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THE HOT SPRING IN THE BASEMENT
Let both curiosity and horror—the latter of which terrorizes us but also holds us rapt, unable to look away—be a motivator for discovery. Embrace the weird, the tiny, the things we’d like to ignore.
—BROOKE BOREL, Infested: How the Bed Bug Infiltrated Our Bedrooms and Took Over the World
IN THE SPRING of 2017, I was in Iceland filming a documentary about microbes.1 As part of the filming, we stood, again and again, beside bubbling, hot, sulfurous geysers where I was meant to point at the geysers and talk on camera about the origins of life. At one point, I was even abandoned at such a geyser, only to wait for the truck to come back to get me.2 Film crews can be unforgiving. While stranded, I had a moment to myself to contemplate the geysers. It was a cold day, and although they smelled sulfurous, I stayed near them. They kept me warm. The water in the geysers was boiling up from fissures in the Earth, warmed by the volcanism beneath the Earth’s crust. In some places, it is easy to forget that the Earth is tectonic, just as one can become numb to the night sky. Not in Iceland. The western and eastern halves of the island are tearing apart and the consequences of this great rip of stone and dirt are hard to miss. Sometimes volcanoes erupt so violently that they darken the sky. And every single day geysers, like those I stood beside, bubble up out of the ground. As they do, they sustain life, life that has far more to do with what is happening in your home right now than you’d ever imagine.
That species survive and thrive in the warmth of geysers was not discovered until the 1960s. Thomas Brock, then at Indiana University, worked in Yellowstone and then also in Iceland, not far from where I stood. Brock was fascinated by the colorful patterns around the geysers. A smeared palette of yellow, red, and even pink gave way to greens and purples. Brock thought these patterns to be the work of single-celled organisms.3 They were. The species present included bacteria but also archaea. The archaea are an entirely separate domain of life, as ancient and unique as the bacteria themselves.4 What was more, Brock discovered that many of the species in the geysers were “chemotrophs,” species able to turn the chemical energy of the geysers into biological energy; they made life from nonlife without the aid of the sun.5 These microbes were of the sort likely to have existed long before photosynthesis ever evolved, their communities akin to some of the first communities. They evoked Earth’s most ancient biochemistry. I could see them growing in a crusty mat around the geysers keeping me warm.
But these were not the only organisms in the geysers. Cyanobacteria were living in the hot water and photosynthesizing. In addition, Brock found bacteria that lived off of the organic matter swirling around in the bubbling water, be it the cells of other bacteria or a dead fly. Superficially, these scavengers were not very interesting. Unlike the chemotrophic bacteria Brock was studying, they couldn’t turn chemical energy into life and instead had to find and consume living and dead bits of other species. However, after some study Brock decided that they belonged to a new species and even a whole new genus. He called the genus Thermus for obvious reasons and the species aquaticus to reflect its habitat. For mammals or birds, finding a new species is a newsworthy event and finding a new genus, an even bigger deal.6 But not for bacteria. It isn’t hard to find new kinds of bacteria, and in terms of the features that microbiologists focus on first, this new species, Thermus aquaticus, didn’t appear terribly interesting: it didn’t form spores. Its cells were yellow rods. It was gram-negative. All true, all mundane. But there was something else.
Brock saw Thermus aquaticus in the lab only when he kept the growing medium (his cultures) at temperatures above 70 degrees Celsius (122 degrees Fahrenheit). It preferred even hotter temperatures and could still live at temperatures as high as 80 degrees Celsius (176 degrees Fahrenheit). The boiling point of water, for context, is 100 degrees Celsius, lower at higher elevations. Brock had grown what were among the most heat-tolerant bacteria on Earth.7 As he would later note, finding this life-form wasn’t hard. It was just that no one else had tried to grow microbes at temperatures so high. Laboratories had cultured samples from hot springs in 55 degrees Celsius culture conditions, too cold for Thermus aquaticus to grow well. Subsequent research has revealed an entire world of bacteria and archaea that can be grown only under very hot conditions. To such microbes, the temperatures at which we live out our ordinary lives are so cold as to be unlivable.
Why bring the story of Thermus aquaticus up in a book on houses? Because the temperatures and conditions found in geyseres and other hot springs, as unusual as they might seem, are very similar to those found around us in our daily lives. A student in Brock’s lab thought it possible that Thermus aquaticus or other similar bacteria were even living, unnoticed, alongside us. To test the idea, the student and Brock probed the coffeemaker in Brock’s lab, a machine that was plenty hot enough to favor Thermus. Given how much the machine helped fuel their work, it would have been an apt place to find the species. It wasn’t there.
Brock found himself wondering about other places around him that contained hot liquids, such as the human body. Human bodies are not nearly as warm as hot springs, but Brock thought perhaps the bacteria might be present anyway, holding out for moments of fever. Who knew? It was easy enough to check. So Brock “produced” a sample of human spit (in an email, he declined to note whether it was his own, which in my experience studying the behavior of scientists means it was). He tried to grow Thermus aquaticus from the spit. Nope, no Thermus aquaticus. He checked human teeth and gums (much as Leeuwenhoek might have). None there either, nor any other heat-loving bacteria. Neither were there any in the lake from which he took a sample, nor in the nearby reservoir. He also checked the cactus in the greenhouse in his building, Jordan Hall. Nothing. Perhaps it really was a bacterial species found only in hot springs.
Just to be sure, Brock checked one more location: the hot water tap in his lab in Jordan Hall. Brock’s lab was two hundred miles from the nearest hot spring. Yet, the lab’s tap water contained what looked to be Thermus aquaticus. This was fantastic. Brock wondered whether the hot water heaters provided the habitat for the microbe—the water in the tap was warm, but not like in a hot spring. The hot water heater itself should be nearly perfect. Maybe the bacteria lived in the hot water heater and every so often, inadvertently, rode downstream to the tap.
Eventually another pair of researchers, Robert Ramaley and Jane Hixson, both of whom also worked at Indiana University, did additional sampling of thermophilic bacteria around Jordan Hall. When they did, they too found a kind of thermally tolerant bacteria. It was similar to the Thermus aquaticus noted by Brock. But it wasn’t identical, so they called it Thermus X-1 for the time being.8 Unlike Thermus aquaticus, it wasn’t yellow. It was clear. Also, it grew faster than did Thermus aquaticus. Ramaley speculated that perhaps it was a new strain of Thermus aquaticus. Maybe the yellow pigment of Thermus aquaticus was an adaptation that protected it from the sun out in exposed hot springs. Perhaps, having colonized water sources in the building, this strain might have lost the ability to produce the expensive and unnecessary pigment. Brock, who had by then moved to the University of Wisconsin, decided it was time to study the Thermus in buildings in more detail.
Brock, along with his lab technician Kathryn Boylen, looked in hot water heaters both in homes and in laundromats near the University of Wisconsin. In laundromats, hot water heaters are often larger and used more consistently than those in homes, such that they might be even more likely to house thermophilic microorganisms. At each site, Brock and Boylen unfastened the drain on a hot water tank and examined what was inside. In hot water heaters, like in hot springs, temperatures can get very hot. In addition, all tap water contains organic material, perhaps enough of it to sustain Thermus aquaticus.
Over a century ago, the ecologist Joseph Grinnell applied the term niche to describe the set of conditions a species needs to survive. The word niche derives from the Middle French word nicher, “to nest.” It was first used in reference to the shallow recesses in ancient Greek and Roman walls in which a statue or other object might be displayed.9 The niches were just the right size for the statues, much as the temperature and food resources in your water heater seem to suit the needs of Thermus aquaticus. But just because a species can survive somewhere doesn’t mean it arrives. Scientists now distinguish between the fundamental niche of a species (those conditions in which it could live) and the realized niche (those conditions in which it does live). The fundamental niche of Thermus aquaticus includes hot water heaters, but whether it was realized was another question altogether.
It was. Brock and Boylen found that species of the genus Thermus live, in addition to in geysers exposed to magma and in the tap water in Jordan Hall at Indiana University, in the hot water heaters of houses and laundromats around Madison, Wisconsin. What was more, the bacteria found in those hot water heaters were tolerant of temperatures as extreme as any at which life had been found anywhere. Brock went to the ends of the Earth to find species of the genus Thermus. He could have made the same discovery around the corner from his laboratory in the back room of the Suds and More.10
Since Brock’s work, no other scientists have yet published papers about the Thermus aquaticus in hot water heaters. A new species of Thermus was, however, discovered in hot tap water in Iceland.11 It turned out to be the same pigment-less species Brock and Boylen found in hot water heaters, a species now called Thermus scotoductus rather than Thermus X-1.12 A graduate student at Pennsylvania State University, Regina Wilpiszeski, has spent the last few years sampling hot water heaters to see whether this is the main species present in hot water heaters. It appears to be: she has found Thermus scotoductus in hot water heaters across the United States. In thirty-five out of a hundred hot water heaters Wilpiszeski sampled, she found Thermus scotoductus. Wilpiszeski’s work is not yet done, but it already raises new questions. Why is this species present in hot water heaters and how does it get there? And why have the many other heat-loving bacteria able to live in hot springs not yet colonized hot water heaters? Why don’t very old hot water heaters take on the colorful microbial complexity of hot springs? So far, none of these questions have been answered.
I suspect different species of heat-loving bacteria live in hot water heaters in other regions. It is easy to imagine the species found in hot water heaters in faraway New Zealand or Madagascar might be totally unique. We don’t know. Much in the way that few followed up on Leeuwenhoek’s efforts, the same has been true for those of Brock.13 Wilpiszeski stands alone. We don’t know whether Thermus scotoductus has any consequences for us or our hot water heaters (be they positive or negative). Nor do we know whether the Thermus scotoductus bacteria in hot water heaters might have some uniquely useful attributes; the same species collected from other habitats seems to be able to make toxic forms of chromium nontoxic, among other tricks.14 But the story of Thermus has been key in the history of the study of life in our houses. It was an indication—indeed, the clearest reminder since Leeuwenhoek’s time—that the ecosystems in our houses are more diverse than we had thought, populated with far more on hand than the pathogens that have received so much focus. Moreover, the Thermus in the water heater spoke to the possibility that the conditions of the modern home could have invited species indoors that never used to live around us, species that had moved in unnoticed. Ultimately, the presence of Thermus in hot water heaters helped, slowly, trigger a broader search for life in homes. It inspired people like me to consider the possibility that Thermus was not alone but instead part of some much bigger story. One can find, in houses, conditions as cold as the coldest colds, as hot as the hottest hots. One can find a microcosm of the world’s conditions. It was entirely possible that these microbes had found and colonized our indoor extremes, but that no one had looked for them. The next revolution in the study of the home awaited new techniques, techniques that would allow microbes to be identified even if they could not be cultured in Petri dishes, techniques that would prove to be dependent on the unusual biology of Thermus itself.
WE HAVE KNOWN for a while now that most species of bacteria cannot be grown in the lab; they are still “unculturable.” We don’t know what food or conditions they need, so even if we sample them, we never see them. This means that for most of the history of microbiology these species were also unstudiable unless a clever and persistent biologist made an unculturable species culturable by figuring out its needs. Such was the case with species of the genus Thermus; they went unseen until Brock tried to grow them at high temperatures. But our ability to see the unculturable life around us has recently changed. It is now possible to study, and understand species we have no idea how to grow. This is thanks in no small part to Thomas Brock’s discovery of Thermus aquaticus and its kin.15
The main tool we now use to initially find and identify unculturable species is really a series of laboratory steps. Those steps often are called a “pipeline,” where pipeline just means the steps need to happen in order.16 Into the beginning of the pipeline, one inserts a sample. Out the other side comes a list of the species, be they living, dormant, or even dead, present in the sample. This pipeline is an approach worth understanding in more detail because we have come to use it again and again in our research.
The pipeline begins with the samples. Once in the lab, samples are put into small tubes that contain a drop of liquid. The samples might be dust, or feces, or water—anything that contains or might contain cells and DNA. The liquid includes soap, enzymes, and tiny round glass beads, each the size of a grain of sand, which help to break open cells, like cracking eggs, to get out their DNA, the bacteria’s genetic code. The tube is then sealed, heated, shaken, and centrifuged. The heavy beads and many cell bits and pieces sink to the bottom of the tube. The treasure, the long strands of less dense DNA, rises to the top to be skimmed off the way you might pull a dead fly from the surface of a swimming pool.17 All of this is pretty straightforward and can be done in an introductory biology laboratory with sleepy students, some of whom have likely ignored most of the instructions.
To identify the different organisms on the basis of the resulting DNA (which has been “extracted” from its cells), we need to read the DNA, a process scientists call sequencing. This is the tricky part. As opposed to microscopes, which make the thing you are looking at appear to be bigger, sequencing techniques make the invisible information in DNA intelligible by first making it more plentiful. The trick was how to make it more plentiful so that the nucleotides of the DNA, its genetic letters, could be read. All DNA, except that in viruses, is double stranded. Two complementary strands are joined by a sort of molecular zipper. It was understood quite early on that if the two strands of DNA could be (gently) unzipped, each strand could be copied, and that this might be repeated until there was enough DNA to work with and decode. The two strands of DNA can be separated using heat. That much was easy. Copying the separate strands of DNA then just required use of an enzyme called polymerase, the same enzyme cells themselves, including human cells, use to copy DNA. You could separate the two strands of DNA, add some polymerase, a primer (the bit of DNA that told the polymerase which section of DNA, which gene, to copy), and some nucleotides, and you’d be on your way. The problem was that temperatures hot enough to pull the two strands of DNA apart were also hot enough to destroy the polymerase. One clumsy, expensive, labor-intensive way around this problem was to add fresh polymerase and primers after each round of heating. This approach worked, but was painfully slow, slow enough that in studying bacteria it was still easier for most microbiologists to just focus on the subset of species that could be cultured and ignore the unknown, unculturable bacteria for the time being.
A solution was forthcoming. The solution was Thermus aquaticus. The polymerase of Thermus aquaticus works at high temperatures. More than that, it works best at high temperatures. This polymerase was exactly what was needed. Several years after Thermus aquaticus was discovered by Brock, it was realized that the polymerase of Thermus aquaticus (nicknamed “Taq”) could be added to DNA at high temperatures and the DNA would be copied rapidly. The copying of DNA using thermally tolerant polymerases, a process called the polymerase chain reaction (PCR), may seem abstract, a minor scientific footnote. Yet it is at the heart of virtually every genetics test being done in the world, whether it is to identify a child’s paternity or the bacteria in a dust sample. The bacterial lineage discovered in hot springs and hot water heaters, a lineage that inspires our quest for unusual life in homes, also provides the enzymes necessary to carry out this quest across modern scientific research.18
Just which gene scientists, technicians, or clinicians copy during the polymerase chain reaction, and how they decode the resulting copies of DNA, depends upon the goal of the study and the technology being used. Studies that attempt to identify all of the bacteria in a particular sample tend to copy a single gene, the 16S rRNA gene, which is so central to the function of bacteria and archaea that it has changed little over the last four billion years. For that reason, scientists can count on the gene being present in any species of bacteria or archaea studied. The gene differs enough among species to allow them to be distinguished, but not so much that it becomes unrecognizable. As for the technologies used for decoding the many copies of this gene, they vary greatly. Some rely on adding labeled nucleotides (those genetic letters) into the samples that have been or are going to be copied. The nucleotides are labeled with substances that can be read by a sequencing machine. The machine begins by reading each copy of the primer, that beginning stretch of nucleotides, and then it reads the letters that follow. It does this for all of what might be billions of individual copies of DNA in a sample, yielding enormous data files in which the code of each and every bit of copied DNA is listed. Those copies are then lumped into groups on the basis of their similarity to each other, and the codes of those groups of sequences can then be compared to the genetic sequences of known species in databases from other studies.19 The mechanics of this process are ever changing, but one thing about them is not. Every year they are cheaper and easier. Handheld sequencing devices are now on the horizon. (Indeed, they already exist but are prone to errors in reading the DNA. With time they will improve.)
Today, then, thanks in no small part to Thermus aquaticus, it is now possible to take a sample and process it through the “sequencing pipeline” in such a way as to identify which species, living and dead, are present in the sample. This can be done without ever seeing or growing any of the species in the sample. Biologists can identify the life in soil, seawater, clouds, feces, and anywhere else. Biologists can identify culturable species but also the many, many species we do not yet know how to culture. Such a reality seemed impossible, inconceivable really, when I was a graduate student. Today, it is ordinary.20 About ten years ago my colleagues and I decided to use such techniques to study the life in homes. At the time it had become possible, and affordable, to take a swab of dust from a door frame, a drop of water from the tap, or even a piece of clothing from the closet and to identify nearly all of the species present in that sample by decoding the DNA in the sample. Leeuwenhoek held his single lens up to the life around him. We would run the life around us through the sequencing pipeline. When we began, we really had no idea what we would find. The results would prove surprising. They were surprising both in terms of the many species we found to be present and in terms of those that were missing.