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.