@article {1737,
	title = {Methane cycling. Nonequilibrium clumped isotope signals in microbial methane.},
	journal = {Science},
	volume = {348},
	year = {2015},
	month = {2015 Apr 24},
	pages = {428-31},
	abstract = {<p>Methane is a key component in the global carbon cycle, with a wide range of anthropogenic and natural sources. Although isotopic compositions of methane have traditionally aided source identification, the abundance of its multiply substituted "clumped" isotopologues (for example, (13)CH3D) has recently emerged as a proxy for determining methane-formation temperatures. However, the effect of biological processes on methane{\textquoteright}s clumped isotopologue signature is poorly constrained. We show that methanogenesis proceeding at relatively high rates in cattle, surface environments, and laboratory cultures exerts kinetic control on (13)CH3D abundances and results in anomalously elevated formation-temperature estimates. We demonstrate quantitatively that H2 availability accounts for this effect. Clumped methane thermometry can therefore provide constraints on the generation of methane in diverse settings, including continental serpentinization sites and ancient, deep groundwaters.</p>},
	keywords = {Animals, Carbon Cycle, Carbon Isotopes, Cattle, Groundwater, Hydrogen, Methane, Methanomicrobiales, Temperature},
	issn = {1095-9203},
	doi = {10.1126/science.aaa4326},
	author = {Wang, David T and Gruen, Danielle S and Lollar, Barbara Sherwood and Hinrichs, Kai-Uwe and Stewart, Lucy C and Holden, James F and Hristov, Alexander N and Pohlman, John W and Morrill, Penny L and K{\"o}nneke, Martin and Delwiche, Kyle B and Reeves, Eoghan P and Sutcliffe, Chelsea N and Ritter, Daniel J and Seewald, Jeffrey S and McIntosh, Jennifer C and Hemond, Harold F and Kubo, Michael D and Cardace, Dawn and Hoehler, Tori M and Ono, Shuhei}
}
@article {432,
	title = {Metabolic response of Geobacter sulfurreducens towards electron donor/acceptor variation.},
	journal = {Microb Cell Fact},
	volume = {9},
	year = {2010},
	month = {2010},
	pages = {90},
	abstract = {BACKGROUND: Geobacter sulfurreducens is capable of coupling the complete oxidation of organic compounds to iron reduction. The metabolic response of G. sulfurreducens towards variations in electron donors (acetate, hydrogen) and acceptors (Fe(III), fumarate) was investigated via (13)C-based metabolic flux analysis. We examined the (13)C-labeling patterns of proteinogenic amino acids obtained from G. sulfurreducens cultured with (13)C-acetate.

RESULTS: Using (13)C-based metabolic flux analysis, we observed that donor and acceptor variations gave rise to differences in gluconeogenetic initiation, tricarboxylic acid cycle activity, and amino acid biosynthesis pathways. Culturing G. sulfurreducens cells with Fe(III) as the electron acceptor and acetate as the electron donor resulted in pyruvate as the primary carbon source for gluconeogenesis. When fumarate was provided as the electron acceptor and acetate as the electron donor, the flux analysis suggested that fumarate served as both an electron acceptor and, in conjunction with acetate, a carbon source. Growth on fumarate and acetate resulted in the initiation of gluconeogenesis by phosphoenolpyruvate carboxykinase and a slightly elevated flux through the oxidative tricarboxylic acid cycle as compared to growth with Fe(III) as the electron acceptor. In addition, the direction of net flux between acetyl-CoA and pyruvate was reversed during growth on fumarate relative to Fe(III), while growth in the presence of Fe(III) and acetate which provided hydrogen as an electron donor, resulted in decreased flux through the tricarboxylic acid cycle.

CONCLUSIONS: We gained detailed insight into the metabolism of G. sulfurreducens cells under various electron donor/acceptor conditions using (13)C-based metabolic flux analysis. Our results can be used for the development of G. sulfurreducens as a chassis for a variety of applications including bioremediation and renewable biofuel production.},
	keywords = {Acetic Acid, Acetyl Coenzyme A, Amino Acids, Carbon Isotopes, Citric Acid Cycle, Electrons, Ferric Compounds, Fumarates, Geobacter, Gluconeogenesis, Oxidation-Reduction, Phosphoenolpyruvate Carboxykinase (GTP), Pyruvates},
	issn = {1475-2859},
	doi = {10.1186/1475-2859-9-90},
	author = {Yang, Tae Hoon and Coppi, Maddalena V and Lovley, Derek R and Sun, Jun}
}
@article {491,
	title = {Elucidation of an alternate isoleucine biosynthesis pathway in Geobacter sulfurreducens.},
	journal = {J Bacteriol},
	volume = {190},
	year = {2008},
	month = {2008 Apr},
	pages = {2266-74},
	abstract = {The central metabolic model for Geobacter sulfurreducens included a single pathway for the biosynthesis of isoleucine that was analogous to that of Escherichia coli, in which the isoleucine precursor 2-oxobutanoate is generated from threonine. 13C labeling studies performed in G. sulfurreducens indicated that this pathway accounted for a minor fraction of isoleucine biosynthesis and that the majority of isoleucine was instead derived from acetyl-coenzyme A and pyruvate, possibly via the citramalate pathway. Genes encoding citramalate synthase (GSU1798), which catalyzes the first dedicated step in the citramalate pathway, and threonine ammonia-lyase (GSU0486), which catalyzes the conversion of threonine to 2-oxobutanoate, were identified and knocked out. Mutants lacking both of these enzymes were auxotrophs for isoleucine, whereas single mutants were capable of growth in the absence of isoleucine. Biochemical characterization of the single mutants revealed deficiencies in citramalate synthase and threonine ammonia-lyase activity. Thus, in G. sulfurreducens, 2-oxobutanoate can be synthesized either from citramalate or threonine, with the former being the main pathway for isoleucine biosynthesis. The citramalate synthase of G. sulfurreducens constitutes the first characterized member of a phylogenetically distinct clade of citramalate synthases, which contains representatives from a wide variety of microorganisms.},
	keywords = {Acetyl Coenzyme A, Bacterial Proteins, Biosynthetic Pathways, Butyric Acids, Carbon Isotopes, Geobacter, Isoleucine, Malates, Pyruvic Acid, Threonine, Threonine Dehydratase},
	issn = {1098-5530},
	doi = {10.1128/JB.01841-07},
	author = {Risso, Carla and Van Dien, Stephen J and Orloff, Amber and Lovley, Derek R and Coppi, Maddalena V}
}
@article {526,
	title = {Microbial incorporation of 13C-labeled acetate at the field scale: detection of microbes responsible for reduction of U(VI).},
	journal = {Environ Sci Technol},
	volume = {39},
	year = {2005},
	month = {2005 Dec 1},
	pages = {9039-48},
	abstract = {A field-scale acetate amendment experiment was performed in a contaminated aquifer at Old Rifle, CO to stimulate in situ microbial reduction of U(VI) in groundwater. To evaluate the microorganisms responsible for microbial uranium reduction during the experiment, 13C-labeled acetate was introduced into well bores via bio-traps containing porous activated carbon beads (Bio-Sep). Incorporation of the 13C from labeled acetate into cellular DNA and phospholipid fatty acid (PLFA) biomarkers was analyzed in parallel with geochemical parameters. An enrichment of active sigma-proteobacteria was demonstrated in downgradient monitoring wells: Geobacter dominated in wells closer to the acetate injection gallery, while various sulfate reducers were prominent in different downgradient wells. These results were consistent with the geochemical evidence of Fe(III), U(VI), and SO(4)2- reduction. PLFA profiling of bio-traps suspended in the monitoring wells also showed the incorporation of 13C into bacterial cellular lipids. Community composition of downgradient monitoring wells based on quinone and PLFA profiling was in general agreement with the 13C-DNA result. The direct application of 13C label to biosystems, coupled with DNA and PLFA analysis,},
	keywords = {Acetates, Biodegradation, Environmental, Carbon Isotopes, Electrophoresis, Polyacrylamide Gel, Geobacter, Phylogeny, Polymerase Chain Reaction, Proteobacteria, Uranium},
	issn = {0013-936X},
	author = {Chang, Yun-Juan and Long, Philip E and Geyer, Roland and Peacock, Aaron D and Resch, Charles T and Sublette, Kerry and Pfiffner, Susan and Smithgall, Amanda and Anderson, Robert T and Vrionis, Helen A and Stephen, John R and Dayvault, Richard and Ortiz-Bernad, Irene and Lovley, Derek R and White, David C}
}
