The Next Climate Change Calamity?: We’re Ruining the Microbiome, According to Human

By David Ewing Duncan

“Human activity is causing a huge imbalance in the global microbiome,” said Craig Venter in his low, rumbling voice. As usual, he was not mincing words. It was 2018. Venter and I were sitting on the deck of Sorcerer II, his 100-foot sailboat, sipping coffee on a cold, misty morning in the Gulf of Maine. Slow, looping waves surrounded the boat as dolphins, off the starboard, leaped up and down in great arcs, their sleek, gray bodies lathered in foam.

What Venter meant is that fossil fuels and other pollutants aren’t just messing with polar bears and Monarch butterflies. They are also changing the invisible world of tiny organisms that sustain life as we know it, something that’s integral to what Rachel Carson called “the fabric of life” in her seminal 1962 book, Silent Spring, an indictment of humans’ folly in polluting their own environment.

This warning has become Venter’s clarion call too. It is a central theme of a new book that he and I have cowritten called The Voyage of Sorcerer II: The Expedition That Unlocked the Secrets of the Ocean’s Microbiome, which lays out the compelling evidence of how Homo sapiens are causing the micro-fabric of our lives to come apart at the seams.

Most non-scientists know little or nothing about this existential threat. And though I’d heard dribs and drabs about it as a science writer, it wasn’t until that damp morning on Venter’s boat that I truly understood the urgency of the matter. At the time, Venter, then 70, was nearing the end of a series of ocean voyages begun in 2003 to collect samples of seawater brimming with microbes, a quest that rival scientists had originally called a fool’s errand. Eventually sailing 75,000 miles, Venter had defied naysayers by taking on board Sorcerer II hundreds of barrels of seawater and then genetically sequencing the billions of microbes each sample contained—a project that ended up reshaping what science now knows about these tiny creatures, which outnumber the known stars in the universe, and connect all life on Earth.

Say hello to the microbiome—the planet’s bacteria, viruses, fungi, and microscopic animals—which have comprised Venter’s playground for the past 30-plus years. More persuasively than anyone, he has proven that these very small creatures are literally everywhere on Earth: in the atmosphere, deep in the ground, in glaciers, on every rose, and in every beating heart of every animal. Some 39 trillion of them are living inside and on your body right now, and you wouldn’t live very long without them. Research suggests they can impact your health and your moods. They might even influence who you fall in love with, the future health of babies, and how long you will live. And that’s just a small part of their outsized impact on us along with every other species of animal or fauna, and how they all relate to each other.

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If you’ve seen either of the Avatar films, microbes are akin to the real-life version of the blue glowing goo that links all life on the movie’s fictional moon, Pandora. Except that microbes don’t glow, and they aren’t blue. But they are the life force of our planet and have been since they first appeared around 3.5 billion years ago. Microbes are why we have an oxygen atmosphere, due to the fact that some of them—microbial phytoplankton in the oceans—“inhale” carbon and “exhale” O2, producing perhaps 60% of all terrestrial oxygen.

All life, including you, evolved from the earliest microbes. And all life is dependent on them for everything from helping you digest that raspberry smoothie you just drank to the bacteria that gobble up and break down every creature that dies and subsequently recycling those chemical components into nutrients for new life.

Craig Venter has been called everything from prickly and arrogant (and worse) to a genius. In the 1990s, he famously led an upstart team that challenged and probably beat a much larger and better-funded federal program to sequence the first complete DNA of a human being. (The race to finish the first map of a human genome was officially declared a tie in 2000 by then President Bill Clinton). In 2010, Venter achieved another huge milestone: creating a human-made genome from scratch, which he inserted into a bacterium that then popped to life. This breakthrough so alarmed President Barack Obama that the White House ordered an urgent assessment of the ethics of designer DNA and the advent of “synthetic biology.”

Venter didn’t accomplish any of this humbly or quietly. He has spent a career overturning the apple carts of scientific orthodoxies and then facing down uproars of protest with an I-told-you-so swagger and often brilliant flourishes of science and technological innovation. For instance, he has unabashedly compared his explorations into the microbiome of the oceans to the young Charles Darwin’s voyages of the 1830s. For biologists, this is a bit like comparing oneself to the Almighty, an attitude that also hasn’t sat well with some in the scientific establishment who have bristled at his provocative ideas and abrasive style, even though he has often been right.

“Craig is a very mercurial and a very tough personality,” observed Ari Patrinos, formerly a senior administrator at the US Department of Energy, which helped fund many of Venter’s projects, “which is not a negative trait, as far as I’m concerned. I think it’s always been a tremendous strength of personality and commitment to the ideas that he’s had. I honestly don’t think he would have been half as successful if he had tried to make peace with people.”

In early 2018, after covering Venter as a science writer for 20 years, I was in his office in La Jolla interviewing him for another project when he asked me to join him in coauthoring a book about his adventures in microland. This launched a four-year adventure in trying to get him to sit still long enough to chat about the book—in between racing vintage sailboats off Nantucket, four-wheeling on his desert ranch near San Diego, and drinking martinis in his sprawling house on the California coast in La Jolla. As a rule, when I pushed him to discuss pure science, he defaulted to deflection, preferring to talk about his sailing adventures on Sorcerer II. Like the time he was nearly eaten by sharks in the Galapagos. Or the day his ship was boarded by armed gendarmes in the Indian Ocean.

“Am I a bit of an adrenaline junky?” said Craig, bearded, bearish, perpetually sunburned. “Yes.”

I also witnessed him getting emotional one night in his La Jolla home when a close friend called to inform him that the friend’s wife, also a friend of Venter’s, had died. As the sun was setting in streaks of orange and red over the Pacific, time seemed to stop as he received the bad news. His face became stoic, with a hint of Old Man and the Sea, a chiseled visage I had glimpsed now and then when he was in deep concentration, captaining Sorcerer II. He quietly hung up and I swear I saw a tear.

With persistence, I was able to piece together what he and his team on Sorcerer II had accomplished during 15 years of voyages that took them from the Black Sea to the North Atlantic to the Sargasso Sea near Bermuda. The routine started with research assistants dropping a pump and special sensors into the sea to measure salinity, temperature, and other ocean metrics. Drawing in around 200 liters of water, the assistants would then ferret out the tiny microbes by straining the samples of seawater through finely meshed filters mounted in the stern. The filters would then be frozen and sent back to Venter’s institute, early on in Rockville, Maryland, and later based in La Jolla, where researchers sequenced and analyzed the treasure trove. Their goals and those of thousands of independent researchers that have used the Sorcerer II data were varied: looking for clues as to how many of these tiny organisms were out there, what they did, and how they were evolving over time; plus insights into developing new sources of energy, drugs, and cleaner industrial chemicals; and ultimately clues to the origins of life itself.

Meeting with dozens of scientists for the book, I also heard very disturbing findings about climate change. Call it a “microbial inconvenient truth,” to borrow from former Vice President Al Gore’s book and films about carbon buildup in the atmosphere. To get a sense of the small-scale changes in the environment, try thinking about what happens when you binge on fast food and upset the balance of microbes in your gut. You get sick.

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This is what we’re doing to the microbiome of the Earth as humans pour the chemical equivalent of fast food into the atmosphere and the oceans—which, among other things, is putting enormous pressure on critical, planet-wide systems that, in the coming decades, could face collapse.

Take the so-called ocean biological carbon pump, which uses phytoplankton to suck in 25–30% of the carbon in the air and produces most of the oxygen we breathe. Scientists are finding that larger phytoplankton are dying off, possibly from increases in the ocean’s temperature and from choking on all that carbon. The flow of nutrients that feed phytoplankton—and fish and other aquatic organisms—are shifting, while pollution from fertilizers and other chemicals flowing from rivers into the oceans are causing dead zones where few or no fish and other macro-life can survive. A dead zone below the mouth of the Mississippi River in the Gulf of Mexico is now almost the size of New Jersey. And it’s growing.

The assault on the microbiome is also contributing to the death of coral reefs, in part because climate change is impacting bacteria that live symbiotically with the coral and are responsible for their vibrant colors, and for keeping the reefs healthy. Climbing ocean temperatures and pollution can cause coral to eject these bacteria, leading to reefs blanching and dying as they turn from colorful to white. In short, the planet’s ecological health is being potentially endangered by the ravaging of the microscopic building blocks that affect every element of the environment at large.

This reminds me of something else Rachel Carson wrote 60 years ago in *Silent Spring—*that nature, in the face of the “chemical barrage” being thrown at it by humans, was “capable of striking back in unexpected ways,” something we’re seeing evidence of everywhere right now. Not only with things we can see and feel, such as the furnace-like heat that has been enveloping the globe this summer—plus melting glaciers, super storms, and all the rest—but also in the world of the Very Small.

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“Most of us have such a human-centric view of the world,” Venter told me not long before we took off to sail the Gulf of Maine—a rare moment when this consummate man of action waxed philosophical—“like the Earth was made for us, and it will keep supporting us no matter what we throw at the environment. It’s not very smart of us. We can’t live in a methane atmosphere, and we can’t live with too much CO2. But that isn’t really given much thought by most people, or by politicians, which is kind of disastrously wrong.”

In the boat on that gray afternoon, Venter reiterated this thought as he gazed out at the sea. He then drew quiet, turning his head to survey the vast panorama around us, a liquid desert with dunes made of H2O that seemed alive as the surface pitched and crested, lifting the ship, and then dropping it in a steady rhythm as the swells grew in intensity.

“A storm is coming,” he finally said, sitting still for a fraction of a second longer before jumping into action to prepare for yet another squall bearing down on him.

Portions of this essay are adapted from The Voyage of Sorcerer II: The Expedition That Unlocked the Secrets of the Ocean’s Microbiome, which will be published on September 12, 2023, by Harvard University Press. The book is copyrighted by © JCVI; sections herein are used with permission.

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