Microbes gave us life

Every week brings news of superbugs, rare parasites, and flesh-eating bacteria. As two microbiologists working at a medical school, we know full well that those threats are real and can’t be dismissed. But the bad news unfortunately elbows aside the untold stories of the microbes that pioneered life on Earth and the diverse microbes that continue to support our lives.

For the past three years, we have been photographing traces of the earliest microbes as well as the output of those at work today. We’ve captured thousands of images of microbes in far-flung landscapes and fantastic micro-scales. What we saw compelled us to share the beauty of the microbial world in a book of photographic essays, “Life at the Edge of Sight.” It sends a different message about microbes than what often appears in the headlines: The most fundamental realities of the microbial world are remarkably positive. Here are a few of these positive realities and even parallels to be drawn between humans and microbes.

Microbes first

Around 4 billion years ago, primordial cells began to form in a hot, chemical-rich broth. One credible storyline starts inside erupting geysers in a thermal region on land, similar to present-day Yellowstone National Park. Minerals on geyser walls catalyzed the formation of simple types of fat molecules and spewed them into nearby pools. As the molecules collected and interacted, these pools became hatcheries of microscopic spheres called vesicles. Meanwhile, RNA molecules arose through other chemical reactions and began to self-replicate inside vesicles. Heat fluctuations and turbulence in the environment eventually kick-started a primitive cellular life cycle and these proto-cells began to divide and reproduce. Those were the first microbes; that was the first life on Earth.

Soon after the first traces of life appear in the geological record, there’s fossil evidence of microbial communities. In those communities, microbes cooperated, competed, and evolved ways of communicating with each other. Much later on, from within those microbial ecosystems — and never separate from them — larger multicellular organisms evolved. Including us.

Invisible chefs

Though we are inexorably linked to the first invisible organisms in an unbroken evolutionary chain, our ancestors had no clue about microbes even as they were helping them. Here’s the story of the making of kombucha, a drink that has become wildly popular.

It begins with someone who once prepared a jug of sweet tea and left it to sit undisturbed. (Some say this happened in ancient China; others say it happened more recently in Russia.) After rediscovering the tea a few weeks later, the forgetful one noticed a thick white layer floating atop the liquid. Feeling adventurous, he or she poured the tea into a cup, leaving the white layer behind, and took a sip. “Mmm!” the experimenter exclaimed. It was a tangy and effervescent.

Little did early kombucha drinkers know they were consuming microbes with every gulp. All they knew was that they could keep remaking the drink and sharing the recipe with others as long as they transferred some of the slimy white layer to the next batch.

Without a microscope, the first people to make the fermented foods and drinks that have been savored for thousands of years around the globe — from cheeses to breads, beers, sakes, and more — had no concept of the microbial communities that made them. In the case of kombucha, the white layer is diverse biofilm ecosystem of yeasts, molds, and bacteria held together by a forest of crisscrossed cellulose fibers. Bacteria that generate acetic acid give kombucha the acidic finish that makes your mouth pucker.

A minority of bad actors

As modern microbiology came to be in the 1800s, pioneers like Robert Koch and Louis Pasteur discovered that microbes were responsible for fermentation around the same time they learned that certain microbes cause deadly diseases. Work on these so-called pathogenic microbes was, and continues to be, a necessary priority. Microbiologists have made great strides in medicine by singling out pathogens and finding ways to kill them. But the work by Koch and Pasteur and others quickly and indiscriminately typecast microbes as germs.

It is easy to understand how that happened. The technologies needed to survey the full diversity and abundance of microbial life had simply not been invented. Now we know that there are up to 1 trillion microbial species on Earth, and only a minute fraction of them cause disease. Nevertheless, much of the fear of microbes lingers in the public consciousness. Imagine if every little boy selling lemonade at a corner stand, every grandmother baking a cake, and every good Samaritan were suddenly placed on the FBI’s most wanted list. Vilifying all microbes for the sake of a few is a mismatch of equal magnitude.

Shifting allegiances

Even the idea of a disease-causing microbe is not as simple as it seems. Take Pseudomonas aeruginosa. This bacterium truly deserves its rank on the microbial most wanted list; it can cause many types of infections, some of them life-threatening. However, many people who come into contact with the microbe aren’t affected by it; most of those harmed by it have an underlying medical condition or a compromised immune system. That means there’s a back and forth with the immune system and it’s this interplay, not just the presence of the microbe, that determines if it will cause disease.

In fact, many bacteria capable of causing infections can and do carry out an honest living in our bodies, in the soil, and elsewhere in the environment. Adding even more nuance, some microbes are harmful or neutral depending on which other microbes are nearby. One species of bacteria might be perfectly civil when it hangs around another species, but the absence of that species brings out the worst in it. That phenomenon is true for Staphylococcus aureus, a species of bacteria that lives in the nasal cavities of some 25 percent of the human population. It is likely kept in check by other nearby bacteria. When it isn’t, it can cause skin and other serious staph infections.

These examples demonstrate that all interactions between microbes and humans are on the spectrum of symbiosis. There are the parasitic “pathogens” that harm humans, “commensal” microbes that live on and inside us without any known positive or negative consequence, and those that benefit us while we mutually benefit them. All of these categories of microbes are symbionts, not just the ones that help us, and one microbial species can shift from one relationship status to another in different times and places.

Makers and maintainers of the biosphere

The microbial world is the foundation upon which all other life rests. The mitochondria that make energy in our cells and the chloroplasts that power photosynthesis in plants got their starts as free-living bacteria. Oceanic cyanobacteria less than a thousandth of a millimeter wide produce much of the oxygen we breathe. Microbes in the soil nourish the roots of plants and transform inert nitrogen gas from the atmosphere into a biologically usable form, playing a key role in the nitrogen cycle and other chemical cycles. Bacteria and fungi actually create soil as they slowly break down plant and animal material, including the leaves in your backyard.

Microbes connect the global food web. Look at your dinner tonight. Whether you are a meat eater, vegetarian, or vegan, there would be no food on your plate without microbes. Let’s say it’s a filet of wild salmon. The salmon came neatly sliced and packaged, but it was once a living part of an ecosystem. As it grew, the fish consumed insects and smaller fish. Those animals ate even smaller ones — crustaceans and other kinds of zooplankton. And the zooplankton, in turn, ate single-celled algae called phytoplankton. Take away those microbes at the bottom of the web and the salmon disappears, too.

Of microbes and humans

Throughout the span of humankind, microbes have enabled societies and posed grave challenges to them. They will do the same in our future. Everyone experiences colds and acute infections, and some will suffer more serious interactions with microbes. But it’s thanks to these invisible organisms that we are alive in the first place and capable of experiencing the best parts of life too.

As we see it, microbial life illustrates an intrinsic duality in nature. Microbes make some of the most delightful things on the planet, like wine and chocolate, and they are capable of unimaginable devastation, like the Black Death. Microbes are social creatures that live in communities shaped by cooperation and competition, and they change their behavior, sometimes for the worse, depending on the company they keep. Sound familiar?

Just as we embrace the goodness in humanity in spite of the terrible few, so too should we strive to balance our negative view of microbial life with these overarching positive messages: Microbes gave us life, and they continue to give us life each and every day.

Scott Chimileski is a research fellow and imaging specialist in the Kolter Lab at Harvard Medical School. Roberto Kolter, who directs that lab, is professor of microbiology and immunobiology and director of the Harvard Microbial Sciences Initiative. They are the authors of “Life at the Edge of Sight: A Photographic Exploration of the Microbial World” (Harvard University Press, September 2017). Images from the book are currently on display in the exhibition “World in a Drop” at the Harvard Museum of Natural History, a precursor to the “Microbial Life” exhibition scheduled to open there in February 2018.