Aerobic Bacteria May Predate Earth’s Oxygen Boom

Bacteria, among the oldest of life forms, have lived in seemingly every possible habitat on the planet, from ocean trenches and mountaintops to hot springs and polar ice. Yet, they have left a limited fossil record, hindering scientists’ efforts to piece together their early evolutionary timeline.

“There is something else that happens with microorganisms,” said Philip Hugenholtz, a microbiologist at the University of Queensland. “They can leave a biochemical trace in the Earth's history because of their metabolism.”

By studying ancient biochemical signatures, Hugenholtz and his collaborators constructed a timeline of bacterial evolution and oxygen adaptation.¹ Their findings, published in Science, suggest that some bacteria could use oxygen millions of years before it became abundant on the Earth, reshaping our understanding of bacterial evolution.

“This is a brilliant study,” said Gaurav Sharma, a computational biologist and microbial geneticist at the Indian Institute of Technology Hyderabad, who was not involved in the study. “It gives a very different perspective which was not known ‘til now.”

To decipher the genes that ancient bacteria would carry, Hugenholtz and his team used an approach called phylogenetic reconciliation. They traced the evolutionary history of thousands of extant genes against the genome history of 1,000 existing bacterial species and inferred their ancestors’ genomes. They then set out to predict whether these organisms used oxygen.

The researchers first compiled a list of genes found in modern aerobic and anaerobic bacteria, which they used to train a machine learning model to determine an organism’s oxygen use based on its genetic makeup. They then applied the model to the ancestral genomes.

Their models predicted that most ancestral lineages were anaerobic, consistent with geochemical records indicating that ancient Earth’s atmosphere was largely devoid of oxygen around 2.5 billion years ago. The researchers observed that many ancient bacteria transitioned to an aerobic lifestyle as the Great Oxidation Event (GOE) occurred about 2.3 billion years ago.² This event, triggered by microbes’ ability to photosynthesize, led to a rise in atmospheric oxygen. Ancient bacteria that had never encountered oxygen either evolved to use it or retreated into oxygen-free environments deep within the planet.

However, the researchers observed that at least three bacterial lineages appeared to use oxygen as early as 900 million years before the GOE. “This was a big surprise,” said Hugenholtz. “At this point, we were pulling our hair out, because [the findings are] going against the perceived wisdom, which is that if you're making oxygen, then that will drive your ability to use oxygen,” he recalled.

The researchers double-checked their analyses to rule out any errors. When everything checked out, they dug into literature in search of explanations for their unexpected findings. They unearthed articles from the 1970s where researchers had hypothesized that ancient microbes may have had the ability to tolerate oxygen before the GOE.³ Hugenholtz and his team reasoned that these lineages may have been exposed to oxygen produced abiotically, such as through the photolysis of water.

Their results also revised the timeline of bacterial evolution, suggesting that the last common bacterial ancestor lived between 3.9 and 4.4 billion years ago, as opposed to 3.5 to 3.8 billion years ago as indicated by some analyses.⁴ This occurred soon after a Mars-sized object crashed into the Earth around 4.5 billion years ago, a cataclysmic event that wiped out any existing life and formed the Moon. “This means that the innovation for making life could happen in a geologically short time, like a few 100 million years,” said Hugenholtz.

This is the first study to show that a group of organisms already carried genes for using oxygen before the oxygenation event, said Sharma. He added that analyzing a broader range of genomes could provide a better resolution of the evolutionary timeline. “We have more than 100,000 genomes [available].”

“I'd like to see [the study] repeated on a larger data set,” agreed Hugenholtz. Nevertheless, he believes that their study offers a framework to map evolutionary histories of other organisms. “Now, I think that we'll really get much better, detailed picture of how life and metabolism evolved on this planet.”