Japan’s hot springs hold clues to the origins of life on Earth

To understand what life was like in this ancient, alien world, researchers led by Fatima Li-Hau (graduate student at ELSI at the time of the research) and her supervisor, Associate Professor Shawn McGlynn (at the time of research), from the Earth-Life Science Institute (ELSI) at Institute of Science Tokyo, Japan, studied a remarkable modern analogue: iron-rich hot springs. These hot springs resemble the chemistry of early Earth's oceans during one of the planet's most dramatic transformations -- the oxygenation of the atmosphere.

Their research shows that primitive microbial communities once relied on iron and trace amounts of oxygen released by photosynthetic microbes to produce energy. This discovery reveals a transitional period when early life turned what was once a toxic byproduct into a valuable energy source, paving the way for oxygen-based photosynthesis to take hold.

The Great Oxygenation Event and Earth's Transformation

Roughly 2.3 billion years ago, the Great Oxygenation Event (GOE) marked a turning point in Earth's history. It was likely driven by Cyanobacteria that learned to harness sunlight to split water and convert carbon dioxide into oxygen through photosynthesis. This process gradually filled the atmosphere with oxygen, transforming its composition into what we breathe today -- around 78% nitrogen and 21% oxygen, with only traces of methane and carbon dioxide, which had previously played a greater role.

The GOE reshaped the course of evolution. Oxygen made complex, multicellular life possible but also created serious challenges for the earlier microbes that had evolved in a low-oxygen world. How these ancient organisms adapted to the arrival of oxygen has remained one of biology's most enduring mysteries.

To explore how early microbes might have survived this transition, Li-Hau and McGlynn's team examined five hot springs across Japan, each with unique water chemistries. These springs (one in Tokyo, two each in Akita and Aomori prefectures) contain high levels of ferrous iron (Fe2+), a form of dissolved iron that was once common in Earth's early oceans but is rare today. In modern, oxygen-rich environments, ferrous iron rapidly oxidizes into ferric iron (Fe3+), which is insoluble. Yet in these springs, the water remains rich in ferrous iron, low in oxygen, and close to neutral pH -- conditions strikingly similar to those of ancient seas.

"These 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," says Shawn McGlynn, who supervised Li-Hau during her dissertation work.

Microbes That Thrived on Iron, Not Oxygen

In four of the five springs, the researchers found that microaerophilic, or low-oxygen-loving, iron-oxidizing bacteria were the dominant life forms. These microbes use ferrous iron as a source of energy, converting it into ferric iron in the process. Photosynthetic Cyanobacteria, which produce oxygen, were also present but in smaller numbers. Interestingly, one of the Akita hot springs displayed a different balance, where microbes relying on non-iron-based metabolisms were more abundant.

By performing metagenomic analyses, the team reconstructed over 200 high-quality microbial genomes to examine how these organisms functioned within their communities. They found that microbes capable of linking iron and oxygen metabolism could convert what was once a toxic compound into a usable energy source, while also maintaining conditions suitable for oxygen-sensitive anaerobes to persist.

These communities were not only recycling iron but also participating in vital processes such as carbon and nitrogen cycling. Even more surprising was the discovery of genetic evidence for a partial sulfur cycle, including genes responsible for sulfide oxidation and sulfate assimilation. Since the springs contained very little sulfur, this points to a "cryptic" sulfur cycle -- an intricate, hidden network of microbial interactions that scientists are only beginning to understand.

"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," says Li-Hau.

Rethinking Early Ecosystems and the Origins of Life

The findings reshape our understanding of Earth's earliest ecosystems, suggesting that primitive microbes harnessed both iron oxidation and trace oxygen from early phototrophs to fuel their metabolism. Like the modern Japanese hot springs, early Earth likely hosted diverse microbial communities -- iron-oxidizers, anaerobes, and Cyanobacteria -- living side by side and influencing oxygen levels in their environment.

"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. By understanding modern analogue environments, we provide a detailed view of metabolic potentials and community composition relevant to early Earth's conditions," says Li-Hau.

Together, these insights deepen our understanding of life's early evolution on Earth and have implications for the search for life on other planets with geochemical conditions similar to those of early Earth.

More Information

Earth-Life Science Institute (ELSI) is one of Japan's ambitious World Premiere International research centers, whose aim is to achieve progress in broadly inter-disciplinary scientific areas by inspiring the world's greatest minds to come to Japan and collaborate on the most challenging scientific problems. ELSI's primary aim is to address the origin and co-evolution of the Earth and life.

Institute of Science Tokyo (Science Tokyo) was established on October 1, 2024, following the merger between Tokyo Medical and Dental University (TMDU) and Tokyo Institute of Technology (Tokyo Tech), with the mission of "Advancing science and human wellbeing to create value for and with society."

World Premier International Research Center Initiative (WPI) was launched in 2007 by Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT) to foster globally visible research centers boasting the highest standards and outstanding research environments. Numbering more than a dozen and operating at institutions throughout the country, these centers are given a high degree of autonomy, allowing them to engage in innovative modes of management and research. The program is administered by the Japan Society for the Promotion of Science (JSPS).