Postdoc and PhD position: Spatial self-organisation of microbial consortia decomposing soil organic matter – SomSOM – Self-organization of microbial soil organic matter turnover (OE197)

Postdoc and PhD position: Spatial self-organisation of microbial consortia decomposing soil organic matter – SomSOM – Self-organization of microbial soil organic matter turnover (OE197)

Project summary

Microbial turnover of soil organic matter (SOM) is key for the terrestrial carbon (C) cycle. Its underlying mechanisms, however, are not fully understood. The role of soil microbes for organic matter turnover has so far been studied mainly from the point of view of microbial physiology, stoichiometry or community composition. In this project, we aim to shed new light on it from the perspective of complex systems science.

Microbial decomposition of organic matter requires the concerted action of functionally different microbes interacting with each other in a spatially structured environment. From complex systems theory, it is known that interactions among individuals at the microscale can lead to an ‘emergent’ system behavior, or ‘self-organisation’, at the macroscale, which adds a new quality to the system that cannot be derived from the traits of the interacting agents. Importantly, if microbial decomposer systems are self-organised, they may behave in a different way as currently assumed, especially under changing environmental conditions.

The aim of this project is to investigate i) if microbial decomposition of organic matter is driven by emergent behaviour, and ii) what consequences this has for soil C and nitrogen cycling. Combining state-of-the-art methods from soil biogeochemistry, microbial ecology, and complex systems science we will

  • Investigate mechanisms of spatial self-organization of microbial decomposer communities by linking microscale observations from experimental microcosms to mathematical, individual-based modelling,
  • Elucidate microbial interaction networks across the soil’s microarchitecture by linking microbial community composition, process rates and chemical composition of spatially explicit soil micro-units at an unprecedented small and pertinent scale.
  • Explore fundamental patterns of self-organisation by applying the framework of complex systems science to high-resolution spatial and temporal data of soil microstructure and process rates.

I am looking for enthusiastic PhD students and postdoctoral researchers interested in carrying out research at the interface between Soil Microbial Ecology, Soil Biogeochemistry and Complex Systems Science in a creative, interdisciplinary team.

I am offering fully funded PhD (4 years) or PostDoc (2.5 years) positions at the Division for Terrestrial Ecosystem Research at the Centre for Microbiology and Environmental Systems Science of the University of Vienna. Our Division and Centre offers excellent opportunities for scientific interactions and collaborations and a vivid, cooperative and friendly working environment, in a city with one of the best living conditions in the world.

More about

Christina Kaiser’s team and research:

Division for Terrestrial Ecosystem Research:

Centre for Microbiology and Environmental Systems Science:

Open positions are available in the different project parts as described below. Applicants must have good communication skills and should be highly motivated and committed to pursuing interdisciplinary research in an international team. Excellent English in speaking and writing is mandatory. The University of Vienna values equal opportunities, as well as diversity (, and lays special emphasis on increasing the number of women in senior and in academic positions. Women are encouraged to apply.

Please send your application including

  • a motivation letter (1-2 pages max; please clearly specifiy the project part/position you are applying for – see below)
  • CV (including scientific publication and presentation activities, if any)
  • Contact details of two possible references

to Positions will be filled as soon as possible and remain open until filled. Evaluation of applications starts in May 2019.

For questions please contact

An updated version of this document is available at


Interactions among decomposer microorganisms in natural soil communities are shaped by their necessity to perform “leaky” functions, for example the release of extracellular enzymes that cleave complex organic molecules into smaller units before they can be taken up into microbial cells. As small molecules are readily diffusible in a liquid environment, this allows other nearby microbes to exploit these enzymatic products (‘public goods’), leading to a spectrum of social behaviours within microbial communities such as cooperation, communication, ‘division of labour’, synchronization and pattern formation.

The aim of this project part is to design and set up experimental microcosms (based on microfluidics), in which microbial decomposer communities can grow under controlled and observable conditions, and to link microscale observations from this experimental setup to mathematical, individual-based modelling (based on Kaiser et al., 2014, 2015; Evans et al., 2016).

I am looking for persons interested in microbial community ecology, in particular spatial self-organization of microbial communities. The team of this project part will be composed of an experimental scientist and a modeler working closely together. Applicants who have a background in both experimental work and modelling are most welcome, and encouraged to apply.

To apply for the ‘experimental’ position, you should have a scientific background (Msc or PhD) in Ecology, Microbial ecology or a related field, while for the ‘modelling’ position a Science degree (Biology, Physics, Mathematics, or similar) combined with proven abilities of mathematical modelling and computer programming is desired. Knowledge of chemical pathways during the degradation of complex organic compounds and of microbial physiology, metabolism and interactions is of advantage, as is knowledge in soil biogeochemistry and complex systems science.



  • Practical experience in molecular microbial ecology
  • experience/interest to work with strain databases and/or metagenomics data to extract and characterize microbial functional groups (with respect to degradation of complex C compounds) (KEGG, Pathfinder…) (this can also be on the side of the modeler)
  • experience with microfluidic approaches in microbial ecology is an advantage
  • experience in cultivation of soil microbes is an advantage
  • microscopy (e.g. CLSM), FISH, Stable isotope tracing, NanoSIMS, HPLC is an advantage


  • Mathematical modelling, ecological modelling, Individual-based modelling
  • background in ecology, microbial ecology or microbial metabolic pathways is an advantage
  • Interest /Knowledge in complex system science
  • Programming (JAVA, or an alternative programming language like C++ allowing you to learn and build on JAVA-based programs)

Each position can be carried out either as a PhD (4 years) or a postdoctoral project (2.5 years) – depending on the suitability and complementarity of the candidates.

More information available here.