Evolution builds complexity from simplicity, new study finds

Art by Julia Jabur

By Luiz Eduardo Del-Bem

Charles Darwin, a pioneer of evolutionary theory, famously envisioned the diversification of life as a great “tree of life. This tree symbolizes how new species arise from a common ancestor – a root that branches out and connects to other lineages. This view emphasizes vertical inheritance, in which genetic material is passed down through generations, accumulating modifications over time.

In the last century, this view was challenged. In 1928, bacteriologist Frederick Griffith published his now classic experiment demonstrating the ability of bacteria to exchange genes. The significance of the results was difficult to grasp at the time because the physical basis of inheritance—DNA and RNA—was not yet known.

Griffith’s experiment showed that genetic material from disease-causing (pathogenic) bacteria could transform harmless (non-pathogenic) bacteria into ones capable of causing disease. This suggested a novel mechanism of inheritance—horizontal gene transfer—in which genes for pathogenicity could be swapped between different strains, bypassing the need for reproduction.

Gene exchange between organisms was considered rare and limited to bacteria for decades. However, the early 21st century brought new evidence that unicellular eukaryotes (organisms with complex, nucleated cells) could also acquire genes horizontally from other organisms. The implications of this process for multicellular eukaryotes, animals, and plants with diverse, tissue-organized cell types remain a fascinating area of ongoing research.

In February of this year, a partnership between my research group at the Federal University of Minas Gerais (UFMG) and Michigan State University made a groundbreaking discovery. Using sophisticated analyses and comparisons of plant and algal genomes, we published a study with unprecedented findings: plants may have exchanged genes with fungi and bacteria during their evolution. But how did we discover this?

For the past 15 years, I’ve been immersed in the fascinating world of plant biochemistry, studying how plants synthesize and break down carbohydrates. This curiosity was sparked when I realized the sheer dominance of plant carbohydrates, such as cellulose, on our planet.  Land plants, remarkably, contain about 80% of the biosphere’s living matter, with carbohydrates typically making up three-quarters of their dry mass.

This makes sense because photosynthesis, the basis of most life on Earth, converts carbon dioxide into sugars. It’s no exaggeration to say that we live on a planet where sugar molecules, linked in countless combinations, reign supreme.

Our research focused on analyzing the evolution of enzymes that break down plant carbohydrate bonds. We discovered that plants have at least 40 gene types encoding these carbohydrate-cleaving enzymes.  Each gene type exists in numerous copies, demonstrating the importance of this process – a modern flowering plant (angiosperm) devotes over 1% of its entire genome to carbohydrate breakdown.

We knew that when the earliest eukaryotic algae emerged more than a billion years ago, they had a limited set of carbohydrate-splitting enzymes – just a few dozen. Some of these ancient enzymes are associated with the breakdown of starch, a vital energy source throughout the plant lineage. This sparked a burning question: if their distant ancestors had such a limited set of enzymes, how did today’s plants acquire their incredible diversity of carbohydrate-cleaving tools?

To solve this mystery, we compared plant genomes to the vast database of known genomes of diverse organisms. Surprisingly, we found that most of the enzymes missing from early plant ancestors were strikingly similar to those found in bacteria and fungi.

This discovery strongly suggests that horizontal gene transfer from bacteria and fungi played a critical role in shaping the evolution of plant carbohydrate metabolism.  Perhaps the vibrant ecosystems we know today, which rely on plants to capture atmospheric carbon through photosynthesis, wouldn’t exist without this unexpected genetic boost from our microscopic bacterial and fungal neighbors.

We hypothesize that most of these gene transfers occurred when plants’ unicellular algal ancestors colonized the land. In these microscopic terrestrial ecosystems, they would have lived alongside fungi and bacteria. Amazingly, today’s towering forests may have descended from these ancient microforests—a world where algae acquired genes from the microbes around them.

This groundbreaking discovery suggests that the complex cellular capabilities of modern eukaryotes may have arisen from the repeated acquisition of genes from different microorganisms. In other words, these organisms may have “borrowed” essential genes throughout their evolution to become what they are today.

Contrary to Darwin’s 19th-century vision, life evolves not simply as a tree, but as an intricate web in which distant branches intertwine unexpectedly through gene exchange. This process of acquiring genes from diverse sources may have been a driving force behind the leap from microscopic, single-celled life to the complex organisms we see today—even humans.

Perhaps we are discovering that complexity results from many simple things coming together. Deep within plants lies DNA from the fungi and bacteria that helped shape our planet—a world where our primate ancestors evolved, jumping from branch to branch like genes on the tree of life.

This text was originally publicated on Serrapilheira’s Ciência Fundamental blog on Folha de S.Paulo