Genomic and Geological Timeline of Bacterial Evolution

A team of scientists, including researchers from the University of Queensland (UQ), has helped establish a more precise timeline for bacterial evolution—revealing that some bacteria used oxygen nearly a billion years before they developed the ability to produce it through photosynthesis.

The international collaboration, which included experts from the Okinawa Institute of Science and Technology, the University of Bristol, Queensland University of Technology, and UQ, focused on how microorganisms responded to the Great Oxygenation Event (GOE). This pivotal moment in Earth’s history occurred around 2.33 billion years ago, shifting the atmosphere from largely oxygen-free to one capable of supporting complex life.

Dating the evolution of bacteria around the GOE has been challenging due to the lack of a complete fossil record. As Professor Phil Hugenholtz from UQ’s School of Chemistry and Molecular Biosciences explained:

“Most microbial life doesn’t leave direct fossils, so we’re missing records from much of Earth’s early biological history. But ancient rocks preserve chemical traces of how bacteria lived and processed nutrients. By analyzing both geological and genomic data, we’ve been able to fill in many of the missing pieces.”

A key breakthrough in the study was treating the GOE as a temporal boundary—assuming that most oxygen-using (aerobic) bacterial lineages likely evolved after this event, unless strong fossil or genetic evidence suggested otherwise.

To map out the evolutionary timeline, the researchers reconstructed ancient genomes and used machine learning to predict whether ancestral organisms depended on oxygen. They also incorporated data from mitochondria and chloroplasts—organelles linked to alphaproteobacteria and cyanobacteria, respectively—helping them anchor bacterial evolution more firmly to the fossil record of early complex cells.

“Our results show that at least three aerobic lineages existed nearly 900 million years before the GOE,” Hugenholtz noted.
“This suggests that oxygen-based metabolism evolved long before atmospheric oxygen levels rose. In fact, the first aerobic transition likely occurred around 3.2 billion years ago in the ancestor of cyanobacteria—indicating that using oxygen preceded making it.”

Dr. Adrián Arellano Davín, the study’s lead author, highlighted the power of integrating advanced technologies with genomic and geochemical data to bring ancient evolutionary events into sharper focus.

“By using machine learning to predict cell function, we can go beyond identifying which bacteria were aerobic. We can also begin forecasting traits in incomplete genomes—like potential antibiotic resistance—that could have implications today.”

The research not only revises our understanding of microbial evolution but also demonstrates how modern tools can help decode the deep past, offering insight into how life adapted to a changing planet.