Members of our laboratory have developed a variety of tools for study of life in extreme environments. These include
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•A numerical approach for quantifying rates of chemical reactions in deep marine sediments (Wang et al 2008.pdf)
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•A method for consistently separating microbial cells from their marine sedimentary matrix (Kallmeyer et al 2008.pdf).
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•An assay for quantifying extremely low levels of a fundamental enzymatic activity (hydrogenase activity) (Soffientino et al 2006.pdf)
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•A method for quantifying rates of hydrogen production by water radiolysis in sedimentary environments (Blair et al 2007.pdf)
Students and post-docs who worked on these projects were co-advised by D’Hondt and Arthur Spivack and/or David Smith. If you’re interested in quantifying subsurface biogeochemical processes, you may also be interested in Spivack’s ex situ technique for quantifying in situ concentrations of dissolved volatile chemicals (such as methane) in high-pressure environments (Spivack et al 2006.pdf).
You can apply the numerical approach of Wang et al. (2008) to your own data by using our computer program. The program is written in Matlab. Download the following three files to run the program: NRR1.m, NRR2.m, and SSErev.m. NRR1 estimates a reaction rate profile from measured concentrations of dissolved chemicals and physical properties, NRR2 quantifies uncertainties of the rates using Monte Carlo simulation of concentrations and SSErev provides the minimization technique used in the program. Our manual for the program (NRR_manual.pdf) describes: (1) how to generate input files for NRR1; (2) how to run NRR1 and NRR2; and (3) how to read and use the outputs from both sub-programs. This short manual is a supplement to Wang et al. (2008), where the basis of the reaction rate program (NRR) was originally described. We recommend that users read the paper and this manual before using the program.
