Scientists have recently identified a microbe that boasts one of the smallest genomes on the planet. What’s particularly fascinating is its heavy reliance on its host: this microbe lacks the genes necessary for metabolism, a fundamental life process. This finding raises questions about the very definition of what constitutes a living organism.
This unexpected discovery, described by Takuro Nakayama, an evolutionary microbiologist at the University of Tsukuba in Japan, was an accident during research aimed at the microbes residing in the single-celled marine dinoflagellate, Citharistes regius, a type of plankton. Upon sequencing the genes within this community, Nakayama and his team stumbled upon some peculiar, minute DNA segments.
These DNA sequences belong to unique archaea, a category of single-celled microbes often found in extreme environments. Archaea are fundamentally different from bacteria in terms of structure, genetic makeup, and metabolic processes.
Nakayama and his colleagues named the newly identified microbe Sukunaarchaeum mirabile—a nod to the Japanese dwarf deity Sukuna-biko-na and the word “marvelous.” With just 238,000 base pairs, Sukunaarchaeum has fewer genes than any known archaea. Their findings were documented in a bioRxiv preprint earlier this year.
What led to such a remarkably tiny genome? Evolution typically drives genetic complexity upward, but sometimes it can lead to simpler genomes—as seen in the cases of certain bacteria and archaea. Nakayama and his team were struck by how far the genes in Sukunaarchaeum have simplified and specialized.
With its minimal genome, Sukunaarchaeum is entirely dependent on its host, C. regius, for crucial energy and nutrients. “It seems unable to produce its own cellular building blocks,” Nakayama observes. “No other microbe has shown such an extreme level of metabolic reliance.”
This microbe appears to straddle a unique category of life, somewhat between archaea and virus. While it has a small genome and is reliant on its host for metabolism—similar to viruses that aren’t typically classified as “alive”—Sukunaarchaeum possesses its own ribosomes and can replicate independently.
To assess just how extraordinary Sukunaarchaeum is, the researchers decided to explore marine environments for potential relatives. By analyzing genetic sequence data from various oceanic locations where C. regius thrives, they found many sequences that might represent a new archaeal lineage.
Nakayama believes this discovery indicates that numerous microbes, which could reshape our understanding of life, might still exist in what he terms “microbial dark matter”—microbes that cannot be cultivated in lab conditions. “Sukunaarchaeum exemplifies the unexpected results found in this ‘natural lab of evolution,’” he explains.
Mart Krupovic, a virologist and microbiologist at Institut Pasteur in France who wasn’t involved in this study, called the finding “remarkable.” He has researched giant viruses that, like Sukunaarchaeum, challenge traditional categorization. These viruses often possess larger and more complex genomes, including genes related to DNA translation, typically associated with cellular life. “It’s fascinating how little we still know about our environment,” he adds.
Nakayama’s next step involves culturing and isolating Sukunaarchaeum in the lab—not just its genetic material—hoping to capture images or videos of it. This research aims to provide insights into its biology, ecological role, and the mechanisms that allow it to exist on the fringe of life.
