All Things Microbial Group: What We Do
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Currently, members of this research group are engaged in a number of activities. The link between these activities is something microbial and the methodology by which we study the particular problem. Traditional microbiology has taught us much about the diversity of the microbial world. Particularly with regard to what microbiota look like and their biochemical processes. While it remains quite true, “That to know it—you have to grow it,” we now know that the bulk of the microorganisms in the environment are incapable of being brought into cultivation. It is too difficult to duplicate an organism’s host environment / ecosystem in a dish in a laboratory. With the advent of modern molecular techniques, we can understand the microbial environment in much greater detail through an examination of DNA present in any environment. Phylogenetic characterization is possible by base-pair comparison of DNA sequence between organisms. Applied to genetically conserved genes, like small sub-unit ribosomal rRNA genes (SSU rRNA), we can begin to understand how organisms are related. We can also look at functional genes—genes that help to facilitate specific pathways like nitrogen fixation, metal reduction or hydrogen utilization. Typically our studies take us to a field site where some microbial process is occurring or is thought to. We sample and characterize the site for associated chemistry / geochemistry, and collect material for DNA analysis back in the laboratory. At the bench, we employ molecular processes of DNA extraction, polymerase chain reaction (PCR), cloning, DNA sequencing, phylogenetic tree building and statistical analyses to characterize the microbiota of the site. Our laboratory is stocked with state of the art equipment that includes, anaerobic chambers, PCR machines, spectrophotometers, “sterile” work spaces, a Leica analytical microscope, an Hitachi TM-1000 Scanning Electron Microscope (SEM) and several computer workstations for data manipulation.
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Research Projects
The DEep Phreatic THermal eXplorer (DEPTHX)
Funded by a NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) grant, this project seeks to develop an autonomous underwater vehicle that is capable of mapping, exploring, and sampling its world in 3-D space. The team responsible for this idea and work includes people from CSM, Carnegie-Mellon University, The University of Texas and the Southwest Research Institute. The robot has been built by the lead design team members at Stone Aerospace in Austin, TX and will be deployed in Cenoté Zacatón, ~2 hours NW of Tampico, Mexico, in the Spring of 2007. This exciting project has as a goal, the sampling of microbial life from deep within the Cenoté, returning that sample to the surface, and telling us where it came from. A variety of instruments and algorithms are on board to allow choice of sampling place. The sample(s) will be collected as both water column samples and biofilm / wall samples with which we can deliver back to our laboratory for molecular phylogenetic characterization. Some useful websites for more information to track our progress are:
http://www.depthx.org/
http://www.ri.cmu.edu/projects/project_544.html
http://www.geo.utexas.edu/zacaton/3D_Mapping/images/DEPTHX.htm
A Blog of our activity can likely be found here:
http://www.stoneaerospace.com/news-/news-zacaton-mission1.php
DEPTHX Images:
The Fish Food Project
In a grant to the National Science Foundation’s Materials Use: Science, Engineering and Society (MUSES) program entitled “Production and use of a novel bacterial protein in aquaculture operations: societal benefits and global ramifications,” we seek to take what has normally been considered a waste stream—bacterial biomass from food production—and turn that in to a beneficial source of protein for farm-raised fish. To do this, we need to characterize the kinds of microbiota present in single cell protein biomass obtained from a brewery waste stream. With that information, we can design and construct machinery to make a high protein content additive for fish meal. Farm raised Talapia can then eat the high protein meal, and farmers can get bigger fish, ready faster, for the marketplace. Some aspects of this work have both anthropologic and economic ramifications, and those are being explored by partners at the University of Colorado, Boulder. Look for updates on this work in the Spring of 2007.
Environmental Hydrogenases in Geothermal Hotsprings
This is an NSF funded project that extends work done as a Postdoc in Norm Pace’s laboratory. We have shown that many, if not most, microbial communities in Yellowstone National Park hotsprings rely upon aqueous molecular hydrogen (H2) concentrations (nM) as a source of electrons to carry out metabolism. Now, we seek to show how this process happens. Presumably, microbial cells of many different kinds, have functional hydrogenase enzymes oxidizing the hydrogen to water. Most hydrogenase enzymes will also carry out this reaction in reverse, producing hydrogen. Thus, this work has functional components to both basic science, i.e., what happens in nature; and the potential for engineered application in the area of bioenergy, i.e., use of microbially produced hydrogen as a fuel source.
Geobiology Interests
For several years I have been thinking about the rock: microbiota interface. How ore bodies form and what microbial processes are involved, for example. For my Ph.D. work I looked at the kinetics of how fast sulfate reducing bacteria can reduce soluble U(VI) to insoluble U(IV). This process could have been responsible for the formation of natural uranium ore bodies, but can now be examined and then utilized for the removal of U in contaminated waters for remediation purposes. I then moved on to characterizing the microbial communities present in the “endolith”—microbes located in the pore spaces of rocks, with a focus on gypsum / halite evaporite salts (photo, top of this page). Currently, we are looking at the communities that make up forming stalactites in a geothermal mine adit. Such communities are likely widespread and greatly aid in the formation of what can be amazing speleothems in caves. The rock:microbial interface is quite amazing and this is why I like to work the International Geobiology Course on Catalina Island (link available, Classes Page).
"More Research, Less Partying...."--is our theme.
