Fantastic Microbes and Where to Find Them

Beneath our feet, beyond the reach of sunlight, and buried in the most unforgiving corners of the planet, an unseen world thrives. Though these environments may seem desolate, and devoid of warmth, light, or sustenance, they are anything but empty. They’re home to extraordinary microbes known as extremophiles, which have adapted to conditions that would destroy most known organisms. Some corrode minerals deep within the Earth, carving out underground caverns. Others survive extreme temperatures in boiling pools or icy tundras. At the same time, others live in the ocean’s deepest trenches, where they flourish at hydrothermal vents by harnessing energy from chemicals instead of sunlight.

As some of Earth’s earliest inhabitants, microbes not only endure—they thrive. But why do these microscopic survivors matter? Their resilience may reveal how life first emerged on Earth—and whether it could exist elsewhere in the universe. Extremophiles are also untapped treasures for potential real-world applications; scientists hope to repeat the success story of the isolation of PCR-enzyme Taq polymerase, which transformed molecular biology, from the heat-loving Thermus aquaticus. In search of the microbial prize, microbiologists venture into some of the most remote and extreme environments on Earth—including the labyrinthine world beneath our feet.

Digging Deep: Snottites and Other Unusual Cave Microbes

Since prehistoric times, caves have played a key role for humans, serving as shelters, sources of water, and even rocky canvases for ancient art. However, as civilizations advanced, reliance on caves waned, and scientific exploration of these subterranean ecosystems slowed. Now, researchers are returning underground, not just to uncover geological wonders but also to explore vibrant ecosystems filled with microbial life. Each cave system is unique—an ideal natural laboratory for studying extremophiles and how life adapts to perpetual darkness.

When geomicrobiologist Diana Northup joined an outings club during her undergraduate studies at West Virginia University, she didn’t expect to fall into caving—literally, she fell in over her head. But that rush of adrenaline captivated her. As she traversed in the darkness, she wondered what kind of organisms lived in the caves. That curiosity launched her into cave research at the University of New Mexico, starting with the unique formations in her New Mexico backyard in Lechuguilla Cave. Her earliest graduate studies were on water samples from Lechuguilla Cave in the 1990s. “When we looked in there, the microbes were just enchanting.”

Lechuguilla Cave, one of the longest caves in the world at nearly 150 miles, is no ordinary cavern. Unlike typical limestone caves formed from the top down by carbonic acid, Lechuguilla is a hypogenic cave—sculpted from the bottom up. Millions of years ago, hydrogen sulfide bubbling up from below reacted with oxygen, forming sulfuric acid that carved out the cave’s dramatic passages and mineral formations.

For scientists, Lechuguilla Cave is a microbial goldmine.¹ Due to its formation, it has been separated from the surface for millions of years. It provides a rare glimpse into ancient mineral deposits and the microbes that may thrive miles away from the cave entrance. The cave has nutrient-limited conditions, forcing microbes to rely on alternative energy sources, such as hydrogen, methane, sulfide, ammonia, or iron.^2,3

Northup set out to investigate how microbes might contribute to the formation of the colorful ferromanganese deposits that coat the cave’s walls. These deposits resembled a sandwich in cross-section, with an outer red (iron) or black (manganese) layer, followed by a corroded carbonate rock layer—known as “punk rock”—and then a bedrock layer beneath.⁴

“At the ferromanganese deposit, we got the punk rock to see who lived in it,” said Northup. These corrosion residues, a few centimeters thick, lay atop the altered carbonate rock up to 10cm. “We chipped away at the carbonate rock, smashing it enough to bring it back for examination.”

The research team first spotted microbial life as coccoid- or filament-shaped structures with microscopy. Genetic analysis revealed iron- and manganese-oxidizing bacteria like Leptothrix and Variovorax paradoxus, along with related unidentified species. These microbes produce acid as a byproduct, accelerating rock wall dissolution and corrosion.

Snottites form in these drips, where the pH can be as low as zero to one—it is very acidic.

—Diana Northup, University of New Mexico

Microbial life in caves isn’t always so picturesque. When exploring the active hypogenic Villa Luz Cave in Mexico, Northup dons a respirator and descends into passages thick with hydrogen sulfide—the source of the cave’s overpowering rotten-egg smell. Gas concentrations can reach 280ppm, far above the 5ppm threshold that triggers alarms.

Northup explained that unusual formations emerge due to the active hydrogen sulfide from the cave’s springs. “When the hydrogen sulfide [gas] reaches the ceiling, it converts into sulfuric acid, which starts dripping. Snottites form in these drips, where the pH can be as low as zero to one—it is very acidic.”

Snottites resemble slimy, dripping stalactites composed of biofilm, teeming with microbes. Researchers have also found snottites in caves with a more neutral pH, but across environments, one bacterial species dominates: Acidithiobacillus thiooxidans, known for oxidizing sulfur and thriving in harsh conditions.⁵ Not only do these cave microbes harbor interesting metabolic activity, but they may also offer biomedical potential.

While soil-dwelling Streptomyces has been a rich source of known antibiotics, caves are untapped reservoirs of novel antibiotics. These extreme environments may hold the key to combating modern antibiotic resistance.⁶ Hazel Barton, a geomicrobiologist at the University of Alabama, explores cave microbiomes and their unique properties for novel applications.

Barton studied antibiotic resistance in Lechuguilla Cave where microbes have been isolated from the surface for millions of years.⁷ If antibiotic use were the primary driver of resistance, these cave microbes should lack it. Yet, Barton’s team found that these cave microbes were resistant to every type of natural antibiotic, highlighting the ancient origins of antibiotic resistance.

One particularly resistant strain, Paenibacillus sp. LC231, was non-pathogenic yet withstood 26 out of 40 tested antibiotics.⁸ Further analysis revealed that its resistance profile closely matched that of surface-dwelling bacteria, reinforcing the idea that antibiotic resistance evolved long before modern antibiotic use.

Cave microbes not only show how life can thrive in extreme, nutrient-poor, light-free environments—so-called "dark biospheres"—but they also offer clues about the potential for life beyond Earth. Barton and her team have also explored Wind Cave, where underground lakes form from groundwater rising through an aquifer rather than surface runoff. “[This cave] is completely isolated from the surface, and that is what makes it a good analog for [Jupiter’s moon] Europa,” remarked Barton. “So, because you've got an icy moon with a shell, there's no communication with the outside. What are the potential chemistries that can support life there?”

When the researchers examined whether these lakes harbored unique microbial life, they were surprised by the results.⁹ “It turned out [to have] the lowest cell counts for any water on Earth apart from somewhere deep in South African gold mines,” remarked Barton. Due to this low biomass, Barton’s team had to filter thousands of liters of water to gather enough DNA for analysis. Despite the low cell counts, the samples held high microbial diversity, dominated by Gammaproteobacteria. Further investigation uncovered a unique metabolic system, where microbes use manganese as an energy source for growth.

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Microbiology

Spelunking for Microbes

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Frozen Frontiers: Hunting Microbes at the Ends of the Earth

Underground cave aquifer lakes, rich in biodiversity, share similarities with the cold deserts at Earth's poles. In both environments, microorganisms must develop specialized strategies to survive. These arid soils withstand freezing temperatures, limited carbon, nitrogen, water availability, strong UV radiation, and frequent freeze-thaw cycles.^10-12 But there is rather limited knowledge of their microbial communities.

Belinda Ferrari, an environmental microbiologist at the University of New South Wales, was first inspired by science at the age of 10 when she received a toy microscope and discovered the tiny swimming creatures in water samples from a duck pond on her family’s farm. Today, Ferrari studies polar microbes in soil, culturing species that were once thought to be unculturable.

In 2005, Ferrari received soil samples collected by the Australian Antarctic Division from the Windmill Islands of East Antarctica as part of a serendipitous collaboration. She was delighted, as samples are rare due to logistical constraints imposed by the remote location.

Antarctic soil bacteria thrive in one of Earth’s harshest environments, making them notoriously difficult to culture using traditional methods. Ferrari took up the challenge of growing the Antarctic microbial inhabitants in the lab. When standard agar media failed, Ferrari developed a new technique: soil slurry, which used non-sterile soil as the growth medium to mimic their natural conditions.¹³ While this approach successfully cultured some microbes, others required more specific conditions, such as exposure to atmospheric trace gases.¹⁴

To explore these elusive microbes further, Ferrari and her team use amplicon sequencing and metagenomics to reconstruct genomes and identify whether the microbes expressed genes involved in oxidizing atmospheric gases like hydrogen, carbon monoxide, and methane. Some of these air-eating bacteria are affiliated with high-elevation desert Actinobacteria, which possess genes for trace gas scavenging.¹⁵

After over a decade of analyzing samples sent by collaborators in 2005, Ferrari set off on her own expedition to the Windmill Islands in 2019. She returned to the same three sites where the original samples were collected, sieving the soil to gather hundreds of new samples to assess how the region’s warming had affected the microbial communities.¹⁶

“We took the same samples, and you know what we wanted to do was try to do all the same types of sequencing studies, get all the same environmental data for all those soil samples, and try and understand what was happening in terms of the soil communities and [note] any changes.”

The scientists predicted that due to warming, there would be increased moisture, a rise in phototrophic species, and a decline in trace gas bacteria. Indeed, their predictions were correct. “We saw an increase in things like Cyanobacteria that carry out photosynthesis, and a decrease in the ones that like dry soils,” remarked Ferrari.

While traversing the icy terrain, Ferrari saw another opportunity for further exploration. “On one of the sites, Robinson Ridge, [had] some beautiful moss beds on it. We ended up focusing on one of the samples there to try and culture it.”

In the lab, Ferrari set up low-nutrient media in tubes, using concentrations 100 to 1,000 times lower than standard levels, and added hydrogen gas to the vials to test the microbes' ability to oxidize hydrogen. However, instead of bacteria, fungi flourished, leading to the collection of a library of over 300 intriguing fungal species.

They're specialized to exist in these different environments, but the important thing is that you do find life.

—Julie Huber, Woods Hole Oceanographic Institution

Ferrari and her team are investigating a few novel fungi, including Penicillium psychrofluorescens sp. nov., an autofluorescent Antarctic fungus.¹⁷ This species cannot use nitrates but can utilize phosphorus from phosphonates via oxidative pathways. It also had 30 biosynthetic gene clusters, suggesting it could produce unique bioactive compounds with potential medical or biotechnological uses.

Excited by these findings, the team is experimenting with culturing fungi alongside bacteria or other fungi to stimulate antimicrobial or melanin production. Ferrari and her team have also partnered with botanical gardens that are interested in characterizing these fungi as novel organisms that could potentially function as plant pathogens.

Other researchers have explored melanin-producing microbes, such as Cryomyces antarcticus and C. minteri, for their resiliency in simulated space and Martian conditions.^18,19 These studies suggest that thick melanin layers shield microbial DNA and cells from extreme environmental stress.

“We’re looking at the organisms that are surviving in Antarctica as a model system for how organisms are surviving stress,” said Ferrari. “Getting a bit of an understanding of how these fungi are surviving in Antarctica might help us understand how to even remediate sites and learn how organisms respond [to different types of] disturbance too.”

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Microbiology

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Beneath the Waves: Microbes Thriving in Hydrothermal Vents and Ocean Worlds

The deep ocean serves as a prime analog for exploring life’s origins and the potential for life on other planets and moons with oceans. This mysterious, alien world—teeming with everything from coral reefs to microscopic life—remains Earth’s final frontier. Covering more than 70 percent of the planet, oceans are home to countless organisms that drive nutrient cycles, power marine food webs, and maintain ecosystem health.^20,21 Understanding how they survive in such extreme conditions is a monumental challenge.

Julie Huber, a deep-sea oceanographer at Woods Hole Oceanographic Institution, is deeply curious about the mysteries of the deep ocean. “I got hooked on this idea of microbes providing insights into how life might work beyond Earth, the origins of life, and that tight connection between the geological history of our planet and life,” said Huber.

Now, she studies how microbes tap into energy from the seafloor—far from sunlight. Her expeditions ferry her and her team out to sea near underwater volcanoes or a seamount, a submarine mountain, and hydrothermal vents—like geysers or hot springs on the ocean floor.

Hydrothermal vents release superheated and chemical-rich water that supports chemosynthesis, microbes can use these chemical compounds instead of light as energy sources.^22,23 These chemosynthetic bacteria then serve as food, supporting an ecosystem of animals such as tube worms, giant clams and mussels, and even octopi. Beyond serving as microbial munchies, the bacteria may offer additional benefits through their biochemical processes and byproducts.

For example, as Huber noted, “There are octopus nurseries [in Costa Rica] that are laying their eggs in these warm fluids leaking out of the seamount.” The reason for their decision to start a family here is still unclear. While some researchers hypothesize that these chemical-rich fluids may help with embryo development, Huber questions if the microbes in those fluids play more roles, like providing new carbon into the ecosystem that benefits the mother octopus or her eggs.

To get a glimpse into these interactions, Huber and her team ferry out to sea to sample from areas from 500 to 3,000 meters below the water’s surface. To collect the water leaking out of the crust at these vents, she uses a pump, equipped with a series of tubes, filters, and metals that are mounted on a remotely operated- or human-occupied vehicle. They also collect sediments and use 16S rRNA sequencing and culturing techniques to gain insights into microbial diversity.²⁴ Researchers can also feed their deep-sea microbes with different isotope labels, to characterize the metabolically active autotrophic microbes.²⁵

“The Earth’s crust is a porous matrix. I think about it like a jar of marbles. Sometimes, there's a lot of space for the water to move through. Sometimes it's like there's not a lot of space,” explained Huber. Different parts of the seafloor host distinct microbial communities. “This water is always moving through the ocean crust, and it's carrying all these nutrients and chemicals and life along with it. Depending on the temperature and the type of rock you're at, the energy available for microbial life changes.”

The Hidden Worlds of Extremophiles Microbes that flourish in extreme environments offer clues into novel biochemical processes, paving the way for industry innovations. Microbes thrive where few others can—pitch-black caves, icy tundras, or deep ocean floors. Scientists don caving gear, brave freezing temperatures, and set sail across the oceans to study these resilient microorganisms. Along the way, they discover microbes that produce novel antibiotics, survive on rock and air, and offer insights into climate adaptation and biotechnology. CAVERNOUS DEPTHS Buried in darkness and isolated from the world for millions of years, cave-dwelling microbes survive on sparse nutrients like iron, manganese, and sulfur. Despite minimal exposure to the outside world, they’ve evolved to produce antimicrobial compounds—potential resources in the search for new antibiotics. Snottites are slimy microbial mats that dangle from cave ceilings and survive in highly acidic environments, like battery acid. Researchers investigate how these microbial communities differ, how they thrive on high concentrations of hydrogen sulfide, and how their activity sculpts cave formations over time. FROZEN FRONTIERS At Earth’s poles, microbes persist in frigid, barren landscapes bathed in relentless light or darkness. These cryophiles have adapted to extract energy from unexpected sources—some even “breathe” hydrogen from the air to fuel their survival. As the climate warms, polar microbes help researchers understand how organisms adjust to rising temperatures and shifting humidity. Bacteria and fungi in polar sediments and mosses endure extreme cold. Some fungi produce dark pigments believed to strengthen their cell walls and protect them from harsh UV radiation. Researchers are studying how these traits help microbes, and potentially astronauts, endure space. SUNKEN REALMS Beneath the ocean’s surface lies a rugged world of seamounts, mud volcanoes, and hydrothermal vents. Scientists deploy deep-sea submersibles to collect samples from these mysterious environments, revealing microbial life that thrives in total darkness and crushing pressure. Hydrothermal vents gush scalding, mineral-rich water that supports chemosynthetic microbes—organisms that turn chemicals into energy. Researchers are studying how these microbes support deep-sea ecosystems, such as octopus nurseries, and provide insights into how life might exist in other ocean worlds.

One of Huber’s sea-scouring trips took her to mud volcanoes in the Western Pacific Ocean. There, she and her team found bacteria living in a highly alkaline environment—a whopping pH of 12.²⁶ But researchers have also found bacteria thriving in mud volcanoes with an acidic pH. “It’s a huge range for life to contest with, and you don't find the same microbe at a pH of twelve and a half that you do at one,” remarked Huber. “They're specialized to exist in these different environments, but the important thing is that you do find life.”

This search for marine microbes reveals not only their ability to survive extreme conditions—such as crushing pressure, searing or freezing temperatures, total darkness, and highly variable pH—but also their essential roles in deep-sea ecosystems. As researchers continue to uncover this microbial diversity, they search for novel compounds with promising antibiotic properties.

These discoveries may also hold clues about life beyond our planet. By studying the extreme environments where these microbes thrive, scientists are gaining a better understanding of the conditions necessary for life. As researchers dive into the depths of the sea, they’re looking for parallels with ocean worlds—Enceladus (one of Saturn’s moons) and Europa, which harbor their vast subsurface oceans beneath their icy crusts. “We're in this really exciting time for ocean world exploration,” said Huber. “I think we are poised to ask the question: How can life exist beyond Earth?”

By studying life in caves, polar regions, and the deep sea, researchers are uncovering key insights into microbial resilience. These isolated and extreme environments—marked by intense pressure, temperature extremes, and nutrient scarcity—harbor microbes that have evolved extraordinary survival strategies. Understanding how these organisms adapt and thrive not only expands researchers’ knowledge of life’s potential on Earth but also shapes the search for life beyond it.