Eduard Ocaña-Pallarès was staring at a genetic puzzle that spans a billion years: how did four completely unrelated groups of organisms all independently invent the same way of eating? The answer, he and his international team discovered, wasn't invention at all—it was borrowing.
The planet's decomposers—fungi, bacteria, and countless other microorganisms that break down dead matter and return nutrients like carbon, nitrogen, and phosphorus back to the soil—are quietly essential to all life. Most of them feed through osmotrophy, a method of absorbing dissolved nutrients directly rather than swallowing prey. But how this feeding strategy evolved independently across such distant branches of the evolutionary tree had remained a mystery. Until now.
A collaboration spanning the Okinawa Institute of Science and Technology, the University of Oxford, the Barcelona Supercomputing Center, and research institutions across Spain has reconstructed how this happened. By analyzing hundreds of gene trees across four distantly related eukaryotic groups—fungi, Pseudofungi, Labyrinthulea, and Teretosporea—the researchers discovered that these organisms didn't evolve osmotrophy in isolation. Instead, they shared genes with each other, passing genetic material across species barriers in a process called horizontal gene transfer.
The timeline is striking: all four groups specialized in osmotrophy between 720 million and 1 billion years ago, a period when Earth's biochemistry was fundamentally different. More remarkably, despite their evolutionary distance, they all developed strikingly similar traits: filamentous networks, tough cell walls, and—most tellingly—a shared metabolic toolkit for survival. That toolkit includes genes controlling nutrient uptake, ion regulation, and anabolic metabolism. The researchers identified 166 cases where horizontal gene transfer likely occurred between these groups, with genetic material moving predominantly between fungi and Pseudofungi, and between Labyrinthulea and Teretosporea.
This finding upends a long-held assumption about how evolution works. "Horizontal gene transfer used to be framed as just a peculiarity that happens in bacteria, with eukaryotes passing genes down vertically to their offspring," explains Professor Gergely Szöllősi, who leads the Model-based Evolutionary Genomics Unit at OIST. "Instead, we show that even in eukaryotes, the branches of the tree of life can, and do, exchange genetic material, and those exchanges can allow entirely new ways of making a living to take hold."
The pattern of gene transfers reveals intriguing ecological clues. Szöllősi notes that the genetic "transfer highways" between certain groups may reflect their shared habitats—some inhabit terrestrial environments while others thrive in water—suggesting that proximity and lifestyle created opportunities for genetic exchange.
But significant mysteries remain. Researchers still don't understand the actual mechanisms driving horizontal gene transfer in eukaryotes. Was foreign DNA acquired directly from the environment, or did viruses act as intermediaries? Ocaña-Pallarès, now a Ramón y Cajal research fellow at Universitat Oberta de Catalunya, acknowledges that "the main question is no longer whether horizontal gene transfer takes place in eukaryotes, but how it occurs." The work, published in Nature Ecology and Evolution, has shifted biology's fundamental understanding of inheritance itself—and opened new questions about how life's most crucial functions came to be.