Weather makers: How microbes living in the clouds affect our lives

BBC News

11-06-2025

Trillions of bacteria, fungi, viruses and single-celled organisms travel the globe high in the atmosphere. Scientists are discovering they play a vital role in the weather and even our health.
Clouds are our lifelong companions. Sometimes they drift overhead as wispy filigrees. On other days, they darken the sky and dump rain on us. But for all our familiarity with these veils of water vapour, they have been keeping a secret from us. Clouds are actually floating islands of life, home to trillions of organisms from thousands of species.
Along with birds and dragonflies and dandelion seeds, a vast ocean of microscopic organisms travels through the air. The French chemist Louis Pasteur was among the first scientists to recognise what scientists now call the aerobiome in 1860. He held up sterile flasks of broth and allowed floating germs to settle into them, turning the clear broth cloudy. Pasteur captured germs on the streets of Paris, in the French countryside and even on top of a glacier in the Alps. But his contemporaries balked at the idea. "The world into which you wish to take us is really too fantastic," one journalist told Pasteur at the time.
It took decades for people to accept the reality of the aerobiome. In the 1930s, a few scientists took to the sky in airplanes, holding out slides and Petri dishes to catch fungal spores and bacteria in the wind. Balloon expeditions to the stratosphere captured cells there as well. Today, 21st-Century aerobiologists deploy sophisticated air-samplers on drones and use DNA-sequencing technology to identify airborne life by its genes. The aerobiome, researchers now recognise, is an enormous habitat filled only with visitors.
Those visitors come from much of the planet's surface. Each time an ocean wave crashes, it hurls fine droplets of sea water into the air, some of which carry viruses, bacteria, algae and other single-celled organisms. While some of the droplets fall quickly back to the ocean, some get picked up by winds and rise up into the sky, where they can be carried for thousands of miles.
On land, winds can scour the ground, lofting bacteria and fungi and other organisms. Each morning when the sun rises and water evaporates into the air, it can draw up microscopic organisms as well. Forest fires create violent updrafts that can suck microbes out of the ground and strip them off the trunks and leaves of trees, carrying them upwards with the rising smoke.
Many species do not simply wait for physical forces to launch them into the air. Mosses, for example, grow a stalk with a pouch of spores at the tip, which they release like puffs of smoke into the air. As many as six million moss spores may fall on a single square metre of bog over the course of one summer. Many species of pollinating plants have sex by releasing billions of airbourne pollen grains each spring.
Fungi are particularly adept at flight. They have evolved biological cannons and other means for blasting their spores into the air, and their spores are equipped with tough shells and other adaptations to endure the harsh conditions they encounter as they travel as high as the stratosphere. Fungi have been found up to 12 miles (20km) up, high above the open ocean of the Pacific, carried there on the wind.
By one estimate about a trillion trillion bacterial cells rise each year from the land and sea into the sky. By another estimate, 50 million tonnes of fungal spores become airborne in that same time. Untold numbers of viruses, lichen, algae and other microscopic life forms also rise into the air. It's common for them to travel for days before landing, in which time they can soar for hundreds or thousands of miles.
During that odyssey, an organism may fly into a region of the air where the water vapor is condensing into droplets. It soon finds itself enveloped in one of those droplets, and updrafts may carry it up deeper inside the water mass. It has entered the heart of a cloud.
Much of what scientists have learned about the life in clouds has come from the top of a mountain in France called Puy de Dôme. It formed about 11,000 years ago when a fist of magma punched up into the rolling hills of central France, creating a volcano that spilled out lava before going dormant just a few hundred years later. For the past twenty years or so, a weather station on top of Puy de Dôme has been equipped with air samplers. The mountain is so high that clouds regularly blanket its peak, allowing scientists to capture some of the life they ferry.
Studies led by Pierre Amato, an aerobiologist at the nearby University of Clermont Auvergne, have revealed that every millimeter of cloud water floating over Puy de Dôme contains as many as 100,000 cells. Their DNA has revealed that some belong to familiar species, but many are new to science.
Scientists who use DNA to identify species are perpetually anxious about contamination, and Amato is no exception. A hawk soaring over Puy de Dôme might fly over Amato's tubes and shake microbes off its feathers, for example. In Amato's laboratory, a graduate student may exhale germs into a test tube. Over the years, Amato has rejected thousands of potential species, suspicious that he or his students have inadvertently smeared skin microbes onto the equipment. But they have confidently discovered over 28,000 species of bacteria in clouds, and over 2,600 species of fungi.
Amato and other scientists who study clouds suspect that they may be particularly good places for bacteria to survive – at least for some species. "Clouds are environments open to all, but where only some can thrive," Amato and a team of colleagues wrote in 2017.
For bacteria, a cloud is like an alien world, dramatically different from the habitats where they usually live on land or at sea. Bacteria typically crowd together. In rivers they may grow into microbial mats. In our guts, they form dense films. But in a cloud, each microbe exists in perfect solitude, trapped in its own droplet. That isolation means that cloud bacteria don't have to compete with each other for limited resources. But a droplet doesn't have much room to carry the nutrients microbes need to grow.
Yet Amato and his colleagues have found evidence that some microbes can indeed grow in clouds. In one study, the researchers compared samples they gathered from clouds on Puy de Dôme to others they collected on the mountain on clear days. The researchers looked for clues to their activity by comparing the amount of DNA in their samples to the amount of RNA. Active, growing cells will make a lot of copies of RNA from their DNA in order to produce proteins.
The researchers found that the ratio of RNA to DNA was several times higher in clouds than in clear air, a powerful clue that cells thrive in clouds. They also found that bacteria in clouds switch on genes essential for metabolising food and for growing.
To understand how these bacteria can thrive in clouds, the researchers have reared some of the species they've captured in their lab and then sprayed them into atmospheric simulation chambers. One kind of microbe, known as Methylobacterium, uses the energy in sunlight to break down organic carbon inside cloud droplets.
In other words, these bacteria eat clouds. By one estimate, cloud microbes break down a million tons of organic carbon worldwide every year.
Findings such as these suggest that the aerobiome is a force to be reckoned with – one that exerts a powerful influence on the chemistry of the atmosphere. The aerobiome even alters the weather.
As a cloud forms, it creates updrafts that lift water-laden air to high altitudes that are cold enough to turn the water to ice. The ice then falls back down. If the air near the ground is cold, it may land as snow. If it is warm, it turns to rain.
It can be surprisingly hard for ice to form in a frigid cloud. Even at temperatures far below the freezing point, water molecules can remain liquid. One way to trigger the formation of ice, however, is to give them a seed of impurity. As water molecules stick to a particle's surface, they bond to one another, a process known as nucleation. Other water molecules then lock onto them and assemble into a crystal structure, which when heavy enough, will fall out of the sky.
It turns out that biological molecules and cell walls are exceptionally good at triggering rain. Fungi, algae, pollen, lichens, bacteria and even viruses can seed ice in clouds. It's even possible that clouds and life are linked in an intimate cycle, not just living and devouring the clouds, but helping them to form in the first place.
One of the best rainmakers is a type of bacteria called Pseudomonas. Scientists are not sure why those bacteria in particular are so good at forming ice in clouds, but it could have to do with the way they grow on leaves. When cold rain falls on a leaf, Pseudomonas may help the liquid water to turn to ice at higher temperatures than it normally would. As the ice cracks open the leaves, the bacteria can feast on the nutrients inside.
Some scientists have even speculated that plants welcome bacteria like Pseudomonas, despite the damage they cause. As the wind blows the bacteria off the plants and lofts them into the air, they rise into clouds overhead. Clouds seeded with Pseudomonas pour down more rain on the plants below. The plants use the water to grow more leaves, and the leaves support more bacteria, which rise into the sky and spur clouds to rain down even more water to nurture life below. If it turns out to be true, it would be a majestic symbiosis, connecting forests to the sky.
Research on the life in clouds also raises the possibility that airborne organisms might exist on other planets – even ones that might seem the worst places for life to survive. Venus, for example, has a surface temperature hot enough to melt lead. But the clouds that blanket Venus are much cooler, and perhaps able to sustain life.
Sara Seager, an astrobiologist at MIT, has speculated that life might have arisen on the surface of Venus early in its history, when it was cooler and wetter. As the planet heated up, some microbes could have found refuge in the clouds. Instead of sinking back to the surface, they may have bobbed up and down in the atmosphere, riding currents for millions of years, she says.
Thinking about Seager's alien aerobiome can make cloud-gazing even more enjoyable. But when we look at clouds, Amato's research has revealed, we are also looking up at our own influence on the world. When Amato and his colleagues have surveyed the genes in the microbes they capture, they find a remarkable number that endow bacteria with resistance to antibiotics.
Down on the ground, we humans have spurred the widespread evolution of these resistance genes. By taking excessive amounts of penicillin and other drugs to fight infections, we favour mutants that can withstand them. Making matters worse, farmers feed antibiotics to chickens, pigs and other livestock in order to get them to grow to bigger sizes. In 2014 alone, 700,000 people died worldwide from infections of antibiotic‑resistant bacteria. Five years later, the toll rose to 1.27 million.
The evolution of antibiotic resistance occurs within the bodies of humans and the animals humans eat. The bacteria endowed with this resistance then escape their nurseries and make their way through the environment – into the soil, into streams, and it turns out, even into the air. Researchers have found high levels of resistance genes in the bacteria floating through hospitals and around pig farms.
But airborne resistance genes can waft even further. An international team of scientists inspected the filters in automobile air conditioners in nineteen cities around the world. The filters had captured a rich diversity of resistant bacteria. It appears, in other words, that resistance genes float through cities.
In recent years, Amato and his colleagues have charted even longer journeys. In a 2023 survey of clouds, they reported finding bacteria carrying 29 different kinds of resistance genes. A single airborne bacterium may carry as many as nine resistance genes, each providing a different defense against the drugs. Every cubic metre of cloud, they estimated, held up to 10,000 resistance genes. A typical cloud floating overhead may hold more than a trillion of them.
Amato and his colleagues speculate that clouds hold such a high number of resistance genes because they can help the bacteria survive there. Some genes provide antibiotic resistance by allowing bacteria to pump the drugs out of their interiors quickly, getting rid of them before they can cause damage. The stress of life in a cloud may cause bacteria to produce toxic waste that they need to pump out quickly as well.
Clouds may be able to spread these resistance genes farther than contaminated meat and water. Once in a cloud, bacteria can travel hundreds of miles in a matter of days before seeding a raindrop and falling back to Earth. When they reach the ground, the microbes may then pass along their resistance genes to other microbes they encounter. Every year, Amato and his colleagues estimate, 2.2 trillion trillion resistance genes shower down from the clouds.
It is a sobering thought to hold in one's mind on a walk through the rain. We walk through downpours of DNA of our own making.
* Carl Zimmer's latest book Air-Borne: The Hidden History of the Life We Breathe is out now.
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