Mots-Clés

Viromics TIme-series Coastal environments

Description

Diversity and temporal dynamics of marine viruses in the Bay of Brest.

Viruses are by far the most abundant and ubiquitous biological entities in the global ocean and infect, through different strategies, up to 10^23 cells each day leading to significant impacts on the ecology and evolution of their hosts (control of host demography and diversity, gene transfer and coevolution), and on the biogeochemical balances of marine systems (Suttle 2007; Breitbart et al. 2018). Despite their major impact, the ecology and dynamics of marine viruses are still poorly understood, in particular in coastal environments, which are characterized by strong seasonal variations of environmental conditions and planktonic community composition. Our knowledge of viruses in these ecosystems has indeed been hindered by the paucity of sampling and technical limitations.
In the Bay of Brest, bacterial communities have been monitored monthly for over 10 years by metagenomics sequencing (the sequencing of all the DNA found in a sample) in the frame of the microbial genomics observatory MicroBrest (coordinated by UMR BEEP, UMR LEMAR, and the observation service of IUEM - UAR 3113). This observatory benefits from the simultaneous monitoring of more than 15 physico-chemical parameters by the national network SOMLIT, bringing a precise characterization of the environmental context. The analysis of the microbial dataset has notably revealed that the physico-chemical parameters only partly explain the variations in microbial community composition, which strongly suggests a role of biotic interactions in controlling the dynamics of microbes (Lemonnier, thesis). In order to quantify the impact of viruses on these microbial communities, a new times series was initiated in 2025 to monitor viruses, through the sequencing of viral DNA (viromes) from monthly samples. Indeed, while viruses are difficult to observe, viromics bring insight into both the taxonomic and the functional diversity of viral communities. The first year of samples are currently being treated in the lab. The combination of the existing microbial time series with this new viral time series constitutes a rare and invaluable dataset to study the interactions between viruses and their microbial hosts, and their ecological and evolutionary consequences (Hevroni et al. 2020; Lopez-Alforja et al. 2025).

Objectives of the internship:

• Establish the first collection of viral genomes from the viromes sampled in 2025-2026 in the Bay of Brest (Sainte-Anne du Portzic)

• Identify the taxonomic and functional diversity of this collection

• Track the temporal dynamics of viral populations, in relation with environmental parameters

To reach these objectives, the selected student will apply and develop skills in bioinformatics (metagenomics assembly, viral annotation, …) and in multivariate statistics. Depending on the advancement of the work and the preferences of the student, other datasets generated by the MicroBrest observatory could be included (long-read metagenomes, HiC metagenomes), and the student will have the opportunity to participate in the sampling and the preparation of viromes. Overall, this work will give insights into the potential persistence of populations, the stability of the viral community and into the impact of environmental conditions on viruses.

Required skills:

• Knowledge of bioinformatics and microbiology

• Ability to work independently in a Unix environment

• Basic knowledge of R or Python

• Initial experience in using metagenomic data would be an advantage

• Interest in marine microbial ecology

Bibliography :

• Breitbart, Mya, Chelsea Bonnain, Kema Malki, and Natalie A. Sawaya. 2018. “Phage Puppet Masters of the Marine Microbial Realm.” Nature Microbiology 3 (7): 754–66. https://doi.org/10.1038/s41564-018-0166-y.

• Hevroni, Gur, José Flores-Uribe, Oded Béjà, and Alon Philosof. 2020. “Seasonal and Diel Patterns of Abundance and Activity of Viruses in the Red Sea.” Proceedings of the National Academy of Sciences 117 (47): 29738–47. https://doi.org/10.1073/pnas.2010783117.

• Lemonnier, Clarisse. n.d. Effect of environmental variations on bacterial communities dynamics: evolution and adaptation of bacteria as part of a microbial observatory in the Bay of Brest and the Iroise Sea.

• Lopez-Alforja, Xabier, Elisabet L. Sà, Maria V . Quiroga, et al. 2025. “Long-Term Decline of Marine Viruses Associated with Warming and Oligotrophication at a NW Mediterranean Coastal Site.” ISME Communications 5 (1): ycaf150. https://doi.org/10.1093/ismeco/ycaf150.

• Suttle, Curtis A. 2007. “Marine Viruses — Major Players in the Global Ecosystem.” Nature Reviews Microbiology 5 (10): 801–12. https://doi.org/10.1038/nrmicro1750.