Earth's first bacteria used oxygen about one billion years earlier than we thought

Life on our planet goes back at least 3.7 billion years, and much of it started small. Researchers have studied microbial life in ancient rocks, but it has remained hard to place microbes on an exact timeline.

New work indicates that some bacteria harnessed oxygen almost one billion years earlier than scientists previously believed.

Led by Dr. Adrián Arellano Davín of the Okinawa Institute of Science and Technology (OIST), this study highlights an unexpected link between early oxygen tolerance and the later rise of photosynthesis.

Understanding the Great Oxidation Event (GOE)

A huge turning point in Earth’s early history is known as the Great Oxidation Event, or GOE for short. It happened around 2.4 billion years ago, when oxygen started building up in the atmosphere for the first time.

Before that, there was barely any oxygen in the air – life existed, but it was mostly tiny microbes that didn’t need it. Or, as we’re learning from this study, a few species of bacteria that learned to use it before it became prevalent in the atmosphere.

At first, that oxygen got soaked up by things like iron in the oceans, but eventually, it started leaking into the air.

Once oxygen began to stick around in the atmosphere, it changed everything. Some life forms couldn’t handle it and died off, but others adapted and thrived.

This event set the stage for more complex life to evolve down the road.

Bacteria used oxygen before air changed

Scientists have assumed that most bacteria stayed anaerobic until the onset of the GOE. The new investigation challenges that assumption.

Clues suggest certain bacterial lineages adapted to oxygen at least 900 million years before the GOE. This surprising result implies that small amounts of oxygen were present in pockets of Earth’s environment.

Such an ability to work with trace oxygen may have paved the way for modern forms of respiration.

Early oxygen use gave bacteria an advantage

Energy production in cells is crucial, and oxygen-based metabolism is notably more efficient than methods that rely on other substances.

Before atmospheric oxygen rose, most organisms relied on anaerobic paths. Gaining even a slight advantage by using oxygen could have given those early aerobic microbes a head start.

“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,” said Professor Gergely Szöllősi, leader of the Model-based Evolutionary Genomics Unit at OIST.

The role of machine learning

Scientists used machine learning alongside phylogenetic reconciliation to reconstruct which ancestral bacteria may have used oxygen.

By looking at patterns across 1,007 modern bacterial genomes, the method predicted points where lineages switched from anaerobic to aerobic lifestyles.

Modern labs have begun using these computational techniques to shed light on evolutionary puzzles that lack physical fossil evidence.

Researchers found that lineages with oxygen-based metabolism spread further and diversified more quickly once the atmosphere changed.

Insights into cyanobacteria

The study points out that cyanobacteria – the group known for introducing oxygenic photosynthesis – may have already been primed to handle oxygen.

Evidence hints that an ancestor of this group had an aerobic phase, which might have helped it develop photosynthetic genes.

“Our work also shows that modeling microbial traits from their genomes using machine learning works well for studying the spread of aerobic metabolisms,” said Dr. Tom Williams, a researcher from the University of Bristol’s School of Biological Sciences.

The presence of genes for managing oxygen could have set the stage for the development of photosynthesis later on.

Existence of oxygen-using bacteria

Scientists mapped bacterial family histories back to the Hadean or earliest Archaean era, roughly 4.4 to 3.9 billion years ago.

Several major groups emerged and radiated well before the GOE. Families that adopted oxygen-based lifestyles were able to thrive and multiply once oxygen became plentiful.

By analyzing both geological and genomic data, researchers placed maximum age limits on groups that rely on oxygen. Anything that needed oxygen to survive could not have existed long before free oxygen was available.

Yet the data showed that a few select lineages managed to eke out an aerobic existence in localized habitats.

A broader perspective

Ancient bacterial evolution remains a tough subject to nail down.

Fossils are rare for microbes, which means researchers must rely on chemical signals in sediments and advanced computational methods. These techniques fill the gaps left by the limited record of ancient life.

“This combined use of different data types can help us figure out not only when bacteria evolved but also how they adapted,” said Dr. Davín.

Cross-referencing oxygen-related genes with global events paints a clearer picture of the factors that steered bacterial diversity.

What comes next

Questions remain about how oxygen pockets formed before the GOE and how widespread they might have been. Scientists are also curious whether other organisms besides bacteria adapted to these oxygen pockets.

Future work may involve examining additional traits, such as antibiotic resistance or carbon fixation, to see how they appeared in tandem with environmental changes.

Understanding ancient microbial lineages can shed light on the conditions that fostered eukaryotes and, eventually, complex life forms like animals and plants.

Early oxygen tolerance in microbes might have played a big part in shaping the biosphere we see today.

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Featured image: An artistic conception of the early Earth, showing a surface pummeled by large impact, resulting in extrusion of deep-seated magma onto the surface. Credit: NASA/Simone Marchi

The study is published in Science.

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