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Microbiology

Current studies include the investigation of the role of viruses in the ecology of communities inhabiting rocks, or endolithic communities and halotolerant microbes living at high pressure, and continued inquiry into microbial viability at high pressures using diamond anvil cells. The challenge is how to interrogate quantitatively these volumetrically tiny worlds where microorganisms clearly exhibit evidence of viability with unknown biochemical modifications.

Microbiology in Extreme Environments — The Geophysical Laboratory has a fully equipped laboratory for microbiological culturing, subsequent biochemical characterization, and experimental studies over a broad range of extreme conditions. The Lab has been involved in studying microbes isolated from hydrothermal vents, fossilized rocks millions of years in age, contaminating the surfaces and cracks of extraterrestrial meteorites, and investigating microbrial viability up to gigapascal pressures in the laboratory using diamond anvil cells. Current studies include the investigation of the role of viruses in the ecology of communities inhabiting rocks, or endolithic communities and halotolerant microbes living at high pressure.

In recent years, microbiologists have developed culture methods to enable them to isolate and grow microbes from deep sea and sub-surface environments. Temperature is only one of many stressors on microbes living in the subsurface. Pressure, high sulfide concentrations, extremes in pH, salinity, and low C availability are some of the many factors that contribute to the designation of extreme environment through their effect on growth limitation and survival at depth. Experiments at the Geophysical Lab were carried out to determine the extremes of pressure tolerance. Conventional diamond anvil cells, tools of the high-pressure materials and Earth science community, are used in these experiments as a clever way of providing a window allowing the observation of cell metabolism and survivability in situ up to pressures of 1 GPa (~ 35 km depth). We have continued to investigate microbial viability at high pressures using diamond anvil cells. The current challenge is how to quantitatively interrogate these volumetrically tiny worlds where microorganisms clearly exhibit evidence of viability with unknown biochemical modifications. Upon recovery, the cultures will be interrogated using RNA microarrays, enabling us to detect up or down regulation of any specific genes as a response to pressure. This interdisciplinary study, funded by the W. M. Keck Foundation, takes advantage of our geobiology and high pressure expertise.

Facilities, equipment and resources available for projects:

Axon 4000B Microarray reader for measuring sample reaction on microarray chips
Labsystems microplate reader for enzyme-linked immunosorbant assays (ELISA)
PAGE gel electrophoresis and blotting apparatus units for macromolecular protein analysis
Ciphergen Protein chip reader for high molecular weight compound analysis, specifically proteins
Bioprobe field ATP Luminometer for enumeration of microbes in soils, sediments, and rocks in the field
Anaerobic chambers (2) for microbial growth
Cepheid Real-time, quantitative PCR and 2 PCR robocyclers for analysis of DNA and RNA
Arrayit, Spot Bot personnel array printer for protein and DNA assays
Agilent 2100 Bioanalyser Lab on a Chip design for instantaneous analysis of proteins and nucleic acids
Field molecular biology laboratory equipped for extracting DNA and running identification.