Projects and Work Packages

Project 1 - Interactions in Underexplored Ecosystems

WP 1.1 - The Small Intestine: an Underexplored Habitat with Implication for Human Health

The small intestine (SI) is an important site for the absorption of (micro-)nutrients, fat digestion, and immunity. Although the SI harbors billions of microorganisms, their interactions and impact on human health remain poorly studied. SIBO (small intestinal bacterial overgrowth) patients, for example, present with vitamin B12 deficiency and report abdominal discomfort. Interestingly, ~40% of patients exhale methane instead of hydrogen, proving the involvement of methanogenic archaea. 
Our goal is to understand the local composition, ecological principles, and dynamics of the SI microbiome. Given our strong expertise on archaea, we will specifically investigate the interaction between the host, the bacteriome, and the archaeome using SIBO as setting of medical relevance. Our key questions are: (i) Where are SI microorganisms located, and how do microbiomes fluctuate during health and disease? (ii) What impacts do microbes have on nutrient uptake and health? (iii) How does the SI microbiome interact with the immune system? 

PhD position (Moschen)          Postdoc position (Moissl-Eichinger) - filled

 

WP 1.2 - The Influence of Invasive Species on Host-Associated Microbiomes 

Species invasions are one of the biggest causes of ecosystem change. Rapid climate shifts will result in redistributions of plant and animal species, changing the natural world beyond recognition and causing massive ecological and economic consequences. Invasive plants and animals have the potential to alter microbial ecosystems where they invade, but so far, most studies of these effects were limited to a few introduced pathogens that hitchhiked on invasive plants and animals. Our central goal is to answer fundamental questions about how native and introduced microbiomes interact to influence the ecological and economic outcomes of biological invasions. For this we will focus on two plant systems as model experimental systems, using a range of methods from molecular omics to experimental microbiome manipulation to investigate the potential roles of the microbiome in invasion success.

PhD position (Petersen and Sessitsch)          Postdoc position (Petersen)          Technician position (Petersen) - filled

 

Project 2 - Interdomain Interactions and Interaction Mechanisms

WP 2.1 - Cross-Kingdom Interactions in the Ectomycorrhizal symbiosis

More than 80% of all plant species are associated with mycorrhizal fungi. They receive a considerable proportion of their host plant’s photoassimilated C, and deliver soil nutrients in return. Extending this partnership to a tripartite symbiosis, mycorrhizal fungi pass on plant C to soil microbes to facilitate nutrient availability. The combined resource exchange at the plant-fungus and the fungus-soil interface is crucial for plant nutrient availability and soil C sequestration. Still, very little is known about its underlying mechanisms. We aim to shed light on this by combining C and N stable isotope tracing with cutting-edge visualisation techniques. We will expose mycorrhizal plants to 13C-labelled CO2 to trace photoassimilated C into mycorrhizal roots and rhizosphere microbial groups. In addition, we will investigate interactions between roots and reduced model microbial communities at the microscale by microfluidic chips (‘root on a chip’) facilitating controlled cell-to-cell interactions between roots, fungal hyphae, and bacteria.

Postdoc position (Kaiser)          Postdoc/High Level Technician position (Ertl) - filled

 

WP 2.2 - Control of Eukaryotic Microbial Populations by Viral Parasites

Viruses greatly outnumber cellular organisms and significantly impact microbial communities and nutrient cycling. However, little is known about how viruses interact with major microbial groups such as heterotrophic protists. Recent evidence suggests that giant DNA viruses (Nucleocytoviricota) are important predators of heterotrophic protists. These giant viruses are highly unusual, with genome and particle sizes comparable to those of bacteria, and a number of features previously known only from cellular organisms. 
This work package aims to investigate viral interactions with protists by employing cutting-edge techniques, including isolation, high-resolution time-series sampling, and advanced sequencing methods. Our overall aim is to uncover novel giant virus diversity and to unravel coupled dynamics of protist and giant virus populations in complex microbial communities to determine to what extent eukaryotic microbial populations are controlled by these viral parasites.

PhD position (Horn) - filled          Postdoc position (Horn)

 

WP 2.3 - Probing interkingdom crosstalk during inflammation

How does inflammation induce shifts in the gut microbiome? Do distinct types of immune responses imprint specific dysbiotic signatures? Are all types of inflammation perceived similarly by the brain?
In this project, we will investigate the effects of distinct infectious agents on the gut microbiome, aiming to understand how the ecological processes between members of the entire community (bacteria, archaea, fungi and viruses) respond to challenge-specific inflammatory cues. Behavioral changes including anorexia and anhedonia are often induced by systemic inflammation; however, whether challenge-specific microbial shifts contribute to induce unique brain states during disease remains unknown. We will use animal models of infection, metagenomics profiling, phage cultivation techniques, gnotobiotic models, behavioral tests and brain network mapping to address these questions.

PhD position (Polz)- filled          Postdoc position (Campbell) -filled          Technician position (Campbell) - filled

 

Project 3 - Chemical Perturbations and Microbiome Functioning

WP 3.1 - Impact of Drugs on Microbiomes in Humans and Wastewater Treatment

Human gut and wastewater microbiomes interact with pharmaceuticals in multiple ways, which can have profound consequences for the treatment of patients and the health of ecosystems that receive pharmaceuticals. In this work package, we will study how commonly used pharmaceuticals and pharmaceutical combinations affect the composition and function of human-associated and environmental microbiomes. Meta-omic techniques in combination with single-cell isotope-probing will be used to quantify abundance and activity changes of small and large intestine human gut microbiome members in response to selected pharmaceuticals in healthy individuals. In parallel, gut microbiome structure and function will be characterized in respective patient cohorts. Complementarily, we will study the biotransformation of pharmaceuticals to better understand the effects of biotransformation products on microbiomes and the fate of pharmaceuticals in environmental systems. To identify enzymes with potential roles in pharmaceutical biotransformation and to derive links between enzyme abundance and biotransformation rates, we will develop workflows based on metaproteomics and protein-reactive chemical probes. The resulting insights will provide guidance for personalized therapy and pave the way for innovative technologies to reduce negative effects of pharmaceuticals on human and environmental microbiomes.

PhD position (Hofmann) - filled          Postdoc position (Wagner M and Berry)

 

WP 3.2 - Impact of Emerging Pollutants on Microbiomes across Systems

Chemical pollution can have profound effects on microbial communities, and thus on biodiversity, ecosystem function, and human health. Here, we aim to understand the reciprocal interactions between non-exhaust emissions (NEE), such as brake and tire wear particles, including their additives, and different human and soil microbiomes. We address the research questions (i) How is the human and soil microbiome affected by exposure to NEE? (ii) Does exposure to NEE induce similar effects in these very diverse microbiomes? (iii) Do these chemical perturbations affect species interactions beyond simple additive effects? (v) Do compositional changes drive functional changes across systems?

Revealing the cross-system effects of chemical pollution on microbiome diversity and functioning will provide an essential knowledge base for designing interventions and setting targets to prevent further planetary harm by chemical pollution.

Postdoc position (Hofmann) - filled          Postdoc position (Loy) - filled

 

Project 4 - Microbiome Responses to Climate and Land Use Change

WP 4.1 - Microbial Interactions under Climate Extremes 

Climate extremes, such as heat waves, extended drought periods and torrential rains, are among the strongest drivers of changes in the functioning of terrestrial ecosystems. At the same time, the frequency and intensity of extreme events are predicted to further increase during the next decades. So far, the response of microbiomes has mainly been studied following one climate extreme, although it is well known that for example heat waves and drought periods commonly occur together. In addition, microbiome responses to recurrent stresses have mainly been studied in further stress periods, while it has remained elusive how alternative stable states of soil microbial communities may affect ecosystem functions during non-stress periods. The main goal of this work package is to comprehensively study the combined effects of heat waves and droughts, followed by subsequent heavy precipitation events, on microbiome interactions in the plant-soil system. 

PhD position (Richter)- filled          Postdoc position (Wöbken) - filled

 

WP 4.2 - Perturbations of Permafrost Microbiomes and the Climate Feedback

Permafrost is thawing because of global warming. The impact of this is vast, rapid and potentially devastating, affecting both humans and natural ecosystems. Key to predicting the permafrost-climate feedback is an understanding of the processes at the permafrost thaw front, where microbial communities are exposed to recurrent perturbations. Moreover, permafrost contains a record locked up in frozen ancient DNA going back thousands to tens of thousands of years, providing unique opportunities to understand microbiome responses to environmental change over long timescales, and allowing informed predictions of the effects of climate
change on Arctic microbiomes.
The key questions of this WP are therefore:
(i)    How have permafrost microbiomes changed from the last glacial maximum to the Holocene and to the present day, and how do these changes reflect the environmental conditions during freezing?
(ii)    How is the growth and turnover of microbial communities of all three domains of life controlled at the permafrost thaw front and what does that mean for the stability of the permafrost carbon?
(iii)    How does the top-down control of these microbial communities unfold by predation (i.e., by protists and phages)?
By addressing these questions in thawing experiments and in sampling along permafrost gradients, we will elucidate specific controls that are prerequisites for modelling of large-scale permafrost thaw feedbacks.

Postdoc position (Rattei)          Postdoc position (Richter)

 

WP 4.3 - Control of nitrous oxide emissions in soils

Soils are the main source of atmospheric nitrous oxide (N2O), a potent greenhouse gas. N2O is a metabolic byproduct of ammonia oxidation by complete ammonia oxidizers (comammox) and by ammonia oxidizing archaea (AOA) and bacteria (AOB), a product of nitrifier denitrification by AOB, and N2O is produced and/or consumed by denitrifying bacteria, archaea, and fungi. In a reductionist approach we will use synthetic microbial communities (SynCom) in gnotobiotic soils to address (i) how soil N2O production/consumption are affected by land use and climate change, and which N cycling populations drive this response, (ii) how metabolic complementation affects N2O emissions, and (iii) whether N2O accumulation feeds back on microbiome structure, e.g., via N2O toxicity. The results will help to minimize agricultural N2O emissions ultimately leading to the development of targeted approaches to manipulate the soil microbiome, and show how and by which mechanisms soil N2O emissions are changed during perturbations. 

PhD position (Wanek) - filled          Postdoc position (Kitzinger)- filled          Technician position (Kitzinger) - filled

 

Project 5 - Microbiome Monitoring and Interventions for Human Health

WP 5.1 - Wastewater Microbiomes for Next-Gen Public Health Monitoring

Wastewater is increasingly recognized as an information-dense footprint of the urban microbiome. But how can this be leveraged to improve public health?
Our ambition is to explore the microbial composition in wastewater, including commensal and pathogenic microbes, to identify patterns that can be linked to human health and inform strategies to improve human well-being. To this end, we will develop and establish sequencing based methods to detect, quantify and genetically characterize a range of microbes. This data will be intersected with available health, demographic and socioeconomic data to explore and identify patterns, associations and interactions between environmental and human health indicators. The expected results will support fundamental research questions about infectious diseases and drive concrete initiatives to positively impact public health.

PhD position (Bergthaler) - filled          PhD position (Berry) - filled          Technician position (Bergthaler) - filled 

One postdoc position is available in this work package. We are looking for applicants with either a focus on microbiology and metagenomics, or data science. If you are interested in this position, please apply for the focus that fits your skills and background through our recruiting platform.

Postdoc - Microbiology/Metagenomics (Bergthaler)          Postdoc - Data Scientist (Bergthaler)

 

WP 5.2 - Principles of microbiome modification & host modulation by fecal microbiota transplantation (FMT)

FMT is an effective therapeutic approach for recurrent C. difficile colitis but indications expand to other diseases like IBD and even cancer immuno-therapy (ICI). Transferred microbiota persists over prolonged periods after FMT and engraftment rates could be artificially modulated by taxonomic matching of donor and recipient microbiota as well as select modification of microbes in the transplant opening the avenue for personalized FMT approaches. Curiously, engraftment rates and efficacy of FMT seems to be disease-context dependent (e.g. IBD vs. ICI). Moreover, host factors besides the taxonomic composition have been largely ignored as potential factors governing efficacy of FMT. We will leverage our large FMT biorepository (donor and recipient samples including stools, biopsies, blood, urine) to comparatively assess host and microbiome features governing efficacy of FMT. We will focus on thus far under-investigated features of FMT including host factors like mucosal transcriptional and immune responses as well as systemic effects in the host (e.g. host-metabolome). 

PhD position (Wagner) - filled          Postdoc position (Gorkiewicz) - filled

 

WP 5.3 - Eavesdropping Interdomain Signals and Modulators 

Cooperative or antagonistic interactions shape the composition and functional output of microbial communities. Relative to intra-kingdom ecological interactions (e.g., bacteria-bacteria), interkingdom communication is less well studied, particularly in the context of the intestinal microbiome.   In this project, we will investigate how the metabolic output arising from intra- and inter-kingdom interactions impact host physiology. To learn how mammalian cells may “listen in” the chemical conversation between commensal microbes, we will test the effects of microbial metabolites and signaling molecules on host immune and metabolic pathways. 

PhD position (Campbell) - filled          Postdoc position (Böttcher) - filled

 

Project 6 - Environmental Interventions

WP 6.1 - Microbiome-Based Improvement of Nitrogen Nutrition in Crop Production

Excessive fertilization causes eutrophication and species extinctions in downstream aquatic systems and promotes climate warming and ozone destruction. It is therefore extremely important to reduce global fertilizer input, particularly the energy-demanding, inefficiently-used and ecologically-costly nitrogen (N) fertilizers. Nutrient turnover in soils is a microbially-driven process that strongly impacts plant nutrition. Hence, modulation of soil- and plant-associated microbiomes represents a promising approach to improve plant N nutrition. Soil- and plant-associated microorganisms contribute to plant nutrition by transforming N compounds into forms that plants can take up. In this project, we aim to identify and isolate microbial consortia that improve N nutrition in agricultural-relevant plants using state-of-the art molecular tools combined with high-throughput isolation techniques. Taken together, this project will assess the complex interactions between nutrient cycling microbiomes, plant nutrition, and greenhouse gas emissions in a multi-disciplinary manner, and develop microbiome-based approaches to improve plant nutrition and curb fertilizer use.

PhD position (Sessitsch) - filled          Postdoc position (Wöbken)

 

WP 6.2 - Microbiome-Enhanced Silicate Weathering

For the world on the verge of missing the Paris Agreement‘s global warming target, Negative EmissionTechnologies (NET) are critical. Enhanced silicate weathering involving the amendment of agricultural soils with reactive silicate minerals is an emerging NET that promises not only to sequester carbon but also to enhance plant growth. The relevant molecular scale biogeochemical weathering processes are strongly influenced by pore-scale heterogeneity caused by variations of redox potential, pH, biogenic compounds etc., which are in-turn influenced by microbial colony formation, mineral aggregation, and secondary mineral formation. Based on this premise, the project will aim to understand overall weathering rates based on the properties of the soil microbiome and the silicate mineral amendments, taking into account the effect of microheterogeneity on the pore-scale and biogeochemical processes on the molecular scale.

PhD position (Pjevac)          Postdoc position (Krämer) - filled

 

WP 6.3 - Role of Selective Sulfur Nutrients across Human and Environmental Microbiomes and for Precision Microbiome Editing

Structure and function of microbiomes are significantly shaped by selective nutrients that provide
exclusive metabolic niches for microorganisms. This project will explore the degradation of plant- and bacteria-derived sulfo(no)lipids across environmental and host-associated microbiomes and their potential as prebiotics for targeted modulation of the microbiome. The key questions here are: (i) What are the common metabolic principles and interaction mechanisms of microorganisms and phages involved in the processing of sulfur-containing organic matter across environmental and host-associated microbiomes? (ii) What is the impact of organosulfur degradation on nutrient cycling and greenhouse gas emissions from soils and on human and plant health? We hypothesize that selective organosulfur nutrients, such as sulfolipid-derived sulfoquinovose, can be used as prebiotics for stimulating beneficial microorganisms and combined with chemical precision tools that simultaneously control detrimental enzymatic processes, such as H2S production, to further enhance target-oriented control of microbiome functions.

PhD position (Wanek) - filled          Postdoc position (Loy) - filled

 

Project 7 - Fundamental Principles of Microbiome Dynamics

The project ‘Fundamental principles of microbiome dynamics’ aims at identifying pattern that unite different systems, and search for principles of microbiome dynamics that are shared across systems. We hypothesize that there are basic rules of community dynamics, which are rooted in fundamental principles of microbial life, such as growth, exchange of metabolites, co-evolutionary constraints, and ecological interactions. Improving our understanding of them will advance microbiome research across disciplines.

The project is structured in three work packages: WP 7.1 on Microbial Growth, Biomass, and Carbon Use Efficiency, WP 7.2. on Microbial Interaction Mechanisms and Networks in Complex Microbiomes, and WP 7.3. on Effects of Oscillating Environmental Conditions and Perturbations on Microbiomes. Postdocs in these work packages are associated to a subproject but will work collaboratively across work packages. They are therefore listed twice on this overview site.

Postdoc 7.1 (Richter) - filled          Postdoc 7.2 (Daims) - filled          Postdoc 7.3 (Kaiser)          Postdoc 2 7.3 (Berry) - filled

 

WP 7.1 - Microbial Growth and Carbon Use Efficiency in Soil

Microbial growth, turnover, carbon use efficiency, and biomass are fundamental aspects that connect microbiomes to ecosystem processes, functions, and services. Understanding these factors in complex (eco)systems is crucial for unraveling the microbiome assembly, functioning, and response to disturbances, aligning with the overall goals of the 'Fundamental Principle of Microbiome Dynamics' project. The specific objectives of this work package are twofold. Firstly, we aim to consolidate existing theories on microbe growth, turnover, growth yield/carbon use efficiency, and biomass. This will enable us to make generalizations applicable to various growth types (e.g., cell division, growth in size) and various environmental and host-associated microbial ecosystems, spanning the boundary between medical and environmental microbiology, including soil and oceans, the mouse gut (as a model), and activated sludge systems. Secondly, we strive to uncover the primary cross-system controls governing growth and turnover at the individual microorganism, population, and community levels. We will particularly focus on elucidating the role of predation and resource availability on growth, size/mass and carbon use efficiency. 

PhD position (Polz) - filled          Postdoc position (Richter) - filled  

 

WP 7.2 - Microbial Interaction Mechanisms and Networks in Complex Microbiomes

Complex microbiomes are shaped by interaction networks involving for example cross-feeding, metabolite exchange, and molecular signaling. These networks are crucial for the survival and growth of environmental and host-associated microbiomes, but our understanding of interaction networks in complex microbiomes remains incomplete. To address this, we will investigate interactions in wastewater treatment plant and human small intestine microbiomes. Metagenomic data will be used for metabolic modeling and machine learning to predict interactions and functional traits. Computational predictions will guide experimental manipulations of living microbiomes, including substrate and metabolite provision and modulation by signaling compounds. Interaction network functioning and restructuring will be monitored by in situ fluorescence and chemical imaging, such as multicolor FISH and confocal microscopy, stable isotope probing linked to Raman microspectroscopy and NanoSIMS, and single-cell transcriptomics. Ultimately, our goal is to enhance predictions of microbiome development in dynamic conditions, aiding the optimization of biotechnological processes and microbiome-targeted therapies.

PhD position (Moissl-Eichinger) - filled          Postdoc position (Daims) - filled

 

WP 7.3 - The effect of oscillating environmental conditions and perturbations on Microbiomes

Sudden and short-lived changes in environmental conditions (‘Pulse perturbations’) can have long lasting effects on microbial communities. They are highly prevalent in natural systems and occur irregularly or in an oscillating fashion. This project will investigate how the history of perturbations events as well as their temporal pattern shape the functionality, resistance and resilience of microbial communities in different environmental and medical systems (i.e. desert biological soil crusts, activated sludge, soil, mammalian gut). By compiling the results from the different microbiome systems and combining it with theoretical modelling we aim to identify potential basic mechanisms of community adaptation to perturbations, as driven by the kind and frequencies of perturbation. Given the high prevalence of pulsed perturbations or environmental oscillations in nature, a better understanding of their effect on the functioning of microbiomes will be essential for managing natural or developing engineered systems.

PhD position (Wöbken)          Postdoc position (Kaiser)          Postdoc position (Berry) - filled