How gene swapping helped build the planet's decomposers

How gene swapping helped build the planet's decomposers Sadie Harley Scientific Editor Alexander Pol Deputy Editor Decomposers are crucial for keeping Earth habitable, breaking down dead biomass and returning key nutrients, such as carbon, nitrogen and phosphorus, to the ecosystem. Most decomposers, including fungi, survive through osmotrophy—a means of feeding by absorbing dissolved nutrients rather than engulfing prey. But how this method of feeding repeatedly arose across the eukaryotic tree of life remains unclear. Now, researchers from the Okinawa Institute of Science and Technology in Japan, the University of Oxford in the U.K., the Barcelona Supercomputing Center, the Institute of Research in Biomedicine (IRB Barcelona), and the Universitat Oberta de Catalunya in Spain, among other institutions, have reconstructed the deep history of osmotrophic specialization in eukaryotes (organisms with complex cells). Their findings suggest that four groups of eukaryotes that have specialized in osmotrophy first arose between 720 million and 1 billion years ago and that they share a toolkit of genes involved in osmotrophic functions. Their results also indicate that horizontal gene transfer—that is, the process by which genes move from one species to another—played an important role in the evolution of these functions. The paper, published in Nature Ecology and Evolution, adds to the slow shift in how biologists think about how life evolves and how genes are inherited. "Horizontal gene transfer used to be framed as just a peculiarity that happens in bacteria, with eukaryotes passing genes down vertically to their offspring," says 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." Digging deep into the history of decomposers In this research, the team compared the genomes of species within four distantly related osmotrophic groups. Apart from fungi, which is the most well-known and studied of these groups, three other eukaryotic lineages also transitioned toward a specialized osmotrophic lifestyle: Pseudofungi, Labyrinthulea and Teretosporea. "Despite sitting on opposite sides of the eukaryotic tree, a suite of traits has repeatedly evolved in these groups as an adaptation to an osmotrophic lifestyle, including filamentous networks and tough cell walls," says lead author Eduard Ocaña-Pallarès, a former postdoctoral researcher in Szöllősi's unit and now a Ramón y Cajal research fellow at Universitat Oberta de Catalunya. "Importantly, they also share a common metabolic toolkit necessary for osmotrophy, including genes involved in nutrient uptake, ion regulation and anabolic metabolism. We wanted to know where these shared genes came from." By analyzing hundreds of gene trees, the researchers identified 166 cases in which horizontal gene transfer was likely to have occurred between these groups, involving genes mostly related to metabolic functions. In particular, horizontal gene transfer occurred predominantly between fungi and Pseudofungi, and between Labyrinthulea and Teretosporea. "It could be that we see 'transfer highways' between these groups because of their shared terrestrial and aquatic ecology, respectively," Szöllősi suggests. Unanswered questions Looking ahead, the researchers pinpoint important directions for future research, including deciphering the actual function of these shared genes within each group. A further mystery is how horizontal gene transfer happened between these lineages. "For example, was it driven by the acquisition of foreign DNA directly from the environment or through viral intermediates?" says Ocaña-Pallarès. "The main question is no longer whether horizontal gene transfer takes place in eukaryotes, but how it occurs. We still know very little about the mechanisms driving this process in eukaryotes." Publication details Eduard Ocaña-Pallarès et al, Signatures of gene transfer in the parallel evolution of osmotrophic specialization in eukaryotes, Nature Ecology & Evolution (2026). DOI: 10.1038/s41559-026-03054-w Journal information: Nature Ecology & Evolution Provided by Okinawa Institute of Science and Technology