Ancient Gene Exchange May Have Shaped the Evolution of Decomposer Organisms

A researcher at the Institute of Evolution of the HUN-REN Centre for Ecological Research and his colleagues, by analysing a large number of evolutionary trees, revealed how decomposer organisms that are on far-flung branches of the tree of life, such as fungi, can possess genes that provide very similar traits. It turned out that around one billion years ago, the ancestors of these organisms, although they were already only distantly related, exchanged genes with each other. This phenomenon, horizontal gene transfer, is common in bacteria, but rare among organisms with a true cell nucleus, that is, eukaryotes.

According to their nutrition, living organisms can be divided into three large groups. Producers are able to produce organic food from inorganic materials, including, for example, photosynthesising plants; consumers, such as animals, feed on the organic matter produced by producers, but are unable to produce it themselves; and decomposers break down the materials of other dead organisms into simpler components – many fungi are typical examples. These nutritional modes did not appear only once but evolved again and again during evolution in groups that are distant from one another.

We now understand the origin of producers and consumers well. For example, the chloroplast needed for photosynthesis entered the plant cell when an ancient eukaryotic cell engulfed a photosynthesising bacterium but did not digest it; instead, it incorporated it into its own system. This is the endosymbiotic theory. The evolutionary origin of decomposers, however, has not been known until now, even though the abilities required for this nutritional mode also evolved many times, in groups distant from one another. Although these groups are independent of one another in terms of descent, according to the latest discovery by evolutionary biologists, they did not acquire their new traits independently of one another.

Gergely Szöllősi, Senior Research Fellow at the Institute of Evolution of the HUN-REN Centre for Ecological Research, and Associate Professor leading the Model-based Evolutionary Genomics Unit at the Okinawa Institute of Science and Technology, and his colleagues revealed in their research that decomposer organisms acquired the genes required for osmotrophy through horizontal gene transfer.

Decomposer organisms usually feed through osmotrophy, meaning that they absorb the dissolved materials of dead organisms. In the study, the researchers traced the evolutionary history of this nutritional mode. They compared the genomes of four distantly related osmotrophic groups: fungi, Pseudofungi, which may be described as “fungus-like” organisms, Labyrinthulea, and Teretosporea, which are closely related to animals. Although these groups are located at very distant points on the tree of life, they possess very similar traits and abilities. Their cell walls are strong, they grow in a defined direction, they form filamentous networks, and they are unable to feed by engulfment, that is, by phagocytosis.

These organisms emerged at roughly the same time, during the Tonian geological period, between 1,000 and 720 million years ago. If we examine their genomes, we see that their gene repertoires are convergent. In other words, although they are very distant relatives, they nevertheless possess similar genes that enable similar metabolic processes. The main question of the study was where their shared genes may have come from. After tracing back the evolutionary descent of several hundred thousand genes, the researchers found 166 gene families that were very likely transferred from one organism to another through horizontal gene transfer. In such cases, organisms that are only distantly related exchange genes with one another.

Among prokaryotic organisms, which do not have a cell nucleus, such as bacteria, this is a common phenomenon, but among eukaryotes, including fungi, it is very rare according to current knowledge. At the same time, at least one fifth of the genetic toolkit required for osmotrophy is provided by such “borrowed” genes. This suggests that, over the past hundreds of millions of years, gene exchange between eukaryotes that are only distantly related may have been more common than previously suspected.