Microbes found in hot springs that mimic early Earth conditions when oxygen was toxic to life

Before forests, animals, or even breathable air, Earth was a completely different place. Over two billion years ago, the planet’s atmosphere held almost no oxygen.

What we now call life had to survive in conditions that would be toxic to most organisms today. Back then, oxygen wasn’t a breath of fresh air – it was a threat.

So how did life adapt when oxygen first started to show up? And what did those early ecosystems look like?

A new study offers a rare glimpse into that ancient world by looking at something surprisingly modern: hot springs in Japan.

These bubbling pools, rich in iron and low in oxygen, turn out to be time capsules for understanding how early microbes may have survived – and even thrived – during one of Earth’s biggest turning points.

When Earth gained its oxygen

Around 2.3 billion years ago, Earth’s atmosphere started to change in a big way. This event, known as the Great Oxygenation Event (GOE), introduced oxygen into the air for the first time in large amounts.

The likely culprits? Tiny green cyanobacteria.

These microbes figured out how to use sunlight to break apart water and release oxygen – a waste product of photosynthesis.

Today, oxygen makes up about 21% of the atmosphere. But before the GOE, it was almost non-existent. Instead, gases like methane and carbon dioxide dominated the air.

For most early life, oxygen wasn’t helpful – it was harmful. This shift forced life to evolve new strategies for survival.

Studying early life through hot springs

The research was led by Fatima Li-Hau in the Earth-Life Science Institute (ELSI) at the Institute of Science Tokyo.

The team looked at five hot springs in Japan to learn how early microbes might have coped with increasing oxygen.

Located in Tokyo, Akita, and Aomori, these springs hold water loaded with ferrous iron (Fe²⁺), much like the ancient oceans.

The hot springs also contain little oxygen and have a near-neutral pH, making them rare examples of modern environments that echo early Earth’s conditions.

According to study co-author Shawn McGlynn, the iron-rich hot springs provide a unique natural laboratory to study microbial metabolism under early Earth-like conditions during the late Archean to early Proterozoic transition, marked by the Great Oxidation Event.

“They help us understand how primitive microbial ecosystems may have been structured before the rise of plants, animals, or significant atmospheric oxygen,” noted McGlynn.

Microbes found in the hot springs

The researchers found that most of the hot springs were dominated by microaerophilic iron-oxidizing bacteria.

These microbes prefer low-oxygen environments and feed on ferrous iron, turning it into ferric iron (Fe³⁺). Photosynthetic cyanobacteria were present too, but they played a smaller role than expected.

One of the hot springs in Akita was different. Instead of iron-oxidizers, it had microbes using non-iron-based metabolisms – an unexpected discovery that points to the variety of ways early life might have adapted.

Turning waste into energy

By studying the DNA of the microbes living in these springs, the researchers pieced together over 200 complete microbial genomes. What they found paints a picture of microbial teamwork.

The microbes that used iron and oxygen didn’t just survive – they helped build an environment where oxygen-sensitive organisms could also live.

The community carried out carbon and nitrogen cycling, and even showed signs of a partial sulfur cycle. That last part was surprising, because the hot springs had very low sulfur content.

This hinted at something called a “cryptic” sulfur cycle – a complex system where microbes recycle sulfur in ways that aren’t easy to detect.

“Despite differences in geochemistry and microbial composition across sites, our results show that in the presence of ferrous iron and limited oxygen, communities of microaerophilic iron oxidisers, oxygenic phototrophs, and anaerobes consistently coexist and sustain remarkably similar and complete biogeochemical cycles,” said Li-Hau.

Transition to an Earth with oxygen

This research suggests that early Earth wasn’t just waiting around for photosynthesis to take over.

Instead, microbes were already finding clever ways to use the small amounts of oxygen around them – and to build ecosystems where different types of organisms could survive together.

“This paper expands our understanding of microbial ecosystem function during a crucial period in Earth’s history, the transition from an anoxic, iron-rich ocean to an oxygenated biosphere at the onset of the GOE,” said Li-Hau.

“By understanding modern analogue environments, we provide a detailed view of metabolic potentials and community composition relevant to early Earth’s conditions.”

The full study was published in the journal Microbes and Environments.

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