As the world turns to green hydrogen and other renewable energy sources, scientists have discovered that archaea – the third form of life after bacteria and eukaryotes – have been producing energy using hydrogen gas and “ultraminimal” enzymes for billions of years.
Specifically, an international team of researchers found that at least nine strains of archaea, a domain of single-celled organisms lacking internal membrane-bound structures, produce hydrogen gas using enzymes thought to exist only in the other two forms of life.
They realized that Archaea not only have the smallest hydrogen-using enzymes compared to bacteria and eukaryotes, but their hydrogen consumption and production enzymes are also the most comprehensively characterized yet.
These small and powerful enzymes appear to have enabled archaea to survive and thrive in some of Earth’s most hostile environments, where there is almost no oxygen.
“People have only recently started thinking about using hydrogen as an energy source, but archaea have been doing it for a billion years,” says Pok Man Leung, a microbiologist at Monash University in Australia who led the study.
“Biotechnologists now have the opportunity to draw inspiration from these archaea for the industrial production of hydrogen.”
Hydrogen is the most abundant element in the universe and is used worldwide to make fertilizers and other chemicals, to treat metals, process food and refine fuels.
However, the future of hydrogen lies in energy storage and the production of steel, which could be produced with zero emissions if renewable energy was used to convert materials such as water into hydrogen gas.
Microorganisms produce and release hydrogen gas (H2) for entirely different purposes, mainly to dispose of excess electrons produced during fermentation, the process by which organisms extract energy from carbohydrates such as sugars in the absence of oxygen.
Enzymes used to consume or produce H2 are called hydrogenases and were first comprehensively explored across the tree of life only eight years ago. Since then, the number of known microbial species has exploded, especially archaea that hide in extreme environments such as hot springs, volcanoes, and deep-sea vents.
However, most archaea are known only from parts of their genetic code found in these environments, and many have not been cultured in the laboratory because it is very difficult.
So microbiologist Chris Greening of Monash University and his colleagues looked for a gene encoding part of one type of hydrogenase, a fast-acting [FeFe] hydrogenases, in more than 2,300 clusters of archaeal species listed in the worldwide database.
They then tasked Google’s AlphaFold2 with predicting the structure of the encoded enzymes and expressed these enzymes in E-coli bacteria to verify that these genes were indeed functional and produced hydrogenases capable of catalyzing hydrogen reactions in their surrogate host.
“Our findings bring us one step closer to understanding how this fundamental process gave rise to all eukaryotes, including humans,” says Leung.
Eukaryotes are organisms whose cells contain a nucleus and membrane-bound organelles such as mitochondria and other useful cellular factories.
All eukaryotes are thought to have arisen from the fusion of anaerobic archaea and bacteria that it engulfed billions of years ago. A second, much later endosymbiosis then gave rise to the ancestors of plants with chloroplasts.
Greening, Leung and their colleagues found the genetic instructions [FeFe] hydrogenases in nine archaeal strains and confirmed that they are indeed active in these microorganisms—three of the three areas of life that use these kinds of enzymes to produce hydrogen.
But unlike bacteria and eukaryotes, further analysis showed that archaea assemble “remarkable hybrid complexes” for hydrogen production needs, linking two types of hydrogenases together.
“These findings reveal novel metabolic adaptations of archaea, simplified by H2 catalysts for biotechnological development and the surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes,” the team writes in their paper.
However, many of the cataloged archaea genomes analyzed in this study are incomplete, and who knows how many more species are yet to be discovered.
It is more than likely that archaea harbor other ingenious methods of energy production that we have yet to find.
The research was published in Cell.