Geomicrobiology of Pristine Environments

Macaroni and stalactite speleothems in the Herrenberg cave, discovered in 2008 during the construction of a high speed train tunnel
Macaroni and stalactite speleothems in the Herrenberg cave, discovered in 2008 during the construction of a high speed train tunnel by the Deutche Bahn
The Herrenbergberg Cave in Germany was discovered during the process of digging a new high speed train tunnel. Before its discovery, it was isolated from the surface.
Sampling a stalagtite from the Herrenberg cave for the presence of bacteria.
A section of Trochitenkalk, which makes up the main aquifer in this region, showing the many pores where micro- and macroorganisms can reside in the rock.
Pitcher plant, Sarracenia purpurea leaves filled with water in a bog in northern Florida.

As microbes are the drivers of biogeochemical cycles, understanding their impact on life-sustaining processes starts with an understanding of their biodiversity in pristine habitats. I am interested in understanding the microbiology of the Earth´s Critical Zone (CZ) and the impact of microorganisms on carbon cycling (Akob and Küsel 2011). The CZ is the heterogeneous environment where complex interactions between rock, soil, water, air, and living organisms regulate the availability of life-sustaining resources. It is a huge region, ranging from the outer extent of vegetation through soils (pedosphere) down to unsaturated and saturated bedrock and it contains all that is necessary to sustain human life. My CZ research focuses on characterizing microbial diversity in pitcher plants (Gray et al. in prep), karstic caves (Rusznyak et al. submitted), and aquifers with the goal of determining the role of microbial populations in carbon cycling.

Karstic caves represent one of the most important subterranean carbon storages on Earth and provide windows into the subsurface. In the newly discovered Herrenberg Cave, Germany, I was involved in investigating the diversity and potential role of bacteria in carbonate mineral formation (Rusznyak et al. submitted). In this work, microbial communities inhabiting stalactites and sediments were identified using DNA- and RNA-based 16S rRNA sequencing. Microbial carbonate precipitation was assessed using cultivation techniques combined with mineral analysis (e.g., Raman spectroscopy, EDX) and microscopy. The combination of various techniques was important for understanding the geomicrobiology of karstic caves and providing a first link between the geochemistry and microbial populations of the cave.

Pristine aquifers of the Hainich region, Germany are the focus of a large on-going interdisciplinary research program at the Friedrich Schiller University Jena. As a post-doc in this project my goal is to elucidate the composition and diversity of microorganisms in these aquifers and link their activity in the deep biosphere to the surface environment. In my work, I am using molecular techniques to target total Bacteria and Archaea communities and functional groups involved in CO2-fixation in groundwater and core samples My goal is to compare the composition of free-living and attached microbial communities to determine how they contribute to subsurface carbon cycling.,

The North American pitcher plant, Sarracenia purpurea, is a unique system for characterizing microbial diversity and carbon cycling but it has been poorly studied from a microbiology perspective. The leaves of S. purpurea trap rainwater, creating a microscopic aquatic habitat with the dynamics of larger aquatic food webs and making it an ideal system for understanding dynamics occurring in an entire food web. Insects, especially ants, fall into the water trapped in the leaf; bacteria and yeast colonize the system, decompose the insects, and liberate nutrients for the plant. A variety of protozoans and a rotifer species also colonize this community and consume the bacteria. The leaves of S. purpurea contain the same species of larvae, protozoans and rotifer species throughout the plant's native geographic range but little is known about the identity of the bacteria in this system. In collaboration with Dr. Sarah M. Gray I am using a combination of 16S rRNA sequence analysis and cultivation techniques to determine if the bacteria forming the bottom trophic level of this community are the same throughout leaves at a local scale (within a bog) and between sites in Florida and New York (the Southern and Northern points of S. purpurea's geographic range). In the future I will identify the functional role of microbial populations to determine what enzymes these organisms utilize for decomposition. This work may also have implications for bioenergy as novel enzymes for cellulose degradation could exist within this system.



Gray, S. M., D. M. Akob, S. J. Green, and J. E. Kostka. Geographic variability in aquatic microbial community composition and diversity in the pitcher plant Sarracenia purpurea. In prep.

Akob, D. M., H. J. Mills, K.-J. Chin, M. S. Humphrys, T. M. Gihring, J. Delgardio, K. Küsel and J. E. Kostka. Quantification of metabolically active Fe(III)- and sulfate-reducing prokaryotes in intertidal marine sediments. In prep.

Rusznyák, A., D. M. Akob, S. Nietzsche, K. Eusterhues, K. U. Totsche, T. R. Neu, T. Frosch, J. Popp, R. Keiner, J. Geletneky, L. Katzschmann, E.-D. Schulze, and K. Küsel. 2011. First insights into bacterial communities inhabiting the pristine karstic Herrenberg Cave. Applied and Environmental Microbiology. In revision 10-2011.

Akob, D. M. and K. Küsel. 2011. Where microorganisms meet rocks in the Earth's Critical Zone. Biogeosciences Discussions 8: 2523-2562.

Diaz, M. C., D. Akob, & C. S. Cary. 2004. Denaturing gradient gel electrophoresis of nitrifying microbes associated with tropical sponges. Proceedings of the 6th International Sponge Conference, Rapallo, Italy, 2002. Bollettino dei Musei e degli Istituti biologici dell'Università di Genova 68: 279–289.