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No. A 2025 study of five Japanese hot springs did not find microbes that have survived for billions of years. It examined living communities in modern, iron-rich, low-oxygen environments that researchers use as analogues for some conditions proposed for early oceans. The distinction matters: the study offers clues about how ancient ecosystems may have worked, not evidence of organisms persisting unchanged since that time.
What scientists found in Japan’s hot springs
Fatima Li-Hau and colleagues sampled five circumneutral, iron-rich hot springs in Japan and used amplicon and metagenomic sequencing to study which microbes were present and what metabolic processes their genetic material suggested they could perform. The paper appeared in Microbes and Environments in 2025; its J-STAGE record was released July 23, 2025, and lists a correction notice dated September 5, 2025. Read the paper and its record on J-STAGE.
The communities were not identical from spring to spring: microbial membership varied with local geochemistry. In four of the five springs, bacteria that oxidize iron in low-oxygen conditions were dominant, according to an Institute of Science Tokyo summary. The journal abstract reports that microaerophilic iron oxidizers from Zetaproteobacteria or Gammaproteobacteria had higher relative abundance than Cyanobacteria at most sites. The study also describes Kowakubi as distinctive, with Hydrogenophilaceae dominant; hydrogen oxidation is discussed as a possible influence there despite abundant ferrous iron. See the study summary and author comments reproduced by ScienceDaily.
The team reconstructed more than 200 high-quality microbial genomes, as reported by the Institute of Science Tokyo. These genomes help researchers investigate the organisms’ potential functions; their presence does not by itself show that every predicted process was occurring at a particular rate in the springs.
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Why the springs offer clues about early Earth
The springs’ iron-rich chemistry and limited oxygen make them useful modern analogues for some conditions proposed for ancient oceans. An analogue shares selected environmental features with a past setting. It is not an ancient ecosystem preserved intact, and the organisms living in it today are not thereby shown to be ancient.
The historical comparison is the Great Oxygenation Event, a major change in atmospheric oxygen that the Institute of Science Tokyo places roughly 2.3 billion years ago. Oxygen was toxic to many organisms adapted to low-oxygen conditions. Studying how present-day microbes coexist around ferrous iron and limited oxygen can help scientists consider possible ecological relationships during that broad transition. The hot-spring study did not date its organisms to the event or measure the event itself. The Institute of Science Tokyo’s explanation of the early-Earth context.
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How iron oxidizers can coexist with other microbes
“Low oxygen” does not necessarily mean that every part of a spring is oxygen-free. The study’s authors describe communities in which microaerophilic iron oxidizers, oxygen-producing phototrophs, and anaerobes coexist. In the authors’ interpretation, oxygen-producing Cyanobacteria may provide oxygen that helps fuel iron oxidation, while other organisms occupy low-oxygen or anaerobic niches. This is a proposed ecological picture drawn from sampled communities and their genomic evidence—not a claim that the same balance applies to every hot spring.
That interaction is relevant to early-Earth questions because it shows how different metabolisms may fit together in an environment with ferrous iron and limited oxygen. Shawn McGlynn, the study supervisor, described the springs as “a unique natural laboratory” for examining microbial metabolism under early-Earth-like conditions during the late Archean to early Proterozoic transition. His statement is reproduced in the ScienceDaily summary.
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What metabolic processes the study detected
The researchers reported shared metabolic potential across the communities, including carbon fixation through the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation and reduction. They also reported genetic evidence associated with nitrogen cycling through dissimilatory nitrate reduction to ammonia and denitrification. These are findings about the sampled organisms’ genetic capabilities and inferred processes; they should not be read as direct measurements of ecosystem-wide rates.
The institutional summary also describes genetic evidence for a partial sulfur cycle despite low sulfur abundance in the springs, calling it a cryptic cycle. That evidence suggests sulfur transformations may be possible even when sulfur is scarce; it does not establish a complete, universal sulfur cycle across hot springs. The summary discusses the reported cycles and microbial genomes.
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What the headline gets wrong—and what the study does show
The phrase “still alive in Japan” can sound as if these organisms have been living continuously since billions of years ago. The study does not support that interpretation: it sampled present-day organisms and used their environments and genomic information to investigate possible analogues of ancient ecology. It establishes neither multi-billion-year lifespans nor an unchanged lineage tracing back to the Great Oxygenation Event.
Its contribution is more specific and useful: five modern Japanese springs show how varied microbial communities in iron-rich, low-oxygen settings can include iron oxidizers, phototrophs, and anaerobes, with evidence of carbon, nitrogen, iron, and partial sulfur cycling. Those observations help researchers develop and assess ideas about early ecosystems without turning a modern analogue into a time capsule.
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The 2025 paper’s J-STAGE record
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