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We are proud to support the following DEBI RCN projects.
Brandon Briggs, Oregon State University
The Effect of Methane on Microbial Community Distributions
in the Ulleung Basin
Host: Eoin Brodie at Lawrence Berkeley National Laboratory
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.
NEW!
Doug LaRowe, University of Southern California, Alberto Robador,
Tina Lin, University of Hawaii
Environmental engergy availability for sulfate-reducing microorganisms
in deep subseafloor basaltic fluids
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.
NEW!
Cassandre Lazar, University of North Carolina Chapel Hill
Enumeration of microbial cells in sediments from the Mediterranean
Sea
Host: Fumio Inagaki at the Kochi Insitute for Core Sample
Research (JAMSTEC, Japan)
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.
Brandi Kiel Reese, Texas A&M University
Bioprospecting novel antimicrobials in the marine deep subsurface
biosphere
Host: Fumio Inagaki at the Kochi Insitute for Core Sample
Research (JAMSTEC, Japan)
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.
> See more on our student
and postdoctoral exchange program.
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