• We seek to understand

    the role of microorganisms in Earth's nutrient cycles

    and as symbionts of other organisms

  • Cycling of carbon, nitrogen and sulfur

    affect the health of our planet

  • Ancient invaders -

    Bacterial symbionts of amoebae

    and the evolution of the intracellular lifestyle

  • The human microbiome -

    Our own social network of microbial friends

  • Single cell techniques offer new insights

    into the ecology of microbes

  • Apply for the DOME International PhD/PostDoc program

Dome News

Latest publications

Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via 15N2 and 13C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a 13C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.

Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D
2015 - FEMS Microbiology Ecology - *Editor's Choice Article*, in press

Intestinal epithelial cell tyrosine kinase 2 transduces interleukin-22 signals to protect from acute colitis

In the intestinal tract, IL-22 activates signal transducer and activator of transcription 3 (STAT3) to promote intestinal epithelial cell (IEC) homeostasis and tissue healing. The mechanism has remained obscure but we demonstrate that IL-22 acts via tyrosine kinase 2 (Tyk2), a member of the Janus kinase (Jak) family. Using a mouse model for colitis, we show that Tyk2 deficiency is associated with an altered composition of the gut microbiota and exacerbates inflammatory bowel disease (IBD). Colitic Tyk2-/- mice have less phosphorylated STAT3 (pY-STAT3) in colon tissue and their IECs proliferate less efficiently. Tyk2-deficient primary IECs show reduced pY-STAT3 in response to IL-22 stimulation and expression of IL-22-STAT3 target genes is reduced in IECs from healthy and colitic Tyk2-/- mice. Experiments with conditional Tyk2-/- mice reveal that IEC-specific depletion of Tyk2 aggravates colitis. Disease symptoms can be alleviated by administering high doses of recombinant IL-22-Fc, indicating that Tyk2 deficiency can be rescued via the IL-22 receptor complex. The pivotal function of Tyk2 in IL-22-dependent colitis was confirmed in Citrobacter rodentium-induced disease. Thus, Tyk2 protects against acute colitis in part by amplifying inflammation-induced epithelial IL-22 signaling to STAT3. 

Hainzl E, Stockinger S, Rauch I, Heider S, Berry D, Lassnig C, Schwab C, Rosebrock F, Milinovich G, Schlederer M, Wagner M, Schleper C, Loy A, Urich T, Kenner L, Han X, Decker T, Strobl B, Müller M
2015 - J Immunol., in press

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira

Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. Despite this, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly utilize urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to utilize formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared to Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.

Koch H, Lücker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H
2015 - Proc Natl Acad Sci U S A, in press

Lecture series

Cool microbes: Assessing the role of acidobacteria communities in carbon and nitrogen cycling processes in arctic tundra soils

Max Häggblom
Department of Biochemistry and Microbiology School of Environmental and Biological Sciences Rutgers, The State University of New Jersey
11:00 h
Seminar Room DOME (2.309)

The genus Pseudovibrio: versatile bacteria with the potential for a symbiotic lifestyle

Stefano Romano
Biomerit research centre, University College Cork
12:00 h
Seminar room DoME (2.309)