A new analysis combining genomics, machine learning, and geochemistry suggests that some bacterial lineages developed the ability to use oxygen hundreds of millions of years before oxygen-producing photosynthesis evolved.
The study, published by a multinational team including researchers from the University of Queensland, the Okinawa Institute of Science and Technology, the University of Bristol, and Queensland University of Technology, reconstructs a timeline of bacterial evolution in the context of Earth’s shifting atmospheric composition. Their findings challenge longstanding assumptions about when bacteria first began to metabolize oxygen.
The Great Oxygenation Event (GOE), which occurred around 2.33 billion years ago, marks the point when oxygen began accumulating in Earth’s atmosphere. Until now, scientists assumed that most aerobic bacteria (those that require oxygen) must have evolved after this event. However, direct fossil evidence for microbial life during that period is sparse.
“Most microbial life leaves no direct fossil record, which means that fossils are missing from the majority of life’s history on Earth,” said Phil Hugenholtz from the University of Queensland’s School of Chemistry and Molecular Biosciences.
To address this, the researchers merged genomic and geological data to estimate the timing of key evolutionary events. The team reconstructed ancestral genomes, then applied machine learning to predict which ancient bacterial lineages were capable of aerobic metabolism.
“The key innovation was using the GOE as a time boundary, assuming that most aerobic branches of bacteria are unlikely to be older than this event unless fossil or genetic signals suggested otherwise,” stated Hugenholtz.
To anchor their evolutionary timeline, the researchers included genes from mitochondria and chloroplasts, organelles in modern eukaryotes that trace their origins to alphaproteobacteria and cyanobacteria, respectively. This allowed them to use more reliable fossil and molecular clock data from early eukaryotes to better infer the timing of bacterial events.
According to their analysis, at least three aerobic lineages of bacteria emerged before the GOEnearly 900 million years earlier. One key transition appears to have occurred in the ancestor of cyanobacteria about 3.2 billion years ago. These results suggest that oxygen use predated the emergence of oxygenic photosynthesis.
Lead author Adrián Arellano Davín highlighted the broader implications of the methods used in the study. “By using machine learning to predict cell function, we can not only predict the aerobic metabolisms of ancestral bacteria but also start to take incomplete genomes to try to predict other traits that could impact the world now, such as whether certain bacteria might be resistant to antibiotics,” he said.
Publication Details
Adrián A. Davín et al., A geological timescale for bacterial evolution and oxygen adaptation. Science 388, eadp1853 (2025). DOI:10.1126/science.adp1853
The study, published by a multinational team including researchers from the University of Queensland, the Okinawa Institute of Science and Technology, the University of Bristol, and Queensland University of Technology, reconstructs a timeline of bacterial evolution in the context of Earth’s shifting atmospheric composition. Their findings challenge longstanding assumptions about when bacteria first began to metabolize oxygen.
The Great Oxygenation Event (GOE), which occurred around 2.33 billion years ago, marks the point when oxygen began accumulating in Earth’s atmosphere. Until now, scientists assumed that most aerobic bacteria (those that require oxygen) must have evolved after this event. However, direct fossil evidence for microbial life during that period is sparse.
“Most microbial life leaves no direct fossil record, which means that fossils are missing from the majority of life’s history on Earth,” said Phil Hugenholtz from the University of Queensland’s School of Chemistry and Molecular Biosciences.
To address this, the researchers merged genomic and geological data to estimate the timing of key evolutionary events. The team reconstructed ancestral genomes, then applied machine learning to predict which ancient bacterial lineages were capable of aerobic metabolism.
“The key innovation was using the GOE as a time boundary, assuming that most aerobic branches of bacteria are unlikely to be older than this event unless fossil or genetic signals suggested otherwise,” stated Hugenholtz.
To anchor their evolutionary timeline, the researchers included genes from mitochondria and chloroplasts, organelles in modern eukaryotes that trace their origins to alphaproteobacteria and cyanobacteria, respectively. This allowed them to use more reliable fossil and molecular clock data from early eukaryotes to better infer the timing of bacterial events.
According to their analysis, at least three aerobic lineages of bacteria emerged before the GOEnearly 900 million years earlier. One key transition appears to have occurred in the ancestor of cyanobacteria about 3.2 billion years ago. These results suggest that oxygen use predated the emergence of oxygenic photosynthesis.
Lead author Adrián Arellano Davín highlighted the broader implications of the methods used in the study. “By using machine learning to predict cell function, we can not only predict the aerobic metabolisms of ancestral bacteria but also start to take incomplete genomes to try to predict other traits that could impact the world now, such as whether certain bacteria might be resistant to antibiotics,” he said.
Publication Details
Adrián A. Davín et al., A geological timescale for bacterial evolution and oxygen adaptation. Science 388, eadp1853 (2025). DOI:10.1126/science.adp1853