The little cell that could: modeling how climate change impacts ocean bacteria

When I was younger, I pictured the ocean as a giant soupy mix of whales, sharks, fish, jellyfish, and dolphins, and marine biologists were the people in scuba gear studying the wildlife. What I didn’t know was that the ocean is brimming with life invisible to the naked eye in every single drop of seawater!

My name is Iris, and I’m one of the lucky people that gets to call myself a marine biologist studying one very specific bacteria, SAR11. Before we get there, let’s talk about how I got into this field. 

From pre-med to pipettes

When I was applying to college, I knew I liked science, and I knew that people who liked science went on to become doctors. Research, as far as I understood it, mostly meant killing mice, and I wasn’t cut out for that. So I was “pre-med” for about half of my college career: checking all the boxes, taking all the classes, volunteering in hospitals in Italy, Taiwan, whatever it took to reach the goal. 

In the middle of a mid-college crisis, I stumbled onto a bioengineering career fair. I wasn’t a bioengineer, but it couldn’t hurt to look. Resume in hand, I walked nervously up to the very first booth I saw: Amyris.

I won’t butcher what the guy at the booth told me, so I’ll put it in my own words. Amyris is a biotech company that genetically engineers yeast, the same yeast behind sourdough and beer, to produce sustainable molecules we use every day. By engineering new genes and pathways in yeast, scientists can use yeast to generate large quantities of a given molecule. 

Their favorite example (and mine) is squalene, a common ingredient in skincare and makeup that’s traditionally harvested from shark liver oil. Instead of hunting sharks, Amyris brews it from scratch in yeast. Fun fact: you’ve probably walked past their products in Sephora!

I was starstruck. Microorganisms like bacteria and yeast aren’t just some invisible force in nature. They have a huge impact on our world, and with the right tools, we can put them to work for our benefit. That was the moment microbiology became something I was completely fascinated by. And that guy from the career fair? He turned out to be my future boss after I started working at Amyris after graduation.

This isn’t a story about Amyris, but it is certainly how I became absolutely fascinated with the enormous role the tiniest things on our planet play.

The ocean is one really productive soup

Let’s pause my story for a moment and talk about the ocean itself.

When we picture climate change and climate change mitigation, most of us look at land and sky: trees, forests, rising temperatures, and carbon dioxide drifting up into the atmosphere. But some of the planet’s most important climate work is happening out of sight: underwater. The ocean is Earth’s largest carbon sink, soaking up roughly 30% of the carbon dioxide we emit. It also captures about 90% of the excess heat trapped by our greenhouse gas emissions, and it produces about half of the oxygen on Earth.

This planet-sized job isn’t being run by the charismatic animals of the sea. It’s not the whales, the sharks, or the sea turtles doing the heavy lifting. It’s the microorganisms, invisible to our naked eye, existing in multitudes in every drop of seawater. 

The amount of bacteria in the ocean is a ridiculous number that sounds fake. The ocean holds an estimated 1.2 × 10²⁹ bacterial cells. That’s over one hundred octillion bacterial cells. There are more bacteria in the sea than there are stars in the observable universe! 

These invisible workhorses are breaking down, recycling, and shuttling carbon through the water column. And as the ocean absorbs more and more of our heat, the water they live in is warming, which changes how these bacteria function and therefore how well the whole system keeps operating. 

My journey from sourdough to marine microbiology

While working at a biotechnology company, I became really interested in the basic biology of microorganisms. I was engineering new parts in the machine without really understanding how the machine worked! 

However, I still wanted to do science that helped the environment, so I decided the best way was to go straight to the source. I wanted to study the microbes actually living out there, figure out what jobs they’re doing, and understand how our actions affect their work. So, I joined Dr. Cameron Thrash’s lab at the University of Southern California as a PhD student, studying the ocean’s most abundant and most widespread bacterium: SAR11.

SAR11 is a group of heterotrophic bacteria, which means they get their energy through consuming carbon molecules (a.k.a. “food”) rather than capturing carbon for their cells from CO2 like a plant. This group of bacteria is so abundant that they can make up nearly a third of all cells in the surface ocean. They’re also found practically everywhere: open ocean, coastal waters, even freshwater. This combination of “wildly abundant” and “basically everywhere” makes SAR11 a fantastic model system for asking how climate change is reshaping the ocean via microbial metabolism.

And here’s what makes SAR11 one of the most interesting bacteria to study. 

1. SAR11 is one of the smallest free-living cells we’ve ever found, with one of the tiniest, most streamlined genomes, or the full set of genetic instructions an organism carries, of anything alive in the ocean. Talk about packing light for a trip! 
2. They also thrive in oligotrophic waters, or environments so nutrient-scarce that most life would starve, which happens to describe most of the open ocean. 
3. They’re taking up all sorts of small, easy-to-digest carbon molecules. 

Since they’re doing this everywhere, all at once, in enormous numbers, we believe SAR11 plays a major role in the ocean’s carbon cycle. 

Studying SAR11 inside and outside the lab 

I  hope you’re convinced that SAR11 is a pretty cool organism to study. Here’s the catch: it is notoriously difficult to grow in the lab, because of all the things that make it so interesting. It’s too small to be easily observed under a normal microscope, and because its genome is so pared down, the requirements for life are very intricate. 

The way I study SAR11 is a two-pronged approach. 

1. In the lab, I grow SAR11 in culture to characterize its phenotypes, or its observable behaviors, like how fast it grows and what kinds of carbon it can feed on.
2. On the computer, I build a model called a metabolic model. A metabolic model is a digital representation of the cell’s entire metabolism. The model captures the organism’s full set of genes, proteins, and the chemical reactions it can run. In other words, it’s a blueprint of everything the cell is capable of doing.

Using this model, I can put SAR11 to the test under challenging conditions and really understand how the cell could be responding on a metabolic level. What happens inside the cell and to the carbon it consumes when coastal waters get saltier as sea level rises? When the ocean gets warmer? A good model doesn’t just describe the bacterium. It can help us understand and predict how the bacteria will respond to changes in its environment. 

What lies on the horizon?

After I’ve built a model validated with my lab experiments, my next steps are to point it at two big questions:

1. Carbon use efficiency: when SAR11 takes up carbon, how much does it keep to build its tiny cell body versus release through respiration as carbon dioxide? And how does that balance shift under climate change and dynamic coastal conditions?
2. Salinity stress: as sea levels rise and coastal waters mix with freshwater, how does a cell this streamlined handle the change?

There’s lots more for me to do, more lab experiments to run, more conditions to test, more of this little cell’s metabolism to map. But by the end, I hope to answer my own questions and leave behind a model the rest of the scientific community can use too.

None of this would be possible without the support of the Wrigley Institute, my advisor Dr. Cameron Thrash, and the Thrash lab. I’m incredibly grateful for the opportunity to develop this research and to learn alongside my interdisciplinary cohort of Wrigley Fellows. And hopefully, I’ve introduced you to the tiny cell in the ocean that could, SAR11!

Iris Wu is supported by the USC Dornsife Wrigley Institute Graduate Fellowship.