Postdoc and PhD position: Fine-scale organization of the soil microbiome across the soil’s physical micro-architecture – SomSOM – Self-organization of microbial soil organic matter turnover (EO198)

Postdoc and PhD position: Fine-scale organization of the soil microbiome across the soil’s physical micro-architecture – SomSOM – Self-organization of microbial soil organic matter turnover (EO198)

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


The aim of this project part is to better understand soil organic matter turnover by understanding the fine-scale organization of the soil microbiome. This will be done by combining methods from soil microbiology and complex systems sciences.

From a microbial perspective, soil is one of the most complex and heterogenous environments on earth. It is organized in spatial micro-units (macro- and microaggregates) in a hierarchical way. Formation and turnover of these aggregates, which are usually from 20 – 5000 μm in diameter, is driven by interactions between physicochemical processes and microbial activity. As soil microbes interact with each other only over very small ‘calling’ distances of a few tens of μm, it is likely that the soil’s microarchitecture shapes the fine-scale organization of the soil microbiome.

In this project part we aim to identify microbial interaction networks across the soil’s microarchitecture and link it to measured parameters of soil organic matter turnover. Towards this goal, we will refine and develop techniques to measure community composition and decomposer functions at the scale of individual aggregates. This project part will combine methods from soil biogeochemical research (i.e. Pyrolysis-GC-MS, stable isotopes, process rates measurements,..), soil microbial ecology (16S rRNA gene amplicon sequencing, metagenomics), with mathematical approaches, theoretical ecology and complex system science to get a better understanding of the intrinsic and extrinsic factors driving the organization of the soil microbiome across scales, and its consequences for soil organic matter turnover.

I am looking for interdisciplinary-thinking scientists interested in combining knowledge of different fields to develop new approaches and ideas to better understand the soil from a soil ‘systems’ perspective. You should have a background in soil microbial ecology, soil biogeochemistry, and/or mathematics, physics or complex systems science, and need to have good communication skills to favor cross-discipline discussions.

There are two positions available, which will be selected to complement each other. To join the team you should have some of the following skills:

  • Background in soil microbial ecology and/or soil biogeochemistry
  • Alternatively, Background in mathematics or physics
  • Interest/Background in theoretical ecology and complex systems science
  • Molecular microbial ecology (16S rRNA gene amplicon sequencing, metagenomics or metatranscriptomics of soil microbial communities)
  • Interest in soil microscale processes and interactions
  • good command of R or another programming language
  • Experience in microbial interaction (co-occurrence) network analysis is an advantage
  • Knowledge/interest in Graph theory
  • Soil chemical analysis (Pyrolysis-GC-MS), phospholipid fatty acids
  • Soil process measurements (Respiration, enzyme activities, N mineralisation)
  • Experience in using stable isotopes in soil ecology

Both positions can be carried out either as a PhD (4 years) or a postdoctoral project (2.5 years) .

More information available here.