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Horizontal Gene Transfer (HGT) is a powerful force generating genomic diversity in bacterial populations. HGT in Streptomyces is in large part driven by conjugation thanks to plasmids, Integrative and Conjugative elements (ICEs) and Actinomycete ICEs (AICEs). To investigate the impact of ICE and AICE conjugation on Streptomyces genome evolution, we used in silico and experimental approaches on a set of 11 very closely related strains isolated from a millimeter scale rhizosphere population. Through bioinformatic searches of canonical conjugation proteins, we showed that AICEs are the most frequent integrative conjugative elements, with the central chromosome region being a hotspot for integrative element insertion. Strains exhibited great variation in AICE composition consistent with frequent HGT and/or gene loss. We found that single insertion sites can be home to different elements in different strains (accretion) and conversely, elements belonging to the same family can be found at different insertion sites. A wide variety of cargo genes was present in the AICEs with the potential to mediate strain-specific adaptation (e.g., DNA metabolism and resistance genes to antibiotic and phages). However, a large proportion of AICE cargo genes showed hallmarks of pseudogenization, consistent with deleterious effects of cargo genes on fitness. Pock assays enabled the direct visualization of conjugal AICE transfer and demonstrated the transfer of AICEs between some, but not all, of the isolates. Multiple AICEs were shown to be able to transfer during a single mating event. Although we did not obtain experimental evidence for transfer of the sole chromosomal ICE in this population, genotoxic stress mediated its excision from the chromosome, suggesting its functionality. Our results indicate that AICE-mediated HGT in Streptomyces populations is highly dynamic, with likely impact on strain fitness and the ability to adapt to environmental change.

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The genomes of five Streptomyces strains belonging to the same soil community were sequenced and assembled. The strains, which were isolated at microscale, belonged to different Streptomyces species. This sample provides access to understand the functioning of a Streptomyces community in an ecological context.

The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.

Streptomyces are rhizospheric bacteria that contribute to soil fertility (recycling of organic matter), plant growth and health. They have among the largest bacterial genomes (12 Mb) with a high genetic variability. The genome variability, observed at the interspecific level has never been addressed within a population, i.e. between sympatric individuals belonging to the same species (Conspecific strains) within the same ecological niche. The objective of this work was to investigate this diversity in the forest soil ecosystem, to estimate its dynamics and its potential functional roles. After sequencing and comparison of the complete genomes, we observed a wide genomic diversity in terms of size, presence/absence of extrachromosomal elements, but also in terms of presence/absence of genes along the chromosome. A large number of insertion and deletion events (indels) from 1 to 241 genes differentiate individuals in the population. Given the close phylogenetic relationship of these strains, the common ancestor of the population is recent, hence the genomic diversity would result from a massive and rapid gene flux. The high prevalence of integrative and conjugative elements in the population suggests that conjugation could act as a driving force of this diversity. Differential production of specialized metabolites (antibiotics) was also used to estimate the impact of genetic diversity on population’s ecology. We were able to show that this production was linked to strain specific genes and that it may constitute a « public good » for the population. We propose that the rapid evolution of the genome contributes to the maintenance of social cohesion mechanisms within these soil bacteria., Les Streptomyces sont des bactéries de la rhizosphère qui contribuent à la fertilité des sols (recyclage de la matière organique), et à la croissance et la santé des plantes. Elles possèdent parmi les plus grands génomes bactériens (12 Mb) et présentent une variabilité génétique importante. Cette variabilité connue au niveau interspécifique n’a jamais été abordée à l’échelle de la population, c’est-à-dire entre individus sympatriques appartenant à la même espèce (souches sœurs) au sein de la même niche écologique. L’objectif de ce travail est de rechercher cette diversité dans les populations de l’écosystème sol forestier, d’approcher sa dynamique et son rôle fonctionnel. Après séquençage et comparaison des génomes complets, nous avons observé une grande diversité génomique en termes de taille, de présence/absence d’éléments extrachromosomiques, mais également en terme de présence/absence de gènes le long du chromosome. Un grand nombre d’événements d’insertions et délétions (indels) comprenant de 1 à 241 gènes différencient les individus de la population. Au vu des liens phylogénétiques étroits entre les individus, l’ancêtre commun de la population est récent, aussi la diversité génomique résulterait d’un flux massif et rapide de gènes. La forte prévalence d’éléments conjugatifs intégrés dans la population suggère que la conjugaison est le moteur prépondérant de cette diversité génomique. La production différentielle de métabolites spécialisés (antibiotiques) a également été utilisée pour estimer l’impact de la diversité génétique sur le fonctionnement de la population. Nous avons pu montrer que cette production était liée à des gènes spécifiques de souches et qu’elle pouvait constituer un bien commun pour la population. Nous proposons que l’évolution rapide du génome participe au maintien des mécanismes de cohésion sociale chez ces bactéries du sol.

The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting the same ecological niche, were sequenced and assembled. This data set offers an ideal framework to assess the genome evolution of Streptomyces species in their ecological context.

International audience; IntroductionAs for plants or animals, the microbes form populations that consist of interacting individuals from the same species. This level of organisation is an operating unit able to respond to biotic stresses coming from other ecological co-inhabitants such as microbes or plants. The sum of these interactions (often occurring at the cellular level) drives responses and ecological traits at higher scales such as in the forest ecosystem. QuestionThe global aim of this project is to assess how a microbial population affects its biotic co-inhabitants in a forest soil and how in return these latter influence the dynamic of the bacterial population. In this study, we focused on this last point and investigated the genomic diversity of a Streptomyces population isolated from grains of rhizospheric soil. ResultsWe selected strains that could be considered as clones, sequenced and compared their genomes. We showed that their genomes presented an unexpectedly large set of variable genes (ca. one third of the population pangenome) indicating that this population had a great evolvability over a short evolutionary time. We showed that this rapid genome dynamics (massive gene fluxes fuelled by mobile genetic element mobility) in bringing different functions in individuals of the population, can help to its functioning. For instance, some metabolites produced by some individuals provide advantage to non-producing conspecifics (public good) in biotic competition. ConclusionThese massive gene fluxes do not occur at long-term evolutionary time but at a scale enabling the population response to environmental changes. This tremendous capacity of evolvability appears as a key factor to favour resilience of the e

International audience; Like for animals, the plant microbiota has a key role on the tree health in participating, for instance, to their growth or their protection against pathogens. Generally, the more a microbiota is diverse, the more efficient it is for its host. Some results suggest that an organisation level of this diversity could be the bacterial population that is composed of interacting sister strains with different capabilities. These variable functions, linked to the genetic diversification of the population, could enable a share of labour and create synergic actions in the niche. In return, the root exudates could affect the microbiota in increasing the frequency of gene transfer and consequently the emergence of new functions within the population. To compare the influence and the efficiency of Streptomyces populations (that belong to root microbiota) in comparison with single isolates for functions in link with the health and the growth of plants. To measure the rhizosphere effect on gene transfer events and their consequences on the diversification of a Streptomyces population.Natural Streptomyces populations are already available. They will be tested in interaction with root systems or in devices mimicking the rhizosphere for the direct or indirect growth of model plants (root development, mineral solubilisation, pathogen inhibition) and the transfer of mobile genetic elements.This project will bring a better comprehension of the ecological functioning of the root microbiota. Firstly, it will enable to define the synergic role of the bacterial population in plant-bacteria interactions and notably for the plant health. Secondly, it will enable to assess the rhizosphere influence on its microbiota and its role on the functional diversification of bacteria.Key words: Microbial population, whole genome comparison, gene transfer, plant response

International audience; La dynamique du génome est cruciale pour son évolution et son adaptation. En comparant les génomes d'une même espèce de Streptomyces issus d'une population sympatrique, nous avons mis en évidence que ces phénomènes de diversification étaient nombreux et rapides et pouvaient impacter le fonctionnement écologique de la population. Un plan d'échantillonnage a été mis en place afin d'obtenir des souches dérivant d'un ancêtre commun proche et avec une histoire évolutive commune récente. Pour ce faire, des Streptomyces ont été isolés à partir de micro agrégats (mm 3) d'un même sol sur une distance maximale de quelques cm. Des souches ont ensuite été sélectionnées pour leur grande proximité taxonomique au niveau intra-spécifique, c'est à dire sur la base de séquences identiques pour le gène codant l'ARNr 16S et un degré élevé de similitude en MLST. Le séquençage du génome de 18 souches de cette population a permis de montrer qu'elles possédaient un chromosome linéaire d'environ 11,7 Mb. La comparaison de leur séquence a révélé une diversification importante au sein de la population avec au moins 25 îlots génomiques (> 10 kb) dispersés le long du chromosome, mais avec toutefois une variabilité plus élevée dans les régions terminales et pouvant dans certains cas affecter l'extrémité chromosomique. En outre, certains isolats divergeaient également par la présence de grands plasmides (100 à 400 kb). Certaines de ces régions variables présentaient des signatures claires d'éléments conjugatifs intégrés, tandis que d'autres comprenaient des gènes de biosynthèse de métabolites secondaires. Au niveau fonctionnel, l'étude comparée des profils d'inhibition des souches de la population a permis de mettre en évidence des différences entre les isolats. Ainsi, certains sont capables d'inhiber des bactéries d'autres genres provenant du même sol et d'autres non. Toutefois, toutes les souches de la population de Streptomyces étaient capables de se développer ensemble, suggérant que les activités inhibitrices fournies par les souches productrices constitueraient des « biens publics » pour l'ensemble de la communauté de Streptomyces. L'inactivation d'un gène appartenant à un cluster de métabolite secondaire (NRPS) spécifique aux souches inhibitrices a permis d'abolir cette activité, amenant une preuve de concept que la dynamique rapide du génome impacte l'écologie de la population et ce notamment par la différenciation du répertoire de gènes du métabolisme secondaire L'ensemble de nos résultats confirment l'hypothèse selon laquelle le haut niveau d'évolutivité du génome de Streptomyces affecte la structuration et l'adaptation des communautés bactériennes dans leur environnement naturel.

International audience; Genome dynamics is crucial for bacterial genome evolution and adaptation. Here we reveal the unexpectedly fast genome diversification occurring within a highly genetically cohesive population of soil bacteria Streptomyces. We applied a reverse ecology sampling strategy in order to isolate sympatric Streptomyces that have diverged within a short evolutionary time. For this purpose, we isolated bacteria from rhizospheric soil aggregates in the range of mm3 size and distant at the centimeter scale. We selected isolates that shared 100% of identity in 16S rRNA sequences and presented a high degree of similarity in MLST and ANI genome comparisons. We concluded that the isolated strains were all highly related at the intra-specific level and according to the sampling scheme should derive from a common ancestor over a very short evolutionary time. By comparing the genome sequences of 18 isolates (genome size ca. 11.7 Mb), we identified at least 25 genomic islands (>10 kb) scattered along the chromosome, but with a higher frequency in the terminal regions of the linear chromosome, including in some cases the chromosomal end. Some of them exhibit clear signatures of integrated and conjugative elements, while some other include secondary metabolite biosynthetic genes. In addition, some isolates also diverge by the presence of large plasmids (100 to 400 kb). Different patterns of inhibitory capacities were distinguished within the population. Hence, while only some Streptomyces isolates exhibited inhibitory activities against other bacterial coinhabitants (e.g. Bacillus), all the Streptomyces strains could develop together. This suggests that inhibitory activities provided by some isolates may constitute ‘public goods’ to the Streptomyces community, and this by the mean of differentiation of the secondary metabolism gene repertoire. As a proof of concept that rapid genome dynamics impacts population ecology, we inactivated a biosynthetic gene cluster gene (i.e. NRPS) specific of one inhibitory strain and observed the abolition of the inhibitory activity. Together our data support the hypothesis that the high level of evolvability of the Streptomyces genome impacts structuring and adaptation of natural bacterial communities.