Dr. Stephanie A. Eichorst

Staff Scientist
University of Vienna
Department of Microbiology and Ecosystem Science
Althanstrasse 14
A-1090 Vienna
Austria
Phone: 0043 14277 91210

MAIN AREAS OF RESEARCH

  • Ecophysiology of soil acidobacteria.
  • Exploring the niches of microbial cellulose degradation in temperate soils.
  • Single-cell method development for investigations in soils.
 
Exploring the function of soil acidobacteria 
 
 
Members of the phylum Acidobacteria are ubiquitous across soils worldwide and comprise a monophyletic bacterial phylum of astonishing diversity. Their common occurrence and high abundance based on ribosomal gene sequences suggest that they are likely a major component of the soil microbial community and play ecologically significant roles in soil processes. Yet, their functions remain largely unknown due to the limited number of cultivated representatives and a paucity of information on their genetic potential (genomic and metagenomic information).  
 
 
 
 
Overall, my goal is to elucidate the ecophysiology and therefore the success and ubiquity of members of the phylum Acidobacteria in soils. To achieve this goal, we use a combination of genomics, transcriptomics, growth-based experiments, enzyme kinetics and molecular analyses to identify key features in acidobacterial strains. In addition, we continuously thrive to isolate new members of the Acidobacteria. I have always been fascinated with cultivation-based approaches and find the outcomes of such experiments extremely rewarding as one can better investigate the potential of the microorganisms in the laboratory. Some of our active investigations are highlighted below.
 
 

 

 

Comparative genomics

  • We embarked on the largest comparative acidobacterial genomic investigation to date, which were supported by growth-based investigations.

  • 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.

  • Bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. 

H2-scavenging ability

  • We revealed another feature that can explain their success in soil - the existence of group 1h [NiFe]-hydrogenase in several soil acidobacterial genomes.

  • We demonstrated the use of this enzyme to scavenge H2 during carbon starvation in acidobacterial strains.

  • Furthermore, we surveyed geographically and edaphically different soils and revealed that acidobacteria are prevalent members of the H2-scavenging community. 

Shallow-breathing acidobacteria

  • Several acidobacterial strains harbor both low- and high-affinity terminal oxidase genes.

  • This respiratory flexibility of the prevalent Acidobacteria could aid in their survival in the heterogenous soil environment. 

 

Some of our acidobacterial strains and research have been highlighted here:

 

Microbial cellulose degradation and development of single-cell methods to investigate soil microorganisms

 
 
Soils contain the largest pool of carbon on Earth. Cellulose is a major source of this carbon, as it comprises ca. 30 to 50% of plant dry weight.Members of the BacteriaArchaea, and Fungi are capable of degrading cellulose in several ecosystems, yet their exact contributions or specific niches remain unresolved. We explore this process using a multidisciplinary approach including process level measurements, stable isotope probing, next generation sequencing along with single-cell approaches such as fluorescence in situ hybridization (FISH) and nanometer-scale secondary ion mass spectrometry (NanoSIMS). Using this approach, we seek to not only identify the active participants in this process, but also identify the different niches of the cellulose-responsive guilds. 
 
 

 

One aspect of our multidisciplinary approach in various research projects is to investigate the active participants in microbial processes at the single-cell level to confirm their activity and to gain additional information at this scale. As such, we are developing pipelines and are optimizing tools that permit the analysis of our targeted processes down to the single-cell level, such as FISH, NanoSIMS and Raman microspectroscopy combined with stable isotope tracers (such as 13C, 15N and D) in complex systems, such as soil. 

 

Some of our developments have been highlighted by the Joint Genome Institute, Science Highlights: A Single-Cell Pipeline for Soil Samples

CURRENT RESEARCH PROJECTS

Microbial mediated cellulose degradation in soil

Single-cell methods in terrestrial ecosystems

Ecophysiology of acidobacteria

PUBLIC OUTREACH

University of Vienna, KinderUni (since 2014-current)
Summer Workshope entitled "What would the world look like without microbes?". Course description: Microbes are all around us and are very important. Imagine what the world would look like without them? Come spend some time at our MIcrobial Exhibition and learn more. We will explore what microbes do in nature, for instance in dirt and in lakes, how they help us make food, and how they help plants to grow. 

 

American International School (2014)

3-day workshop for school childgren entitled "An Underground Adventure. Dirt - The Scoop on Soil". This 3-day workshop was a synthesis of presentations, discussions and hands-on activities to develop an awareness and appreciation for soil and soil microorganisms. The themes covered topics such as "What is Soil?", "What lives in soil?", and what we can do to save/preserve the soil, along with a question-and-answer session with students.