PhD Patterns of Gene Expression in Marine Phytoplankton-virus Interactions

PhD Patterns of Gene Expression in Marine Phytoplankton-virus Interactions

Working at the UvA

About the position 

Despite their minute size, marine phytoplankton are vital for marine ecosystem productivity and play a key role in global carbon and nutrient cycling. However, like all life on Earth, phytoplankton are susceptible to viral infections. Viral-induced mortality (viral lysis) of phytoplankton cells redirects the flow of energy and elements with expected far-reaching consequences for ocean ecosystem structure and functioning. Yet, phytoplankton viral lysis rates are poorly constrained. Additionally, to what extent viral infections affect phytoplankton host stoichiometry and functional traits as well as how this is influenced by (global climate change-induced) environmental stressors are understudied. Moreover, a comprehensive understanding of the geographical distribution of virus and phytoplankton host traits is lacking. These knowledge gaps prevent incorporation of virus-host dynamics in global ecosystem and biogeochemical models. Only by integration of complementary expertise, ranging from viral ecology, phytoplankton ecophysiology, molecular biology, and biological oceanography, to large scale bioinformatic data analysis and mathematical modelling, can we effectively bridge the knowledge gaps that limit our current understanding and predictive power of how viral infections impact phytoplankton communities and associated biogeochemical fluxes.

This PhD position is part of the NWO-funded PHYVIR project, which aims to elucidate marine phytoplankton-virus interactions from local to global scales. It focuses on five interlinked objectives, related to the above-mentioned knowledge gaps. The research spans from genetic analysis and controlled experiments to oceanic expeditions and global ecosystem models. The project consists of 5 PhD and 2 Postdoc positions and is led by Prof. Corina Brussaard (NIOZ, coordinator), Prof. Jef Huisman (University of Amsterdam), Prof. Dedmer van de Waal (NIOO), Dr. Susanne Wilken (University of Amsterdam) and Dr. Thomas Hackl (University Groningen).

Working at the UvA

About the position 

Despite their minute size, marine phytoplankton are vital for marine ecosystem productivity and play a key role in global carbon and nutrient cycling. However, like all life on Earth, phytoplankton are susceptible to viral infections. Viral-induced mortality (viral lysis) of phytoplankton cells redirects the flow of energy and elements with expected far-reaching consequences for ocean ecosystem structure and functioning. Yet, phytoplankton viral lysis rates are poorly constrained. Additionally, to what extent viral infections affect phytoplankton host stoichiometry and functional traits as well as how this is influenced by (global climate change-induced) environmental stressors are understudied. Moreover, a comprehensive understanding of the geographical distribution of virus and phytoplankton host traits is lacking. These knowledge gaps prevent incorporation of virus-host dynamics in global ecosystem and biogeochemical models. Only by integration of complementary expertise, ranging from viral ecology, phytoplankton ecophysiology, molecular biology, and biological oceanography, to large scale bioinformatic data analysis and mathematical modelling, can we effectively bridge the knowledge gaps that limit our current understanding and predictive power of how viral infections impact phytoplankton communities and associated biogeochemical fluxes.

This PhD position is part of the NWO-funded PHYVIR project, which aims to elucidate marine phytoplankton-virus interactions from local to global scales. It focuses on five interlinked objectives, related to the above-mentioned knowledge gaps. The research spans from genetic analysis and controlled experiments to oceanic expeditions and global ecosystem models. The project consists of 5 PhD and 2 Postdoc positions and is led by Prof. Corina Brussaard (NIOZ, coordinator), Prof. Jef Huisman (University of Amsterdam), Prof. Dedmer van de Waal (NIOO), Dr. Susanne Wilken (University of Amsterdam) and Dr. Thomas Hackl (University Groningen).

All about this vacancy

What are you going to do?

As PhD candidate for PHYVIR’s subproject-3, you will contribute to improving our understanding of the interplay between viruses and their phytoplankton hosts. Specifically, this project aims to elucidate how viral infection alters host gene expression and how this links to changes in functional traits and stoichiometry of infected phytoplankton hosts. You will participate in the project’s two scientific cruises, perform on-deck incubation experiments, and analyze resulting meta-transcriptomes. You will closely collaborate with the other PhDs, working on cultured virus-host pairs to assess altered gene expression and functional traits in controlled laboratory experiments.

Tasks and responsibilities: 

  • develop a PhD thesis plan, prepare and perform the research, analyze the samples and data;
  • actively exchange ideas and results within the larger PHYVIR team;
  • supervise MSc students who wish to do an internship on marine phytoplankton virus ecology;
  • present your results at meetings and scientific conferences;
  • publish your results in international scientific journals.

Your profile

We are looking for an enthusiastic and motivated candidate, with a keen interest in marine viral ecology and phytoplankton host-virus interactions. You enjoy bioinformatic analyses, are well-organized, have a collaborative personality but are also able to work independently.

Your experience and profile:

  •       A MSc degree in environmental microbiology, marine ecology, or closely related discipline;
  • Strong motivation to develop as a scientist;
  • Strong oral and written communication skills in English;
  • Experience with analysis and interpretation of omics data is a plus;
  • Prior (marine) fieldwork experience is a plus;

 

Our offer

A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is 1 October 2025. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students. For this position the University Job Classification profile “Promovendus” (PhD candidate) applies. Your salary will be €2,901 gross per month in the first year and will increase to €3,707 in the final year, based on full-time employment of 38 hours per week. This does not include 8% holiday allowance and 8.3% year-end allowance. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Universities of the Netherlands is applicable.

Besides the salary and a vibrant and challenging environment at Science Park, we offer you multiple fringe benefits:

  • 232 holiday hours per year (based on fulltime) and extra holidays between Christmas and 1 January;
  • multiple courses to follow from our Teaching and Learning Centre;
  • a complete educational program for PhD students;
  • multiple courses on topics such as leadership for academic staff;
  • multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses;
  • 7 weeks birth leave (partner leave) with 100% salary;
  • partly paid parental leave;
  • the possibility to set up a workplace at home;
  • a pension at ABP for which UvA pays two third part of the contribution;
  • the possibility to follow courses to learn Dutch;
  • help with registration at UvA- Housing for a studio or small apartment when you’re moving from abroad. 

Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

All about this vacancy

What are you going to do?

As PhD candidate for PHYVIR’s subproject-3, you will contribute to improving our understanding of the interplay between viruses and their phytoplankton hosts. Specifically, this project aims to elucidate how viral infection alters host gene expression and how this links to changes in functional traits and stoichiometry of infected phytoplankton hosts. You will participate in the project’s two scientific cruises, perform on-deck incubation experiments, and analyze resulting meta-transcriptomes. You will closely collaborate with the other PhDs, working on cultured virus-host pairs to assess altered gene expression and functional traits in controlled laboratory experiments.

Tasks and responsibilities: 

  • develop a PhD thesis plan, prepare and perform the research, analyze the samples and data;
  • actively exchange ideas and results within the larger PHYVIR team;
  • supervise MSc students who wish to do an internship on marine phytoplankton virus ecology;
  • present your results at meetings and scientific conferences;
  • publish your results in international scientific journals.

Your profile

We are looking for an enthusiastic and motivated candidate, with a keen interest in marine viral ecology and phytoplankton host-virus interactions. You enjoy bioinformatic analyses, are well-organized, have a collaborative personality but are also able to work independently.

Your experience and profile:

  •       A MSc degree in environmental microbiology, marine ecology, or closely related discipline;
  • Strong motivation to develop as a scientist;
  • Strong oral and written communication skills in English;
  • Experience with analysis and interpretation of omics data is a plus;
  • Prior (marine) fieldwork experience is a plus;

 

Our offer

A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is 1 October 2025. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students. For this position the University Job Classification profile “Promovendus” (PhD candidate) applies. Your salary will be €2,901 gross per month in the first year and will increase to €3,707 in the final year, based on full-time employment of 38 hours per week. This does not include 8% holiday allowance and 8.3% year-end allowance. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Universities of the Netherlands is applicable.

Besides the salary and a vibrant and challenging environment at Science Park, we offer you multiple fringe benefits:

  • 232 holiday hours per year (based on fulltime) and extra holidays between Christmas and 1 January;
  • multiple courses to follow from our Teaching and Learning Centre;
  • a complete educational program for PhD students;
  • multiple courses on topics such as leadership for academic staff;
  • multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses;
  • 7 weeks birth leave (partner leave) with 100% salary;
  • partly paid parental leave;
  • the possibility to set up a workplace at home;
  • a pension at ABP for which UvA pays two third part of the contribution;
  • the possibility to follow courses to learn Dutch;
  • help with registration at UvA- Housing for a studio or small apartment when you’re moving from abroad. 

Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

Your place at the UvA

About us

The Institute for Biodiversity and Ecosystem Dynamics (IBED) is one of eight research institutes of the Faculty of Science at the University of Amsterdam. The research at IBED aims to unravel how ecosystems function in all their complexity, and how they change due to natural processes and human activities. At its core lies an integrated systems approach to study biodiversity, ecosystems and the environment. IBED adopts this systems approach to ecosystems, addressing abiotic (soil and water quality) and biotic factors (ecology and evolution of plants, animals, and microorganisms), and the interplay between those. The IBED vision includes research encompassing experimental and theoretical approaches at a wide variety of temporal and spatial scales, i.e. from molecules and microorganisms to patterns and processes occurring at the global scale. The University of Amsterdam has excellent high performance computing facilities. Furthermore, IBED has a dedicated computational support team with specialized knowledge of bioinformatics, (geo)database management and scientific programming. IBED also works with non-academic partners to deliver transdisciplinary science for society.

The position will be based in the Department of Freshwater and Marine Ecology. The department of Freshwater & Marine Ecology aims to increase our understanding of the biodiversity and dynamics of freshwater and marine ecosystems from the level of molecules and genes to entire ecosystems.

Want to know more about our organisation? Read more about working at the University of Amsterdam.

More about the UvA

The University of Amsterdam is ambitious, creative and committed. An inspiration to students since 1632, a vanguard player in international science and a partner in innovation.
The University of Amsterdam is the largest university in the Netherlands, with the broadest range of courses on offer. An intellectual hub with 42,000 students, 6,000 staff and 3,000 PhD students. Connected by a culture of curiosity.

Your place at the UvA

This is where you will be working

About us

The Institute for Biodiversity and Ecosystem Dynamics (IBED) is one of eight research institutes of the Faculty of Science at the University of Amsterdam. The research at IBED aims to unravel how ecosystems function in all their complexity, and how they change due to natural processes and human activities. At its core lies an integrated systems approach to study biodiversity, ecosystems and the environment. IBED adopts this systems approach to ecosystems, addressing abiotic (soil and water quality) and biotic factors (ecology and evolution of plants, animals, and microorganisms), and the interplay between those. The IBED vision includes research encompassing experimental and theoretical approaches at a wide variety of temporal and spatial scales, i.e. from molecules and microorganisms to patterns and processes occurring at the global scale. The University of Amsterdam has excellent high performance computing facilities. Furthermore, IBED has a dedicated computational support team with specialized knowledge of bioinformatics, (geo)database management and scientific programming. IBED also works with non-academic partners to deliver transdisciplinary science for society.

The position will be based in the Department of Freshwater and Marine Ecology. The department of Freshwater & Marine Ecology aims to increase our understanding of the biodiversity and dynamics of freshwater and marine ecosystems from the level of molecules and genes to entire ecosystems.

Want to know more about our organisation? Read more about working at the University of Amsterdam.

More about the UvA

The University of Amsterdam is ambitious, creative and committed. An inspiration to students since 1632, a vanguard player in international science and a partner in innovation.
The University of Amsterdam is the largest university in the Netherlands, with the broadest range of courses on offer. An intellectual hub with 42,000 students, 6,000 staff and 3,000 PhD students. Connected by a culture of curiosity.

Important to know

Your application & contact

If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the ‘Apply’-button on the vacancy’s webpage. We accept applications until and including 11 July 2025.

Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

  • a detailed CV including publications if there are any and the months (not just years) when referring to your education and work experience;
  • a letter of motivation;
  • the names and email addresses of two references who can provide letters of recommendation.

Only complete applications received within the response period via the link below will be considered. A knowledge security check can be part of the selection procedure.(for details: national knowledge security guidelines)

We will invite potential candidates for interviews soon after the closing date. Online interviews will be held on July 24th and in-person interviews will be held on August 11th.

Do you have any questions, or do you require additional information? Please contact:

Dr. Susanne Wilken, Associate Professor, [email protected]

Diversity, Equity & Inclusion

As an employer, the UvA maintains an equal opportunities policy. We value diversity and are fully committed to being a place where everyone feels at home. We nurture inquisitive minds and perseverance and allow room for persistent questioning. With us, curiosity and creativity are the prevailing culture.

Important to know

Your application & contact

If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the ‘Apply’-button on the vacancy’s webpage. We accept applications until and including 11 July 2025.

Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

  • a detailed CV including publications if there are any and the months (not just years) when referring to your education and work experience;
  • a letter of motivation;
  • the names and email addresses of two references who can provide letters of recommendation.

Only complete applications received within the response period via the link below will be considered. A knowledge security check can be part of the selection procedure.(for details: national knowledge security guidelines)

We will invite potential candidates for interviews soon after the closing date. Online interviews will be held on July 24th and in-person interviews will be held on August 11th.

Do you have any questions, or do you require additional information? Please contact:

Dr. Susanne Wilken, Associate Professor, [email protected]

As an employer, the UvA maintains an equal opportunities policy. We value diversity and are fully committed to being a place where everyone feels at home. We nurture inquisitive minds and perseverance and allow room for persistent questioning. With us, curiosity and creativity are the prevailing culture.

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