Transcription
There's something kind of absurd at the heart of life on Earth. In the words of one scientist, it's a cruel joke. And it goes like this: All living organisms need nitrogen to survive. It's a key part of proteins and DNA. And our atmosphere is absolutely packed with nitrogen.
But here's the cruel part. The one enzyme that can pull nitrogen out of the air so that living organisms can use it? That enzyme basically falls apart in the presence of oxygen. Meaning that plants, and animals, and fungi are surrounded by nitrogen that they can't use. The only organisms that can pull this nutrient from the air are the ones that can survive without oxygen. Pretty much just super simple microbes. Because of this, the entire natural world relies on these tiny microorganisms to get nitrogen.
This was an ironclad rule of biology. No organism from the complex side of the tree of life could pull nitrogen out of the air. But today, one microorganism has rewritten this rule, in a way that could change everything from the future of food to our understanding of life on Earth.
It all started in the '90s on a research boat in the middle of the ocean. On that boat was an oceanographer named Jon Zehr. Now, Jon didn't study whales or dolphins or coral reefs. He studied nitrogen-fixing bacteria. Jon was on the hunt for new kinds of bacteria in the ocean, and he was using something pretty cutting edge for the time: DNA. His plan was to test samples of seawater for a key nitrogen-fixing gene, in the hope that he might find something that other scientists had missed. And, well, it worked.
Almost immediately, he found a species previously unknown to science. As he looked at the gene he'd found, he could get a pretty good clue of what this new bacteria should look like. So, he popped it under the microscope, expecting to see that bacteria everywhere, but it wasn't there. He couldn't see anything that matched what he was looking for. For many years, at the beginning of the story, we had found this gene sequence. We would look under the microscope and we could not see them. So, for years, we were actually studying this organism with no idea what it actually looked like.
Jon and his colleagues chased the bacteria around the world, finding fingerprints everywhere, but never finding the bacteria itself. What Jon could see was the bacteria's DNA. And that was even weirder. You see, it was supposedly a photosynthetic bacteria, but it didn't seem to have the genes to photosynthesize. It had also lost all sorts of other genes that it really should need to survive. In fact, it seemed to have lost about 80% of its entire genome. So, how was it even alive?
Well, over years of studying this, Jon started to notice a pattern. Every sample of seawater that contained this mystery bacteria DNA also contained DNA for this one specific species of algae. Jon realized that his bacteria had been hiding in plain sight. The reason he couldn't see it under the microscope was because all along it had been inside of the algae. And that's also why the bacteria could survive even with all those missing genes because the algae was feeding it. This algae was the missing puzzle piece that Jon had been chasing for years.
And unbeknownst to him, across the ocean was a Japanese scientist who'd spent her career studying that exact puzzle piece. This is Kyoko Hagino. She's an algae scientist from Kochi, Japan. And just like Jon, her story also started in the late '90s, with a microorganism that changed the course of her career. She was part of a paleontology research team studying tiny algae fossils on the ocean floor. Out of all of the little fossils that Kyoko would look at under the microscope, there was one that absolutely captivated her. It was a type of algae called Braarudosphaera bigelowii. Kyoko fondly just calls it Bigelowii. At certain points in Bigelowii's life, it surrounds itself with this beautiful geometric shell. But no one really knew anything about the algae living inside.
This mesmerizing algae? This was what Kyoko wanted to study. But no one else seemed to share her fascination. At the time, Kyoko was having trouble finding a position at a university. At the same time, she was taking care of her young kids and was moving to a new city where her husband had found work. Everything in her life seemed to be sending a clear message that she should just drop it and find something else to study. But Kyoko just couldn't do that. For whatever reason, there was something about this algae that just absolutely enamored her, and she wanted to learn everything about it, even if that meant studying it on her own.
So she and her daughter started taking trips to the beach, collecting samples of seawater in the hopes of finding this elusive algae. Over the years, they ended up taking hundreds of these trips. They did this so often that her daughter genuinely didn't know that people went to the beach for other reasons, like to go swimming. Kyoko would then spend hours at home with the microscope searching for Bigelowii cells and individually picking them out when she'd find them. This was incredibly time consuming. But it was kind of the only way to study them. No matter what she did, the cells just wouldn't grow in a test tube.
For years, Kyoko worked on growing a culture without any kind of university salary. To make ends meet, she ended up picking up a part-time job washing test tubes in a lab. One day, she was talking to one of the scientists there, and he suggested adding a strange ingredient to her culture. It wasn't a chemical or anything else you'd normally find in a lab. It was a type of noodle called tokoroten. And to Kyoko's amazement, the noodles were just what Bigelowii needed. After years, the culture started to grow.
Now that she had a culture, she could finally grow enough cells to answer some of the big questions about this organism. And there was one big question on the top of Kyoko's mind. You see, over the course of her many years studying Bigelowii, she'd noticed something kind of weird. It had all the normal components of an algae cell, but then it also had this other thing. And just as she was puzzling over what it could be, she stumbled on an article that had just come out in the American journal Science. It was Jon's article. The article followed the story of his hunt for the invisible nitrogen-fixing bacteria and ended with his theory that the bacteria was likely living inside of a species of algae called Braarudosphaera bigelowii.
That strange object that Kyoko had noticed. It was the nitrogen-fixing bacteria that Jon had spent so many years searching for. Our paper came out. She realized that what we were studying might be that black body and she found that this thing she had been studying actually had the same gene sequence that I had been chasing for years. Neither one of us knew that the two things went together.
Kyoko and Jon had both spent their careers trying to solve a scientific puzzle with no idea that they each held the other's missing piece. And now that they had a culture, they had the chance to unravel a mystery that would end up going deeper than they'd ever imagined. Let me explain. You've probably heard of symbiotic relationships in nature. Two organisms each helping the other out. The fish from Finding Nemo is a good example of this. It looks after the sea anenome in exchange for a safe place to live. But these relationships can get closer and closer. You have organisms that live inside of other organisms like corals, which get food from the algae that live in them. And you even have cells that live inside of other cells. Until at a certain point these relationships become something more than symbiotic.
Now, this line is kind of mind bending and it's only been crossed a few times in the history of life on Earth. It's the line where two organisms fuse into one. The two famous examples of this are mitochondria, the powerhouse of the cell found in you and me and every other complex life form on Earth, and chloroplasts, the parts of plant cells that do photosynthesis. Both of these examples started as separate organisms that got so close that they became one. Now they're not separate organisms anymore. They're organelles, little organs inside of other cells. So this line is a really big deal and the question was: had Bigelowii crossed it? Well, with the culture and Jon and Kyoko's expertise, they could actually answer that question. And so they teamed up.
Kyoko sent the culture to Jon's lab, and hoped to visit California as the experiment went on. I think I have a picture in my office of when the culture arrived. We sat around as a lab and we decided the ten things we were going to do first because we didn't know how long the culture would stay alive anyway and within three days the COVID lockdown started. The pandemic threw a wrench in all of their plans. Japan put up very strict travel restrictions, and they lasted for several years meaning that after everything Kyoko couldn't join in person. Jon and Kyoko were still hungry for answers and they decided that the show must go on. Kyoko still had funding from a grant she shared with Jon, and she helped as much as she could from afar. But otherwise, Jon's lab once again forged ahead to better understand how these two pieces fit together.
And pretty quickly, they started to find clues. Like Bigelowii and the bacteria always divided at the same time, and they grew at the same rate in ways that looked really similar to mitochondria or chloroplasts. But the real smoking gun came from Tyler Coale, a postdoc in Jon's lab. He was studying Bigelowii's DNA and the proteins that it made with it. And he ended up uncovering something very weird. Bigelowii had all of these random extra genes for proteins it wasn't actually using. And on the very ends of each of these random genes, there was this one specific sequence of DNA that kept showing up over and over.
So, what was going on? Remember how Jon's bacteria had all those missing genes? This discovery would end up solving that mystery. Let's imagine Jon's bacteria needs proteins A through E to do something really important, like store energy. But it only has the genes for proteins A, C, and E. Normally, these missing proteins would mean death, except for the fact that its host, Bigelowii, had evolved the genes for proteins B and D. This is what all those random sequences were. They were the genes for all the proteins that Jon's bacteria was missing. And that little bit of DNA on the end of each of the sequences, they were essentially delivery instructions to send the protein over to the bacteria.
This discovery was huge because this kind of system had only been seen a small handful of times in mitochondria and in chloroplasts. This was the smoking gun. Bigelowii had crossed the line. That nitrogen-fixing bacteria that Jon had spent his entire career studying? It wasn't a bacteria anymore. It had become a part of Bigelowii. And all it needed was a name. Jon and his team called this new organelle the nitroplast.
Before this discovery, the rule was that only simple organisms like bacteria could pull nitrogen out of the air. No plants, no animals, no fungi. But this discovery rewrote that rule. This was the first organism on the complex side of the tree of life that could pull nitrogen out of the air.
But this isn't just a big deal for biologists. It could also fundamentally reshape the way we grow food. Since plants can't get nitrogen from the air, farmers often have to use synthetic fertilizer to help them grow. Fertilizer requires a ton of energy to produce and it creates a lot of pollution when it eventually gets washed downstream. But imagine if we didn't need fertilizer. What if plants could pull nitrogen straight out of the air? This has long been the dream of crop scientists. And with the discovery of the nitroplast, it showed that this was possible. Here is an organism that has figured out how to do it. This organism has done what you know decades of biotech couldn't do, right? It has engineered this capability in into this cell. It's natural to think that there might be lessons here that we could learn. The downer is it's really difficult to go from what we know about the nitroplast to engineering a plant. And yet, if you don't take one step, you're not going to make a hundred steps.
Already researchers are studying the nitroplast, in the hopes of one day creating plants that can make their own fertilizer. But while Tyler and Jon and Kyoko are all excited about the potential impacts of their discovery, for them, it's never really been about changing the world. Instead, they spent their careers studying this tiny organism, not knowing what they'd find, but with the hope that whatever they discovered could teach them a little more about how the natural world works. And on that front, there's so much more to learn. There still exists these types of biological mysteries out there to be solved and unexpected things coming out of basic science. Well, because you never know, you know, and some of the biggest advances might come from things that you didn't expect. And this might be a case like that.