• Centre for Microbiology and Environmental Systems Science

  • CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • EDGE - Environmental Geosciences

  • TER - Terrestrial Ecosystem Research


Latest publications

In situ abundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica.

Sulphide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulphidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labelling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photopigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3% ± 7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulphur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulphur bacteria (Halochromatium sp.) contributed only 1.8% ± 1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulphur bacteria and one of a purple sulphur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth.

Pjevac P, Dyksma S, Goldhammer T, Mujakić I, Koblížek M, Mussmann M, Amann R, Orlić S
2019 - Environ. Microbiol., 10: 3896-3908

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.

Riva A, Kuzyk O, Forsberg E, Siuzdak G, Pfann C, Herbold CW, Daims H, Loy A, Warth B, Berry D
2019 - Nat Commun, 10: 4366

Life at 0 °C: the biology of the alpine snowbed plant Soldanella pus

All plant species reach a low temperature range limit when either low temperature extremes exceed their freezing tolerance
or when their metabolism becomes too restricted. In this study, we explore the ultimate thermal limit of plant tissue formation
exemplified by a plant species that seemingly grows through snow. By a combination of studies in alpine snowbeds and
under controlled environmental conditions, we demonstrate and quantify that the clonal herb Soldanella pusilla (Primulaceae)
does indeed grow its entire flowering shoot at 0 °C. We show that plants resume growth under 2–3 m of snow in mid-winter,
following an internal clock, with the remaining period under snow until snow melt (mostly in July) sufficient to produce a
flowering shoot that is ready for pollination. When snow pack gets thin, the flowering shoot intercepts and re-radiates longwave
solar radiation, so that snow and ice gently melt around the fragile shoot and the flowers emerge without any mechanical
interaction. We evidence bud preformation in the previous season and enormous non-structural carbohydrate reserves
in tissues (mainly below ground) in the form of soluble sugars (largely stachyose) that would support basic metabolism for
more than 2 entire years under snow. However, cell-wall formation at 0 °C appears to lack unknown strengthening factors,
including lignification (assessed by confocal Raman spectroscopy imaging) that require between a few hours or a day of
warmth after snow melt to complete tissue strengthening. Complemented with a suite of anatomical data, the work opens a
window towards understanding low temperature limits of plant growth in general, with potential relevance for winter crops
and trees at the natural climatic treeline.

Körner C, Riedl S, Keplinger T, Richter A, Wiesenbauer J, Schweingruber F, Hiltbrunner E
2019 - Alpine Botany, 129: 63-80

Lecture series

Exploring and Exploiting the Chemistry of Microbial Interactions

Thomas Böttcher
Department of Chemistry, University of Konstanz, Germany
12:00 h
Lecture Hall HS2, UZA1, Althanstrasse 14, 1090 Wien

Computational modeling and learning methods for metagenomics of microbial and viral communities

Prof. Dr Thomas Rattei
Department of Microbiology and Ecosystem Science, University of Vienna, Austria
16:30 h
Eberhard Clar-Saal (2B 204), Althanstrasse 14 UZA II, 1090 Vienna

Global wildfires - trends, impacts and their role in the carbon cycle

Dr Cristina Santin, Prof. Dr Stefan Doerr
Department of Geography, Swansea University, UK
16:30 h
Eberhard Clar-Saal (2B 204), Althanstrasse 14 UZA II, 1090 Vienna