• Our new home

    since summer 2021.

  • Hunting for microbes since 2003

  • 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

  • The human microbiome -

    Our own social network of microbial friends

  • Ancient invaders -

    Bacterial symbionts of amoebae

    and the evolution of the intracellular lifestyle

  • Marine symbioses:

    Listening in on conversations

    between animals and the microbes they can't live without

  • Single cell techniques offer new insights

    into the ecology of microbes

  • Doctoral School in Microbiology and Environmental Sciences

  • PhD program in Microbial Symbioses

    A special FWF funded track in our doctoral school

Dome News

Latest publications

Sulfur and methane oxidation by a single microorganism.

Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic-anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, '' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox-rDsr pathway and the SI system. Strain HY1 employed the Calvin-Benson-Bassham cycle for CO fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic-anoxic interface environments.

Gwak JH, Awala SI, Nguyen NL, Yu WJ, Yang HY, von Bergen M, Jehmlich N, Kits KD, Loy A, Dunfield PF, Dahl C, Hyun JH, Rhee SK
2022 - Proc Natl Acad Sci U S A, 32: e2114799119

Limnospira fusiformis harbors dinitrogenase reductase (nifH)-like genes, but does not show N2 fixation activity

East African soda lakes (EASLs), some of them world-renowned for their large flocks of flamingos, range amongst the most productive aquatic ecosystems worldwide. The non-heterocytous filamentous cyanobacterium Limnospira fusiformis (formerly Arthrospira fusiformis or Spirulina platensis), forming almost unialgal blooms, is supposed to be a key driver in those ecosystems and is gaining increasing attention because of its nutritional value. Compared to phosphorus and carbon availability, these lakes show reduced nitrogen supply. We studied the possibility of molecular nitrogen (N2) fixation in Limnospira, as contradictory statements have been published, and some closely related taxa were confirmed as N2 fixers (diazotrophs). We cultivated nine isolates originating from various EASLs under nitrate-rich and nitrate-depleted conditions. We detected dinitrogenase reductase (nifH)-like genes in all strains; however, the genes grouped within nifH cluster IV that mostly contains nitrogenases not functioning in N2 fixation. Accordingly, incubations with 15N2 gas did not support N2 fixation activity of the investigated strains. Under laboratory conditions, all strains faded during nitrate-depleted growth after approximately three weeks. Both phycocyanin and chlorophyll-a dropped to a threshold, and chlorophyll fluorescence indicated a severe problem with nitrogen supply. In summary, our data indicate that the investigated Limnospira fusiformis strains are not capable of N2 fixation.


Schagerl M, Angel R, Donabaum U, Gschwandner AM, Woebken D
2022 - Algal Research, 66: 102771

Phage-host coevolution in natural populations.

Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.

Piel D, Bruto M, Labreuche Y, Blanquart F, Goudenège D, Barcia-Cruz R, Chenivesse S, Le Panse S, James A, Dubert J, Petton B, Lieberman E, Wegner KM, Hussain FA, Kauffman KM, Polz MF, Bikard D, Gandon S, Rocha EPC, Le Roux F
2022 - Nat Microbiol, 7: 1075-1086

Lecture series

DOME Lecture: “'Dark oxygen' - an electron acceptor for productive and diverse microbial communities in ancient groundwaters"

Emil Ruff
Marine Biological Laboratory, Massachusetts, USA
12:00 h
hybrid, UBB HS 2

DOME Lecture: "Creating a “niche” and making the most of it: Bacteria – insect interactions in a mutualistic endosymbiosis"

Anna Zaidman-Remy
Institut National des Sciences Appliquées, Lyon, France
12:00 h
hybrid, UBB HS 2

DOME Lecture: "A physical niche regulates a complex microbiome in the Drosophila gut"

William Ludington
Department of Embryology, Carnegie Institution of Science, Maryland, USA
14:00 h