The Department of Marine Microbiology and Biogeochemistry (MMB) of the Royal Netherlands Institute for Sea Research (NIOZ) is recruiting a Research Assistant (1.0 FTE). We offer an appointment for the duration of the project, for 5 years.
THE DEPARTMENT
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 experimental 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 Ph.D. 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.
THE ViBRANT-SEA PROJECT
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.
THE CANDIDATE
We seek a highly motivated team member with strong quantitative skills in some or all of the following areas: Next Generation Sequence data analysis, Python, R or bash scripting, Linux (command line), data analysis, data manipulation, statistics, image analysis, and machine learning.
The selected candidate will provide different bioinformatics analyses and data management support for the 5-year duration of the project. The ideal candidate will have at least a bachelor's degree in bioinformatics, computational biology, scientific computing and/or data science, and a proven track record of applying bioinformatics tools. The international character of the institute and department require that the candidate possess excellent English oral and written communication skills. The 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)
- Writing scripts for custom molecular data analysis, including e.g., data management, database searches, data integration
- Troubleshooting problems and answering computational/bioinformatic questions
- Performing image analysis ideally including machine learning methods to increase throughput
- Performing analyses using a variety of statistical methods
- Organizing, archiving, and submitting sequencing data and metadata to public repositories
WHAT WE EXPECT
- Positive attitude, open mind, and willingness to take on new challenges
- Organized 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, coding ability
- Flexibility in adapting to the needs of the project and other team members
- Efficiency and accuracy, working independently and as part of the team
- Interest in developing new methods, using analytical software and skills in data processing and archiving
WHAT WE OFFER
- Opportunities to complement your computational skills with laboratory skills needed to generate high throughput sequencing data if desired
- Opportunities to creatively analyze and integrate amplicon, metagenomics and image data and thereby contributing to research on biodegradable plastic biodegradation
- Interactions with researchers with backgrounds from a broad range of environmental microbiological topics
- Excellent computing facilities
- Support from an enthusiastic research team, as well as molecular analysts, bioinformaticians and computational infrastructure personnel to work with you
- Further skills development via workshop or online course material
CONDITIONS
- Employment of this full-time position at Royal NIOZ is by NWO-I, for a temporary duration of 5 years.
- Salary compliant with CAO-WVOI (Collective Labour Agreement for Dutch Research Institutes) in scale 8 or 9.
- 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%.
- 2nd class public transportation for work related travel is reimbursed 100%.
- 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.
The closing date for this position is June 1, 2024.
