in a domain different from the biological features it is usually known for. A message that resonated with many current research interest of the Villefranche lab.

— · —

MedPlanet, a scientific network to study Mediterranean fish larvae

For the last two days, the MedPlanet group met in Leucate/Le Barcarès. The objective of MedPlanet is to regroup all teams working on late-stage fish larvae (post-larvae) in the Western Mediterranean. These two days were an opportunity to finally meet in person many potential collaborators, and to present the work we have been doing as part of this PUF project. The discussion highlighted that interactions between the behaviour fish larvae and the constraints of their physical environment should be one of the main focus point of research in the coming years. Good for us since this is exactly the question we have been focussing on for the last two years! This meeting also opened the possibility for a wider collaboration between RSMAS, OOV, and other teams in Spain and Italy, to disseminate instruments and techniques which were developed through our partnership (swimming tunnels, DISC orientation device, etc.). Exciting times!

Here is a photo of us in front of the Centre de Recherche sur les Ecosystèmes Marins (CREM) in Le Barcarès, which hosted us. The meeting was partly financed by the EU LIFE+ project SUBLIMO, coordinated by Philippe Lenfant.

group photo

— · —

The 24/7 fish larvae week

Most coastal fish larvae recruit (i.e. come back from the ocean to the coast) during the night. We took advantage of this to collect them using light traps (they are attracted by light at night) and study them the next day. We observed that they seem to arrive in localised pulses, because different traps would collect very different amounts of fish larvae during the same night. Robin Faillettaz' thesis committee, including Claire Paris from RSMAS, suggested that we look more into this, to confirm or infirm the existence of such pulses. If larvae indeed travel in patches, that has important consequences for their orientation (organisms orient better when in groups), survival (survival probability of each individual is increased in a group), advection by currents (local phenomena would affect the whole group) etc. All questions we are very interested in to understand the physical-biological interactions occurring during the larval stage of fishes.

To detect such pulses, we decided to survey the recruitment of fish larvae at night every 40 min, for a week, prior to the new moon, when most recruitment occurs. But, we also needed to continue our daytime observations of behaviour (orientation and swimming abilities) because it was the last opportunity to get data on the species we were currently studying: the damsel fish Chromis chromis. This species is very interesting because it is very abundant in the Mediterranean and damselfishes are widespread geographically and common where they are present. It therefore provides opportunities for comparison with other ecosystems, in particular the tropical systems studied at RSMAS.

So we assembled a team of researchers and students from the Observatory of Villefranche to achieve the 24/7 sampling effort we needed. We surveyed fish recruitment for seven nights in a row, measured the swimming speed of about 20 damselfish larvae and deployed 40 more in the DISC. We did not get as many fish larvae as we expected but only time will tell what we will be able to do with this data.

The nights were long but the rewards of the sunset and sunrise over the bay of Villefranche made up for the cold, wet hours in between. On the plus side, we all know more about the star constellations visible this time of year! The day-time activities allowed us to complete our dataset for Chromis chromis, now we just need to proceed with the analysis.

We owe a big thank you to all the volunteers who helped us: Mégane Tetaz, Laurent Gilletta, Léo Lacour, Sakina Ayata, Federica Ferrando, Morgane Maillard, Fabio Benedetti, Hubert Bonnefond, and Cécile Guieu. Here are a few pictures taken during this very intense week.

Nights1 Nights1 Nights2 Nights3 Nights4 Nights5 Nights6 Nights7 Nights8 Nights9 Nights10 Nights11 Nights12 Nights13 Nights14 Nights15 Nights16 Nights17 Nights18 Nights19

— · —

DISCing in Villefranche

This year's main goal is the study of the orientation capabilities of fish larvae and how those can influence their dispersal by ocean currents. This work started earlier through the internships of several students and the cooperation of researchers at LOV and RSMAS. This cooperation was made more concrete when Claire Paris, from RSMAS, flew to Villefranche to participate in field work. The goal was to deploy the Drifting In Situ Chamber (DISC) instrument, two copies of which were in Villefranche, to study the orientation of as many species as possible.

It was a very intense time (although the pictures might not do justice to the amount of work) but also very productive. We collected orientation data but also swimming speeds for two species: Diplodus annularis (a sea bream) and Oblada melanura (the saddled seabream). Both species are abundant in the area and fished by the local, traditional fishery. That meant 85 deployments of the DISC over a several days. The weather was not necessarily our best ally so achieving this number was kind of a feat in itself. But we had a few good weather days, with plenty of fish larvae, as you can see below, and we made the most out of them.

Now the data is collected, stored, backed up and being processed. We hope to get the results by the end of the summer.

The downtimes (the bad weather days) were opportunities to discuss the future of the project with Claire. We came to the conclusion that doing similar experiments at night would be the best next step, because most of these species actually recruit on the coast during the night.

Claire is also co-supervising Robin Faillettaz PhD thesis and we took advantage of her being here to hold a very productive thesis committee. Robin had the opportunity to present his work so far, most of which done in the framework of this PUF-funded project, and to outline the last year of his PhD. The committee gave very useful comments and advice for the future. In particular, a more detailed inspection of the dynamics of fish recruitment, during the night. But more on that later…

Disc Claire1 Disc Claire2 Disc Claire3 Disc Claire4 Disc Claire5 Disc Claire6

— · —

Studying fish larvae behaviour

One definition of behaviour is "the way an animal reacts to a stimulus from its environment". This is what we strive to explore in the case of fish larvae with this year's PUF funding. We record the characteristics of the physical environment of fish larvae, their orientation behaviour and then try to relate the two. We achieve this with the Drifting In Situ Chamber, an instrument co-developed by Claire Paris in RSMAS and myself in Villefranche. But the ability to orient would be nothing without the ability to move at significant speed. So we also measure the swimming speed of those fish larvae by making them swim against a flow of know velocity. Both aspects are completely unexplored in the Mediterranean.

This work was started with the help of two interns from the Master in Oceanography and Marine Environment (OEM) of Université Pierre et Marie Curie. Agathe Blandin (for the orientation part) and Elysanne Durand (for the swimming speed part) were efficient, dedicated and produced very good results. Together with Robin Faillettaz, the PhD student working on that project, and Federica Ferrando, an Erasmus intern working on the VISUFRONT cruise of last year but who lent a hand when needed, we formed a great team!

Fish larvae team

Now we are continuing the work on new species with Claire Paris who came from RSMAS to experience field work in the Mediterranean with us. We are making good progress and it is nice to have the original team reunited here. Still, we miss Agathe' and Elysanne's enthusiasm and efficacy and wish them a very good summer.

— · —

The "SpeedyLarvae" project

With my colleague and friend Agathe Blandin, I have been working at the Ocean Observatory of Villefranche-sur-Mer a project financed by the PUF partnership with the Rosenstiel School of Marine and Atmospheric Sciences.

My 2-months internship there was meant to be the "first study ever done" on Mediterranean fish larvae swimming speed.. and it was! I made cute little larvae swim in the swim tunnel that arrived just before me, while being in a fridge (actually, a cold room) all day long. But fortunately for my suntan, I had the opportunity to go almost every day on the boat to drop off and take back the light traps designed to catch the larvae, and that was amazing! Also, we spent hours with PhD student Robin Faillettaz trying to identify the fish species we worked on. When we finally found the key to differentiate Spicara smaris from Boops boops, only the word "Eureka" can describe how we felt.

But getting back to what's important : the larvae. They could swim pretty fast; indeed, the ones we tested could swim faster than the ambient current found in the area, so they can not be considered plankton!

Eventually, those data and more to come, paired with those from the Drifting In Situ Chamber collected by Agathe, will allow improving models that predict larval dispersal, leading to a better management of fish stocks in the Mediterranean Sea.

I am very grateful to my supervisor Jean-Oliver Irisson and to Robin Faillettaz for their commitment in my experience and for making it much more than just a first year MSc internship, but also a great scientific and human experience that makes you not want to leave the lab until 7 or 8 pm everyday ;)

Elysanne 1 Elysanne 2 Elysanne 3 Elysanne 4 Elysanne 5

— · —

Mediterranean fish larvae, Drifting In Situ Chamber and me ... a love story

For my first year of MSc internship, I had the opportunity to be part of the PUF project and the partnership between the Rosenstiel School of Marine and Atmospheric Sciences and the Ocean Observatory of Villefranche-sur-Mer. The aim of my study was to gather the first dataset of orientation abilities of post-flexion Mediterranean fish larvae by using the mini-DISC, an instrument developed at RSMAS. After setting up that that transparent floating and drifting structure with the help of Claire Paris and Cédric Guigand, from RSMAS, we have been able to detect and quantify the orientation of 3 common Mediterranean species : Boops boops (the bogue), Spicara smaris (the picarel) and Spondyliosoma cantharus (the black seabream). Yeepy !!

Being on the field to deploy the DISC was a huge experience and a privilege, even if it was not easy at the beginning (due to a rough Mediterranean Sea). I took great pleasure in discovering all of the technologies developed for this project and in learning how to work with it.

There are still a lot of work to do and thanks to that experience, I can say that I am motivated in helping progressing science in that field of research.

This internship was full of discoveries and I thank my two supervisors Jean-Olivier Irisson and Robin Faillettaz for their patience, their trust and for having been so present during these 2 months.

Agathe 1 Agathe 2 Agathe 3 Agathe 4 Agathe 5 Agathe 6

— · —

My adventure in Miami is coming to an end…

The PUF program gave me the occasion to study my semester at the University of Miami, on the RSMAS campus. I got the opportunity to study three different classes:

  • Biological and Physical Interaction, taught by Claire Paris and Josephina Olascoaga. I learned to use Matlab and the Connectivity Modelling System. The CMS is a very interesting tool, it allows to look at the trajectories of particles as well as the connectivity between those particles and some settlement area. I worked on a very interesting final project for this class; the dispersion of larvae around hydrothermal plumes. I mostly used the CMS to draw the trajectories of the larvae if they were released around a hydrothermal plume.
  • Coral biology and ecology, taught by Dr Andrew Baker. I've learned everything there is to know about the corals and their importance in ecology. Many specialist came to this class to give lectures and shared their different point of view on the future of coral reefs. I also had a final project to work on: I decided to present the diversity of deep coral reefs and how they are threaten by bottom trawling.
  • Biogeochemical of the ocean taught by Denis Hansell. I've learned a wonderful tool: the Ocean Data View. I've understood a lot on the distribution of chemicals around the ocean and how the interaction of ocean and atmosphere is really considerable.

Classes were a great learning experience. I am definitely taking some knowledge home. The second part of this adventure was the internship. My project "Finding Nemo" came to an end and I got to do the statistics on the data. Different results came out, some larvae oriented and others not. It rose some very interesting questions! The behavioral data collected in DISC experiments could be potentially changing for studies of larval dispersal. DISC data will provide critical inputs to a new generation of biophysical larval dispersal models.

I must admit I had hard times at the beginning of my internship but it's normal. I've learned to do research, to learn about the DISC project, to analyze and well organize data. I've learned to work independently, to ask questions to everyone around me. I've learned so much from my lab mates; Andrew Kough, Matt Foretich and Erica Staaterman. Claire Paris shared her contagious passion about science and reef larvae and I'm definitely going to keep up with her research. I am thankful to the Paris Lab for everything that I've learned during this adventure. And I would like to thank Jean-Olivier Irisson for giving me this opportunity.

For anyone who wants to do this exchange program: you will learn a lot. Whatever your research field, studying in an international lab is a rewarding experience. You will grow personally and professionally. Be courageous and make that step, it's worth it.

Laurianne 1 Laurianne 2 Laurianne 3

— · —

An internship at RSMAS

I went to RSMAS for four months in order to do my second year of Masters’ internship. I worked within the CIMAS team, under the supervision of Dr David Die to carry out a biodiversity study of a Marine Protected Area (Pulley Ridge HAPC) in the Gulf of Mexico, to see the spatial and temporal evolution of the sharks' community at the scale of the West Florida Shelf. This study is interesting because this preliminary work will help for the determination of the best extension area for the Pulley Ridge HAPC and for the creation of a bio-economic model in the future, for fishery management. On a personal point, I gained a lot of autonomy with different software like ArcMap, Access and PRIMER. I also improved my English (and a few words of Spanish!) and now I know that I can survive in a tropical country ;)

It was very pleasant to work at RSMAS which offers a lot of services and opportunities to learn more about all the different aspect of the Oceanography. And every workday, it was a pleasure to bike from my home to Virginia Key (the location of RSMAS) which offers a perfect view of Miami downtown (see the picture: Miami by night!).

I would like to thank Jean-Olivier Irisson for this PUF partnership and his help in statistics, David Die for allowing me to do my internship under his supervision and the PhD students for helping me with the different software! And thanks to everyone else for their help and friendship.

Chloe Miami By Night

— · —

Mel and larval fish

My internship at RSMAS is focused on the impact of mesoscale eddies, season and water temperature on early life history traits of larval fish in the Florida Keys. Mesoscale eddies are hydrographic structures of which influences on the delivery of fish larvae to reefs have been shown in this area. The water temperature is one factor likely driving the growth of larvae. Understand the key processes operating during the early life of fish is important to improve models and figure out how populations are connected and replenished over time and in this way improve the protection, conservation and management of marine species. In these perspectives, my study was undertaken to examine growth rates and pelagic larval duration of reef fishes 1) that were “delivered” by eddies or arrived at the reef when eddies were not present (2) under the seasonal water temperature variation influence. The hypothesis is that conditions inside the eddy and summer temperature are better for growth and survival. In order to test this one, larvae have been measured and their otoliths (calcified structures with daily deposition) were dissected out, imaged, and analyzed. Lab-work and data analysis were and are a pleasure thanks to the sympathy and help of my advisor, Dr. Evan D'Alessandro, and my lab-mate, Iris.

Mel Fish

— · —

VISUFRONT at Ocean Science Meeting

For seven months, since the end of the VISUFRONT cruise using ISIIS in the Mediterranean Sea, we have been working hard sorting a few percents of the millions of images that we collected. And we are progressing: the very first results were published as a poster at the Ocean Science Meeting 2014 in Honolulu, Hawaii!

This trip was made possible thanks to the PUF program that sponsored it and I would like to acknowledge it once more. Not only for letting me go the flagship destination that Hawaii is but also because participating to an Ocean Science Meeting is such a fascinating experience. There are so many people, over 5500, gathered in the same building that it could become overwhelming. But the meeting was so enjoyable that everyone was speaking to each other creating a huge melting-pot of knowledge and being in the middle of that was unique.

So many people also means so many posters, and I was one of the 3000 that were exposed. Yet, my poster attracted quite a few people, PhD students as well as researchers, and I was busy explaining it for (more than) the entire duration of the session, until we got kicked out by the security. I didn't know wether people would find any interest in these preliminary results, but they did, which shows that our data is valuable and it we will be even more once everything get processed! If you want to have a look at my poster, it's there:

In addition to meeting many new people, this week also allowed me to meet with Pr. Claire Paris, my PhD co-supervisor from RSMAS, and her team. We discussed the forecoming field season using the DISC to study the orientation of Mediterranean fish larvae.

I'm finally back to sorting ISIIS frames in my office in Villefranche, but with tons of nice memories from that conference in Hawaii and new perspectives for analyzing our data in the future, thanks for that!

Robin At OSM 1 Robin At OSM 2 Robin At OSM 3

— · —

A quest into fish larvae olfaction

During this spring's break from classes I was fortunate enough to travel to the Laboratoire d'Océanographie de Villefranche in Villefranche-sur-Mer as part of this PUF program. While the trip began on Sunday with some sightseeing in the beautiful, postcard-esque city, we quickly got to work on Monday. My host, Dr. Jean-Olivier Irisson, had invited me there to continue work on two projects investigating the behavior of larval fishes.

The first two days were spent discussing the hardware and software used in conjunction with the Drifting In Situ Chamber (DISC), a Lagrangian observation system that records the behavior of marine larvae in their natural settings. Our first goal was finalize the design of our custom-engineered compass for the system, and our second goal was to plan the export of the data analysis software to a more user-friendly format.

compass 1 compass 2

We took a break from this project on Wednesday when we travelled to Marseille and visited Dr. Emmanuel Villermaux, a Professor at the Université de Provence and Institut Universitaire de France. We had a very productive meeting planning an experiment to investigate the potential use of infotaxis in larval fishes. The hypothesis is that larvae may navigate to their settlement locations by coming into contact with discrete patches of advected odor and using the times and locations of these “hits” to infer the location of their homes.

Upon returning to Villefranche we continued development of software for the DISC, but spirits were especially high on Friday when Dr. Irisson's lab received a brand-new toy to be used by PhD student Robin Faillettaz : a Loligo swim tunnel. As I had previous experience with this instrument, I was able to provide some valuable information in setting up the chamber as well as suggestions for future use.

On Saturday I began my journey home, which was nearly derailed by a social movement that shut down the airport buses in the city of Nice. Fortunately, the kind people in Villefranche had taught me just enough French in my week's stay for me to find my way to the airport by other means. Now that I am home I am already looking forward to future opportunities to visit the beautiful country of France and continue my work with Dr. Irisson and Robin.

Matt 1

— · —

Swim tunnel test

This year's research is about the behavioural abilities of fish larvae and how it interacts with their physical environment. We will study both their swimming speed and their ability to orient in the open ocean. Today, we received the swim tunnel, ordered from Loligo systems which will allow us to measure the ability of fish larvae to swim against a flow. Check out the video on the product page to understand how the tunnel works. While the principle of the recirculation of water within the double layered tunnel can seem complex, it was quite easy to set up; in particular because Matthew Foretich, a PhD student from RSMAS, was here to help us. Matt spent a week to study Loligo's products as part of class at RSMAS. He was able to give us small tips and highlight details which will help use the tunnel successfully in the future. Here are Robin and Matt setting the tunnel up.

Loligo 1

But, today, as kids receiving a present on Christmas, we couldn't wait to try it. So we set everything up as fast as we could, popped a weeks-old juvenile fish into the tunnel, and turned the turbine on. Here is a video of the result. We start with a slow speed, then crank the speed up and the small Mullidae keeps up with it very well, and we finally come back to a reasonable speed before letting the fish out, back to its quiet and comfortable aquarium. We then examine the flow inside the tunnel by injecting dye in the water. We leave it to you to guess the nature of this dye. Remember this is a french-american cultural exchange program ;)

— · —

Multivariate stats class open

The multivariate stats class which was well received by RSMAS students last year (check Dan's, Erica's and Jessica's impressions) is now open for registration. It will be dispensed as a summer school, from July 7th to July 25th. The description of the summer school is only available in French unfortunately but check the last page of the description of all classes in Villefranche for an english summary. Interest students should contact with a CV and letter explaining their interest for the class. They will then need to fill the registration form. Registration closes on April 11th.

See you soon in Villefranche!

— · —

My adventure in Miami

An adventure. The risk you take to go study or work outside of your comfort zone, outside your own country, in another language.

The opportunity that the PUF program gave to me was, for me, an amazing adventure in perspective, an opportunity that wouldn't happen twice, so I grabbed it. I was crazy (or smart) enough to take this occasion to go study one semester in a sunny state of the USA, where the meaning of Miami is more like beach, sun, shopping, dancing, Cuban music and spring break vacation for most of the American students.

I was given the occasion to go study my second semester (first year graduate program, spring semester in the US) at the Rosentiel School of Marine Atmospheric Sciences (RSMAS pronounced razmas). I chose three classes from a list, which I tried to diversify: Biological and Physical Interactions (a modeling class), Biogeochemistry of the ocean and one original class that is unique to the school, a Coral Biology class.

My first surprise was the number of student in each class, three in BPI and Biogeo and twelve in Coral Biology. I was used to be part of big groups, up to twenty nine students, and there I found myself on an almost one to one basis in class! But it makes things so much easier. I feel free to talk to the teachers and they have more time to help the students. The English it not so complicated and scientific vocabulary is pretty much the same… So classes are one cool part of the adventure!

The second part of my adventure is the internship. I had the chance to get a spot in Dr. Claire Paris' laboratory and work on data that was collected in the Dean Blue Hole in the Bahamas! Too bad I wasn't there a year before. The goal is to find the clues of the orientation of fish larvae, thanks to the help of the DISC, a device which goes underwater and where a larvae is followed by a GoPro camera. Part of my work is to click on the position of the larvae for each picture that was taken during a deployment of the DISC. With an average of 600 picture per deployment and 200 deployments, I decided to call this project "Finding Nemo!" to make it more fun. Then when I'll be done with the data I will be able to work on it with R.

Daily, my life at Miami began with difficulties, the administration wasn't ready for me, papers were missing, I had to get keys and a pass to get in the buildings and I didn't had any for a week… The place where I stay is very good, the landlord is really nice and my room is much bigger than the one I used to have in Paris, for a cheaper price. Everyday it's sunny and warm, I get to take the shuttle to school for free and I get to see a beautiful view of all Miami every day. It did take me a month to get use to everything, and at beginning February two other students from the French OEM Masters degree arrived, so now I feel less crazy. Things are getting much better and life is good, so to be continued ☺ !

And let me introduce you to Jack, a juvenile lobster we caught with Andrew Kough one night, who is now growing in the lab so that we can study it.

Jack 1 Jack 2

— · —

Miami experience

Miami is, at first glance, from the plane window at night, a huge shiny square of a city. Later, the "magic city" also appears infinite (when walking), slow (when driving, due to traffic jams), latino (when taking the bus) and hot (when riding a bike).

RSMAS' campus is a great place to work. Labs are well furnished and large. The restaurant offer a view to the sea, good food (even for vegetarian people, and even with a smile) and a bar after 5 p.m. (3 days/week). The beach volleyball field, the pontoon, the beach itself and even the library are nice places to take a break.

RSMOIDS are smiling, friendly and relaxed. Especially my lab team, which debates about a paper a week, sometime with some crepes, and that is a really interesting way to work.

Finally, I was struck by two points. The first one is the number of seminars (at least 3 a week) where you can find students, professors and researchers together. The second one is… the excessive use of the air conditioning (almost 10°C of difference between outside and inside) that forces me to wear everyday the only sweatshirt I brought to Miami!

Here is a view of the cafeteria building from RSMAS' beach.


— · —

First impressions

From the beginning, the temperature and humidity put me in this tropical atmosphere where Spanish is the second national language.

The first day at RSMAS was dedicated to the administrative paperwork, with the help of Julie Houston and Meagan Zubkoff. But also the creation of my internet connection (taking more than 3 hours when you are unlucky like me) with the help of all the staff of IT service. During the rest of the week, few administrative appointments were needed for the J-1 Visa status at the different campuses of the University of Miami (RSMAS campus but also Main Campus). This first week is eventful, forces us to quickly become familiar with life in Miami (transit, the pace of life, …) and helps us to discover the infinite streets of Miami with all its different facets.

After all these adventures I had the pleasure to discover the RSMAS campus with all its advantages : numerous labs, a great restaurant where we can see the olympic games :), a library with free coffee, tea and hot chocolate, beaches with a great view, a lot of seminars with excellent teachers…

Miami is a city full of surprises and these 5 months here promise to be rewarding!

Chloe 1 Chloe 2

— · —

The DIVAMAR class in Banyuls

I think the course did a very good and comprehensive job with its practical work activities. It allowed us to put the theory we learned previously and during the course into practice. Additionally, it was great getting to know a little piece of France, getting to know some of the culture of the region, and the beautiful scenery all around. It was also great to get to know new people and make friends with them — Ilan

Visiting the Banyuls Marine Station for the DIVAMAR course was a good way to expand my current knowledge of physiology to species and topics beyond my normal study area of acid-base balance in marine fish. In DIVAMAR, we were able to examine how various species including marine bacteria, phytoplankton, and fish respond to changes in light conditions. In addition to lectures on photoacclimation and photoadaptation, we were also able to practice new laboratory techniques. For my PhD research, I don’t often do a lot of field work so it was interesting to take a short research cruise to learn how water samples are taken for various analyses (and also to get a great view of the Banyuls bay area!). Right downstairs from our classroom, we were also able to visit a historic aquarium and take a look at some of the local marine species — Rachael


— · —

Fisheries modelling by David Die

The main part of Dr David Die's intervention was about fisheries and how modelling can help sustain this business. He introduced us to the different types of institutions that prepare scientific reports to guide politicians in their decisions. He also gave us clues to answer the huge mystery: how can scientists predict the maximum stock that fishermen should catch to have a profitable and sustainable fishery.

Here are some comments from students who followed his lectures:

"Very interesting teacher, really interesting lectures about tuna fisheries and the challenge to deal with over fishing. To have lecture from an external professor was an unique and amazing opportunity that ended in a great success. The only regrettable fact of this experience is that it was a little bit short to share knowledge in its entirety." Kento

"It was really fascinating to know how fisheries quotas are being calculated. Nice to see how model can be applied it several types of work. "Adrian

"It was a nice change from phytoplankton and zooplankton. He was a very enthusiastic professor and I really enjoyed his lectures. It would have been nice to work on Matlab or to do something with Leslie matrices." Molly

"It was really interesting to have courses about top predators and also show the aim of modelling for management and conservation. I agree with Molly he was a very nice professor, social, close to us who really wanted to show us what his job is and issues he can has in a field like fishery management." Julie D.

"The lectures were really interesting. The topic presented and the way the teacher explained them stirred up my curiosity all the time. It was a pleasure meet a person with such experience and very open towards the student." Chiara

"The world is running around a model and he is the King of applied modelling. Fisheries need scientific modellers to take the power back! We trust in the power of the models, we trust in fisheries, we trust in David Die!" Anonymous

"Really interesting lecture about population dynamics of marine fishes. It will be particularly useful to know how modelling can help to manage fisheries. David Die was very enthusiastic to share his knowledge with us and we learn a lot from his experience". Julie B.

Here are a few pictures of David "in action" and with the students on the "promenade des professeurs" (yes, professors have their own promenade in Villefranche!).

Daviddie1 Daviddie2 Daviddie3 Daviddie1

— · —

Andrew Bakun receives Albert 1er medal in Monaco

Andrew Bakun, a professor at RSMAS who has been coming to Villefranche for two years as part of this PUF program, just received the Albert 1er medal from the Oceanographic Institute of Monaco. This medal is awarded every year to honour a lifetime of work in the field of oceanography. It is the most prestigious award from the Oceanographic Institute.

I was delighted to attend the award ceremony and to chat with Pr Bakun again. I was also very pleasantly surprised to see that most of the examples and concepts that Pr Bakun presented in his acceptance speech were the same he presented to the students in Villefranche a few weeks earlier. Maybe not all of them realised how lucky they were to get such a lecture as part of their Masters, but it made it even more concrete how great it is to be able to host Pr Bakun thanks to the support of this PUF project.

Here is the press release of the University of Miami, the video presentation of Pr Bakun shown during the ceremony and a few pictures.

BakunMonacoAward1 BakunMonacoAward1

— · —

Classes by Andrew Bakun

Thanks to the partnership between the Ocean Observatory of Villefranche-sur-Mer and the Rosenstiel School of Marine and Atmospheric Sciences, Andrew Bakun came to Villefranche this year again. This professor from the university of Miami, one of the main specialists in fisheries dynamics, gave four lectures incorporated within the framework of the master students' course. Their overall topic was physical-biological interaction in the ocean, focusing on variability in complex adaptive systems. This meeting happened during the course: "response of pelagic ecosystems to environmental changes". His four lectures were complementary, in order to understand the mechanisms acting at the population level under anthropic and environmental forcings. To do so, several ecological concepts (news for most of us) were presented. They were more based on physical contribution than most of the concepts developed in this unit, and were illustrated by historical examples. It was also instructive because Andrew Bakun gave classes different from our usual courses, trying to rise questions more than give answers. Finally, this was a great opportunity for us to improve our knowledge and see a different pattern from the French way of teaching.

— · —

An internship at RSMAS

I am a Master student in Oceanography and Marine Environments from the University Pierre and Marie Curie of Paris, with a specialization in anthropization, management and conservation of marine habitats. I went to RSMAS for four and a half months in order to do my second year of Masters’ internship. I worked under the supervision of Dr Elizabeth Babcock and PhD candidate Bill Harford to assess for Glover’s reef spiny lobster fishery the bias in abundance and fishing mortality resulting from a depletion model, in comparison to the outputs from an individual-based model developed by Bill Harford. This study is really interesting because it has a crucial perspective for fishery management at Glover’s Reef, which is a marine protected area including a no-take reserve; but also more generally for areas located nearby marine protected areas, as it raises the issue of considering individuals from a no-take reserve as part as the fishable stock or not. The further purpose of this study would be to determine the total allowable catch to be implemented to have a sustainable fishery, and therefore to evaluate the bias resulting from different management strategies. On a personal point, it also allowed me to learn about stock assessment procedures and to understand the functioning of individual-based model. I also gained a lot of autonomy with R and discovered another programming language, Java. But even more, it confirmed my vocation to work in fishery sciences in addition to marine ecology and conservation. It was really interesting and instructive to discover another education system, and working at RSMAS was such a rewarding experience.

Indeed, RSMAS is a really great place to study any aspect of oceanography, to enlarge your knowledge and satisfy your curiosity, as it regroups many labs working on various disciplines. Anyone is likely to find something (if not many things) to be interested by. There are many occasions to discover other fields of study within and from biological oceanography, one of the main being the WetLab after-works. The WetLab is also a great place to spot manatees, dolphins, sharks, rays, tarpons, and seabirds.

I would like to thank my advisor, Elizabeth Babcock, and PhD candidate Bill Harford, for allowing me to do my internship under their supervision, and for the help, time and assistance they provided me. I am also grateful to Jean-Olivier Irisson for creating this partnership between our universities and for his help in preparing my departure to Miami, as well as the PUF organization for funding this wonderful experience. Thanks to David Die too for taking us on a fishing trip with his class. And thanks to everyone else for help, friendship, and good moments!

Caroline1 Caroline2

— · —

The VISUFRONT people

The dust has settled. The cruise is now over. The Miamians are back in Miami. ISIIS is in a container, on a ship, sailing back towards the US. The cruise gear has been put back in the drawers, crates and shelves in Villefranche. And what are we left with? A little sleep deprivation, many memories and a lot of data. Quite a few megabytes of physical data and about 18 terabytes of images. That is 9 transects across the Ligurian current to examine the frontal structure, 7 transects along the current to examine small-scale patchiness and diel variability, and 15 transects cutting into the same water mass during the Lagrangian experiment.

The collection of this amazing dataset was made possible by the cleverness, dedication, and hard work of the team of this cruise. I dealt with the organisation so I get to thank everyone and it is with great pleasure that I do so.

There was the core of the VISUFRONT team, the four of us who stayed on the ship the whole time and manned the long 12 hours shifts between 3 am and 3 pm: Jessica, Robin, Cédric, and myself. There was Bob, who made it a point to come even though he was in the middle of a complicated move across the US to a new job. There was the jellies-team: Léo, Fabien, and Martin, relentless at counting jellies, all night long. There was our CTD expert, Vincent, who left his soon-to-deliver wife ashore to come with us for two days and make the reference CTD casts which will allow to inter-calibrate all instruments. There was the drifter team: Simone and Mireno, who came on the ship, as well as Annalisa and Anne, who made the drifters available, and allowed us to track a water mass for nearly 48 h. There were Laurent and Hassane who coordinated the gliders upstream of us, with the help of Florent who also tested a new jellyfish-watching camera mounted on an Argo float. There was Grigor, who so efficiently coordinated the arrival and departure of the gear with the authorities of the Nice harbour (and rescued our GPS signal on a Sunday night!). There were Laurent and Émilie who helped us set up the UVP on the first day. There was Marie who documented all this with her camera. There were all the people who participated to the discussions to set up this sampling plan: Louis, Philippe, Claire, etc. And finally, there was the crew of the ship, the Tethys, who proved to be efficient, competent, yet fun to work with: Renaud, Stéphane, Fred, Laurent, Gwen, Michael, and Bertrand.

To all of them, a very deep and sincere Merci !

Group With Bob Group Front Group Front 2

Jessica Tethys Jessica Loading Isiis 3 Martin Martin And Robin Cedric Fabien Martin And Jessica Glasses People Fred People Laurent People Michael Sunset

— · —

The main finding of this cruise

Even if it is not finished yet, we can already certify that this cruise was a complete success. We do not have figures and papers published, but we do have concrete results. Not about larval fish ecology nor any other scientific topic, but about an extraordinary, almost unbelievable, extremely useful matter. Indeed, everyone in the scientific crew learnt to do a bowlin knot, with just ONE HAND. Amazing, isn't it?! Here is a picture to help you picturing our studious evening!

Bowlin Knot

— · —

Final along-front transect

This is our last sampling day and everything went fine over the last few days. But after all the troubleshoots we have been fighting (with success!), this last day could not be a usual one. The plan was to do a transect following the drifters trajectory from 36 h ago. By doing that, we would get a quite perfect along-current transect if the oceanographic conditions did not change much, which was a fair assumption. It seemed simple, but actually appeared pretty challenging since storms were expected in the early afternoon. It was 6:30 am, we had plenty of time and we decided to stick to the plan. The ship and ISIIS were set up at 7:20 am and Jessica took over for me.

A few minutes later, the weather started to become harsher and a curtain of rain along with lightning caught us. Visually amazing. Until the actual "visual" was reduced to 30 m. The captain started to be concerned about our gear and warned us that from now on, the responsibility was ours in case of damage if we wanted to keep ISIIS in the water. Surprisingly, there were no more end-of-the-cruise-tiredness-because-we-slept-about-5-hours-per-night. It was like we had drank 5 Redbulls each (although we didn't drink any… that day). Everyone has is own reaction to adrenaline. Jessica was hilarious and "sooo excited" while I was trying to figure out how I was going to pull up ISIIS on board with a limited number of bumps. Long story short, rain stopped before paying in the cable, ISIIS made it and we even got a beam of sunlight right when it landed on deck.

Storm 1 Storm 2 Storm 3 Storm 4 Storm 5 Storm 6

We could therefore finish our sampling with plankton tows on the way back, in order to compare that data with ISIIS images. This last sampling day was successful… until winds came up to 30 knots during the plankton tows and constrained us to go straight to a safe anchorage behind Lérins Islands. We stayed there the rest of the day and started packing before picking up the remaining float and glider tomorrow.

— · —

Nocturnal observations

One of the secondary aspects of the VISUFRONT cruise has been to collect surface observations of jellyfish. The common Scyphozoan jellyfish species in the Ligurian Sea is the Mauve Stinger (or Méduse Rose in French) Pelagia noctiluca. This species has been present within the Mediterranean for at least 100 years and has periods of high abundance alternating with several years of low abundance. The species arrives on the coasts throughout the year, but attracts considerable media attention by tourists and swimmers being stung in the summer. Throughout the Mediterranean it is perceived as a problem species, but despite long observational records very little is known about the biomass of the species or even how long it lives. The research from VISUFRONT will go some way to providing a wider spatial view of this species.

Unfortunately for the researchers, Pelagia seems to respond to light and spend the day deep in the water (possibly as deep as 700m), coming to the surface at night in large numbers to feed. Even the light of the moon is sufficient to send it swimming down into the depths if exposed to it for too long. Only those animals arriving close to shore, possibly in poor condition appear to respond less towards the light. So to observe these animals the use of a spotlight and work during the night hours (currently 21:30-05:00) is required. The team from the L'Observatoire in Villefranche-sur-Mer took turns with Leo Berline, Fabien Lombard and Martin Lilley alternating to observe the night-sea.

Within the light of the spotlight, halfway back along the side of the boat, you can see about 40 m2 at a time. The aim is to count the number of Pelagia passing this ‘window' and record the changing physical conditions of the sea on a regular basis. Observations at the 4-knot cruising speed of ISIIS are relatively easy as long as there aren't large waves, but faster speeds or a swell make the conditions more difficult. At times you find yourself being mesmerised by empty green-blue moving water, and are then brought back to reality by the arrival of a jellyfish. These calm times were rare, unless we were observing before dusk, and 5-50 jellyfish were common in a five minute period. At times there was a carpet of jellyfish all facing different ways at the surface, using their long tentacles to fish plankton, and competing for space. When this is the case you are forced to count in 10s, 20s or 50s at a time and the numbers rack up to over 1000 individuals on several occasions.

The night-time labour is not without reward as you spend so much time staring at the sea occasionally other organisms are either surprised or attracted to the light source as it goes by. Small fish seem to use the light to hunt, Sunfish have been seen, and occasionally dolphins zip through the light on their way to play on the bow-wave. The downsides of course are prolonged periods staring at a moving sea, which can cause stomach upsets in those not acclimatised to the motion of the ship. Equally sleeping during the day can lead to disorientation and confusion as to what the day is, when the next meal will come and quotes like "is it morning?" and "See you ‘tomorrow', when I have slept". At times it is also hard to motivate yourself to continue on for another five minutes, without the use of energy drinks or caffeine.

All in all, it provides an opportunity to look into a world that few people have had the chance to observe and those coming to question the ‘compteur de méduse' have been frequently surprised to see the jellyfish. If you don't observe the world you'll just remain oblivious to that which is passing your port-hole. Personally though, it is possible to get too much of a good thing and I will be glad to get back to a normal schedule once again next week. It has provided plenty of food for thought and posed further questions about the life of these nocturnal creatures.

Counting Jellies 1 Counting Jellies 2 Red Bull

— · —

Lagrangian studies

We finished our cross-current and along-current transects on Thursday, July 25 and headed back to Nice harbour for the evening to pick up some more scientists and get ready for the Lagrangian studies. Fabien Lombard from LOV, who had come on board for the previous two nights to observe and count Pelagia noctiluca, switched with Martin Lilley (LOV) who joined us for the remainder of the cruise. Two other scientists from Italy, Simone Marini and Mireno Borghini, who work with Annalisa Griffa, also brought drifters that will be used for the Lagrangian studies.

The goal of the Lagrangian portion of the VISUFRONT cruise is to track a water mass over 36h hours using drifters and continuously sample this water mass with ISIIS. The drifters, designed to passively drift with the current, transmit their GPS location every ~ 15 minutes, so we can see their past trajectory and estimate their future location. We aim to sample in transects perpendicular to the drifter tracks. This is particularly interesting because in our other transects (cross-current and to a lesser degree, the along-current ones) we are crossing over different water masses, so we have both a spatial and temporal pattern to tease apart. With the Lagrangian studies, we theoretically are sampling the same "space" (in terms of water mass) over time, so we can isolate the temporal signal in the ISIIS data. In my opinion, this is probably the most novel component of the VISUFRONT cruise; we had never sampled in a Lagrangian fashion with ISIIS and been able to truly isolate the temporal signal in the fine-scale movements of plankton. With these experiments, we are able to ask questions about the diel vertical migration patterns of organisms within multiple trophic levels and size ranges.

However, as fitting with the theme with the rest of the cruise, things did not go entirely according to plan. We lost a day of sampling at the beginning of the Lagrangian portion of the cruise because we had to go to BOUSSOLE to rescue a glider that had lost its connection with the mainland. The drifters were supposed to go in at nighttime according to our original sampling plan, so going to BOUSSOLE and back would result in an entire day lost. (We ended up doing some plankton tows so it wasn't entirely lost, though.)

Glider 2 Glider 1

Upon returning to the coast and putting the drifters into the water, we could not initially obtain accurate GPS positions for the drifters – the positions we were getting by SMS were completely useless. After quite a bit of troubleshooting, we figured out that we could obtain the drifter positions using geoborders' website, so that put us back on track to do the Lagrangian transects.

We sampled with the drifters for nearly 48 hours before pulling them out of the water due to weather concerns. Reports of a bad storm had been coming for the past couple days, and it is supposed to hit later today, on the 28th. So, instead of sampling until tomorrow (the 29th), we are cutting our Lagrangian studies even shorter. However, 48 hours of near continuous Lagrangian sampling is pretty good, so we are pretty happy with what we got. Thus, this morning, we pulled the drifters out, dropped the Italian scientists off in Nice, and are heading out again to brave the winds, swell and rain.

Drifters 1 Drifters 2 Drifters 3 Drifters 4

Provor Preparation 1 Provor Preparation 2 Provor Preparation 3 Provor Preparation 4

— · —

A better understanding

It’s Sunday, July 28 at 3:30 am and I am starting one of my last night shifts. We have been working in twelve hour shifts, from 3 am to 3 pm, 3 pm to 3 am. Robin and I (Jessica) have been shift partners, and Jean-Olivier and Cédric have been manning the other shift. Between the four of us, we have recorded and watched nearly 15 terabytes of ISIIS images, accounting to a total of nearly 100 hours of black and white pictures flying by the screen at 1/14th of a second a piece.

This is my first ISIIS cruise since the summer of 2011, when the Cowen Lab did a series of cruises in the Gulf of Mexico (some of the data for my PhD) and this one has definitely been one of the most enjoyable cruises I’ve participated in. Part of it has been the effortless camaraderie of the four of us and the ease of working together, part of it has been the inherent scientific interest of this project, with its different components (lagrangian studies, diel vertical migration studies, plankton in mesoscale frontal features).

Isiis 2

A third and rather large component of why it has been such a fun cruise is something I didn’t know to expect but now make total sense. As I have progressed along in my PhD studies and delved deeply into the ecology of gelatinous zooplankton (and have looked at hundreds of thousands of ISIIS images along the way), I have developed an instinct for, understanding of, and expertise in many of the organisms that are zooming across the screen in milliseconds. Thus, when I see a bunch of large Prayid (likely Lilyopsis spp.) siphonophores at 100 m, Mertensid ctenophores casting a sticky thin web of tentacles, or a huge surface patch of doliolids, I not only know what I’m seeing (finally!) but also am starting to register in my head why they are in certain places, or in particular orientations in the water column. It’s been really neat for me, as I sit here taking notes on ISIIS images as we collect them, to be able to think beyond the "what is that dark blob over there?" and consider the ecology and behavior of these underappreciated organisms, for we are seeing them in an unprecedented manner. To be able to observe fine-scale patterns and patches (some of these organisms occur in patches just 1-2 meters high) has been fascinating and incredible for me. On this cruise, in the middle of the Mediterranean, I truly feel like I’m "eavesdropping" on the secret lives of these sea drifters.

Here are a few images we captured, most of them taken straight out of ISIIS, some cropped and zoomed. Remember that those are taken in situ, at 4 knots, at the rate of 14 images per second!

Frame Grab01 Frame Grab02 Frame Grab03 Frame Grab04 Frame Grab05 Frame Grab06 Frame Grab07 Frame Grab08 Frame Grab09 Frame Grab10 Frame Grab11 Frame Grab12 Frame Grab13

— · —

A few transects later

We have now been successfully sampling the Ligurian current for the past three days!

Of course there were still a few bumps in the road. Despite our efforts to dry the inside of the camera pod of ISIIS, which took in a little sea water on Sunday, condensation was still forming on the lens when ISIIS was in warm surface waters, obscuring the images. But with a more intense cleanup of the pod and optical system, and with the help of the crew's hairdryer (!) we managed to dry it completely and it has worked beautifully since.

We could not communicate with UVP and ISIIS simultaneously, so we had to devise a startup sequence that would allow us to set UVP up before we started communicating with ISIIS. This eventually worked and we could deploy the ISIIS+UVP (now happy) couple for a few days. However, we then realised it was a much more intense deployment schedule than what is usual for these instruments. We deployed them for over 14h straight, with pauses of only a couple hours between deployments, when ISIIS had been used for a maximum of 8h and UVP profiles are usually not longer than 5 h. This was taking a toll on the gear and we were loosing bolts and nuts here and there. We decided to take out the UVP from inside ISIIS to avoid damaging the instruments.

En Route Sunset Net Panoramic Isiis Dry Lab Dry Lab Pano

We still have a few 20 miles transects with both instruments taking images, all sensors working and complemented by the ship's data collection at the surface. By interpolating and plotting the hydrological data collected by ISIIS in real-time, we were able to tell when we crossed the front and to pay attention to the differences in the biology between sides of the front, since ISIIS images are displayed live while sampling. Here are a few rough interpolations of the salinity, fluorometry, and oxygen across the frontal structure. We had a well defined front with a thin surface layer. The biological communities looked very different on both sides of the front from our sneak peak to ISIIS data. Now we need to proceed with the analysis!

Salinity Fluoro Oxygen

— · —

First ISIIS deployments

Monday, July 22 marked the fifth day of the cruise and we felt ready to give ISIIS a go in the water. In the process of calibrating the camera before leaving Nice, we realized that the images seemed a little too dark. We then checked everything – the line scanning rate, the camera software, and then the camera pod itself. Upon opening it, saw that the camera pod was flooded from our 2 m test dunk in Nice harbor the previous evening. Good thing that the water was only minimal and did not damage the equipment – and, if we had not done the test dunk the previous night, and if we had not noticed the slight abnormality in the image darkness, we would have tried to run ISIIS on a regular transect (to 100 m)… and had been completely screwed.

Leaving Nice Isiis Uvp Light Test

After a bit of scrambling to dry out the interior of the camera pod, we take off for test runs in Monaco waters. We had to sample in Monaco on Monday because the French Navy had closed off all French waters for three days. However, the thin strip of Monaco waters we were able to sample in cut perpendicular to the Ligurian current, so we were able to get roughly the same kind of transect that we would have sampled had we been able to adhere to our original plan. We finished Monday’s sampling by heading to the BOUSSOLE point at midnight to start our regular transects. The transect between Nice and the BOUSSOLE point has been studied by LOV for quite some time, using both ship cruises and remote systems such as gliders. It is therefore well known in terms of the physics and allows us to build on this knowledge.

Isiis Deployment 1 Isiis Deployment 2

— · —

Setting up ISIIS

Our first challenge upon receiving the ISIIS container was the winch. We typically use a University of Miami winch for ISIIS because it is already equipped with a fiber optic cable and appropriate connectors for communicating with ISIIS. The ship did not have the appropriate hydraulic connectors for the winch, so we had to contact some other specialist suppliers who said that, since it was after work hours on a Friday, we could either receive the hydraulics in Nice on Tuesday (way too late!), or we could go to their shop, 45 minutes north of us, on Saturday morning. We chose the latter option and Jean-Olivier drove up in the mountains north of Nice, with the chief mechanic of the ship, to come back 2 hours later with the proper connectors and hoses… and a big smile on their faces.

Installing Winch

The problematic winch connectors

Meanwhile, we unpacked the main ISIIS computer and discovered that it would not turn on properly. The computer would power on but went immediately into a Startup Restore and never started up completely. This could potentially be a huge problem – without the main ISIIS computer, we would not be able to communicate with ISIIS at all. Resolved to solve the problem quickly, Cédric took apart the insides of the computer and discovered the culprit was a cable that had come detached. A cable that went to the CD-ROM drive, of all things. But he plugged the cable back in and the whole system powered up beautifully. Voilà! A simple solution!

… Only that when we powered up the computer, we discovered that the two main programs for communicating with the ISIIS mainframe and camera were missing. They were nowhere to be found. Not in the Program Files, not in the Recycle Bin, not anywhere on the computer. After a lot of tinkering and asking our best friend Google, it appeared to be due to the Windows 7 Startup Restore, which will delete all new executable files on your computer since the previous system backup, which evidently happened prior to the installation of these two crucial programs. All that without a hint of warning of course. Genius. Grrrrr…

We did not have independent copies of these programs, as they came came pre-installed on this system we ordered from Prime Test, the company that built the software for us. And we could not get in contact with them – they were in Boca Raton, Florida, and, at the time, it was 2 am on Saturday morning. We sent an urgent email, left voicemails and texts… but just had to wait. Thankfully, they responded quickly and after a whole night of cloning hard drives (as failsafe), restoring old versions of the system and reinstalling the ISIIS programs, we could get it to work.

Setting Up Computer

A looong night setting up the computer

Those computer problems ended up costing us over a day. We had initially anticipated that set up would take one day, but it ended up taking both Saturday and Sunday. Through the set-up, we could observe the dynamic duo of Jean-Olivier Irisson (informatics) and Cédric Guigand (mechanics) tackling all of our problems, one by one. This pair needs to work together more often. We solved the UVP communication issue (faulty cable), the ISIIS - UVP power mismatch issue (discharge the UVP to the ISIIS power levels), the lack of GPS signal from the ship (reroute through another GPS system onboard, thanks to another miraculous intervention by Grigor Obolensky, late on a Sunday night. Thank you again Grigor!), and our diminishing supply of wine and chocolate (send Jessica on a purchasing mission). We slowly checked off items on our Hit List and ran a successful test-dunk of ISIIS in the Nice harbor.

The Hit List Isiis Uvp Close Isiis Test 1 Isiis Test 2 Isiis Test 3 Isiis Test 4 Isiis Test 5 Isiis On Board Nice At Night

— · —

VISUFRONT has started

Thursday, July 18 marked the first day that we had ship time aboard the Tethys II. Tethys II is a CNRS vessel, serving multiple institutions' research and teaching activities in the Mediterranean. This year, this busy vessel only has 15 free days out of 356. Three UPMC teaching courses use the Tethys II (two Masters courses and one undergraduate course), as well as a whole suite of researchers. We had the fortune of securing ship time for 13 days for the VISUFRONT cruise. Our first task upon arriving in the morning was to go through the safety briefing, which included proving our competency in donning on all the safety gear, including the full immersion suit.

Due to the looming thunderclouds in the distance and the increasing frequency of lightening strikes, the science team happily went through the safety exercises, thinking – well, better safe than sorry. Shall we also note that at this point, it had not rained in Nice in over a month? What great timing these clouds had!

Lightning Safety Bob Safety Jo Safety Robin Safety Cedric Safety Jessica

The VISUFRONT team showing their commitment to safety (Bob, Jean-Olivier, Robin, Cedric, and Jessica). Marie, from mon océan & moi came for the day to shoot pictures and we thought we would avoid her the embarrassment and not show hers ;)

But wait! More good news. We find out that due to French Navy activities, we would be restricted from sampling in French coastal waters (even beyond the typical naval activity zones) for three entire days during our 13 day cruise: Saturday through midnight Monday, July 20-22. There was only one other option: the small city-state of Monaco, whose narrow strip of waters were not controlled by the French Navy. But we would have to put a proposal in to Monaco and hope that it could be approved by Friday. Furthermore, because of the way that marine research permits are granted, even though we applied for these research permits more than half a year in advance, we would not find out until the week before whether or not we could sample during the next week. The whole cruise could be compromised. But ever the optimist, Jean-Olivier pressed on, assuring everyone it would be fine. Some of us wondered what he truly felt inside…

At that point in the morning, we were out of port, and since ISIIS was still on its way from Spain, we proceeded to sample with a Régent net along a transect from Nice towards the BOUSSOLE point (a buoy deployed by LOV which provides reference data for water-color satellites). The first few nets that we ran did not inspire the group with a whole lot of confidence, as the most interesting things we caught were a bunch of calycorphoran siphonophores, three adult Pelagia noctiluca, the purple-striped jellyfish, and some P. noctiluca ephyrae (young). Says Robin Faillettaz with a crinkle on his nose, "I think I am allergic to Pelagia."

Pelagia Img Pelagia Closup

The evening of the first day found us back in Nice harbor for a couple hours before leaving at 11 pm for BOUSSOLE to sample through the morning along a cross-front transect towards Nice. At each station, we sampled using a Régent net, CTD and the UVP. Vincent Taillandier, Research Engineer at LOV, joined us for the day to run the CTDs.

Net Deployment Net Deployed Bob Looking At Sample Net Sample Uvp Deployment Ctd Deployment

Phronyme 1 Phronyme 2

The only problem was, we could not get the UVP to work. After the first couple stations, we realized the problem was that the UVP had no power. But even with full power, we still could not consistently communicate with it to download the data. We knew that the data was being collected, because 10% of the time, we could actually connect with it and be able to download all the data it had collected. But there seemed to be no rhyme or reason to why it would or would not connect. We would need to contact Marc Picheral, who happened to be on a 6 month TARA cruise in the Arctic. There was an email address we could reach him at – as his ship in the Arctic had satellite internet – but we had no internet. Less than 20 km from the coast of France… We would have to wait until we were back in Nice to contact him.

Cedric Robin Uvp Cedric Uvp

Cédric and Robin trying to understand what is wrong with the UVP

We finished our transect and made a bee-line straight for the Port of Nice, as we had just received word that ISIIS had arrived in France and had gotten picked up by the truck to bring it to Nice. We wanted to meet the truck at the harbor when it arrived, so it would not turn back around and leave. Our 18-meter marine vessel was racing a 8-meter long truck to Nice. Go, go, go.

We arrive in Nice and voilà, the truck is there with ISIIS onboard. At the sight of ISIIS, all of us – particularly Cédric – look anxiously to see what condition it is in after its trans-Atlantic travel. From the surface, it looks good…

Loading Isiis 1 Loading Isiis 2 Loading Isiis 3 Loading Isiis 4 Loading Isiis 5 Loading Isiis 6 Loading Isiis 7 Loading Isiis 8 Loading Isiis 9 Loading Isiis 10

ISIIS and the accompanying gear being loaded on the the ship

We move ISIIS, the winch, and the computers from the shipping container on board the Tethys II. Thanks to Grigor Obolensky, from LOV, who organised everything with the staff of Nice's harbor, this is done in a swifty 30 minutes. To the lay person, nothing looks damaged. But Cedric, with his keen eye, notices that the container floor is littered with screws from the winch and ISIIS. Vibrations from the travel must have been so strong and sustained as to dislodge all these screws. At this point, no one had any clue how bad the damage would be. This was 5 pm on Friday afternoon.

To be continued…

— · —

The ISIIS crisis

The preparation of the VISUFRONT cruise, the main research action of this year's PUF program, has been an uphill battle the entire way. Perhaps we should rename this cruise "The ISIIS crisis: a study of Murphy's Law," because nearly everything that could have gone wrong has gone wrong. To mark the battles that we have had along the way, here we go:

  1. The In Situ Ichthyoplankton Imaging System (ISIIS), the main instrument to be used on our cruise, was shipped from Miami during the first week of June by freight, and was supposed to arrive in France on July 5, and at the latest by July 12, way in advance for our July 18 start date. On July 11, we find out that ISIIS missed its transfer upon arrival in the Mediterranean and would be stuck in Algeciras, Southern Spain, for at least a week. We wouldn't expect it in Nice until July 19 at the earliest. There were no other solutions available for shipping ISIIS for an earlier arrival.
  2. The Underwater Video Profiler (UVP) that we were supposed to be using broke down. It would not be repaired in time for the cruise. In the several years that UVP5 has been in existence, it has not broken down even one time. I guess there must be a first time for everything. We looked into getting a replacement UVP from Marseille, but that took time to secure and someone to go fetch it from Marseille (3 hours away from Nice).
  3. The glider that was dedicated to VISUFRONT also broke down. A new one was being set up by someone who later called in sick. The glider would be ready for the cruise but would not be released in advance of the cruise as we had planned. There is another glider in the water at the moment, so we will have some preliminary data, but not at the temporal resolution we were expecting. This complicates sampling planning because we need to know where the front is located.
  4. Annalisa Griffa's ARGO float would not be usable during VISUFRONT. However, another similar float developed in Villefranche can be deployed, so we would not lose that aspect of the cruise.

This was all happening the week before the cruise was supposed to start. The University of Miami / RSMAS crew all arrived within a day of each other, but from very different locations. Cedric Guigand arrived in Villefranche-sur-Mer from the North of France on Monday, July 15, and then Bob Cowen from Oregon and Jessica Luo from Miami flew into Nice on July 16.

Fortunately for us, Fabien Lombard was already making a trip to Marseilles for another purpose and picked up their UVP for the VISUFRONT cruise, arriving back in Villefranche on the evening of Wednesday, July 17. Also, according to our super freight ship tracker, ISIIS has left Spain and was on its way to France. Things are looking up… For the moment.

— · —

The VISUFRONT cruise

The VISUFRONT scientific cruise is the main research action of our PUF-sponsored program this year. The goal of this cruise is to deploy an array of instruments to study physics and biology in the ocean at the same very high scale, as we initially described in our proposal.

We will deploy the In Situ Ichthyoplankton Imaging System, developed at RSMAS, coupled with the Underwater Video Profiler, developed at LOV. Both instruments take images of the plankton. The UVP focuses on small particles while ISIIS focuses on large, hence rarer, organisms (such as larval fish = ichthyoplankton). ISIIS also collects data about the physical properties of the water and this will be intercalibrated and compared with a CTD and gliders.


Armed with this data-collecting arsenal, we hope to understand how organisms such as fish larvae or jellies respond to their environment. We will focus on a region where physical forcings are strong: the front of the Ligurian current. This current separates coastal waters from more oceanic waters and the combination of the current and the mixing of those water masses makes for a very interesting environment.

As a first step, we plan to sample along transects both across and along the front, to capture the variability in both directions. The we will deploy drifters and floats which will track a parcel of water as it is moved by the current and we will sample this parcel of water repeatedly to see how it evolves through time.

Map Transects Map Drifters

— · —

About Robin

Robin Faillettaz, a PhD student from France, spent a few months in Miami thanks to the support of the PUF. There he worked with senior scientists but also with many of RSMAS' PhD students. Here are the impressions of a couple of them.

Erica — Robin was a pleasure to get to know – he is enthusiastic and smart, and we have many of the same research interests. He was a great help to us during our recent field work – he was willing to work hard and always maintained a positive attitude and curiosity for the world around him. It is great to know that I now have a colleague across the ocean who is asking similar questions in a different ecosystem. I look forward to collaborations for years to come.

Andy — I am a graduate student of Professor Claire Paris who had the pleasure of working with Robin Faillettaz while he was at RSMAS as part of the PUF program. Robin was a quiet, polite, and gentlemanly visitor to our scientific community, but left an overwhelmingly positive impression on all of us. He was an active participant in lab meetings helping us prepare talks for broader dissemination, and gave practical advice on figure preparation. Robin also had a keen interest and photographic eye for the local wildlife and unique flora and fauna of South Florida and the Caribbean as evidenced by his enthusiasm during journeys out to the Everglades and in the Bahamas. He had a playful sense of humor and tried to teach some bullheaded American's French, while his grasp of English steadily improved during his tenure with us. Robin was a great visitor to our lab, and I look forward to having him come back again some day.

— · —

Caroline Ton's internship at RSMAS

Caroline Ton's thesis involved conducting an analysis of how the movement of spiny lobsters between fished and unfished zones can bias the estimates of abundance and fishing mortality rates from fisheries data. We used an individual-based model (IBM) of lobster movement built by Ph.D. student Bill Harford to generate simulated fisheries “data” under a range of scenarios about movement of lobsters, and the distribution of fishing effort. Caroline then applied a fisheries stock assessment model to the “data” generated by the IBM to determine how well the true abundance and true fishery mortality rate could be estimated. Interestingly, she found that abundance (in the fished zone) was fairly well estimated even with high movement rates, but that the fishing mortality rate estimates were quite biased with large amounts of movement. Her results will help us estimate how much bias there may be in our estimate of an appropriate sustainable catch level of spiny lobsters at Glover’s Reef.

— · —

The RSMAS experience

I'm a french PhD student working on larval fish distribution, dispersal and behaviour in the Mediterranean Sea. As you may know, there is no better place than RSMAS to improve my expertise on that subject. With that purpose, I just spent two and a half months in that beautiful and brain stimulating place! And this was made possible by the PUF project that supported my travel expenses and housing!

I had the chance to learn about the three main topics of my research, starting on the first day of my arrival with larval fish distribution. I first participated ("observed" would be more adapted) in the coupling of UVP and ISIIS with Jean-Olivier, Marc and Cédric, that will be produce a brand new in situ observation tool which will be used for the VISUFRONT cruise in a few weeks.

After the french team went back to France, I was introduced to the "french crew" of RSMAS with whom I spent most of my lunches and wetlabs, tanning (burning) on the terrace of The Commons.

I started working on the main objective of my stay in RSMAS: using the Connectivity Modelling System (CMS), a dispersal model that was developed by the Physical-Biological Interactions Laboratory, under the supervision of my Ph.D co-advisor, Pr Claire Paris. The major advantages of this model are the behavioural components implemented that permit to model active particles. During my stay, I adapted the CMS to oceanographical data from the western Mediterranean Sea, generated by two different physical models (Nemo and Mars3D). Here is an example of a simulation with passive particles over 45 days and 16 different releasing locations.

Robin Cms Simulation

Now that I'm able to run the CMS in this region, I will need to collect behavioural data in order to implement realistic behaviour in the model. And my stay in RSMAS offered the opportunity to learn how to do so!

Indeed, I participated in a two weeks field trip using the Directional In Situ Chamber (DISC), which was also developed in RSMAS, and allows to determine orientation behaviour in larval fish, one of the major factor influencing their dispersal. Next year, I will be doing the same experiment, following the same protocol, offshore Villefranche-sur-Mer. Again, this was precious knowledge that I will be bringing back to France!

As icing on the cake, I ended my stay with the Larval Fish Conference where I presented a poster and during which I met several leading figures of larval fish science. I had very interesting interactions with them about larval fish distribution, i.e. for the VISUFRONT survey with ISIIS, dispersal modelling and behavioural capabilities of fish larvae.

I can't write about everything and everyone I met, that would be too long, but as a short conclusion I'd like to say that I had a wonderful and productive time in Miami. I would also like to thank everyone who has been very helpful and nice to me, spending time trying to answer my numerous questions (special thanks to Pr Paris's lab PhD students for the CMS and the rest), sharing ideas and culture. I hope I will come back soon!

Merci à tous et merci le PUF !

Robin1 Robin2

— · —

Integrating UVP and ISIIS

The main goal of our last week of work in Miami was the physical an electronic integration of the Underwater Vision Profiler (UVP) into the In Situ Ichthyoplankton Imaging System (ISIIS). Marc Picheral developed the UVP in Villefranche and it is now sod by the company Hydroptics. It is becoming a standard for the measurement of the vertical flux of particulate organic mater in the ocean. The UVP focuses on imaging small and abundant particles and planktonic organisms. ISIIS has been developed by Cédric Guigand, in Bob Cowen's lab, and the company Bellamare. Its focus is rather on larger, and rarer, organisms such as fish larvae and larger jellyfishes. The integration of these two instruments will therefore allow us to study the distribution of two main compartments of the plankton synchronously. Exiting data to look forward to (and a lot of it). Here are Cédric's impression after this week of work with Marc as well as a few pictures of the two beasts being joined together.

We had a very productive time with Marc Picheral and Jean Olivier Irisson. The UVP training went very well as well as the integration of the UVP into the ISIIS vehicle. After 3 busy days under the supervision of Marc we had the all integrated system working on the bench, now I can't wait to put our UVP/ISIIS in the waters offshore Villefranche this summer!

Uvpisiis1 Uvpisiis2 Uvpisiis3 Uvpisiis4 Uvpisiis5 Uvpisiis6 Uvpisiis7 Uvpisiis8 Uvpisiis9 Uvpisiis10

— · —

Building bridges

I spent a busy week in Miami meeting with people and building on the collaboration sponsored by the PUF.

Together with Marc Picheral and Robin Faillettaz, we interacted with Bob Cowen's group, Cédric Guigand in particular, to integrate the Underwater Video Profiler imagined by Marc in Villefranche within the In Situ Ichthyoplankton Imaging System built by Cédric in RSMAS. You will get to read more on this from Marc and Cédric shortly.

Bob, Robin and I discussed the sampling strategy and the data analysis of our scientific cruise this summer, during which the now-coupled ISIIS and UVP will be deployed.

I met with Claire Paris and her team of post-docs and PhD students. We had long and productive discussions regarding the instrument and software we will use to study the orientation of fish larvae next year. The Drifting In Situ Chamber (DISC) instrument has changed a lot since the last time I used it with Claire and her team have made progress with the software I initially wrote. Now that it has grown so much, we need to re-think it. It will be a busy and exiting time.

I also met with Chris Langdon and we discussed the possibility of a collaboration between his group and Jean-Pierre Gattuso in Villefranche, which the PUF program could sponsor.

On the education side, I had the pleasure to meet again with Arthur Mariano (around a wonderful lunch) and Andy Bakun, who both came to teach in Villefranche. We agreed they would come to give the same lectures next year and I am sure students will benefit greatly from this.

Andy Bakun let me teach a lecture on the response of ichthyoplankton (larval fish) to physical forcing in the ocean, within his "Physical oceanography" class. The short format of those lectures (1h15) was difficult to adjust to for me but I hope it was well received. I, at least, was very pleased to get such a large and interested audience!

Finally I met with Elizabeth Babcock and Martin Grosell to discuss future plans for teaching collaborations, involving statistics in particular. A lot of good ideas emerged and we will be happy if some of them at least come to life through the PUF.

So, overall, a very productive week. I am very glad this program allowed us to do so much. I will finish by thanking Claire who hosted me once again, and Bob Cowen and Su Sponaugle for the wonderful diner we all shared in their house.

— · —

Imaging the ocean

Through the PUF project, I visited the Rosenstiel School of Marine and Atmospheric Sciences to talk about imaging systems for the observation of the pelagic ocean.

I gave a seminar titled "Studying pelagic ecosystem dynamics by in situ observation of plankton and particles size distributions using optical cameras". The summary was:

Quantifying chemical elements fluxes through trophic webs and from the surface to the deep ocean requires the ability to detect and identify all organisms and particles in situ and in a synoptic manner. An idealized sensor should observe both the very small particles and protozoa and the extremely large particles such as aggregates, and plankton. Such an instrument would reveal an astonishing amount and diversity of living and non-living particles present in parcel of water and help to understand their dynamics. It is very important to distinguish particles nature (living, non living, organic, minerals) because it has an impact on elements pathways within trophic webs and on vertical fluxes. Unfortunately past sensors did not achieve this goal easily because of their inability to determine particles nature or to be deployed in a synoptic manner. However, recent technological developments now allow better measuring in situ particles and plankton optical properties and size distributions in a way that synoptic surveys are possible. Using recent examples from the literature, my presentation deals with particle and plankton size distributions to show how they help to understand the processes responsible for particulate organic carbon attenuations with depth and the impact of mesoscale hydrodynamics on particle and plankton accumulation or dispersion. I will present the future of imaging technologies to be mounted on autonomous vehicle in a way that coastal or open seas may be monitored using gliders and profiling floats (ARGO floats). Finally, I will suggest how these new data sets could be integrated into size-structured mathematical models of biogeochemical fluxes.

During my stay, I also had two meetings, one with Bob Cowen and his group and one with Claire Paris. The first one was about image recognition, the second was about database and data organization.

We agreed that imaging the pelagic ecosystem needs to be organized in a way that data can be inter-comparable and available easily for collaborations among scientists and also for educational purposes. Probably each system should operate on its own way (including web based application for image analysis and storage) and then there should be a web based application able to cope with the different systems. We will continue to collaborate (in the next weeks) to propose for next ASLO-AGU meeting in Hawaii a workshop on imaging plankton.

Here is a picture of me with Bob Cowen's group. From left to right: Cedric Guigand, Jessica Luo, Bob Cowen, Lars Stemmann, Adam Greer.

Lars In Miami

— · —

Five weeks in Villefranche

I would like to thank the faculty, students and staff of the Ocean Observatory of Villefranche for the opportunity to study and work at the Lab for five weeks, particularly the instructors of the Exploratory Multidimensional Analysis in Environment (AME2) course, Jean-Olivier Irisson, Sakina-Dorothée Ayata, and Stéphane Gasparini, as well as the numerous other scientists I had the pleasure of interacting with: Marc Picheral, Fabien Lombard, Lars Stemmann, Martin Lilley and Robin Faillettaz.

I stayed at the Lab between January 7 and February 9, 2013. During the first three weeks, I took the AME2 course, which covered topics such as constrained and unconstrained ordination, time series, clustering, and discriminant analyses. The course mostly utilized the statistical programming language R, but also other statistical programs such as TANAGRA, PATH and SYSTAT. The unofficial textbook for the course was Legendre and Legendre’s Numerical Ecology (1998 and 2013). Like Erica and Dan commented, the three week course structure is very intensive, but taught extremely well. I appreciated the opportunity to be completely immersed in the subject matter, to learn useful techniques that are not commonly taught in the US (e.g. correspondence analysis), and the introduction and experience working with R. For me, the class was most valuable as a broad introduction to multivariate statistics that gave me the tools to delve more deeply into other specialized and derivative methods, many of which are based on these core statistical tools (PCA, CA, RDA, etc). Being able to now decipher Legendre and Legrendre’s Numerical Ecology is alone worth the three weeks of class, not to mention all the programming tools that we learned.

The crème de la crème of my stay was actually the two weeks following, in which I stayed at Oceanography Lab of Villefranche (LOV) to work with Jean-Olivier Irisson and applied the techniques and tools I learned from the course to start analyzing data for my PhD. At the same time, I also worked with Marc Picheral to learn how to use ZooProcess, a program designed to process and analyze in situ images of plankton, and evaluate how well ZooProcess could be used on data from the In Situ Ichthyoplankton Imaging System (ISIIS), an imaging tool I am using for my dissertation. This was a very productive time for me, and I especially enjoyed the exchange of ideas, perspectives and expertise with the scientists in the LOV plankton team, many of whom work on topics similar to my research interests.

Villefranche-sur-Mer is a beautiful place to be in the wintertime, and in my free time, I enjoyed visiting Nice, the Southern Alps, Monaco and running along the hilly and stunning coastline of the Côte d’Azur.

I am looking forward to this continued partnership between the two institutions and hope that the exchange of students, researchers and faculty will lead to many more productive and enriching collaborations. Thank you to PUF for this funding opportunity and especially to Jean-Olivier Irisson for his time.

jessica0 jessica1 jessica2

— · —

New location, new analysis techniques

My time at OOV was memorable and worthwhile, not only because of the beautiful location and a welcome change of scenery compared to Miami, but also because of the excellent training we received in the Multivariate Statistics course. I was impressed with the quality of the teaching and was happy with the choice of topics that were taught. Some methods I had heard of, but never tried, and other methods were completely new. I am excited to begin to apply these new methods to my PhD research. Taking the course in a 3-week time span was challenging, but I think it worked well to be 100% focused on one topic for a short period of time, rather taking a whole semester to learn the material. I was also happy to spend some time learning how to use R, a programming language that was completely new to me.

The facilities at OOV are very nice, and it is a real treat to spend time on such a beautiful coastline. Day trips to Nice and Monaco are very do-able and not expensive. Having the weekends off was wonderful, not only to have time to study but also to have some time to explore. For future students, I highly recommend exploring the hills above Villefranche (there is a beautiful castle up on the hillside with gorgeous views), and also enjoying some French food at the restaurants in Villefranche and Nice.

I am very grateful for this opportunity. Thanks, PUF and OOV!

Erica2 Erica3 Erica4 Erica5

— · —

Multivariate Stats in Villefranche - Multiple Descriptors Correlate with a Great Time

Villefranche is that quiet, beautiful Mediterranean town that you know you have to visit someday, and the Ocean Observatory of Villefranche-sur-Mer (OOV) is nestled right in the heart of it. Similarly, the multivariate statistics course we've taken over the past few weeks (AME2) is the course that every marine ecology or oceanography graduate student knows will be indispensable to their career. The teaching of the course was truly superb – they even managed to teach me these techniques, believe it or not – and the application of theoretical techniques on representative ecological datasets using R statistical packages provided me with tools I simply was not aware of before. The OOV masters students are driven, studious and friendly, and made the class not only competitive and stimulating, but also memorable and fun. It's easy to become so consumed by the material that evenings and weekends are spent experimenting with your newfound statistical prowess, but don't forget to go for a hike, check out Nice, or maybe even take a day trip to the nearby French Alps or Monaco. A truly memorable experience, indispensable information and an incredible opportunity. Thanks OOV!

Here are a few pictures of Villefranche and Nice which I took during my stay.

Dan1 Dan2 Dan3 Dan4 Dan5 Dan6 Dan7 Dan8 Dan9

— · —

Multivariate stats class now international

The multivariate stats class of Villefranche (AME2) was the last one to be taught in French. Not any more. This year, Stéphane Gasparini, Sakina-Dorothée Ayata and myself switched to English because three students from RSMAS were coming to take the class. We took advantage of this change to modify the content slightly too. Over the course of three weeks, we covered ordination methods (PCA, CA and MCA), clustering (hierarchical and K-means), data series analysis, as well as an introduction to various statistical software including the R language. But we also added MDS, RDA and variance partitioning, hence fulfilling common requests from previous students.

Erica, Jessica and Dan seem to have enjoyed the class and you should be able to read their impressions soon. Jessica is staying in Villefranche for two more weeks and she will be putting this new knowledge to use immediately, with the analysis of her PhD thesis data.

Here are pictures of this year's AME2 class, on the sea-side of the Galeriens building.

Ame2jan1 Ame2jan2

— · —

Six weeks of modelling and a bit of fun

Overall, we found the Marine Environment Modelling course to be very interesting and informative. We enjoyed the overall content of the course and the experience was very rewarding. We have never had a class that really discussed the formulation of models, so going through the process really provided a feel for some of the assumptions and considerations that go into it. In particular, we were really grateful for the chance to build and learn about the NPZ models as we hear a lot about them in ecosystem-based fishery management, but rarely delve into the specifics or inner-workings. Essentially, they're usually just considered in a "black-box" context which is really unfortunate if your goal is to consider the entire ecosystem. However, it was easy to see how each model we addressed could be applied in the field (bioenergetics, IBMs, etc.) and it was great to receive some background into how these models may be formulated.

The pace of the course took some getting used to and it was somewhat difficult to keep all of the information in mind. The last week of class, while studying for the exam, we had completely forgotten some topics that were discussed earlier in the course! But, while it was very intensive, we were definitely capable of keeping up with the workload so it wasn't unreasonable.

We liked how the daily lessons were designed: lectures in the mornings and labs in the afternoon. We found it very difficult to pay attention to another round of lectures in the afternoon, so we were quite happy when we were instead given a lab and set off to go forth and code.

All of the people were great. Our professors were passionate for the topics that they covered and were approachable. They also made themselves available for further help outside of the classroom. The students welcomed us as if we spoke the language. We have a lot of good memories with the students (from various dinners to trips into the surrounding towns) which really helped release some of the stress from the intensive workload. Even the various staff members of the buildings were friendly.

We also enjoyed residing at the O.O.V. station. The rooms were very comfortable, and we loved falling asleep to the sounds of the waves as well as waking up to watch the sunrise across the bay (what could be more relaxing than that). Although bathrooms and showers were shared, they were kept very clean. Above all, we were very appreciative of having access to a kitchen and laundry room throughout our stay.

Here are a few pictures to share our experience. Together with us, they feature Jean-Olivier Irisson (PUF project's coordinator), Lars Stemmann and Fabien Lombard (the Modelling course supervisors) and some of the other students.

Holly Matt00 Holly Matt01 Holly Matt02 Holly Matt03 Holly Matt04 Holly Matt05 Holly Matt06 Holly Matt07 Holly Matt08 Holly Matt09 Holly Matt10 Holly Matt11 Holly Matt12 Holly Matt13 Holly Matt14 Holly Matt15 Holly Matt16

— · —

Arthur Mariano's impressions

I would like to thank the Observatoire Océanologique de Villefranche sur Mer for providing me a stimulating research and teaching environment during my November visit. The help, the good energy, and the hospitality of Jean-Olivier Irisson is very much appreciated. I really enjoyed my lunchtime conversations about research, oceanographic courses, and the skill set required of students to do cutting edge research. Your modular teaching approach containing both theoretical and practical components, such as research projects, requiring coding and numerical computations, is very effective. I think that it is a great idea that more physical oceanography is being introduced into your curriculum.

The best part of being a professor is interacting with the best students and the students in the program are excellent. I hope I conveyed to the students the importance of using the Lagrangian viewpoint for exploring the ocean and its biology, as well as, the importance of mathematics for analysis and modeling. Please email me any questions about my lectures or about your research. In particular, I enjoyed my conversations with Robin Faillettaz about his research and for the opportunities to get out on the water and sample the bay.

Besides all of the exciting science going on, the local region is beautiful and every meal was superb. I look forward to future collaborations with the Observatoire Océanologique de Villefranche sur Mer, its faculty, and the students. Cheers,

— · —

Arthur Mariano is in Villefranche

After Andy Bakun in September, Arthur Mariano travelled from RSMAS to Villefranche-sur-Mer. Pr Mariano came for a week to teach and discuss research. He gave three lectures: one to students in the Oceanographic Instrumentation class (Lagrangian exploration of the ocean), and two to students in the Marine Ecosystems Modelling class (Lagrangian data analysis and Lagrangian modelling and data assimilation). Through a research seminar, he introduced his point of view on "Forward and Inverse Lagrangian Prediction" to the research and teaching staff of the LOV. In between all this, Pr Mariano took the time to discuss his research and his experience in teaching physics with the staff of Villefranche sur Mer and the students. Here are a few pictures during a lunch break discussion with (from left to right) Robin Faillettaz, Jean-Olivier Irisson, Lars Stemmann and Louis Legendre, as well as with the students he taught, in the modelling and instrumentation classes.

mariano1 mariano2 mariano3 mariano4

— · —

Students impressions about Andrew Bakun's lectures

Professor Bakun's classes were very interesting and rewarding. They allowed us to review the complexity of the marine systems and understand their flexibility. Oftentimes, when acquiring knowledge, we tend to think that processes are linear and many concepts are learned as facts. But indeed, life is intriguing!

In these four classes, the concept of systems was re-evaluated giving a more holistic view; while referring to different examples, Pr. Bakun managed to explain the relationship between physical (eg. eddies) and biological components (eg. fish larvae); he added on the complexity of the relationships that could occur. These lectures also unraveled the surprising adaptability of some organisms, for example the bluefin tuna. Overall, the professor provided us with great ideas for our future research and how to approach scientific problems without forgetting the importance of thinking globally.

— · —

Andrew Bakun's impressions

It was my great pleasure to visit beautiful Villefranche during the week of 24-28 September and to present lectures at the Observatoire Océanologique. My visit was extremely pleasant and satisfying. I was extremely impressed by the interest and energy of the students, and I dearly hope that they, in turn, might have been nearly as impressed by my presentations which introduced and explored a theme of 'marine ecosystems as complex adaptive systems'. All in all, I found the entire experience to be highly enjoyable and stimulating. I wish to thank Jean-Olivier in particular, who coordinates the program on the French side, as well as all colleagues I met there, including my very old friend, Louis Legendre. I truly hope it might be possible to return to Villefranche next year for an opportunity to repeat the experience.

— · —

Final cruise dates

The scheduling of the oceanographic cruise for our research project around frontal dynamics is now finalized. We will spend 13 days on the N.O. Tethys from July 18th to July 30th 2013. Now we can prepare the sampling plan properly; and this will likely be done in a very positive atmosphere because we should be able to partner with other European institutions to give an even larger international dimension to the project… and spend more time at sea!

— · —

Andrew Bakun is in Villefranche

Andrew Bakun flew into Nice on Saturday, Sept 22nd. After a nice week-end, an intense week of discussions and teaching started. He presented a seminar titled "Greenhouse gas, upwelling favorable wind, and the future of coastal ocean upwelling ecosystems" on Tuesday. Unfortunately the current directors of the lab and the observatory are both away for the week but we had a great lunch with Louis Legendre, the former director of the Laboratoire d'Océanographie de Villefranche. Pr Bakun then gave four lectures, on Wednesday and Thursday, trying to instil in the young minds of students of the OEM Master that marine ecosystems are complex adaptive systems. Finally, Friday should be a day for discussions, in the lab and at a restaurant.

bakun1 bakun2 bakun3 bakun4 bakun5 bakun6 bakun7

— · —

Ten reasons to go to Nice

As the first people from RSMAS are travelling to Villefranche-sur-Mer, Air France magazine has a timely piece titled "Ten reasons to go to Nice", written in French and English. Nice is just next to Villefranche and these suggestions should help fill in the week-ends.

10 Reasons To Go To Nice

— · —

Ship time granted

Our research project around frontal dynamics is centered around an oceanographic sampling campaign in the Ligurian sea. So we need a ship. In France, the operation of oceanographic vessels is centralized and handled, partly, by the CNRS. To get a ship, research proposals are submitted and ship time is allocated based on the scientific merit of the projects and their feasibility. We are delighted to report that we have just been granted the 13 days we asked for on the N.O. Tethys.

The decision letter highlights some weaknesses in the proposal of course, which we will correct, but the campaign has been provisionally programmed from July 11th to July 24th 2013, and this is great news.

Nest step: gliders!

— · —

Email announcement

The following email was sent today to all staff members and students of OOV and RSMAS as well as to the international studies office of UPMC and to the directors of the Oceanography Master of UPMC.

Hello everyone, Bonjour à tous,

Nous nous en excusons mais les communications autour de ce projet, commençant avec cet email, seront faites en Anglais uniquement, pour plus de simplicité.

We are very pleased to let you know that a joint Partner University Fund ( project between the Rosenstiel School of Marine and Atmospheric Sciences (RSMAS - and the Ocean Observatory of Villefranche (OOV - has just been funded! This project will support and promote education exchange, research collaboration and technological innovation between RSMAS and OOV. This initial funding is focused on the study of "Physical-biological interactions at mesoscale in the ocean", though the development of future topics is encouraged. Indeed, this grant is for a three year period but should serve as the basis for a longer term relationship between our two institutions, which have much in common.

Information is available on the project’s website: and here is a quick summary.

This grant will:

  • allow students to take classes and spend internships at both institutions; the intent is that 3 or more students will travel to the partner institution each year;
  • support travel expenses of professors and students between Villefranche and Miami (air fare and living expenses) for teaching and taking classes;
  • enhance opportunities for applications to further grants dedicated to the travel of PhD students from the US to France (Chateaubriand scholarships) or from France to the US (Fulbright scholarships);
  • greatly facilitate co-supervision of PhDs (co-tutelle arrangements), even for already on-going PhDs;
  • provide support for two joint research projects, regarding the description of bio-physical interactions at very high resolution along a front (year 1) and the in situ study of the behavior of planktonic organisms (year 2).

This email announcement serves to both introduce this opportunity and to point to required action for participation. In the short term, we need to:

  • organize the trips of professors and students wanting to be involved in classes at OOV for the 2012/2013 Academic Year. Classes last from 3 to 6 weeks and topics span pelagic ecosystems, operational oceanography, chemical pollution, modelling, GIS, satellite imagery and multivariate statistics. See for more information.
  • collect internship opportunities at RSMAS for OOV Master students (5 months, from Feb to June 2013). Students will have advanced academic training in oceanography and will be funded for their trip. See for more information.

If a selection among student applicants is necessary, it will be based on academic merit and standing (grades at previous exams, specified milestones met, etc.), pertinence of the course/internship in the thesis project, and relevance of the subject to the theme of the partnership. The selection committee will comprise the project coordinators and the leaders of research projects or of teaching units when appropriate.

Please spread the word and get in touch if you are interested. We look forward to a fruitful collaboration!

The project coordinators,

Jean-Olivier Irisson, OOV
Martin Grosell, RSMAS
Robert K Cowen, RSMAS

It's started!

— · —

100% funded!

We received the official decision letter from the executive director of the Partner University Fund. Eleven projects were selected this year. The very good news this letter carries for us is that the full amount we asked for in the grant proposal was allocated. This amount represents a bit less than 30% of the cost of the project. The rest corresponds to salaries or in kind money that has already been raised. We are therefore in a position to carry out the projects we envisioned completely.

We thank the grant review committee and the steering committee for their work.

— · —


We received the good news on July 3rd: the joint project between the Ocean Observatory of Villefranche-sur-mer and the Rosenstiel School of Marine and Atmospheric Sciences has been selected for funding by the Partner University Fund. The results are now officially announced on the fund's website.

We do not know know the amount of funds awarded yet, but we are very thankful and honored to be among the (very short) list of projects supported. We look forward to a very fruitful collaboration. The next three years will be exciting!