Royal Netherlands Institute for Sea Research (NIOZ)

PhD Student "Physiological diversity and ecological niche of JTB255 Bacteria in marine sediments"

The department of Marine Microbiology and Biogeochemistry (MMB; principal investigator dr. Pierre Offre) is looking for a highly motivated PhD Student with a keen interest in microbial physiology who would like to support the research of a diverse and ubiquitous group of marine benthic bacteria: JTB255.

VACANCY ID: 2018-007
CLOSING DATE: April 5th, 2018


Research at the department of Marine Microbiology and Biogeochemistry (MMB) strongly focuses on the physiology of marine microorganisms and their role in marine biogeochemical cycles, which are investigated in a variety of marine environments, including tidal flats, coral reefs, and the deep ocean. The department has a widely acknowledged expertise in organic geochemistry, especially for its research knowledge of membrane lipid biomarkers. Those lipid biomarkers have a broad range of applications in the study of extant ecosystems (e.g. to investigate the trophic structure of ecosystems or trace inputs, loss, and cycling of biogenic materials) but also in deciphering past climate changes and reconstructing microbial evolution. The department is equipped with state-of-the-art laboratories, analytical equipment, and bioinformatics resources. Technical support is excellent.

The research team of dr. Pierre Offre, the principal investigator, has a key interest in characterizing the metabolic and physiological traits of marine microorganisms and understanding how those traits drive the cycling of nutrients and the assembly of biological communities. Those overarching goals are addressed in several research lines, one of which focuses on the metabolic and physiological diversity of JTB255 bacteria.

JTB255 is a group of Gammaproteobacteria, which is common in marine benthic environments (coastal and deep-sea) and therefore represents one of the core groups of the global sediment microbiome. Until recently, JTB255 was only known as a cluster of 16S rRNA gene sequences but several partial genomes and one complete genome have now been obtained. Investigations of those genomes suggest that JTB255 bacteria include chemoorganoheterotrophs, some of which also have a potential for chemolithoautotrophy.


In this project, you will characterize the range of electron donors and carbon sources used by a cultivated strain of the JTB255 group as well as its growth and substrate uptake kinetics. Among several classes of substrates, the project will emphasize growth on lipids and the broad variety of related compounds, which are important drivers of the health and stability of marine ecosystems and also function as determinants of the bioaccumulation of pollutants.

Niche separation between the cultivated strain and more widely investigated lipid-degrading bacteria will be investigated using comparative analyses of their physiology and genomes. We will attempt to enrich additional strains of JTB255 bacteria using knowledge acquired from the characterization of the strain that is currently available.


You are a highly motivated young researcher with an MSc degree in microbiology or microbial ecology. You are eager to elucidate the lifestyle and traits of microorganisms and you are willing to work across disciplines using experimental work on cultivated bacterial strains, ecological molecular approaches, and comparative genomics.

Some experience in handling and maintaining bacterial cultures is strongly desired but experience in comparative genomics and/or knowledge of biochemistry (especially microbial metabolisms) would also be advantages. You will be working in an international research environment. A very good command of spoken and written English is therefore essential.


Employment of this position at Royal NIOZ is by NWO-I (The Netherlands Organization of Scientific Research). We offer a 4-year full time position with an excellent salary, a pension scheme, a holiday allowance of 8% of the gross annual salary, a year-end bonus, and flexible work arrangements. You may expect very attractive secondary employment conditions. We offer generous relocation expenses for employees coming from abroad and support with finding accommodation.

For additional information about this vacancy, please contact Dr. Pierre Offre .

For additional information about the procedure, please contact Jolanda Evers (senior HR advisor).

posted: 14 February 2018     Please mention EARTHWORKS when responding to this advertisement.