Microbial evolution provides clues on history of life
Microbes play a critical role in ecosystems and human health and have evolved over time in order to thrive. Major advances in sequencing techniques are now providing a wealth of data on the diversity of microbial life, providing insights into how they function and how they have evolved. “A key question is how they produce and conserve energy,” explains EvolPhysiol project coordinator Filipa Sousa(opens in new window) from the University of Vienna(opens in new window). “While computers run on electricity, living things use ATP (adenosine triphosphate, the primary energy-carrying molecule in cells).” Humans produce ATP by breathing oxygen. Some microbes however have developed mechanisms to produce ATP not only from oxygen, but from other sources such as sulfur and nitrogen.
Getting inside microbes
The EvolPhysiol project, supported by the European Research Council(opens in new window), sought to study the ways in which microbes have learned to produce ATP, and how this has evolved over time. The project focused in particular on archaea and bacteria, two groups of single-celled microorganisms that are known to be everywhere. “Our key objective was to get insights on these microbes,” says Sousa. “We wanted to understand the global diversity of microbes today and then go back in time.” The project built on the fact that biology is highly modular. “At different levels, life is often made up of building blocks, like Lego,” adds Sousa. “Proteins, say, can be reorganised to build different things. This allows for different functions, and for organisms to deal with different compounds.” The project team also ‘looked’ inside proteins to identify cofactors that are frequently reused by organisms. “This means that when they evolve, they don’t have to invent everything from scratch,” explains Sousa.
Large genomic databases and sequences
The project dealt with thousands of genomes. Large genomic databases were filtered for quality, and sequences compared to find proteins. “The fun part was trying to make sense out of all this data, while taking into account biological and geological considerations,” says Sousa. This work unearthed some very unexpected results, for example regarding the sulfur cycle. The standard consensus was that archaeoglobus must have received this functionality from bacteria. “While we identified that a key enzyme involved in the sulfur cycle was probably from bacteria, the rest of the pathway was a result of synonymous replacement (a change in the DNA sequence in which the produced amino acid sequence is not modified),” notes Sousa.
Identification of new biotech applications
The sheer amount of data generated meant that the project team was unable to look through everything, and several aspects of the project, such as microbial diversity, are ongoing. “Continuing our quest to see the evolution of these building blocks is the direction in which I want to continue,” remarks Sousa. “I think it is in our human nature to know where we came from.” Sousa points out that our planet – estimated to be around 4.5 billion years old – was once populated only by archaeal bacteria. Understanding how these microbes co-evolved with the environment can tell us a great deal about our distant past, and also perhaps benefit our future through the identification of new biotech applications. “The more we know about them, the more we can use them in our favour,” she adds.
