Dark Matter Scientist, Investigative Reporter, and Marine Biologist, All in One.

You probably see the words “dark matter” and think of physics–the mysterious stuff that fills our universe even though we can’t observe it. Or maybe you think of witchcraft and sorcery. But if you work in the Stepanauskas lab at Bigelow you know that I’m referring to “microbial dark matter”, which is no less exciting than any of the above! Here’s why.
Microbes live almost everywhere on Earth, from ocean depths to volcanic lava to your own stomach, and make up most of the world’s biodiversity. Despite this abundance, we know almost nothing about most of them. That’s because for most of modern science we’ve studied microbes by growing them in culture, which is a problem because we haven’t actually figured out how to grow most of them in culture. Luckily, over the past few decades scientists have developed techniques to study microbial life without the need for culturing it, leading them to discover a LOT of new microbes that aren’t closely related to any that we knew about before–whole new branches on the tree of life! Hence, microbial dark matter: the vast, mysterious majority of the world’s microbes that we can’t grown in lab and barely understand. Poor things.
Among the techniques that helped us get here is single cell genomics, which was pioneered in part by the Stepanauskas lab here at Bigelow. Essentially, you take an environmental sample, sort individual cells out of it, and sequence their genomes. These genomes are kind of a blueprint for the cells, so we can study them and learn who they are without actually growing them in a lab.
That all sounds rather theoretical, so you might be wondering what I actually do all day.
Since my research is all computational, I walk to Bigelow every morning (in open-toed shoes! Perks of not working in a lab) and plant myself at my desk, which has this incredible view.
Once there, I fire up my laptop and analyze the genomes of bacteria belonging to a specific “dark matter” phylum, meaning that these organisms are so different from other bacteria that they form a whole new phylum. For reference, that’s about as different as a flatworm and anything with a backbone. For further reference, humans, lizards, and fish all belong to the same phylum. It’s pretty unbelievable that we’re still discovering entirely new phyla — imagine being a bacterium, discovering a flatworm, and then finding out that humans, lizards, and fish exist too.  And don’t forget that we still haven’t grown any of these bacteria in a lab. All we have of these bacteria are their genomes, which are basically just millions of letters, and my job is to “read” these genomes and look for clues about who these bacteria are. What do they look like? Where do they live? What do they eat? How similar are they? It’s more like interviewing actually–I like to think of it as investigative journalism of sorts.
My work is a constant reminder of how much diversity of life is out there, and of how much we don’t know about it yet. After all, my phylum is one of many that have yet to be characterized, and new ones are being discovered all the time. I’m feeling pretty lucky to be at a place like Bigelow that’s such a pioneer in this discovery, and where I can be a dark matter scientist, an investigative reporter, and a marine biologist, all at once.
Michael Chen is an REU intern in the Stepanauskas lab.
Dark Matter Scientist, Investigative Reporter, and Marine Biologist, All in One.