Rosa Rubicondior: Creationism Refuted - The Subterranean Microbes That Make Creationists Sick

Karen Lloyd

Buried Alive: The Secret Life of Deep Earth Microbes

What if we could peer back through deep time and see what single-celled organisms looked like—not just thousands, but hundreds of millions of years ago—and compare them to their living descendants? It would be a revelation for science… and a nightmare for creationists.

That’s precisely what geobiologist Karen Lloyd and her team at the University of Southern California (USC) are uncovering. They study microorganisms that have made an incredible journey: born in the depths of the ocean, slowly buried under a relentless rain of sediment, and then carried by plate tectonics into the deep Earth, where subduction dragged them beneath continental crust. There, cut off from oxygen and sunlight, they survived for millions of years in a slow-motion existence, drawing nutrients from the surrounding rock. Their metabolic rates became so low they could no longer replicate, yet they endured by “breathing”—in the biochemical sense—through redox reactions, extracting energy from electrons provided by whatever electron donors the rocks could supply. Some have even evolved the ability to “breathe” carbon dioxide, something unknown among terrestrial life.

These organisms’ existence is a direct challenge to creationist dogma—not only because they have persisted for timescales far beyond the Bible’s allowance, but because they reveal how even apparently simple single-celled organisms can diverge and adapt over geological epochs. Environmental pressures have driven them into extraordinary evolutionary niches, each defined by what they have learned to “breathe.” Moreover, they exist in environments in which life as we know it couldn't survive, yet creationists insist that Earth was intelligently created, perfect for life, which begs the question, which life? The life that breathes using arsenic, lives for millions of years deep underground with almost no metabolic activity and survive in the heat and acidity of volcanic hot springs, or life the breathes oxygen and needs a regular supply of water and a narrow range of ambient temperatures in which to survive without special equipment?

An overview of extremophile microorganisms and the electron donors they rely on: How Extremophiles Harvest Energy

Many extremophiles operate as chemolithoautotrophs — they oxidise inorganic substances to gain electrons and fix carbon dioxide for growth [1, 2]. They may also function heterotrophically or mixotrophically, using organic substrates depending on availability [2].

Common Electron Donors Employed by Extremophiles

Molecular Hydrogen (H₂)
Many hyperthermophilic archaea use H₂ as a direct electron donor, coupling it to electron acceptors like nitrate, sulfate or oxygen, depending on the species [1]). In bioelectrochemical systems, hydrogenase enzymes mediate direct electron uptake from H₂, although this remains a disputed mechanism thermodynamically [3].
Reduced Sulfur Compounds
Thermoacidophiles such as Acidianus species and Sulfolobus solfataricus oxidise sulfide (H₂S), elemental sulfur (S⁰), or thiosulfate as electron donors, especially in acidic hot springs or volcanic environments [4].
Ferrous Iron (Fe²⁺)
Extremophiles like Acidianus ferrooxidans and other Sulfolobales oxidise Fe²⁺ to gain electrons, often in conjunction with sulfur metabolism, thriving in iron- and sulfur-rich geothermal settings [4, 5].
Organic Compounds
Some extremophiles and electroactive microorganisms oxidise simple organics like acetate or lactate. For instance, Thermincola species are noted for using lactate to generate extracellular electrons shed into biofilms or electrodes [6].

Interactions with Solid Electron Sources

Some extremophiles are electroactive microorganisms, capable of obtaining electrons from insoluble sources like metals or electrodes:

Geobacter species (e.g. G. metallireducens) oxidise organic substrates (like acetate, ethanol) and transfer electrons to insoluble minerals (Fe(III), Mn(IV), or even U(VI), V(VI)) via direct contact, nanowires, or secreted shuttles [7, 8].
Others function as electrotrophs, oxidising extracellular electron donors (e.g. metals or electrodes treated as cathodes), supporting metabolisms relying on CO₂ fixation via electroautotrophy [9].

Example Organisms & Specialized Metabolisms

Sulfolobus solfataricus

Electron donor: H₂S, S⁰, H₂, organic compounds
Notes: Thrives in acidic, high‑T volcanoes; fixes CO₂ via rTCA or HP/HB cycle [5].

Acidianus spp.

Electron donor: Fe²⁺, H₂, sulfur compounds
Notes: Thermoacidophiles from hot springs; versatile among inorganic donors [4].

Geobacter spp.

Electron donor: Acetate, ethanol, organic acids
Notes: Transfers electrons to insoluble Fe/Mn/U oxides; forms conductive pili (“nanowires”) [8, 10].

Thermincola sp.

Electron donor: Lactate
Notes: Known for strong extracellular electron generation to electrodes [6].

Environmental Contexts & Implications

Hydrothermal vents and volcanic environments: These settings offer rich sources of H₂, reduced sulfur, ferrous iron and other metals that feed extremophiles’ redox metabolism [4, 9].
Deep subsurface and ocean floor: Microbes buried under sediment can persist by using mineral substrates and hydrogen gas generated by geological activity—a deep-time survival strategy [9, 11].

Why It Matters

Understanding these electron donor pathways is crucial for:

Evolutionary insights: These metabolisms mirror what early Earth life might have used, showing how life adapts to minimal energy and extreme conditions.
Biotechnology: Many extremophiles power microbial fuel cells, bioelectrosynthesis, or bioremediation, thanks to their ability to transfer electrons to electrodes or reduce toxic metals [9, 11].
Astrobiology: Their resilience informs the search for life in extraterrestrial environments with limited organic carbon or sunlight [12].

Karen Lloyd describes these hidden worlds and their evolutionary lessons in her book, Intraterrestrials: Discovering the Strangest Life on Earth. The story is also featured in the USC Dornsife College of Letters, Arts and Sciences magazine: USC Dornsife.

Buried Alive: The Secret Life of Deep Earth Microbes
Discover a vast, previously unknown world of microbial life that survives — and even thrives — for hundreds of millions of years in some of the planet’s harshest environments.

After a grueling descent into the crater of Costa Rica’s Poás Volcano, pioneering geobiologist Karen Lloyd paused to catch her breath as she took in the dramatic beauty of the landscape, then turned to the local researcher next to her.

“So,” she asked, glancing warily at the sputtering crater of acid at her feet, “what’s our exit strategy again if this thing goes off?”

“That’s easy,” he laughed. “Just turn around and admire the view. Because it’s going to be the last one you’ll ever see.”
Fortunately for Lloyd and her colleagues, their research expedition to collect samples of subsurface life from the subduction zone around the volcano passed without incident.

But just 54 days later, the sputtering burst into a furious torrent of ejected boulders and the spectacular view disappeared, engulfed in a dark, mushrooming cloud of volcanic ash as Poás erupted in what was Costa Rica’s most serious volcanic episode in more than 60 years.

For Lloyd, known for her groundbreaking work in microbial geochemistry, that moment eight years ago was more than a brush with danger — it was a reminder of the high-stakes environments her field depends upon to gain understanding of the deep workings of our planet.

Over the past two decades, that understanding has undergone a radical shift. Lloyd, Wrigley Chair in Environmental Studies and professor of Earth sciences, is part of a global group of scientists behind a major discovery that is transforming how we think about life on Earth. The scientists revealed the existence of a vast, previously hidden world of living biomass inside the planet’s crust. This biosphere consists of active microorganisms, hundreds of millions of years old, that are thriving in extreme environments once thought uninhabitable.

As Lloyd details in her new book, Intraterrestrials: Discovering the Strangest Life on Earth, these subsurface microbes can survive in boiling water, acid — even bleach. Some can “breathe” rocks, metals or electrons. Some are hundreds of thousands of years old. All live in ways completely alien to us surface dwellers.

Overcoming the challenges of sample contamination to find conclusive proof took years of painstaking work, but the evidence is now overwhelming. These deep-life microbes are real. They’re alive and they have decidedly weird lifestyles — doing strange, fascinating things we’re only just beginning to understand.

Karen Lloyd

To hunt them down, Lloyd and her colleagues explore permafrost in the Arctic, hot springs in Iceland, rift basins in the American Southwest, and volcanoes in Costa Rica, New Zealand and the Andes. In these places, tectonic activity squeezes ancient groundwater to the surface — much as we might wring out a washcloth — creating natural laboratories for studying Earth’s hidden biosphere.

Each location offers a different window into Earth’s deep history, where materials are exchanged between the surface and the subsurface world. In New Mexico’s rift basins, the ground stretches apart, pulling up ancient fluids. In Idaho, springs near old Yellowstone hotspots mark how the continent has drifted. Iceland, in contrast, sits atop both a spreading center and volcanic hotspot, producing a radically different subsurface chemistry.

Subsurface Survivors

Lloyd — a marine biologist by training whose work builds on the trailblazing research of USC Dornsife professors Kenneth Nealson and the late Katrina Edwards and Jan Amend — also explores microbial life thriving beneath the ocean floor. This research into deep sea sediments enables Lloyd to dive not just into the ocean, but into time itself, peering back to the dawn of life on Earth.

Her team uses drills, push cores and even submersibles to retrieve mud from the ocean bottom, extracting it in cores and slicing it into layers to analyze the microbial life within.

Deep-ocean mud might not sound too thrilling an environment, but to Lloyd it’s a portal into a mysterious and exciting secret world.

Imagine, she says, being a microbe. You fall to the seafloor in a slow rain of organic detritus — dead plankton, river runoff, sunken particles. Then you’re buried, grain by grain. You end up meters below the sea, where nothing much happens. For hundreds of thousands — sometimes hundreds of millions — of years.

... and you keep living for all that time. These are not lively lives. There’s not enough energy down there to reproduce. But they persist — barely — metabolizing just enough to survive.

Karen Lloyd

The implication is staggering — and not just because some of these single-celled organisms may have been alive for a hundred million years. Despite their similar appearances under a microscope, the genetic differences of these organisms are far more profound than any between humans and other visible forms of life on Earth.
They’ve been down there changing slowly, unnoticed for nearly as long as Earth has had life.

Karen Lloyd

The Life Beneath

On the surface, life displays dazzling diversity — from towering sequoias to luminous jellyfish, from scuttling ants to graceful giraffes. But even the most alien-looking organisms we can see are remarkably close cousins, evolutionarily speaking.

I look at my children and then at a jellyfish — clearly different species. But when we look at their DNA, we find that we only diverged from jellyfish a few hundred million years ago.

Karen Lloyd

That may sound like a long time ago — but in evolutionary terms, it’s a mere blink of an eye, particularly when compared to the timescale of subsurface microbes. They diverged from one another billions of years ago.

There are 100 billion billion billion living microbial cells underlying all the world’s oceans. That’s 200 times more than the total biomass of humans on this planet. And those microbes have a fundamentally different relationship with time and energy than we do.

Karen Lloyd

Another striking way that subsurface life forms differ from those on the surface of the planet — and from each other — lies in what they breathe.

Most visible life on Earth either respires oxygen, ferments, or photosynthesizes — and that’s it. But some species of subsurface life can ‘breathe’ every metal on the periodic table, including arsenic, while others breathe carbon dioxide. That’s not something any visible life form can do.

Karen Lloyd

To “breathe,” in this context, means to harvest energy through redox reactions — chemical exchanges through which electrons are transferred. When those reactions are coupled to energy production inside the cell, it’s called respiration. For microbes buried deep underground, oxygen often isn’t even part of the equation.

Even more fascinating, metal-breathing microbes are not confined to one lineage. Just as diverse organisms on the surface have evolved to breathe oxygen, metal breathers appear on wildly different branches of the tree of life — a testament to life’s adaptability and the evolutionary forces shaping it far beneath our feet.

It makes perfect sense when you think about it. They’ve had 10 times more time to evolve in different directions. They’ve been down there, changing slowly, unnoticed, for nearly as long as Earth has had life. Now, the cutting-edge methods we are developing to study the subsurface have enabled us to discover that there are branches on the tree of life that we never knew existed until now — lineages of life that had gone undetected for billions of years.

Karen Lloyd

This realization reshapes our understanding of biology. It suggests that we’ve only scratched the surface — literally — of life on Earth.

Fine-Tuned — But for Whom? Creationists often claim the Earth is “fine-tuned for life”, usually meaning human life or the life forms we see on the surface. But the planet’s real track record tells a different story:

Most of Earth’s habitable space — by volume — is deep underground or beneath the ocean floor, in total darkness, high pressure, and chemical extremes.
The oldest and most persistent life on the planet are microorganisms adapted to those conditions, not large animals or plants.
These organisms can metabolise hydrogen, iron, sulphur, and even carbon dioxide — compounds that would be toxic or useless to us.

If Earth is “fine-tuned” for anything, it’s for microbes that thrive in places where humans would die instantly. Our comfortable surface world is a tiny, temporary exception in a planet-wide biosphere dominated by extremophiles.

Bottom line: The “fine-tuning” argument collapses when you ask, fine-tuned for whom? For most of Earth’s history — and most of its present — life is nothing like us.

Practical Potential

This extraordinary endurance isn’t just biologically fascinating, it may have real-world applications. One of Lloyd’s collaborators at USC Dornsife, Andrew Steen, associate professor of biological sciences and Earth sciences, is investigating whether protein-stabilizing microbes could help extend the shelf life of vaccines without refrigeration — a breakthrough that could revolutionize access to healthcare in parts of the world with limited resources.

Lloyd’s trip to Costa Rica — which sits on a subduction zone — also helped solve a puzzle with implications for the climate: Why does carbon dioxide escape in massive plumes from the country’s volcanoes, but only in tiny puffs from its hot springs?

Her team discovered that deep underground, microbes and rock reactions were converting the gas into carbonate minerals, locking it into rock before it reached the surface. That insight could inform carbon capture strategies. Instead of releasing CO₂ into the atmosphere, we could pipe it underground, where microbes would help turn it to stone. In some cases, with hydrogen present, microbes can even convert CO₂ into methane — creating a usable energy source, although with climate trade-offs.

From vaccine preservation and carbon capture to enzyme stabilization and insights into aging, Lloyd’s research has far-reaching potential. But she’s quick to point out that real-world benefits aren’t her primary focus.

I’m not looking for any particular solution or benefit. My goal is to push the boundaries of what we know to best provide for other people who are doing practical stuff. That’s the promise of blue-sky research.

Karen Lloyd

Still, her excitement about the possibilities is palpable.

If we can make such a big breakthrough from just one study, then imagine what else is waiting to be discovered down there?” Lloyd says. “This new field of geobiochemistry is going to have huge implications — maybe even predicting earthquakes or finding life beyond our planet.

Karen Lloyd

It could even, she says, help us understand the origin of life itself.
Life buried deep within the Earth’s crust may seem irrelevant to our daily lives. But this weird, slow life may hold the answers to some of our planet’s greatest mysteries — and challenges.

Karen Lloyd

Attentive readers might have spotted what seems to be something of a paradox here. On the one hand, the microorganisms were said to be so lacking in sources of energy that they were unable to reproduce, and on the other hand, they evolved into the different niches to exploit the different available electron donors.

This is resolved by considering the mechanism by which they found themselves 'trapped' in subterranean rocks, which was slow and gradual, creating exactly the conditions for increasing evolutionary pressure while there was energy enough to replicate and evolve in response to that intense selection pressure before entering what was, in effect, suspended animation.

Properly understood, these discoveries present creationists with two deeply inconvenient facts about life on Earth. The first is sheer timescale. The microorganisms studied by Karen Lloyd and her colleagues have existed in their present form for millions — in some cases, tens or even hundreds of millions — of years, far beyond the 6,000–10,000 years allowed by biblical creation narratives. Their journey from the ocean floor, down through layers of sediment, and in some cases into the deep crust by the process of subduction, takes millions of years at rates far too slow to fit within any young-Earth model. The geological context alone obliterates any claim that the Earth is only a few thousand years old.

The second challenge comes from their evolutionary story. These microorganisms are not identical relics from the past — they are survivors of ancient lineages that have diversified over geological time to use different electron donors in their metabolism. This is textbook adaptive evolution: environmental pressures and changing chemical conditions favoured some variants over others, producing the range of metabolic strategies observed today. Even though individual microbes in the deepest, most energy-starved zones may not reproduce, their ancestors evolved these traits long before they were buried. Creationists must either accept that these changes took place — meaning evolution is real — or invent ad hoc explanations that deny observable biochemical diversity.

They also undermine another popular creationist trope — that the Earth is “fine-tuned for life”. Fine-tuned for what life? Not for humans, or for the surface biosphere at all, but for microorganisms that thrive in lightless, high-pressure, chemically extreme conditions deep beneath our feet, metabolising compounds that would kill most surface life. If anything, the Earth’s most stable, long-term habitats are these inhospitable zones, and the most persistent life forms are not large animals or flowering plants but microbes adapted to conditions utterly alien to us. The idea that the planet was designed with us in mind collapses when you realise that for most of Earth’s history, and for most of its habitable volume even today, life has belonged to organisms that neither need nor want the conditions we call “Earth-like”.

Finally, these organisms dismantle the creationist claim that life exists in neatly fixed “kinds”. Here we have single-celled organisms that look superficially similar yet differ profoundly in their biochemistry, shaped by environmental history. What unites them is not some fixed, immutable “design” but the fact that they are all products of an evolutionary process that equips them to survive in wildly different chemical landscapes. The fossil record of their habitats, the plate tectonics that moved them there, and the molecular evidence of their metabolisms together form a seamless narrative in which life adapts over immense spans of time — precisely what evolutionary biology predicts, and precisely what biblical literalism cannot accommodate.

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