University Place

The Microbial Planet

This is our final University Roundtable of the Spring semester. I’m Renee Meiller and I am a member of the committee that chooses our speakers. Before we begin, please join me in thanking this year’s sponsors of the University Roundtable. Those include the Office of Learning and Talent Management, the Chancellor’s Office, the Wisconsin Union and the Office of the Secretary of the Academic Staff. We are very lucky to have today’s speaker back at UW-Madison. Jo Handelsman earned her PhD here at UW Madison in Molecular Biology, after which she enjoyed a 24-year career at our university. That included 22 years as a faculty member in Plant Pathology and another two years as a Professor and Chair of the Department of Bacteriology. She left briefly to conduct some important business. In addition to serving as a Professor at Yale University, she also was Associate Director for Science in the White House Office of Science and Technology Policy serving under former President Barack Obama. We are excited this Plant Pathologist has, forgive my pun, returned to her Wisconsin roots. Jo now is Director of our Wisconsin Institute for Discovery. And as her laboratory name might suggest, she also oversees the Handelsman Lab in the Institute. Her group focuses on understanding diversity in microbial communities and their role in infectious disease. In addition to her service as Director of the Discovery Institute, she is a Vilas Research Professor in the Department of Plant Pathology. She also is in high demand as a lecturer, so we’re excited to have her today, for example she recently spoke at the American Association for the Advancement of Science. It is an honor and pleasure to introduce her today. Jo Handelsman, Director of the Wisconsin Institute for Discovery, welcome. [applause]

– Well thank you, Renee, for the lovely introduction and the welcome back to Wisconsin, which I can say has been just an absolute delight and a privilege to experience over the last year. It’s been great to be in Wisconsin, at the university and at our wonderful Wisconsin Institute for Discovery, so, thank you again for welcoming me. Well, it’s a real pleasure to be here. I, in the past, in my past life in Madison I was a great fan of the Roundtable because I always found it such a great place to meet interesting people from across campus. So I hope you’ve all had enough time to meet your table mates and learn something about another part of campus. I’m going to tell you today about another part of campus as well as a part of the world that you may not think about too much, a part of the world that we can’t see, by definition, because it’s microscopic, but nonetheless is what drives most important elements of our planets and our bodies and everything else around us. And so I’m going to talk about the, what I call The Microbial Planet, from a perspective of an idea that has bothered me forever, that even though people don’t appreciate microorganisms, we call them germs and we disrespect them in all sorts of ways, all we seem to want to do is get rid of them if you watch modern television.

Microbes in fact do run all of the important processes in us and around us and keep our Earth healthy, keep ourselves healthy and I’d like to, today, convince you of that. Somebody once called me a lobbyist for the microbe, so I apologize if this sounds like an ad, but I do market my microbes because it is a fact that the microbes rule the Earth and rule us and I hope to convince you of that today. So I want to cover four questions. First, what are microbes? Because people often hear the word and they’re not quite sure what that encompasses. And then why do we think they’ve gotten such a bad name. Why do we talk about them as germs and bad things that we should wash away or sterilize away? And then ask the question, do microbes make us human? And I think this is becoming both a philosophical question as well as a biological one that is quite serious. How much of who we are, as humans and as functional beings, both physically and mentally and behaviorally are we because of our microbes? And then finally, how do our microbes influence the Earth around us? So starting with what the microbes are. So there are several groups of organisms that make up the microscopic world. One group are the viruses, this is a colorized version of one of the prettier viruses that we have. These are the tiniest of the microbes and they can’t live by themselves. These are the microbes that live in association with other organisms, we probably know them well because of the diseases that they cause in humans. There are also well-known eukaryotes which are the higher organisms, although of course I think bacteria are the highest organisms around so I think that’s a misnomer, but we’ll get to that. These organisms are cellular, they have cells, they also are microscopic, but they also have nuclei and they have parts to their cells. And that’s the definition of a eukaryote, they have a nucleus and various other organelles or sub-compartments. The biggest of those are the microscopic worms on the right, the nematodes. And those are sometimes debated to be microbes because they can get big enough that you can see them with the naked eye, but I include them because I think they’re a really interesting group of organisms. The protists, I’ll talk about one that caused a very important famine in history. Those are less well known because they’re harder to study, we haven’t been able to culture them in the laboratory for the most part and they’ve been somewhat ignored in many fields.

The fungi have gotten most of their attention in plants because they’re the most important group of organisms that kill and make plants sick. And then there are the prokaryotes and these are the so called lower, but I think top of the heap organisms. These are the ones that don’t have nuclei, don’t have sub-cellular compartments. They’re unicellular organisms and there are two groups of them. And I’ll talk in a minute about some of the reorganization of the Tree of Life that we’ve learned about in the last 30, 40 years that tells us that there are two groups of prokaryotes, one are the archaea and one are the very well-known bacteria. And for a long time these were thought to be one group and then it turned out that evolutionary understanding shows that they developed on very different paths many, many years apart in evolutionary history. The bacteria are the ones, the microbes that I’ll be talking about mostly today and they’re typically the ones you hear a lot about. Besides the viruses, probably the bacteria are the most famous ones and they will include organisms like the one shown on the lower right, which is Lactococcus lactis, which is, has, was actually proposed as our state microbe because it is the cheese making organism. Just as an aside, that organism passed muster by the Assembly of Wisconsin, but then died in the Senate.

And we’re just starting a campaign to rejuvenate it because the Senate said, oh, we have more important things to do than discuss microbes, even though we had explained that a multi, multi-billion-dollar part of our economy is based entirely on microbes. And then a few month later it passed the State Pastry. [laughter] So we knew how busy they were. Which is Kringle, if you want to know. So the bacteria are wonderful microbes like Lactococcus that makes cheese and then some that aren’t as friendly, like Staphylococcus, Streptococcus, many that cause disease. So why is it that people don’t appreciate the power of the microbes to keep the world happy and healthy? Why is it that we have this negative view of microbes? And I think it goes back to the many plagues that affected the human species for many, many centuries, probably ever since we started living in groups on Earth. And these were of course devastating, bacterial for the most part infections, the plague being, the Black Plague being one of the most popular examples and it was remembered very well by Albert Camus, in the book The Plague. There are many others, the Black Death, I mean the names are all very intimidating and you can see that art has commemorated these terrible scourges on human existence very well. And I think it’s the breadth of their devastation that has left such an indelible mark in peoples’ minds of the very visible impact when millions of people die from an epidemic. Similarly, these are all depicting bacterial plagues, in this case it’s a plague caused by a protist, one of those eukaryotic organisms I mentioned. And this was the Irish Potato Famine which was caused by a microorganism that just devastated all the potatoes in Ireland in a two-year period in the 1840s and led to a mass extinction of people of Irish, on the island of Ireland and also enormous immigration to this country and to Canada. And so this microorganism had a tremendous impact, in fact the population of Ireland has never recovered to what it was in the 1840s.

The potato was a tremendous boon to, I apologize, that’s my, the potato was a boon to the Irish people and allowed their population to grow tremendously. And after the Potato Famine wiped out many of the potatoes as well as the people the population was never able to recover. But of course we owe a great debt to the Irish Potato Famine because of all of the people of Irish decent that live in this country now. So it had for decades and decades an enormous impact on the movement of the Irish from Ireland to the New World. So that was a really high impact event, devastating event that changed Irish history forever, changed the relationship, worsened the relationship, between the Irish and the British, the effects of which are still being felt today. But in the 20th century we began to understand some of these plagues and these enormous devastating events that affected human history. We started understanding them in a new way and the first was the etiology of disease. This happened at the end of the 19th century and then into the 20th century, when we began to understand that microbes actually do cause disease. And it’s surprising that the microbes were suspected for centuries, literally, before it was actually shown rigorously that microbes cause human and animal and plant disease. In the 20th century, we began to understand the immune system and that enabled us to take advantage of vaccines, which gave us immunological protection against many pathogens that have affected people throughout history. And gave us an immunity not only to the disease, but I think of a sense of immunity of our own selves to the invasion by these kinds of pathogens.

I think we became a little bit less afraid of them and perhaps dismissive of them because of vaccines. But the most important event of the 20th century was the discovery of antibiotics. And this happened in 1929 when Alexander Fleming found on a Petri dish in his lab a fungus called Penicillium mold, that was able to produce this zone of no growth around it. And so the white, the bright white circular thing is the mold and then the other organism growing on the plate is Staphylococcus, a pathogen. And he found that the mold was secreting this chemical that inhibited the growth of the bacterium. And he immediately recognized the impact of this, that if we could harness this, if we could use this new chemical penicillin in treating infectious disease, we could have a completely different relationship with the microbes and even things that couldn’t be subjected to vaccines would be manageable, at least among the bacterial pathogens. But you can see that that zone of inhibition is really very tiny and that meant that there wasn’t very much penicillin being produced by this mold in Fleming’s hands. And so the discovery was wonderful from a very basic standpoint, but it didn’t end up in a commercial setting or able to be used broadly in people for well over a decade. And in fact there’s stories of people approaching Fleming and saying my child is dying and can you give us some penicillin? And Fleming could make so little penicillin that he would give the child penicillin and then he would collect the urine which had the penicillin in it that had gone through the body and repurify it from the child and give the penicillin back again, that’s how precious this substance was and of course that was not viable on any kind of large scale. So it was really during World War II that antibiotics took hold in a meaningful way in human health.

And that started with Kenneth Raper who was a Professor here at UW in his later years. But at the time during the war that he did the work I’ll talk about, he was actually at a USDA facility in Peoria, Illinois. And I had the pleasure of knowing Ken Raper at the end of his life and he was the ultimate gentleman scientist. He always came to work looking like this, he was in the Bacteriology Department here when I was a graduate student, he always wore a tie, he always wore a hat and he always wore a suit and then sat at his microscope all day long. And he did this very, very basic science on these obscure organisms that very few people even know exist, called the slime molds. But during the war, he knew that there was a higher calling, that basic research was great and he eventually returned to that, but there was a real need and that was the discovery of penicillium mold strains that would produce enough penicillin to actually be useful in a practical way. And so during World War II he set up a search in Peoria, where his lab was, for strains of penicillium mold which grows, I’m sure you’ve all seen it on your bread or your melons or fruits and vegetables, it’s that beautiful, I think, see I’m biased. [laughter] Blue green mold that you find when some of your foodstuffs get old. And so he put out a call in the community of Peoria and said anybody who gets penicillium mold on your food, please bring it to the lab.

And it turned out that it was actually his own technician, Mary Hunt, who saved the day. She picked up a melon in the local market and it had this beautiful blue green film on it and she knew that was penicillium mold. And that strain of penicillium still to this day produces more penicillin than any other natural strain anyone’s ever found. And it was just this freak of nature that produced massive amounts of this incredible compound that we know of as penicillin. And Moldy Mary as she’s known in the world of bacteriology was commemorated in a painting that hangs on this campus. And you can see her picking up her melon in the market, that has the penicillium strain on it. Well the rest really is history because World War II became the first war in history when more people died directly of bullets and bombs and the armaments of war than of the infections that resulted from their injuries. And that was because once Raper and Hunt had their strain, they immediately took it to a drug company which took it into immediate large-scale production and shipped enough penicillin over to the troops in Europe that it saved millions and millions of lives and of course since then has been, has continued to save lives to this day. And I love this ad from during the war, this was in Life Magazine and it’s an ad that says, “Thanks to penicillin he will come home. ” And if you can see the picture it’s a soldier being treated with penicillin the drug. This really changed history because now simple ear infections, all sorts of fevers and diseases that used to be a threat to our health to the point that many children died, infant mortality was incredibly high before antibiotics, suddenly these became manageable diseases. These became diseases that one survived to tell about instead of dying from the infection.

And only today are we beginning to emerge from that glorious era of antibiotics controlling our diseases because we’re now seeing such high levels of resistance among many, many of the pathogens that we can’t treat them anymore. Unfortunately, due to a series of different reasons there’s a lack of new antibiotics coming from industry and the result is we have a lack of new antibiotics, we have resistance to the old ones and you can see where that leads. We have all these pathogens now that can’t be treated with the antibiotics we have in hand. So we’re now facing a crisis that could, has a potential to put us back to a time that’s far worse than where we were during World War II and before because now we have such a dense population on Earth. People are living in such close quarters in so many large cities that infectious disease is a much more serious problem than it would have been in the 1930s and before. So we’re facing a health crisis today that does bring the bacteria back to light in their very negative role as inciters of disease. But it’s also important to remember that after the penicillium mold all, almost all of the other antibiotics that were discovered were produced by bacteria. And so we are using what’s probably a form of natural warfare between bacteria to make our antibiotics. And so even though the bacteria have this terrible name for causing human disease, they’re also the means for curing human disease through antibiotics. So the 20th century saw this incredible change in our relationship with microorganisms. And I think it’s historical that we have this despicable attitude about microorganisms being bad and dangerous because it turns out that the vast majority of them are helpful and healthy for us and not negative. It’s interesting that in the early 20th century this was actually appreciated by a very small number of people. But this manuscript was found a few years ago and does anyone recognize the handwriting? Well I’ll show you what the manuscript says. It’s actually a novel and it’s about a bacterium living among bacteria in the human body. And some of the text on this first page of it is really significant. For example it says, we know that the human race was saved from destruction in the beginning by the microbe. We know that the most valuable citizen of the Earth was the microbe and that the human race could no more do without him, should be her, but OK, typo, [laughter] than it could without the sun and the air. Now who wrote this? This was we think in, it was never turned into a book, it was never completed, but it is a long novel and this is 1906 we think and it was written by Mark Twain. So in the early 20th century he happened to live near one of the earliest Bacteriology Departments in the country which was at U. Conn in Connecticut. And he went to some lectures by Professor HW Conn and that’s actually mentioned in his novel and he was absolutely enthralled by the idea of the microbes.

So even then, there were people who appreciated, including Mark Twain and the Professor who taught him Bacteriology, that the microbes living within us are a benefit, keeping us healthy, protecting us and that we couldn’t live without them. And so it took us a long time to catch up with that. And it took, in fact, most of the 20th century for the rest of the world to recognize that in fact the microbes are absolutely essential to life. I think, and this is unproven, but I think it was ulcers that made the difference. And ulcers were a disease that were attributed for decades and decades to the kind of food you ate. People would say, you know, hot food causes ulcers, people would say stress caused ulcers, genetics, there were all sorts of explanations for ulcers. But it turned out in the late 20th century, the 1980s actually, there was a study of ulcers. So that’s what a stomach ulcer looks like, it’s this horrible little wound in the stomach and extremely painful. And there was a study done by a group in Australia that was convinced that it was actually bacteria in the stomach that caused ulcers. And the scientist who purported this idea couldn’t get anyone to listen, the medical community literally laughed at him. So eventually he took a culture of what he believed to be the ulcer causing organism that he had isolated from the stomachs of ulcer patients and he drank a large quantity of the culture. And in fact he did get ulcers and he eventually treated himself with antibiotics and cured them. And that changed the entire view of the medical profession of ulcers, but also of many, many other diseases. He eventually got the Nobel Prize and people stopped laughing at him [laughter] and we now know today that we can treat ulcers very effectively with antibiotics because in fact they are caused by a bacterial infection. But what was striking was the realization that there are functions of bacteria that we don’t recognize. There was a certain arrogance about microbiology, I think, for most of the 20th century, that we know most of the causes of disease, we know most of the functions of bacteria and we know who all the bacteria are. When I first entered this field we thought we knew the full breadth of Bacteriology. And in fact we found out, based on first ulcers, because people couldn’t culture these organisms at first, it was the group in Australia that learned how to do that and people believed because they couldn’t culture anything from the stomach, they believed the stomach was sterile. Well the stomach is not sterile, there are bacteria that are fully well adapted to living in the stomach. And this is Helicobacter pylori, the causal agent of ulcers. And I believe it was the discovery of that organism that was essentially invisible to people throughout medical history until this work was done, that changed peoples’ minds and had us as microbiologists scratching our heads saying well what else are we missing out there? What else can’t we see or what else can’t we culture? And that led to a revolution in the way that microbiologists do what they do.

Until that point, from the late 19th century, 1878 actually, the first Petri dish was used and organisms were cultured in the laboratory on Petri dishes and from then on, for more than a hundred years, that was essentially the core of microbiology. Everything that could be cultured was studied and everything that couldn’t be cultured was ignored. And that’s a little bit of an overstatement but not much. Everyone wondered why would you study anything that you couldn’t culture because all bacteria were cultured. But it turns out that in the late 20th century scientists discovered that most of the microorganisms in us, on us, around us, in the Earth, in the ocean cannot be cultured in the Petri dish. And so we had to move to other methods for describing those organisms and those became largely DNA-based methods. So DNA was the chemical that could be isolated from essentially every organism in the environment whether you could culture it or not. In fact some of the methods literally involved extracting DNA directly from sea water or from soil without ever isolating the bacteria in any way, that circumvents the need for culturing. And we could begin to see in an abstract way because we could see the DNA and we could sequence the DNA, we began to see the diversity of life that was lurking in us and around us that had eluded us because these organisms didn’t grow, for the most part, on our Petri dishes.

And so the DNA revolution in microbiology has totally transformed our view, not just of microorganisms, but in fact of the whole biological world. So this is a tree that developed from the methods, the DNA-based methods that came out of that era. And where many of us probably have heard of the Five Kingdom Model on the Tree of Life, has anyone learned that? Yeah, most of us learned that in high school, they still teach it in high school, well it’s completely wrong. [laughter] And we now know that because we can do evolutionary studies about the, all the organisms that exist and we can get DNA from all these organisms. And if you look at this Tree of Life, as we now know it, it’s fascinating because all of it is microbial except a little bit up in the upper right. And so the animals and the plants are visible, those are macroscopic. Everything else in that tree, including even most of the eukaryotes that we think of as the big organisms, are microscopic. And so the bacteria and the archaea have represented the vast majority of evolutionary history. The lower eukaryotes, which are the microscopic ones, represent the vast majority of eukaryotes. And the diversity among all of those organisms so far overshadows the diversity of animals and plants that we can’t even put numbers to that. The diversity of all these other organisms hasn’t even been described fully. We know of what we think of hundreds of thousands of them, but there are probably many millions and that leaves many left to be discovered.

So once people began to recognize that in fact the microbial world, the biological world was far more complex than we had given it credit for from our culturing, we began to study all the environments that had been cultured previously and asked what were we missing in those environments? And so the first one I want to talk about is the human microbiome because it’s of interest to all of us because it’s what keeps us healthy and also makes us sick. One of the environments that was discovered to contain a much greater diversity of organisms than was previously suspected, is the human colon and this is known as the gut microbiome. And it’s the site of probably most of the organisms of the human body and in fact it’s most of the cells of the human body. And you heard me right, most of the cells in the human body are microbes living in the gut and other environments on us. We found that, decades ago, that there are actually hundreds of species living in the gut. We used to know of a few and functions of even fewer but what is truly amazing is that there are 10 times as many microbes in and on the human body as there are human cells.

So that makes us question our identity, are we human or are we microbe? [laughter] We’re actually mostly microbe is the answer. We’ve found since then that microbes influence our immune system and so without a normal gut microbiota or microbiome we don’t develop a normal immune system. So they’re absolutely essential for us to become what we ultimately become as mature humans. And they clearly protect us from chronic disease and I’d like to give you a few examples just because it’s become such a fascinating field. And you probably have read some of this in the paper but you’re going to be reading a lot more about the impact of the microbiome on chronic disease. So strong connections have been made between the human microbiome, the composition of the microbiome which means which organisms are there and which ones aren’t and diabetes, colon cancer, heart disease, in fact they’ve found that HDL/LDL ratios, one critical feature in predicting heart disease are determined in part by microorganisms. And even things, behavioral things like Tourette’s Syndrome was one of the early things that was associated with bacterial infection, so that’s a behavioral characteristic. Probably the most dramatic example was the study of obesity. And in this they took microbiome samples, so gut microbiome, complex mixtures, no culturing involved, and they transferred those samples from humans to germ free mice, so these are mice that are grown without any microbes, they’re sterile inside and out from birth. And what they found was that if you transfer the microbes from a lean person, the mouse stays lean. But if you transfer the microbes from an obese person you can induce obesity in the germ-free mouse. So this is, was one of the very early causal relationships that was demonstrated between the microbiome and a characteristic or a disease of humans. Some of the ones that I find the most interesting and that are forming a large project within the Wisconsin Institute for Discovery are the relationship between the microbiome and brain diseases. So one that has caught a lot of peoples’ attention is depression. There was a paper that was called Catching the Blues and it meant that you can actually transfer the depressive characteristics from one organism to another by transferring microbes.

And so the experiment was taking the microbes from depressed people, putting them into germ free mice and finding that those mice begin to express the behaviors of depressed mice. And I can tell you about depressed mice if you want to know, it’s very sad. Germ free mice were noticed very early on these are ones without any microbes in them or on them to grow more slowly, so clearly they needed their microbes for normal growth, but they also were less aggressive and the males were much less likely to eat their babies. So this is a behavioral thing that I expect we have a couple of lawyers in the room, I expect we’re going to start seeing this showing up in the courts. You’ve heard of the Twinkie defense? Well I think we’re going to hear my microbes made me do it. [laughter] And then a study that came out just a few months ago from here at UW from Federico Rey and Barb Bendlin’s labs showed that in fact Alzheimer’s seems to have a link. And it’s not yet causal, but it’s a strong association between Alzheimer’s symptoms and the gut microbiota. And they found that there was a dramatic difference in the composition of the gut microbiota between patients with Alzheimer’s and those without. But even some patients without Alzheimer’s symptoms had altered spinal fluid that were the markers for Alzheimer’s in their spinal fluid and that correlated with the microbiome changes. So we don’t know of course if the people with those changes might go on to develop Alzheimer’s or not, but there does seem to be an association between the microbiome.

And of course the next step is to determine whether the microbiome is a result of that disease or is actually causing it and perhaps there’s a route to altering the course of the disease. So I hope you’re convinced by now that you are not really human, you are truly a mass of microbes. And in fact your microbes affect who you are, what you look like, how you behave, how healthy you are and even the choices you make. One of the things that I love about the microbes is that they crave certain foods and they make us crave those foods. And there was a paper a few years ago that showed that microbes being fed chocolate actually make us crave chocolate. So it’s not us, it’s the microbes, you can blame them. [laughter] But the microbes have much broader impacts than just on the human system. The world around us is just completely shaped by microbes. And this started probably longer ago than this, but about three billion years ago bacteria evolved that started producing oxygen. And after hundreds of millions of years enough oxygen built up in the environment around the Earth that two things happened. One, there was oxygen to breathe, so aerobic organisms, ones like us that depend on oxygen, could survive on Earth.

Before that everything was anaerobic, oxygen free. And the second important thing was that the oxygen eventually reached such a high concentration that it started inducing chemical reactions and forming ozone, which is a complex of three oxygen atoms. And the ozone layer which is above our atmosphere is critical for life on land because it filters out ultraviolet light which kills life. And so there was a pretty dramatic moment in history when oxygen built up to a high enough concentration that life began to move from the ocean to land, land plants began to evolve. And you can see on this graph the formation of the ozone layer shown on the, in the dotted line and the formation of the oxygen layer is the solid line which is a little lower. What is striking is that the vast diversification of life, the what’s known as the Cambrian Explosion, happened after oxygenation of the atmosphere. And so the incredible variety of life forms that we see around us today could not have happened without the formation of both the oxygen atmosphere to breathe and then the ozone layer above that to filter out UV light. So that was three billion years ago and the microbes have very generously continued to produce oxygen for us, but they’ve done lots of other things, too. Carbon fixation, something we hear an awful lot about because carbon dioxide in the atmosphere is one of our major greenhouse gases, it turns out that although the trees and plants get all the credit for photosynthesis, more than half of that photosynthesis is done by microbes in the ocean.

And so and they were the early ones, they did photosynthesis long before the plants evolved. So the microbes in the ocean are fixing carbon dioxide, taking carbon dioxide out of the air and into the ocean and they’re releasing oxygen to cleanse and nourish the atmosphere. So critical to the balance of gases on Earth are these microbes that carry out photosynthesis. Another thing they do is not so great. So we know that cars produce a large amount of carbon compounds that end up in the atmosphere. There are about a billion cars on Earth and the carbon dioxide and other carbon compounds that they produce are responsible for a large portion of what we know of as global climate change. But interestingly, there are about the same number of cows on Earth, there are about 1. 5 billion cows on Earth. And they don’t produce all that much carbon dioxide they produce some, but more importantly they release vast amounts of methane. And methane turns out to be 20 times worse as a greenhouse gas than carbon dioxide. And so the effect of the methane produced by cows is equivalent to the carbon dioxide produced by cars in terms of the impact on the greenhouse effect and climate change and global warming. The organisms that do this of course are not the cows, cows, can’t blame them, but it’s their microbes.

And this is an example of what the cow’s rumen looks like, which is a mass of billions of microbes living together in a community and one of the things that that community produces is methane. They also nourish the cows and make it possible for cows to eat things like hay that we can’t digest, but the cow’s microbes can. But then one of the negative side effects is this production of methane. And so there’s a lot of thought about how could we manipulate cows and their microbes so that there’d be less methane produced by cow production? So those are a few of the things that our atmosphere is shaped by that is due, are due to microbial activity. There are other things that happen in our atmosphere and one that we’re not very aware of in North America and probably most people aren’t generally because you can’t see it that often, is the movement of soil. And it turns out that five billion tons of soil leave the Sahara Desert, the Gobi Desert, the deserts of Asia and Africa and are deposited, for the most part, in the Americas, mostly South America. And so, for example, the very rich Brazilian soil that we know exists in South America, is due in very large part to this highly mineralized soil that is lifted by wind processes called aeolial processes, from the other continents and then brought down and deposited in the Americas. It turns out that the stabilization of those deserts is a microbial function.

And so on the top left you see a series of microbes that live on the top crust of sand in deserts and beach sand as well. And you can see those long strands, those are long, sticky strands of polysaccharides that have the ability to gum up the sand and clump it together. The same thing happens in soil, this is an important aspect of microbial nourishment in soil. The microbes produce these long, sticky polymers that stick clods of soil together, giving the soil the structure that’s required for healthy plants and healthy soil. So without the microbes we would be losing even more sand from the deserts because the microbes form this crust on the surface of the sand preventing it from being lifted off, at least preventing everything but the five billion tons that are removed very year. So we know that the atmosphere is dramatically changed by microorganisms, we know the deserts are stabilized and the movement of soil across the world is greatly influenced by the microorganisms, but what else do they do? Something that hasn’t been studied probably as much as it should be is the role of the microbes in bio, in precipitation, so we call it bioprecipitation.

So there is a bacterium that was discovered here at Madison to have a very unusual property. It grows on plant leaves, that was no big surprise. But then it was found, in the Plant Pathology Department in the 70s, that after a rain this bacterium called Pseudomonas syringae, grows rapidly on leaves. And so after particularly heavy rainstorms, we see these enormous, skyrocketing populations of Pseudomonas syringae. When the leaves then dry and the sun comes out and it’s windy, Pseudomonas syringae can take off from those leaves and get carried in air currents. So all of that isn’t terribly surprising, but it turns out that it’s very significant because of one gene that this bacterium contains and that’s called the ice nucleation gene. It enables this bacterium to cause water that is otherwise liquid, so below the absolute freezing point which is zero degrees Centigrade water can actually do what we call supercooling, it stays as a liquid even though it’s below the freezing point at which it could be a solid, well when this bacterium is present even at very high temperatures very close to zero, like minus one, minus two, this bacterium can cause ice to form.

So this was initially found to be important for plants, that when plants freeze when the temperature just dips a little bit below freezing it is often because of the ice nucleating bacteria because usually plants don’t freeze, the water on them doesn’t freeze when it’s just minus two or so below zero, it usually takes to minus six or minus eight. But this bacterium turns out to cause ice formation. Well that turns out to be important because the Pseudomonas syringae cells can also get into the clouds, they’ve been detected in the atmosphere. And if you know a little bit about raindrop formation it starts with an ice nucleus that forms an ice crystal. And then as the raindrops come down to Earth those crystals melt and that’s why we see them as rain. So a question that still remains unanswered but there are great suspicions about it, is that Pseudomonas syringae gets into the clouds, it acts as a nucleus for ice formation and induces rain. And there’s actually something we do as humans that’s a parallel to this. You may have heard of seeding clouds with silver iodide. Well it turns out silver iodide is the best ice nucleus known outside of these bacteria which are the best in nature, silver iodide isn’t found very much in nature, but when we use it as a substance to seed the clouds, exactly what I described happens.

There’s a nucleation of ice crystals and that eventually causes rain to occur, raindrops to form and a rain event to occur. So is Pseudomonas syringae having the same effect? We don’t know, but there are some evolutionary arguments that suggest that that’s how Pseudomonas syringae gets around in the world, it goes up to the clouds, the clouds move and then it induces crystallization of water and raindrops to form and then it comes back to Earth where it can eat the good food produced by plants and then it carries out its cycle even more, it goes on. Another thing that Pseudomonas syringae does and WARF actually had the patent on this for 17 years, is to help ski resorts make snow. Because it turns out that this ice nucleation ability lowered the energy needed to produce snow under conditions where it was cold but not cold enough to get snow. And so you could nucleate the formation of ice crystals and eventually snowflakes with this bacterium. And that was a process, I think it’s still used, WARF just doesn’t make money from it anymore, but it’s a process that’s been used across ski slopes over the world. So these are some of the things that we know microorganisms do. And then there are the things that we don’t yet quite know about and that’s, for example, the role in weather. There’s probably a role but it hasn’t been proven yet. So before I stop I just want to remind you of a couple of other things that you should be grateful to your microbes for. This is a coffee plantation in Hawaii and these are the coffee beans that form on the coffee plants. Well, it turns out we wouldn’t have coffee if it weren’t for the microbes.

And in addition to nourishing the soil and doing all the things that all crops benefit from microbes in, the coffee beans have to be fermented before they’re taken to roasting. And it’s the bacteria that live on the beans when they’re formed that do that fermentation. So it’s a completely natural process, a natural inoculum of organisms on those beans. Similarly, my other favorite food, chocolate is made by a similar process. And it turns out that cacao, the plant that chocolate comes from, has these fruits that contain the seeds that are the chocolate source and those have to be fermented to free the seeds from the environment around them in these very dense fruits. And there’s some evidence that the flavor of chocolate is dramatically affected by the composition of that community that ferments them. And that’s why chocolate from various places sometimes can vary in flavor because the bacteria conveys some of the flavor to the chocolate. So as you’re thanking your microbes for keeping you healthy and keeping the planet healthy, I also encourage you to acknowledge their role in nourishing us with chocolate and coffee. [laughter] There are hazards of forgetting about the microbes. And one really, one event really brought this home to scientists.

This was Biosphere 2, this was an experiment in Arizona to see if they could recreate the biosphere, the environment of the Earth and get a functional ecosystem going that would mimic the Earth and so thus Biosphere 2. And after months this experiment completely failed. They couldn’t keep the oxygen levels high enough and the people in Biosphere 2 had to leave because they were so sick from oxygen deprivation and carbon dioxide poisoning, the plants didn’t grow quite right. And the scientists scratched their heads forever about why their equations didn’t work. They had done all these calculations of the organisms that needed to be there and the balance and they, the oxygen should have been much higher by their calculations. And as we now know they were forgetting the microbes and that’s a pretty big part of the balance of oxygen and carbon dioxide in an environment. So just as the scientists in Biosphere 2 ignored the microbes to their hazard, we also only ignore them at our own hazard on Planet Earth. So for keeping our planet happy and healthy, we need to keep our microbes happy and healthy as well. Thanks for your attention. [applause]