I was honored to receive a DEBI RCN Graduate Student Education Exchange grant for research at the IODP Kochi Institute for Core Sample Research in Kochi, Japan. During the month of July 2010, I worked with Dr. Fumio Inagaki and other members of his lab group to learn his techniques of cell enumeration and flow cytometry. The experience of working in his lab allowed me to go beyond the typical collaboration based on brief meetings and email exchanges alone. I was able to step outside of my comfort zone and have a research experience in an unfamiliar culture. I learned much more than research techniques including overcoming communication barriers, building collaborations, and cultural exchanges. I discovered that the basic standards of science are global and although communication was difficult with a few lab members, the language of science transcended that and we continued to learn from each other regardless. The methods I have learned in Japan have given me the ability to expand on my skill set and apply it to various environments. Since working with Dr. Inagaki, the techniques I have learned have allowed me to work on samples collected from research cruises in the Gulf of Mexico and IODP Leg 325 in the Great Barrier Reef. Dr. Inagaki encouraged me to ship and work on my own samples in order to return to my home institution with data that I am able to directly incorporate into my dissertation. We have since discussed other collaboration opportunities and I look forward to what the Research Coordination Network can provide in the future.
The DEBI/C-DEBI research exchange gave me the opportunity to travel to Lawrence Berkeley National Laboratory (LBNL) to work with Dr. Eoin Brodie. While at LBNL, I was able to learn and adopt a new microarray technology for subseafloor microbial ecology investigations. The PhyloChip is a microarray that contains probes for Bacterial and Archaeal 16s rRNA genes and uses parallel hybridization to minimizes the influence of dominant organisms; therefore, it is highly sensitive to rare microbes. In addition, to this data the research exchange provided necessary funding for me to finish my dissertation. The research exchange funds allowed two sites in the Ulleung Basin to be fully analyzed and incorporated into my dissertation “Geomicrobiology of sediment containing methane”. This collaboration also introduced me to how research is conducted at a national laboratory. This information is valuable in deciding my future career path. Whatever that path may be the collaboration and techniques that I learned will continue beyond graduate school, as we are planning future studies using the PhyloChip. For more on this method, see Briggs, Pohlman, Torres, Reidel, Brodie and Colwell’s 2011 AEM paper Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane.
Enumeration of microbial cells in subsurface samples is an important baseline approach in our understanding of microbial life and ecosystems. This method has proven a challenge as non-specific fluorescent signals due to sediment particles impede efficient detection and counting of microbial cells. Therefore, the proposed travel exchange took place at Fumio Inagaki’s laboratory (JAMSTEC) in Kochi (Japan) in order to carry out computer-based automatic cell counting for gravity core sediments fixed on board during the DARCSEAS cruise in the Eastern Mediterranean Sea. This method is based on washing sediments with hydrofluoric acid, and staining with SYBR Green I in order to eliminate fluorescence of non-biological background while discriminating at the same time against background fluorescence of unspecifically stained organic material whose emission wavelengths are slightly offset from the peak of the SYBR Green I fluorescence emission window (Morono, 2009). This innovative technique will allow processing the large number of cell count samples generated during the cruise. This will in turn enable robust statistical comparison between samples as it will eliminate the bias of human counting. This information will prove useful in quantifying the microbial population in the sediment samples of the Mediterranean Sea. This travel exchange will also be very beneficial for learning this new method and training with the leading experts on this field of research.
Sulfate reducing microorganisms (SRM) may play a significant role altering upper oceanic crustal fluids when suitable electron donors, such as hydrogen or organic matter, are available. The habitability of such an environment with respect to sulfate reduction depends on the competition of microbial communities for substrates, which is largely dictated by the energetics of catabolic and anabolic processes. Although sulfate reduction has been observed in fluids taken from the upper ocean crust in Juan de Fuca Ridge flanks, the electron donors (EDs) used by SRM have not been identified, nor has the energy required for organic synthesis been determined. As a result, a collaboration is underway to characterize the EDs that are plausible candidates for the SRM in the Juan de Fuca system and to quantify the amount of energy these microorganisms require to synthesize biomolecules. This is accomplished by carrying out thermodynamic calculations that take into account the physicochemical properties of the resident fluids. Specifically, the Gibbs energy of reactions describing the reduction of sulfate by various EDs and the synthesis of amino acids from inorganic precursors is being calculated at the temperature, pressure and compositional conditions prevailing in particular Juan de Fuca sample site locations.
The immediate objective is to learn techniques of intact polar and apolar lipid analysis (IPL and AL, respectively) in the Hinrichs Lab (MARUM, Bremen, Germany). Analysis will be conducted in several sections from five sediment cores collected in a cross-shelf transect during the LARISSA 2012 research expedition in the Weddell Sea. This work would be undertaken in a three-month graduate student research exchange. The overarching research objective is to assess the changes in sedimentary microbial community structure and the input of organic matter as the Larsen A embayment (Weddell Sea) transitioned from an oligotrophic sub-ice shelf, dark system to a photosynthetic open ocean system. These changes will be verified and related to the ice shelf collapse in space and time. The results will be merged with geochemical (concentrations of methane, sulfate, sulfide, dissolved inorganic carbon, and nutrients), geological (Lead 210 dating, diatom counts and chlorophyll concentration) and genetic profiles (i.e. bacterial and archaeal 16S rDNA sequencing and metageomics data) generated by collaborators in the NSF-funded LARISSA Program.