As the world turns to green hydrogen and other renewable energy sources, scientists have discovered that archaea – the third life form after bacteria and eukaryotes – have been making energy for billions of years using hydrogen gas and ‘ultra-minimal’ enzymes.
Specifically, the international team of researchers found that at least nine phyla of archaea, a domain of single-celled organisms without internal membrane-bound structures, produce hydrogen gas using enzymes thought to be found only in the other two life forms.
Archaea, they realized, not only have the smallest hydrogen-consuming enzymes compared to bacteria and eukaryotes, but their enzymes for consuming and producing hydrogen are also the most complex yet.
These small and mighty enzymes have seemingly enabled archaea to survive and thrive in some of the most hostile environments on Earth, where little to no oxygen is found.
“People have only recently started thinking about using hydrogen as an energy source, but Archaea have been doing this for a billion years,” said Pok Man Leung, a microbiologist at Monash University in Australia who co-led the study.
“Biotechnologists now have the opportunity to take inspiration from these archaea to produce hydrogen industrially.”
Hydrogen is the most abundant element in the universe and is used worldwide to make fertilizers and other chemicals, treat metals, process food and refine fuels.
But the future of hydrogen lies in energy storage and steel production, which could be produced emission-free if renewable energy is used to convert materials such as water into hydrogen gas.
Micro organisms produce and release hydrogen gas (H2) for entirely different purposes, mainly to carry off excess electrons produced during fermentation, a process in which organisms obtain energy from carbohydrates such as sugars without oxygen.
Enzymes used for the consumption or production of H2 are called hydrogenases, and it was only eight years ago that they were extensively studied for the first time throughout the tree of life. Since then, the number of known microbial species has exploded, especially archaea, which lurk in extreme environments such as hot springs, volcanoes and deep-sea vents.
However, most archaea are only known thanks to parts of their genetic code found in these environments, and many of them have not been grown in the laboratory because it is very difficult to do so.
That’s why microbiologist Chris Greening and colleagues at Monash University looked for the gene that codes for part of one type of hydrogenase, a fast-acting [FeFe] hydrogenases, in more than 2,300 clusters of archaeal species included in a global database.
They then instructed Google’s AlphaFold2 to predict the structure of the encoded enzymes, and expressed those enzymes in E.coli bacteria, to check whether those genes were actually functional and produced hydrogenases that could catalyze hydrogen reactions in their surrogate host.
“Our finding brings us one step closer to understanding how this crucial 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.
It is believed that all eukaryotes emerged from the union of an anaerobic archaea and a bacterium that swallowed it billions of years ago. A second, much later endosymbiosis then led to the ancestor of plants, with chloroplasts.
Greening, Leung and their colleagues found the genetic instructions for [FeFe] hydrogenases in nine archaeal phyla and confirmed that they are indeed active in those microorganisms – making them three of the three domains of life that use these types of enzymes to make hydrogen.
But unlike bacteria and eukaryotes, further analyzes showed that archaea assemble ‘remarkable hybrid complexes’ for their hydrogen production needs, fusing two types of hydrogenases together.
“These findings reveal novel metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2metabolize enzymes,” the team writes in their article.
However, many of the cataloged archaea genomes analyzed in this study are incomplete, and who knows how many species remain to be discovered.
It’s more than likely that Archaea harbors other ingenious ways to make energy that we have yet to find.
The research was published in Cell.