In the dim waters off the Japanese coast, scientists have stumbled upon something that shouldn’t exist. Or at least not by the rules we thought biology followed.
While sequencing DNA from a tiny marine plankton, a team led by Ryo Harada at Dalhousie University discovered an unexpected loop of genetic material. The fragment didn’t match anything they had seen before. What it turned out to be has stunned researchers: a strange microorganism that straddles the fine line between virus and cellular life.
In their new study, researchers describe Candidatus Sukunaarchaeum mirabile. Sukuna, after a mythological Japanese deity of small stature, and mirabile, meaning “marvelous” in Latin.
“This extreme specialization… challenges our fundamental understanding of the minimal requirements for cellular life,” the researchers wrote.
A Genome Barely There
To understand why this tiny organism has made such a splash in the scientific world, we need to look at its genome.
At just 238,000 base pairs, Sukunaarchaeum’s genome is the smallest ever recorded for any archaeon. That’s less than half the size of the previously smallest known archaeal genome. By comparison, some viruses have far more genetic material. Yet unlike viruses, which hijack the machinery of their hosts entirely, Sukunaarchaeum carries some of its own replication tools.
“Its genome is profoundly stripped-down, lacking virtually all recognizable metabolic pathways, and primarily encoding the machinery for its replicative core: DNA replication, transcription, and translation,” the authors wrote in their study.
It has genes for ribosomes, tRNAs, and mRNAs. These components are the scaffolding of life: the tools by which cells read their genomes and build proteins. Viruses don’t have them but this archaeon does.
That makes it an evolutionary paradox—an organism that can replicate its genetic code but is otherwise almost entirely dependent on its host. It neither makes its own food nor contributes to its host’s survival, unlike symbiotic bacteria that exchange nutrients. Sukunaarchaeum, it seems, is just along for the ride.
Virus-Like—but Still a Cell
The discovery pushes against the fragile fence science has built around what defines life.
Viruses are usually disqualified from the category because they can’t reproduce or carry out metabolism on their own. Cells, on the other hand, can. Sukunaarchaeum does just enough to place it among cells, but only barely. It may represent the closest cellular entity discovered to date that approaches a viral strategy of existence.
Its genome is laser-focused on one thing: replication. Out of 189 protein-coding genes, over half are dedicated to reading and copying DNA. Almost none serve other biological functions.
It is, as the researchers put it, “a viable cell seemingly stripped down to its replicative core.”
That’s not something even the most minimal symbiotic bacteria do. For example, Carsonella ruddii, which lives inside sap-feeding insects, has a similarly tiny genome. But even it retains genes for energy and amino acid production. Sukunaarchaeum does not.
A Stranger Among Archaea
Even its ancestry is an enigma. Phylogenetic trees place Sukunaarchaeum as a “deep-branching” member of the domain Archaea—a domain that includes extremophiles and gave rise to eukaryotes, the group that includes plants, fungi, and animals. But it doesn’t belong to any known phylum.
Depending on the computational model used, it might be closest to the mysterious Nanobdellati or perhaps Halobacteriota. Both are groups known for their small genomes and fast evolution. But the phylogenetic trees disagree, and the statistical support for any exact placement is weak.
This may be a lineage unto itself. The branch on the tree of life it occupies is so long and so isolated that it may represent a completely new major group of archaea.
Hidden in Plain Sight
The team discovered Sukunaarchaeum by diving deep into the genetic soup of a marine plankton cell called Citharistes regius. The cell came from the waters off Shimoda, Japan, and was part of a study into the microscopic community it hosts.
Among the usual suspects like cyanobacteria and proteobacteria was a mystery genome. It later turned out to be a complete circle of DNA from Sukunaarchaeum.
To confirm this wasn’t a fluke, researchers turned to the global Tara Oceans project, which surveys the ocean’s microbial life. There, too, they found Sukunaarchaeum’s genetic fingerprints, but only in the fraction of samples associated with larger single-celled eukaryotes.
This suggests that Sukunaarchaeum and its relatives live on or inside bigger planktonic hosts. It’s unlikely they float freely in the ocean. But what they do to their hosts—friend, foe, or freeloader—remains an open question.
Rethinking the Limits of Life
This isn’t the first time scientists have found an organism that breaks the rules. Over the past two decades, new techniques in metagenomics have revealed a parade of previously unknown microbes. Some of them—like the DPANN archaea or the Candidate Phyla Radiation bacteria—have already forced biologists to redraw the microbial tree of life.
But Sukunaarchaeum is different.
It practically dances on the line between life and virus. It lives, but only just. It replicates, but does little else. It carries the architecture of a cell, but behaves like a virus. It raises an unsettling possibility: that the difference between life and non-life may not be a clean break, but a continuum.
“The discovery of Sukunaarchaeum pushes the conventional boundaries of cellular life,” the team concluded, “and highlights the vast unexplored biological novelty within microbial interactions.”
As scientists continue to explore the hidden networks of microbial life—inside cells, across oceans, and in the soil beneath our feet—organisms like Sukunaarchaeum offer a reminder: the living world is far stranger than we imagined.
The study was published in the preprint server bioRxiv.
