Rosa Rubicondior: Refuting Creationism - Clues to Abiogenesis In Japan's Hot Springs

Hot springs in Japan give insight into ancient microbial life on Earth – ELSI｜EARTH-LIFE SCIENCE INSTITUTE

It’s been a dreadful week for creationists as yet another published paper undermines one of their favourite claims and further reduces the god-shaped gap on which they increasingly depend — the so-called abiogenesis gap. This argument rests on the delusional assumption that if science has not yet fully explained something, then it never will — and therefore creationism wins by default. The history of science, of course, shows the opposite: today’s mysteries are tomorrow’s discoveries.

This time, the blow comes from a publication in the journal Microbes and Environments, which describes how five hot springs in Japan provide natural analogues of the conditions in which the first living organisms could have evolved. These springs are rich in diverse chemical and thermal gradients, making them excellent testbeds for exploring how life can thrive in extreme conditions and use non-traditional energy sources.

The study was conducted by a team led by Fatima Li-Hau, then a graduate student at the Earth-Life Science Institute (ELSI), Tokyo Institute of Science, with Associate Professor Shawn McGlynn as her supervisor. Their work focused on the microbial communities found in these hot springs, which range from moderately warm to boiling.

The main findings and how it refutes creationism:

Microbes in these environments exploit alternative metabolic pathways, such as oxidising hydrogen gas or reducing sulphur, instead of relying solely on sunlight or oxygen.
The hot springs represent a spectrum of geochemical conditions similar to those thought to exist on the early Earth.
By studying these ecosystems, researchers can observe how organisms adapt to extreme and fluctuating conditions, providing clues to the resilience and diversity of early life.

In short, the hot springs act as natural laboratories for studying life’s origins.

Why This Matters for Abiogenesis

Creationists insist that life could not have emerged without a designer, but studies like this steadily chip away at that claim. They show that the fundamental requirements for life — sources of energy, chemical gradients, and environments that sustain self-replicating chemistry — are not only possible but occur naturally.

Far from being a miracle, the emergence of life appears increasingly as a natural outcome of geochemistry meeting biology. Every discovery of organisms exploiting novel energy pathways or surviving in harsh conditions makes the creationist claim of impossibility look ever more hollow.

Closing the Gap

The so-called “God of the gaps” argument has always been a fragile strategy, relying on ignorance as its only strength. But ignorance shrinks with every scientific advance. The hot springs of Japan now provide another piece of the puzzle, helping scientists understand how life might have begun in Earth’s distant past — and perhaps how it could arise elsewhere in the universe.

For creationists, the gap into which they squeeze their god is narrowing once again.

The research is described in an ELSI press release:

Hot springs in Japan give insight into ancient microbial life on Earth
Iron-oxidising bacteria in the iron-rich hot springs suggest early microbes used iron and trace oxygen, not sunlight, as their primary energy source during the planet’s shift from a low-oxygen to a high-oxygen atmosphere about 2.3 billion years ago.

Hot spring sampling
The picture shows Fatima Li-Hau preparing to sample water and sediment from a hot spring at low tide.
Credit: Natsumi Noda, ELSI

Earth was not always the blue-green world we know today: the early Earth’s oxygen levels were about a million times lower than we now experience. There were no forests and no animals. For ancient organisms, oxygen was toxic. What did life look like at that time then? A recent study led by Fatima Li-Hau (graduate student at ELSI at the time of the research) along with the supervisor Associate Professor Shawn McGlynn (at the time of research) of the Earth-Life Science Institute (ELSI) at Institute of Science Tokyo, Japan, explores this question by examining iron-rich hot springs that mimic the chemistry of Earth’s ancient oceans around the time of one of Earth’s most dramatic changes: the oxygenation of the atmosphere. Their findings suggest that early microbial communities used iron along with oxygen released by photosynthetic microbes, for energy, revealing a transitional ecosystem where life turned a waste product of one organism into a new energy source before photosynthesis became dominant.

The Great Oxygenation Event (GOE) occurred around 2.3 billion years ago and marked the rise of atmospheric oxygen, likely triggered by green Cyanobacteria that used sunlight to split water, subsequently converting carbon dioxide into oxygen through photosynthesis. The result is that the current atmosphere is around 78% nitrogen and 21% oxygen, with only traces of other gases such as methane and carbon dioxide, which might have played a greater role before the rise of oxygen. The GOE fundamentally changed the course of life on Earth. This high amount of oxygen allows us animals to breathe, but it also complicates life for ancient life forms, which were almost unaware of the O₂ molecule. Understanding how these ancient microbes adapted to the presence of oxygen remains a major question.

To answer this, the team studied five hot springs in Japan, which are rich in varied water chemistries. Those five springs (one in Tokyo, two each in Akita and Aomori prefectures) are naturally rich in ferrous iron (Fe²⁺). They are rare in today’s oxygen-rich world because ferrous iron quickly reacts with oxygen and turns into an insoluble ferric iron form (Fe³⁺). But in these springs, the water still contains high levels of ferrous iron, low levels of oxygen, and a near-neutral pH, conditions thought to resemble parts of the early Earth’s oceans.

One of the five hot springs
A panoramic picture of a hot spring from the source to the ocean.
Credit: Fatima Li-Hau, ELSI

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.

Professor Shawn Erin McGlynn, co-corresponding author
Earth-Life Science Institute (ELSI)
Institute of Science
Tokyo, Japan.

In four of the five hot springs, the team found microaerophilic iron-oxidising bacteria to be the dominant microbes. These organisms thrive in low-oxygen conditions and use ferrous iron as an energy source, converting it into ferric iron. Cyanobacteria, known for producing oxygen through photosynthesis, were also present but in relatively small numbers. The only exception was one of the Akita hot springs, where non-iron-based metabolisms were surprisingly dominant.

A view of a hot spring
A close-up picture of the sediment and rocks of one of five hot springs during low tide, showing iron oxide mineral precipitates.
Credit: Fatima Li-Hau, ELSI.

Using metagenomic analysis, the team assembled over 200 high-quality microbial genomes and used them to analyse in detail the functions of microbes in the community. The same microbes that coupled iron and oxygen metabolism converted a toxic compound into an energy source and helped maintain conditions that allowed oxygen-sensitive anaerobes to persist. These communities carried out essential biological processes such as carbon and nitrogen cycling, and the researchers also found evidence of a partial sulfur cycle, identifying genes involved in sulfide oxidation and sulfate assimilation. Given that hot springs contained very little sulfur compounds, this was a surprising discovery. The researchers propose that this may indicate a “cryptic” sulfur cycle, where microbes recycle sulfur in complex ways that are not yet fully understood.

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.

Fatima Li-Hau, co-corresponding author.
Earth and Planetary Sciences Department
Institute of Science
Tokyo, Japan.

The research suggests a shift in our understanding of early ecosystems, showing that microbes may have harnessed energy from iron oxidation and oxygen produced by early phototrophs. The study proposes that, similar to these hot springs, early Earth hosted ecosystems were composed of diverse microbes, including iron-oxidising bacteria, anaerobes, and Cyanobacteria living alongside one another and modulating oxygen concentrations.

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.

Fatima 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.

Ocean near a hot spring
A picture of the Sea of Japan as seen from one of five hot springs, where Shawn E. McGlynn is conducting sampling. Orange discharge of oxidated spring water can be seen flowing into the sea.
Credit: Fatima Li-Hau, ELSI

Publication:
Li-Hau,Fatima; Nakagawa,Mayuko; Kakegawa,Takeshi; Ward,L.M.; Ueno,Yuichiro; McGlynn,Shawn Erin
Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan
Microbes and Environments (2025) 40(3), ME24067; DOI: 10.1264/jsme2.ME24067

Abstract
Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H₂ as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N₂ fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth’s oceans became oxygenated at the onset of the Great Oxidation Event.

Putative evidence for life extends to some of the oldest graphitic inclusions, as far back as ~4.1 billion years ago (Gya), where carbon isotope ratios suggest metabolic activity (Bell et al., 2015). However, little is known about the types of organisms that inhabited early Earth and the ecology expected (Crowe et al., 2008; Planavsky et al., 2011; Poulton and Canfield, 2011.1). One major control parameter differentiating contemporary and early Earth environments is atmospheric and oceanic oxygen concentrations. Multiple lines of evidence suggest that O₂ was on the order of 1,000,000 times lower than present levels until the great oxygenation event (GOE) at around 2.4 Gya (Holland, 1986; Lyons et al., 2014; Catling and Zahnle, 2020), which marks the transition from the Archean Eon to the Proterozoic Eon. This difference in oxygen concentration and the reasons behind it are critical for our understanding of biosphere productivity and early Earth’s ecosystems. In the low oxygen conditions of early Earth, the size of the biosphere would have been muted, perhaps 1000 times less than present day values (Ward et al., 2019c). Biological O₂ is generated through oxygenic photosynthesis, which today provides the largest flux of organic carbon and biomass at the Earth’s surface (Quéré et al., 2018; Ward and Shih, 2019.1). Meanwhile as a substrate, oxygen serves as a powerful electron acceptor, allowing life to utilize a diverse range of electron donors as power sources (Amils, 2011.2). The accumulation of oxygen in the atmosphere at around 2.4 Gya provoked changes on Earth’s mineralogy and metal reservoirs that opened new metabolic possibilities and may have been a springboard leading to the contemporary biosphere (Raymond and Segrè, 2006), making the transitory period of the GOE of great interest. This brings forward the question of how early microbial communities utilized the increasing concentrations of oxygen alongside other electron donors and how aerobes and microaerophiles interacted with anaerobic community members.

Here we focus on Japanese ferrous (Fe²⁺) iron carbonate rich hot springs to gain perspective on the types of communities and ecosystem processes which may have been operative as the Earth became oxygenated. In a similar way that terrestrial analogs are valuable for theorizing about other planetary bodies, analogue environments are also valuable for considering early Earth environments which were very different from today. At these sites, one or more conditions similar to those on early Earth or other planets can be found (Léveillé, 2010). Ferrous iron-rich surface environments are scarce on modern Earth as present oxidizing conditions quickly convert it to its insoluble ferric (Fe³⁺) form. Because of this scarcity, our understanding of iron-rich environments expected on the early Earth is yet limited.

Some consensus exists on the geochemical constraints that shaped Precambrian oceans: During the Archean, an anoxic (Cloud, 1968; Holland, 2002), ferruginous (~100 μM Fe²⁺) (Planavsky et al., 2011), circumneutral ocean was present (Krissansen-Totton et al., 2018.1). Then, copious amounts of oxygen started accumulating globally at the onset of the GOE marking the Proterozoic (Catling, 2011.3). It has also been suggested that local “oxygen oases” could have existed after the evolution of oxygenic photosynthesis, but before the GOE (Anbar et al., 2007). In search for environments on today’s Earth which may recapitulate these conditions, stratified lakes with bottom iron-rich water layers have been studied to gain insights into ancient ecology and host microbial communities capable of exploiting iron as an electron donor/acceptor (Crowe et al., 2011.4; Walter et al., 2014.1; Camacho et al., 2017). One limitation of these studies is that the conditions are achieved at depths in which phototrophy occurs only by specialized organisms capable of surviving on 1% of surface irradiance or less or with phototrophy being completely absent (Julià et al., 1998; Lehours et al., 2007.1; Romero-Viana et al., 2010.1; Descy et al., 2012). Amongst previous studies at surface environments (Pierson et al., 1999; Inskeep et al., 2005; Hegler et al., 2012.1; Ward et al., 2017.1; Clair et al., 2019.2; Kotopoulou et al., 2019.3; Ward et al., 2019.4a), community composition and activity varies. For example, at the ferrous iron-rich Chocolate Pots spring (Yellowstone National Park, USA), rapid abiotic iron oxidation outcompetes iron oxidizers (Clair et al., 2017.2); at other sites, such as Crystal Geyser (Colorado, USA) (Probst et al., 2018.2), the potential for iron cycling has been suggested but other metabolic pathways, centered on the high quantities of nitrates and sulfates seem to be more active; whereas in subsurface marine iron-rich systems, aerobic and anaerobic iron oxidizers are directly involved in nitrogen cycling (McAllister et al., 2021). Here, we surveyed five iron-rich hot springs of Japan which could serve as analogues for Neoarchean to Paleoproterozoic oceans on the basis that they contain ferrous iron in ranges near what is expected in the Archean (~40–120 μM) (Catling and Zahnle, 2020), have circumneutral pH, and have lower oxygen concentrations than modern atmosphere-equilibrated water. These variables, extremely rare today, position these springs as analogous to conditions which may have been expected as the early Earth became oxygenated. By comparing surficial iron-rich hot springs, we sought to increase our understanding of the role of Fe²⁺ as a driver of microbial community composition, investigating the geochemistry, microbial taxonomy membership, and bulk metabolic potential.

Fig. 1.
Map showing the location of hot springs in the study. Locations are marked with red circles.

Fig. 2.
Pictures of the hot springs sampled in this study. Kowakubi hot spring [1, 2, and 3]: Source well showing microbial mats and iron oxides. Tsubakiyama hot spring [4, 5, and 6]: Spring water flowing from source tube, outflow of the spring to the ocean showing oxidation of fluid and close-up of source microbial mat. Furutobe hot spring [7, 8, and 9]: Spring water flowing from tube, pump to the bathing area, bathing area. OHK hot spring [10, 11, and 12]: Close-up to microbial mats and travertine deposition at the spring source. Jinata hot spring [13, 14, and 15]: Spring source during low tide, aerial view of spring at rising tide, sediments at low tide.

Li-Hau,Fatima; Nakagawa,Mayuko; Kakegawa,Takeshi; Ward,L.M.; Ueno,Yuichiro; McGlynn,Shawn Erin
Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan
Microbes and Environments (2025) 40(3), ME24067; DOI: 10.1264/jsme2.ME24067

Copyright: © [year] The authors.
Published by [publisher]. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Of course, this study doesn’t purport to fully solve abiogenesis in one stroke — the origin of life is a puzzle too intricate for any single paper. But what it does accomplish is to turn one more “impossible” claim of creationism into a domain of plausible natural chemistry. The hot springs of Japan demonstrate that life can harness iron, oxygen, and subtle geochemical gradients in ways that align with what we might expect from Earth’s earliest ecosystems.

In the words of Shawn McGlynn, “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.”

And Li-Hau emphasises the consistency of the phenomena across varied sites, with, “Despite differences in geochemistry and microbial composition across sites, … communities of microaerophilic iron oxidisers, oxygenic phototrophs, and anaerobes consistently coexist and sustain remarkably similar and complete biogeochemical cycles.”

That is the kind of language that disarms the “gap argument.” It shows scientists not grasping at miracles, but methodically uncovering mechanisms that once lay behind the veil of uncertainty. Creationists who demand a supernatural explanation now find themselves on a shrinking stage. The more we learn, the less room remains for a divine placeholder—unless one insists on believing beyond evidence. And of course it refutes the ludicrous claim by creationists that biomedical scientists are abandoning 'materialist' science and adopting creationism as a better explanation of the observations.

Advertisement

What Makes You So Special? From The Big Bang To You

How did you come to be here, now? This books takes you from the Big Bang to the evolution of modern humans and the history of human cultures, showing that science is an adventure of discovery and a source of limitless wonder, giving us richer and more rewarding appreciation of the phenomenal privilege of merely being alive and able to begin to understand it all.

Ten Reasons To Lose Faith: And Why You Are Better Off Without It

This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.

Amazon