Subsurface Carbon Cycling

Geomicrobiology of Caves, Groundwater, and Mofettes

The Critical Zone (CZ) is the region of the Earth that encompasses the outer extent of the vegetation down to the lower limits of groundwater. This heterogeneous and complex region of the Earth includes soils and terrestrial ecosystems and can reach to > 200 m below the surface. The CZ contains all that is necessary to sustain human life. While the importance of the CZ is unrivaled, the relationships between its constituent parts is not as well understood. Most studies of the interactions between life on the surface and life below the surface have concentrated the Pedosphere, the uppermost layer of soil, reaching just a few meters below the surface. However, life extends below the pedosphere, down through the subsurface to aquifers and caves teeming with life, before hitting bedrock. The lower boundary of the CZ is the point where life no longer influences rock and is unknown as modern microbiology is constantly extending the depth of known organisms. The deepest zones of the CZ are where much of the groundwater resides and the processes taking place may influence life at the surface through the water and gas transport. Despite the putative importance of the subsurface on life at the surface, important questions remain about the links between it and surface environments. In our research, we are particulary interested in understanding how subsurface carbon cycling impacts the rest of the CZ.

We are addressing these questions in three environments: karstic caves, limestone aquifers (Hainich groundwater well transect), and mofettes. In these projects we are investigating the diversity and activity of indigenous organisms involved in CO₂-fixation (autotrophic prokaryotes), carbonate biomineralization, and organic matter degradation. Our cave and aquifer projects fall within the framework of an interdisciplinary project at FSU Jena, called AquaDiv@Jena.

In total, we hope to be able to gain some insight into the processes and relationships that govern Critical Zone biology. With climate change and growing human impact, a complete understanding of the processes maintaining natural resources, is absolutely crucial. With this work, we hope to begin to uncover these unanswered questions about life in this narrow, but vitally important section of the planet.

Herrenberg Cave

The newly discovered cave Herrenberg Cave in Thuringia provides us a unique opportunity to examine microorganisms in a pristine environment. It was originally discovered in April 2008 during the building of a tunnel for the Inter City Express (high-speed) railway line from Erfurt to Nürnberg. The construction crew originally tried to fill the cavity with concrete, but stopped after 500 m³. Speleologists were then consulted and the cave exploration came shortly thereafter with ~ 700 meters mapped. The cave developed along the southern fault of the Thuringian Forest in triassic limestone and is a strikingly beautiful cave with many speleothems as well as 3 lakes inside.

Click here to see the Herrenberg Cave on a map >>

After a scientific sampling trip in January 2009 the cave and the entrance were permanently closed with concrete. With the samples we obtained on this trip we investigated the overall bacterial diversity (clone libraries) as well as isolated carbonate-precipitating bacteria (Rusznyak et al. 2012). We found high microbial diversity in the cave and the communities were similar to those found in other subsurface environments. In addition, we were able to show that isolates from the cave can precipitate calcite and are potentially involved in speleothem formation in situ. We also observed species-dependent morphological differences in carbonate crystals and are currently working to assess the influence of cell surface properties on carbonate formation using atomic force microscopy (AFM).

Hainich Groundwater Well Transect

A groundwater well transect was constructed in the Thuringian basin for the AquaDiv@Jena project during 2010-2011. Starting in the Hainich National Park, the transects run parallel to the direction of water flow down from elevated forests of the Hainich to less elevated fields in the basin below. This orientation will allow our researchers to correlate land use patterns with above and belowground biodiversity along the transect.

Click here to see the groundwater well transect on a map >>

To date there are altogether 10 groundwater wells established at the five sampling sites along the transect. The wells are sampled regularly for geochemistry, hydrology, and microbiology. In addition to water sampling, passive samplers are installed to allow for microbial colonization over longer periods of time between water sampling.

The main goal of our research is to characterize the diversity of microbial Prokaryotes and Eukaryotes and to link this diversity to biogeochemical cycling within aquifers. The research of Dr. Denise Akob and Dr. Anna Rusznyak focuses on characterizing active and CO₂-fixing Bacteria in groundwater and aquifer core material. To do this, they employed pyrosequencing of bacterial 16S rRNA genes and carbon fixation genes (e.g., Rubisco genes). Research of Patricia Geesink, Dr. Martina Herrmann, and Dr. Ute Risse-Buhl focuses on characterizing microbial Eukaryotes in the aquifer by targeting 18S rRNA genes. In an associated project, Dr. Martina Herrmann and Sebastian Opitz aim to characterize nitrogen cycling microbial communities in the aquifer. Our hope is that by combining the results of these studies we can begin to understand microbial food webs in the Hainich aquifer and determine the microbial impact on carbon and nitrogen cycling.

Mofettes

A mofette is the exhalation of volcanic CO₂ directly derived from the upper mantle that has temperatures <90°C. They occur along geological disturbances and can lead to CO₂ concentrations in the soil gas phase of up to 100%. Mofettes provide a unique environment to study the effects of extreme CO₂ on ecosystems and microbial life. The capture and storage of CO₂ in geological structures (CCS) is a proposed method for reducing anthropogenic CO₂ emissions. However, leakage of these structures might lead to high CO₂ concentrations which might severely damage the health of humans and ecosystems. Therefore, mofettes are ideal natural analogs for understanding the potential effects of extreme CO₂ concentrations.

We study mofettes near Hartousov, Czech Republic, which are controlled by active magmatic activity. The work of Felix Beulig aims to characterize metabolically active microbial community structure in mofette soils and determine their interaction with the upstreaming CO₂.