Moira Donovan is a freelance journalist reporting on the environment and climate change, with a particular focus on the ocean. Her stories on subjects such as fisheries management, ocean pollution and carbon dioxide removal have appeared in Hakai Magazine, the Guardian and the Economist, and on CBC Radio, and have won awards from the Canadian Association of Journalists and the Society of Environmental Journalists.
HALIFAX, Nova Scotia — On a bright day in mid-November, a small Canadian Coast Guard vessel called the Sigma T is bobbing gently in the near-freezing water of the Halifax Harbour. Aboard, three technicians get to work attaching weighted plastic containers called Niskin bottles to a cable. The cable drops the bottles 60 meters into the Atlantic Ocean. More bottles follow like pearls on a string: 30 meters, 10, five, one.
Once the bottles are full of seawater, they’re hauled back to the surface, where the technicians begin to decant their contents, working quickly in the cold but getting slightly soaked in the process. Some of the water is directed into glass vials and mixed with chemicals to test for dissolved oxygen; other samples are processed for nitrogen and dissolved inorganic carbon. The rest of the water goes into jugs covered in duct tape and is then sent off to Dalhousie University to be filtered and analyzed by microbiologists.
What’s in those jugs is the reason I’m here. Scientists have been sampling this exact part of the harbor, the Bedford Basin, since the early 1990s to examine minute changes in microbial plankton. These waters are teeming with microbial life, tiny beings with complex names like Braarudosphaera bigelowii and Thalassolituus haligoni. Although they’re invisible to the naked eye, we depend on microbes for our survival.
“Each week is different from another,” one of the technicians, Magda Waclawik, tells me while directing water from the Niskin bottles into containers. “It sounds like it would be monotonous, but it’s not.”
Waclawik is the program manager of the Bedford Basin Time Series, a program that provides an ecosystem profile of the harbor through weekly sampling. This repetitive and largely unseen work shows up in scientific discoveries; even in these well-studied waters, Waclawik and her colleagues have helped identify new species. In parallel, microbes in these waters — and everywhere else on the planet — are working indetectably too.
Microbes outnumber the stars in the galaxy. In the ocean, they produce roughly half of the oxygen on Earth, while playing an essential role in cycling carbon dioxide out of the atmosphere and making essential nutrients available to other organisms.
On land, microbes are no less essential, cycling carbon and nutrients and forming the soil crusts that prevent deserts from eroding. Even the air is thick with microbes, which are believed to shape cloud formation and precipitation. Despite being practically imperceptible, microbes play an outsize role in every way, even making up the largest proportion of biomass on the planet, apart from plants, mostly trees.
“Microbiology is the beauty of the world,” says Jack Gilbert, a microbial ecologist at the Scripps Institution of Oceanography at the University of California, San Diego. “It is a fundamental truth of biology on this planet that it is all microbial. We just happen to be biased towards the fact that we’re more important.”
Many of the planet’s microbiomes, however, are under serious threat, with untold numbers of species and ecosystems flickering silently out of existence. Despite this, conservationists have largely failed to recognize the urgency of protecting microbes. There is no Red List to track the decline of microbial species, no microbial frozen zoos, no microbes adorning heart-stirring billboards.
The exact consequences of microbial biodiversity loss are still unclear. Yet as the primary microbes that produce oxygen in the ocean decline in warming waters and gut bacteria disappear — potentially fueling everything from a rise in autoimmune diseases to an alteration of the ocean’s carbon cycle — scientists say we’re risking irreversible changes to the planet’s unseen life-support system.
“The world is at a critical inflection point,” says Gilbert. “If we don’t do something now, shit’s going to get real, and microbiology needs to be considered in this space.”
Understanding that we are facing a catastrophe, microbiologists have spent the last few years making the case for why conservation, long the domain of plants and animals, must also apply to the tiniest life forms. Such a shift would bring considerable challenges. Conservation efforts are already stretched thin enough without factoring in micro-scale organisms. And how do you conserve something you can’t even see?
But the reality is that we need microbes much more than they need us. If we want them to continue sustaining life on Earth — at least, our lives — we need to act before it’s too late.
Safeguarding Microbial Ecosystems
At age 22, Arwyn Edwards very nearly disappeared into a glacier.
It was 2006 and he was on his way to sample microbes from a site on Norway’s Svalbard Archipelago when the scree slope he was traversing moved underneath him, sending him careening down the incline. As he slid, he desperately flailed his ice axe and managed to save himself from plunging into a swift-moving stream that would have swept him away deep into the ice. Just like that, he was almost gone without a trace.
Last summer, Edwards returned to the same spot on Svalbard. It was the glacier that had vanished: In under two decades, it appeared that a 12-story building’s worth of the ice had disappeared.
“When you see something as big and as majestic as a glacier … being destroyed, juxtaposed against where my corpse would have ended up,” Edwards said, “it just really brings it home that these are environments which are profoundly changing within our timescales because of our actions.”
“Many of the planet’s microbiomes are under serious threat, with untold numbers of species and ecosystems flickering silently out of existence.”
As a microbiologist, Edwards knows it’s more than ice that’s being lost.
Glaciers are the largest freshwater reservoir on the planet, home to dazzlingly diverse microbiomes that are often distinct to each glacier. At the surface, easy-going generalist bacteria live in the snow itself, snacking on a range of nutrients. In the summer, microalgae with red pigments swim through the snow seeking sunlight during large blooms, painting the white with a pinkish hue. Embedded in the ice surface, clumps of minerals bound together by cyanobacteria form brown spots that darken the ice. In the resulting melted potholes, a menagerie of microbial life — thousands of species of microbes: bacteria, algae, fungi, protozoa, diatoms, tardigrades, rotifers and viruses — flourishes.
Farther down in the ice is a low-abundance community of 100 to 1,000 cells per millimeter — “not much more alive than what’s coming out of your tap,” Edwards says. At the glacier bed are microbes that haven’t seen the sun in millennia. “You can have something that’s basically a hangover from before the last ice age [and] you can have things that are just changing day by day within meters of each other,” says Edwards.
As climate change rapidly increases temperatures in the Arctic, these eclectic microbiomes are increasingly vulnerable. Edwards has taken microbial samples from glaciers for his research only for those ecosystems to disappear by the time his work was published.
In an Arctic Ocean that’s losing sea ice, in soils modified by intensive agriculture, in degraded coral reefs — and inside the industrialized human body — human influence is disrupting microbial diversity with incalculable consequences.
“What if that glacier held the microbe that could make the next penicillin … or something that had a solution to climate change?” asks Edwards. “We will never have the opportunity to explore and investigate that functionality and that diversity because it’s just been lost.”
This urgency also weighs on Maria Gloria Dominguez-Bello, a microbiologist with Rutgers University who studies the development of the human microbiome. She has documented how the features of modern life — antibiotics, C-sections, infant formula, sanitation and processed food — reduce microbial diversity in the human body. She has also found that in some American adults, gut microbial diversity is around half that of mostly uncontacted Indigenous people from the Amazon basin, with bacteria like Bifidobacterium infantis — which is crucial for digesting breast milk, boosting the immune system and influencing bacterial biodiversity in the gut — seeming to disappear in infants as societies industrialize.
A series of micro-catastrophes in Dominguez-Bello’s life pushed her toward a potential solution. She carried her own collection of human microbiome samples with her when she left Venezuela after the 1999 revolution and sustained it through annual hurricanes after moving to Puerto Rico only for it to be almost wiped out by power outages during Hurricane Sandy in New York, where she eventually settled. Then she watched a documentary on the Svalbard Global Seed Vault, a backup storage facility for seeds to safeguard the world’s crop diversity, and thought: Why not do the same for microbes? Two years later, the Microbiota Vault Initiative was born.
Dominguez-Bello and her co-founders launched the Initiative in 2025 as a means to preserve entire microbial ecosystems. While there are already many collections of microbial isolates (strains of microorganisms isolated and cultured in a lab), there are very few collections of specimens, meaning ice, soil, feces or other microbial environments. This matters because roughly 99% of microbes currently can’t be cultured. Preserving only the isolates risks missing the vast majority of microbial life.
For now, the Initiative is focused on human-associated microbes and has started to receive specimens of feces and fermented food, with samples from threatened ecosystems like melting glaciers to follow. Eventually, these will be housed in a facility in a cold and politically stable country; the Initiative is searching for the right property in Switzerland. This vault will serve as a backup — the original samples will remain with the researchers who collected them, with the Initiative planning to offer free DNA sequencing on deposits, provided the data is open-access.
Ultimately, the Initiative aims to create a lifeline. If we wait to act, we could reach a point at which too many microbes are gone for us to enlist their help in ensuring a habitable planet. The Initiative is a hedge against that outcome. “When we decide to be more rational, then we need that biodiversity to restore ecosystems,” Dominguez-Bello says. “We need more research, and meanwhile, we need to preserve.”
“We need microbes much more than they need us. If we want them to continue sustaining life on Earth — at least, our lives — we need to act before it’s too late.”
Edwards, who is a senior researcher in biosciences at Aberystwyth University in Wales, is considering this too. When field research was restarting after the pandemic, nearly every glacier ecology laboratory in the U.K. had some kind of freezer failure, he says — including his own. Painstakingly collected samples melted to puddles. “I realized that our samples were very vulnerable. I already knew that the field sites were very vulnerable. I started to think, well, what’s left?”
He and other researchers are now in the process of establishing an international cryo-microbiome biobank to safely conserve samples of disappearing ecosystems. “We’re going to lose these places,” he says. “Now is our opportunity to try and salvage what we can.”
But conserving microbes doesn’t stop with freezers.
Microbes Get A Seat At The Table
In 2010, Gilbert, the microbial ecologist, embarked on an audacious plan: to catalogue microbial diversity from every biome on planet Earth. Over 10 years, he and his colleagues analyzed thousands of samples gathered from microbiologists’ freezers using DNA sequencing and mass spectrometry to get the genetic profile and function of microbes from as many ecosystems as possible.
But Gilbert knew something else was needed. Technological advancements were shaping a better picture of the global microbiome, and the picture was frightening. “We can see that things need conserving because they have a unique genetic character which will disappear if they are killed,” says Gilbert. “What we need is global leadership to pay attention to this.”
At a five-day conference in San Diego last May, Gilbert and other microbiologists made their case for why conservationists should care about microbes the same way they care about plants and animals (or “macrobes,” as Gilbert calls them). One microbiologist in the group told me that at that meeting, there was debate over prioritizing microbial conservation when overall biodiversity is in such dire straits.
Nonetheless, the group insisted that microbes should have a seat at the table, and in 2025, the International Union for the Conservation of Nature (IUCN) approved the first-ever Microbial Conservation Specialist Group, with the goal of charting the threats to microbial communities and coordinating their conservation.
The group’s approach is multifaceted, including coordinating biobanking initiatives, such as the Microbiota Vault Initiative, and integrating microbiology into existing conservation strategies for ecosystems or species. It also aims to map microbial conservation hotspots — like the planet’s melting cryosphere or the Cuatro Ciénegas Basin, an imperilled oasis for ancient bacteria in the Mexican desert — and to develop criteria for listing microbes on the IUCN’s Red List (the same list that tracks the conservation status of around 175,000 lifeforms, from the redwood to the axolotl).
Gilbert says the case for conservation rests on the fact that all the life we can see with our eyes depends on the life we can’t see. Without it, there is no Earth as we know it — and what we know of microbes is only barely beginning to scratch the surface.
“There are trillions of strains of bacteria,” he estimates, pointing to the variety found even within a single species, like E. coli. “You have sub-species, some of which are more different from each other than you are from a fungus. The diversity is so extraordinary and so, so poorly understood. There’s your freaking wonder.”
Yet in many ways, microbes challenge the usual ways of thinking of conservation.
Conservation Under The Microscope
When microbial samples come out of the Bedford Basin and off the Sigma T, they’re ferried to a range of laboratories, including a densely packed labyrinth of rooms in a building on Dalhousie University campus in Halifax. Here, researchers are trying to understand the importance of not just what microbes are, but what they’re doing.
Take B12, says Erin Bertrand, a marine biogeochemist at Dalhousie and the lab’s principal investigator. It’s produced by only bacteria and archaea, yet it’s essential to life, starting with the microscopic phytoplankton at the bottom of the food chain. In the Southern Ocean and the North Atlantic, Bertrand’s lab has shown that the amount of B12 that bacteria produce limits phytoplankton productivity — and therefore everything else. “It’s such an easy way to see how microbial activity and the interconnections between marine microbes drives major processes that are absolutely essential for us.”
Despite the centrality of microbes, Bertrand is hesitant about a conservation framework. Conservation has traditionally pitched humans against nature, she says; ideally, we would see humans as inseparable from the world microbes create — which we disrupt at our peril.
“If we wait to act, we could reach a point at which too many microbes are gone for us to enlist their help in ensuring a habitable planet.”
“When people ask me if we’re worried about microbes going extinct … I think the microbes are going to be fine. It’s just the services that they provide and the roles that they play in the ecosystems are going to change dramatically,” she says. “Is that good for us or bad for us? And who is ‘us’ — which group of people are we talking about? Those are the kinds of questions that I think are really important right now.”
Microbial function both bolsters and complicates the case for conservation. At the microbial level, evolution can happen with head-spinning speed. Bacteria and archaea can swap genes like baseball cards through lateral gene transfer. When there’s significant selective pressure — say, through the use of antibiotics or an influx of pollution — unrelated bacteria can share (or steal) genetic material to take on useful new functions. It’s in this way, some scientists hypothesize, that microbes acquire the ability to live in extreme environments, like hydrothermal vents or hot springs.
This not only confounds our way of thinking about life, it also begs the question of what conservation is meant to accomplish. Unlike life at the macro scale, where restored ecosystems can take decades to recover — if they recover at all — microbial communities often bounce back quickly after a disturbance, says Rob Beiko, a professor of bioinformatics at Dalhousie. They may not be the same microbes, he says, but do we care if a species is driven to extinction, so long as the function is preserved? “It’s like, yeah, here’s a thing that did a job before. And yeah, we killed it. But some other organism in the environment can pick up those capabilities.”
To complicate this further, even within a named species of microbes, members can vary so much that they have completely different functions, Beiko says. “When you put a name on something, there’s this implication that everybody in that group does the same thing, and so that should be your unit of conservation, like a deer or a brown bear. But there’s a lot more complexity under the hood [and] this is our job, to wrestle with this.”
Beiko is part of the Microbiome Stewardship Initiative, an international research group investigating practices to protect microbiomes from human disturbance. The group grapples with complex questions about microbial conservation. “When we talk about preserving a community, do we care about preserving specific species, or genera, or strains? Do we care more about specific functions?” Beiko asks. “It’s a really challenging problem and you will get different answers from different people.”
Respect For Microbes
In 2004, the astrobiologist Charles Cockell published a paper with a title that, at the time, people found puzzling: “The Rights of Microbes.” Speaking to me over Zoom, Cockell says that in the decades since, there’s been a recognition that the idea of microbial rights is not as absurd as it once sounded. He points out that our circle of moral regard has already flexed to include nonhuman animals and entities.
In Western thought, the idea of animal rights dates back to 18th century thinkers like Jeremy Bentham, and has even expanded to include ecosystems, like rivers, over time. Indigenous worldviews have also long emphasized relationality with nonhuman beings. Excluding microbes because they’re too small to see is illogical, Cockell suggests: If bacteria were the size of polar bears, and polar bears a micron in size, would it make ethical sense to care about the beauty of polar bears less, and bacteria more?
Having worked on planetary protection, a set of practices developed to avoid contaminating other planets with Earth organisms and vice versa, Cockell knew that as lax as people can be about protecting microbial life on Earth, they could have “this very, very dogmatic, extremely opposite reaction towards microbes on Mars,” which have piqued immense interest. Yet if that reaction is predicated on respect, it should apply equally to life on Earth, Cockell argues.
“[There are] microbes with the same cognitive capacities as the microbes on Earth; they probably evolved from some phylogenetic tree — they may even be related to life on Earth for all we know,” he says. “It makes no sense to have an environmental ethic that is wildly different on two planets.”
“Ideally, we would see humans as inseparable from the world microbes create — which we disrupt at our peril.”
The respect for microbes has limits: Cockell thinks it’s reasonable to kill microbes if human needs require it, like the much-celebrated eradication of the smallpox virus in the 1970s. But our growing knowledge of the diversity of microbes and their role in the biosphere makes a stronger case for respecting their intrinsic value. “If we’re going to have a robust environmental ethic, it should apply to microbes as much as macro-life,” he says. “Microbes are part of that growing environmental awareness.”
That environmental awareness includes acknowledging that by destroying microbiomes, we ultimately destroy ourselves, because it’s not just the planet that’s microbial — we are too. With the oxygen we breathe, with the food we digest, we are intertwined beings, both human and microbe. Yet there’s still a divide: Without us, there is still life. Without microbes, there is nothing. Microbial conservation could give us the humility to recognize this reality.
Back on the Sigma T in the Bedford Basin, technicians begin packing up the equipment and prepare to head back to the wharf. Once, they saw a Mola mola, a massive sunfish that can grow to be more than 10 feet long — “it just swam past us and gave us a look,” says Waclawik — but they rarely spy anything big. Therein lies the challenge for microbial conservation: The presence of a fish that can be as big as a compact car is arresting, and we miss it when it’s gone. A microbe one-twentieth the width of a human hair, no matter how important, is much harder to notice.
As a last step, the technicians drop a zooplankton net in the water and show me the filtered results. The container seems full of macroscopic wigglers, tiny maroon threads that swirl like confetti through the liquid, butWaclawik tells me it’s actually nothing special: In the spring and the fall, by contrast, the water will be brown or green with microbes.
Describing them, she becomes enthusiastic: Dinoflagellates, single-celled eukaryote protists, are “clever beasts” who steal pigment, “and they look cute. They’re very sweet.” Diatoms, silica-based microalgae that sparkle like snowflakes under a microscope, “are also very pretty.”
Incredibly, in this ordinary cup of seawater, are invisible beings that show all the wonder of this world — something worth saving, if we only look.
