A PhD position is available for the Horizon2020 Project: Marine Biodiversity as Sustainable Resource of Disease-Suppressive Microbes and Bioprotectants for Aquaculture and Crop Diseases (MARBLES).

MARBLES will use a novel and systematic approach to access and exploit marine microbial biodiversity for sustainable bioprospecting to discover microbial consortia and bioactive molecules for application in aqua- and agriculture and in the clinic. MARBLES' ecology-based bioprospecting strategy will focus on unique host-microbe interactions in marine environments, including marine sponges, microalgae and fish, which rely on their microbiomes and microbial natural products for disease resistance. Partners’ existing microbial collections and new ones generated during MARBLES will be harnessed for the discovery of novel natural products and synthetic microbial communities. For this, MARBLES will use a systems-wide genomics approach to uncover the bioactive agents in disease-suppressive microbiomes. Also, MARBLES will explore host- and microbe-derived chemicals that elicit production of bioactive compounds, as elicitors to revitalise drug screening. The deliverables will be microbes and consortia and bioactive natural products, their derivatives and elicitors, which can be harnessed to fight infectious diseases in the agrochemical and aquaculture industries and in healthcare. Besides highly innovative, the approaches will be cost-effective and will offer advantages from both environmental and health perspectives in comparison to existing alternatives. The sustainable production of bioprotectants will increase the effectiveness of fish production - reducing the pressure on harvesting wild fish - and aid the transition of the crop agriculture sector towards bio-based and circular solutions. MARBLES will work closely together with a panel of companies from the EU aquaculture, crop protection biotechnology and health sectors.

NATURALIS Biodiversity Center, Leiden, The Netherlands


The functional microbial diversity and biosynthetic gene clusters (BGCs) diversity in sponges

Supervisors:  Nicole de Voogd & Detmer Sipkema

More information and full job advertisement at https://www.naturalis.nl/en/about-us/phd-marbles

The aim of the PhD-project is to link global sponge biodiversity patterns to both overall microbial diversity and biosynthetic gene cluster (BGCs) diversity in selected sponge families and orders in a variety of marine environments, such as the deep sea, coral reefs and large enclosed water bodies.
Marine sponges are invertebrate animals that harbour a diverse and often specific microbiome. These serve both as degraders of organic compounds providing nutrients to the sponge host, but also as producers of secondary metabolites acting as defence mechanism. The sponge microorganisms have a large potential for the production of bioactive compounds. The identification of biosynthetic gene clusters (BGC’s) in bacterial genome sequences has become a powerful tool for natural product discovery. So far, many different BGC’s have been identified in a variety of sponges that play a key role in microbiome/sponge interactions and distinct chemistry of certain sponge species. In the present study, functional diversity of BGC’s will be assessed using metagenomics sequencing and metatranscriptome analysis to detect global biodiversity patterns within sponges to be linked to both overall microbial and BGC diversity. 

The PhD position fits within the research of Prof Dr Nicole de Voogd (Naturalis Biodiversity Center and Leiden University) and Dr Detmer Sipkema (Wageningen University and Research) who will act as daily supervisors. Prof Dr Nicole de Voogd investigates microbial communities of sponges in tropical marine ecosystems (for more information: https://www.naturalis.nl/en/nicole-voogd) and Dr Detmer Sipkema research is focusing on metagenomics, cultivation and bioactivity of sponge-associated microbes. Scientific director of Naturalis Prof Dr Koos Biesmeijer and Prof Dr Nicole de Voogd will act as promotors.
The PhD candidate will be housed in Naturalis (Leiden, the Netherlands), but regular short-term visits to WUR are required. A PhD training program is part of the agreement and you will be enrolled in the Graduate School of Leiden University. 

General requirements and skills

Preferably the candidate has the following skill set:

● A general interest in marine invertebrates and symbioses, ideally with an affinity to sponges and experience with scientific diving and willingness to do fieldwork is a pre, but not a prerequisite;

● background in molecular techniques, preferably some expertise in next-generation sequencing methods; 

● eager to do molecular lab work;

● excellent knowledge of the English language (written and verbal);

● scientific and critical attitude, excellent time management and organizational skills; 

● ability to work independently as well as collaboratively within the team;

● good communication skills;

● willingness to supervise BSc & MSc students 

We offer

A contract (36 hours per week) for a period of one year, to be extended with three more years after a successful first year evaluation (4y in total), and a monthly starting salary of € 2,840.- (circa € 37,500.- gross per year). The successful candidate will be employed by Naturalis in Leiden. Naturalis Biodiversity Center offers an inspiring working atmosphere with effective and efficient supervision of our PhD candidates. Our Research Coordination Office also provides ample support to our scientific staff. Our institute promotes gender equality and wants to enhance the diversity of staff members. Feel free to contact Prof Dr Nicole de Voogd with questions about the position: Nicole.devoogd@naturalis.nl


Applicants are invited to submit their application, including a cover/motivation letter, CV and two letters of recommendation. Please use this form for your application no later than August 27, 2021, 17.00h CEST. Interviews are foreseen to take place in the second week of September. The PhD position is expected to start October 1st 2021 at the earliest.

Naturalis endorses the Cultural Diversity Code. In the case of equal suitability, preference is given to the candidate who reinforces diversity within the team.

Application deadline:
Location: Leiden, The Netherlands