When the waters south of Miami turned Jacuzzi hot this summer, topping out at 101.1 degrees Fahrenheit in Manatee Bay, scientists agonized over the impact on parrotfish, grunts, spiny lobsters and coral reefs. But what about the invisible world of the ocean’s microbiome that we can’t see—one of bacteria, fungi, algae and viruses?

Before you say “ewww,” you should know that these tiny creatures, which on Earth number more than stars in the universe, connect all life on our planet. Scientists have found them deep in ocean chasms, and in volcanic vents, glaciers, caves and mines. They provide most of the oxygen in the atmosphere and help organisms digest food and manage immune systems. When creatures—including people—die, microbes decompose them, releasing carbon, nitrogen and phosphates that create new life. Roughly 38 trillion bacteria live inside and on you right now. Without bacteria and all that they do, you wouldn’t stay alive very long.

Nor will humans fare well on a planet where our indiscriminate use of fossil fuels and industrial chemicals continues to alter the delicate balance of microbes that sustain our ecosystem, into one that does not. Billions of years of evolution have shifted the Earth from a carbon-rich atmosphere to one drenched in oxygen. Over those eons, microbes mostly accomplished this terraforming by feeding on carbon and producing the oxygen we breathe as a byproduct, a process that humans seem hell-bent on reversing unless we act quickly to preserve the world of the very small by radically reducing carbon emissions and the indiscriminate use of other chemicals.

Humans are subjecting the Earth’s microbiome to the equivalent of what happens when you eat fast-food burgers and potato chips 24/7. You get a bellyache, or worse, in part because processed foods and high fructose corn syrup alter the composition of bacteria in our gut, decreasing the influence of “good” bacteria and increasing “bad” bacteria. Likewise, carbon and other pollutants alter the microbiome of Earth and undermine planetwide ecological systems that most people are only vaguely aware of.

For example, tiny ocean microbes called phytoplankton not only produce much of the oxygen on Earth, but also sequester almost 30 percent of the carbon produced by humans each year. Called the marine biological carbon pump, or just the biological pump, the system that supports phytoplankton is increasingly under threat as sea temperatures rise and phytoplankton drown in carbon. “We’re lucky we have the oceans to sponge up so much CO₂,” says Chris Dupont, an oceanographer and microbiologist at the J. Craig Venter Institute in La Jolla, Calif. “If the pump that drives this ever stopped working, we’d be in big trouble.”

Rising levels of CO₂ make seawater more acidic. This harms microbes sensitive to changes in pH. Pollution from phosphates and nitrogen from fertilizers on land are flowing from rivers into oceans and causing dead zones where the water is hypoxic, containing less than two parts per million of oxygen, an environment where few (or no) fish, or other marine life can survive. A dead zone below the mouth of the Mississippi River in the Gulf of Mexico has reached the size of New Jersey and, while it fluctuates in size according to the season and from year to year, overall it has been growing bigger. Globally, the number of dead zones has doubled every decade since the 1960s and now number in the hundreds, occurring from the Baltic Sea to the coasts of Latin America and Africa and the Great Lakes. The largest dead zone in the world is a 63,700-square-mile swath of the Gulf of Oman, almost the size of Florida.

Warming oceans and out-of-control chemical use cause coral reefs to eject bacteria and tiny algae called zooxanthellae that live in their tissue and provide them with important nutrients. Zooxanthellae help remove waste and fend off pathogens and are responsible for coral’s vibrant colors. Their loss contributes to reef’s dying, bleached white. More heat in the North Atlantic also spurs rising levels of a toxic bacteria species called Vibrio, which causes intestinal illnesses, including cholera, in humans, according to a 2016 study. Vibrio vulnificus, the so-called flesh-eating bacteria, and Karenia brevis, a toxic algae species that can kill fish and cause respiratory and other problems in manatees, sea turtles and humans, are among other nasty pathogens on the rise along parts of the North Atlantic coast. These microbes are often associated with “red tides” that are increasingly inundating the coasts of Florida and other shores as algae thrive in warmer waters and gorge on nutrients in fertilizer runoff.

Scientists can only guess what hot-tub level temperatures off Florida are doing to microbes living there. “One-hundred-degree Fahrenheit water will obviously change the microbiome, but in truth we do not know the ramifications,” marine biologist Jack Gilbert of the University of California, San Diego, told me. “Microbes are highly adaptable, but as these changes become more routine, we will see a shift in community dynamics and their metabolic activity that could have ramifications throughout the food chain.”

As the world moves to limit human activity contributing to climate change, it’s critical that the effect on Earth’s smallest creatures be considered alongside concerns for more photo-friendly species like Adélie penguins, wild tulips, piper plovers—and the aforementioned parrotfish and spiny lobsters. That’s a point made in a new book, The Voyage of the Sorcerer II: Explorations into the Microbiome of the Oceans, which I co-authored with geneticist Craig Venter. The book describes his two decades of work scouring the world’s oceans for microbes from a 100-foot sailboat.

“It’s hard to get the attention of politicians and others about what’s happening,” says Dupont. But scientists are trying. For instance, in 2019, a group of 34 microbiologists published a paper titled “Scientists’ Warning to Humanity: Microorganisms and Climate Change.” The authors put “humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.”

As we think small about climate change it becomes clear that nature is responding to the ongoing chemical assault by “striking back in unexpected ways”—a warning delivered in 1962 when marine biologist Rachel Carson wrote Silent Spring. Six decades later we’re seeing what she meant with superhot oceans, heat domes, raging fires, floods, crop losses and superstorms. Now we can add that nature is striking back through Earth’s smallest creatures, as humanity shifts the microscopic life that sustains us to a planet that, more and more, does not.

This is an opinion and analysis article, and the views expressed by the author or authors are not necessarily those of Scientific American.