Le GDR3692 organise

avec le soutien de l'Université de Nantes

Webinar : Microbial Horizontal Evolution

Thursday June 10th, 2 to 4 pm
Organizers : Samuel Chaffron and Damien Eveillard (LS2N Université de Nantes)

Program: 3 webinars and then a roundtable

Registration at https://forms.gle/7TRqenzFKxeduJtk6

The continuous accumulation of (environmental) genomics data accompanied with recent computational developments allow us to gain a more comprehensive understanding of the promiscuous role of mobile genetic elements (MGE) and horizontal gene transfer (HGT) in shaping prokaryotic genomes, across space (ecology) and time (evolution), in various habitats. This webinar dedicated to microbial horizontal evolution will showcase three presentations highlighting recent and exciting research advances in the field, followed by a short open discussion with all attendees, on the magnitude and scales of microbial horizontal evolution in the wild.

Dr. Thomas Hackl Max Planck Institute for Medical Research, Heidelberg, Germany
Tycheposons - novel mobile genetic elements abundant in marine viruses and vesicles shape Prochlorococcus' genomic plasticity

Horizontal gene transfer accelerates microbial evolution, promoting diversification and adaptation. The globally abundant marine cyanobacterium Prochlorococcus has a highly streamlined genome with frequent gene exchange reflected in its extensive pangenome. The source of its genomic variability, however, remains elusive since most cells lack the common mechanisms that enable horizontal gene transfer, including conjugation, transformation, plasmids and prophages. Examining 623 genomes, we reveal a diverse system of mobile genetic elements – cargo-carrying transposons we named tycheposons – that shape Prochlorococcus ’ genomic plasticity. The excision and integration of tycheposons at seven tRNA genes drive the remodeling of larger genomic islands containing most of Prochlorococcus ’ flexible genes. Most tycheposons carry genes important for niche differentiation through nutrient acquisition; others appear similar to phage parasites. Tycheposons are highly enriched in extracellular vesicles and phage particles in ocean samples, suggesting efficient routes for their dispersal, transmission and propagation. Supported by evidence for similar elements in other marine microbes, our work underpins the role of vesicle- and virus-mediated transfer of mobile genetic elements in the diversification and adaptation of microbes in dilute aquatic environments – adding a significant piece to the puzzle of what governs microbial evolution in the planet’s largest habitat.

Dr. Olaya Rendueles Garcia, Institut Pasteur, France

The capsule: The best defense is not always a good offense

Extracellular capsules constitute the outermost layer of some bacteria and establish the first contact between the cell and its environment. Capsules are best known for their role in clinical settings, where they increase survival upon phagocytosis by eukaryotic cells and lower the sensitivity to antibiotics. They are thus considered a major virulence factor. Capsules evolve fast by horizontal gene transfer, but paradoxically, it has often been proposed that capsules hinder the transfer of genetic information between cells, presumably because they constitute a physical barrier to DNA acquisition, and thus limit adaptability.
In our lab, we combine experimental and computational approaches to understand how the capsule evolves, and how it influences species adaptation and evolution by altering the rates of horizontal gene transfer. We first developed a computational tool to identify capsules in genomes. This allowed us to show that bacteria encoding capsules are better colonizers and are dominant in most environments. We then analysed thousands of bacterial genomes for the evidence of an association between genetic exchanges (or lack thereof) and the presence of a capsule system. This challenged the established paradigm that capsules limit gene transfer and showed that bacteria with capsule systems are more genetically diverse, carry more mobile genetic elements and have fast-evolving gene repertoires, which may further contribute for their success in colonizing novel niches. As an experimental model, we use K. pneumoniae, a gram-negative bacterium belonging to the Enterobacteriaceae family and considered an opportunistic pathogen and a major multi-drug resistant (MDR) bacterium. We specifically address the metabolic costs and benefits of the capsule in diverse environments and the mechanisms by which it evolves. Further, our work suggests that the capsule drives gene flux by differential interactions with mobile genetic elements such as phages and plasmids. Taken together, our work highlights that the capsule is a keystone cellular structure that drives adaptation at all evolutionary time scales. 

Dr. Jesse Shapiro, McGill University, Canada
Pangenome evolution on human time scales

A pangenome is the total set of genes encoded by all members of a species or population. In bacteria, pangenomes can be orders of magnitude larger than an individual genome size, due to extensive gene mobility by horizontal gene transfer (HGT). It is actively debated to what extent mobile gene evolution (and resulting pangenome structure) is shaped by selection (niche adaptation) or drift (neutral evolution). I have recently suggested that this controversy can be resolved by explicitly considering natural selection at the level of the gene versus at the level of the genome. Crucially, whether mobile genes are considered ‘adaptive’ or not depends on the time scale considered. For example, we have identified very recent horizontal gene transfer (HGT) events into Vibrio cholerae from other species in the human gut microbiome. Most of these events are likely only a few days old, since cholera infections are very short. Some of these HGT events may be adaptive within an infection (e.g. modulating biofilm formation) but are likely maladaptive over long time scales – since they are never observed in other patients. Building upon these results, I will describe an analysis of mobile genes in the healthy human gut to test whether global patterns of mobile gene evolution (i.e. over millions of years of evolution, and without ecological context) also hold over short evolutionary time scales, among genes and genomes that are ecologically connected in the same environment. To do so, we used public microbiome data estimate to ask how mobile gene evolution (i.e. census and effective population size) is driven by the human host, the mobile gene family, or the bacterial host genome, and discuss the implications for our models of the population genetics of pangenomes.

video here