Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation

Abstract

A Gram-negative, rod-shaped, motile bacterium, strain Rf4 T , 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 Rf4 T 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 Rf4 T were regular, motile rods, 1.2-2.0 mm long and 0.5-0.6 mm in diameter, with rounded ends. Cells had one lateral flagellum. Growth was optimal at pH 6.5-7.0 and 32 6C. With acetate as the electron donor, strain Rf4 T 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 Rf4 T oxidized the following electron donors: acetate, lactate, pyruvate and ethanol. Phylogenetic analysis of the 16S rRNA gene sequence of strain Rf4 T placed it in the genus Geobacter. Strain Rf4 T was most closely related to 'Geobacter humireducens' JW3 (95.9 % sequence similarity), Geobacter bremensis Dfr1 T (95.4 %) and Geobacter bemidjiensis Bem T (95.1 %). Based on phylogenetic analysis and phenotypic differences between strain Rf4 T and closely related Geobacter species, this strain is described as a representative of a novel species, Geobacter uraniireducens sp. nov. The type strain is Rf4 T (5ATCC BAA-1134 T 5JCM 13001 T ).

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

“…Comparison of the G. uraniireducens transcriptome in cells grown in sediments vs defined medium Geobacter uraniireducens was studied, because it was isolated from the uranium-contaminated site in Rifle, Colorado, and its 16S rRNA gene sequence matched one of the sequences that predominated during in situ uranium bioremediation (Shelobolina et al, 2008). Microarray comparisons between G. uraniireducens cells grown in sediments vs the soluble electron acceptor, fumarate, showed that 1964 genes (1084 upregulated, 882 downregulated) had at least a twofold difference in transcript levels (Table 2; Supplementary Tables S1 and S2).…”

“…Contrary to the often-repeated statement that the most environmentally relevant microorganisms cannot be studied in pure culture, it has become increasingly apparent that pure cultures of some of the most environmentally relevant organisms can be recovered (Chisholm et al, 1992;Button et al, 1993;Rappe et al, 2002;Konneke et al, 2005;Nevin et al, 2005;Giovannoni and Stingl, 2007;Shelobolina et al, 2008;Holmes et al, 2008a). When these organisms are available in pure culture, it is possible to combine genome sequence information with physiological, transcriptomic and proteomic studies.…”

“…Molecular and culturing studies have demonstrated that Geobacter species are the predominant microorganisms in a wide diversity of subsurface environments in which dissimilatory Fe(III) reduction is an important process for the degradation of both natural organic matter and organic contaminants or for the stimulation of in situ bioremediation of metal-contaminated subsurface environments (Rooney-Varga et al, 1999;Anderson et al, 2003;Lovley et al, 2004;North et al, 2004;Coates et al, 2005;Lin et al, 2005;Sleep et al, 2006;Holmes et al, 2007;Winderl et al, 2007). By designing an isolation medium that mimics subsurface conditions, it has become possible to isolate Geobacter species that have 16S rRNA gene sequences that are identical or highly similar to the 16S rRNA sequences that predominate in Fe(III)-reducing subsurface environments Shelobolina et al, 2008;Holmes et al, 2008a).…”

“…Geobacter species are a group of organisms from which it has been possible to obtain pure culture isolates of microorganisms known to be environmentally relevant Shelobolina et al, 2008;Holmes et al, 2008a). Molecular and culturing studies have demonstrated that Geobacter species are the predominant microorganisms in a wide diversity of subsurface environments in which dissimilatory Fe(III) reduction is an important process for the degradation of both natural organic matter and organic contaminants or for the stimulation of in situ bioremediation of metal-contaminated subsurface environments (Rooney-Varga et al, 1999;Anderson et al, 2003;Lovley et al, 2004;North et al, 2004;Coates et al, 2005;Lin et al, 2005;Sleep et al, 2006;Holmes et al, 2007;Winderl et al, 2007).…”

Field-Based Detection and Monitoring of Uranium in Contaminated Groundwater using Two Immunosensors

“…Both the site and the field bioremediation research have been described extensively elsewhere [5][6][7] and a more complete description of the ongoing work at the Old Rifle UMTRA site may be found at http://www.pnl.gov/nabir-umtra/intro.stm. In the summer of 2008, much of the research activity was focused upon the collection of samples for proteomic analyses [5,[8][9][10][11], and timely information about the extent of uranium immobilization or remobilization in groundwater samples was useful to the research team in the timing of sample collection.…”