A PhD position is available at the Institute of Biology, Leiden University within the EU Horizon 2020 MARBLES project - Marine biodiversity as sustainable resource of disease-suppressive microbes and bioprotectants for aquaculture and crop diseases.

Marine microorganisms are a largely untapped resource for bioactive molecules. In this project, the  marine microbial biodiversity will be used to harness the potential of such microorganisms to protect their host and for the production of novel antimicrobial agents. As hosts, we focus on fish, algae and sponges. Within this specific PhD project, we will identify microbes that protect their host from infections, elucidate how they communicate with their host, and identify the compounds and the biosynthetic gene clusters (BGCs) that specify their biosynthesis. We will focus on the regulatory networks that control the gene expression of the BGCs and the molecular triggers and cues that elicit the production of compounds that are not produced under routine growth conditions. BGCs that specifically respond to host-derived and other elicitors will be analysed using bioinformatic tools to identify the underlying regulons and reconstruct transcriptional regulatory networks. The data will then be used to prioritise specific regulons associated with pathogen responses. The elicitors that active silent BGCs will be harnessed for (re-)screening of strain collections. Novel culturing and eliciting approaches will be applied to express, extract and identify the bioactive molecules of interest. Comparative metabolomic analysis and molecular networking will support the identification of specific BGCs and their bioactive molecules that are likely implicated in disease suppression. Genetic manipulation of individual microbes or microbial communities will provide further insights into the role of specific strains and their BGCs in disease suppression. The successful candidate will work closely with other PhDs and PDs within the MARBLES consortium.

Aims of the Project:

• Identify elicitors that activate the production of cryptic compounds;
• Unravel the regulatory networks and regulatory elements that control cryptic BGCs for prediction of their elicitation;
• Initial assessment of candidate molecules via metabolomics and molecular networking;
• mutagenesis of BGCs in individual microbes and in microbial communities;
• develop microbes and compounds for application in aqua- and agriculture.

Key responsibilities

• Microbial screening to identify and select bacteria with antimicrobial activity;
• Testing and Identifying chemical or marine elicitors that activate the production of cryptic metabolites;
• Application of molecular biology and mutagenesis techniques such as CRISPR-Cas;
• Extraction and purification of microbial bioactive compounds;
• Production of bioactive molecules from selected BGCs in native and heterologous hosts;
• Collaborate with other scientists in the MARBLES consortium.

• MSc degree in molecular microbiology or similar discipline with strong affinity for Biochemistry;
• Strong knowledge and experience in microbiology and molecular biology techniques;
• Expertise is systems biology and interest in global regulatory networks;
• An interest in the role of microbial communities in host protection;
• Experience with metabolomics will be of added value;
• Good communication (verbal and writing) skills in English.

We offer a  full-time 1 year term position for initially one year. After a positive evaluation of the progress of the thesis, personal capabilities and compatibility the appointment will be extended by a further three years. Salary range from € 2.395,- to € 3.061,- gross per month (pay scale P in accordance with the Collective Labour Agreement for Dutch Universities).

Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses (8.3 %), training and career development and sabbatical leave. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. Candidates from outside the Netherlands may be eligible for a substantial tax break. For more information, see the website.All our PhD students are embedded in the Leiden University Graduate School of Science.

Our graduate school offers several PhD training courses at three levels: professional courses, skills training and personal effectiveness. In addition, advanced courses to deepen scientific knowledge are offered by the research school.

Diversity
Leiden University is strongly committed to diversity within its community and especially welcomes applications from members of underrepresented groups.

Leiden University

The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are committed to expand fundamental knowledge by curiosity and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future.

The research carried out at the Faculty of Science is very diverse, ranging from mathematics, information science, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The research activities are organised in eight institutes. These institutes offer eight bachelor’s and twelve master’s programmes. The faculty has grown strongly in recent years and now has more than 2300 staff and almost 5000 students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together. For more information, see the website of the Faculty of Science.

The research within the Institute of Biology Leiden (IBL) aims to work on the science base of biodiversity and health, which is reflected in our leading principle Harnessing Biodiversity for Health. We perform innovative curiosity-driven research to answer fundamental questions, and solutions-driven research to help solving major societal challenges. The latter include protecting nature’s biodiversity, creating sustainable biotechnology and agriculture and increasing good health. Our research focuses on four Research Themes: Bioactive Molecules, Host-Microbe Interactions, Development & Disease and Evolution & Biodiversity. Located in a thriving scientific environment with our Faculty of Sciences,  Naturalis Biodiversity Centre, the Leiden University Medical Centre and the Leiden Bioscience Park, IBL offers an exciting, internationally oriented and inclusive place to work and study.