The hunt for a rare microorganism

Tiny Matters

For centuries, scientists have looked through microscopes to witness the worlds of cells and tiny creatures that exist all around us. In this episode, Sam and Deboki learn what it takes to hunt down a rare microbe, and why it matters for how we understand evolution and the connections between species today.

Transcript of this Episode

Sam: When we’ve talked about microbes on Tiny Matters, we’ve either talked about them causing disease or as potential cures. But microbes are so much more than either of those things. They’re organisms with their own lives.

Deboki: For centuries, scientists have looked through microscopes to see what those lives might be like, also sometimes spotting microscopic creatures that have become very familiar in scientific lore. These kinds of multicellular microbes pop up over and over again in papers, like the chubby, resilient, eight-legged tardigrade, also known as a water bear or moss piglet. And we all love to read about their exploits, partly because they tell us a lot about our world.

But there are a lot of microbes out there, and some of them are much harder to find than others.

Sam: Welcome to Tiny Matters. I’m Sam Jones and I’m joined by my co-host Deboki Chakravarti. Today we’re going to talk about what it takes to hunt down a rare microbe, and why it matters for how we understand the world today.

Deboki: Sam, you and I have a very similar scientific background. In graduate school, we both worked with cells. I studied human immune cells, and you mostly studied neurons in the olfactory system, which means that we’ve both had to spend a pretty significant chunk of our lives looking at the way that those cells live and function.

Sam: Yeah—lot of years, whole lot of experiments.

Deboki: When I looked at my little human immune cells through a microscope, it was just to check on how they’re doing. To be honest, they’re kind of cute. They’re very round, they have a large nucleus, so they just look like these little polka dots floating around the screen. But that’s only if things were going well.

Sometimes when I looked through the microscope, I wouldn’t see my round little happy dots. Instead, they would look more like a crumpled up piece of paper, like they’d sort of just popped and turned into a wrinkled mess.

Sam: That doesn’t sound good.

Deboki: Yeah, it absolutely was not good. It meant that my cells had died, and usually the culprit was probably a bacteria or fungus or something else that had somehow managed to sneak its way into my experiment and wreak havoc on the cells I was studying, contaminating the culture and killing the cells in the process.

Sam: Cell contamination is the worst. There was a weird fungal infestation in one of the cell culture hoods in the lab I did my grad school work in and it didn’t impact what I was doing directly but some of my colleagues lost months worth of work and I felt so awful for them.

Deboki: Yeah, that sounds miserable. I’m telling this story of bacterial woe because when I finished my PhD, I had a very narrow vision of how to think of microbes like bacteria and fungi in the context of science. I thought of them as either genetic tools that let me do my research, or I thought of them as things that contaminated my experiments.

But I’d never really thought of them as individual organisms that have their own lives that I just happened to interrupt with my own scientific needs. And I definitely never really thought that I would find those lives fascinating all on their own.

That all changed when I started writing for a YouTube series called Journey to the Microcosmos, which features microscopy done by James Weiss, who we’ve affectionately dubbed our master of microscopes. And the thing to know about James is that he really, really, really loves his microscope.
James Weiss: I stay awake all night and I sleep all day, and then I wake up around like 6:00 pm, 7:00 pm and then I make my first cup of coffee, and then I just sit in front of my microscope, and then I spend probably around like 10 hours, 12 hours a day just doing microscopy and checking a bunch of samples under the microscope and investigating them and trying to find something interesting. I've never failed to find something interesting, so there's something always interesting there to just, you know, take my attention and just get me captivated maybe in a way.

Sam: That is love and dedication. James got his start in microscopy six years ago with something that was definitely going to have lots of microscopic stuff in it: wastewater.

James: It started as a college lab course, so I was studying environmental engineering here, and then we needed to check these wastewater treatment plants, basically human waste, bottled in disgusting looking jars and stuff. And so during this lab course, we just needed to check this water, and I thought it's gonna be really dull, you know? And I put just one drop on a slide and just, you know, covered it with a piece of glass and put it under the microscope. And it was like, love at first sight. I, I don't know if anything in life got my attention this much this quickly. It was unbelievable. It was a rotifer I learned later, but it was so weird. It looked like a worm and looked like an animal. It looked like, I don't know, chainsaw. It was so weird. There were also beautiful things. There was one testate amoeba. It looks like… this amoeba just builds a shelf for itself, and it looks yellowish in color. It looks like a little gem, and it was mind blowing. And so this lab course was just two hours a week, and it wasn't enough for me.

Sam: I love that something as gross as human waste could be so beautiful… if you just look close enough.

Deboki: Yeah, agreed. And James wouldn’t be the first microscopist to think so. One of my favorite science anecdotes is about Antonie van Leeuwenhoek, a 17th century scientist who is considered one of the fathers of microscopy because of just how many things he would study under the microscope, including...

Sam: Let me guess, poop.

Deboki: Yes, you would be correct.

Leeuwenhoek was having a not-so-great stomach day, and he figured why not put it to good use. So he studied his own stool under the microscope, describing the strange creature he found in there. It had a long body with a flat belly, and several foot-like extensions coming off of it.

Centuries later, his biographer Clifford Dobell used that description to retroactively diagnose Leeuwenhoek with giardiasis, a disease that happens when the parasite Giardia duodenalis finds its way into your intestines.

Sam: Giardia is a single-celled eukaryote, which means that it’s a type of organism called a protist. Protists make up a good chunk of the microbes throughout the world. But there are also bacteria and archaea, which are prokaryotes. And then you have fungi like yeast, and multicellular microbial animals like tardigrades and rotifers. The diversity in the microbial world is immense, and scientists have been studying the way these organisms are all related so that we can better understand how life began and evolved.

Deboki: One way scientists do this is through taxonomy, the process of organizing the evolutionary relationships between organisms. Identifying and categorizing microbes has helped us understand how Earth became rich with oxygen, how life transitioned from single cell to multicellular forms, how sexual reproduction evolved, and so much more. And for centuries, scientists were doing it the way that James does it, by looking under the microscope.
Of course, it hasn’t all been wastewater and questionable stool samples. The primary requirement for finding microbes is water, so even a puddle can hold all sorts of fascinating life. For James, his samples have come from all over the world, from scientists studying beaches or fjords. But he also gathers many of his own samples by diligently going to a particular pond in Warsaw where he lives.

James: So I go out to sample ponds, uh, lakes, rivers, any sort of water bodies. And these things can be temporary or permanent water bodies. So it can be just a puddle on the street, or it can be a huge lake. So I just collect some samples and the dirtier it looks the better it gets.

Sam: I love that—the dirtier it looks, the better it gets. Makes perfect sense. So during one of his excursions, James ended up coming back with something he had long hoped to find, a protist called Legendrea loyezae.

Deboki: There’s really no other way to describe it. The Legendrea loyezae is weird-looking. Sometimes I think of it as kind of like a spaceship with tentacles, which is weird enough on its own.

Sam: It is very strange looking, but the Legendrea loyezae is also something else: it’s rare. It was first reported in 1908, and up until James came across it, only four other people had reported seeing it.

And if it’s hard to find an organism, it’s also hard to study it. In the scattered reports of the Legendrea loyezae, details about their tentacles and behaviors remained fuzzy. And when scientists found similar organisms, it became difficult to figure out whether or not they were closely related because there just weren’t enough descriptions of Legendrea loyezae to compare them to.

Deboki: But then James became the fifth person to report having found the Legendrea loyezae.

James: I was looking for it for so long, I was sampling this smelly hydrogen sulfide—it smells like rotten eggs. And I was hoping to find it and it took me years to find some, but when I finally found one, it was just mind blowing. It looks so weird.

Sam: But unfortunately James couldn’t marvel at it for too long.

James: So I was so excited to find my first cell, but unfortunately, I needed to kill it because it's side effects of wanting to do some science. You need to fix your specimen for genomic research. You need to just kill it and preserve it in your freezer for DNA analysis. I wasted my first cell, let's say, in this way. But I knew that they were living there, so I needed to find a second cell or a third cell.

Sam: So James spent the next few months on the lookout for more Legendrea, collecting more water from the same pond where he’d found the first one and spending hours sifting through his samples under the microscope.

James: It's just like me taking a drop, putting on a slide and just going through it under the low magnification, just, you know, so I can see everything quite quickly and just wiping it off and checking another drop. And I did that for months. And then I found the second cell.

Sam: And finding more Legendrea loyezae meant that James had the opportunity to see them doing something that had never been seen before.
James: I think on the second day or the third day of me finding this cell and keeping it alive in a humidity chamber I saw that this cell extended its tentacles that trail behind the cell. They were like 10 times longer than their usual structure. So apparently it was able to extend these things. It was a wonderful moment in my life because I knew that nobody has ever seen this. I get so excited, and when I get excited, I call my professor. She's also my best friend. So I was on the phone and the cell was just standing, you know, under the microscope, and nobody was looking at it. I was just like, making circles in my room, in my living room, talking to my professor, just saying, oh my god it extends a tentacles. And we were just repeating the information that we know about them. You know, nobody has seen it, okay, what do we do now? What, what should I do? So I documented this extended morphology of the cell for a couple of days. And then all of a sudden this cell was just contracting the tentacles when I was recording it and swimming away. I think it's one of my favorite videos I've ever recorded. It is wonderful. It makes a really, really tiny difference in science, but it made a huge difference in my life.

Deboki: So James was watching this rare microbe extend and contract its tentacles, which is cool, but it might not seem particularly exciting when you think of all the organisms out there that have tentacles.

In the case of Legendrea loyezae, though, it’s actually very consequential. Remember how we talked about the fact that scientists had had a hard time figuring out some of the relationships between Legendrea loyezae and other similar-looking microbes? James’ observation helped to clear up some of those taxonomic relationships—in other words, how the organisms were grouped based on shared characteristics.

Sam: In particular, there was another species called Legendrea belleraphon, which looked like Legendrea loyezae except that its tentacles situated in a row around the cell, unlike Legendrea loyezae which only had tentacles at the end of its cell. And in 1967, a scientist decided on the basis of that difference alone that these two species belonged to different genuses, so he renamed Legendrea belleraphon to Thysanomorpha bellerophon.

Deboki: It’s not quite clear why this taxonomic splitting ended up happening though. The scientist who had decided to make that divide had never actually seen Legendrea loyezae or Thysanomorpha bellerophon. He was simply going off other descriptions, and as we said, those descriptions were rare.

James: This scientist is in 1967, he changed the names without seeing any cells, without any investigation. So he didn't add any more information to the diagnosis of the species. And he didn't improve anything. He didn't do anything. He just decided, okay, this is called this now, and this is called this now, and that's it.

Sam: But James’ videos showed that the differences that existed in those descriptions weren’t so stark after all, that the tentacles of Legendrea loyezae and Thysanomorpha bellerophon actually might be more similar than they appeared in those initial observations.

So based on what he saw, James and his professor argued that the Thysanomorpha genus shouldn’t exist, and that Thysanomorpha bellerophon should be reunited with the Legendrea loyezae as Legendrea bellerophon. You can picture it as like a fun little microscopic family reunion.

Deboki: And that first cell he sacrificed for genetic work has also provided useful data that will help in further studies of the Legendrea family.

Sam: We started out this episode talking about our own experiences with microbes in the lab. And it’s interesting to think about how James’ work fits in with that. When microbiology began as a field, a lot of it was built on scientists and hobbyists like James who were dedicated to the microscope. Their observations formed essential descriptions of creatures who shape every facet of our lives.

Deboki: When it came to taxonomy, using the way microbes look to classify them made a lot of first. If you have two organisms with similar shapes or similar features or similar behavior, it makes sense to assume they might be more closely related to each other in the evolutionary scheme of things.

But appearances can be deceiving. Sometimes two organisms look alike because their two separate evolutionary paths converged on the same thing, like bird wings and bat wings. Those evolved separately. So although they might look closely related, they aren’t actually. Over the past century, as our tools to study organisms at the genetic level have greatly advanced, there’s been a shift away from using morphological comparisons to instead using genetic comparisons to figure out how evolutionary families are formed. And that’s been tremendously useful for our understanding of microbes and evolution.

But for James, focusing on genetics alone means seriously missing out.

James: I know some scientists, they have so much information about the genomes of this one specific organism, for example, but they’ve never seen that organism under the microscope. So if somebody outside of the field just looks at this data, they're not seeing anything beautiful, they're not seeing anything interesting. It’s just, you know, it's a bunch of information. It's great, it's science, but it's not influencing people to start working with microbes. But when you do microscopy, you see it's unbelievable.

Sam: Let's do our first tiny show and tell of 2023. Am I first or you first?

Deboki: I have no idea.

Sam: I'm happy to kick things off. So there was a recent, and by recent, I mean early-ish January paper that came out in Nature Climate Change, where researchers were looking at possible impacts of deforestation of the Amazon rainforest. So as you can probably tell, this is not a super uplifting tiny show and tell, but it's an important one. I'll, I'll start by saying that the Amazon rainforest, as we all know, is very important, more important than I think I realized in some ways the amount of carbon capture from all the trees in the Amazon, it's important for air quality, it's important for a lot of things. And the Amazon rainforest is considered one of the world's tipping points. I hadn't realized this was a term that people use in climate science, but generally you have this happening relatively slowly.

I mean, humans are speeding things up like crazy, but relatively slowly, but then all of a sudden they reach this tipping point that can lead to a sudden permanent change that can't be undone by just, say, planting a billion more trees in the Amazon rainforest. This international team of climate scientists found evidence that deforestation in the Amazon rainforest is influencing weather in Tibet, which I thought was very interesting because Tibet is 15,000 kilometers away, which for us in the US is over 9,000 miles. So these researchers figure this out by analyzing global climate data covering 1979 to 2019, and then combine that with data showing how much rainforest was cut down across those years. And they found that warmer temperatures in the Amazon correlated with rising temperatures in Tibet as well as the West Antarctic ice sheet. And they also found that when it was raining more in the Amazon, there tended to be less precipitation in both of those regions as well.

And so they started kind of finding these associations and then also linking that to deforestation. Why does it matter? Well, previous research had already shown that warming in Tibet was moving at a much faster rate than the global average, but also thinking about this tipping point, this sort of point of no return, if that's reached in the Amazon, these scientists are saying, well, this could also be the tipping point for Tibet temperatures and rainfall would be permanently impacted. So none of this was shocking to me, really. I mean, I'd love to hear what you think Deboki, because I'm assuming you're probably not totally shocked by this, but I think it's a reminder of how climate is global. It's not something that's just happening in one place and only impacting that place.

Deboki: Yeah, totally. I didn't study atmospheric dynamics. I didn't learn about weather really, as part of my science experience, I guess. I mean obviously I learned about weather as a kid and I, I read the news. I look at weather and like we've all had to learn about the climate and everything, but I remember in college I was dating, well, now my husband, but he did environmental engineering for his major in college, and he would explain to me about how weather systems in one thing apply to another, where you're like, oh, it's all connected. I see it now. It's fascinating. And then also so bleak because we've managed to mess up so much of it.

Sam: Right? No one wants to deal with climate change, but if you think about a lot of regions that are being impacted, the people being impacted are not necessarily the people that are leveling parts of the rainforest, right? Yeah. So they're dealing with the consequences, but they're not getting this like, monetary benefit that comes from clearing land and selling stuff from the Amazon. It's a little depressing.

Deboki: Yeah. It makes such a big difference on how we think about environmental policy. You can set up laws in one country and think, oh, this, this is only about that country. But it's, it's not, it's, it's about people who have had no choice in the matter.

Sam: All right. Let's see. Do you have something less depressing for me Deboki?

Deboki: I absolutely do. And I just wanna be clear that when I thought of this today, I had completely forgotten a lot of what we talked about in our episode today. So I did not expect for it to be so closely related, but I've just wanted to talk about this article since it came out in November and it just lined up really. I'm just recommending an article—it’s one of those tiny show and tells for me because I think you all should read it because it's a delightful. This was published in the Defector by Sabrina Embler, and it's titled An Oral History of the Time Six Doctors Swallowed Lego Heads to See how long they'd Take To Poo.

Sam: This is definitely more delightful than what I just shared. Okay, great.

Deboki: Yes. And it's part of the underlying theme that I feel like has been in this episode of like people studying their own poop, right? This is something that all microscopists did. It's also something that these doctors decided to do a while back because they wanted to know. So this is about a paper that was published in the Journal of Pediatrics and Child Health that documents six doctors who decided to see what happens when they swallow a Lego head, and to see how long it would take for them to poop out the Lego head. It's an oral history, which is a format that I have a lot of thoughts about because I read it a lot. As someone who loves to read celebrity gossip and articles about pop culture, it's a format that I have mixed feelings about, but it's so perfect for this story.

So the doctors involved, they work in pediatrics, so they've had to deal with plenty of parents who bring in their kids who have just swallowed something like coins or Legos. And what they were kind of realizing is that there's actually some data about how long it takes for these kids to, you know, expel coins. There really isn't as much data about how long it takes to poop out Lego heads. The doctors were also driven by an ulterior motive, which was to be published in the Christmas issue of the bmj, which is a very serious medical journal. But around Christmas it publishes gr goofy research papers and ultimately, like, just spoiler alert, they didn't publish this one because it involves self experimentation. Because yes, the six doctors decided as a group, they were gonna swallow some Lego heads, and they were gonna, they were gonna see how long it took for them to poop that out.

And I just, if you're, if you're having a day where you need to be, you know, like if you've just been dealing with the enormity of climate change or if just something's been going wrong with your day, I definitely recommend reading this article because it's so delightful. But also, I think it's scientifically kind of interesting because they talk about how they develop their methodology because they gotta figure out when they poop out the Lego head, which means they gotta figure out how they're gonna gather the poop and how they're going to look through it to find the Lego head. So there's just, there's actually a decent amount of technical information around all of this. And so it does make the article a little gross at times. So if you don't like reading about poop, then you know, maybe this will not be as delightful for you. But I do think that this was a great read. So I highly recommend it.

I am absolutely going to read this immediately following our conversation today. I'm so excited. Thank you Deboki. We needed that.

I'm so glad I could help.

Sam: So good. All right. Shall we close it up?

Deboki: Thanks for tuning in to this week’s episode of Tiny Matters, a production of the American Chemical Society. Our exec producer is my co-host, Sam Jones.

Sam: This week’s script was written by Deboki and was edited by me and by Matt Radcliff. It was fact-checked by Michelle Boucher. Episode audio was edited by Russell Silber. The Tiny Matters theme and episode sound design are by Michael Simonelli and the Charts & Leisure team. Our artwork was created by Derek Bressler.

Deboki: Thanks so much to James Weiss for joining us. If you have thoughts, questions, ideas about future Tiny Matters episodes, send us an email at You can find me on Twitter at okidoki_boki.

Sam: And you can find me on Twitter at samjscience. See you next time.