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Investigating factors that govern biological N2 fixation in soil by CHIP-SIP


Supervisor: Dagmar Wöbken

PhD student: Marlies Dietrich

Group: Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science



Elucidating microbial participants in plant-associated processes

My PhD aims to investigate the influence of different factors (plant root exudates, nutrient impact and climate change conditions) on the community composition and activity of a particular functional guild of plant-associated microbes – free-living diazotrophs, as well as the effect of fungi on bacterial/archaeal root-associated communities. The effect of nutrient impact and plants on the diazotroph communities in an Austrian grassland was assessed by sequencing the dinitrogenase reductase (nifH) gene. Different plant species (2 grass and 2 herb species) grown in a long-term nutrient deficiency experiment and the associated soil-plant microhabitats (bulk soil, rhizosphere, rhizoplane, root) were investigated. By sequencing transcripts reverse transcribed into cDNA, diazotrophs actively expressing the nifH genes were identified. Different microhabitats host distinct diazotroph communities that are shaped by nutrient deficiency. In order to gain insights into the dependence of free-living diazotrophs on plant-derived carbon sources, 15N2 tracer assays were applied showing that diazotroph activity depended on the provision of root exudates. In order to identify which exact compounds drive responses in diazotroph communities, the actual root exudate composition was measured in the field. Follow-up incubations are being performed to assess if specific root exudate compounds stimulate specific members of the diazotroph community.

In an additional approach, ChipSIP is being applied to identify active diazotrophs in grassland soils. This novel technique combines advantages of both, community identification by microarrays and analysis of stable isotope incorporation by NanoSIMS, representing a high throughput and high sensitivity method. In order to build the phylogenetic CHIP, the existing microbial diversity was characterized by sequencing the 16S rRNA gene from DNA and cDNA samples using Illumina and PacBio technologies. Sequence data were used to design specific probes for the construction of a customized microarray in collaboration with Jennifer Pett-Ridge, Xavier Mayali, Erin Nuccio (Lawrence Livermore National Laboratory, USA) and Mark Somoza (Inorganic Chemistry, University of Vienna). Samples from a climate change experiment were incubated with 15N2-gas and will be analyzed for the active diazotrophs using the ChipSIP approach.


In my third project, I investigate the effect that ectomycorrhizal fungi might have on plant-associated microbial communities. The ectomycorrhiza fungal communities inhabiting different beech tree-associated habitats (litter, bulk, soil, rhizosphere, mycorrhizal root tips) were investigated by sequencing of the ribosomal internal spacer region. The data were combined with already existing 16S rRNA amplicon data of bacteria/archaea derived from the very same samples to determine whether different fungal communities host specific bacterial/archaeal communities. Specifically, the fungal and bacterial/archaeal communities are being analyzed in mycorrhizal fungi hotspots (mycorrhizal root tips) using network analysis in collaboration with Alicia Montesinos- Navarro (Centro de investigacion sobre desertificacion, Valencia).


Co-Supervision by Andreas Richter and Michael Wagner, secondment by Dr. Jennifer Pett-Ridge (Lawrence Livermore National Laboratory, USA) on the CHIP-SIP procedure.


Please find a list of publications here.

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