In a quiet laboratory in Tsukuba, Japan, scientists have spent two years reading the genetic language of thousands of microorganisms, searching for a capacity that plants have long possessed: the ability to pull carbon dioxide from the air and transform it into life. What they found — 306 microbial strains carrying the machinery for carbon fixation, 173 of them previously unknown to science in this regard — does not yet change the world, but it expands the map of what living things can do, and by extension, what we might ask them to do on our behalf.
Researchers identify 300 microbial strains with CO2-fixing potential from 'microbial dark matter'
Many microorganisms can fix CO2 in the dark, where plants cannot.
Mark
So they looked at 6,700 microbial strains and found 300 that can fix CO2. That sounds like a big number. Is it?
Mimi
It depends on what you're comparing it to. For context, the collection holds over 32,000 strains total. So they're saying roughly 4 to 5 percent of the ones they analyzed have this capability. That's not trivial.
Luke
But wait—they analyzed 6,749 strains, and found 306. The summary says 300. Which is it?
Mimi
306 is the precise number from the research. The summary rounded down.
Mark
And of those 306, how many were actually new discoveries?
Mimi
173 of them belong to genera—that's a taxonomic grouping—where CO2 fixation had never been reported before. So those are the genuinely novel candidates.
Luke
But "never reported" doesn't mean they don't actually do it. It means nobody had looked or published about it. There's a difference.
Mimi
True. The genetic signature is there. Whether the organism actually performs CO2 fixation under real conditions is something that still needs to be tested.
Mark
What would make this useful? Like, why does this matter beyond the catalog?
Mimi
The idea is that if you're trying to develop a carbon-capture technology, or a bioprocess that uses microbes to reduce CO2, you can now request specific strains from this collection that have the genetic potential to do what you need.
Luke
Assuming the culture conditions can be figured out. The researchers themselves said they might need to change how they grow these organisms to unlock the ability.
Mark
So it's a starting point, not a solution.
Mimi
Exactly. It's foundational work. It opens doors for applied research, but it doesn't solve the problem itself.
The Pulse
- With climate pressure mounting, the search for biological carbon capture has grown urgent — yet the microbial world, vast and largely unmapped, has remained a largely untapped frontier.
- Analyzing 6,749 prokaryotic genomes over two years, a RIKEN research team uncovered 306 strains with CO2-fixing genes, nearly half belonging to genera where this ability had never before been documented.
- The discovery disrupts assumptions: some of these organisms may fix carbon not through light, but through hydrogen or sulfur, and may thrive in oxygen-free environments where conventional biology would not look.
- Researchers believe that adjusting laboratory conditions could awaken dormant fixation abilities in these strains, opening a path from genetic potential to measurable, real-world function.
- The immediate result is a catalog — a searchable, requestable list of 306 strains now tagged with a specific capability, ready to be matched to industrial or environmental carbon capture needs worldwide.
In a quiet laboratory in Tsukuba, Japan, scientists have spent two years reading the genetic language of thousands of microorganisms, searching for a capacity that plants have long possessed: the ability to pull carbon dioxide from the air and transform it into life. What they found — 306 microbial strains carrying the machinery for carbon fixation, 173 of them previously unknown to science in this regard — does not yet change the world, but it expands the map of what living things can do, and by extension, what we might ask them to do on our behalf.
In Tsukuba, Japan, a research team at RIKEN's BioResource Research Center spent two years doing the kind of work that is essential and unglamorous in equal measure: reading through the genomes of nearly 6,750 bacteria and archaea, one by one, looking for a specific genetic signature. The question they were asking was deceptively simple — which of these organisms can fix carbon dioxide?
The collection they drew from is one of the world's most carefully documented microbial libraries, holding over 32,000 strains gathered from researchers across the globe, each with a recorded origin and growth history. Yet no one had ever systematically screened it for carbon fixation potential. Senior Research Scientist Shingo Kato decided to change that. His team searched for genes associated with the Calvin-Benson cycle — the same biochemical pathway plants use during photosynthesis to convert CO2 into organic matter.
The results were striking. Of the 306 strains that carried the relevant genetic machinery, 173 belonged to genera with no previously documented CO2 fixation ability. These were organisms that science had simply never thought to ask. What makes them particularly interesting is their potential fuel source: unlike plants, some of these microbes may fix carbon using hydrogen or sulfur compounds, and some may do so in oxygen-free environments — conditions that open possibilities far beyond what photosynthesis can reach.
Postdoctoral researcher Arisa Nishihara noted that altering culture conditions in the laboratory might awaken fixation abilities that currently lie dormant, suggesting the gap between genetic potential and active function may be narrower than it appears.
The practical outcome for now is a catalog. The Japan Collection of Microorganisms can tag these 306 strains with a verified capability, allowing research teams worldwide to identify and request organisms suited to specific carbon capture applications. Kato's broader ambition, embedded in RIKEN's TRIP initiative, is to layer artificial intelligence over this biological data — using what is known about where microbes live, what they consume, and how they behave to predict where they might be most useful in industry.
The work remains firmly in the domain of basic science. But it represents a meaningful incursion into what researchers sometimes call microbial dark matter — the vast, poorly understood majority of Earth's bacterial and archaeal life. What Kato's team has done is illuminate one small corner of that darkness, and ask not just what these organisms are, but what they might one day be asked to become.
Somewhere in a laboratory in Tsukuba, Japan, researchers have been quietly working through the genomes of thousands of microorganisms, looking for a particular genetic signature. What they found could matter for how we think about capturing carbon from the air—not through machines, but through life itself.
The Japan Collection of Microorganisms, housed at the RIKEN BioResource Research Center, holds over 32,000 strains of bacteria and archaea gathered from researchers around the world. These are not random samples. Each one comes with a documented history: where it was found, how it grows, what conditions it needs. The center distributes more than 4,000 strains annually to laboratories across the globe. But until recently, no one had systematically asked a simple question: which of these organisms can fix carbon dioxide?
A team led by Senior Research Scientist Shingo Kato decided to find out. They took 6,749 prokaryotic strains—6,262 bacteria and 487 archaea—and searched their genomes for genes associated with the Calvin-Benson cycle, the biochemical pathway that plants use to convert CO2 into organic matter during photosynthesis. The work took two years. Arisa Nishihara, a postdoctoral researcher on the team, later admitted with a laugh that this was exactly the kind of grueling project she had hoped someone else would tackle.
What emerged from that analysis was striking. The researchers identified 306 strains carrying the genetic machinery for CO2 fixation, belonging to 147 different genera. But here is where the finding gains weight: when they cross-referenced this genetic data against the scientific literature, they discovered that 74 of those genera already had documented evidence of CO2 fixation. The other 73 genera did not. This means 173 individual strains—organisms that had never been known to fix carbon—suddenly became candidates for further investigation.
The significance lies partly in what these organisms might use as fuel. Plants need light to fix carbon. Many microorganisms do not. Some of the newly identified candidates appear capable of fixing CO2 using hydrogen or sulfur compounds, and some may thrive in oxygen-free environments. Nishihara noted that by adjusting culture conditions—changing the chemical environment in which these organisms grow—researchers might unlock CO2 fixation abilities that currently remain dormant in the laboratory.
This is not yet applied technology. No one is deploying these microorganisms at an industrial scale to scrub CO2 from the air. But the research has created something more fundamental: a catalog. The Japan Collection of Microorganisms can now tag 306 strains with a specific capability, allowing researchers worldwide to search for organisms suited to their particular needs. A team working on carbon capture in a specific industrial setting, or in a particular geographic location, can now consult this list and request the strains most likely to work for them.
Kato and his colleagues are part of a larger RIKEN initiative called TRIP, which aims to integrate research infrastructure and data across disciplines. The vision extends beyond cataloging. Kato spoke of using artificial intelligence not just to identify CO2-fixing microorganisms, but to predict how they might be deployed in specific industries and research contexts. The raw data—which microbes live where, what they eat, how they reproduce—becomes the foundation for computational models that could accelerate the discovery of practical applications.
For now, the work remains in the realm of basic science. But it represents a shift in how researchers approach a vast, largely unmapped territory. Scientists estimate that millions of species of bacteria and archaea exist on Earth, yet only a fraction have been formally described or grown in a laboratory. This realm of poorly understood microbial life is sometimes called microbial dark matter. What Kato's team has done is take one small corner of that darkness and shine a light on it, asking not just what these organisms are, but what they might do.
Notable Quotes
Many microorganisms can fix CO2 in the dark, whereas photosynthesis by plants requires light. If we could harness this ability in places where light doesn't reach, it would contribute to a low-carbon society.— Shingo Kato, Senior Research Scientist
By changing culture conditions, we may be able to discover microorganisms that exhibit CO2 fixation ability.— Arisa Nishihara, postdoctoral researcher
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Climate & Environment