Logo der Universität Wien

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




The sensitivity of terrestrial ecosystems to climate change is complex and is regulated by a range of factors which depend on the ecosystem and include interactions between biotic and abiotic factors. Biotic factors include plants, soil fauna and free-living - as well as symbiotic - soil microbes. Several studies have indicated microbes as main players mediating soil nutrient transformations and biogeochemical cycles. Changing global conditions, as for example increased global mean temperatures, altered precipitation regimes, and increased atmospheric CO2 concentrations are known to cause biodiversity loss and decrease ecosystem functionality, thus having repercussions on biogeochemical element cycling. Grasslands cover 40% of the Earth's surface and provide many ecosystem services ranging from food production to preservation of biodiversity. In grasslands, the availability of nitrogen (N) in forms that can be taken up by soil biota, is often the most important factor limiting primary productivity. Soil N availability is likely to be affected by changing climate over the next decades due to potential changes in community structure and altered nutrient demand.

The responses of an ecosystem to climate change strongly depend on the interplay of factors determining production, stabilization and decomposition of soil organic matter. Nitrification links mineralization to N loss processes by producing oxidized forms of N. These compounds can be assimilated into biomass or fuel other microbial biological pathways that lead to the production of potent greenhouse gases such as NO and N2O. Nitrification is a two-step process that starts with the oxidation of ammonium to NO2- by canonical bacterial and archaeal nitrifiers. The discovery of microbes that catalyze both steps of nitrification has received a lot of attention from the scientific community and called for a reassessment of the relative contribution of each microbial group to nitrification.

The most common ways of studying N-related processes include quantification of nutrient pools, enzyme assays, and determination of gross transformation rates. Such studies have increased our understanding of the role of microbes in regulating N cycling but leave the link between taxonomy and function incomplete. The advent of molecular tools in microbial ecology together with the application of stable isotope probing (SIP) techniques have allowed the identification of new players on the N cycle  in different ecosystems.


On my PhD, I will be looking into the identity of active microbial groups responsible for organic N cycling in grassland soils and whether these functional communities are altered by climate change. In my PhD this is done through the use of CHIP-SIP, a microarray-based method that allows the simultaneous detection of a multitude of taxa involved in particular processes on a single run, at much lower isotope enrichment than traditional SIP. Additionally, I will attempt to link the identity and abundance of bacterial nitrifiers to the corresponding gross nitrification rates in grasslands under a climate change scenario.  Finally, I will use total RNA metatranscriptomics to simultaneously assess the identity and gene expression levels of microorganisms involved in organic N cycling under short and long term soil warming. Altogether, these approaches will provide valuable additions to our understanding of microbial nitrogen cycling in soils, as well as the responses of different grassland types to climate change.


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


Please find a list of publications here.

University of Vienna | Universitätsring 1 | 1010 Vienna | T +43-1-4277-0