2. OUR MICROBIAL PLANET Our planet began as a lifeless sphere of molten rock about 4.5 billion years ago But a billion years later,its oceans were teeming with free-living cells.Somehow, in ways still opaque to science,life arose in those primordial seas.Some say the first building blocks arrived as dust falling from outer space,the so-called panspermia hypothesis.Others argue that self-replicating molecules coalesced in clay deposits at the bottom of the ocean,in hot hydrothermal vents or in foamy bubbles created from waves breaking on the shores.We still don't have an explanation for how it all began. Nevertheless,we have some pretty basic ideas of how life operates,how simple rules give rise to complexity,and how the richness of our planet's diversity came into being All of biology-the ratcheting of life-rests on the enduring principles of evolution,competition,and cooperation first forged in those oceans. We live on a microbial planet that is totally dominated by forms of life too small to be seen by the naked eye.For about 3 billion years,bacteria were the sole living inhabitants on Earth.They occupied every tranche of land,air,and water, driving chemical reactions that created the biosphere,and set conditions for the evolution of multicellular life.They made the oxygen we breathe,the soils we till the food webs that support our oceans.Slowly,inexorably,through trial and error across the deepness of time,they invented the complex and robust feedback systems that to this day support all life on Earth. It's difficult for the human mind to grasp the concept of deep time,of billions of years of microbial activity churning inorganic matter into the stuff of life.It is a concept emanating from geology,from our understanding of how continents formed, drifted,broke apart,crashed into one another,built mountain ranges and eroded them away with wind and rain over billions of years.And yet the bacteria were here long before even the giant supercontinents,Laurasia and Gondwana,which go back a half billion years or so and from which our present continents have descended 6
2. OUR MICROBIAL PLANET Our planet began as a lifeless sphere of molten rock about 4.5 billion years ago. But a billion years later, its oceans were teeming with free-living cells. Somehow, in ways still opaque to science, life arose in those primordial seas. Some say the first building blocks arrived as dust falling from outer space, the so-called panspermia hypothesis. Others argue that self-replicating molecules coalesced in clay deposits at the bottom of the ocean, in hot hydrothermal vents or in foamy bubbles created from waves breaking on the shores. We still don’t have an explanation for how it all began. Nevertheless, we have some pretty basic ideas of how life operates, how simple rules give rise to complexity, and how the richness of our planet’s diversity came into being. All of biology—the ratcheting of life—rests on the enduring principles of evolution, competition, and cooperation first forged in those oceans. We live on a microbial planet that is totally dominated by forms of life too small to be seen by the naked eye. For about 3 billion years, bacteria were the sole living inhabitants on Earth. They occupied every tranche of land, air, and water, driving chemical reactions that created the biosphere, and set conditions for the evolution of multicellular life. They made the oxygen we breathe, the soils we till, the food webs that support our oceans. Slowly, inexorably, through trial and error across the deepness of time, they invented the complex and robust feedback systems that to this day support all life on Earth. It’s difficult for the human mind to grasp the concept of deep time, of billions of years of microbial activity churning inorganic matter into the stuff of life. It is a concept emanating from geology, from our understanding of how continents formed, drifted, broke apart, crashed into one another, built mountain ranges and eroded them away with wind and rain over billions of years. And yet the bacteria were here long before even the giant supercontinents, Laurasia and Gondwana, which go back a half billion years or so and from which our present continents have descended. 16
John McPhee in his classic book Basin and Range,collected in Annals of the Former World,captures our place in this vast chronology with a wonderful analogy:"Consider the earth's history as the old measure of the English yard,the distance from the king's nose to the tip of his outstretched hand.One stroke of a nail file on his middle finger erases human history." Or consider another comparison.If 3.7 billion years of life on Earth were compressed into a twenty-four-hour clock,our hominid ancestors would have appeared 47-96 seconds before midnight.Our species,Homo sapiens,arrived on the scene 2 seconds before midnight. But there is another mind-boggling concept needed to appreciate the vastness of our microbial world.Microbes are invisible to our naked eye,with a few exceptions that reinforce the rule.Millions can fit into the eye of a needle.But if you were to gather them all up,not only would they outnumber all the mice,whales. humans,birds,insects,worms,and trees combined-indeed all of the visible life- forms we are familiar with on Earth-they would outweigh them as well.Think about that for a moment.Invisible microbes comprise the sheer bulk of the Earth's biomass,more than the mammals and reptiles,all the fish in the sea,the forests. Without microbes,we could not eat or breathe.Without us,nearly all microbes would do just fine The term microbe refers to several types of organisms.In this book,I will be talking mostly about the domain of bacteria,also called prokaryotes,single-cell organisms that lack a nucleus.But that doesn't mean they are primitive.Bacterial cells are complete,self-contained beings:they can breathe,move,eat,eliminate wastes,defend against enemies,and,most important,reproduce.They come in all shapes and sizes.Some look like balls,carrots,boomerangs,commas,snakes, bricks,even tripods.All are exquisitely adapted for how they make a living in this world,including those,as I'll elaborate in the next chapter,that thrive on and within our bodies.When they go AWOL.we are in trouble. Another microbial domain,called archaea,superficially resemble bacteria but, as their name suggests,they are a very old,very deep branch of the tree of life with different genetics and biochemistry and an independent evolutionary history. Originally found in extreme environments,such as hot springs and salt lakes, archaea actually may be found in many niches,including the human gut and belly button The third branch of microbial life is composed of eukaryotes,single cells with a nucleus and other organelles that provide the building blocks for more complex, multicellular forms of life.Over the last 600 million years,eukaryotes have given rise to insects,fish,plants,amphibians,reptiles,birds,mammals-all the"big"life from ants to redwoods that you can see around you.However,some primitive eukaryotes are lumped in with microbes,including fungi,primitive algae,some amoebae,and slime molds. 17
John McPhee in his classic book Basin and Range, collected in Annals of the Former World, captures our place in this vast chronology with a wonderful analogy: “Consider the earth’s history as the old measure of the English yard, the distance from the king’s nose to the tip of his outstretched hand. One stroke of a nail file on his middle finger erases human history.” Or consider another comparison. If 3.7 billion years of life on Earth were compressed into a twenty-four-hour clock, our hominid ancestors would have appeared 47–96 seconds before midnight. Our species, Homo sapiens, arrived on the scene 2 seconds before midnight. But there is another mind-boggling concept needed to appreciate the vastness of our microbial world. Microbes are invisible to our naked eye, with a few exceptions that reinforce the rule. Millions can fit into the eye of a needle. But if you were to gather them all up, not only would they outnumber all the mice, whales, humans, birds, insects, worms, and trees combined—indeed all of the visible lifeforms we are familiar with on Earth—they would outweigh them as well. Think about that for a moment. Invisible microbes comprise the sheer bulk of the Earth’s biomass, more than the mammals and reptiles, all the fish in the sea, the forests. Without microbes, we could not eat or breathe. Without us, nearly all microbes would do just fine. The term microbe refers to several types of organisms. In this book, I will be talking mostly about the domain of bacteria, also called prokaryotes, single-cell organisms that lack a nucleus. But that doesn’t mean they are primitive. Bacterial cells are complete, self-contained beings: they can breathe, move, eat, eliminate wastes, defend against enemies, and, most important, reproduce. They come in all shapes and sizes. Some look like balls, carrots, boomerangs, commas, snakes, bricks, even tripods. All are exquisitely adapted for how they make a living in this world, including those, as I’ll elaborate in the next chapter, that thrive on and within our bodies. When they go AWOL, we are in trouble. Another microbial domain, called archaea, superficially resemble bacteria but, as their name suggests, they are a very old, very deep branch of the tree of life with different genetics and biochemistry and an independent evolutionary history. Originally found in extreme environments, such as hot springs and salt lakes, archaea actually may be found in many niches, including the human gut and belly button. The third branch of microbial life is composed of eukaryotes, single cells with a nucleus and other organelles that provide the building blocks for more complex, multicellular forms of life. Over the last 600 million years, eukaryotes have given rise to insects, fish, plants, amphibians, reptiles, birds, mammals—all the “big” life from ants to redwoods that you can see around you. However, some primitive eukaryotes are lumped in with microbes, including fungi, primitive algae, some amoebae, and slime molds. 17
Here is another kind of scale.Everyone is familiar with a family tree.Your ancestors are lined up by generation with the oldest great-grandparent first, followed by your grandparents,and so forth,expanding the numbers with each generation.Now imagine a family tree of all life on Earth.There are so many forms of life that rather than a tree,it looks more like a bush,with branches extending in all directions.Imagine for the moment that it is a round bush,with the first generation,the origin,near the center and the branches extending outward.Next, let's place us humans on the bush,somewhere around eight o'clock on a watch dial. Now for the quiz.Where is the life-form on farms that we call corn on that bush?All things equal,we don't think that we are so close to corn,which,after all, is a green plant maybe it is halfway around the bush?Wrong,it is at about 8:01.If humans and corn are so close,who is taking up the rest of the bush of life and its branches?The answer:It is mostly bacteria.For example,the distance between E. coli and Clostridium-two common bacteria-is much greater than the distance between corn and us.Humanity is just a speck in the massively bacterial world.We need to get used to that idea. And then there are viruses,which are,strictly speaking,not alive;they propagate by invading and co-opting living cells.We think about viruses like the flu,the common cold,herpes,and HIV as problems of humans.But most of the viruses in the world are completely irrelevant to us;their targets are bacterial cells, not animal cells like ours.In the oceans,the number of virus particles is unfathomable,more than all the stars in the universe,living off the myriad bacteria in the waters.Over the billions of years that viruses and microbes have been duking it out,each has evolved weaponry to defeat the other.It reminds me of the classic Spy vs.Spy comic strip in Mad magazine.In fact,one possible treatment for bacterial diseases in humans involves harnessing phages-viruses that kill bacteria -an idea I discuss near the end of the book While many types of microbes inhabit and shape our world,my main focus here is on bacteria and what happens when we kill them indiscriminately with potent drugs.Although there are plenty of eukaryotes (such as Plasmodium falciparum, one of the major causes of malaria)that lead to great misery,the problems they pose are of a different nature.And there are viruses that cause much harmthink about HIV-but they do not respond to antibiotics and are a topic for a different day Microbes make their homes everywhere we look.The ocean is home to unimaginable numbers of them,though some estimates give a flavor to their ubiquity.At least 20 million types of marine microbes(possibly a billion)make up 50-90 percent of the ocean's biomass.The number of microbial cells in the water column,meaning sea surface to sea floor,is more than 10 to the 30th,a nonillion,or 18
Here is another kind of scale. Everyone is familiar with a family tree. Your ancestors are lined up by generation with the oldest great-grandparent first, followed by your grandparents, and so forth, expanding the numbers with each generation. Now imagine a family tree of all life on Earth. There are so many forms of life that rather than a tree, it looks more like a bush, with branches extending in all directions. Imagine for the moment that it is a round bush, with the first generation, the origin, near the center and the branches extending outward. Next, let’s place us humans on the bush, somewhere around eight o’clock on a watch dial. Now for the quiz. Where is the life-form on farms that we call corn on that bush? All things equal, we don’t think that we are so close to corn, which, after all, is a green plant; maybe it is halfway around the bush? Wrong, it is at about 8:01. If humans and corn are so close, who is taking up the rest of the bush of life and its branches? The answer: It is mostly bacteria. For example, the distance between E. coli and Clostridium—two common bacteria—is much greater than the distance between corn and us. Humanity is just a speck in the massively bacterial world. We need to get used to that idea. And then there are viruses, which are, strictly speaking, not alive; they propagate by invading and co-opting living cells. We think about viruses like the flu, the common cold, herpes, and HIV as problems of humans. But most of the viruses in the world are completely irrelevant to us; their targets are bacterial cells, not animal cells like ours. In the oceans, the number of virus particles is unfathomable, more than all the stars in the universe, living off the myriad bacteria in the waters. Over the billions of years that viruses and microbes have been duking it out, each has evolved weaponry to defeat the other. It reminds me of the classic Spy vs. Spy comic strip in Mad magazine. In fact, one possible treatment for bacterial diseases in humans involves harnessing phages—viruses that kill bacteria —an idea I discuss near the end of the book. While many types of microbes inhabit and shape our world, my main focus here is on bacteria and what happens when we kill them indiscriminately with potent drugs. Although there are plenty of eukaryotes (such as Plasmodium falciparum, one of the major causes of malaria) that lead to great misery, the problems they pose are of a different nature. And there are viruses that cause much harm—think about HIV—but they do not respond to antibiotics and are a topic for a different day. * * * Microbes make their homes everywhere we look. The ocean is home to unimaginable numbers of them, though some estimates give a flavor to their ubiquity. At least 20 million types of marine microbes (possibly a billion) make up 50–90 percent of the ocean’s biomass. The number of microbial cells in the water column, meaning sea surface to sea floor, is more than 10 to the 30th, a nonillion, or 18
1.000 x 1 billion x 1 billion x 1 billion.This is equal to the weight of 240 billion African elephants. The International Census of Marine Microbes,a decade-long project that has been sampling marine microbes from more than twelve hundred sites around the world,estimates there may be one hundred times as many microbial families (genera)as previously thought.Everywhere scientists have looked,some species dominate in terms of numbers and activity.But in what came as a surprise,they also found many species represented by fewer than ten thousand individuals (a puny number for bacteria),including one-off singletons.They concluded that many rare bacteria in the oceans are lying in wait,ready to bloom and become dominant if environmental changes favor them.The same concept holds true for the microbes that inhabit our bodies.The ability to "lurk"for long periods of time in small numbers and then spontaneously"bloom"is an important feature of microbial life. Many marine microbes are so-called extremophiles.They live in hydrothermal vents where boiling water rich in sulfur,methane,and hydrogen rises from the mantle to meet frigid water,forming conelike chimneys.It is a hellish mixture of acids and heavy chemicals,but it is one in which rich communities of bacteria thrive in the absence of oxygen and sunlight.We see the same thing in the superhot pools and geysers at Yellowstone National Park in Wyoming and in the bubbling tar lake found on the Caribbean island of Trinidad.Bacteria also live in the massive glaciers of Antarctica and under the frozen depths of the Arctic Ocean. Oceanic crust composed of dark,volcanic rock at the bottom of the sea, encompassing 60 percent of Earth's surface,is home to perhaps the largest populations of microbes on the planet.Its resident microbes live off energy obtained from chemical reactions between water and rock. Recently,bacteria have been found munching on plastic particles floating in the open oceans.Although a slow process,at least one thousand different species are involved in converting this "plastisphere"to a healthier biosphere.Other than dump plastic in the ocean,we didn't do anything to stimulate these bacteria.From among the countless varieties floating about,some found their way to the plastic,and those that found it a favorable food source grew in numbers-natural (plastic)selection in action The deepest place on Earth,the Marianas Trench,was recently found to support an active microbial community with ten times more bacteria than those in the sediments of the surrounding abyssal plain.And gigantic mats of microbes-the size of Greece-live on the seafloor off the west coast of South America by consuming hydrogen sulfide. Abundant microbes are lofted by winds,including hurricanes,where they persist and may even make their living high in the skies.They help form cirrus clouds and nucleate ice particles to make it snow.They influence both weather and climate as well as recycle nutrients and decompose pollutants. 19
1,000 × 1 billion × 1 billion × 1 billion. This is equal to the weight of 240 billion African elephants. The International Census of Marine Microbes, a decade-long project that has been sampling marine microbes from more than twelve hundred sites around the world, estimates there may be one hundred times as many microbial families (genera) as previously thought. Everywhere scientists have looked, some species dominate in terms of numbers and activity. But in what came as a surprise, they also found many species represented by fewer than ten thousand individuals (a puny number for bacteria), including one-off singletons. They concluded that many rare bacteria in the oceans are lying in wait, ready to bloom and become dominant if environmental changes favor them. The same concept holds true for the microbes that inhabit our bodies. The ability to “lurk” for long periods of time in small numbers and then spontaneously “bloom” is an important feature of microbial life. Many marine microbes are so-called extremophiles. They live in hydrothermal vents where boiling water rich in sulfur, methane, and hydrogen rises from the mantle to meet frigid water, forming conelike chimneys. It is a hellish mixture of acids and heavy chemicals, but it is one in which rich communities of bacteria thrive in the absence of oxygen and sunlight. We see the same thing in the superhot pools and geysers at Yellowstone National Park in Wyoming and in the bubbling tar lake found on the Caribbean island of Trinidad. Bacteria also live in the massive glaciers of Antarctica and under the frozen depths of the Arctic Ocean. Oceanic crust composed of dark, volcanic rock at the bottom of the sea, encompassing 60 percent of Earth’s surface, is home to perhaps the largest populations of microbes on the planet. Its resident microbes live off energy obtained from chemical reactions between water and rock. Recently, bacteria have been found munching on plastic particles floating in the open oceans. Although a slow process, at least one thousand different species are involved in converting this “plastisphere” to a healthier biosphere. Other than dump plastic in the ocean, we didn’t do anything to stimulate these bacteria. From among the countless varieties floating about, some found their way to the plastic, and those that found it a favorable food source grew in numbers—natural (plastic) selection in action. The deepest place on Earth, the Marianas Trench, was recently found to support an active microbial community with ten times more bacteria than those in the sediments of the surrounding abyssal plain. And gigantic mats of microbes—the size of Greece—live on the seafloor off the west coast of South America by consuming hydrogen sulfide. Abundant microbes are lofted by winds, including hurricanes, where they persist and may even make their living high in the skies. They help form cirrus clouds and nucleate ice particles to make it snow. They influence both weather and climate as well as recycle nutrients and decompose pollutants. 19
Down on the ground,microbes are in charge of soil,one of our most precious resources.Projects to sample soil bacteria worldwide are just getting under way in what some experts call the search for Earth's dark matter,an undertaking akin to figuring out the nature of unknown realms of the cosmos. We know that microbes make the planet habitable.They decompose the dead, which is a very useful service.And they convert or "fix"inert nitrogen in the atmosphere into a form of free nitrogen that can be used by living cells,benefiting all plants and animals.After the Deep Water Horizon oil spill in the Gulf of Mexico,bacteria ate up much of the contamination because they were able to supplement the nutrients in the oil with nitrogen that they could remove from the air to form a complete meal for themselves Microbes live in rocks.For example,in South Africa's Mponeng gold mine, bacteria survive with the help of radioactive decay as uranium splits water molecules,releasing free hydrogen,which the bacteria combine with sulfate ions to make dinner.They even mine the gold.Delftia acidovorans uses a special protein to convert floating ions of gold,which are toxic to it,into an inert form of the metal that precipitates from the surrounding water and accumulates in mineral gold deposits.Meanwhile,perhaps the world's toughest bacterium,Deinococcus radiodurans,lives on radioactive waste But my favorite was described several years ago.Geologists were drilling an exploratory well and studying the cores that came up.From one core taken a mile down,they found only three constituents:basalt (a form of bedrock),water,and bacteria-loads of them.These bacteria made their living and reproduced on just rock and water Finally,whole industries are based on harnessing microbes to do our bidding, from making the bread that nourishes us,the alcohol we drink,to the modern drugs engineered by the biotech field.It is fair to assume that bacteria can do just about any chemical process that we might assign to them.In their endless variety are found untold capabilities.We just have to define the problem and go after the right microbes to solve it or we will need to reengineer them.But those exciting possibilities are subjects for another time. The story of microbes is a saga of limitless warfare and also endless cooperation. Since most people are familiar with Darwinian competition and survival of the fittest,I'll start there. Darwin's careful observations showed that there always was variation among individuals of any species,from birds to humans.He developed his theory of evolution by positing that when variants exist,nature will "select"the one(s)that are best adapted (the fittest):these are the ones that best complete their life cvcle and have descendants.They outcompete the other variants.Over the course of time 0
Down on the ground, microbes are in charge of soil, one of our most precious resources. Projects to sample soil bacteria worldwide are just getting under way in what some experts call the search for Earth’s dark matter, an undertaking akin to figuring out the nature of unknown realms of the cosmos. We know that microbes make the planet habitable. They decompose the dead, which is a very useful service. And they convert or “fix” inert nitrogen in the atmosphere into a form of free nitrogen that can be used by living cells, benefiting all plants and animals. After the Deep Water Horizon oil spill in the Gulf of Mexico, bacteria ate up much of the contamination because they were able to supplement the nutrients in the oil with nitrogen that they could remove from the air to form a complete meal for themselves. Microbes live in rocks. For example, in South Africa’s Mponeng gold mine, bacteria survive with the help of radioactive decay as uranium splits water molecules, releasing free hydrogen, which the bacteria combine with sulfate ions to make dinner. They even mine the gold. Delftia acidovorans uses a special protein to convert floating ions of gold, which are toxic to it, into an inert form of the metal that precipitates from the surrounding water and accumulates in mineral gold deposits. Meanwhile, perhaps the world’s toughest bacterium, Deinococcus radiodurans, lives on radioactive waste. But my favorite was described several years ago. Geologists were drilling an exploratory well and studying the cores that came up. From one core taken a mile down, they found only three constituents: basalt (a form of bedrock), water, and bacteria—loads of them. These bacteria made their living and reproduced on just rock and water. Finally, whole industries are based on harnessing microbes to do our bidding, from making the bread that nourishes us, the alcohol we drink, to the modern drugs engineered by the biotech field. It is fair to assume that bacteria can do just about any chemical process that we might assign to them. In their endless variety are found untold capabilities. We just have to define the problem and go after the right microbes to solve it or we will need to reengineer them. But those exciting possibilities are subjects for another time. * * * The story of microbes is a saga of limitless warfare and also endless cooperation. Since most people are familiar with Darwinian competition and survival of the fittest, I’ll start there. Darwin’s careful observations showed that there always was variation among individuals of any species, from birds to humans. He developed his theory of evolution by positing that when variants exist, nature will “select” the one(s) that are best adapted (“the fittest”); these are the ones that best complete their life cycle and have descendants. They outcompete the other variants. Over the course of time, 20