1 trillion species 3 billion years how we used AI to trace evolution of bacteria on Earth
them still unknown to science. These microbes play crucial roles in various ecosystems, from breaking down organic matter to producing oxygen. Understanding and protecting microbial diversity is essential for maintaining a healthy planet. Advances in technology have enabled scientists to study these microscopic organisms in greater detail than ever before. Continued research is needed to unlock the full potential of microbial communities for sustainable solutions.
Bacterial Evolution: Unveiling Earth's History
There are roughly a trillion species of microorganisms on Earth – the vast majority of which are bacteria. Bacteria consist of a single cell. They do not have bones and are not like big animals that leave clear signs in the geological record, which thankful paleontologists can study many millions of years later. This has made it very hard for scientists to establish a timeline of their early evolution. But with the help of machine learning, we have been able to fill in many of the details.
Our new research, published today in Science, also reveals some bacteria developed the ability to use oxygen long before Earth became saturated with it roughly 2.4 billion years ago.
Monumental Events in Earth's History
About 4.5 billion years ago, the Moon formed violently when a Mars-size object collided with Earth, turning its surface into molten rock. If life existed before this cataclysm, it was probably destroyed. After that, the current ancestors of all living beings appeared: single-celled microbes. For the first 80% of life’s history, Earth was inhabited solely by these microbes.
Nothing in biology makes sense except in the light of evolution, as evolutionary biologist Theodosius Dobzhansky famously said in 1973. But how did the evolution of life proceed through the early history of Earth?
The Great Oxidation Event
One thing geology teaches us about is the existence of another monumental event in the history of Earth, 2.4 billion years ago. At that time, the atmosphere of the Earth changed dramatically. A group of bacteria called the cyanobacteria invented a trick that would alter the story of life forever: photosynthesis. Harvesting energy from the sun powered their cells. But it also generated an inconvenient waste product, oxygen gas. Over the course of millions of years, oxygen in the atmosphere slowly accumulated.
Before this “Great Oxidation Event”, Earth contained almost no oxygen, so life was not ready for it. In fact, to uninitiated bacteria, oxygen is a poisonous gas, and so its release into the atmosphere probably caused a mass extinction. The surviving bacteria either evolved to use oxygen or retreated into the recesses of the planet where it doesn’t penetrate.
The Bacterial Tree of Life
The Great Oxidation Event is especially interesting for us not only because of its impact on the history of life but also because it can be given a clear date. We know it happened around 2.4 billion years ago – and we also know most bacteria that adapted to oxygen had to live after this event.
By using the planet-wide geological event of the Great Oxidation Event effectively as a “fossil” calibration point, our approach produced a detailed timeline of bacterial evolution. Combining results from geology, paleontology, phylogenetics, and machine learning, we were able to refine the timing of bacterial evolution significantly.
Our results also revealed a surprising twist: some bacterial lineages capable of using oxygen existed roughly 900 million years before the Great Oxidation Event. This suggests these bacteria evolved the ability to use oxygen even when atmospheric oxygen was scarce.
Remarkably, our findings indicated that cyanobacteria actually evolved the ability to use oxygen before they developed photosynthesis. This framework not only reshapes our understanding of bacterial evolutionary history but also illustrates how life’s capabilities evolved in response to Earth’s changing environments.