In this perspective in Nature Microbiology, researchers lay out strategies for better understanding of the ocean microbiome. For Nature Methods, I recently did two stories about ocean research, in particular about the ocean microbiome and the ocean virome. You can find the pieces here: Why the ocean virome matters and Trawling the ocean virome.
As Chris Bowler explained--he is with the Institut de Biologie de l’École Normale Supérieure-- viruses control population numbers of organisms in the ocean they infect, they move genes around, thus “lubricating the ocean.” They contribute to biogeochemical cycles of the minerals carbon, nitrogen and phosphorus that all life depends on.
Bowler is scientific director of the Tara Oceans consortium, which involves many organizations around the world. He was scientific coordinator of the Tara Oceans expedition, which produced copious data about the ocean. an expedition is currently underway called Mission Microbiomes.
A team of scientists recently explored how one might assess the biosynthetic potential of the ocean microbiome at the global scale. They integrated ocean microbial genomes to set up a phylogenomic and gene functional database. As they point out in their paper they mined this database and "uncovered a diverse array of biosynthetic gene clusters (BGCs)." You can find the resources they present here and their Nature paper here.
You do not necessarily have to be the ocean-faring type to analyze data from ocean expeditions. As ETH researcher Shinichi Sunagawa, who is corresponding author on the afore-mentioned Nature paper, pointed out to me, that Tara Ocean's data troves can be found for instance, in the European Nucleotide Archive (ENA), Pangeaea, Cyverse, iVIRUS and on Genoscope.
I reached out to the foundation to find out more about what it does. Here is a conversation with Romain Troublé, executive director of the Tara Ocean Foundation. You can find this podcast, for example, on Apple podcasts, Google podcasts, Spotify and Amazon Music. And right here. A transcript is pasted in below.
Note: These podcasts are produced to be heard. If you can, please tune in. Transcripts are generated using speech recognition software and there’s a human editor. But a transcript may contain errors. Please check the corresponding audio before quoting.
Speaking for the ocean: A conversation with Romain Troublé
We have to speak for the ocean because nobody speaks for the ocean in fact.
That’s Romain Troublé, executive director of the Tara Ocean Foundation, or since it’s based in France, Fondation Tara Océan, which is an organization devoted to the ocean and ocean research.
You will hear more about Romain Troublé and from him in this podcast. And about ocean research, the boat Tara and a two-year project currently underway called Mission Microbiomes and how this is connected to the fashion house agnès b.
Hi and welcome to Conversations with scientists, I’m Vivien Marx. Just briefly about this podcast. For my stories, I interview scientists around the world and these podcasts share more of what I find out and hear. I recently did a story on ocean research, in particular the ocean microbiome and ocean viruses. Links to the pieces in Nature Methods and on the Nature.com blogs are in the show notes. Why the ocean virome matters and Trawling the ocean virome
The stories look at the work ongoing in a number of labs that focus on the difficult tasks of assessing the ocean’s microbiome including the ocean’s viruses.
You have perhaps heard of the gut microbiome, the many microbes in our gut that play a large role in maintaining our health. The ocean microbiome plays a similar role in our planetary health. A massive research effort is underway to better understand the roles the ocean’s microbiome plays. Here’s Romain Troublé:
Romain Troublé [1:30]
I really see an analogy, although we cannot compare the two microbiomes. Our microbiome in our guts, we don’t have it we do not live, we cannot live without these people. I like the analogy with the ocean, the big equilibrium of the planet depends on the microbiome in the same way we depend on our microbiome. The analogy is important for people to understand, because the ocean is not made of whales and dolphins. The ocean is 60% made of microbes and they are doing many things for us every day. How can we share this story that when you see plastic in the ocean, chemicals, on warming, you have an effect on something that brings you life and something that make the planet a living planet. I think this is very important for people to understand.
Microbes may be tiny but they are mighty in the way they are involved in regulating ocean ecology. Microbes affect the health of our planet because, for example of the role they play a role in food webs. Since we like breathing, we can thank the ocean’s microbes for that. And there are also viruses in the ocean that matter, in good ways.
Romain Troublé [3:00]
Viruses they are part of the puzzle, one of the jigsaw pieces. They work together with many others and they produce what we need as living organisms on the plant. It’s magical, it’s pretty crazy, all these people are moving, moved by the currents. Some days they are South African, other days, they are Namibian. They don’t really care about the limits mankind has put into place. Despite all this movement, this dynamic, they keep doing what they do, producing oxygen, they keep storing carbon dioxide. This is a great mystery of the century, how can we decipher how these microscopic people is behaving.
It's logistically hard and expensive to study the oceans’ microbes. You need to collect samples, many samples of, for example, plankton and other marine microbes. And take the samples to the lab and analyze the genomic information you collected about microbes in those samples. You have to tease out which pieces of genomic material are in the samples and which organisms those snippets are from. That’s genomic detective work on a gigantic scale.
First and foremost in this work, you need a boat. And in this case there is a schooner called Tara, which has a crew and which travels the world’s oceans. Scientists come on board for weeks or months at a time. You will hear more about this from Romain Troublé and what to do if you are interested in coming aboard Tara yourself:
The foundation has many partners and supporters and has run a number of expeditions that have yielded loads of publicly available data. So even if you are not the ocean-faring type, you can look at the data, play with it, analyze it, while sitting high and dry on land.
But it’s not the kind of ocean data you might expect, like tallies of, say, coral reefs or whale populations. The data are about the ocean’s microbes. I asked Romain Troublé, the foundation’s executive director, what fundamentally matters to him about this work.
Romain Troublé [5:15]
We have to speak for the ocean, because nobody speaks for the ocean in fact, with a very humble. Because we are sailors. I’m a sailor myself. The founders are sailors. When you’re a sailor, you’re kind of a humble person, because you know weak and how little you are facing the sea. We’re kind of nothing. We have to be conscious of that. I think that’s something that characterizes a lot about the spirit of this project: low key.
Romain Troublé is a sailor and a scientist. And as a sailor-scientist he wants to help others to study and try to understand the ocean and its microbes. He is motivated by curiosity and his love of the sea.
I think it’s about curiosity. Indeed I used to sail a lot. I used to sail 300 days a year in my life at one stage in bays, across the world. Daily sailing
So as a sailor-scientist, he. Wait he spent 300 days a year at sea?
Romain Troublé [6:20]
300 days a year for two or three years a year, in sports regattas. When we met the scientists who were willing to go and meet the invisible of the planet. I had the background in molecular biology I understood by training, five years, I stopped just before the PhD, I understood kind of what they wanted to do. Although I was not really aware what would be the outcome of it . It was incredible to figure out. When we swim around, what we have around us it’s completely crazy it’s billions of organisms all over the place.
Billions of microbes play roles in all kinds of aspects of ocean ecology and planetary health. There’s lots to decipher and understand.
What caught my eye as I looked at photos from Tara Oceans expeditions is that Tara sails say: agnes b. on it. That’s a fashion brand called agnès b that carries the name of the designer Agnes Trouble. I wondered how fashion is connected to ocean research. As it turns out, the family is keen on the ocean and ocean science Romain Troublé is agnès B’s nephew. France has a big coastline and also a long track record of ocean exploration and research. Romain Troublé reminds me tho that this caring about the ocean is not unique to France.
Romain Troublé [8:10]
No, it’s not French. Although we had famous sailors in the past. It’s not French at all, the French people work in the field, not at sea. Like every human being. If you ask an Islander for the Pacific if he is an ocean man, he will say ‘we are not ocean men’. They care about what they do on land, they don’t like to go to sea much. I think it’s part of a human. I love sailing, there’s no place I am better than when I am on the ocean. The freedom of it. The face to face with nature. Could be hard, can be mild. For the fashion brand it was more the love of the ocean we got from the grandfather, father of the stylist agnès b, who was the father of my cousin Etienne, who was the founder of this project. It’s more a love for the ocean that sent us here, it led my father to sail the Olympic Games two times. It’s kind of a family issue.
A family issue indeed. There’s agnès b., there’s her son Etienne Bourgois who started the project and who is director of Tara Ocean Foundation. There’s Romain Trouble’s father, a sailor and Romain Troublé nephew of agnès b, and who is executive director of the foundation.
Romain Troublé [9:50]
For me the sea is the origin of everything, it’s like the liquid when we are in the belly of our mother amniotic liquid, that is sustaining all life on Earth. It’s the way I see it and I think it’s pretty true. We all come from there. The organisms are maintaining the life we have today as it is. The water, the physics of it, but also the life we have in it. There is a divide between the physical scientist who denies success to the biologist, because biology is not really a science. There is a lot of stories between these two fields.
Some scientists study the physics and chemistry of the oceans and others focus on the biology of the ocean. And between them you can find a cultural divide.
That’s for sure, it’s not a divide, it’s a huge gap.
Now to the practicalities. To do ocean research you need a boat. Tara is a 36-meter long schooner.
Romain Troublé [11:10]
The boat Tara was bought by my aunt agnès b and her son Etienne.
The boat was originally owned by explorer Jean-Louis Etienne. He had naval architects design for his purposes, which was exploration.
Yeah, he was an explorer, he sold the boat to Peter Blake.
Peter Blake, actually it’s the New Zealander Sir Peter Blake, was also an explorer. I say ‘was’ because he was murdered during an expedition in the Amazon. The expedition was focused on global warming and pollution. But then pirates the boat.
Romain Troublé [11:50]
Our planet is not everywhere like the US or Europe, our planet is full of surprises full of people who don’t think the way you think. But also full of people who are starving for living. That can be interested in the money of others. That’s what happened to Peter. People wanted to get some dollars and some watches and get off the boat like that. It was a tragedy because Peter decided to defend himself. His widow Pippa is very keen, she is with us, she is following what we do. I speak to her, she’s very happy of the legacy.
Romain Troublé knew Peter Blake because they both had been sailors.
Romain Troublé [12.40]
I knew him from sailing. Racing against him, losing all the time, I sailed America’s Cup twice against us. and twice he won.
In English you call that a frenemy
Frenemy, well he was a nice guy.
When agnès b and Etienne Bourgois bought the boat, it was, to them, about continuing Peter Blake’s legacy.
Romain Troublé [13:05]
When they bought the boat, they said we want to continue what Peter started, keep talking about the ocean, We want to do some science, as well. Promote science and that’s what we did. The success is here. The papers you saw, they show the excellence is here. I like to say it’s a cool excellence.
The Tara expeditions have generated a lot of data for scientists to analyze and use.
Romain Troublé [13:35]
We have put a lot of data into the game. What is pretty interesting and what is pretty unique is that we have done this for the last ten years with the same approaches. All the data from the plankton in the high seas, from the plankton along the coasts, the reefs of the Pacific.
We have done this over the next ten years, with the same approaches. All the data from the high seas, coasts, from the coral reefs, on the plastic ecosystems, all is intercorrelated. You can ask questions to anything. Billions of questions. It’s what we see in the papers coming out from teams we have never met before and who have new ideas, new questions. That’s completely incredible.
When the boat is at sea, the daily tasks all about sample and data collection
Romain Troublé [14:30]
On the boat, we don’t do research, in fact. On Tara, we don’t do research, we collect. We are collectors, as. Uch as we can. Every day and night. The money we collect from sponsors, private sponsors, we have the obligation to be as efficient as possible. To bring the most data, the best quality data we can. My personal goal.
During expeditions Tara is out at sea for a long time. And it’s 36 meters in length so it’s tight quarters, I asked Romain Troublé what it takes to become part of the crew. People have to be physically and mentally fit.
Romain Troublé [15:15]
People need to be hard at work, it’s repetitive work, always timed work. To have good science, good data, you have to repeat every day, every two days what we did two days before with the same quality. Rigor is one of the very important qualities. And the will to spend life kind of locked down on the boat with other people for a long time. Fit is one thing but also psychologically be happy to share with the others in a small space.
If you are listening to the podcast and want to become involved with these expeditions, there are several ways to do so. Romain Troublé explains.
Romain Troublé [16.10]
They can apply to be sailors. But all the scientific work is done by the labs. And people are brought to the boat by the labs. For the last two years, for the Mission Microbiomes, they never stopped to send people on board.
Also we have artists in residence onboard Tara. We have welcomed so far 10 artists so far, for 3 weeks each ion residence. We have applications, usually 300 applications for 8-10 places. It’s a lot of people who want to come. I think art is really really important
We need art to think the future, we need art ways that we have never thought about. We need utopia to go forward in this world. We underestimate a lot the power of the art to show use new thinking.
Also to reach out to people who never cared about the ocean, never cared about the sciences They care about emotion. It’s funny because many artists come on board to have projects on microbiome or on the ocean. In the end they are so moved by the people, by the microcosmos, microscopic way of being together on a small boat, the adversity. Sometimes they change their work, they work on the people interactions, they are moved the value of this.
The expedition currently underway is called Mission Microbiomes. Since the early Tara Oceans expeditions techniques for analysis have advanced and the plan is with Mission Microbiomes to use long-read sequencing, Hi-C sequencing to capture chromatin organization on a genome-wide scale and the researchers will also be using various types of imaging. The teams are also focusing on microplastics in the ocean.
Romain Troublé [18:15]
Plastic is made of oil, it’s hydrophobic, stick to it in the water. Organisms, pollutants, they are in fact concentrators of pesticides, it sticks to the plastics. It’s kind of an accumulator of chemicals, but also it’s a fantastic substrate for organisms to stick on it, like to a rock on the coast. Sunny place we call it the plastisphere. It’s funny, the plastic is not the same, if you change the plastic chemical, polystyrene or polypropylene, it’s not the same ecosystem. They are specific to the type of plastics.
Mission Microbiomes which has collected a lot of data on the ocean microbiome and on microplastics wraps up this fall and has been ongoing for two years. Tara and the crew have been sailing along the coasts of Europe Africa and South America. Tara has also stopped along the way, for example Dakar, Capetown, Rio de Janeiro, Buenos Aires and other cities, too. When Tara stops, people come on board and that includes policymakers and children and young people. For the younger generations who come on board, the message, says Romain Troublé shouldn’t be one of doom and gloom about the state of the oceans and what might happen to the oceans
Romain Troublé [19:50]
The message that is important to me is the message we bring to the people, not only science, not only knowledge, not only the doom and gloom of pollution and climate change. A lot of anxiety. But I think we should show that there is a way. You can choose the work that’s on the good side of the issue. And to show people if you choose the right side, the right companies who work toward solutions, rather than to other issues, you are going to have a happier life, you are going to enjoy your life in fact. Just in your daily life, choose the right path, choose the positive path and not the negative path. Because the job you do, you can do in an oil company, you can do it in other companies.
What makes people anxious about climate change and all this stuff, is not the climate change itself, it’s the fact that we don’t move to find a solution. This is what makes people Anxious. As soon as you start moving in your daily life in the way you consume, which company you work for. Then you move, then you are not anxious anymore.
We speak to kids now and then. We cannot tell kids “everything is f*cked up, we f*cked up everything. Yeah, we have problems, but we need to work on solutions. 2 degrees will be better than 3 degrees and 3 degrees will be better than 4 degrees. You have to fight for the future you want. The young students, they have the power. If they don’t choose companies who are negative on climate change and all these issues and go to work on the solution-driven companies. The value of a company is the people who make it.
That was Conversations with scientists. Today’s episode was about the ocean microbiome and ocean research and a little about the fashion designer agnès b and her family and their commitment to ocean research. And it was with Romain Troublé, executive director of the Tara Ocean Foundation. And here’s a shoutout and thank you to Camille Lextray from Tara Ocean Foundation who helped me organize this podcast.
And I just wanted to say, because there is confusion about these things sometimes, Tara Ocean Foundation did not pay to be in this podcast. This is independent journalism that I produce in my living room. I’m Vivien Marx thanks for listening.
The schooner Tara (Credit: V. Hilaire, Fondation Tata Océan)