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PhD position: "Bioinformatics and Systems Biology in the ViBRANT SEA-project"

  • 't Horntje, Texel, Noord-Holland, Netherlands
Marine Microbiology & Biogeochemistry (MMB)

Job description

Validating Biodegradation Rates and Reactions Applying Novel Technologies and Systems Ecology Approaches (ViBRANT-SEA) is an Advanced European Research Council (ERC) supported project that is recruiting a PhD Candidate (1.0 FTE). This position is vacant within our Department of Marine Microbiology and Biogeochemistry (MMB) of the Royal Netherlands Institute for Sea Research (NIOZ) and in collaboration with the Institute for Biodiversity and Ecosystem Dynamics (IBED) Department at the University of Amsterdam (UvA).


The Department of Marine Microbiology and Biogeochemistry (MMB,) is located on Texel. The MMB Department studies microbial communities in all types of marine environments, from estuaries to the deep ocean, from the deep past to the present. Using field and expermental approaches and a variety of analytical, (bio)chemical and genomic techniques, we study the diversity, evolution, physiology and activity of eukaryotes, bacteria, archaea, and viruses in diverse marine environmental settings. We do so by a variety of analytical chemical, biochemical and modern genomic techniques. The MMB Department is well-equipped with laboratories for molecular analyses and state-of-the-art bioinformatics facilities. The MMB technical and scientific staff is international, diverse, and has approximately 80 members, including PhD students, postdocs, and Master students from more than 15 different countries. A group of sixteen staff scientists and fifteen research assistants (junior and senior) form its support core.


Plastic Marine Debris (PMD) is now considered a planetary boundary threat and the “Plastic Cycle” a biogeochemical cycle. The impacts of single-use plastic litter in marine environments have prompted a search for greener alternatives such as the biodegradable/ compostable plastics polyhydroxyalkanoates and polylactic acid already being used for consumer goods. The diversity of microbes, their enzymes, and their role in influencing the rates of plastic biodegradation in nature remains poorly characterized – particularly in cold or low-oxygen marine waters and seafloor, where most PMD accumulates. The impact of lag duration, pH, hydrostatic pressure, and potential priority effects of initial microbial colonizers remain vital but unaddressed concerns. In addition, the impact of plastic, its breakdown products, and additives on marine organisms and ecosystems is largely unquantified. Two urgent questions are how long does plastic last in the marine environment and what are the impacts on ecosystems. This technology-enabled project aims to quantify biodegradation rates of biodegradable plastics and plastic-associated additives in the field and under controlled laboratory conditions, and to develop a fish model system for toxicity tests to fill these knowledge gaps.

This project will generate novel microbial metagenomes from global plastic samples collected during cruises and from biodegradation experiments to create a comprehensive list of genes and enzymes linked to biodegradation of biodegradable plastic in marine environments. It will be the first to combine in situ respirometry, stable isotope probing, and advanced imaging techniques to measure biodegradable plastic biodegradation rates,

while visualizing microbe-microbe interactions on the plastic surface, revealing cellular mechanisms occurring during active biodegradation.

Finally, it will develop the first marine fish organoid model for consistent and efficient testing of toxicity due to plastics and additives.

Job requirements


We seek a highly motivated candidate as a team member with a background in bioinformatics, computational biology, systems biology, microbiology, and molecular biology with the ambition to become a scientist. In this PhD-trajectory you will be jointly supervised by Prof. dr. L.A. Amaral-Zettler (NIOZ/UvA) and Dr. D. Mende (UvA/University Medical Center). The ideal candidate will have a master’s degree in bioinformatics, computational biology, systems biology or related fields and a proven track record of applying bioinformatics tools. The international character of the institute and department require that the candidate possesses excellent English oral and written communication skills. Key responsibilities for this position are;

  • Performing molecular biology data analysis on all three domains of life (Bacteria, Archaea and Eukarya) using custom analysis pipelines (e.g. amplicon, genomic, metagenomic, metatranscriptomic data analysis)
  • Identifying novel biodegradation-associated enzymes via interrogating metagenomic and metatranscriptomic datasets generated from archived and newly generated samples
  • Designing Fluorescence In Situ Hybridization (FISH) rRNA and mRNA probes from amplicon and metagenomic/metatranscriptomic libraries
  • Using Machine Learning methods to analyze image data
  • Organizing and submitting sequencing data and metadata to public repositories


  • A positive attitude, open mind, and willingness to learn and take on new challenges
  • A highly organized, strong work ethic, excellent documentation skills, and attention to detail
  • Experience with high-throughput molecular data analysis
  • Competence in data analysis using R or python, proficient unix/linux skills, ability to write well-structured open-source code with proper documentation
  • Flexibility in adapting to the needs of the project and other team members
  • Efficiency and accuracy working independently and as part of the ViBRANT-SEA team
  • Interest in developing new methods, using analytical software and skill in data processing and archiving


  • A supervised PhD-trajectory of 4 years, in which we support you to become a full blown scientist
  • Opportunities to complement your computational skills with laboratory skills needed to generate high throughput sequencing data if desired
  • Interactions with researchers with backgrounds from a broad range of environmental microbiological topics
  • Excellent computing and laboratory facilities
  • Support from an enthusiastic research team as well as molecular analysts, bioinformaticians and computational infrastructure personnel to work with you
  • Optional opportunities to assist in teaching undergraduates and master students
  • An opportunity to join a research expedition


  • A temporary contract for 40 hours a week for the duration of 4 years at Royal NIOZ is by NWO-I. The initial contract will be for a period of 1 year and after satisfactory Go-No Go -evaluation in the 9th month, it will be extended for the total duration of 4 years. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and scientific meetings.
  • Salary compliant with CAO-WVOI  (Collective Labour Agreement for Dutch Research Institutes) 
  • 338 annualized holiday hours for a full-time 40-hour work week.
  • Pension scheme via ABP, 8% holiday allowance and a year-end bonus of 8.33%. 
  • Employment benefits plan to exchange a portion of your salary for days off or vice versa or can be used to purchase a bicycle with tax benefits.
  • We offer relocation expenses for employees coming from abroad and support with finding accommodation.


If this profile matches your background and skills, and you are interested in the job, we look forward to receiving your application. You can apply online via the button below. Applications should include the following information:

  • a detailed CV including the months (not just years) when referring to your education and work experience
  • a letter of motivation
  • the names and email addresses of three references willing to write a letter of recommendation

Only complete applications received within the response period via the link below will be considered. We want to be a transparent institute with a healthy working climate and an inclusive culture, where people from diverse backgrounds and gender bring their talents and further develop these talents. We aim for inclusive decision-making processes and expect our leadership to show visible commitment, awareness of bias, and cultural intelligence.

For additional information about this vacancy, please contact Prof. Linda Amaral-Zettler (ViBRANT-SEA Principal Investigator) for substantial questions regarding the position or project. For all procedural question please email to

The closing date for this vacancy is 1 June 2024. The interviews will be held  on June 3 and 4 (online) and June 6 and 7 on site at NIOZ.