Dataset Information

Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site.

ABSTRACT: The Department of Energy's Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.

SUBMITTER: Koribanics NM

PROVIDER: S-EPMC4395306 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site.

Koribanics Nicole M NM Tuorto Steven J SJ Lopez-Chiaffarelli Nora N McGuinness Lora R LR Häggblom Max M MM Williams Kenneth H KH Long Philip E PE Kerkhof Lee J LJ

PloS one 20150413 4

The Department of Energy's Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reductio ...[more]

PMID: 25874721

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Project description:RNA-based biomarkers have been successfully detected at field sites undergoing in situ bioremediation, but the detection of expressed enzymes is a more direct way to prove activity for a particular biocatalytic process of interest since they provide evidence of potential in situ activity rather than simply confirming presence and abundance of genes in a given population by measurement of DNA copies using qPCR. Here we successfully applied shotgun proteomics to field samples from a trichloroethene (TCE)-contaminated industrial site in southern Ontario, Canada that had been bio-augmented with the commercially available KB-1TM microbial culture. The KB-1TM culture contains multiple strains of Dehalococcoides mccartyi (D. mccartyi) as well as an organohalide respiring Geobacter species. The relative abundances of specific enzymatic proteins were subsequently compared to corresponding qPCR-derived levels of DNA and RNA biomarkers in the same samples. Samples were obtained from two wells with high hydraulic connectivity to the KB-1TM-bioaugemented enhanced in situ bioremediation system, and two control wells that showed evidence of low levels of native organohalide respiring bacteria (OHRB), Dehalococcoides and Geobacter. Enzymes involved in organohalide respiration were detected in the metaproteomes of all four field samples, as were chaperonins of D. mccartyi, chemotaxis proteins, and ATPases. The most highly expressed RDase in the bioaugmentation culture (VcrA) was the most highly detected enzyme overall in the bioaugmented groundwater samples. In one background groundwater well, we found high expression of the Geobacter pceA RDase. The DNA and RNA biomarkers detected using qPCR-based assays were a set of orthologs of Dehalococcoides reductive dehalogenases (VcrA, TceA, BvcA, dehalogenase "DET1545"), and the Ni-Fe uptake hydrogenase, HupL. Within a sample, RNA levels for key enzymes correlated with relative protein abundance. These results indicate that laboratory observations of TCE-bioremediation biomarker protein expression are recapitulated in field environmental systems and that both RNA and protein biomarker monitoring hold promise for activity monitoring of in situ populations of OHRB.

Project description:Phosphate fertilization contributes to an input of uranium (U) in agricultural soils. Although its accumulation and fate in agricultural soils have been previously studied, its colloidal transport and accumulation along slopes through erosion have been studied to a lesser extent in viticulture soils. To bridge this gap, the contents and potential mobility of U were investigated in vineyard model soils in the Rhineland-Palatinate region, Germany. In addition to elevated U contents, U was expected to associate with colloids and subject to erosion, thus accumulating on slope foots and in soils with fine structure, and reflecting a greater variability. Moreover, another expectation was the favorable erosion/mobility of U in areas with greater carbonate content. This was tested in three regional locations, at different slope positions and through soil horizon depths, with a total of 57 soil samples. The results show that U concentrations (0.48-1.26 ppm) were slightly higher than proximal non-agricultural soils (0.50 ppm), quite homogenous along slope positions, and slightly higher in topsoils. Assuming a homogeneous fertilization, the vertical translocation of U in soil was most probably higher than along the slope by erosion. In addition, carbonate content and soil texture correlated with U concentrations, whereas other parameters such as organic carbon and iron contents did not. The central role of carbonate and soil texture for the prediction of U content was confirmed using decision trees and elastic net, although their limited prediction power suggests that a larger sample size with a larger range of U content is required to improve the accuracy. Overall, we did not observe neither U nor colloids accumulating on slope foots, thus suggesting that soils are aggregate-stable. Lastly, we suggested considering further soil parameters (e.g., Ca2+, phosphorus, alkali metals) in future works to improve our modelling approach. Overall, our results suggest U is fortunately immobile in the studied locations.

Dataset Information

Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site.

Publications

Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site.

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