• CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • TER - Terrestrial Ecosystem Research

DMES News

  • David Berry appointed Full Professor

    09.01.18
    People

    David Berry was appointed Full Professor for Intestinal Microbiology at the University of Vienna as of January 1, 2018. Great start into the new year, congratulations!

  • Congratulations - Msc Stefan Gorka

    22.12.17
    People

    Congratulations to Stefan Gorka, who successfully defended his Master thesis "Carbon and nitrogen exchange between plant roots, ectomycorrhizal fungi and soil bacteria in the mycorrhizosphere of Fagus sylvatica“ on Thursday 21 December 2017! Excellent, Stefan.

  • SEACUE: New FWF Project for Jörg Schnecker

    07.12.17
    News

    Jörg Schnecker has recently received funding for a new project called "SEACUE - Seasonal dynamics of soil microbial carbon sequestration" from the Austrian Science Fund (FWF). 

    Congratulations Jörg!

  • Saint Nicholas was here!

    06.12.17
    News

    Saint Nicholas visited DOME to hand out presents to the good Domies and to encourage them to continue doing their best, making DOME a fun and welcoming place for everyone!

Latest publications

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from thirteen bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the thirteen newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth’s ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF
2018 - ISME J, In press

In situ observation of localized, sub-mm scale changes of phosphorus biogeochemistry in the rhizosphere

Aims We imaged the sub-mm distribution of labile P and pH in the rhizosphere of three plant species to localize zones and hot spots of P depletion and accumulation along individual root axes and to relate our findings to nutrient acquisition / root exudation strategies in P-limited conditions at different soil pH, and to mobilization pattern of other elements (Al, Fe, Ca, Mg, Mn) in the rhizosphere. Methods Sub-mm distributions of labile elemental patterns were sampled using diffusive gradients in thin films and analysed using laser ablation inductively coupled plasma mass spectrometry. pH images were taken using planar optodes. Results We found distinct patterns of highly localized labile P depletion and accumulation reflecting the complex interaction of plant P acquisition strategies with soil pH, fertilizer treatment, root age, and elements (Al, Fe, Ca) that are involved in P biogeochemistry in soil. We show that the plants respond to P deficiency either by acidification or alkalization, depending on initial bulk soil pH and other factors of P solubility. Conclusions P solubilization activities of roots are highly localized, typically around root apices, but may also extend towards the extension / root hair zone.

Kreuzeder A, Santner J, Scharsching V, Oburger E, Hoefer C, Hann S, Wenzel WW
2018 - Plant and soil, 1-17

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed the largest (to date) comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8, and 23 (n=24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. In contrast to earlier studies, our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Amongst many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic N sources (such as extracellular peptidases), were detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2, now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large-scale acidobacteria genome analysis reveals traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.

Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D
2018 - Environ Microbiol, in press