Tawaran Beasiswa S3: PhD – “Ecophysiology, metagenomics and lipidomics of nitrite-oxidizing bacteria under oxygen deprivation”

This project is part of the Gravitation Research Program SIAM – Soehngen Institute of Anaerobic Microbiology (https://www.anaerobic-microbiology.eu/).The PhD project will be developed at the Department of Marine Microbiology and Biogeochemistry, Royal NIOZ, Texel (Principal Investigator dr. Darci Rush), and at the Department of Microbiology, Radboud University, Nijmegen (Principal Investigator dr. Sebastian Lücker).

LOCATION:              NIOZ TEXEL (with frequent visits to Radboud University Nijmegen)

VACANCY NR.:        2019 – 73

CLOSING DATE:       30-09-2019     

THE DEPARTMENT

Researchers in the Department Marine Microbiology and Biogeochemistry (MMB) aim to understand the crucial role that microorganisms play in regulating global biogeochemical cycles, including primary productivity, carbon sequestration, and changing climate. To support this research, the Royal NIOZ has a sea-going research fleet to collect marine water column and sediment samples. MMB also offers world-leading in-house analytical facilities for both lipid and molecular techniques.

At Radboud University, the microbiology research has focused on the discovery of new (an)aerobic ammonium, nitrite and methane-oxidizing microorganisms, and the elucidation of their genomes and metabolisms. The RU Microbiology department provides ample opportunity for scientific cooperation, in particular in the areas of microbial (eco)physiology equipped with state-of-the-art bioreactor facilities and analytical (GC, GC-MS, HPLC) equipment, microbial (meta)genomics using high-throughput sequencing and bioinformatics, microbial cell biology with advanced electron microscopic facilities and Microbe-Host interactions.

THE PROJECT

This project is part of the Gravitation Research Program SIAM – Soehngen Institute of Anaerobic Microbiology (https://www.anaerobic-microbiology.eu/).The PhD project will be developed at the Department of Marine Microbiology and Biogeochemistry, Royal NIOZ, Texel (Principal Investigator dr. Darci Rush), and at the Department of Microbiology, Radboud University, Nijmegen (Principal Investigator dr. Sebastian Lücker). 

This project will describe the ecophysiology of nitrite-oxidizing bacteria (NOB) under extreme oxygen limitation with the ultimate aim of understanding the effects low oxygen environments have on their lipid profile and nitrite-oxidizing capacity. To achieve this, the study will focus on Nitrospina-like bacteria enriched from marine oxygen-depleted environments. Moreover, sedimentary records will be evaluated for novel biomarker lipids to reconstruct nitrification in past biogeochemical cycling and retrace the history of NOB in marine OMZ.

Using the state-of-the-art methodology and instrumentation at NIOZ, NOB pure culture and marine enrichments cultured by the PhD candidate will be analysed for novel biomarker lipids. NOB pure culture maintenance and enrichment of novel Nitrospina-like NOB from OMZ water samples will be performed at RU using stat-of-the-art bioreactor setups. From this data, we will develop biomarker proxies to analyse their abundance and metabolism in available sediment record samples at NIOZ.

This research will be conducted in the framework of the Soehngen Institute for Anaerobic Microbiology SIAM (Gravitation grant ‘Zwaartekracht’, from the Dutch Ministry of Education, Culture and Science).

THE CANDIDATE

The ideal candidate holds a MSc degree in (organic) geochemistry, microbial ecology, marine sciences, chemical oceanography, (analytical) chemistry and/or a related field. Expertise in microbiology would be advantageous. You are well-organized and methodical in the lab but also willing to get your hands dirty while sampling and analyzing natural systems, often under demanding conditions. Fieldwork at sea can be expected during this PhD position.

You are eager to communicate your findings at (inter)national conferences and in peer-reviewed publications and you have excellent computer and software skills.

The inter-disciplinary and international research environments at the Royal NIOZ and at RU suit you well, and you have an excellent command of the English language in speaking and writing.

CONDITIONS OF EMPLOYMENT

We are offering fulltime positions for 4 years, a pension scheme, a yearly 8% vacation allowance, year-end bonus and flexible employment conditions. Conditions are based on the Collective Labour Agreement of Research Centers. The position will be located on Texel. Cost of relocation and help with housing is provided by NIOZ.

FURTHER INFORMATION

Additional information about the vacancy can be obtained from: Dr. Darci Rush (Research Scientist).

Additional information about the procedure can be obtained from Alexandra Noppeney (Sr HR Advisor).

Interviews will be held on November 6th 2019.

Press Release: Workshop on Zooxanthellae Isolation

Pada hari Senin (29/7/2019), Departemen Ilmu Kelautan sukses melaksanakan kuliah umum dan dilanjutkan dengan workshop yang di berikan langsung oleh Prof. Ranjeet Bhagooli dari University of Mauritius. Acara ini dibuka langsung oleh Dr. Agus Trianto, S.T., M.Sc selaku Ketua Prodi Ilmu Kelautan dan dihadiri oleh 19 peserta.

Prof. Ranjeet telah melakukan kegiatan pengajaran dan pelatihan di Undip dari tanggal 24 Juli hingga 5 Agustus 2019 melalui program World Class Professor yang merupakan hibah dari Kementerian Riset, Teknologi dan Pendidikan Tinggi (Ristekdikti) ke pada Dr. Ir. Diah Permata Wijayanti, M.Sc.

Melalui kegiatan ini, diharapkan civitas akademika Departemen Ilmu Kelautan mampu meningkatkan lab skill untuk mengisolasi Zooxanthellae serta mengkaji respons stresnya atas perubahan iklim global saat ini.

Discussion between Dr. Dwi Haryanti and Prof. Ranjeet
Observation of Zooxanthellae
Morphological characteristics of the observed Zooxanthellae