Dr. Stephanie A. Eichorst
University of Vienna
Department of Microbiology and Ecosystem Science
Division of Microbial Ecology
Althanstr. 14
A-1090 Wien
phone: +43 1 4277 76603

Complex Carbon Degradation in Terrestrial Ecosystems
Funding: Marie Curie International Incoming Fellowship (S.A. Eichorst)
Soils contain the largest pool of carbon on Earth. Cellulose is a major constituent of this carbon since it is a key component of plant structural carbon. Members of the bacteria and fungi are essential for degrading cellulose and thus are essential for cycling carbon. However, the majority of our knowledge on cellulose degradation has been restricted to organisms that we can grow in the laboratory. The reliance on these growth-based methods to understand soil function can be misleading.
While a postdoctoral researcher at Los Alamos National Laboratory (Los Alamos, NM, USA), I employed a molecular-based approach, DNA-stable isotope probing (SIP), to identify active cellulolytic bacteria and fungi across edaphically and geographically different soils. I am continuing this work in Dr. Dagmar Woebken's group in the Division of Microbial Ecology to better delaminate the specific bacterial and fungal populations' contributions to cellulose degradation in soils and reveal (any) systematic differences in the time course of cellulose degradation among these active microbial populations. In addition, I am investigating various edaphic drivers (such as different types of C and N sources) that can drive the process of cellulose degradation and the associated active communities. By varying the edaphic properties we hope to better understand the importance of the groups and their unique niches for this process. Our study site is a local beech forest soil in the Viennese Forest, Klausen-Leopoldsdorf (see image), from which we collect soil samples for microcosms experiments.
We are using a combination of approaches including activity and enzymatic assays, SIP, next generation sequencing and single-cell approaches to determine and to quantify the in situ contributions of active cellulolytic microorganisms in the soil environment in a previously unachievable manner.
Investigating the function of the ubiquitous Acidobacteria in terrestrial environments - from genome to in situ analysis
Funding: FWF Austrian Science Fund (PI: Dagmar Woebken, Co-PI: S.A. Eichorst)
Members of the phylum Acidobacteria are found in soils worldwide. They comprise a monophyletic phylum of astonishing diversity, similar to the proteobacteria, with 26 currently recognized subdivisions. Their common occurrence and high abundance based on ribosomal gene sequences suggests that they are likely a major component of the microbial community in soil and play ecologically significant roles in the soil environment. However, their roles remain largely unknown due to the limited number of cultivated representatives and a paucity of information on their genetic potential (genomic and metagenomic information).
The overarching goal of this project is to elucidate the ecophysiology and therefore the success and ubiquity of members of the phylum Acidobacteria in terrestrial ecosystems by combining genomic, growth-based, molecular and in situ functional analyses. Our goal is to better link the genetic potential of acidobacteria with their in situ functions in the soil. We have a unique opportunity to analyze the genomes of multiple strains in subdivisions 1 and 3 to understand the genetic potential across representatives of these dominant subdivisions due to a successfully awarded Joint Genome Institute Community Sequencing Project. The expected scientific outcome include: (1) identify genes that help explain their ubiquity in soils; (2) develop acidobacterial primers for functional gene analysis and expression studies in environmental samples, linking genome potential with environmental function; (3) explore acidobacteria ecophysiology with growth-based and environmental in situ experiments combined with NanoSIMS analysis; and (4) develop additional cultivation/enrichment strategies to isolate additional strains in this phylum.
  1. Berthrong S, Yeager CM, Gallegos-Graves L, Steven B, Eichorst SA, Jackson RB, Kuske CR. Nitrogen fertilization has a stronger effect on soil N-fixing bacterial communities than elevated atmospheric CO2. Appl Environ Microbiol. 2014 Mar 7.
  2. Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons BA, Singer SW. Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ Microbiol. 2013 Sep;15(9):2573-87.
  3. Gans JD, Dunbar J, Eichorst SA, Gallegos-Graves LV, Wolinsky M, Kuske CR. A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil. Nucleic Acids Res. 2012 Jul;40(12):e96.
  4. Eichorst SA, Kuske CR. Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing. Appl Environ Microbiol. 2012 Apr;78(7):2316-27.
  5. Gladden JM, Eichorst SA, Hazen TC, Simmons BA, Singer SW. Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia. Biotechnol Bioeng. 2012 May;109(5):1140-5.
  6. Liu KL, Porras-Alfaro A, Kuske CR, Eichorst SA, Xie G. Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes. Appl Environ Microbiol. 2012 Mar;78(5):1523-33.
  7. Dunbar J, Eichorst SA, Gallegos-Graves LV, Silva S, Xie G, Hengartner NW, Evans RD, Hungate BA, Jackson RB, Megonigal JP, Schadt CW, Vilgalys R, Zak DR, Kuske CR. Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide. Environ Microbiol. 2012 May;14(5):1145-58.
  8. Challacombe JF, Eichorst SA, Hauser L, Land M, Xie G, Kuske CR. Biological consequences of ancient gene acquisition and duplication in the large genome of Candidatus Solibacter usitatus Ellin6076. PLoS One. 2011;6(9):e24882.
  9. Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA. New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol. 2004 Aug;70(8):4748-55.
  10. Eichorst SA, Kuske CR, Schmidt TM. Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria. Appl Environ Microbiol. 2011 Jan;77(2):586-96.
  11. Eichorst SA, Breznak JA, Schmidt TM. Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl Environ Microbiol. 2007 Apr;73(8):2708-17.

Teaching Participation
  1. International FISH Course 2013
  2. UE Practical Course in Molecular Microbiology, Microbial Ecology and Immunobiology. Diversity and Function of Uncultured Microbes in Medical and Environmental Samples. 2014

Public Outreach
  1. Article describing Dr. Eichorst's drive as a scientist (English version and Deutsch version).
  2. American International School - 3-day workshop for school children entitled "An Underground Adventure. Dirt - The Scoop on Soil".
    This 3-day workshop was a synthesis of presentations, discussions and hand-on activities to develop an awareness and appreciation for soil and soil microorganisms. The total number of participants was ca. 90 school children. The theme of the first day was "What is Soil?". We discussed the properties and components of soil. Different soil types were brought in so one could gain an appreciation for them. The theme of the second day was "What lives in soil?". We discussed the different types of life in soil - microorganisms, plants and animals, talked about soil as a growth medium for food, and the different soil layers or the soil profile. The final day culminated with a discussion of what we can do to save/preserve the soil, jobs with soil and a question-and-answer session with the students.
  3. University of Vienna, KinderUni. Summer Workshop entitled "Adventures into the microbial world".
    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 Microbe Exhibition and learn more. We will explore what microbes do in nature, such as dirt and lakes, how they help us make food, and how they keep us healthy.