Direct microbial reduction and subsequent preservation of uranium in natural near-surface sediment

Abstract

The fate of uranium in natural systems is of great environmental importance. X-ray absorption near-edge spectroscopy (XANES) revealed that U(VI) was reduced to U(IV) in shallow freshwater sediment at an open pit in an inactive uranium mine. Geochemical characterization of the sediment showed that nitrate, Fe(III), and sulfate had also been reduced in the sediment. Observations of the sediment particles and microbial cells by scanning and transmission electron microscopy, coupled with elemental analysis by energy dispersive spectroscopy, revealed that uranium was concentrated at microbial cell surfaces. U(IV) was not associated with framboidal pyrite or nanometer-scale iron sulfides, which are presumed to be of microbial origin. Uranium concentrations were not detected in association with algal cells. Phylogenetic analyses of microbial populations in the sediment by the use of 16S rRNA and dissimilatory sulfite reductase gene sequences detected organisms belonging to the families Geobacteraceae and Desulfovibrionaceae. Cultivated members of these lineages reduce U(VI) and precipitate iron sulfides. The association of uranium with cells, but not with sulfide surfaces, suggests that U(VI) is reduced by the enzymatic activities of microorganisms. Uranium was highly enriched (760 ppm) in a subsurface black layer in unsaturated sediment sampled from a pit which was exposed to seasonal fluctuations in the pond level. XANES analysis showed that the majority of uranium in this layer was U(IV), indicating that uranium is preserved in its reduced form after burial.

FIG. 1.

Normalized U L3-edge absorption spectra for fresh and incubated aquatic black sediments and a subsurface black sediment (fresh, inc, and black, respectively) along with those for U(IV) and U(VI) standards from UO₂ and UO₃, respectively.

FIG. 2.

(A) Backscattered electron image of uranium-bearing phases (arrows) found in the aquatic sediment and an associated EDX spectrum. (B) Backscattered electron image of framboidal pyrite in the sediment and an associated EDX spectrum. (C) TEM image and EDX spectrum (∼30 nm spatial resolution) of a prokaryotic cell in the sediment that had accumulated iron and sulfur. (D) TEM image and EDX spectrum of a prokaryotic cell from the sediment that had accumulated uranium, iron, and sulfur.

FIG. 3.

Evolutionary distance dendrogram of P4 clones within the δ-Proteobacteria subdivision based on 639 nucleotides of 16S rRNA. Families and the genus Desulfomonile are bracketed to the right.

FIG. 4.

Evolutionary distance dendrogram of P4 clones based on 237 inferred amino acids of DSR genes. Families and the genus Desulfomonile are bracketed to the right. For multiple nearly identical clones (>97% identity), the number of multiples is given after the clone name of a representative clone. Accession numbers for the GenBank/EMBL/DDBJ databases are provided if the clone or organism name is not unique.