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🔬Biology8 min read

Endosymbiotic Theory

Every cell in your body contains structures that were once free-living bacteria. About two billion years ago, one cell swallowed another and, instead of digesting it, kept it alive. Everything complex that has ever lived on this planet is the result of that one improbable event.

In plain English

Your cells contain mitochondria. You have heard this. Mitochondria are the "powerhouses of the cell," the structures that produce ATP, the energy currency every cell uses to do anything at all. Without mitochondria, you could not exist. In fact, without mitochondria, nothing more complex than a bacterium could exist.

Here is the thing about mitochondria: they are not part of the cell in the way that a liver is part of a body. They have their own DNA, separate from the DNA in the cell's nucleus. They have their own ribosomes, which differ from the cell's ribosomes. They divide by binary fission, the same way bacteria divide. Their inner membrane closely resembles the outer membrane of a specific group of bacteria called alphaproteobacteria. They are, in almost every molecular detail, bacteria.

They are bacteria that, roughly two billion years ago, were absorbed by a larger cell and never left. Instead of being digested, they entered into a permanent partnership. The host cell provided a safe environment and raw materials; the absorbed bacterium provided efficient energy production. Over billions of years, most of the mitochondrial genes migrated into the host cell's nucleus. The bacterium became an organelle. It became a part of you.

This is endosymbiotic theory. It explains where your mitochondria came from. It implies something stranger than it first appears: you are a composite organism. You contain, in every cell, the descendants of an ancient bacterial partnership. You are more than one thing.

Five things to file under "wait, what?"

  • Lynn Margulis proposed this in 1967 and was rejected fifteen times. Her manuscript, On the Origin of Mitosing Cells, was rejected by fifteen academic journals before finally being published. The scientific establishment considered the idea that bacterial symbiosis could produce a new kind of cell to be either obvious or impossible, no one was sure which, but the consensus was that it was wrong. Margulis persisted. The discovery of mitochondrial DNA in the 1960s, and subsequent molecular analysis confirming the relationship to alphaproteobacteria, vindicated her completely. She is now considered one of the most important biologists of the twentieth century.

  • The same thing happened with chloroplasts. Plant cells contain chloroplasts, the structures that carry out photosynthesis. Chloroplasts have their own DNA, their own ribosomes, and divide independently. They are closely related to cyanobacteria, the ancient photosynthetic bacteria that once transformed Earth's atmosphere by producing oxygen. About 1.5 billion years ago, a cell absorbed a cyanobacterium in the same way it absorbed the ancestor of the mitochondrion. That event is why plants are green, why they can make food from sunlight, and why Earth's atmosphere has enough oxygen for complex life.

  • This event happened exactly once. All eukaryotes, every plant, animal, fungus, and protozoan on Earth, are descended from a single ancestral cell that acquired its mitochondrion. This merger happened once, produced a single lineage, and that lineage diversified into everything complex that has ever lived. The improbability of this single event is one reason some scientists believe complex life may be rare in the universe: the prokaryote-to-eukaryote transition required a chance event that may not happen very often.

  • Mitochondria have their own genome, but it is shrinking. The ancestral alphaproteobacterium had several thousand genes. Human mitochondria retain only 37. The rest were transferred to the nucleus over billions of years. This gene transfer is still ongoing: researchers have found cases of mitochondrial DNA inserting itself into nuclear chromosomes in living organisms. The mitochondrion is slowly becoming less of an independent entity, its genome dissolving into the host. In hundreds of millions of years it may have no DNA of its own at all.

  • We inherit mitochondria from our mothers. Sperm cells contain mitochondria in their tails, which power the swimming. When a sperm fertilises an egg, the sperm's mitochondria are usually destroyed. The mitochondria in every cell of your body are therefore descended from your mother's mitochondria, which came from her mother's, and so on back through an unbroken maternal line. This mitochondrial inheritance is the basis of mitochondrial DNA analysis used in genealogy and archaeology, tracing human migration through the female line over hundreds of thousands of years.

The full story

The world before eukaryotes

For the first two billion years of life on Earth, all life was prokaryotic: simple cells without a membrane-bound nucleus or complex internal structures. Bacteria and archaea ruled a world of shallow seas, evolving extraordinary metabolic diversity. Some metabolised sulphur, some produced oxygen, some lived in boiling springs or hypersaline lakes. But none of them were complex. None of them had the internal scaffolding to become multicellular.

Then, around two billion years ago, something new appeared: a cell with a nucleus. The first eukaryote. How the nucleus itself formed is still debated. The leading hypothesis involves fusions between archaeal and bacterial cells, but the details remain unclear. The acquisition of the mitochondrion was a central event: it gave the proto-eukaryote an energy supply vastly more efficient than fermentation, enabling the larger, more complex cell to survive and thrive.

The energy breakthrough

Why does energy matter so much? Bacteria are limited in size partly by their energy production. They generate ATP across their outer membrane. To increase energy production, a bacterium would need to increase its membrane surface area, which means increasing its size, which means it needs more energy, and around you go in a circle that caps bacterial complexity.

The mitochondrion solves this problem by acting as an internal energy factory. The cell can grow larger without reducing its energy efficiency per unit volume, because the mitochondria, which number in the hundreds to thousands per cell, provide distributed, high-capacity energy production throughout the cell interior. This is what made complex cells possible, and complex cells are what made complex life possible.

Estimates suggest that eukaryotic cells can produce around 100,000 times more energy per gene than prokaryotic cells. This surplus funded the evolution of complexity: the nucleus, the internal membranes, the cytoskeleton, the capacity for specialised cell types, and multicellularity itself.

Lynn Margulis and the science of difficult ideas

Lynn Margulis's story is worth dwelling on because it illustrates how science works in practice, as opposed to how it is usually described. The accepted story of science is that it proceeds by hypothesis, evidence, and rational updating of views. The actual history is often messier: established consensus resists challenge, institutions reject heterodox ideas, and correct theories sometimes wait decades for acceptance.

Margulis was not a fringe figure making wild claims without evidence. She was a rigorously trained biologist making a specific, testable claim supported by cytological evidence. The claim contradicted the then-dominant view that organelles had evolved from within cells, and the resistance was partly about that contradiction.

When molecular evidence, the discovery that mitochondrial ribosomes more closely resemble bacterial ribosomes than eukaryotic cytoplasmic ribosomes, made the symbiotic origin of mitochondria undeniable, the field moved quickly to acceptance. Margulis later proposed other symbiotic origins that remain contested. But the core theory of mitochondrial and chloroplast endosymbiosis is now textbook biology.

What it means to be an individual

Endosymbiotic theory has a quiet but profound implication: the boundary of the individual organism is less clear than we suppose. You are not a single, unified biological entity. You are a collaboration between a lineage of archaeal-derived cells and the descendants of bacteria that joined them two billion years ago. Add in the gut microbiome, roughly as many bacterial cells as human cells, contributing to digestion, immunity, and possibly mood and cognition, and the picture of the "individual" becomes blurrier still.

The concept of the "holobiont," the organism plus all its associated microbes considered as a single evolutionary unit, is a live area of research. Whether the holobiont is the right level at which to understand evolutionary selection is debated. But the starting point for that debate is the recognition that the organism was never as bounded or as singular as we assumed.

We are, at minimum, a partnership that has lasted two billion years.

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