This paper, in many ways, sums up the journey of my PhD. Funnily enough, the idea behind it came to me in the very first weeks after I started. I had arrived at ETH Zurich with the wonderfully terrifying blank slate of a PhD project in front of me: phytoplankton-bacteria interactions.
So, naturally, I asked what seemed to me like a very simple question: does the coccosphere, the calcium carbonate shell of coccolithophores, protect them from bacterial attack?
It sounded suspiciously simple. Surely, I thought, someone must have looked at this before. Coccolithophores build these beautiful mineral structures around themselves, bacteria interact with phytoplankton all the time, and some bacteria can kill algae. Surely someone, somewhere, had tested whether the shell acts as a kind of armor.
Color me surprised when it turned out that, no, not really.
At the time, I thought this was excellent news. What a lovely, low-hanging-fruit kind of hypothesis. What I had not yet fully appreciated was that in biology, “simple” is often just a trap laid by the universe on unsuspecting PhD students.
Before starting my PhD, I trained as a chemist. I studied chemistry at the University of Edinburgh and, for the most part, loved the clarity of it. Of course, chemistry has its own particular ways of breaking your spirit. Sometimes you get a crystal when you were supposed to get a liquid. Sometimes the reaction turns blue when it was supposed to stay white. Sometimes you sneeze and there go three weeks of work. And sometimes the rotary evaporator does indeed seem to be acting with a type of personal malice.
But usually, when something failed, there was at least a fighting chance that you could figure out why. Maybe the temperature was wrong. Maybe the solvent was wet. Maybe someone had never learned how to clean glassware properly (see also: menace to society). There was cause and effect, or at least the comforting illusion of it.
My first real encounter with biology came during my master’s thesis, where I worked with coccolithophores from a materials chemistry perspective. We were interested in whether calcification was influenced by hydrostatic pressure. After years of staring at spectra and getting excited or devastated depending on whether a peak appeared in one place or another, it was a relief to work with something I could actually see. Admittedly, to the naked eye it mostly looked like green sludge, but under the microscope, and especially under the SEM, these organisms were rather astonishing. Tiny single cells wrapped in elaborate armor made of calcium carbonate plates.
That was enough to convince me that maybe biology was not as bad as I had thought in high school. Maybe I could find my green thumb after all.
Which brings us back to the start of my PhD, and my supposedly simple question.
The first decision was which coccolithophore to work with. For the real biologists reading this, yes, I now understand why people like model organisms. Coccolithophores have one too: Emiliania huxleyi--technically Gephyrocapsa huxleyi now, although it will probably always be Emiliania to me. It has been studied extensively, its genome has been sequenced, its growth conditions are known, and many people have spent many years making it comparatively well behaved.
So naturally, I did not choose it.
Instead, I chose Coccolithus braarudii, a large, heavily calcified coccolithophore. Scientifically, it made sense. It has a substantial coccosphere, it is large enough to track relatively easily, and although it is not always the most abundant coccolithophore in the ocean, its heavy calcification means it can make an important contribution to calcium carbonate production. Also, it is very pretty, but obviously that was not the reason why I chose it.
I ordered the strain, prepared the artificial seawater, added the nutrients, remembered that C. braarudii needs silicon despite not being a diatom (it likes to be special, which would become a recurring theme throughout this journey) and waited.
And then waited some more.
After two weeks, the time I had read it should take to reach a decent density, I looked under the microscope and found almost nothing. At first, I assumed this was because I did not know how to use the microscope properly, which was partly true. Unfortunately, it was also because there were almost no cells in the flask.
What followed was several months of changing everything. Trace nutrients. Vitamins. Silicon. No silicon. Temperature. Flasks. Plastic. Glass. Different batches of medium. Different flavours of hope. I played classical music to them. I played the Imperial March. None of it worked particularly well.
At some point, people in the lab stopped asking me how I was in the morning and started asking, “How is braarudii?” The answer was usually: uncooperative, thanks for asking.
Then, one day, Dr. Zachary Landry made a suggestion that changed everything. The Stocker lab had once worked on corals, and although that project had ended, an aquarium remained in the lab, ruled by a female clownfish with distressingly sharp teeth and a male clownfish who appeared to have accepted his fate. The aquarium contained essentially the same artificial seawater I was using, with one major difference: it had passed through the digestive tract of two clownfish and whatever microbial mystery was going on in the tank.
Zach suggested that, since algae often grow better in filtered natural seawater, perhaps I should try filtered aquarium water. Before anyone asks why I did not use filtered seawater from the beginning, I invite you to consider the geographical location of ETH Zurich.
To my amazement, it worked. C. braarudii grew. I was delighted. For about three months.
Then the aquarium developed a bloom of something deeply unhelpful, and braarudii decided that cooperation had been a brief phase in its life and it would now like to die again.
At that point, I changed projects and, armed with everything I had learned from my previous mistakes, turned my attention to the model organism Emiliania.
For the next two years, C. braarudii lingered in the background of my PhD like an unresolved side quest. Of course, during that time, while receiving less attention than ever before, it mysteriously started growing better. This was partly thanks to more stable, self-prepared artificial seawater, and partly, I suspect, because biology enjoys irony.
Eventually, near the end of my PhD, I returned to the question I had asked at the beginning. Does the coccosphere protect coccolithophores from bacterial attack?
This time, the cells grew. The experiments worked. And the simple little hypothesis that had started it all turned out to be worth asking. When calcified, C. braarudii was remarkably resistant to Phaeobacter inhibens, a bacterium known to kill algal cells. But when we removed the coccosphere, the same alga became vulnerable.
Looking back, I find it funny that the idea I had in the first few weeks of my PhD ended up becoming one of the final pieces of it. At the beginning, I thought the hard part would be designing the experiment. In the end, the hard part was convincing a tiny calcifying alga to remain alive long enough so I could kill it with bacteria.
There is probably a lesson in there somewhere about patience, persistence, and the dangers of thinking that a biological question is ever as simple as it sounds. But mostly, this paper is the story of a stubborn question, an even more stubborn organism, and the long, ridiculous, wonderful process of getting an experiment to work.
You can read the paper if you want to know how I finally got my revenge on C. braarudii by stripping off its shell and exposing it to bacteria. Perhaps, given everything I put it through, it is not so mysterious after all why braarudii lost the will to live.