Oxygen metabolism in bacteria arose before Earth’s Great Oxidation Event
Summary author: Walter Beckwith
American Association for the Advancement of Science (AAAS)
Bacteria may have adapted to oxygen well before Earth’s atmosphere was saturated with it, according to a new study. Researchers who traced microbial evolution over billions of years – using machine learning and other methods – show that the evolution of oxygen tolerance predated the Great Oxidation Event (GOE) and may have been crucial not only for the origin of oxygenic photosynthesis in Cyanobacteria but also for the evolution of the planet’s atmosphere. The findings underscore the dynamic relationship between biological evolution and Earth's geological history. Microbial life has dominated Earth’s history for at least 3.7 billion years. However, given the sparse presence of the planet’s first lifeforms in the fossil record, particularly in deep geological time, little is known about their evolution. In lieu of fossil evidence, researchers use geochemical records of microbial biological activity to estimate the ages of key bacterial lineages and their metabolic innovations. The GOE, ~2.4 billion years ago (Ga), marked the accumulation of atmospheric oxygen. This transformative event is thought to have been driven by the emergence of oxygenic photosynthesis – an evolutionary innovation attributed to Cyanobacteria that likely arose ~3.22 Ga. Yet despite this innovation that predated the GOE, it is thought that most life remained anaerobic until the GOE, when atmospheric oxygen levels began to rise. The extent to which aerobic life existed before the GOE remains a subject of debate and the evolutionary timelines of oxygen-adapted bacterial lineages remain poorly constrained.
To address this gap, Adrián Davín and colleagues constructed a species tree of Bacteria using 1,007 genomes spanning bacterial taxonomy. Then, using machine learning and phylogenetic reconciliation, Davín et al. identified distinct evolutionary signatures for oxygen adaption in bacterial genomes and predicted lineages where ancestorial transitions from anaerobic to aerobic lifestyles occurred. This allowed the authors to trace the evolution of oxygen use in bacteria across deep time. According to the findings, early aerobic bacteria emerged before the GOE, around 3.22 to 3.25 Ga, suggesting that aerobic metabolism evolved in some lineages – likely the ancestors of cyanobacteria – before oxygenic photosynthesis emerged. Following the GOE, there was an intense diversification of aerobic metabolism, which contributed to higher rates of diversification in oxygen-adapted lineages compared to anaerobic ones.
Journal
Science
Article Title
A geological timescale for bacterial evolution and oxygen adaptation
Article Publication Date
4-Apr-2025
Molecular clock analysis shows bacteria used oxygen long before widespread photosynthesis
Scientists use the Great Oxidation Event and how organisms adapted to it to map bacterial evolution
Okinawa Institute of Science and Technology (OIST) Graduate University
image:
Bacterial evolution and oxygen adaptation: A timeline built from genomic, fossil, and chemical data. Colors show oxygen states: anaerobic (blue), aerobic (red), and proportion of aerobic lineages in modern bacterial phyla (purple shades). Analysis includes mitochondria and plastids to leverage eukaryotic fossil data. Land plants and animals are shown for time reference.
view moreCredit: Davín et al., 2025
Microbial organisms dominate life on Earth, but tracing their early history and evolution is difficult because they rarely fossilize. Determining when exactly a particular group of microbes first appeared is especially hard. However, ancient sediments and rocks hold chemical clues of available nutrients that could support the growth of bacteria. A key turning point was when oxygen accumulated in the atmosphere around 2.3 billion years ago. Scientists have used this oxygen surge and how microbes adapted to it to map out bacterial evolution.
In a new study published in Science, researchers from the Model-Based Evolutionary Genomics Unit at the Okinawa Institute of Science and Technology (OIST) and their international collaborators have constructed a detailed timeline for bacterial evolution and oxygen adaptation. Their findings suggest some bacteria could use trace oxygen long before evolving the ability to produce it through photosynthesis.
The researchers focused on how microorganisms responded to the Great Oxygenation Event (GOE) some 2.3 billion years ago. This event, triggered in large part by the development of oxygenic (oxygen-generating) photosynthesis in cyanobacteria and carbon deposition, fundamentally changed Earth’s atmosphere from one mostly devoid of oxygen to one where oxygen became relatively abundant, as it is today.
Until now, establishing accurate timescales for how bacteria evolved before, during, and after this pivotal transition has been difficult due to incomplete fossil evidence and the challenge of determining the maximum possible ages for microbial groups – given that the only reliable maximum limit for the vast majority of lineages is the Moon-forming impact 4.5 billion years ago, which likely sterilized the planet.
The researchers addressed these gaps by concurrently analyzing geological and genomic records. Their key innovation was to use the GOE itself as a time boundary, assuming that most aerobic (oxygen-using) branches of bacteria are unlikely to be older than this event – unless fossil or genetic signals strongly suggest an earlier origin. Using Bayesian statistics, they created a model that can override this assumption when data supports it.
This approach, however, requires making predictions about which lineages were aerobic in the deep past. The team used probabilistic methods to infer which genes ancient genomes contained, and then machine-learning to predict whether they used oxygen. To best utilize the fossil record, they leveraged fossils of eukaryotes, whose mitochondria evolved from Alphaproteobacteria, and chloroplasts evolved from cyanobacteria to better estimate how and when aerobic bacteria evolved.
Their results indicate that at least three lineages had aerobic lifestyles before the GOE – the earliest nearly 900 million years before – suggesting that a capacity for using oxygen evolved well before its widespread accumulation in the atmosphere. Intriguingly, these findings point to the possibility that aerobic metabolism may have occurred long before the evolution of oxygenic photosynthesis. Evidence suggests that the earliest aerobic transition occurred in an ancestor of photosynthetic cyanobacteria, indicating that the ability to utilize trace amounts of oxygen may have allowed the development of genes central to oxygenic photosynthesis.
The study estimates that the last common ancestor of all modern bacteria lived sometime between 4.4 and 3.9 billion years ago, in the Hadean or earliest Archaean era. The ancestors of major bacterial phyla are placed in the Archaean and Proterozoic eras (2.5-1.8 billion years ago), while many families date back to 0.6-0.75 billion years ago, overlapping with the era when land plants and animal phyla originated.
Notably, once atmospheric oxygen levels rose during the GOE, aerobic lineages diversified more rapidly than their anaerobic counterparts, indicating that oxygen availability played a substantial role in shaping bacterial evolution.
“This combined approach of using genomic data, fossils, and Earth’s geochemical history brings new clarity to evolutionary timelines, especially for microbial groups that don’t have a fossil record,” Prof. Gergely Szöllősi, leader of the Model-based Evolutionary Genomics Unit, highlighted.
“Our work also shows that modelling microbial traits from their genomes using machine learning works well for studying the spread of aerobic metabolisms and might also be a useful approach for exploring how other traits emerged and interacted with the planet's shifting environment across geological time,” Dr. Tom Williams, a researcher from the University of Bristol’s School of Biological Sciences, explained.
Molecular clock analysis header Image (OIST)
Credit
Kaori Serakaki (OIST)
Journal
Science
Method of Research
Computational simulation/modeling
Subject of Research
Cells
Article Title
A geological timescale for bacterial evolution and oxygen adaption
Article Publication Date
4-Apr-2025
