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Home > Thèses et HDR > Thèses en 2020

23/09/2020 - Sungeun LEE

by Laurent Krähenbühl - published on , updated on


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Sungeun Lee defends his PhD on Sept. 23, 2020 at 4:00 PM.
Place : Ecole Centrale de Lyon, Bâtiment W1, visio conference only.

Title : Virus-host interactions across a soil pH gradient at the community and individual scale

Jury :
Rapporteurs :
- M. Michael DUBOW, Professeur, Institut de Biologie Intégrative de la Cellule, Gif-sur-Yvette, France
- Tim URICH, Professeur, Universitat Greifswald, City, Allemagne
Autres membres :
- Graeme W. NICOL, DR CNRS, Ecole Centrale de Lyon, Directeur de thèse (Ampère)
- Christina HAZARD, Ecole Centrale de Lyon, co-Directeur de thèse (Ampère)
- Sophie ABBY, Laboratoire TIMC-IMAG, La Tronche, France
- Joanne EMERSON, University of California, Davis, CA, Etats-Unis
- Timothy M. VOGEL, Professeur, UCBL (Ampère)

Abstract :
Soil viruses have potential to influence microbial community structure and subsequent ecosystem functioning by directly affecting the abundance of host cells by lysis and through their ability to transfer genes between hosts. Although our understanding of soil viral diversity and functioning has increased, the role of viruses and their interactions with prokaryotes in soil is limited. To gain a better understanding of virus-host interactions in soil, a long-term pH-manipulated soil gradient, which microbial community structure changes across, was investigated. The main objectives of this thesis were to 1) determine the influence of microbial community structure and soil pH on viruses using metagenomics and viromics (Chapter II), 2) determine the infectivity of soil viral populations from co-localized and foreign pH soil niches using a plaque assay approach combined with hybrid metagenomics sequencing (Chapter III) and 3) identify virus populations infecting specific soil microbial functional groups, specifically methanotrophs (Chapter IV) and nitrifiers (Chapter V), using DNA stable isotope probing combined with metagenomic deep sequencing. Viral community structure was found to change with soil pH, demonstrating that viral communities are tightly linked to host populations, but also may have narrow host ranges. Analysis of clustered regularly interspaced short palindromic repeats (CRISPR) arrays revealed dynamic virus-host interactions, with the number and size of CRISPR arrays distinct across contrasting pH soil. Profiling of the host-virus linkages between soil pH, suggests that viruses play a critical role in shaping the composition and function of the soil prokaryotic community. Surprisingly, greater infectivity of a host bacterium by virus populations was found when viruses and host bacterium were not co-localized in the same pH soil. Coevolutionary processes between the host and virus populations, such as restriction modification/virus-encoded methyltransferase and CRISPR-Cas system/spacer mutation, provide evidence for local adaptation, and that virus-bacterial host interactions play an integral part in the susceptibility of a host to infection and consequently in the regulation of soil bacterial populations. Targeting specific microbial functional groups via stable isotope probing allowed analysis of individual host-virus populations. Tracking carbon flow through prokaryotic and viral populations revealed active interactions between viruses and methanotroph and nitrifier hosts, and soil pH niche preferences. Evidence of horizontal gene transfer and virus-encoded auxiliary metabolic genes, such as glycoside hydrolase families, peptidases, particulate methane monooxygenase subunit C (pmoC), nitrogenase (nifH) and cytochrome cd1-nitrite reductase, supports that viruses are significant contributors to host functioning and carbon and nitrogen cycling in soil. Overall, this work demonstrated that soil viruses are important regulators of microbial communities through specific host lysis and dynamic virus-host interactions.

Key Words:
microbial community, viral community, soil, deep sequencing, DNA stable-isotope probing, plaque assay, virus-encoded auxiliary metabolic genes, soil microbial food-web, virus-host interactions, coevolutionary processes.

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