@article {471,
	title = {Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments.},
	journal = {ISME J},
	volume = {3},
	year = {2009},
	month = {2009 Feb},
	pages = {216-30},
	abstract = {To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.},
	keywords = {Colorado, DNA, Bacterial, Environmental Microbiology, Gene Expression Profiling, Geobacter, Geologic Sediments, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Sequence Analysis, DNA, Uranium},
	issn = {1751-7370},
	doi = {10.1038/ismej.2008.89},
	author = {Holmes, Dawn E and O{\textquoteright}Neil, Regina A and Chavan, Milind A and N{\textquoteright}guessan, Lucie A and Vrionis, Helen A and Perpetua, Lorrie A and Larrahondo, M Juliana and DiDonato, Raymond and Liu, Anna and Lovley, Derek R}
}
@article {484,
	title = {Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation.},
	journal = {Int J Syst Evol Microbiol},
	volume = {58},
	year = {2008},
	month = {2008 May},
	pages = {1075-8},
	abstract = {A Gram-negative, rod-shaped, motile bacterium, strain Rf4T, which conserves energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation, was isolated from subsurface sediment undergoing uranium bioremediation. The 16S rRNA gene sequence of strain Rf4T matched sequences recovered in 16S rRNA gene clone libraries constructed from DNA extracted from groundwater sampled at the same time as the source sediment. Cells of strain Rf4T were regular, motile rods, 1.2-2.0 microm long and 0.5-0.6 microm in diameter, with rounded ends. Cells had one lateral flagellum. Growth was optimal at pH 6.5-7.0 and 32 degrees C. With acetate as the electron donor, strain Rf4T used Fe(III), Mn(IV), anthraquinone-2,6-disulfonate, malate and fumarate as electron acceptors and reduced U(VI) in cell suspensions. With poorly crystalline Fe(III) oxide as the electron acceptor, strain Rf4T oxidized the following electron donors: acetate, lactate, pyruvate and ethanol. Phylogenetic analysis of the 16S rRNA gene sequence of strain Rf4T placed it in the genus Geobacter. Strain Rf4T was most closely related to {\textquoteright}Geobacter humireducens{\textquoteright} JW3 (95.9 \% sequence similarity), Geobacter bremensis Dfr1T (95.4 \%) and Geobacter bemidjiensis BemT (95.1 \%). Based on phylogenetic analysis and phenotypic differences between strain Rf4T and closely related Geobacter species, this strain is described as a representative of a novel species, Geobacter uraniireducens sp. nov. The type strain is Rf4T (=ATCC BAA-1134T =JCM 13001T).},
	keywords = {Bacterial Typing Techniques, DNA, Bacterial, Genes, rRNA, Genotype, Geobacter, Geologic Sediments, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Species Specificity, Uranium},
	issn = {1466-5026},
	doi = {10.1099/ijs.0.65377-0},
	author = {Shelobolina, Evgenya S and Vrionis, Helen A and Findlay, Robert H and Lovley, Derek R}
}
@article {530,
	title = {Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site.},
	journal = {Appl Environ Microbiol},
	volume = {71},
	year = {2005},
	month = {2005 Oct},
	pages = {6308-18},
	abstract = {The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.},
	keywords = {Acetates, Biodegradation, Environmental, Deltaproteobacteria, DNA, Bacterial, DNA, Ribosomal, Ferric Compounds, Fresh Water, Geologic Sediments, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sulfates, Uranium, Water Pollution},
	issn = {0099-2240},
	doi = {10.1128/AEM.71.10.6308-6318.2005},
	author = {Vrionis, Helen A and Anderson, Robert T and Ortiz-Bernad, Irene and O{\textquoteright}Neill, Kathleen R and Resch, Charles T and Peacock, Aaron D and Dayvault, Richard and White, David C and Long, Philip E and Lovley, Derek R}
}
