Niels Bohr, the Nobel laureate in Physics and father of the atomic model, is famously supposed to have said, “It is difficult to make predictions, especially about the future.” Our uncertainty about whether he actually said this or not, some attribute the quote of the legendary baseball player (and philosopher) Yogi Berra, highlights that making predictions about the past can be equally challenging. However, reconstructing the distant past and tracing how and when life adapted to new conditions, such as the rise of oxygen on Earth, requires making exactly such predictions.
“In a recent study published in Science, a multinational collaboration led by Gergely Szöllősi, senior research associate at HUN REN’s Institute of Evolution and the head of the Model-based Evolutionary Genomics Unit at the Okinawa Institute of Science and Technology (OIST), Tom Williams’ lab at the University of Bristol and Adrian Davin from Phil Hugenholtz’s group at the University of Queensland constructed a detailed timeline for bacterial evolution and oxygen adaptation, with a specific focus on how microorganisms responded to the Great Oxygenation Event (GOE) some 2.33 billion years ago. This event, triggered in large part by the innovation of oxygenic photosynthesis in cyanobacteria, fundamentally changed Earth’s atmosphere from mostly devoid of oxygen to one where oxygen became relatively abundant. Until now, establishing accurate timescales for how bacteria evolved before, during, and after this pivotal transition has been hampered by incomplete fossil evidence and the challenge of determining the maximum possible ages for microbial groups—given that the only credible maximum for the vast majority of lineages is the Moon-forming impact 4.52 billion years ago, which likely sterilised the planet.
The researchers addressed these gaps by turning to the geological and genomic records in tandem. Their key innovation was to use the GOE itself as a temporal constraint, assuming that most aerobic (oxygen-using) bacterial lineages are unlikely to be older than this event—unless fossil or genetic signals strongly suggest an earlier origin. They introduced a Bayesian approach that uses this assumption as a “soft” maximum, allowing for exceptions where the data warrant it. This approach, however, requires making predictions about which lineages were aerobic in the deep past. To do so, the team deployed machine-learning algorithms that aggregate signals across the entire genome, thereby robustly inferring oxygen tolerance from incomplete ancestral gene repertoires. To best leverage the fossil record, they incorporated genes from mitochondria (branching with Alphaproteobacteria) and chloroplasts (branching with Cyanobacteria), enabling additional fossil-based calibrations from the eukaryotic record and thereby improving dating accuracy.
Their results indicate that at least three aerobic lineages appeared prior to the GOE—by nearly 900 million years—suggesting that a capacity for using oxygen evolved well before its widespread accumulation in the atmosphere. Intriguingly, these findings also point to the possibility that aerobic metabolism may have predated the evolution of oxygenic photosynthesis. For instance, the earliest inferred aerobic transition occurred around 3.2 billion years ago in the common ancestor of two cyanobacterial groups, indicating that the ability to utilise trace oxygen may have facilitated the later emergence of genes central to oxygenic photosynthesis. Moreover, the study estimates 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. 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. The researchers argue that this combined approach of using genomic data, fossils, and Earth’s geochemical history brings new clarity to evolutionary timelines, particularly for microbial groups that lack a straightforward fossil record. It also offers a powerful framework for exploring how other microbial traits arose and interacted with the planet’s shifting environment across geological time.
Photo: Banded Iron Formation (BIF): sedimentary rocks that record the rise of atmospheric oxygen during the Great Oxidation Event (GOE)
