When a primitive cell engulfs an aerobic bacterium, the structure that forms is a mitochondrion. This is the core event described by endosymbiotic theory, and it happened roughly 1.5 billion years ago. The engulfed bacterium was never digested. Instead, it survived inside its host, kept producing energy using oxygen, and over vast stretches of time became a permanent organelle: the mitochondrion found in nearly every complex cell alive today.
How Endosymbiotic Theory Explains the Event
Endosymbiotic theory proposes that the complex cells making up animals, plants, and fungi (eukaryotes) didn’t evolve all their internal machinery from scratch. Instead, some of their most important organelles started out as free-living bacteria that took up residence inside a simpler host cell. The mitochondrion is the clearest example of this process.
The host cell was likely a type of archaeon, a single-celled organism belonging to one of the ancient domains of life. This host was anaerobic, meaning it couldn’t use oxygen for energy. The bacterium it internalized was aerobic, capable of breaking down nutrients using oxygen to produce large amounts of ATP, the molecule cells use as fuel. The partnership gave the host access to a far more efficient energy source than it had on its own. Over time, the bacterium lost the ability to live independently, transferred many of its genes into the host’s nucleus, and became what we now call the mitochondrion.
What the Ancestral Bacterium Was
Phylogenetic analyses consistently place the ancestor of mitochondria within the alphaproteobacteria, a large and diverse class of bacteria. The specific group it belonged to is still debated. Proposed candidates have included the order Rickettsiales, the family Rhodospirillaceae, and the genus Rickettsia. More recent network-based analyses suggest mitochondria share a common ancestor with a broad group containing most alphaproteobacterial orders except Rickettsiales. What’s clear is that the engulfed bacterium was a proteobacterium that could perform oxidative phosphorylation, the oxygen-dependent process that generates ATP efficiently.
How the Bacterium Got Inside
The exact mechanism of internalization remains one of the open questions in evolutionary biology. The classic version of endosymbiotic theory, first championed by Lynn Margulis, assumed the host cell used phagocytosis to ingest the bacterium, much like an amoeba swallowing a food particle. Phagocytosis involves wrapping the cell membrane around a target, pinching off an internal compartment, and pulling the target inside.
There’s a problem with this idea, though. Phagocytosis is a complex process that depends on a flexible internal skeleton made of actin proteins, something modern archaea don’t have. Alternative models, sometimes called “mitochondrion-early” hypotheses, argue that the bacterium entered the host through a simpler mechanism, possibly parasitic infection or a slow physical engulfment driven by membrane protrusions, and that sophisticated cell-swallowing machinery only evolved afterward. The hydrogen hypothesis, for instance, proposes that the relationship began as a metabolic partnership: the bacterium produced hydrogen and carbon dioxide as waste, and the archaeal host depended on those molecules for its own metabolism. Physical proximity eventually led to internalization.
Evidence That Mitochondria Were Once Bacteria
Several features of modern mitochondria look strikingly bacterial, and these similarities are the strongest evidence for endosymbiotic theory.
- Circular DNA. Mitochondria carry their own small genome, and it’s circular, just like bacterial chromosomes. This DNA is organized into protein-associated clusters called nucleoids, again mirroring bacterial genome structure. Human mitochondrial DNA is tiny compared to a free-living bacterium’s genome because most of the original genes migrated to the host cell’s nucleus over evolutionary time.
- Double membrane. Mitochondria are enclosed by two membranes. The inner membrane is thought to derive from the original bacterium’s cell membrane, while the outer membrane likely came from the host cell’s membrane wrapping around the bacterium during engulfment.
- Own ribosomes. Mitochondria build some of their own proteins using their own ribosomes. These ribosomes are distinct from the larger ones (80S) found in the surrounding cell cytoplasm. In mammals, mitochondrial ribosomes sediment at 55S. They were originally expected to match bacterial ribosomes (70S) exactly, but they’ve diverged significantly: they contain about half as much RNA and nearly twice as much protein as bacterial ribosomes. Still, their basic functional properties resemble bacterial ribosomes more than they resemble the cell’s own cytoplasmic ribosomes.
- Binary fission. Mitochondria divide by splitting in two, the same basic method bacteria use to reproduce. They don’t arise from scratch inside the cell.
What the Host Cell Gained
The payoff for the host was enormous. Aerobic respiration, the oxygen-using process that mitochondria perform, extracts far more energy from food molecules than anaerobic metabolism can. This is why mitochondria are often called the powerhouses of the cell. Every major lineage of eukaryotes uses aerobic respiration, and it’s localized in the mitochondria.
Beyond ATP production, mitochondria also took on other metabolic roles. They help build clusters of iron and sulfur that serve as essential components of many enzymes throughout the cell. Over time, the host installed its own proteins into the mitochondrial membrane, including a transporter that swaps the cell’s spent energy molecules (ADP) for freshly made ATP from inside the mitochondrion. This transporter essentially turned the former bacterium into a dedicated energy-export machine for the host.
Why This Matters for All Complex Life
The acquisition of mitochondria wasn’t a minor upgrade. Current evidence suggests that all living eukaryotes either possess mitochondria or descend from ancestors that once had them and lost them secondarily. In other words, no lineage of complex cells appears to have evolved without this partnership. The hydrogen hypothesis predicted exactly this pattern: that the merger between host and bacterium was the founding event of eukaryotic life itself, not something that happened later to an already complex cell.
A parallel event occurred when an early eukaryote engulfed a photosynthetic cyanobacterium, giving rise to chloroplasts in plants and algae. But the mitochondrial partnership came first and is more universal. Every cell in your body that has a nucleus also has mitochondria, typically hundreds or thousands of them, each one a distant descendant of a free-living bacterium that was swallowed roughly 1.5 billion years ago and never left.