projects

Molecular and biochemical characterization of the nitrogen regulatory network and stress response in Methanosarcina mazei.

Methanosarcina mazeiArchaea represent the second domain of Prokarya. They are phylogenetically distant to Bacteria and share many features more similar to their eukaryotic than their bacterial counter parts (e.g. transcription and translation machineries). Working with the model archaeon Methanosarcina mazei, we study and aim to understand the overall regulatory network of the nitrogen metabolism and stress response. Besides classical genetic and biochemical approaches we achieve genome-wide transcription analysis using whole genome DNA microarrays and RNAseq approaches (high through put sequencing of cDNA libraries) to analyze individual regulatory networks and potential cross talks between different regulons. Besides regulation on the transciptional level by proteins, currently our main focus is to study the role of non-coding regulatory RNAs in stress response of M. mazei to understand the regulatory mechanisms of those small RNAs on the molecular level. (funded by the DFG)


Analysing the M. mazei immune system 

The second classes of regulatory RNAs we are studying are so called crRNAs, which are part of the Prokaryotic immune system - the CRISPR/Cas system - in M. mazei. The CRISPR (clustered regularly interspaced short palindromic repeats) system has been only recently discovered as defense system against exogenous nucleic acids in bacteria and archaea. In contrast to other gene transfer and phage defense mechanisms it allows a highly adaptive and heritable resistance mechanism that incorporates sequences derived from foreign elements into the respective CRISPR locus. Thus, the CRISPR system represents an adaptive immune system of the Prokaryotes. We are aiming to unravel the function of several Cas proteins and complexes in M. mazei, and achieve an insight regarding crRNA processing and potentially on methanoarchaea / phage dynamics. (funded by DFG, FOR1680)


Analysing the M. mazei immune system

Enriched methanoarchael phages

Enriched methanoarchael phages


The innate immune system encountering methanogenic archaea

Archaea the second domain of Prokarya are phylogenetically distant to Bacteria and Eukarya, which is expressed in genetic differences as well as structural differences of the cell wall. Though methanogenic archaea form part of the indigenous microflora of the human gut, until today it is not clear whether antimicrobial peptides (AMPs) affect them as the archaeal cell envelope differs profoundly in terms of chemical composition and structure from that of bacteria. In this project we are addressing if and how antimicrobial peptides act against (methano)archaea and study the response of the innate immune system encountering Methanosphaera stadtmanae and Methanobrevibacter smithii, both considered to be inhabitants of the human gut, and M. mazei. (funded by the DFG)

M. smithii

Methanosarcina


Analysing supra gingival biofilm formation

We are investigating the gingival bacterial colonization and the role of bacterial virulence factors for the epithelial (innate) immune response during biofilm formation using molecular and biochemical tools. The community structures, colonization profiles and the functional diversity of microorganisms involved in the formation of biofilms are analysed over a 21 day period applying next generation pyro-sequencing. Simultaneously the clinical inflammation processes as well as the epithelial immune response are analysed in close collaboration with Dr. Jörg Eberhardt (Medizinische Hochschule Hannover). (funded by the DFG)

Analysing supra gingival biofilm formation


Gene mining for novel enzymes and drugs from marine environments

It has been estimated that > 99 % of microorganisms observable in nature typically can not be cultivated by using standard techniques. Thus, a large fraction of the diversity in an environment is still unknown. Our approach is to use the genetic diversity (DNA) of the micro-organisms in a certain environment as a whole to encounter new genes and gene products for various purposes (e.g. new biocatalysts; microbial drug molecules; novel components, which prevent biofilm formation). The genetic diversity is accessed by isolation of DNA followed by direct cloning of functional genes from environmental samples. In Kiel, we are mainly focusing on marine environments, which are highly diverse (collaboration with the GEOMAR, Kiel).

We are interested to increase our knowledge on marine microbial consortia and biofilms on biological and non-biological surfaces. In order to understand the ecological aspects and interspecies communication in mixed biofilms on a molecular level we are using metagenomic technologies. Here one focus is to identify novel components which interfere with biofilm formation by degradation, suppression or inhibition of signal molecules for interspecies and intraspecies communication and thus prevent mixed biofilm formation. (Funded by the BMBF, Chembiofilm)

In collaboration with the Medical Department (Institute for Clinical Molecular Biology) and the GEOMAR we analyze the mechanisms of host-microbial interactions in marine environments. The goal of this project is to develop model systems, which may lead to understand human barrier diseases (see also 'The Future Ocean').

PolypEphyraMedusa


Control biofilm of Klebsiella wildtype Biofilm of recombinat Klebsiella expressing a QQ-ORF


Oceanic biological nitrogen fixation: Sensitivity to changes in dissolved oxygen

Nitrogen (N2) fixation is a key control on the oceanic nitrogen inventory. In many oceanic regions, growth of phytoplankton is N limited because oceanic N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, and NO3-) by anaerobic microbial processes. Oxygen minimum zone (OMZ) waters play a crucial role in regulating the availability of nutrients, nitrogen (N) in particular. Within this project we investigate in close collaboration with Dr. Marcel Kuypers’ group at the MPI Bremen the effects of oxygen concentration on nutrient regeneration, N-loss as N2-production, and N2-fixation in OMZ Waters. Rate measurements for various N-cycling processes are performed via incubation experiments with stable isotope-labeled substrates, and the microorganisms involved will be identified using molecular biological techniques.

Web-pages of SFB754 - Climate - Biogeochemistry Interactions in the Tropical Ocean

On Cruise SFB 754

SFB 754 (2)

Diagrams


Regulation of nitrogen fixation in Klebsiella pneumoniae.

K. pneumoniae is able to reduce molecular nitrogen to ammonia under oxygen- and nitrogen-limiting growth conditions. Synthesis of the key enzyme nitrogenase is regulated in response to molecular oxygen and combined nitrogen by the two regulatory proteins NifA and NifL as well as the nitrogen sensory protein GlnK. Our research is focused on the characterization of the cellular signal perception and transduction of the oxygen and nitrogen signal towards NifL and NifA by genetic, biochemical and molecular biological methods. (Funded by the DFG)

Regulation of nitrogen fixation in Klebsiella pneumoniae