• 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

  • Microbial Symbioses

    University of Vienna PhD program

  • Apply for the DOME International PhD/PostDoc program

Dome News

Latest publications

Culture-independent tracking of Vibrio cholerae lineages reveals complex spatiotemporal dynamics in a natural population.

Populations of the bacterium Vibrio cholerae consist of dozens of distinct lineages, with primarily (but not exclusively) members of the pandemic generating lineage capable of causing the diarrhoeal disease cholera. Assessing the composition and temporal dynamics of such populations requires extensive isolation efforts and thus only rarely covers large geographic areas or timeframes exhaustively. We developed a culture-independent amplicon sequencing strategy based on the protein-coding gene viuB (vibriobactin utilization) to study the structure of a V. cholerae population over the course of a summer. We show that the 26 co-occurring V. cholerae lineages continuously compete for limited space on nutrient-rich particles where only a few of them can grow to large numbers. Differential abundance of lineages between locations and size-fractions associated with a particle-attached or free-swimming lifestyle could reflect adaptation to various environmental niches. In particular, a major V. cholerae lineage occasionally grows to large numbers on particles but remain undetectable using isolation-based methods, indicating selective culturability for some members of the species. We thus demonstrate that isolation-based studies may not accurately reflect the structure and complex dynamics of V. cholerae populations and provide a scalable high-throughput method for both epidemiological and ecological approaches to studying this species.

Kirchberger PC, Orata FD, Nasreen T, Kauffman KM, Tarr CL, Case RJ, Polz MF, Boucher YF
2020 - Environ. Microbiol., in press

Using Colonization Assays and Comparative Genomics To Discover Symbiosis Behaviors and Factors in Vibrio fischeri.

The luminous marine Gram-negative bacterium () is the natural light organ symbiont of several squid species, including the Hawaiian bobtail squid, , and the Japanese bobtail squid, Work with has shown how the bacteria establish their niche in the light organ of the newly hatched host. Two types of strains have been distinguished based upon their behavior in cocolonization competition assays in juvenile , i.e., (i) niche-sharing or (ii) niche-dominant behavior. This study aimed to determine whether these behaviors are observed with other strains or whether they are specific to those isolated from light organs. Cocolonization competition assays between strains isolated from the congeneric squid or from other marine animals revealed the same sharing or dominant behaviors. In addition, whole-genome sequencing of these strains showed that the dominant behavior is polyphyletic and not associated with the presence or absence of a single gene or genes. Comparative genomics of 44 squid light organ isolates from around the globe led to the identification of symbiosis-specific candidates in the genomes of these strains. Colonization assays using genetic derivatives with deletions of these candidates established the importance of two such genes in colonization. This study has allowed us to expand the concept of distinct colonization behaviors to strains isolated from a number of squid and fish hosts. There is an increasing recognition of the importance of strain differences in the ecology of a symbiotic bacterial species and, in particular, how these differences underlie crucial interactions with their host. Nevertheless, little is known about the genetic bases for these differences, how they manifest themselves in specific behaviors, and their distribution among symbionts of different host species. In this study, we sequenced the genomes of isolated from the tissues of squids and fishes and applied comparative genomics approaches to look for patterns between symbiont lineages and host colonization behavior. In addition, we identified the only two genes that were exclusively present in all strains isolated from the light organs of sepiolid squid species. Mutational studies of these genes indicated that they both played a role in colonization of the squid light organ, emphasizing the value of applying a comparative genomics approach in the study of symbioses.

Bongrand C, Moriano-Gutierrez S, Arevalo P, McFall-Ngai M, Visick KL, Polz M, Ruby EG
2020 - mBio, 2: in press

Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan.

Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.

Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF, Hehemann JH
2020 - Nat Microbiol, 8: 1026-1039

Lecture series

Ecology of ammonia oxidizers in engineered aquatic environments

Josh Neufeld
Department of Biology, University of Waterloo, Canada
19.03.2020
12:00 h
Webinar

Ammonia oxidising archaea: From environments to enzymes

Laura Lehtovirta-Morley
University of East Anglia
30.01.2020
12:00 h
Lecture Hall HS2, UZA1, Althanstrasse 14, 1090 Wien

Metals and microbial respiration: the molecular basis of bioelectricity production and greenhouse gas destruction

David Richardson
University of East Anglia, Norwich Research Park, Norwich, UK
23.01.2020
12:00 h
Lecture Hall HS2, UZA1, Althanstrasse 14, 1090 Wien