The environment drives microbial trait variability in aquatic habitats

A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes

Représentation graphique à l'aide de l'outil Circos des données d'expression de gènes de type RNAseq. Application au peuplier

il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATIONLe peuplier de l'Ouest ou Populus trichocharpa a vu son génome séquencé depuis 2006, son annotation structurale et fonctionnelle reste quand à elle encore en constante évolution. Une croissance rapide ainsi qu'un petit génome et une importance économique sont autant de qualités qui font du peuplier un bon modèle pour l'étude des arbres forestiers et fruitiers à intérêt agronomique. Aujourd'hui les techniques de séquençages à très haut débits facilitent l'étude de l'expression des gènes jusqu'au génome entier. C'est en identifiant et caractérisant ces gènes, qu'il devient alors envisageable de définir des profils d'expression qui permettront par la suite d'étudier la réponse de l'organisme à son environnement. Le présent rapport expose les différentes étapes qui ont permis la représentation graphique à l'aide de l'outil Circos de données d'expression de gènes de types RNAseq chez le peuplier pour des individus soumis ou non à un stress hydrique. Étant donné que les résultats expérimentaux du PIAF ne sont pas encore sortis au moment de mon stage, un jeux de données similaires est utilisé ici, tiré de la publication de Cossu et al., 2014

Écologie des bactéries symbiotiques associées aux coraux et corallinales de l'Océan Pacifique : du génome à la communauté

Les récifs coralliens tropicaux dépendent de communautés microbiennes complexes qui régissent les cycles biogéochimiques, maintiennent la santé des hôtes et soutiennent l'homéostasie de l'écosystème. Il est essentiel de comprendre l'écologie complexe des microorganismes des récifs coralliens pour préserver ces précieux écosystèmes. Cependant, le rôle fonctionnel précis des communautés microbiennes des récifs reste mal connu. En particulier, l'association entre les coraux et les bactéries de la famille des Endozoicomonadaceae, considérée comme un symbiote bactérien crucial pour les coraux, n'est toujours pas bien définie. Les micro-organismes tels que les Endozoicomonadaceae semblent essentiels à la survie de l'hôte corallien adulte, mais l'installation des larves est un autre élément important pour la santé des coraux. Il a récemment été démontré que le succès du recrutement des larves dépendait des algues calcaires encroutantes (CCA) sur lesquelles elles s'installent. Plus précisément, les communautés microbiennes associées aux CCA peuvent jouer un rôle crucial, mais nous savons très peu de choses sur ces communautés. Les objectifs généraux de cette thèse étaient d'étudier la diversité des espèces et le potentiel fonctionnel des communautés microbiennes associées aux coraux tropicaux et aux CCA. Le chapitre 2 s'est concentré sur les Endozoicomonadaceae associées à trois espèces de coraux dans l'océan Pacifique. Il a révélé que différentes espèces de coraux présentent des stratégies distinctes de relations hôte-symbionte. Nous avons identifié trois nouvelles espèces de symbiotes, chacune présentant des adaptations fonctionnelles distinctes qui peuvent être à l'origine de la relation hôte-symbiote. L'environnement n'a généralement qu'un faible effet sur la composition de la communauté d'Endozoicomonadaceae, tandis que la lignée génétique de l'hôte est importante pour certains coraux. Nous suggérons que la relation entre les Endozoicomonadaceae et le corail peut aller de relations stables de co-dépendance à des associations opportunistes. Dans le chapitre 3, nous avons décrit les communautés microbiennes associées à différentes espèces de CCA à travers des échelles spatiales et défini les facteurs contrôlant leur composition. Nous avons également vérifié s'il existait des liens entre les communautés microbiennes de la CCA et des larves de corail. Nos résultats suggèrent que le microbiome des algues de la CCA n'agit pas comme un réservoir microbien pour les larves de corail en développement. Cependant, nous avons observé que les communautés microbiennes des recrues coralliennes différaient en fonction de leur association avec différents types d'algues. Nous concluons que les CCAs et leurs bactéries associées influencent la composition du microbiome des recrues coralliennes. De plus, nous montrons que différentes espèces de CCA présentent des communautés microbiennes distinctes, avec un signal potentiel de phylosymbiose, suggérant l'adaptabilité du microbiome au cours de l'évolution. Dans le chapitre 4, nous avons étudié le potentiel fonctionnel des communautés microbiennes des CCAs. Nous avons démontré que les CCAs abritent des communautés fonctionnelles distinctes bien qu'elles partagent une forte base commune. Les communautés microbiennes des deux espèces de CCAs que nous avons ciblées n'a pas montré de différences claires dans leur capacité à produire des inducteurs de recrutement larvaire. Cependant, les capacités fonctionnelles d'induction n'étaient pas homogènes entre les genres microbiens des espèces de CCAs. Nous suggérons que les communautés microbiennes ne déterminent pas directement le comportement de recrutement des larves, mais qu'elles améliorent ou atténuent plutôt la réponse induite par la CCA et l'environnement.Tropical coral reefs depend on complex microbial communities that drive biogeochemical cycles, maintain host health, and support ecosystem homeostasis. Understanding the complex ecology of coral reef microorganisms is essential for the preservation of these precious ecosystems. However, the precise functional role of the reef microbial communities remains poorly known. In particular, the association between corals and bacteria of the Endozoicomonadaceae family, believed to be a crucial coral bacterial symbiont, is still not well defined. Microorganisms such as Endozoicomonadaceae appear essential for the survival of the adult coral host, but larval settlement is another important element for the corals’ fitness. The success of larval recruitment has recently been shown to depend on the Crustose Coraline Algae (CCA) on which they settle. More precisely, microbial communities associated with CCAs may play a crucial role, yet we know very little about these communities. The overall objectives of this thesis were to study the species diversity and the functional potential of the microbial communities associated with tropical corals and crustose coralline algae (CCA). Chapter 2 focused on Endozoicomonadaceae associated to three coral species across the Pacific Ocean. It revealed that different coral species exhibit distinct strategies of host-symbiont relationships. We identified three new symbiont species, each with distinct functional adaptations that may drive the host-symbiont relationship. The environment had generally only a small effect on Endozoicomonadaceae community composition, while the genetic lineage of the host was important in some corals. We suggest that the relation between Endozoicomonadaceae and the coral can range from stable co-dependent relationships to opportunistic associations. In Chapter 3, we described the microbial communities associated to different CCA species across spatial scales and defined the factors controlling their composition. We also tested if their were some links between the CCA and coral larvae microbial communities. Our results suggest that the CCA microbiome does not act as a microbial reservoir for the developing coral larvae. However, we observed that the microbial communities of coral recruits differed depending on their association with different types of algae. We conclude that CCAs and their associated bacteria influence the composition of the coral recruits’ microbiome. Additionally, we showed that different CCA species exhibit distinct microbial communities, with potential signal of phylosymbiosis, suggesting adaptability of the microbiome through evolutionary time. In Chapter 4, we studied the functional potential of CCA microbial communities. We demonstrate that CCA harbor distinct functional communities despite sharing a strong core functional metabolisms. The microbial community of the two CCA species that we targeted did not show clear differences in their ability to produce coral larvae inducers. However, inducing functional capabilities were not homogenous across microbial genera between CCA species. We suggest that microbial communities do not directly determine the behaviour of larvae settlement, but rather enhance or mitigate the response induced by the CCA and the environment

Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere

International audienceIn environmental metagenomic experiments, a very high proportion of the microbial sequencing data (> 70%) remains largely unexploited because rare and closely related genomes are missed in short-read assemblies. The identity and the potential metabolisms of a large fraction of natural microbial communities thus remain inaccessible to researchers. The purpose of this study was to explore the genomic content of unassembled metagenomic data and test their level of novelty. We used data from a three-year microbial metagenomic time series of the NW Mediterranean Sea, and conducted reference-free and database-guided analysis. The results revealed a significant genomic difference between the assembled and unassembled reads. The unassembled reads had a lower mean identity against public databases, and fewer metabolic pathways could be reconstructed. In addition, the unassembled fraction presented a clear temporal pattern, unlike the assembled ones, and a specific community composition that was similar to the rare communities defined by metabarcoding using the 16S rRNA gene. The rare gene pool was characterised by keystone bacterial taxa, and the presence of viruses, suggesting that viral lysis could maintain some taxa in a state of rarity. Our study demonstrates that unassembled metagenomic data can provide important information on the structure and functioning of microbial communities

New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics

International audienceAdvances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome

Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean

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A strong link between marine microbial community composition and function challenges the idea of functional redundancy

Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes

Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea

The Archaea Marine Group II (MGII) is widespread in the world’s ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group’s metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean Sea to test if the taxonomic diversity within the MGIIb family (Candidatus Thalassarchaeaceae) reflects the presence of different ecotypes. The MAGs’ seasonality revealed a MGIIb family composed of different subclades that have distinct lifestyles and physiologies. The vitamin metabolisms were notably different between ecotypes with, in some, a possible link to sunlight’s energy. Diverse archaeal proteorhodopsin variants, with unusual signature in key amino acid residues, had distinct seasonal patterns corresponding to changing day length. In addition, we show that in summer, archaea, as opposed to bacteria, disappeared completely from surface waters. Our results shed light on the diversity and the distribution of the euryarchaeotal proteorhodopsin, and highlight that MGIIb is a diverse ecological group. The work shows that time-series based studies of the taxonomy, seasonality, and metabolisms of marine prokaryotes is critical to uncover their diverse role in the ocean

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages

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High-throuput workflow for RNAseq data treatment linking laboratory data server and remote parallel calculation platform

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