On the hunt for giant microbes along the California coast

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By Jean-Marie Volland

This is a short story of how my wife, my daughter and I, armed with two microscopes, took an RV and went hunting for giant microbes along the California coast.

Before we get there, let me introduce myself and give you some context. My name is Jean-Marie Volland, I am a French marine biologist from Guadeloupe island, a French overseas region in the southern Caribbean Sea. I arrived in California three years ago to join an amazing network of scientists who are interested in big biological questions such as: What is the origin of life? How did simple microscopic cells evolve to large and complex organisms? Do we know all forms of life or can we still discover new lineages? These are really important questions that are not going to get definitive answers for anytime soon, but we have to start somewhere…

Simple life versus complex life

Life as we see it with our human eyes everyday is mostly our pets, our plants, our fellow human friends and family. Add to this, insects, birds, fish, corals, reptiles, snails, worms, and pretty much anything you can find in a zoo or an aquarium and you will have about nothing percent of the entire biodiversity that exists on Earth.

In fact, all these organisms, big enough to be seen with the naked eye, belong to a very small branch of the tree of life we call the Eukaryotes. The most widespread forms of life by far — 99.9% of species — and also the most ancient, belong to two other groups: bacteria and archaea. They are microscopic and relatively simple cells that are virtually everywhere. They are in and on our bodies, in the soil, in the air, and in ponds, lakes and oceans. There is also a big difference between Bacteria and Archaea, and the Eukaryotes that appear to fill our landscapes: that is, the presence of a more complex basic unit of life, i.e., a more complex cell (there are other differences as well, but we won’t go into those details here). Compared to bacterial and archaeal cells, the complex eukaryotic cell safely keeps its DNA — the genetic blueprint for life — in a protected place called the nucleus. It doesn’t matter how small or how large Eukaryotes are, or if they swim or fly or run, they are all made of complex cells.

This is where it gets even more interesting. We know that complex cells emerged about 1.8 billion years ago when two simple bacterial and archaeal cells decided to cooperate and establish a permanent association. This association, what we call a “symbiosis”, created a new more complex eukaryotic cell. To raise the stakes, these complex eukaryotic cells somehow also managed to join together to form highly differentiated structures that we see in eukaryotes but are absent in bacteria, such as bones and hearts and livers. This is the fascinating story of evolution: how did all this happen? How did complex life emerge out of simple life forms?

What exactly happened 1.8 billion years ago and why it happened only once is the million-dollar question that we are just beginning to answer.

Why the giant bacteria?

I know what you’re thinking, this is all great but what does it have to do with the giant microbes from California? Well, here is the connection. Since we cannot go back in time 1.8 billion years ago to study the first eukaryotic cell, maybe we can try to find something that looks a little bit like it in today’s world. What we are after are modern symbiotic associations between simple life forms such as bacteria so we can observe the process as it may have happened billions of years ago.

One place we may find relevant examples of symbiosis is in environments that still resemble primordial Earth, environments that are similar to what happened billions of years ago. These environments are very different than what you and I are comfortable with, they can be hot, acidic and full of strange gases. It is in these environments we can find bacteria that do odd things and grow to giant proportions- such as using the energy contained in chemicals like hydrogen sulfide. Hydrogen sulfide (H2S) is a nasty chemical, and is in fact very toxic to humans, so much so that evolution made us very good at detecting its distinct smell of rotten eggs to prevent us from poisoning ourselves with it. But for some bacteria it is food, and it allows them to thrive and become giants. Bacteria are normally about 0.002 mm long but some of them that grow on hydrogen sulfide can develop into large filaments of several centimeters. These giant bacteria are big enough to host other regular size bacteria and establish a symbiosis with them — this is what we are looking for.

To find these little giants, I normally would have organized a sampling trip with my colleagues. We would have shared a car, booked hotels, and maybe met with a scientist or two at marine biology stations close to sampling sites. But with the Covid-19 pandemic, I had to come up with an alternative. Sharing a car, staying in hotels, or meeting other scientists in labs was not recommended anymore. On top of that, schools and daycare were closed and like everyone else we had our child at home with us while still working full time. So, we improvised. We decided to take the trip together, my wife (who is also a scientist), my five-year-old daughter and me. Since we couldn’t go to a host lab, we opted to bring the lab with us to the field. We rented a RV which we made into a lab on wheels by bringing sampling and dissecting tools as well as a light and a stereoscopic microscope equipped with a camera. We went grocery shopping, packed a few clothes, wet suits, masks and snorkels, and here we are loading everything in the RV, ready to start a 4 day socially distanced scientific expedition as family.

A family scientific expedition

In the late afternoon, we left the San Francisco bay area and drove a few hours south. We spent our first night in the middle of pumpjacks and fields near Bakersfield. The next morning, we drove down to beautiful Santa Monica, looking for a sampling spot around Venice Beach. I snorkeled around for about two hours while my wife and daughter went for a stroll along the Venice Canals. I did not find anything interesting and the only surprising encounter underwater was an electric scooter covered in algae. At the end of the day, we met my friend Fabian and his family in Venice and had a socially-distanced dinner together. I’ve known Fabian since high school in Guadeloupe; he is also a scientist and he too immigrated to California a few year ago. I had told him about the trip and he decided to join me for the dive planned the next morning.

The next day, day three of our endeavor, we set out to sample the marine environment at White Point Beach in San Pedro, Los Angeles. We geared up, and with the help of our dive instructor, we first swam at the surface around the rugged coastline for about 20 minutes before diving about 30 feet down to the seafloor. The seafloor was composed of mudstone which had been folded by tectonic movement now forming parallel lines. Cracks in the rock allow ground water to flow through in a series of vents. After about 15 minutes we found what we were looking for — hydrothermal vents. In these vents, the water is very hot (about 85 degrees or more) and very rich in hydrogen sulfide. We later found that you could smell the sulfur even at the surface!

The seafloor was mostly covered in algae and the occasional large starfish, sea cucumber and anemones, but the vents displayed completely different communities of organisms. And we found what we were looking for, white hair-like filaments swaying in the current, the giant white sulfur eating bacteria that could hold answers to our questions. We sampled the white bacteria for another 30 minutes, finally surfacing above the vent before swimming back to the shore. I took the precious samples back in the RV where we had set up two microscopes.

My wife and I spent the next five hours dissecting and sorting the different large sulfur bacteria that I had collected. Our daughter, very interested in these giant microbes, helped us sort them out at the microscope from time to time (between watching cartoons of course). When both your parents are microbiologists, you learn how to hold a Pasteur pipette and look through the eyepieces of a microscope quite early.

After a long day we packed our things and drove further south. That night we slept at a rest area, and managed to reach San Diego in the morning. After a hearty breakfast (and more cartoons), we drove to Carlsbad for a last sampling session in the Batiquitos Lagoon. There are no vents here, but the muddy sediment produces hydrogen sulfide in a relatively quiet body of seawater. Here I found some other large sulfur bacteria growing on sunken wood or seashell debris.

After lunch in the RV and some more work at the microscope, we moved to La Jolla Shores and decided to relax a bit and enjoy the beach together. After equipping our daughter with her first small mask and snorkel, I took her with me in the water. She was so excited, she screamed in her snorkel when she saw small groups of fish passing in front of her. After half an hour in the water she was freezing but happy. She did not want to leave, and repeatedly told me through chattering teeth, “I’m not even cold!” I took her back to her mom and decided to go snorkeling one last time. Right after re-entering the water, I saw a leopard shark passing right in front of me — a befitting end to wind up this unusual family trip.

Back in the lab…

We are now back in the East Bay up in Northern California. The sampling trip was a success — we collected thousands of the giant bacteria we were interested in and we have started analyzing them. One surprise was to find these large bacterial filaments growing not only on rocks but also on living sea snails, covering their shell like a white fur. We will sequence their genome and look at them more closely with laser and electron microscopes to see if we can detect symbiotic associations with other microbes.

So while one trip ended, we have just started on this interesting journey of scientific discovery. We may or may not find examples of symbiosis, at least the kind we are looking for, but what continues to amaze me is the incredible beauty and diversity that we have here on Earth. Something that we take for granted, and even one day may disappear because we failed to notice the damage we were causing to the environment. Still, I am an optimist. Today as a society we are all trying our best to rectify such damage — it might take time but we will get there. Meanwhile we will continue our search for the origins of life in the beautiful waters of California, and when we can travel, the southern Caribbean Sea.

See video from this journey uploaded to YouTube and stay tuned for the next episode!

Jean-Marie Volland is a scientist specializing in Microbiology and Microscopy at LRC Systems

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