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Evolution of Physiology: The link between Earth and Life

Periodic Reporting for period 2 - EvolPhysiol (Evolution of Physiology: The link between Earth and Life)

Reporting period: 2020-08-01 to 2022-01-31

As humans, we wonder about our history. We wonder how, at a certain place and a certain time, life arose within a lifeless planet. From that time on, life has evolved to reach today’s levels of biodiversity, in where microbes have learned a multitude of different ways to get nutrients from their surroundings and survive. However, the exact ways microbes nowadays explore the environment in terms of how they conserve their energy and obtain nutrients from the surroundings are highly diverse, and still not fully understood. From an evolutionary point, it is clear that all of this diversity did not arise at once. Thus, stepwise transitions, from simpler to more complex energy harnessing solutions, must have existed. While phylogenetic trees based on universal genes can be generated for thousands of lineages at a time, they do not represent the genome as a whole. Moreover, backbone tree based approaches assume that genes within genomes tend to share the same evolutionary history. It is becoming increasingly clear that the evolution of microbial traits, the evolution of bioenergetics processes, is decoupled from the evolution of ribosomal lineages, mainly due to Lateral Gene Transfer (LGT).

The goal of this project is to better understand how microbes harness energy from their environment, how they learned to use new ones, and how this process unfolded during microbial evolution. This will involve large-scale comparative phylogenetic analysis of genes involved in, and genomically associated with, energy-harnessing systems combined with experimental data, using as evolutionary constraints geochemical records of available environmental energy sources.
A database containing publicytly available information regarding growth conditions of isolated organisms was collected and is being analysed. In addition, over 195 thousand publicicly available genomes were downloades and filtered for comtamination and completeness. These genomes are at the basis of all phylogenetic analysis regarding the evolution of the different building blocks of metabolic pathways. Several selected traits are being analysed in terms of taxonomic distribution as well as evolutionary history. Of note, the combination of experimental and bionformatics analyses lead us, in collaboration with experts in the field, to identify a new complex involved in sulfate reduction within Vulcanisaeta, and archaeal lineage isolated in Russia.
The expected outcome of this proposal will be not only the characterization of extant microbial diversity but also how bioenergetics systems have evolved over time. In particular, we envision the following major results from this project: i) the characterization of extant microbial energy-conservation solutions in terms of diversity and chimerism; the evolution of ii) major
energy-harnessing traits; iii) and of pathways associated with them; iv) the identification and evolution of the finite
modules in biology; and v) the establishment of an order of events within microbial physiological evolution leading to a fuller understanding of life’s history.

Independent of the final outcome, the results from this project will strengthen the ties between geochemistry and microbiology, and hence stimulate the dialogue across disciplines to further our understanding of Life – a subject that attracts the interest from both researchers and the society in general.
Microbial diversity from genomes