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The Microbiome
Earth formed about 4.5 billion years ago when a disc-shaped cloud of dust and gas collapsed into a primordial sphere. It was lifeless and molten and reeked of lethal gases. When it finally cooled, a newly solid crust allowed liquid water (via special delivery from comets) to collect on the surface.
A billion years later, this hellish planet had been transformed. It was now slathered with free-living, single-cell organisms called prokaryotes and archaea. They amassed themselves into shallow microbial mats at the bottom of the ocean and on the sides of towering volcanoes. In fact, these original inhabitants survive to this day in the coldest and hottest regions of land and sea. And they can feed on just about anything, including ammonia, hydrogen, sulfur, and iron.
One of the great mysteries of biology is, how did all this life arise? How did nonliving chemicals manage to invent cell membranes and self-replication, to feed and repair themselves? Scientists used to think that a “primordial soup” was struck by lighting and suddenly organic life sparked into being—a la Frankenstein.
Current theories are only a little more prosaic. More recent evidence, based on a genetic analysis of known microbes, traces life’s origins to deep-sea hydrothermal vents that spew out boiling gases.1 In other words, the first cell we can know about by analyzing modern genes fed on hydrogen gas in a hot, pitch-dark, iron-rich, sulfurous environment. It had figured out how to obtain energy to live.
For millions of years, microbial mats pretty much ran things. Gradually, through countless real-life experiments driven by evolutionary forces, some of the microbes developed the ability to use the energy in sunlight to turn carbon dioxide and water into food. This process, known as photosynthesis, released massive amounts of oxygen. The air you breathe was made by those microbes. It still is.
We mention this background to help you get your head around a fact that is difficult to grasp: we humans live on a planet that is run by and for invisible microbes. For 3 billion years, they were its sole owners. They created our biosphere, maintaining global cycles involving carbon, nitrogen, sulfur, phosphorus, and other nutrients. They made all the soil. Last but not least, they set the conditions for the evolution of multicellular life, meaning plants and animals, including us.
The number of bacteria on Earth is estimated to be a nonillion: 1030 (10 to the 30th power, i.e., 10 followed by 30 zeros). That’s more than the number of stars in our galaxy. The number of viruses is at least two orders of magnitude greater. According to a new estimate, there are about 1 trillion species of microbes on Earth and 99.999 percent of them have yet to be discovered.2 If we lined them all up end to end, the “bug chain” would stretch to the Sun and back 200 trillion times.
That means all of microbiology is built on less than 1 percent of microbial life. We have only sequenced fifty thousand of their genomes for our databases. The rest are mysterious. We can’t grow them in our labs. They have no names. Their functions are not known. We are surrounded by microbial dark matter.
Organisms that we call microbes are grouped into three domains: Bacteria, Archaea, and Eukaryota. These domains are radically different from one another—far more different genetically than humans are from a squid or even a pine tree.
Microbes in the first domain, Bacteria, are what most of us think of when we talk about bugs or germs. They are single-cell organisms lacking a nucleus. But they are not primitive. They can move, eat, eliminate waste, defend against enemies, and reproduce with remarkable efficiency.
Microbes in the second domain, Archaea, are single-cell organisms that look very much like bacteria under a microscope but have unique ways of making a living. They stem from a different branch on the tree of life, with different genes and biochemistry. Many of them are extremophiles that thrive in environments like boiling hot springs and salty lakes. But others live in milder climates, in the oceans and even in the human gut and skin.
The third domain is the Eukaryota, in which we find the microbes of the Fungi and Protista kingdoms. These Fungi are not toadstools in a forest but a single-celled version of this kind of life. You are undoubtedly familiar with yeasts, valuable for making bread, beer, and wine. But some, such as Candida, can also cause unpleasant infections. The Protista are single-celled relatives of plants, animals, and fungi. They are the latest incarnation of our microbial ancestors.
Finally, and somewhat contentiously, we have the viruses. While it’s debatable whether they’re alive, there’s no doubt that they are incredibly efficient at replicating themselves by harvesting the cellular machinery of cells around them.
Collectively, these microbiota—the bacteria, archaea, fungi, protists, and viruses—constitute the microbiome of a particular plant, animal, or ecosystem.
Nevertheless, we have some pretty good ideas for how life operates and how simple rules give rise to complexity. All of biology is based on principles of evolution, competition, and cooperation. And microbes are masters at cooperation. The waste product of one microbe helps feed its neighbor. They care where they are and who is with them. And they share genetic information, passing it not only to their progeny but to their neighbors as well—even across species.
As for competition, the microbial world is a stage for endless war. Bugs that eat the same foods struggle to find ways to outwit their neighbors. As sworn enemies, bacteria and viruses have been duking it out for billions of years and, in so doing, have invented just about every chemical reaction, every defensive and offensive strategy imaginable, every survival trick in the book of life.
Another mind-boggling fact is that all these invisible microbes outweigh all visible life by a factor of 100 million. Collectively they are heavier than all the plants and animals—all the whales, elephants, and rain forests—that you can see around you.
Visible life is overwhelmingly composed of eukaryotes—single cells that contain a nucleus and that evolved over the last 600 million years into everything big. You are a eukaryote because the cells that make up your body are eukaryotic. Yet unlike microbial eukaryotes, which only have a single cell, your body is made up of tens of trillions of cells that have differentiated into all the different body parts—each of which still has your genetic code locked in its nucleus. As we’ll see in Chapter 2, collectively, your eukaryotic cells have developed many special relationships with microbes.
But before we get to the human microbiome, let us entertain you with some of the more hostile habitats that microbes call home.
Bacteria and archaea have been discovered living in Martian-like conditions on volcanoes in South America, with no water, extreme temperatures, and intense levels of ultraviolet light. They extract energy and carbon from wisps of gases flowing from Earth’s interior.
The oceans contain at least 20 million kinds of marine microbes that make up 50 to 90 percent of the ocean’s biomass. There is a mat of bacteria on the seafloor off the west coast of South America that covers an area roughly the size of Greece. Mud pulled from more than five thousand feet below the seafloor off Newfoundland was found to be teeming with microbes.
Bacteria at hydrothermal vents inhabit everything—rocks, the seafloor, and the insides of mussels and tube worms. They thrive in highly acidic, alkaline, or salty boiling water under high pressure and heat. Some heat-loving thermophiles grow at 235 degrees Fahrenheit. They lend the deep blue, green, and orange colors to Yellowstone’s boiling ponds.
Microbes dwell in the rocks found in the world’s deepest gold mines. In fact, they can “eat” gold, sequestering it like Lilliputian miners.
Recently, a new genus of bacteria, Candidatus frackibacter, has been found living inside hydraulic fracturing wells in Appalachian Basin shale beds. Similarly, acid-loving microbes make their home in mine drainage sites.
After the Deepwater Horizon oil spill in the Gulf of Mexico in 2010, microbes gorged themselves on oil and natural gas. They chewed through a toxic stew of hydrocarbons.
Microbes eat plastic. As much as 8 million metric tons of the stuff are dumped into our oceans every year. Trouble is, each piece of plastic takes at least 450 years to decompose. The Great Pacific Garbage Patch, a floating vortex of plastic waste far out to sea, is home to about a thousand different kinds of microbes living on the debris. Landfills contain mountains of polyethylene terephthalate, a plastic used to make water bottles, salad spinners, and peanut butter jars. While it’s the most recycled plastic in the United States, two-thirds of it escape our household bins. Researchers recently screened 250 samples of sediment, soil, wastewater, and sludge to see if any microbe might like to eat the plastics. One volunteered: Ideonella sakaiensis.
They even munch uranium. Fungi have been deployed to absorb radiation from tainted water at the Fukushima nuclear reactor in Japan.
Some bugs make their living forty miles high up in the sky. In the upper atmosphere, they help form clouds, snow, and rain. When raindrops land on the leaves of trees and shrubs, the bacteria within them can cause water to freeze, creating ice crystals even when they wouldn’t form otherwise. These crystals damage plant tissues, allowing the microbes to get inside. Once there the microbes can exploit the resources of the plant (of course the plant thinks of this as an infection!).
Bacteria can survive in space. They rode in all the space shuttles and are ensconced in the International Space Station. The Russians exposed microbes to space for a year, outside of the Mir space station, and some survived. NASA scientists suspect that water channels emerge sporadically on Mars and would like Curiosity, the robotic rover that is tooling around, exploring the terrain on Mars, to take a look. But since the rover may carry Earth’s microbes, which would thrive rapidly in the water, they can’t take the chance of getting too close for fear of contaminating this off-world water source.
They also live closer to home. Extremophiles have been found in dishwashers, hot-water heaters, washing machine bleach dispensers, and hot tubs. They are on every household surface and even in your tap water. We harness them to make food, drugs, alcohol, perfumes, and fuel. Nearly every antibiotic is derived from microbes.
And if all this isn’t enough, they eat you when you die.
Copyright © 2017 by Jack Anthony Gilbert, Rob Knight, and Sandra Blakeslee