Dataset Information

Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress.

ABSTRACT: Two Burkholderia spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS-25 and SRS-46 spiked with U and evaluated the microbially-mediated depletion with concomitant genomic and proteomic analysis. Both strains showed a rapid depletion of U; draft genome sequences revealed SRS-25 genome to be of approximately 8,152,324 bp, a G + C content of 66.5, containing a total 7604 coding sequences with 77 total RNA genes. Similarly, strain SRS-46 contained a genome size of 8,587,429 bp with a G + C content of 67.1, 7895 coding sequences, with 73 total RNA genes, respectively. An in-depth, genome-wide comparisons between strains 25, 46 and a previously isolated strain from our research (Burkholderia sp. strain SRS-W-2-2016), revealed a common pool of 3128 genes; many were found to be homologues to previously characterized metal resistance genes (e.g., for cadmium, cobalt, and zinc), as well as for transporter, stress/detoxification, cytochromes, and drug resistance functions. Furthermore, proteomic analysis of strains with or without U stress, revealed the increased expression of 34 proteins from strain SRS-25 and 52 proteins from strain SRS-46; similar to the genomic analyses, many of these proteins have previously been shown to function in stress response, DNA repair, protein biosynthesis and metabolism. Overall, this comparative proteogenomics study confirms the repertoire of metabolic and stress response functions likely rendering the ecological competitiveness to the isolated strains for colonization and survival in the heavy metals contaminated SRS soil habitat.

SUBMITTER: Agarwal M

PROVIDER: S-EPMC6315756 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Proteogenomic Analysis of <i>Burkholderia</i> Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress.

Agarwal Meenakshi M Pathak Ashish A Rathore Rajesh Singh RS Prakash Om O Singh Rakesh R Jaswal Rajneesh R Seaman John J Chauhan Ashvini A

Cells 20181212 12

Two <i>Burkholderia</i> spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS- ...[more]

PMID: 30545132

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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

Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress.

Publications

Proteogenomic Analysis of <i>Burkholderia</i> Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress.

Similar Datasets

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