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Unraveling microbial nitrogen utilization and turnover in soil by Chip-SIP


Supervisor: Andreas Richter

PhD student: Joana Silva

Group: Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science



Linking the structure and function of microbial communities in their natural environment is arguably one of the most compelling challenges of today’s microbial ecology. Nucleic acid and phospholipid fatty acid stable isotope probing techniques (SIP) techniques are most commonly used to connect substrate utilization and microbial identity. These techniques are, however, not suited to study the microbial utilization of nitrogen-containing compounds, due to sensitivity issues and the lack of nitrogen in PLFAs. Recently, a proof of concept for a new method called Chip-SIP has been published (Mayali et al. 2011, ISME J), demonstrating that combining the isotope array approach (Adamczyk et al. 2003, AEM) (which does not work for N because of the lack of a suitable radioactive N isotope) with NanoSIMS measurements, allows the sensitive tracing of 15N into nucleic acids.

This novel approach allows us, for the first time, to define the role of microbial groups in N turnover at a very fine phylogenetic resolution and to cover microorganisms of all domains of life (archaea, bacteria and fungi). The proposed PhD project shall focus on (a) the question which soil microbial taxa are mainly involved in the decomposition of high molecular weight organic N (e.g. chitin, peptidoglycan, protein, humus) and thus play a key role in terrestrial N cycling, (b) whether there are differences in the uptake and utilization of easily assimilable N forms (e.g. amino acids, amino sugars, ammonium or nitrate) in various microbial taxa, i.e. if there are different microbial N utilization strategies and (c) whether nitrifying AOA and AOB are utilizing ammonium for energy and biomass production or if biomass is preferentially build up from organic N sources. The proposed PhD project is closely linked to project of Dagmar Woebken. The microarray that will be used in this project will be designed in close collaboration to target the microbial community in a bulk and a rhizosphere soil of a managed grassland ecosystem. The experiments will be conducted in mesocosms allowing us to amend the 15N-labelled substrates to and, in some approaches, to grow plants in these soils that can be labelled with 13CO2.


Co-Supervision: Dagmar Woebken, Michael Wagner; Secondment: Jennifer Pett-Ridge (Lawrence Livermore National Lab, USA).

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