Planktonic communities, especially those in coastal areas, are strongly affected by global change drivers (e.g. heatwaves, land-use change and increased of water run-off). Opportunistic pathogens – microbes that switch between non-pathogenic and pathogenic lifestyles – are predicted to increase globally across several taxa in the coming years due to the suboptimal living conditions of the marine biota caused by anthropogenic changes. Among planktonic microbes, about 30% of ”unresolved” relationships (yet to be described as beneficial or antagonistic) take place between microbial eukaryotes also called protists.
Labyrinthulomycetes is a group of ubiquitous protists present in marine and estuarine environments. They have a cosmopolitan distribution, from tropics to polar regions and are found as free living cells or attached to a wide range of substrates such as marine plants, macroalgae and corals. Some species are known for their saprotrophic lifestyle (feeding on dead and decaying organic matter) and therefore have an important role in the degradation of phytoplankton litter. Yet, some species have been described opportunistic parasites of clams, juvenile abalone, corals, seagrasses and diatoms. In contrast with their fungi counterparts (e.g., chytrids), the underpinning ecology and diversity of Labyrinthulomycetes remain little studied.
What do we want to accomplish?
We will investigate Labyrinthulomycetes genetic diversity and its global distribution. We will use data from publicly available high-throughput environmental sequencing studies (metabarcoding - the high throughput sequencing of a given marker gene) targeting plankton communities present on metaPR2 . This database contains 59 datasets corresponding to more than 6,000 samples, including samples from Oslo fjord. The database is accessible through both a web-based interface (https://app.metapr2.org) and an R package.
What will you learn during the Master?
You will learn all the steps, from field work to data processing, involved in acquiring metabarcoding data. Metabarcoding today is the golden method used in diversity studies and conservation/monitoring programs.
You will have the opportunity to:
- join the monthly sampling cruises conducted at the Oslofjorden
- get integrated with PhD-student, postdoc and other Master students participating on the Oslofjorden time series
You will learn:
- the different field work strategies to obtain planktonic samples
- how the samples are processed in laboratory
- how to manipulate and work with large metabarcoding datasets using R
- how to document your analysis workflows with GitHub and RMarkdown
- how to perform phylogenetic reconstructions to describe and define genetic diversity of microbial eukaryotes
- how to write documents using the LaTeX script language
What can we offer?
We offer a safe space for learning through achievements and failures, alone and in partnership with others. We welcome individuals of all ages, backgrounds, beliefs, ethnicities, genders, gender identities, gender expressions, national origins, religious affiliations, sexual orientations, and any other visible and non-visible differences. All members of our research groups are expected to contribute to a respectful, welcoming and inclusive environment for every other member.
supervisor: Assoc Prof Adriana Lopes (GEEK Laboratory) and co-supervisors: Prof Bente Edvardsen & CNRS Daniel Vaulot