Research Fields

Links from the Phyllosphere to the Soil

Canopy Crane


Tree in the Hainich CZE

Photos: Canopy Crane in the floodplain hardwood forest in Leipzig (top); Tree in the Hainich Critical Zone Exploratory (bottom).



Researchers: Martina Herrmann, Carl-Eric Wegner

Phyllosphere microbial communities modulate ecosystem functions by influencing the function and fitness of their respective host plants. Besides, they represent a reservoir for the vertical transfer of microbes from canopies into deeper layers including soil. We are interested in exploring and identifying parameters that contribute to phyllosphere microbial community assembly and factors that are linked to mobilization.

In particular, we aim at answering the following questions:  What is the effect of tree species, canopy height, and season on the functional diversity of forest canopy microbiota?  To what extent are forest canopy and soil microbiomes linked by vertical transfer of microorganisms via throughfall and stemflow?  Which microbial groups are preferentially mobilized from soils?  In this context, we are also particularly interested in microbial groups involved in nitrification.


Functional Microbial Diversity of the Subsurface Biosphere



Photos: Groundwater wells of the Hainich Critical Zone Exploratory (CZE) in Thuringia, Germany (top); Groundwater sampling at a well along the Hainich CZE (bottom). More Photos....


Researchers: Martin Taubert, Martina Herrmann, Will Overholt, Lijuan Yan, Patricia Geesink, Markus Krüger, Constantinos Xenophotos

The main goal is to characterize functioning of the groundwater microbiome. Using gene-centric and genome-centric approaches we identify key players of biogeochemical cycles. We want to understand what is driving the subsurface biosphere. Rate measurements provide insights in CO2 fixation rates. Moreover, we want to gain insight into the entire aquifer food web structure by studying prokaryotes and eukaryotes from multiple trophic levels. Our research focuses on limestone aquifers located in the Hainich region in Thuringia, Germany, in an innovative research platform, the Hainich Critical Zone Exploratory (CZE), within the framework of the DFG-funded Collaborative Research Centre SFB 1076 AquaDiva at FSU Jena.


Chemical Interactions / Metabolomics



Photos: Schlöppnerbrunnen fen in Northern Bavaria, Germany  (50°07’55’’N, 11°52’52’’E) (top); Lake 77 located in a former lignite mining region in Germany (bottom).


Researchers: Rebecca Cooper, Stefan Kügler, Qianqian Li

We are particularly interested in understanding iron cycling in peatlands and acidic lakes with a focus on identifying and characterizing what mediates the interactions between microorganisms and the transformation of Fe. The objective of our current research in the slightly acidic, Fe-rich Schlöppnerbrunnen fen is to elucidate the role of metallophores and other chemical mediators involved in multi-layered interaction networks.  Additionally, we aim to gain further insights into interspecies cell-cell communication of microbes involved in different parts of the Fe-cycle. The main goal of our research in the acidic Lake 77 in a former lignite mining region in Germany is to characterize the microbial key players that form iron-rich pelagic aggregates and to understand microbe-microbe and microbe-mediator interactions. Using comparative metabolomics, we try to identify the chemical structures of metallophores and chemical mediators within mult-organism communities and in these natural systems.


Microbial Carbon Metabolism

Life as we know it is made of carbon. Carbon is subjected to constant transformation and recycling, which is summarized in the global carbon cycle. Governed by top-down and bottom-up processes, the global carbon cycle is primarily controlled by the balance between photosynthesis and respiration. Given that the aformentioned interplay is prone to disturbance, we are interested in how top-down and bottom-up processes are affected by distinct biogeochemical settings in diverse environments.

Our focus is on addressing the following objectives:  What is the significance of methylamine as combined carbon/nitrogen resource for microbes in freshwater environments?  How important is dark carbon fixation in the terrestrial subsurface?  How prominent is methylotrophy in terrestrial environments, and how large is the hidden diversity of methylotrophic organisms?  Identifying factors that govern the relative contribution of carbon fixation and complex carbon breakdown to microbial biomass assimilation.




Carl-Eric Wegner - Microbial carbon turnover in complex ecosystems


Photo: Pier at Cromer Beach, UK.


Martin Taubert - Functional biodiversity of aquatic methylotrophs

Sieving soil in the Hainich CZE

Photo: Sieving of soil samples in the Hainich Critical Zone Exploratory.


Rachael Akinyede - The dark side of CO2 fixation in soil



Last Update: 13.06.2018