Scientific programmer/Data scientist – SomSOM – Self-organization of microbial soil organic matter turnover (OE196)

Scientific programmer/Data scientist – SomSOM – Self-organization of microbial soil organic matter turnover (OE196)

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: http://ter.csb.univie.ac.at/people/christina-kaiser

Division for Terrestrial Ecosystem Research: http://ter.csb.univie.ac.at/

Centre for Microbiology and Environmental Systems Science: http://cmess.csb.univie.ac.at/

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 (http://diversity.univie.ac.at/), 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 christina.kaiser@univie.ac.at. Positions will be filled as soon as possible and remain open until filled. Evaluation of applications starts in May 2019.

For questions please contact christina.kaiser@univie.ac.at.

An updated version of this document is available at http://ter.csb.univie.ac.at/open-positions

Introduction

In the course of the project our existing individual-based microbial community model (Kaiser et al., 2014, 2015; Evans et al., 2016), which is written in Java, need to be further developed and refined by different members of the team. I am looking for an enthusiastic data scientist/scientific programmer to coordinate these efforts and support the whole team with programming, data management and data visualization.

You should ideally have a background in informatics (Bsc, Msc, or HTL/HBVLA degree), or alternatively a science (i.e. physics, mathematics, biology,…) background with experience in computer programming (JAVA) and data management. Professional experience in team software development is a big plus. You should be interested in soil ecology and complex systems science, and have a communicative and open personality.

The successful candidate will be responsible for

  • coordinating the programming efforts of the team members, implementing critical parts yourself and support the team with your expertise.
  • efficient code and version management and deposition/maintainance of the source code in public repositories.
  • assisting in creating and implementing a data management plan for depositing experimental data obtained in the project in public repositories in a reproducible way.
  • exploring and implementing options for the visualization of complex datasets such as microbial interaction networks, pore networks etc. (f.e. based on Gephi or other tools).

I offer a part-time position (20 hours) for 2 years in a creative and vivid scientific team at the Terrestrial ecosystem research/Centre for Microbiology and Environmental systems science. This position will be central for the modeling part of the project, and the successful candidate will be, if interested, involved in the science as much as in the technical aspects of it.

References

Evans S, Dieckmann U, Franklin O, Kaiser C. 2016. Synergistic effects of diffusion and microbial physiology reproduce the Birch effect in a micro- scale model. Soil Biology & Biochemistry 93: 28–37.

Kaiser C, Franklin O, Dieckmann U, Richter A. 2014. Microbial community dynamics alleviate stoichiometric constraints during litter decay. Ecology Letters 17.

Kaiser C, Franklin O, Richter A, Dieckmann U. 2015. Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils. Nature Communications 6.

More information available here.

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