New Research Suggests Independent Origins of Life for Bacteria and Archaea

A study led by biologists at the Institute of Molecular Evolution at Heinrich Heine University Düsseldorf (HHU) has unveiled significant insights into the origins of life on Earth. Published in Science Advances, the research explores the chemical reaction networks utilized by the earliest living cells and the energy sources that powered these reactions. Evidence suggests that free-living cells may have emerged independently for bacteria and archaea.

Approximately 4 billion years ago, as Earth transitioned into a habitable environment, two distinct forms of primitive cellular life, pioneer bacteria and archaea, began to emerge. “We would see two very different kinds of cells emerging, pioneer bacteria and pioneer archaea, making their first attempts at life outside the confines of a hydrothermal vent,” stated Natalia Mrnjavac, the lead author of the study.

The research team examined genomes, protein structures, and chemical reactions to investigate early microbial evolution, particularly the time before fully free-living cells existed. William Martin, a senior author of the study, remarked, “These comparisons are giving us unprecedented insights into the phase of evolution when metabolism catalyzed by enzymes was arising from spontaneous reactions catalyzed by metals in the Earth’s crust.”

Reconstructing the Early Metabolism

The researchers focused on a full array of chemical reactions essential for cells to manufacture fundamental biological components like amino acids, RNA bases, and vitamins. This metabolic network consists of 420 interconnected reactions derived from materials available on early Earth, including hydrogen gas, ammonia, and CO2.

What stood out in the findings was the lack of evolutionary conservation of enzymes responsible for these reactions between bacteria and archaea. Martin noted, “The surprise is that the enzymes that catalyze those reactions are not conserved across the evolutionary divide that separates bacteria and archaea. We found that the last universal ancestor of all cells, LUCA, possessed enzymes for only about half of the reactions of metabolism, while the other half was catalyzed by metals.”

This suggests that early metabolism was more dependent on environmental conditions compared to modern cellular metabolism. Harun Tüysüz, an inorganic chemist and co-author, added, “Metals that naturally occur in hydrothermal vents can replace a surprisingly large number of enzymes in metabolism.”

The Evolution of Catalysis

The research reconstructed four stages in the early evolution of biological catalysis, beginning with metal-driven reactions followed by a stage where metals and enzymes worked in tandem. As evolutionary paths diverged for bacteria and archaea, newly evolved enzymes gradually replaced environmental inorganic catalysts.

The study revealed instances of parallel evolution where both lineages developed distinct enzymes for the same metabolic reactions. Mrnjavac pointed out, “These parallel inventions could have paved the way to the independent emergence of free-living bacteria and archaea.” This evolutionary independence possibly enabled the two groups to thrive away from the dependency on hydrothermal vent chemistry.

Energy Sources for Early Metabolism

Crucial to the study was understanding energy supplies before the advent of ATP-based metabolism. Manon Schlikker from the Düsseldorf team identified palladium, a naturally occurring metal in hydrothermal vents known for its catalytic properties, as a potential energy source for early cells. The team discovered that phosphite, found in these vents, can react with organic compounds in the presence of palladium, facilitating metabolic phosphorylation reactions without the need for ATP.

Schlikker explained, “When we react phosphite with organic compounds, we get metabolic phosphorylation reactions overnight in water. It’s amazing, and it makes early evolution a lot easier to grasp.” This finding provides a plausible mechanism for how early metabolic processes might have obtained the necessary energy to function.

Implications for Understanding Life’s Origins

This research marks the first comprehensive study of the complete metabolic reaction network. The results show that while all living organisms may share one genetic code, the emergence of life forms—bacteria and archaea—occurred through two independent trajectories. Martin emphasized, “The new data leave only one conclusion: the bacterial and archaeal lineages made the transition to the free-living state independently.”

The international research team included scientists from various institutions, including the Universities of Canterbury, Rostock, Constance, Ottawa, Strasbourg, and Tübingen, as well as the Max-Planck Institute for Terrestrial Microbiology in Marburg and the IMDEA Materials Institute in Madrid.