8 The Merger
Imagine you are a chemist, and you have exactly one test tube.
Not one test tube on the bench while your equipment cupboard holds dozens more. One test tube — that’s it. Every reaction you run has to happen in that single vessel. Acid and base, oxidation and reduction, synthesis and degradation – all dumped together in the same pot, all at the same time. Whatever you make is immediately exposed to whatever else is in there. If one reaction produces something fragile, the next reaction may destroy it before you can use it.
That is the prokaryotic cell. For roughly two billion years, bacteria and archaea ran the planet’s chemistry inside a single compartment: the cytoplasm. To be fair, they had a second compartment too – the periplasmic space, the thin zone between the inner membrane and the outer cell wall. So call it two test tubes. “But two tubes is certainly not enough for a good chemical laboratory!”1
And yet prokaryotes thrived. They invented photosynthesis, nitrogen fixation, sulfur cycling, methanogenesis. They reshaped the atmosphere and the ocean floor. They did extraordinary chemistry with minimal architecture.
But there were things they could not do. They could not run an oxygen-consuming reaction in one room while running an oxygen-sensitive reaction next door. They could not isolate their DNA behind a membrane and control who got access. They could not build a body made of trillions of differentiated cells, because differentiation requires compartments within compartments – a bureaucracy of nested enclosures, each with its own chemistry, its own imports and exports, its own protected interior.
For that, you need more test tubes. Many more.
The question is: how do you get them?
8.1 The compartment problem
The answer that evolution found is so strange it took biologists a century to accept it. You do not evolve compartments from scratch. You swallow another cell and keep it alive inside you.
This is the story of the eukaryotic cell – the kind of cell that makes up every animal, plant, fungus, and protist on Earth. It is the story of the most consequential merger in the history of life. And it began not with a mutual agreement but with one cell engulfing another.
Before we get to the meal, though, we need to understand what the eukaryotic cell actually solved. The word “eukaryote” means “true kernel” – a reference to the nucleus, the membrane-bound compartment where the genome lives. But the nucleus is only the most visible upgrade. Look inside a eukaryotic cell under an electron microscope and you find a landscape of internal membranes: the endoplasmic reticulum folded into sheets and tubes, the Golgi apparatus stacking its cisternae, lysosomes loaded with digestive enzymes, peroxisomes handling dangerous oxidation reactions, and – most crucially for our story – mitochondria and, in photosynthetic lineages, chloroplasts.
Each of these is a separate reaction chamber. Each maintains its own internal chemistry, buffered from the rest of the cell by a lipid bilayer. The endoplasmic reticulum can fold proteins under conditions that would wreck the cytoplasm’s redox balance. Lysosomes can run acid hydrolysis at pH 5 while the cytoplasm holds steady at pH 7. Mitochondria can maintain a proton gradient across their inner membrane precisely because that membrane is sealed – a private reservoir of electrochemical potential, insulated from the larger cell.
This is what compartmentalization buys you: the ability to run incompatible processes simultaneously. Not by compromising, not by time-sharing, but by physical separation. The chemist’s dream: a laboratory with as many test tubes as you need.
The prokaryotic cell had none of this internal architecture. It was the open-plan office of biology – everything in one room, everyone hearing everyone else’s conversations. Efficient, in a way. Fast, certainly. But fundamentally limited in the complexity of chemistry it could orchestrate.
8.2 A bridge between worlds
For a long time, the origin of eukaryotes was a black box. Prokaryotes on one side, eukaryotes on the other, and a vast gulf of cellular complexity between them. Then, in 2015, a team of researchers pulled something remarkable out of the Arctic Ocean.
The samples came from deep-sea sediments near a hydrothermal vent field called Loki’s Castle, on the Mid-Atlantic Ridge between Norway and Greenland, at a depth of 3,283 meters.2 The organisms they found were not eukaryotes. They were archaea – prokaryotes, single-celled, lacking nuclei and internal membranes. But their gene set told a different story.
These archaea, dubbed Lokiarchaeota, carried genes that no one expected to find in a prokaryote.3 Genes for actin-like cytoskeletal proteins – the molecular scaffolding that eukaryotic cells use to change shape, crawl, and engulf particles. Genes suggesting the capacity for membrane remodeling. Genes hinting at the ability to do something that was supposed to be a eukaryotic monopoly: phagocytosis, the act of wrapping your cell membrane around another object and pulling it inside.
Lokiarchaeota did not have a nucleus. They did not have mitochondria. But they had the genetic toolkit that could, in principle, lead to both. They were closer to eukaryotes than any other prokaryote ever found – a bridge between the two great domains of cellular life.
Lokiarchaeota was the first discovered member of what is now called the Asgard superphylum – a group of archaea named after figures from Norse mythology (Loki, Thor, Odin, Heimdall).4 Phylogenetic analyses consistently place eukaryotes within the Asgard archaea, not as their sister group.5 This means that eukaryotes did not diverge from archaea; they emerged from within them. The “three domains of life” model (Bacteria, Archaea, Eukarya) may need to be revised to a “two domains” model, with eukaryotes as a highly derived branch of the Archaea. The discovery did not answer every question about eukaryotic origins, but it narrowed the search space dramatically.
The picture that emerges is this: somewhere around 1.8 to 2.2 billion years ago, an archaeal cell – perhaps something like Lokiarchaeota, perhaps a close relative – took a step that prokaryotes had been building toward for billions of years.67 It had already evolved the cytoskeletal machinery to reshape its membrane. It had already developed some capacity for engulfing particles. And at some point, it engulfed a bacterium and did not digest it.
That bacterium was an alpha-proteobacterium – an aerobic organism that could use oxygen to burn organic molecules with extraordinary efficiency. Inside the archaeal host, the swallowed bacterium kept breathing. It kept producing ATP. And over time, what started as a captured meal became something else entirely: a permanent resident, a co-dependent partner, and eventually an organelle.
That organelle is the mitochondrion. Every mitochondrion in every eukaryotic cell on Earth descends from that single, ancient engulfment event.
8.3 The spectrum of integration
The transformation from free-living bacterium to mitochondrion did not happen overnight. It was a long, slow slide from partnership to dependence to irreversible fusion – a process that took hundreds of millions of years and that we can still watch happening today, frozen at different stages in different organisms.
[FIGURE: The integration spectrum. A horizontal arrow labeled “Independence” on the left and “Organelle” on the right. Four organisms are placed along the spectrum at increasing integration: (1) Ruthia magnifica – full genome, complete metabolic independence, inside a clam; (2) Elysia chlorotica – stolen chloroplasts, temporary, non-heritable; (3) Carsonella ruddii – 160 kb genome, cannot replicate alone; (4) Mitochondrion – ~16 kb genome, fully integrated organelle. Caption: “The path from symbiont to organelle is a one-way ratchet. Every lost gene tightens the bond.”]
Think of it as a spectrum. At one end, a bacterium lives inside a host cell but retains its full genetic and metabolic independence: it could, in principle, be extracted and grown on its own. At the other end, the bacterium has lost so many genes that it is no longer an organism at all – it is an organelle, a part of the host, unable to exist independently. Between these extremes lies every shade of partnership, dependence, and dissolution.
The living world is full of symbioses caught at different points on this spectrum. They are windows into the past – snapshots of the process that produced mitochondria and chloroplasts, still unfolding in real time.
8.3.1 The chemist in the dark: Ruthia magnifica
The ocean floor, several kilometers below the surface, is usually a desert. No light penetrates. There is no photosynthesis. The only food drifting down from the productive surface waters is a thin, unreliable drizzle of organic particles – “marine snow” – barely enough to sustain the sparse communities of the abyssal plain.
But where the Earth’s crust is cracked, where hydrothermal fluids seep upward carrying hydrogen sulfide and methane, the desert blooms. Around these vents and seeps, life is dense, improbable, and vivid: tube worms with blood-red plumes, ghostly white shrimp, and clusters of giant clams pressing their tissues against the chemical-rich water.
The giant clam Calyptogena magnifica is one of these vent animals. It lives along the edges of hydrothermal vents on the ocean floor, and its secret is inside its gill cells.8 There, packed into specialized host cells called bacteriocytes, lives Ruthia magnifica – a gamma-proteobacterium that has traded the open ocean for a captive existence inside an animal.
Ruthia is a chemoautotroph. It fixes carbon from CO\(_2\) via the Calvin cycle, just as a plant does, but it does not use sunlight as its energy source. Instead, it oxidizes sulfur compounds. Hydrogen sulfide flows in from the vent fluid; Ruthia strips electrons from it, storing elemental sulfur in intracellular granules, then oxidizing the sulfur further to sulfite and sulfate, extracting energy at each step. That energy drives carbon fixation, and the organic molecules Ruthia produces feed the clam.
The clam, in turn, provides Ruthia with a stable physical environment, a supply of oxygen (delivered via the clam’s blood), and access to the hydrogen sulfide welling up from below. It is a partnership: the bacterium is the chemist, the clam is the house.
What makes Ruthia remarkable is what its genome reveals: it has retained a complete set of genes for chemoautotrophic life.9 It can still, in principle, do everything a free-living sulfur-oxidizing bacterium can do. Its genome has not yet suffered the erosion that afflicts more deeply integrated symbionts. It is still biochemically independent, still carrying the full toolkit of an autonomous organism.
Ruthia magnifica is early on the spectrum. It is an intracellular symbiont, yes – committed to life inside a host – but it has not yet traveled far down what we might call the path of inevitable degradation. It is a captured bacterium whose genome still encodes the full machinery for independent life.
8.3.2 The shrinking genome: Carsonella ruddii
Now move to the other end of the spectrum.
Psyllids are small, sap-sucking insects – relatives of aphids – that feed on the phloem of plants. Plant sap is a poor diet. It is rich in sugars but deficient in essential amino acids, the building blocks that animals need to construct proteins but cannot synthesize on their own. Any insect that commits to a sap-only diet faces a nutritional crisis.
Psyllids solved this problem the way many insects have: they enlisted a bacterium. Inside specialized cells in the psyllid’s body lives Candidatus Carsonella ruddii, a gamma-proteobacterium that synthesizes the amino acids missing from the plant sap. The partnership is ancient and obligate – neither the insect nor the bacterium can survive without the other. “Successful symbiosis was the decisive factor allowing psyllids to feed only on plant sap.”10
But look at Carsonella’s genome, and you see something startling. At just 160 kilobases, it is among the smallest genomes of any known cellular organism – smaller than many viruses. It has lost genes for DNA repair, for the synthesis of its own cell wall, for most regulatory functions. It cannot make its own nucleotides. It cannot replicate without help from the host. Gene after gene has been shed, discarded as redundant once the host cell could supply the missing function.
Carsonella is so reduced that some biologists have questioned whether it should still be called a living organism. It is closer to an organelle – a piece of cellular machinery, maintained by the host, performing a specific biochemical task, unable to exist in any other context.
The trajectory from symbiont to organelle is a one-way street driven by a simple evolutionary logic. Once a function is reliably supplied by the host, the symbiont’s gene for that function is no longer under selection. Mutations accumulate. The gene degrades, shrinks, and eventually disappears. Each lost gene makes the symbiont more dependent on the host, which in turn makes further gene loss more likely. The result is a ratchet: integration deepens with every deletion, and there is no going back. Carsonella’s 160-kilobase genome represents a late stage of this process. Mitochondria, with their even smaller genomes (typically 15-20 kilobases in animals), represent a still later stage. The endpoint is complete gene transfer to the host nucleus, at which point the distinction between “symbiont” and “organelle” dissolves entirely.
8.3.3 The borrowed factory: Elysia chlorotica
Between the deep-sea vent and the psyllid gut, there are stranger partnerships. Consider the sea slug Elysia chlorotica, a small, leaf-shaped mollusk that grazes on algae in the tidal marshes and shallow coastal waters of eastern North America.
When E. chlorotica feeds, it does something unusual. It punctures algal cells and sucks out the contents, digesting most of the cellular material. But it does not digest the chloroplasts – the photosynthetic organelles. Instead, it captures them intact and incorporates them into the cells lining its own digestive tract. There, surrounded by animal tissue, the stolen chloroplasts continue to function. They absorb light, split water, fix carbon. The sea slug photosynthesizes.11
The chloroplasts are not inherited. They do not reproduce inside the slug. Each generation of E. chlorotica must acquire them anew by feeding on algae. This is not a permanent merger but a temporary theft – kleptoplasty – that hints at how the permanent acquisition of photosynthesis might have begun, billions of years ago, when an ancient eukaryote engulfed a cyanobacterium and never let go.
E. chlorotica is a living thought experiment: what does the early stage of chloroplast acquisition look like? Perhaps something like this – a predator that learns to keep its prey’s machinery running, harvesting the products, and gradually becoming dependent on them.
8.3.4 The perfect commune: the three-way lichen
If Ruthia is the early stage and Carsonella is the late stage, then lichens represent something else: the fully realized partnership, stable and successful, maintained not by genomic erosion but by ecological complementarity.
A lichen is not a single organism. It is a composite: a fungus (the mycobiont) that provides the structural scaffold, intertwined with one or more photosynthetic partners. In the simplest lichens, the partner is a green alga that performs photosynthesis, converting light and CO\(_2\) into organic carbon that feeds the fungus. But in the most sophisticated lichens, there is a third partner: a cyanobacterium that fixes atmospheric nitrogen, supplying the nutrient that neither the fungus nor the alga can obtain on its own.12
Three organisms, three metabolic capabilities, woven into a single body. The fungus cannot photosynthesize. The alga cannot fix nitrogen. The cyanobacterium cannot build the protective, water-retaining structure that allows the whole consortium to survive on bare rock, on tree bark, in deserts, in the Arctic. Together, they form an organism so self-sufficient that lichens are among the first colonizers of newly exposed surfaces – lava flows, glacial till, concrete.
This is what Markov calls “the greatest perfection of the system” – not the deepest integration, but the most balanced.1314 Each partner retains its own genome, its own cellular identity, its own metabolic autonomy. The lichen persists not because its members have lost the ability to live alone, but because the partnership is so productive that breaking it apart would be a catastrophic downgrade for everyone involved.
The symbiotic rabbit hole goes deeper than three partners. In Yellowstone National Park, a fungal endophyte (Curvularia protuberata) lives inside a panic grass (Dichanthelium lanuginosum), conferring tolerance to the extreme soil temperatures near geothermal vents – but only when the fungus itself is infected by a specific virus (CThTV). Remove the virus, and the thermal tolerance disappears. Three-way symbiosis: a virus in a fungus in a plant, all three needed for survival at the thermal limit.15
8.4 Oases in the dark
The story of Ruthia and Calyptogena is not an isolated curiosity. It is one example of a phenomenon that rewrites our understanding of what powers life on Earth.
Hydrothermal vents and cold seeps are cracks in the ocean floor where reduced chemicals – hydrogen sulfide, methane, hydrogen – leak upward from the Earth’s interior. In the surrounding darkness, where photosynthesis is impossible, these chemicals are treasure. They are electron donors, fuel for chemoautotrophic bacteria that can oxidize H\(_2\)S or CH\(_4\) using dissolved oxygen (or, in its absence, sulfate or nitrate) and use the energy to fix carbon from CO\(_2\).
These bacteria are the primary producers of the deep sea. They are the base of the food web in every vent and seep ecosystem, just as photosynthetic organisms are the base of the food web at the surface. But the relationship between the chemoautotrophs and the animals that depend on them is far more intimate than the usual predator-prey story.
Consider the tube worm Riftia pachyptila, one of the iconic animals of the hydrothermal vent community. Riftia has no mouth, no gut, and no anus.16 It cannot eat. Instead, its body is packed with a specialized organ called the trophosome, which is filled with chemoautotrophic bacteria. The worm absorbs hydrogen sulfide and oxygen from the vent water through its blood-red gill plume and delivers both to the bacteria via a specialized hemoglobin that can bind H\(_2\)S and O\(_2\) simultaneously.17 The bacteria oxidize the sulfide and fix carbon. The worm lives on the surplus.
Other vent animals filter chemoautotrophic bacteria from the water. Others host them on their body surfaces. The giant clam Calyptogena hosts Ruthia inside its gill cells. In every case, the pattern is the same: animals at the vent do not live by catching food from above. They live by partnering with bacteria that can harvest the chemical energy pouring out of the Earth.18
Symbioses of autotrophs and heterotrophs play a huge role in the biosphere – and nowhere is this role more visible than in the deep sea, where the entire ecosystem is built on partnership between organisms that can make food from chemicals and organisms that cannot.19
8.5 The pattern
A pattern runs through every example in this chapter. It is the same at every scale, in every environment, repeated across billions of years:
Partnership forms. Integration deepens. Independence erodes. What was once a relationship between two organisms becomes a single organism with a complex interior.
Ruthia still has a complete genome. Carsonella has lost most of hers. Mitochondria have transferred the vast majority of their genes to the host nucleus and retained only a handful – just enough to build the core machinery of the electron transport chain, the very apparatus that made the partnership worthwhile in the first place. Chloroplasts tell the same story: once free-living cyanobacteria, now organelles with shrunken genomes, dependent on the host for most of their proteins.
The trajectory is always the same. A free-living organism enters a host – by predation, by accident, by mutual convenience. If the partnership is beneficial, both partners persist. Over time, the symbiont loses genes it no longer needs, because the host supplies the missing functions. Each lost gene tightens the bond. The symbiont becomes dependent. The host reorganizes around the symbiont’s contributions. Eventually, the line between “two organisms” and “one organism with internal compartments” blurs and then vanishes.
The trajectory is a mechanism, not an analogy. And it is the mechanism that built the eukaryotic cell.
8.6 The merger itself
We can now reconstruct the event – or rather, the long process – that created the eukaryotic cell.
An archaeal cell, perhaps a member of the Asgard lineage, had already evolved the rudiments of a cytoskeleton and the capacity for membrane remodeling. It could reshape its surface, extend projections, and wrap itself around objects. At some point – roughly 1.8 to 2.7 billion years ago based on molecular clock estimates, with most analyses favoring about 2 billion years ago – this archaeal cell engulfed an alpha-proteobacterium.
The bacterium survived. Perhaps it was resistant to digestion. Perhaps the archaeal cell’s degradation machinery was incomplete. Whatever the reason, the bacterium persisted inside the host, and the two organisms began a relationship that would transform both of them beyond recognition.
The alpha-proteobacterium brought a gift: aerobic respiration. It could use oxygen – by then increasingly available in Earth’s atmosphere, thanks to billions of years of cyanobacterial photosynthesis – to completely oxidize organic molecules, extracting far more energy per glucose molecule than any anaerobic pathway could provide. The archaeal host gained access to an energy supply of unprecedented efficiency.
In return, the host provided the bacterium with a stable environment and a steady supply of organic substrates. The partnership was metabolically complementary: the host could do things the symbiont could not, and vice versa.
Over time, the two genomes began to merge. Genes moved from the symbiont to the host nucleus – a process called endosymbiotic gene transfer that continues to this day in some lineages.20 The symbiont shed genes for functions that the host could supply. The host evolved new systems for importing proteins into the symbiont, targeting gene products across the double membrane that still marks the mitochondrion as a descendant of a gram-negative bacterium.
The prokaryotic cells had taken another step towards further strengthening of integration. They merged into a single body, abandoned cellular individuality, and combined their chromosomes into one coordinated genome.21
The result was a new kind of cell. A cell with internal membranes. A cell with a nucleus. A cell with a dedicated energy-producing organelle. A cell that could grow large, because the mitochondria distributed throughout its cytoplasm provided ATP wherever it was needed, breaking the surface-area-to-volume constraint that keeps prokaryotic cells small.
This was the birth of the eukaryotic cell.
Why did this matter for cell size? Prokaryotic cells generate ATP at their cell membrane. As a cell grows larger, its volume (which determines energy demand) increases as the cube of its radius, while its membrane surface area (which determines ATP supply) increases only as the square.22 Large prokaryotic cells face an energy crisis: demand outpaces supply. Mitochondria solve this by internalizing the energy-producing membranes. A eukaryotic cell can increase its volume and simply add more mitochondria, each with its own chemiosmotic membrane. The internal membrane surface area scales with volume, not with the cell’s external surface. The merger did not just add a metabolic capability. It removed a fundamental architectural constraint.23
And then it happened again.
A eukaryotic cell – already carrying its mitochondrial passengers – engulfed a cyanobacterium. The cyanobacterium was not digested. It persisted, still photosynthesizing, still fixing carbon from CO\(_2\) using sunlight. Over time, it too lost genes, transferred others to the host nucleus, and became an organelle: the chloroplast.24
This second merger gave rise to the photosynthetic eukaryotes: the green algae that would eventually crawl onto land and become plants. Every leaf on every tree, every blade of grass, every strand of kelp carries the descendants of that engulfed cyanobacterium – a free-living organism that became a permanent component of another cell, billions of years ago.25
8.7 The architecture of consequences
What did the merger make possible?
In the short term: larger cells with more energy, more internal organization, and the capacity to run complex biochemistry in separated compartments.
In the medium term: multicellularity. Once you have a cell with a nucleus and mitochondria, you have a cell that can specialize. You can devote some cells to digestion, others to locomotion, others to reproduction. You can build tissues, organs, bodies. The step from single-celled eukaryote to multicellular organism is not trivial, but it is a step that has been taken independently dozens of times in evolutionary history – always by eukaryotes for complex, tissue-level multicellularity – prokaryotes have evolved only rudimentary forms (filamentous cyanobacteria, myxobacterial fruiting bodies).26 The compartmentalized architecture of the eukaryotic cell is the necessary precondition for the kind of multicellularity that builds bodies.
In the long term: everything you see when you look around. Every animal, every plant, every fungus, every protist. The forests. The coral reefs. The grasslands. The humans. All built from eukaryotic cells. All carrying mitochondria. All descended from that ancient merger between an archaeon and a bacterium.
For roughly two billion years, life was prokaryotic: single-celled, small, metabolically brilliant, but architecturally constrained. The merger changed the boundary conditions. It did not violate any physical law. It did not require any new chemistry. It simply reorganized existing capabilities – archaeal information processing, bacterial energy metabolism – into a new configuration that could do things neither partner could do alone.
8.8 What competition could not build
There is a standard story about evolution that emphasizes competition: organisms fight for resources, the fittest survive, the losers go extinct. It is not wrong, but it is radically incomplete.
Competition can sharpen. It can optimize. It can hone a blade to a finer edge. But competition did not build the eukaryotic cell. Competition did not invent photosynthetic animals or nitrogen-fixing lichens or the entire kingdom of plants.
Partnership did.
The merger that produced the eukaryotic cell was not a competitive victory. It was an act of integration – two lineages that had been separate for perhaps a billion years, combining their capabilities into something neither could achieve alone. The alpha-proteobacterium did not “win” by becoming a mitochondrion. The archaeal host did not “conquer” its symbiont. Both gave up their independence. Both were transformed. And the result was not a compromise but an escalation – a cell more powerful, more versatile, and more architecturally complex than anything that had come before.
The same logic runs through every example in this chapter. The tube worm and its chemosynthetic bacteria. The psyllid and Carsonella. The sea slug and its stolen chloroplasts. The lichen’s three-way commune. In each case, the partnership creates capabilities that no single organism possesses. In each case, integration – not competition – is the creative force.
This is not to say that competition is unimportant. Symbiotic partnerships must still compete with other organisms and other partnerships for resources and space. Selection still acts. But the raw material that selection acts on – the new forms, the new metabolic capabilities, the new body plans – comes disproportionately from mergers.
Lynn Margulis, who spent decades championing the endosymbiotic theory against fierce resistance from the biological establishment, put it simply: “Life did not take over the globe by combat, but by networking.”
8.9 The deep continuity
There is one more thing to notice. The merger between the archaeon and the alpha-proteobacterium was not a break in the pattern we have traced through this book. It was a continuation.
In earlier chapters, we watched prokaryotes cooperate: sharing electrons across species boundaries, forming syntrophic partnerships where one organism’s waste is another’s fuel, building biofilms where metabolic labor is divided among specialists. The logic of symbiosis – the advantage of metabolic complementarity – was already ancient when the eukaryotic merger happened.
What changed was the intimacy. In a biofilm, partners live side by side. In syntrophy, they exchange metabolites across a shared boundary. In the eukaryotic merger, one partner moved inside the other. The membrane that once separated two organisms became the double membrane of the mitochondrion – a fossil boundary, still visible under the electron microscope after two billion years.
The step from syntrophy to endosymbiosis is not a conceptual leap. It is a change in distance: from micrometers apart to nanometers apart to zero distance, to full enclosure. The driving force is the same: metabolic partnership is more efficient when transport distances are short. The closer the partners, the faster the exchange, the less energy lost to diffusion. Endosymbiosis is syntrophy taken to its logical extreme.
And the step from endosymbiosis to organelle is not a conceptual leap either. It is a change in commitment: from a partnership that could in principle be dissolved to one that cannot. Gene transfer cements the bond. Genomic erosion makes it irreversible. What was once a relationship becomes an anatomy.
8.10 You are a community
Every cell in your body contains hundreds of mitochondria. Each mitochondrion carries its own small circular genome – a remnant of the alpha-proteobacterial chromosome that has been shrinking for two billion years. That genome still encodes a few essential components of the electron transport chain, the molecular machinery that performs aerobic respiration. The rest of the mitochondrion’s proteins are encoded in your nuclear genome and imported across the double membrane after synthesis.
Your mitochondria replicate independently of your cell’s division cycle. They have their own DNA polymerase, their own ribosomes (which are bacterial-type ribosomes, not eukaryotic-type), their own translation machinery. When a cell divides, the mitochondria are parceled out to the daughter cells, not constructed from scratch. They are inherited, in an unbroken line of descent, from the mitochondria of the previous generation – all the way back, across billions of cell divisions, to the original engulfed bacterium.
If you eat a salad, the chloroplasts in the lettuce leaves tell the same story from a different chapter. They too carry their own circular DNA. They too have bacterial ribosomes. They too descend, in an unbroken line, from a cyanobacterium that was swallowed and never released.
You are, quite literally, a community. Not a metaphorical community – an actual one. Your cells are chimeras: archaeal information systems running on bacterial power plants, enclosed in membranes whose lipid chemistry reflects both lineages. The merger is not something that happened to a distant ancestor. It is something that is still happening, right now, in every cell, in the continuous conversation between your nuclear genome and your mitochondrial genome, in the import of proteins across the mitochondrial membranes, in the division of mitochondria within your cells.
Two billion years ago, two prokaryotes merged. They abandoned cellular individuality. They combined their capabilities into a single body. And from that body came everything that followed: the algae, the plants, the fungi, the worms, the clams, the insects, the fish, the mammals, and – eventually, improbably – the chemist who now has all the test tubes she needs.
But the prokaryotic world that made the merger possible did not disappear. It continued – and continues – to run the planet’s chemistry. The syntrophic partnerships, the closed biogeochemical cycles, the layered communities we traced in earlier chapters are still at work in every sediment, every aquifer, every water column on Earth. The next chapter asks: can we write down the equation that describes what they do?
8.11 Takeaway
- Prokaryotic cells are limited by having essentially one or two internal compartments; eukaryotic cells solve this with internal membranes that create many separate reaction chambers.
- The eukaryotic cell arose from a merger: an archaeal host (likely related to the Asgard archaea) engulfed an alpha-proteobacterium that became the mitochondrion; chloroplasts arose from a later engulfment of a cyanobacterium.
- Living symbioses – from Ruthia (early, genome intact) to Carsonella (late, genome nearly gone) – show snapshots of the same trajectory that produced organelles: partnership, gene loss, irreversible dependence.
- Hydrothermal vent ecosystems demonstrate that symbiosis between autotrophs and heterotrophs can sustain entire communities in the absence of sunlight.
- The creative force behind the most consequential innovations in the history of life – eukaryotic cells, photosynthetic eukaryotes, multicellularity – was not competition but integration.
Markov (2010) notes that prokaryotic cells are limited to one or two compartments (cytoplasm and periplasmic space), constraining the complexity of chemistry they can perform simultaneously. (Markov 2010)↩︎
Spang et al. (2015) reported the discovery of Lokiarchaeota from deep-sea sediments at Loki’s Castle hydrothermal vent field; the genome revealed eukaryotic signature proteins (ESPs) including actin homologs, suggesting phagocytic capacity. (Spang et al. 2015)↩︎
Spang et al. (2015) reported the discovery of Lokiarchaeota from deep-sea sediments at Loki’s Castle hydrothermal vent field; the genome revealed eukaryotic signature proteins (ESPs) including actin homologs, suggesting phagocytic capacity. (Spang et al. 2015)↩︎
The Asgard superphylum includes Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota, all named after Norse deities; see Zaremba-Niedzwiedzka et al. (2017). (Zaremba-Niedzwiedzka et al. 2017)↩︎
Eme et al. (2017) review phylogenetic evidence placing eukaryotes within the Asgard archaea, supporting a two-domain tree of life (Bacteria and Archaea, with eukaryotes as derived archaea). (Eme et al. 2017)↩︎
Molecular clock estimates for the origin of eukaryotes range from 1.6 to 2.7 Ga, with most analyses converging on ~2.0 Ga; see Parfrey et al. (2011). (Parfrey et al. 2011)↩︎
Betts et al. (2018) estimate the last eukaryotic common ancestor (LECA) at 1.84 Ga using a calibrated molecular clock. (Betts et al. 2018)↩︎
Newton et al. (2007) sequenced the Ruthia magnifica genome (1.16 Mb) and found it encodes a complete sulfur oxidation pathway and Calvin cycle, indicating metabolic autonomy. (Newton et al. 2007)↩︎
Newton et al. (2007) sequenced the Ruthia magnifica genome (1.16 Mb) and found it encodes a complete sulfur oxidation pathway and Calvin cycle, indicating metabolic autonomy. (Newton et al. 2007)↩︎
Nakabachi et al. (2006) reported the 160-kb genome of Carsonella ruddii, the smallest bacterial genome known at the time, lacking genes for DNA repair, cell wall synthesis, and most regulatory functions. (Nakabachi et al. 2006)↩︎
Rumpho et al. (2008) describe kleptoplasty in Elysia chlorotica, where stolen chloroplasts remain photosynthetically active for months; nuclear-encoded algal genes have been transferred to the slug genome to support chloroplast maintenance. (Rumpho et al. 2008)↩︎
Nash (2008) provides a comprehensive treatment of lichen biology, including tripartite lichens with fungal, algal, and cyanobacterial partners. (Nash III 2008)↩︎
Markov (2010) notes that prokaryotic cells are limited to one or two compartments (cytoplasm and periplasmic space), constraining the complexity of chemistry they can perform simultaneously. (Markov 2010)↩︎
Nash (2008) provides a comprehensive treatment of lichen biology, including tripartite lichens with fungal, algal, and cyanobacterial partners. (Nash III 2008)↩︎
Márquez et al. (2007) demonstrated that thermal tolerance in Dichanthelium lanuginosum requires both a fungal endophyte (Curvularia protuberata) and a mycovirus (CThTV) infecting the fungus. (Márquez et al. 2007)↩︎
Riftia pachyptila lacks a mouth, gut, and anus; all nutrition is supplied by endosymbiotic sulfur-oxidizing bacteria in the trophosome; see Childress et al. (1987). (Childress and Fisher 1987)↩︎
Riftia hemoglobin has separate binding sites for O₂ and H₂S, allowing simultaneous transport of both; see Arp et al. (1987). (Arp, Childress, and Vetter 1987)↩︎
Dubilier et al. (2008) review chemosynthetic symbioses in marine animals, emphasizing that vent and seep ecosystems are powered by bacterial primary production rather than photosynthesis. (Dubilier, Bergin, and Lott 2008)↩︎
Dubilier et al. (2008) review chemosynthetic symbioses in marine animals, emphasizing that vent and seep ecosystems are powered by bacterial primary production rather than photosynthesis. (Dubilier, Bergin, and Lott 2008)↩︎
Endosymbiotic gene transfer (EGT) moves genes from organellar genomes to the nucleus; thousands of genes have been transferred from the mitochondrial ancestor to the eukaryotic nucleus; see Timmis et al. (2004). (Timmis et al. 2004)↩︎
Lane and Martin (2010) argue that the energetic advantage of mitochondria—internalized ATP-producing membranes—explains the 200,000-fold genome size difference between prokaryotes and eukaryotes. (Lane and Martin 2010)↩︎
Lane and Martin (2010) argue that the energetic advantage of mitochondria—internalized ATP-producing membranes—explains the 200,000-fold genome size difference between prokaryotes and eukaryotes. (Lane and Martin 2010)↩︎
Lane (2005) provides an accessible account of mitochondrial bioenergetics and the surface-area-to-volume constraint on prokaryotic cell size. (Lane 2005)↩︎
Keeling (2010) reviews the origin and diversification of plastids via primary and secondary endosymbiosis; primary plastids arose once from a cyanobacterial ancestor. (Keeling 2010)↩︎
Archibald (2009) traces the evolutionary history of plastids, including multiple independent secondary endosymbiotic events in diverse eukaryotic lineages. (Archibald 2009)↩︎
Grosberg and Strathmann (2007) document that complex multicellularity evolved independently at least 25 times, always in eukaryotes; prokaryotic multicellularity is limited to simple forms. (Grosberg and Strathmann 2007)↩︎