The endosymbiont theory (also called endosymbiotic theory) proposes that mitochondria and chloroplasts, the energy-producing structures inside complex cells, were once free-living bacteria. Billions of years ago, a host cell engulfed these bacteria, and instead of digesting them, the two organisms formed a permanent partnership. Over time, the engulfed bacteria became the organelles we see today in virtually all plants, animals, fungi, and other complex life. The idea has been discussed for over a century and is now one of the most well-supported explanations in evolutionary biology.
How the Theory Works
The core idea is surprisingly simple. An ancient cell, likely one that could not use oxygen for energy, swallowed a smaller bacterium that could. Rather than being destroyed, the smaller cell survived inside the larger one. The oxygen-breathing bacterium provided its host with a far more efficient way to generate energy, and in return, the host provided protection and nutrients. This arrangement proved so successful that the two organisms became inseparable, eventually functioning as a single cell.
This process, called endosymbiosis (literally “living together inside”), happened in steps. First came the ancestor of mitochondria, the organelles that power nearly all complex cells. Later, in the lineage that would become plants and algae, a second engulfment occurred: a cell that already had mitochondria swallowed a photosynthetic cyanobacterium. That cyanobacterium became the chloroplast, the organelle responsible for photosynthesis. Because these events happened one after the other, the idea is sometimes called the serial endosymbiosis theory.
When It Happened
Genomic analyses estimate the earliest symbiotic event leading to eukaryotic cells occurred roughly 2.7 billion years ago, with the mitochondrial event following around 1.8 billion years ago. Both dates align with a critical shift in Earth’s atmosphere: photosynthetic bacteria were pumping out increasing amounts of free oxygen. For anaerobic organisms, rising oxygen was toxic. Partnering with an aerobic bacterium that could not only tolerate oxygen but harness it for energy would have been an enormous survival advantage.
Who Proposed It
The Russian botanist Konstantin Mereschkowsky first articulated the idea in the early 1900s. He argued that plastids (the structures responsible for photosynthesis in plant cells) were not organs the cell built on its own but were “reduced cyanobacteria” that had entered a host cell and established a symbiotic relationship. He even proposed that the cell nucleus itself originated from an engulfed prokaryote, though that particular claim remains debated.
The theory was largely ignored for decades until Lynn Margulis (then Lynn Sagan) revived and expanded it in a landmark 1967 paper. Margulis proposed that the ancestor of mitochondria was an aerobic bacterium ingested by an anaerobic host, and that chloroplasts originated from engulfed cyanobacteria. She also suggested that flagella, the whip-like structures some cells use to move, came from yet another type of engulfed bacterium, though that part of her hypothesis has not gained wide acceptance. Her paper was rejected by roughly 15 journals before being published, but the evidence that accumulated over the following decades proved her central claims correct.
Evidence From DNA
The strongest evidence comes from the genetic material inside mitochondria and chloroplasts themselves. Both organelles carry their own DNA, separate from the DNA in the cell’s nucleus. Mitochondrial DNA is circular, structurally resembling bacterial chromosomes rather than the linear chromosomes found in the nucleus. When researchers sequence mitochondrial genes and compare them to bacterial genomes, the match points clearly to an ancestor within a group of bacteria called alpha-proteobacteria. Chloroplast genes, similarly, trace back to cyanobacteria. Nearly all protein-coding genes in chloroplast genomes originated from cyanobacterial ancestors.
Beyond the DNA itself, the gene expression machinery inside these organelles is bacterial in character. Both mitochondria and chloroplasts use ribosomes (the molecular machines that build proteins) that are more similar to bacterial ribosomes than to the ribosomes floating in the rest of the eukaryotic cell. Bacterial and organelle ribosomes are classified as 70S, while the ribosomes in the main body of a eukaryotic cell are larger, at 80S. This distinction is so consistent that certain antibiotics designed to target bacterial 70S ribosomes can also affect mitochondrial function, which is why some antibiotics carry side effects related to energy metabolism.
Evidence From Cell Structure
Both mitochondria and chloroplasts are surrounded by two membranes. The inner membrane is thought to correspond to the original bacterium’s own membrane, while the outer membrane is believed to come from the host cell’s membrane that wrapped around the bacterium during engulfment. This double-membrane architecture is exactly what you’d predict if one cell swallowed another.
Chloroplasts share additional structural features with cyanobacteria. Both contain flattened internal membranes called thylakoids, where the light-driven reactions of photosynthesis take place. Both use chlorophyll a as their primary photosynthetic pigment and have membranes rich in a specific type of fat molecule called galactolipids. Some chloroplasts even retain traces of peptidoglycan, the rigid material that forms bacterial cell walls. This is found in certain algae and primitive plant groups.
Both organelles also reproduce by binary fission, splitting in two just as bacteria do, rather than being built from scratch by the cell. A cell cannot generate new mitochondria or chloroplasts on its own; they always arise from the division of existing ones.
Primary vs. Secondary Endosymbiosis
The engulfment of a cyanobacterium by a non-photosynthetic cell is called primary endosymbiosis. It produced the chloroplasts found in plants, green algae, and red algae, all of which have a two-membrane envelope matching the two membranes of the ancestral cyanobacterium.
But the process didn’t stop there. In several independent events, other eukaryotic cells engulfed algae that already had chloroplasts. This is called secondary endosymbiosis, and it explains the photosynthetic structures in organisms like brown algae, diatoms, and euglenids. The telltale sign is extra membranes: while primary chloroplasts have two surrounding membranes, secondary chloroplasts typically have three or four. Each additional membrane is a fossil record of another round of engulfment. Some of these secondary plastids even retain a tiny remnant of the engulfed alga’s nucleus, a vestigial structure called a nucleomorph.
The Hydrogen Hypothesis
While the broad strokes of endosymbiotic theory are well established, scientists still debate exactly what drove the original partnership. The traditional view holds that the host benefited from the symbiont’s ability to use oxygen for energy. An alternative model, known as the hydrogen hypothesis, flips the story. It proposes that the host was an archaeon (a type of simple cell distinct from bacteria) that depended on hydrogen gas for its metabolism. The symbiont was a bacterium that produced hydrogen as a metabolic waste product. In this scenario, the host initially kept the symbiont around for its hydrogen output, and the ability to use oxygen for energy came later. The hydrogen hypothesis neatly explains why some modern eukaryotes have mitochondria-like organelles that still produce hydrogen instead of consuming oxygen, suggesting the partnership may have begun in oxygen-poor environments rather than oxygen-rich ones.