Open positions

Postdoc position on the ecology and evolution of giant viruses

We are seeking a bioinformatic postdoctoral researcher for the ERC funded project “CHIMERA”.

CHIMERA investigates the role of mobile genetic elements in the ecology and evolution of giant viruses. These viruses are abundant in soil and aquatic environments, infecting a wide range of protist hosts. Besides unusually large particle sizes, giant viruses possess complex “chimeric” genomes, including genes that were likely acquired from their hosts as well as bacteria that infect the same hosts. Unique is the presence of mobile genetic elements, that may play an important role in host-parasite co-evolution, whereby the same molecular systems are employed by hosts and parasites for defence and subsequent counter-defence. The holder of this position will support the project by studying the competition and interactions between viruses, bacteria and their hosts, from the micro (in a controlled laboratory environment) to the macro scale (in the wild). The research will be conducted as part of a Starting Grant from the European Research Council under the supervision of Anouk Willemsen.

Tasks:

Specific research tasks will be tailored to the candidate. These can include:

• Field work to obtain samples.
• Prepare samples for targeted metagenomics and single-cell sequencing.
• Bioinformatic analyses on the sequence data.
• Possibility to do laboratory work with the obtained samples (e.g. microscopy, flow cytometry).

General tasks include:

• Active participation in research, publication, administration and communication activities.
• Collaborate with members of the research team.
• Present work output in group and departmental seminars.
• Disseminate results at national and international conferences.
• Supervision of trainees and students.

Profile of the Candidate:

• PhD degree (or equivalent) in Biology/Microbiology/Virology/Molecular Biology/Systems Biology/Computational Biology or a related subject.
• Expertise in bioinformatic analyses
• High ability to express yourself both orally and in writing.
• Very good organizational skills.
• Ability and willingness to work independently as well as in a larger team.
• Willingness to acquire new methodological skills required for the project.
• Excellent command of English (written and spoken).

For further information, please contact: Ass.-Prof. Dr. Anouk Willemsen (anouk.willemsen@univie.ac.at)

Application deadline: 30th November, 2023

PhD position on microbial methane cycling in aquatic ecosystems

A fully funded (4-year) PhD position is available at the Division of Microbial Ecology (DOME) at the Centre for Microbiology and Environmental Systems Science (CeMESS), University of Vienna, Austria. The PhD candidate will conduct research within the framework of the Austrian Science Fund (FWF) START Grant “METHANIAQ” under the supervision of Barbara Bayer, PhD.

Project description:
Aquatic ecosystems are a major source of the potent greenhouse gas methane, accounting for half of the global methane emissions. Biogenic methane is microbially produced in anoxic sediments and typically rapidly consumed by methanotrophic microorganisms, largely limiting emissions to the atmosphere (=”microbial methane filter”). Enhanced eutrophication due to human activities has been linked to increases in methane emissions from coastal ocean and lake ecosystems. Yet, it is unclear how such changes in environmental conditions affect the in situ activities of methanotrophic microorganisms. The PhD candidate will conduct research to understand the impacts of eutrophication on methane consumption in lakes and coastal zones.

Project-related tasks include:
• Laboratory experiments with methanotrophic microorganisms
• Methane measurements at multiple lake and/or ocean sites
• Metagenomics of in situ microbial communities
• Data analyses and preparation of scientific publications
• Presenting work output in department seminars and at conferences
• Co-supervision of trainees and students

The successful candidate will benefit from a collaborative and international research network. We thrive to be an inclusive, welcoming and safe environment for people of all backgrounds, ethnic identities and gender identities.

Ideal start date is January 2024 with some flexibility to start later.

Requirements:
Interested candidates (f/m/d) should have a MSc degree (or equivalent) in Microbiology/Ecology/Aquatic Sciences/Geochemistry or a related field. A strong interest to learn new methodological skills required for the project is essential. Previous experience with laboratory and/or fieldwork is of advantage. The candidate must have the ability to work independently but also in research teams. Self-motivation, creativity and curiosity are essential assets. Willingness to plan and conduct fieldwork in lake and/or ocean environments is required. The candidate must have good organizational skills and a very good level of spoken and written English.

How to apply:
For informal enquiries or to apply, please contact Barbara Bayer (barbara.bayer@univie.ac.at). For applications, please send a short (max. 1-page) cover letter (highlighting your main interests and relevant experience) and your CV (including the contact information for 2 references). For full consideration, please send your application until October 15th.

Postdoctoral position in the Group of Dagmar Woebken

EXPLORING SURVIVAL AND RESUSCITATION MECHANISMS OF DESERT SOIL BACTERIA

The Woebken Group is accepting applications for a Postdoctoral position.

Background:

Microorganisms in drylands have to endure long periods of drought, interrupted by unpredictable and very short periods of rain. Dormancy - an inactive state or a state of reduced metabolic activity - has long been regarded as a prerequisite for desert soil microorganisms to survive such drought periods. However, as dormancy cannot be sustained indefinitely, phases of resuscitation must also play an important role for long-term survival of desert soil microorganisms and thus for maintaining microbial diversity in one of the harshest environments on the planet.

Project:

In this project, we are investigating the desiccation survival mechanisms of soil microorganisms and the molecular mechanisms of resuscitation. This will be achieved by applying genome-resolved metatranscriptomics of desert soil microbial communities, building upon knowledge gained by our recent metagenomic investigation of biological soil crusts from the Negev Desert, Israel. In situ community transcription patterns will be combined with single-cell activity assays, employing a recently developed heavy water-NanoSIMS assay to detect anabolically active cells, and process measurements.

Requirements:

Candidates should had a PhD degree in microbiology or biological sciences. A background in microbial ecology (ideally soil microbial ecology) with experimental or fieldwork experience is necessary. A comprehensive understanding of microbial physiology, along with generating and interpreting meta-genomic or metatranscriptomic data is mandatory. We expect the candidate to be creative and innovative with her/his/their research ideas. Proficiency in spoken and written English is mandatory. Good scientific writing and verbal communication skills are necessary. The ability to work and communication in a team is essential.

For additional details, please see the pdf.

Please enclose the following documents to your application:

• Letter of motivation (1-2 pages)
• Curriculum Vitae
• University certificate(s), including grades
• Two letters of recommendation

Please send your application as a pdf to dagmar.woebken@univie.ac.at with the subject "Postdoc-position Survival and Resuscitation". 

Master's Student in the group of Martin Polz

We are looking for a highly motivated master's student interested in the co-evolutionary interactions of bacteria and their viruses. The master thesis project is taking place in the research group of Prof. Martin Polz at the Department of Microbial Ecology (DoME) at the University of Vienna. The duration of the project is for six-months.

Background:
Due to the immense evolutionary pressure imposed by phages, bacteria have evolved many mechanisms to evade phage infection and killing, for example, well-known CRISPR-Cas and restriction-modification systems. In turn, bacteriophages have developed various strategies to bypass immunity for successful infection. Yet, the diversity of phage evasion strategies and mechanisms of their action remain largely unknown. Therefore, it is essential to study phage-host interactions to understand the ecological dynamics of microbes and for potential application in phage therapy.

Project:
The master thesis project will study candidate counter-defense proteins of Vibrio phages which act as a counterplay against defense mechanisms of marine Vibrio bacteria. The project will include molecular cloning of the bacterial defense systems and viral counter-defense proteins in a laboratory strain of Vibrio, as well as bioinformatics and viral infection experiments.

Requirements:
Candidates should hold a BSc degree in Biology (particular emphasis in microbiology, microbial ecology, molecular biology, or similar). The applicant should have previous laboratory experience, particularly in the fields of microbiology and molecular biology. We are looking for a master's student who is highly motivated, with good communication skills, and ability to work in a large department with numerous labs. Our lab consists mainly of foreign scientists; therefore, candidates should have excellent English writing and oral communication skills.

Please enclose the following documents to your application:
• Letter of intent
• Curriculum Vitae
Please send it to: martin.f.polz@univie.ac.at