THE CONTEXT OF PERSISTENCE, THE BACTERIAL DIMENSION
I wrote a song in 2013 called “Past Is Dead” that paints a picture of my beliefs about population wars. The title of the song is ironic, because the past is very much alive, yet we are often willfully blind to the fact that our past has a huge influence on our present. The first line of the song is “Strewn about the battlefields of life are the remainders of history,” and when I look at the world I see ancient history that is very much alive in the present. This is true on both a cultural level and, as we will see, on a genetic and cellular level, within our own bodies. More important, I recognize that the past lives on in a mixture of both the winners and losers of history. We are a global population that is constantly assimilating, and there is no absolute delineation between the populations of the conquered and the conquerors.
I believe that modern humans are poised to acknowledge the cold truth that ultimately there are no victors and no vanquished in life, and that no one is ultimately entirely good or inherently evil. If we, as the intellectual community of modern world citizens, can make this idea accepted, then humans will coexist more peaceably, and we can focus on changing how we deal with other species in the interest of creating a sustainable future.
When I read the history of warfare, I am less interested in the myth of who is the perceived victor than I am in the resulting longer-term assimilations. Yet our culture is obsessed with the belief that winning means complete domination of your opponent, as if war is some kind of competition with a clear prize for the winner. If this is correct, then why do we have winners and losers existing side by side today? In short, it is because of the persistence of populations and the futility of extermination.
In this and the next few chapters we’re going to examine this persistence on every level from micro to macro, first looking at how replicating populations such as microscopic organisms (microbes) and viruses work within our bodies, how they have persisted and replicated since the origin of the biosphere, long before our species evolved. We like to think of ourselves as autonomous, self-regulating beings. The reality is that each one of us is controlled in part by other microscopic beings.
For starters, the genetic material we carry is possibly as much as 43 percent viral. In other words, viruses that infected our ancestors millions of years ago have effectively been incorporated into our genome. Clearly some sort of compromise was reached over the years, with the host species providing a haven for viral DNA.
Furthermore, the bacteria in our guts were once thought to be important only in regard to the digestion and absorption of food; but it is now clear that our bacterial microbiota is involved in developing our immune system and is critical to our overall well-being.
In another area researchers are currently exploring how parasites, such as the feline parasite Toxoplasma gondii, can actively change our brains and our behavior. The parasite changes its host’s behavior to be attracted to, rather than frightened by, cats. Rats infected by T. gondii exhibit signs of curiosity, excitement, and even sexual attraction to the smell of cat urine. The virus benefits from the change because it needs to return to a feline host to reproduce, but obviously this scenario does not end well for the rats. Humans infected with T. gondii exhibit equally strange changes in personality and behavior (infected men show more oppositional defiance and jealousy; infected women become more warm hearted and moralistic), though thankfully the infection in humans rarely ends with the host being eaten by cats.
The fact that viruses can rewrite our genetic code, bacteria can affect our mood, and parasites can change our decision-making processes and lessen our inhibitions has interesting implications. One possibility is that we might begin to consider “ourselves” as a coalition of many populations, rather than one definitive “I.” Perhaps one driver of evolutionary success is how well we maintain our internal environment—how well we care for the billions of microbes that dwell within and on us. We are all stewards of our own unique internal environment; perhaps learning to care for it will encourage us to care for our external environment as well.
The general public easily confuses bacteria, parasites, and viruses (just ask any doctor who has been asked for antibiotics to treat the flu), yet they have little in common beyond their microscopic size and the fact that they impact human lives on a daily basis. Let’s take a closer look first at the way bacteria coexist both with us and within us, affecting our external environment, health, and emotional well-being.
My house is built on rural land in the Finger Lakes region of upstate New York. The geology below the concrete foundation is fascinating; a few feet under our house is a thick deposit of unconsolidated glacial sediments sitting atop a huge stack of ancient strata. These gray and black sedimentary rocks have numerous features that indicate an ancient biological signature in the history of their formation. Furthermore, the stratigraphy (the orientation and sequence of the sedimentary rocks) in this region belies a unique geology that reveals the historical setting of our land over the last 400 million years.
Reading history in rocks is like interpreting a map. It requires a good imagination and keen observation. The stratigraphic rock record isn’t a map of places, however, but of time. Stratigraphers piece together bits and pieces of evidence found in the sediments to reconstruct the geological events of the past. This information allows them to slowly build a picture of the succession of evolving environments that were laid down, layer upon layer, through geologic time.
Stratigraphers have been studying sedimentary rocks for more than two hundred years. One of their most meaningful discoveries is conclusive proof of bacteria in 3.5-billion-year-old sediments. This shows us that bacteria were the first living things to flourish on our planet. Although bacterial cells are very difficult to find as fossils, the chemical evidence they left behind gives us lasting clues that they were as productive in the past as they are now. Bacteria were everywhere, long before the advent of “higher” organisms like plants or animals.
We have a hay field and a large vegetable garden on our property; we spend a lot of time maintaining and encouraging the alfalfa, tomatoes, and kale to grow. This means that we know our dirt, and the rocks that lie beneath it, pretty well. The sedimentary rocks that form the bedrock under my house, and the surrounding outcrops in the nearby gorges and glens, are gray. The color is important; it gives us an easy clue to the history of the rocks. Black and gray sedimentary rocks were deposited under oxygen-free conditions. No oxygen means no oxidation; i.e., no rust. Other sedimentary rocks (such as those in the Four Corners region out west) are red; they contain hematite, an iron-rich mineral that rusts when it is exposed to oxygen. These red beds react like this because they were formed in conditions of oxygen abundance, in the presence of photosynthetic organisms. Yet no matter what their color, all sedimentary rocks contain the same basic set of minerals. They are, after all, the eroded bits and pieces of mountains, floodplains, or reefs. The big difference is where these “bits” ended up and what was—or wasn’t—waiting for them when they got there.
Let’s say our “bits” ended up in a shallow marine basin. In today’s climatic conditions such places are warm, bathed in abundant sunlight, and are inviting habitats for photosynthetic microbes. These microbes in turn produce oxygen, which can rust iron grains as sediment accumulates. Terrestrial basins, such as those in the deserts of the southwestern United States, also produce red beds because the abundant oxygen in the atmosphere rusts residual iron in the sediments. This can also be seen in tropical soils of the Amazon basin today, as well as in regions of the Sonoran Desert, where seasonal rivers produce a rich reddish landscape.
Deep-ocean basins, however, are a different story altogether. Sediments pour into them from large river systems that drain continental highlands. Deep basins are devoid of sunlight and therefore less hospitable to photosynthetic microbes; this means no oxygen—as we see today in the Black Sea. Sediments pour in, and the finer-grained materials that are destined to become future shales and mudstones remain black and gray as they come to rest in the deepest portion of the basin. Without oxygen no rust forms.
There’s another crucial component that makes these deep-water sediments different from red beds: biological debris. Dead photosynthetic microbes accumulate over time and pile up in thick layers underneath tons of sediments in deep basins in total darkness beyond the ocean depth that sunlight can penetrate. The photic zone is only the upper one hundred meters of water depth in the ocean. The sunlight that penetrates, and the warmth of this zone, creates a habitat that is teeming with algae and other small life forms. When these tiny creatures die they drift slowly to the seafloor thousands of meters below. Plant debris from the land and nearshore environment also gets washed into the ocean basin and begins to settle on the seabed. All this biological detritus contains appreciable amounts of sulfur, particularly red algae.27 Anaerobic bacteria that live in deep-ocean basins use sulfur to create energy. The color of black shales comes from pyrite, a sulfur-rich mineral that forms when bacteria are actively producing hydrogen sulfide. However, this process, like most processes that generate energy, creates a byproduct, in this case hydrogen sulfide gas. Hydrogen sulfide is highly destructive to shells and bones. It dissolves calcium carbonate, so it is not uncommon to find black shales devoid of fossilized skeletal parts. Impressions in the mud might be present, but no skeletons are found in these deep-ocean basins where bacteria are busy churning out hydrogen sulfide.
Black shales are best known to petroleum geologists for one simple reason: They contain fossil fuels. The anaerobic bacteria—aka extremophiles—that produce the hydrogen sulfide consume some portion of the dead organisms for energy, particularly the sulfur. The sulfur comes from the cell walls of red algae, so the bacteria can gorge themselves on that while leaving the lipid portion of their meal uneaten. All cell membranes are made of lipids, and it’s this leftover oily portion that collects and becomes hydrocarbons known as kerogen, which infuses the sedimentary rocks. Most oil or gas reserves are a direct product of the molecular remnants of photosynthetic algae and bacteria that died and settled on the seafloor28 and then formed kerogen. The kerogen, safe on its inhospitable basin floor, remains undigested and unused by other organisms and is eventually converted into oil and gas.
The plants and animals that were compressed into the sedimentary rocks below my house died in the Middle Devonian, 400 million years ago. However I, like many other landowners in the northeastern United States, am still dealing with the direct consequences of those organisms. The lack of skeletal fossils, the black color of the rocks, the horizontal stratification of the glens and cliffs, the smell of hydrocarbon in the well water. All these things are constant reminders of the past worlds that existed in this part of upstate New York, and of the factors I had to confront when our house was being built.
Our recently built farmhouse is the picture of modern convenience, utility, and wise environmental sustainability. Although it is rather large by urban standards, it uses far less energy than most houses half its size. This is accomplished by using the most modern building materials available and heating strategies that weren’t very common even twenty years ago. Hopefully they will become standard or be surpassed in the next twenty years.
One of the key elements of our sustainability effort is a fully self-contained water budget. We have a well that draws from an aquifer 120 feet below the surface. Our used water (politely called “gray water”) is essentially recycled because it empties from the main sewage pipe into a tank full of digesting bacteria that reside within a thousand-gallon holding tank. When the bacteria have digested all the waste from our household, the gray water spills out into a labyrinth of pipes that extend hundreds of feet away from the house. In this “leach field” the household effluent returns to the soil, where it percolates and the water eventually rejoins the aquifer hundreds of feet below. We also capture water off our barn during rainstorms and store it underground in thousand-gallon containers. All the irrigation of our gardens and lawns and water for car washing comes from our rainwater capture systems.
One caveat about our water, however, comes from the nature of the sedimentary rocks below our property. We live roughly twenty-five hundred feet above the Marcellus Shale, a large Devonian formation that has been in the news recently because of the biological treasure enclosed within its layers.
The Marcellus Shale is one of many sedimentary rock units that stack up like a layer cake throughout upstate New York, Pennsylvania, West Virginia, and Ohio. These rocks were deposited around 400 million years ago. The subsurface beneath our house is composed of neat layers that contain some fossils and lots of hydrocarbons. It has not been disturbed by tectonic forces. Whatever was buried down there 400 million years ago remains.
This is not always the case for ancient sediments. Tectonic movements can bring ancient sedimentary rocks up from the deep and leave them on display for us to view. Some of the best examples of this are seen along Southern California’s highways and country roads. I’ve spent a lot of time driving either to or from Los Angeles. The huge broken slabs of sedimentary rock that jut up along the sides of the mountain highways impress me as much today as they did when I was a teenager, seeing them for the first time. These rocks are still moving; the San Andreas Fault is compressing them at the rate of roughly six centimeters per year, though most Californians choose to underplay its explosive potential as they build their homes and work within this powerful fault zone.
Sedimentary rocks, and their record of the ancient world, are all around us. They can be seen relatively undisturbed in areas that don’t experience violent earthquakes or any kind of active tectonic disruption. The Colorado Plateau is a good example. The plateau is like a huge layer cake of rocks three thousand feet thick, which have gently risen without folding, warping, or compressing. Within the last 3.5 million years (recently, by geologic standards) the Colorado River’s massive discharge eroded its banks and began to cut through the layers of this undisturbed sediment pile. The result is the Grand Canyon, one of the most magnificent sights in the natural world.
From the rim of the canyon, you can peer down and see the Colorado River three thousand feet below. It’s still carving its way through the rock—although now it has reached “basement” rocks so old and changed from heat and pressure that they don’t even look like sediments anymore. From your vantage point on the rim, however, you will notice that you are standing on a white-colored sedimentary unit that is also visible miles away across the gaping divide of the canyon. This rimrock, the Kaibab limestone, is like the topmost piece of plywood on a stack at the hardware store. The layers below it can be thought of as sheets laid down in progressive sequence. The absence of tectonic folding and squeezing allowed for the great revealing of undisturbed layers in canyons that were eroded by the river below.
The Great Lakes region is another undisturbed showcase of Paleozoic sediments. I’ve driven through Wisconsin to central Illinois, across to Pittsburgh and Cleveland, and over all of upstate western New York many times. There is a quieter, homey, more rural vibe here than in the Grand Canyon region. But the rocks are similar in their horizontality.
The forces that shape the Western landscape are big and dramatic; there is something attention getting about the tectonics and mountain building and canyon carving that dominate the vast open vistas of the American West. Back east our landscape is softer and less extreme, in part because our most noticeable landscape features were formed by glaciers. Until twenty-two thousand years ago—during the Pleistocene Epoch—much of this region was covered by a sheet of ice that was more than two thousand feet thick. The winter season lasted longer, the summers weren’t sufficiently long or hot to melt all the snowfall, and gradually year after year ice became layered and piled up on the horizontally undisturbed sedimentary rock layers below.
The thick ice sheet wasn’t stagnant. Ice moves like water, just much more slowly. It carves its way down a gravitational gradient—from highland to lowland—just like a stream. Glaciers can carve valleys, however, much wider and more rounded in profile than water can. The continental glaciers of the eastern United States carved wide valleys and deep holes for hundreds of miles as they advanced from colder Canadian regions to their terminus in southern Illinois and New Jersey.
As the climate began to warm (twenty-two thousand years ago), the rate of melting exceeded the snowfall accumulation, and the ice sheet began to retreat northward, up to the cold Arctic latitudes where they originated. As they retreated, they left huge piles of debris along their edges. These debris piles are everywhere, forming the rolling hills and skyline ridges throughout the southern Great Lakes region and Finger Lakes of New York State.
Our Eastern geology may be less dynamic than its Western equivalent—we have cozy glens and eroded hollows rather than lofty mountains and fault-bound basins—but it is equally beautiful. Some of the most dramatic scenery in the East can be found alongside the rushing waterfalls and streams that flow through the glacial amphitheaters only miles from my front door. The cliffs along the Great Lakes, and the gorges that feed the Finger Lakes, for example, are lined with sedimentary rock cliffs hundreds of feet tall. A rim of unconsolidated Pleistocene sediment caps these cliffs. Forest trees cling tenaciously to the deep soil that rims the gorges and cliffs. Our farm’s immediate area is full of dramatic gorges and waterfalls that plunge down the cliff faces; just down the road, in the village of Montour Falls, the She-Qua-Ga Falls seem to pour over a handful of Early American houses still standing at the base of the cliff. In the winter the falls freeze over, but you can still hear the water rushing beneath them. I have to remind visitors not to get too close to the iced-over creeks and rivers, lest they break through the fragile crust and get swept away.
Two hundred and fifty feet away from our house sits a glen with a raging creek at its base. We are comfortably situated on a rolling meadow; under the topsoil lies about eighty feet of Pleistocene gravel left behind by the retreating glacier that passed through here roughly ten thousand years ago. Drilling our water well was an education on just how much sediment was left behind.
As the drillers plunged deeper into the earth, their steel drill, boring down inch by inch, sent tiny bits of broken rock and debris in its wake, back up to the surface. Solid rock was struck about 78 feet down. Still no water of appreciable volume. They switched to a different drill bit, one that could cut through the solid rock with ease. Mudstone, siltstone, sandstone, more mudstone. Layer after layer they plunged, until eventually, at 120 feet, they struck a high-volume water “seam” and our well was established.
The water slowly rose to fill the hole bored by the shaft of the drill. The drillers sank a steel pipe vertically down the shaft to contain the water as it gurgled up toward the surface. As it spilled out onto the ground, it brought with it fine sediment, clay, and the gaseous remnants of bacteria; a faint smell of methane emanated from the pipe.
Geologic maps of New York reveal that the sedimentary rocks into which our well was drilled continue down in layer-cake fashion. If the drill had bored two thousand feet, it would have reached the “mother lode” of local hydrocarbon lore, the Marcellus Shale.
What makes the Marcellus unique in our region is the kerogen it contains. Kerogen, as already mentioned, is formed from decayed animal and plant matter that eventually accumulated in deep-ocean basins, which, in turn, eventually formed black shale. Think of this shale deposit as a huge compost pile 391 million years old. Conditions were just right to cause a chemical alteration in that decaying heap of algae and plant debris; an alteration that some unimagined future organisms—with big brains, strong backs, and weak foresight—would exploit for their own evolution. Anoxia (the lack of oxygen) prevented the organic debris from breaking down.
Under “normal” conditions, like here on Earth’s surface, or in nearshore environments, oxygen is plentiful. Oxygen breaks down dead organic tissues either by allowing aerobic bacteria to consume them, or by enabling an oxidizing chemical reaction. Both of these processes break down organic debris (through oxidation). When an animal dies, the chemical “attack” of oxygen degrades the carcass. Aerobic microbes and other animals can help this process. They eat the carbon and use it to make organic “building blocks” for their biological needs. Oxygen gets released as CO2 gas in this process of oxidative respiration. So, on the surface of Earth, carbon is constantly being converted in the presence of oxygen, which results in the disintegration of all dead organisms.
A lack of oxygen is a problem for human health, but historical anaerobic conditions have proved to be a boon for those humans who make their living in energy extraction. The Marcellus Shale was the perfect environment for the creation of hydrocarbons. The organic material was buried rapidly, there was no oxygen, and the sediment pile grew thick. With depth comes heat. At just the right depth, and with the right amount of heat, the organic remains might get “cooked” into crude oil. Under other conditions of heat and pressure, however, the kerogen is converted into methane gas. The gas in the Marcellus Shale is still down there today, as it has been for nearly 400 million years, now trapped under thousands of feet of lithified sediments.
Time is important in this process; the sediments quickly accumulated to form the Marcellus Shale. For five million years, dead organisms drifted into the Marcellus basin and were rapidly buried by more sediment. As the basin continually filled up with sediments and dead microbes, the conditions at the bottom changed and were no longer sufficient to “cook” the organic material into oil or gas. Gas production slowly came to a halt. Eventually the sediment pile reached the shallower well-oxygenated ocean-surface waters. By the end of the Middle Devonian (383 mya), the basin was shallow enough to support a well-developed coral reef, which we recognize today as a geological formation called the Tully Limestone.
The Tully Limestone was a fully formed coral-reef community that basked in the healthy glow of the Devonian intertidal photic zone. If we could travel back in time to experience it in its living glory, we might vaguely recognize some of the animals living on the reef. At the very least they would be recognizable as “seashells by the seashore.” At the bottom of this pile of Devonian sedimentary rocks, however, is a completely alien world. This environment, like the depths of the Black Sea today, was devoid of any web of complex “higher” organisms, only bacteria that can withstand the toxic conditions.
Anoxic oceanic basins are hotbeds of bacterial anaerobic communities. These populations live in the presence of methane the same way we are surrounded by oxygen. Some give off methane as a by-product, and some eat methane for their energy needs. These organisms were there during the formation of the Marcellus sediments, and they are still with us today, as I discovered the day we turned on the tap water in our new house.
When we first drew up our plans for the house we decided that a reliable well was crucial. However, we got more than we bargained for. We quickly learned that in this region wells often have problems with methane. Also known as “swamp gas,” it can smell offensive when you go to wash your face or draw some water for a kettle.
This embarrassing smell isn’t the water but instead the methane, the most common waste product of anaerobic bacteria. It’s not the bacteria’s fault; they’ve been doing fine for hundreds of millions of years until we came along and invited them into our house through a brand-new well pipe and plumbing system. We can’t blame them for expanding their population into this new, wide-open habitat that we created.
The smooth interior surface of the pipes might be glassy and shimmering to our naked eye, but to a bacterium those pipe walls have deep canyons, crenulations, and caverns. Bacteria can easily get into these and form colonies. In the language of microbiology, these are called biofilms, microscopic layers of dead and living bacterial colonies built one generation upon another.29 Folded and crenulated, these films create surfaces of attachment for all kinds of other bacteria. When water is stagnant, biofilms may become anoxic from lack of oxygen circulation. But when turbulent water disrupts the tranquillity of the anaerobic colonies, oxygen is brought in and the flow washes them away. Some biofilms persist even through relatively constant water flow. But in general, the more water flowing through the pipes, the lower the incidence of biofilm buildup. Still, there are thousands upon thousands of potential habitats that are just perfectly suited for anaerobic bacteria within the pipes leading to your faucets. These microhabitats are where the anaerobic bacteria that release methane reside.30
We have one major advantage in this population war between us and the odiferous bacteria—and it’s a great little twist, straight out of War of the Worlds. The element that we depend on for our most basic environmental need, oxygen, kills our opponents the second they are exposed to it. Anaerobic bacteria die when they come into contact with oxygen. In our house this happens when they are sieved through the aeration screen on the faucet’s mouth. So we are left with no threat from their carcasses, simply the unpleasant gaseous emissions from their colony.
Still, they don’t go without putting up a fight. Interior plumbing has been a fixture of American life for at least 150 years, so a lot of houses have long histories of infection by methane producers. Some pipes are probably so infused with bacterial colonies that they will never be treatable with conventional whole-house filters. This is why faucet filters that are placed under the sink are so popular—they are farthest downstream, so it’s less likely that there will be a big colony in the short run of pipe to spigot, where deadly oxygen reigns.
In our house, however, there is a peculiar phenomenon where some pipes have momentary blasts of methane acridity and some seem pure. This is a puzzle that required some review of our building plans. One day our plumbing contractor finished connecting the elaborate labyrinth of pipes that led to our three bathrooms, kitchen, and laundry room. It was time, he said, to hook up the “main line” water pipe that came from our well. At this initial stage only one bathroom and the laundry room had finished plumbing, and the house wasn’t yet protected by a whole-house filtration system. Still, the plumber wanted to test the well pump and get some water into the house.
The water that finally flowed through the first tap was cloudy with clay, and there was a faint smell of methane gas from each of the fixtures. Where did this smell come from? Basically there were two possibilities: The first could be ancient gas from a Devonian population of methane producers. We might have hit a “seam” of gas that had migrated through cracks upward from the Marcellus Shale into our well. Or it could be a biogenic source of methane being produced today by living bacteria much closer to the surface. These populations thrive wherever there are appropriate habitats with low oxygen levels and easy access to carbon (such as the dead piles of leaves, animals, and microbes in swamps or bogs). Either way bacteria, whether living or long dead, were the problem.
So the real question for mitigating the plumbing problems in your house is: Are the faucets emitting a methane smell because of biogenic processes or is it a consequence of tapping into a fossil hydrocarbon reservoir? If it’s the latter, you might have to drill a new water well, but you could also get rich if you sell off the hydrocarbon resource to a gas company.
If, however, your problem is from biogenic methane, then you have to control the bacterial population in order to solve the problem. Eventually we bought and installed a whole-house filter and placed it upstream from the pipes in the house. By the time we connected the rest of the house plumbing we could be sure that no bacteria could come into our house because of the physical barrier provided by the whole-house filter. Not even bacteria can pass through a filter with a pore-space diameter of one micron—bacteria are about ten microns wide.
We are lucky in that our infection was limited to two taps in our house. We have neighbors whose hundred-year-old pipes are completely infected. It’s unlikely they will ever be free of the bacteria and their accompanying biogenic methane.
Our house-building episode is one tiny incident in an evolutionarily brief moment in time. Bacteria and their close relatives were the first living creatures on our planet, yet we are only just starting to truly understand how they have adapted to our evolution and how they continue to shape human lives. Bacteria were discovered only in 1687, by a Dutch amateur scientist called Antoni van Leeuwenhoek; his unique skill at grinding lenses allowed him to build very early microscopes. He studied samples of tooth plaque and observed “very little living animalcules, very prettily a-moving.”31 Yet it took many years for scientists to begin to understand what bacteria were and how they operated. It wasn’t until 1850 that a Hungarian surgeon, Ignaz Semmelweis, observed a connection between patient health, infectious diseases, and hand washing and other basic hygienic practices. Before that, surgeons washed their hands after surgery, but didn’t bother doing so before they operated (or between consecutive operations). They didn’t see the point.
In the last fifty years we’ve been encouraged to think of bacteria as some sort of invisible enemy, one that must be controlled and preferably eradicated for the sake of our family’s health. The manufacturers of Lysol must have made a fortune from products that promise to sanitize every crevice of your home, car, or child. Antibacterial gels are ubiquitous. We are waging a full-scale war on an invisible army, though what eludes most germophobes is that by applying chemicals or antibiotics to populations of microbes we kill only a portion of them. Some bacterial individuals have genetic resistance to the compounds we administer. Even if only one in ten thousand individuals survives the first chemical onslaught, it can reproduce quickly to build back the population numbers to replace those who succumbed. The new generation of microbes will be resistant to the chemicals previously used because each individual was born of the ancestor that survived the initial dose of chemical warfare. Hence a so-called superbug is born—one that is resistant to all forms of antibiotic or “disinfectant” compounds.
As our human population increases it is inevitable that we will come into contact with more and more microbial populations. Our historical tendency has been to try and eradicate other populations with the belief that it somehow makes us safer. It has become clear, however, that it is important to maintain a balance with the bacteria whose interests are sometimes at odds with ours. Some small efforts to protect ourselves are preferable for maintaining a healthy balance between “us” and “them,” rather than trying to eradicate all bacteria. Physical barriers—such as my water filters—are one way of controlling a nasty microbe population. But modern humans have discovered and manufactured chemical barriers as well. Soap and toothpaste use a substance called surfactant to stop surfaces from clinging to one another; in this case it disrupts the attraction between dirt or bacteria and our skin or teeth. Antibiotics, if they’re not overprescribed, can be a useful, manageable shield against bacteria. They work by interfering with the growth and replication of individual bacteria. Today drug companies manufacture these substances synthetically, but in the early part of the twentieth century they were discovered from natural sources.
The Scottish bacteriologist Alexander Fleming was the first person to prove that a fungus called Penicillium notatum produced a substance that was toxic to bacteria. Others had made similar demonstrations before him—they were using other fungi of the same genus to show that certain “molds” could prevent bacterial growth. But Fleming formalized the medical treatment of many infections, including syphilis, using these substances produced by the Penicillium fungus. He named the wonder substance penicillin in 1929.
Fleming found the antibacterial action of penicillin by accidentally leaving a fungus-laced petri dish too close to a bacterial colony in his laboratory. However, Penicillium is not normally found in laboratories. Instead it lives in forest and field soil, where it forms a weblike structure that is hundreds of micrometers in size. There is a practical reason for Penicillium’s deadly touch: It protects the fungi from bacterial parasitizing invaders who might otherwise compete with the fungi for food sources. Penicillium feeds by secreting chemicals that break down the carbon found in dead and dying plant and animal matter. It then absorbs the partially digested carbon-rich broth, mixed with water. In this process, a protective penicillin secretion surrounds the fungi colony; this secretion acts biochemically to weaken the bacteria’s cell walls and render them helpless against osmotic pressure from surrounding water.32
Antibiotics were one of the most profound discoveries of the twentieth century. Treatable infections such as tonsillitis used to be potentially deadly; left untreated they could lead to sepsis and possibly death. However, tonsillitis and other bacterial infections are no longer necessarily lethal; penicillin made them survivable. We have, however, grossly and foolishly overprescribed and misused antibiotics over the last fifty years; some of the bacteria that survive have become superbugs, increasingly resistant to Fleming’s great discovery.
Our relationship with antibiotic-resistant bacteria is a case of evolution in action; we can’t completely exterminate a disease-causing population of bacteria any more easily than we can eliminate the malaria parasite, or eradicate methane producers from our household pipes. A tiny subset of these populations, either hiding out in undiscovered anonymity, or immune to our counterattacks, can easily rebuild and reinfect us. These “enemies” live on, proliferate, and persist.
Superbugs can be horrifying—such as the flesh-eating MRSA epidemic that is rife in hospitals—and wretchedly life ruining—such as Neisseria gonorrhoeae, which no longer responds to any antibiotics in 30 percent of cases; the United States now sees 246,000 drug-resistant gonorrhea infections a year.33 The CDC estimates that 23,000 people die every year—in the United States alone—of infections from antibiotic-resistant bacteria.
The drug companies are aware of this problem; they have taken this population war and continually tweaked it to an advantage since Fleming’s first discovery. We have discovered other organisms, not merely fungi, which also have antibiotic substances. Other bacteria, viral particles, synthetic molecules, and even phagocytic protozoa have been used to fight infections. (A phagocyte is a cell that can eat smaller cells by engulfing them, a process known as “phagocytosis.”)
Bacteria can be a political topic too. Municipal drinking water is treated with multiple chemicals in huge holding tanks millions of gallons in size. These chemicals vary from city to city, or town to town. For instance, Ithaca, New York, doesn’t add fluoride to the water, whereas in Los Angeles it is added to help prevent tooth decay. The people of Portland, Oregon, recently voted to prevent the city from adding fluoride to its water because most voters saw it as a chemical additive that was essentially polluting their relatively pristine drinking water.34 It’s easy to criticize fluoridation as simply a conspiracy or socialist agenda if you believe that fluoridated water is not the best way to improve dental health. The majority of voters in Portland believed that the city had no right to add medicine or any other ingredient to the drinking water. They thought it was a matter of political ideology instead of public health. But fluoridation—like vaccination—was one of the great civic health initiatives of the twentieth century. Public fluoridation is a well-documented and safe deterrent to the mouth bacteria that cause dental caries.35 As the humans debate, the bacteria proliferate. In Portland the only “winners” are the bacteria living in the mouths of the city’s most impoverished residents, who can’t afford to visit a dentist regularly.
I recognize the potential damage that chemicals can cause; however, you have to balance the possible harm against proven benefits. Human beings tend to have very short memories, and it’s been one hundred years since the last cholera outbreak in America. But there’s a reason our grandparents embraced fluoridation, vaccination, and, in the case of cholera, chlorination; these programs were much needed, and they saved many, many lives. Chlorine should be the least controversial chemical added to municipal water. In most cities you can smell the chlorine very easily by putting your nose next to the stream of water coming out of the faucet. It’s not quite as strong as when you visit an indoor swimming pool, but chlorine is readily recognizable. Usually a trip to the country to see your hick cousins makes you aware that there is a difference between the city water you’re used to and the stuff that comes from the well. First and foremost, there’s no chlorine smell.
The chlorine is added to create a hostile environment for bacteria. It combines with water to form acids that oxidize enzymes and other proteins. This oxidation poisoning kills bacteria quickly. Unfortunately oxidation poisoning is also stressful on human cells, especially those such as skin and respiratory linings, and prolonged exposure can lead to cancers. Chlorinated drinking water systems have been in safe operation for decades, exposure levels are sufficiently low that they don’t cause cancer or any other malady. But if you can avoid it, especially through the use of mechanical filters, like those we have in our well-water system, your cells will thank you.
Understanding some basic facts about microbial populations and being aware of their history is the key to sorting out numerous problems of everyday life, from house construction to public health. But having this knowledge—knowing the source of a malady, having an appreciation for the history of the organisms that cause it, and having the tools appropriate for treatment—isn’t always the path to a cure. Instead of eradication, it’s often more prudent to accept the presence of others and strike a compromise. After all, in any confrontation between microbes and humans the microbes will have a significant upper hand: sheer numbers, the ability to colonize, and the fact that they have persisted since the origin of life, at least 3.8 bya.
The next logical question, then, is, How can these populations be controlled? We may eventually be able to get rid of the methane in our house, but I know that these organisms will not go away, nor do I believe the world would be a better place without them. Bacteria are necessary and essential engines in our environment and, as we will see, also necessary to the proper “education” and function of our immune systems. Even with our whole-house filter in place, I acknowledge that my life is intricately intertwined with microbes. They are far more numerous than one can easily imagine.
Bacteria are ovoid and relatively simple in shape—like tiny sacs. They are diverse metabolically, but they tend to be small, on the order of one to ten microns in diameter. One micron equals one 1000th of a millimeter. The dimension of these organisms is hard to imagine, but one thing that is easy to understand is the need for special optical equipment and staining techniques in order to see them. Bacteria are at least ten times smaller than the average human cell from skin, muscle, or immune system. Because of their tiny size, they are magnificent at hiding in places where chemicals cannot penetrate and larger cells cannot kill them.
It takes a little imagination to picture the world of bacteria. When you are only a few microns wide, a seemingly smooth surface—say a human tooth—becomes a rough and ugly landscape, full of deep fissures and jagged peaks. No matter how diligently you brush, the junctions between mouth surfaces, such as between a tooth and its surrounding soft gum tissue, are almost impossible to keep clean. The spaces are simply too tight and the junctions too deep. It is precisely these places where bacteria find an ideal home and undergo their population growth.
Small size and simple metabolism are keys to the great ecological success of bacteria. But perhaps their greatest “achievement,” if you will allow the anthropomorphizing, is their evolutionary longevity. Simply put, bacteria were here first, and likely will be here last as well. These simple colonies of bacteria didn’t do much by our standards of accomplishment. Yet they are crucial to life on our planet; they are engines of environmental change. Because the descendants of these long lines are still with us, we can study what they do and imagine the world in which they first appeared.
The fossils of bacteria are called by the same name as their modern descendants, cyanobacteria.36 They occur as ovoid pairs of cells—only a few microns wide—or longer strands of numerous rectangular cells that may form straight or sheetlike colonies. They can tolerate very high salinity, very low oxygen (they are anaerobic), very high temperatures, and they thrive in intense sunlight. This last point reveals the key to their role as early environmental manipulators.
It’s important to understand how microbe populations have changed our environment. They are responsible for creating some of the basic requirements for life on our planet. If bacteria ceased to exist, our fundamental ecological necessities would collapse, and we would quickly die. In fact most familiar life forms would vanish in a matter of days.
For instance, the atmosphere is the ultimate source of nitrogen for all of the biosphere’s myriad of species. From bacteria to baleen whale, from slime mold to Salmonella, and from millipede to humankind, nitrogen forms the basis of all the protein building blocks for all life on Earth. All proteins are composed of amino acids, all of which have nitrogen compounds as a fundamental component. Roughly 78 percent of the air we breathe is made of nitrogen, but none of this nitrogen exists in a usable form.
Nitrogen is biologically inert. That’s why, for instance, it doesn’t react with your lung tissue. Unlike oxygen, which gets absorbed by the lung epithelium, nitrogen simply passes into the lungs and passes right back out with every breath.
We build our connective tissues, muscles, enzymes, blood, and virtually all the other tissues of our bodies out of proteins, but we have to get the nitrogen for those proteins by eating other proteins. So what is the ultimate source of nitrogen?
Every molecule of biologically viable nitrogen that enters the biosphere comes from a chemical transformation of atmospheric nitrogen brought about by bacteria. If it were not for these nitrifying bacteria busily converting nitrogen gas (N2) into ammonia (NH3), there would be no source of nitrogen for the basic protein and nucleic-acid building blocks of plants, animals, protists, fungi, or bacteria. This process of bacterial activity is known as nitrogen fixation, and it nicely exemplifies the role of bacteria as environmental or ecological engines. If this engine failed, the biosphere would collapse.
What about oxygen? Oxygen comprises roughly 21 percent of the air we breathe. Without it all animals would cease to exist. Humans can stand only a few short minutes of anoxia before severe brain damage sets in, followed by rapid shutdown of all organs and tissues. Unlike nitrogen, oxygen gas is extracted directly from the environment by passing air or water over delicate tissues in all vertebrates. Fishes use gills, terrestrial vertebrates use lungs. In each case oxygen diffuses directly across epithelial tissues in these specialized organs, and we literally steal molecules from the air in each breath. We don’t need bacterial help to breathe, but we do need bacteria in order to have something to breathe in the first place!
We often think of plants as the organisms responsible for creating oxygen, through the process of photosynthesis in their leaves. But in fact it is now widely agreed that the photosynthetic organs of plants are the evolutionary descendants of free-living bacteria. All photosynthesis therefore has a bacterial origin. Photosynthesis is a chemical process that converts carbon from CO2 into sugar and results in the liberation of oxygen (O2) as a waste product. The rock and fossil records prove that the bacterial engine of oxygen production has been running for billions of years.
Have you ever stopped to think about where the air that you breathe comes from, or what the original building blocks of the biosphere were? It’s understandably easy to overlook the fact that our survival is tied into a larger web of life; but only by understanding and accepting the roles of other organisms can we hope to manage the future of our species. The population wars of the past—a series of countless interactions stretching back 3.5 billion years—brought us to this moment.
It is possible that other types of simple cells existed back then, but no trace of them has ever been found. The most conservative estimate is that there were only very primitive biological systems at the dawn of Earth’s biosphere. Slightly older sediments do, however, reveal biochemical signatures that indicate photosynthesis was present 3.8 billion years ago.37 Presumably this was caused by ancestors of the oldest fossils found around 3.5 bya. Therefore geologists are reasonably confident that more than one type of bacterial community was active around the time of the earliest fossils.
Bacterial engines were cranking in the Precambrian, and they haven’t stopped since. The sediments reveal these bacterial signatures throughout geologic time, as seen in the Marcellus Shale. The pipes of our houses reveal that those microbial engines are still at work. We can try to stop them with filtration systems, antimicrobial substances, and antibiotics. However, bacteria are so small that we often don’t realize that they have us surrounded. Even more foolishly, we concentrate on eradicating them without first acknowledging the fact that we are dependent on them for our own lives.
The human body is composed of so many individual cells that it boggles the mind simply to contemplate such a large population size. Let’s say, for the sake of discussion, that ten trillion cells38 make up a single human being. All of them carry the same genes because they originated from a single original source, a fertilized egg, or zygote. Shortly after fertilization the egg cell divides and begins a long cascade of events known as differentiation and cell division. Cell numbers and cell types proliferate throughout this development.
Various divisions of labor spring up as tissues give rise to organs and the embryo begins to materialize. By the time the individual matures into adulthood, most of its cells come to equilibrium and stop dividing. Some, however, lie in relative dormancy, waiting to be called into action in case of injury or infection, at which time they undergo cell division once more to build up their population size and repair damaged tissue. Some still are in constant turnover throughout life, such as skin, blood, the male gonads, and the alimentary canal.
Ten trillion cells is a huge number. However, recent discoveries show that bacteria—once again—outnumber us, this time on our most literal “home turf,” our own bodies. We host, either within or on the surface of our bodies, almost 100 trillion cells that carry DNA different from our own. All these cells contribute to our well-being and decision making. They are microbes that have formed a unique symbiotic union with our bodies. We all carry an entire ecosystem around within us. And no two ecosystems are the same.
Something is keeping these 100 trillion cells busy; their well-being relies on our personal decisions, and we are only very slowly starting to understand how our seemingly “personal” choices are shaped by the microscopic individuals that live within or on us. We can imagine that our own cells are doing something to enhance our lives, even if we don’t know exactly what it is. But it is very difficult to acknowledge that ten times more individual cells are working simultaneously alongside them in a microscopic biome—a microbiome—to make us who we are (A biome is a region with characteristic species that is distinct from other regions due to the complexion of its community of species.)
Roughly 99 percent of these cells are anaerobic bacteria that live in the gut. These bacteria break down nutrients that your own cells cannot digest (such as the vegetable product cellulose) and give off gas as a waste product, methane. Your stomach and intestines are full of harsh acids and other fluids that kill most types of living things. Our bacterial partners in digestion, however, are descendants of ancestors that were there when the first rocks were forming on the planet, at a time when only extremely inhospitable environments blanketed Earth, billions of years before any kind of “higher” organisms appeared. Of course they are happy living in the harsh intestinal environment in our guts—it reminds them of “home!”
It’s not only cellulose, however, that is being broken down in your gut. Humans are unique among mammals in many ways, but one that stands out is our ability to eat so many varieties of plants and animals. We owe this not to our own specialized cells in our intestines, but to the microbiome composed of bacteria. There are at least one thousand different bacterial “species”.39 Each one of these specializes in releasing particular enzymes that break down various constituents of our highly varied diets.
The genes carried by our gut bacteria determine which digestive enzymes are activated in the digestion of our food. It has been estimated that the microbes in our guts carry 150 times the number of genes that we have in our entire genome.40 This gives us an enormous metabolic boost and means that there are hundreds of times more products we can digest because of this symbiosis with microbes. We can let the microbes handle the chemical breakdown of foodstuffs, and we can both share the results. The benefits of this symbiotic relationship are huge; our freedom to choose food from many sources makes us highly adaptable. The microbiome is also highly adaptable; it is a community of different species of bacteria that can shift its variety and abundance in response to the food choices of the host. The practical upswing is that if one food source runs out, we can eat another. We can travel beyond the boundaries of a traditional food source with relative confidence that we will find something else to eat.41
Bacteria are essential to our health. But we give something to them as well; our intestines are a two-way street. Bacterial individuals are able to acquire genes from host cells and from one another, even though they are a completely different species. This means that many of the bacteria living inside us are carrying some of the enzyme-producing genes of humans. In a sense they are competing with us, using the same enzymes to digest food for themselves that we have eaten. Our body keeps these competitive bacteria in check with bile salts and immunoglobin, two substances released by specialized human cells in the gut.42 But it’s also clear that we benefit from their by-products. For instance, we can digest the sugars that they inadvertently produce through fermentation43 and we also digest the constant supply of dead bacterial individuals that expire every hour. Each of us is a steward of the other in a very real sense. Our own cells are “irreversibly dependent”44 on the community of microbes that lives inside our bodies.
Our bodies, and in turn what we consider to be “ourselves,” are very much a collaborative effort, and one we have less control over than we like to think. An emerging field in biology focuses on the “gut-brain axis.”45 From studies on other living vertebrates as well as on humans, it is clear that hormonal signals in the gut travel along sensory neurons (brain cells) in the central nervous system to the brain and affect not only foraging behavior (decisions about when and what to eat) but also mood, anxiety, cognition, and pain. Many of these hormonal cues come from the bacterial populations in the gut. This means that some of our most cherished behaviors—being in a good mood, caring about others, working hard, and the like—are not strictly determined by our own sense of autonomy, and therefore they are potentially out of our control. Organisms—ones that carry completely different genes from our own—interfere with our ideas about how to take care of ourselves. Furthermore, it’s been shown that dietary changes rapidly affect the makeup of symbiotic species we carry in our guts. This means that vegetarians, for instance, have a different set of bacteria—and equally important, a different set of non-native bacterial genes being activated—than those who eat a diet rich in meat.46 Think about that for a minute. If different subgroups of humans have different gut flora, due to dietary constraints such as vegetarianism, other differences in culture and lifestyle might be explained by what bacteria they carry.
It seems, then, that we have to see our microbial partners as an extension of ourselves. If we think of ourselves as a huge group of microscopic individual cells living in a shared environment, then what does it mean to be an individual in the first place? If we care about ourselves, we have to protect and serve the intestinal flora as well as our own somatic cells by treating them well. This could be as simple as eating yogurt occasionally for digestive health47 or refusing to take unnecessary doses of antibiotics because of the damage they cause to all species of bacteria—not just the pathogenic kind, but the helpful partners in our digestive tract as well. It also means, however, having awareness of the invisible population inside us that could cause damage if it grows out of equilibrium.
One classic example is the bacterial gut species called Helicobacter pylori. It infects many but not all of us. At low population levels it is a perfectly benign member of the intestinal microbe community. It eats the occasional products of inflammation that occur naturally from time to time along our stomach lining. Usually we can tolerate low levels of inflammation—it occurs naturally whenever we eat certain foods that are difficult to digest, especially industrially produced mass-market foods. In fact Helicobacter’s presence in low numbers also promotes those same inflammation episodes. If the inflammation gets out of hand, however, the presence of Helicobacter is no longer benign. This microbe was discovered only relatively recently to be the main cause of peptic ulcers, a painful ailment that causes bleeding and degradation of the stomach tissue. And there is a chronic component too. Even the low-level inflammation caused by H. pylori can, over ten or twenty years, develop into stomach cancer.48
Yet the prevalence of H. pylori in so many intestines tells a story that beautifully illustrates how we are inheritors of past circumstances. As it turns out, the presence of this bacterium in our guts prevents other bacteria from taking up residence there. A sort of competitive exclusion is in place: The H. pylori excludes other bacteria by secreting deadly toxins. What sorts of “other” bacteria are excluded? The very same species that cause food poisoning in humans. As we saw with sickle-cell disease, there is an evolutionary trade-off to this population war; if you carry H. pylori you get perpetual protection every day against getting food poisoning49 but you also have a very slight chance (around 2 percent over twenty years) of getting stomach cancer. In other words if you can keep this bacterial population at a low level you are healthier than people who’ve eradicated the bacteria permanently by frequent use of antibiotics. Those who habitually use antibiotics may permanently destroy the low-frequency presence of H. pylori, resulting in a higher risk of stomach cancer.
It’s easy to see how this phenomenon was produced by evolution. In the past humans didn’t live so long. Life expectancy was roughly thirty years in Roman times. That number had increased to merely fifty years at the beginning of the twentieth century.50 A chronic disease that waits, say, twenty years before it starts to take its toll, such as stomach cancer, would not have impaired anyone throughout most of human evolution because people may have had only twenty years of maturity and reproduction before meeting their early death. Nowadays we have fifty years of maturity (at least) and a much longer time to develop slow, chronic, diseases. Stomach cancer cases have increased because humans are living longer. The longer you live, the more likely chronic diseases—such as those caused by populations with genes other than your own—will bring about your demise.
The presence of a healthy gut microbiota, including H. pylori, however, could have greatly improved one’s fitness early on in human evolution as brave individuals branched out in their adventurous attempts to try new foods. Those who carried the right combination of bacteria in their guts avoided potentially deadly attacks of food poisoning, and could digest a wider array of plant compounds. It’s only now—since so many members of our species are increasing in life expectancy—that we have to deal with the chronic effects of one of those bacterial strains growing out of proportion, such as we see in ulcers caused by H. pylori. But treatment in old age is not so simple.
By eradicating H. pylori entirely from the gut, with antibiotics for instance, we can cure ulcers. But it appears as though there is a concomitant increase in acid reflux in populations where the incidence of this bacterium is lowest.51 Over time acid reflux can cause adenocarcinoma, a different type of tumor that affects intestinal and other glands.
By all accounts, then, we have to see the microbes in our guts as coevolutionary partners, meaning that they evolved alongside us throughout the history of our species. They prefer to live inside our guts because it is a suitable habitat, like the ones in which they originally evolved billions of years ago—that is, ones with extreme levels of pH, far away from the deadly activity of both sunlight and oxygen. Their ancestors probably lived in our ancestors’ guts, and the entire lineage evolved together. If we view these other species as participants in our evolution, then clearly the common idea that microbes must be destroyed so that we may live antiseptically is utter nonsense.
The narrative of absolute “good vs. bad” doesn’t apply here. When organisms interact, they do so because the trajectory of history has brought them into contact. There is no reason to assume that this interplay of species has ultimate winners or losers. Instead we should focus on restoring what has been destroyed through mismanagement or improving historical conditions to make life better for ourselves, which also means maintaining suitable habitats for our coevolutionary partners.
Whether it’s the dark, oxygen-free recesses of our home’s plumbing, the highly acidic stomach cavity, or the deep-ocean sediment basins full of hydrogen sulfide, bacterial microbes thrive on today’s Earth in habitats that have been around since the beginning. Fossils from 3.5 billion years ago, and chemical signatures in Earth’s oldest sedimentary rocks, prove that microbial communities existed at that time. Population wars began, it seems, with the very origin of the planet, as soon as appropriate environments had taken shape.
It is hard to know how many species made up those early prokaryotic communities. (All organisms fall under one of two grand categories: Prokaryotes, bacteria, and archaea are unicellular and lack a nucleus. Eukaryotes, the other category, can be unicellular or multicellular, and all have nuclei, among other organelles.) But it is estimated that there are roughly 8.6 million species of plants, animals, fungi, and protists living today, and there are as many as 10 million free-living and symbiotic microbe species.52 A large portion of these prokaryotes are doing pretty much the same thing they’ve been doing for billions of years, metabolically speaking. They are ecological engines converting molecules of their surroundings into cellular building blocks. Through all their collective activities they release excretions of gas that alter the atmosphere or surrounding aquatic environment. This mechanistic activity drives the biosphere forward in time as we confront the present day. Each one of us is merely a passenger on board this evolutionary dynamo. But unlike all species that came before, we have the unique ability to imagine the future and manage it to some degree.