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Josephine Rapp


Postdoctoral fellow

Department of Biochemistry, Microbiology and Bioinformatics, Université Laval

Charles-Eugène-Marchand Building
1030 avenue de la Médecine
Université Laval
Quebec, Canada
G1V 0A6





Projet de recherche

Microbe-virus interactions in cryospheric habitats of the Arctic's Last Ice Area


The cryosphere, that portion of the planet where most of the water is frozen, has been incurring significant losses in both areal extent and volume over the last decades due to climate change. While mostly frozen, cryospheric habitats are home to diverse and specialized microbial and viral populations that play critical roles for ecosystem functioning. The extreme settings that characterize these environments may foster unique interactions and altered ecologies of microbes and their viruses, with implications for microbial evolution and adaptation, yet modern molecular tools are only now starting to be applied to study these ecosystems.


As part of the Sentinel North "Last Ice Microbiomes and Arctic Ecosystem Health" project, I will study the microbial communities and their viruses that live in different types of cryo-environments in the Last Ice Area. Specifically, I will use metagenomic analyses to resolve microbial diversity and metabolism in different habitats, and will investigate whether and how it is affected by viral infection. One of my overarching research questions is whether old and stable ice environments allow for the establishment of specific types of microbe-virus interactions that cannot form under younger and more short-lived environmental settings. With ongoing environmental changes, old and thick ice features are being lost and will eventually be replaced by more transient habitats.

Study sites

We will collect samples for this project from the Ward Hunt Ice Shelf and the surrounding sea ice off the coast of northern Ellesmere Island, Nunavut, Canada. Targeted types of cryo-environments include shelf ice, permanent lakes on the ice shelf surface, thawing and refreezing each year, as well as meltwater rivulets. Further, we will sample seawater and sea ice during an expedition to the Beaufort Gyre aboard CCGS Louis S. St-Laurent, aiming to collect the microbial communities that eventually feed into the ice environments of the Last Ice Area.

Material and methods

We will collect samples on 0.02 µm pore size Anotop filters that capture eukaryotes, prokaryotes and viruses. My focus will be on prokaryotes and viruses for this project. I will extract total community DNA from these filters and use shotgun metagenomic sequencing to access the genomic information encoded by both microbes and viruses. I will reconstruct microbial genomes and their metabolism, and identify viral sequences in the same datasets. In silico virus-host matching, as well as the prediction of viral lifestyle and identification of virally-encoded auxiliary metabolic genes will shed light on specific interactions and the effect of environmental settings on these relationships.

Expected results

Results from this study will help us to better understand the diversity and function of the microbial communities in these extreme and threatened Northern habitats. They will provide some of the first genomic insights into their metabolic capabilities and the role of microbe-virus interactions for community structure and ecosystem functioning. I expect to see differences in both biodiversity and type of interaction between comparably stable and old cryohabitats, i.e. ice shelf and multi-year sea ice, and more transient and short-lived features, i.e. meltwater lakes and young ice, with "aged" communities featuring more specific and synergistic interactions, and younger communities exhibiting a more diverse, but unspecific pool of functions that allow short-lived relationships.

Location of the research sites

Scientific communications

Labbé, M., Thaler, M., Pitot, T.M., Rapp, J., Vincent, W.F., Culley, A.I., 2022. Climate-endangered arctic epishelf lake harbors viral assemblages with distinct genetic repertoires. Applied and Environmental Microbiology, 88(17), e00228-22. DOI: 10.1128/aem.00228-22.

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