Eight fully funded PhD positions:


1) Physiology and ecology of the neonatal gut microbiota

Duration of contract: 4 years 
Planned starting date: ASAP 
Place of work: University of Vienna/AIT
Main supervisor: David Berry

Project description:

Extremely premature infants, which are born before the 28th week of gestation and weighing <1,000 grams, are a highly vulnerable patient group. They frequently experience early-life brain injury that can lead to life-long neurological impairments. Recent research suggests that the gut microbiome can affect the immune system and brain development. As the neonatal gut microbiota-immune-brain axis is important in both short- and long-term neurological diseases, it is a promising target for early-life therapeutic intervention. In order to achieve this, a deeper understanding of the interplay between the microbiome, the immune system, and the brain in early life is urgently needed. This project aims to determine how dysfunction in the gut microbiota-immune-brain axis in extremely premature infants contributes to brain damage and long-term cognitive impairment. The molecular mechanisms underlying the etiology of these neurodevelopmental issues will be addressed in three project areas focused on the components of the axis: the gut microbiome, immune system, and brain.

The NeoGIBA project will take a stepwise, bottom-up approach to test how the gut communicates with the brain using cutting-edge model systems. Promising leads will be integrated in pre-clinical models to test novel intervention strategies. Specifically, we will determine interactions in the microbiome and how the microbiome communicates with the immune system. We will also dissect how cell-cell interactions propagate gut-derived signals to drive neuronal inflammation, focusing on immune cells as central mediators of the axis. We will characterize intestinal events preceding systemic inflammation and will test the impact of microbial components and inflammatory cues on microglial activation and neuronal cell development and physiology. We will then examine how a dysfunctional axis impacts cognition in pre-clinical models and an established patient cohort.

This project aims to make a major advance in the field by comprehensively investigating how the neonatal gut microbiome and its metabolites interact with the immune system and neurodevelopment. The project will provide fundamental insights into gut microbial ecology and immune- and neurodevelopment. It will contribute to novel translation-oriented strategies for early-life therapeutic interventions to improve the health of premature infants.

Position description:

We are looking for a highly motivated PhD candidate to develop, coordinate, and carry out the multidisciplinary project above. The candidate will be supervised by David Berry and will work in a team with other PhD students as well as Clarissa Campbell (host-microbe interactions and immunology, Centre for Molecular Medicine), Isabella Wagner (cognitive neuroscience, University of Vienna), Benedikt Warth (systems biology and metabolomics, University of Vienna), and Lukas Wisgrill (immunology and neonatology, Medical University of Vienna).

The candidate will be responsible for characterizing the microbiome and metabolome of extremely premature neonates using genome-resolved metagenomics and untargeted metabolomics. Additionally, they will characterize the physiology and ecology of isolates of the core gut microbiome. These results should provide insights into the function and assembly of the neonatal gut microbiota and serve as the basis for other work in the research team. Specifically, they will shed light onto the importance of species-specific physiological tolerances and capabilities as well as ecological interactions in determining microbiota assembly and succession. Additionally, they will inform practical strategies for promoting potentially beneficial microbes and conferring colonization resistance against important early-life enteric pathogens including Klebsiella pneumoniae and other pathobionts and immunomodulatory microbes.

The ideal candidate should meet the following criteria: background in microbiology, molecular biology, or related fields; experience working in a microbiology or molecular biology laboratory; programming skills (e.g., Python, R) and motivation to expand those; excellent written and spoken English; excellent skills in project planning and independency in problem-solving; ability to work in a multidisciplinary, international team. 

Experience with experimental design and gut microbiome analysis is strongly desired. 

(Optional) Skills list:

  • Anaerobic cultivation
  • Microbial physiology
  • Genomics analysis
  • Bioinformatics / mathematical modeling expertise
  • Experimental design

Keywords for the position:

Gut microbiota assembly, bacterial physiology, microbial ecology, early life microbiome, gut-brain axis


2) Biodegradable Polymer Degradation in Compost Environments

Duration of contract: 4 years 
Planned starting date: ASAP 
Place of work: University of Vienna/AIT
Main supervisor: Sarah Pati

Project description:

Plastic waste and the global occurrence of plastic/polymer micro- and nanoparticles in the environment has been identified as a major concern regarding environmental health and safety. Most polymer types used in products nowadays are persistent and undergo only very slow degradation, if at all. Environmentally friendly alternatives do exist in bio-degradable polymers, especially PLA and PBAT. It could be shown that these polymers undergo fragmentation and biodegradation/-mineralization within relatively short timeframes. Being proposed as suitable materials for collecting household bio-waste, there is a scientific discussion about how and how fast the fragmentation and complete biodegradation occurs in composting facilities and how the degradation proceeds below the fragment particle sizes which still can be quantified by e.g. Raman microscopy, hence in the size range below 10 µm. The project is a university-industry collaboration and the objective of this PhD project is to implement a sampling, sample preparation and analytical strategy to then quantify the fragmentation and degradation kinetics of biodegradable polymers in different composting procedures which are conducted in the EU member states.

Position description:

We are looking for a highly motivated PhD candidate to develop, coordinate, and carry out the project described above. The candidate will be supervised by Sarah Pati, Thilo Hofmann and Frank von der Kammer (Department of Environmental Geosciences, University of Vienna).

The candidate will be responsible for the development and optimization of the complete analytical workflow required to quantify degradation kinetics in compost and compost amended soil samples: ranging from sampling strategies for heterogeneous samples, homogenization, particle extraction and matrix-separation to the spectral-microscopic identification, counting and sizing of the polymer fragments found in real-world compost and soil samples. The candidate will coordinate the scientific work of the university and industry partners, plan and conduct interlaboratory comparisons and support the method standardization activities towards CEN/ISO. Comparisons of degradation efficiencies of different composting regimes in e.g. Austria, Germany and Italy will be a central part of the case-studies conducted within this project.

The ideal candidate should meet the following criteria: background in chemistry, environmental chemistry and analytics or related fields. Experiences in the analysis of micro-/nanoplastics and/or nanomaterials in complex environmental samples, working in a laboratory tailored for particle analysis and motivation to expand those. Excellent written and spoken English; excellent skills in project planning and independency in problem-solving; ability to work in a multidisciplinary, international team.

Practical experience in electron- and spectral-microscopic techniques (e.g. SEM, micro-FTIR, micro-RAMAN) is highly desired.


Cluster of Excellence

The following five PhD positions are embedded within the recently established FWF-funded Cluster of Excellence: "Microbiomes Drive Planetary Health”. For more information on the Cluster and the individual Work Packages please visit the following pages:

Application started on March 27, 2024 and continues until positions are filled. 


3) The Influence of Invasive Species on Host-Associated Microbiomes 

Cluster of Excellence Work Package: WP 1.2

Duration of contract: 4 years 
Planned starting date: ASAP 
Place of work: University of Vienna/AIT
Main supervisor: Jillian Petersen and Angela Sessitsch
Supervision team: Matthias Horn

Project description:

A number of plants are part of a “blacklist” of invasive species in Europe. The plants of the “blacklist” are considered to have the capacity to change natural environments, influence native vegetations and displace native plant species. In central Europe the most aggressive invasive plants include the knotweed species Fallopia (Reynoutria) japonica (Japanese knotweed) and F. sachalinensis (Sakhalin knotweed) (EPPO Lists of Invasive Alien Plants, 2023). The reason for the success and invasiveness of Fallopia spp. is associated with its clonal propagation and by its capacity to produce a number of secondary phenolic compounds with potential allelopathic activities (Martin et al., 2020, NeoBiota 56: 89-110; Stefanowicz et al., 2021, Sci Total Environ. 767:145439). These phenolic compounds including condensed tannins, catechin, chlorogenic acid, emodin and others and might be part of the reason for the reduction of total fungal (25%) and bacterial (30%) biomass reduction. Other studies suggest an overall increase of bacterial diversity in plant microbiomes, especially in environments with allelopathic compounds produced by invasive plant species (Torres et al. 2021, BMC Ecol Evo 21, 172). Other invasive species with strong allelopathic compound production but distinct reproduction strategy include Impatiens glandulifera (Himalayan balsam), where the phenolic naphtoquinones play an important role (Block et al., 2019, Plant Direct 3: e00132).

The PhD student will perform the following tasks: 

  • Assess whether invasive plants have specific rhizosphere, endophytic or epiphytic microbiomes
  • Assess whether there are specific functions associated with these microorganisms, including high adaption to the invasive species or metabolization of the allelopathic substances
  • Assess whether the microbiome plays a role in the shaping of the invasive character and negative influence on other plants
  • Assess whether there are selective pressures shaping the plant microbiome

4) Impacts of bacterial associated ectomycorrhizal fungi on forest fungal and tree growth

Cluster of Excellence Work Package: WP 2.1

Duration of contract: 4 years 
Planned starting date: ASAP 
Place of work: University of Vienna
Main supervisor: Mark Anthony
Supervision team: Christina Kaiser, Carlos Gustavo Arellano Caicedo, Christine Moissl-Eichinger, Dagmar Woebken, Andreas Richter

Project description:

This project aims to understand the ecology of ectomycorrhizal fungal associations with bacteria in the environment and its influence on tree growth and development. A rich community of bacteria with unique ecological strategies inhabit the exterior and interior mycelium of ectomycorrhizal fungi, but we are only beginning to understand the functional ramifications of these tripartite interactions (bacteria-fungi-plant). This project uses microfluidics, mesocosms, and field experiments to cross scales and produce a harmonious framework of the impacts of co-occurring bacteria on ectomycorrhizal fungal and forest tree growth and development.

Ideally, you will already possess, but more importantly have a keen interest in developing your expertise in fungal ecology, fungal and bacterial culturing, plant ecology, plant-microbe interactions, and/or genomics. This position also involves fieldwork and includes multiple excursions to Switzerland. Candidates should hold an MS degree in biology, microbiology, or a related field. 


5) Emerging pollutant transformation and reactive oxygen species formation by oxygenase enzymes in different microbiomes

Cluster of Excellence Work Package: WP 3.2

Duration of contract: 4 years 
Planned starting date: ASAP 
Place of work: University of Vienna
Main supervisor: Sarah Pati
Supervision team: Thilo Hofmann, Christine Moissl-Eichinger, Andreas Richter

Project description:

This subproject aims to investigate the transformation of emerging pollutants, such as tire additives, pharmaceuticals, and consumer products, by oxygenase enzymes in various microbiomes. Oxygenase enzymes play a crucial role in degrading pollutants in the environment by transforming a wide range of compounds into more polar and bioavailable products. However, under certain conditions, these enzymes exhibit poor efficiency in oxygen utilization, leading to the unintended production of reactive oxygen species (ROS). The PhD candidate in this project will perform exposure experiments with emerging pollutants and microbial communities from soil, freshwater, wastewater, and the human lung. In addition, methods will be developed to identify transformation products and quantify ROS. The outcomes of these experiments will determine whether a negative impact of (emerging) pollutants on environmental and human microbiomes can arise not only from the toxicity of the pollutants and their transformation products but also from the production of ROS by oxygenase enzymes. The ideal candidate has a background in environmental or analytical chemistry and a keen interest in studying organic pollutant transformation with high-resolution mass spectrometry and/or stable isotope techniques.


6) Survival and resuscitation mechanisms of desert soil bacteria

Cluster of Excellence Work Package: WP 7.3

Duration of contract: up to 4 years 
Planned starting date: Summer 2024 
Place of work: University of Vienna
Main supervisor: Dagmar Wöbken
Supervision team: Christina Kaiser, Holger Daims, David Berry

Project description:

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.

In this project, we are investigating the mechanisms of desert soil microorganisms that allow desiccation survival and resuscitation. This will be achieved by applying genome-resolved metatranscriptomics of desert soil microbial communities. In situ community transcription patterns will be combined with single-cell activity assays (such as heavy water-NanoSIMS) to detect anabolically active cells and process measurements.

The ideal candidate for this position should have a background in microbiology or microbial ecology and experience in molecular tools to investigate diverse microbial communities (such as amplicon sequencing). The candidate should be excited to apply cutting-edge molecular approaches to identify active community members (i.e. via stable isotope probing) and interested in -omics data analyses. 


7) The effect of seasonal oxygen fluctuations on aquatic microbiomes

Cluster of Excellence Work Package: WP 7.3

Duration of contract: 4 years 
Planned starting date: Summer 2024 
Place of work: University of Vienna
Main supervisor: Barbara Bayer
Supervision team: Christina Kaiser, David Berry

Project description:

Extensive human activities (e.g., agriculture, industrial production, and sewage discharge) have led to increased eutrophication of lakes and marine coastal zones. As a result, aquatic ecosystems are more frequently affected by hypoxia or anoxia, and coastal bottom waters often display strong seasonal fluctuations in oxygen concentrations. Oxygen availability can have a major impact on microbial metabolism and thus likely affects microbial community composition and microbiome functioning. The PhD candidate will investigate changes in microbiome functioning in response to oxygen depletion by combining metagenomic and -transcriptomic sequencing with activity measurements using stable- and radioisotope approaches. Our goal is to further understand if microbial communities are better adapted to oxygen depletion if they have previously experienced anoxic events.

Project-related tasks include: 

  • Microbial activity measurements and community profiling in coastal marine ecosystems
  • Metagenomics and -transcriptomics 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. The ideal candidate has experience with/or a strong interest in applying isotope techniques and bioinformatics methods. Willingness to plan and conduct fieldwork in coastal ocean environments is required.


8) Microbiome-Enhanced Silicate Weathering

Cluster of Excellence Work Package: WP 6.2

Duration of contract: 4 years 
Planned starting date: ASAP
Place of work: University of Vienna
Main supervisor: Petra Pjevac
Supervision team: Andreas Richter, Stephan Krämer, Peter Hinterdorfer, Thomas Böttcher

Project description:

The PhD Student will investigate the effect of soil microorganisms and mineral/rock preparations (type of rock powder, grain size, aggregation state) on enhanced silicate weathering rates and weathering product. Mineral bag experiments will be performed in situ on the field to investigation microbe-mineral interactions on the micro-scale, including weathering, secondary mineral formation, and depleted layer formation in relationship to microbial colonization, and to beneficial identify microbial consortia that enhance weathering. Experimental setups will include microbial cultures and agricultural soil microcosm, where effects of microbial colonization, inoculations and microbiome transfer on enhanced silicate weathering and carbon sequestration will be analyzed and quantified.


Gender equality, diversity and non-discrimination

© Manuel Lavoriero

The University pursues a non-discriminatory employment policy and values equal opportunities, as well as diversity (http://diversity.univie.ac.at/). The University lays special emphasis on increasing the number of women in senior and in academic positions. Given equal qualifications, preference will be given to female applicants.

The University of Vienna has an institutionalised gender equality policy and within this framework VDSMES strives to strengthen the career development of female scientists at all qualifications levels and to support compatibility between family and work/training.

The Gender Equality and Diversity unit of the University of Vienna provides services which, based on the issue of gender equality, aim at ensuring equal opportunities for all university members.