• 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

Single cell stable isotope probing in microbiology using Raman microspectroscopy

Microbial communities are essential for most ecosystem processes and interact in highly complex ways with virtually all eukaryotes. Thus, a detailed understanding of the function of such communities is a fundamental prerequisite for microbial ecologists, applied microbiologists and microbiome researchers. Using single cell Raman microspectroscopy, biochemical fingerprints of individual microbial cells can be obtained in a fast and nondestructive manner. If combined with stable isotope probing (SIP), Raman spectroscopy can directly reveal functions of single microorganisms in their natural habitat. This review provides an update on various SIP-approaches suitable for combination with different Raman scattering techniques and illustrates how single cell Raman SIP can be directly combined with the omics-centric analysis pipelines generally applied to investigate microbial communities. 

Yun Wang Y, Huang WE, Cui L, Wagner M
2016 - Curr Opin Biotechnol, in press

Single cell genome and group-specific dsrAB sequencing implicate members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling

The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (‘DEH-C11’) with a 16S rRNA gene that affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments, was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. Genes encoding dissimilatory sulfite reductase (Dsr) suggest DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr-loci, dsrAB were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences affiliated with the DEH Dsr-clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH. DEH-C11 also harboured genes encoding reductases for arsenate, dimethyl sulfoxide and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate this RdhA may not be a terminal reductase. Other genes indicated nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognised role in sulfur cycling, and reveal potential for expanded catabolic and respiratory functions among subsurface DEH.

Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker B, Petersen DG, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A, Adrian L
2016 - mBio, In press

Biotransformation of two pharmaceuticals by the ammonia-oxidizing archaeon Nitrososphaera gargensis

The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the archaeal ammonia monooxygenase gene (amoA) in nitrifying activated sludge. Given the increasing interest in and potential importance of ammonia-oxidizing archaea (AOA), we investigated the capabilities of an AOA pure culture, Nitrososphaera gargensis, to biotransform ten micropollutants belonging to three structurally similar groups (i.e., phenylureas, tertiary amides, and tertiary amines). N. gargensis was able to biotransform two of the tertiary amines, mianserin (MIA) and ranitidine (RAN), exhibiting similar compound specificity as two ammonia-oxidizing bacteria (AOB) strains that were tested for comparison. The same MIA and RAN biotransformation reactions were carried out by both the AOA and AOB strains. The major transformation product (TP) of MIA, α-oxo MIA was likely formed via a two-step oxidation reaction. The first hydroxylation step is typically catalyzed by monooxygenases. Three RAN TP candidates were identified from nontarget analysis. Their tentative structures and possible biotransformation pathways were proposed. The biotransformation of MIA and RAN only occurred when ammonia oxidation was active, suggesting cometabolic transformations. Consistently, a comparative proteomic analysis revealed no significant differential expression of any protein-encoding gene in N. gargensis grown on ammonium with MIA or RAN compared with standard cultivation on ammonium only. Taken together, this study provides first important insights regarding the roles played by AOA in micropollutant biotransformation.

Men Y, Han P, Helbling DE, Jehmlich N, Herbold C, Gulde R, Onnis-Hayden A, Gu AZ, Johnson DR, Wagner M, Fenner K
2016 - Environ Sci Technol, in press

Lecture series

Importance of chemosymbiotic lucinid bivalves in seagrass community functioning

Matthijs van der Geest
Université de Montpellier
20.01.2016
11:00 h
Seminar room DoME (2.309), UZA 1

The contribution of phage-mediated gene transfer to microbial genome evolution

Tal Dagan
Christian-Albrechts-Universität zu Kiel
23.10.2015
13:30 h
Seminar room DoME (2.309)

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
11.09.2015
11:00 h
Seminar Room DOME (2.309)