Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation.

A site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilized in situ through intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A paired t test indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion. Castellaniella had the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing genera Geothrix, Desulfovibrio, Ferribacterium, and Geobacter decreased significantly, whereas the denitrifying Acidovorax abundance increased significantly after groundwater invasion. Additionally, seven genera, i.e., Castellaniella, Ignavibacterium, Simplicispira, Rhizomicrobium, Acidobacteria Gp1, Acidobacteria Gp14, and Acidobacteria Gp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.IMPORTANCE High-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites.

Distribution of uranium and thorium in dolomitic gravel fill and shale saprolite.

The objectives of this study were to examine (1) the distribution of U and Th in dolomitic gravel fill and shale saprolite, and (2) the removal of uranium from acidic groundwater by dolomitic gravel through precipitation with amorphous basaluminite at the U.S. DOE Oak Ridge Integrated Field Research Challenge (ORIFRC) field site west of the Oak Ridge Y-12 National Security Complex in East Tennessee. Media reactivity and sustainability are a technical concern with the deployment of any subsurface reactive media. Because the gravel was placed in the subsurface and exposed to contaminated groundwater for over 20 years, it provided a unique opportunity to study the solid and water phase geochemical conditions within the media after this length of exposure. This study illustrates that dolomite gravel can remove U from acidic contaminated groundwater with high levels of Al(3+), Ca(2+), NO(3-), and SO4(2-) over the long term. As the groundwater flows through high pH carbonate gravel, U containing amorphous basaluminite precipitates as the pH increases. This is due to an increase in groundwater pH from 3.2 to ∼6.5 as it comes in contact with the gravel. Therefore, carbonate gravel could be considered as a possible treatment medium for removal and sequestration of U and other pH sensitive metals from acidic contaminated groundwater. Thorium concentrations are also high in the carbonate gravel. Thorium generally shows an inverse relationship with U from the surface down into the deeper saprolite. Barite precipitated in the shallow saprolite directly below the dolomitic gravel from barium present in the acidic contaminated groundwater.

Phosphorus retention in a constructed wetland system used to treat dairy wastewater.

The aim of this study was to develop an input/output mass balance to predict phosphorus retention in a five pond constructed wetland system (CWS) at Greenmount Farm, County Antrim, Northern Ireland. The mass balance was created using 14-months of flow data collected at inflow and outflow points on a weekly basis. Balance outputs were correlated with meteorological parameters, such as daily air temperature and hydrological flow, recorded daily onsite. The mass balance showed that phosphorus retention within the system exceeded phosphorus release, illustrating the success of this CWS to remove nutrients from agricultural effluent from a dairy farm. The last pond, pond 5, showed the greatest relative retention of 86%. Comparison of retention and mean air temperature highlighted a striking difference in trends between up-gradient and down-gradient ponds, with up-gradient ponds 1 and 2 displaying a positive quadratic relationship and down-gradient ponds 3 through 5 displaying a negative quadratic relationship.

Deposition of uranium precipitates in dolomitic gravel fill.

Uranium-containing precipitates have been observed in a dolomitic gravel fill near the Department of Energy (DOE) S-3 Ponds former waste disposal site as a result of exposure to acidic (pH 3.4) groundwater contaminated with U (33 mg L(-1)), Al3+ (900 mg L(-1)), and NO3- (14 000 mg L(-1)). The U containing precipitates fluoresce a bright green under ultraviolet (UV) short-wave light which identify U-rich coatings on the gravel. Scanning electron microscopy (SEM) microprobe analysis show U concentration ranges from 1.6-19.8% (average of 7%) within the coatings with higher concentrations at the interface of the dolomite fragments. X-ray absorption near edge structure spectroscopy (XANES) indicate that the U is hexavalent and extended X-ray absorption fine structure spectroscopy (EXAFS) shows that the uranyl is coordinated by carbonate. The exact nature of the uranyl carbonates are difficult to determine, but some are best described by a split K(+)-like shell similar to grimselite [K4Na(UO2)(CO3)3 x H2O] and other regions are better described by a single Ca(2+)-like shell similar to liebigite [Ca2(UO2)(CO3)3 x 11(H2O)] or andersonite [Na2CaUO2(CO3)3 x 6H2O]. The U precipitates are found in the form of white to light yellow cracked-formations as coatings on the dolomite gravel and as detached individual precipitates, and are associated with amorphous basalumnite [Al4(SO4)(OH)10 x 4H2O].

Uranium removal from contaminated groundwater by synthetic resins.

Synthetic resins are shown to be effective in removing uranium from contaminated groundwater. Batch and field column tests showed that strong-base anion-exchange resins were more effective in removing uranium from both near-neutral-pH (6.5)- and high-pH (8)-low-nitrate-containing groundwaters, than metal-chelating resins, which removed more uranium from acidic-pH (5)-high-nitrate-containing groundwater from the Oak Ridge Reservation (ORR) Y-12 S-3 Ponds area in Tennessee, USA. Dowex 1-X8 and Purolite A-520E anion-exchange resins removed more uranium from high-pH (8)-low-nitrate-containing synthetic groundwater in batch tests than metal-chelating resins. The Dowex 21K anion-exchange resin achieved a cumulative loading capacity of 49.8 mg g(-1) before breakthrough in a field column test using near-neutral-pH (6.5)-low-nitrate-containing groundwater. However, in an acidic-pH (5)-high-nitrate-containing groundwater, metal-chelating resins Diphonix and Chelex-100 removed more uranium than anion-exchange resins. In 15 m L of acidic-pH (5)-high-nitrate-containing groundwater spiked with 20 mg L(-1) uranium, the uranium concentrations ranged from 0.95 mg L(-1) at 1-h equilibrium to 0.08 mg L(-1) at 24-h equilibrium for Diphonix and 0.17 mg L(-1) at 1-h equilibrium to 0.03 mg L(-1) at 24-h equilibrium for Chelex-100. Chelex-100 removed more uranium in the first 10 min in the 100mL of acidic-(pH 5)-high-nitrate-containing groundwater ( approximately 5 mg L(-1) uranium); however, after 10 min, Diphonix equaled or out-performed Chelex-100. This study presents an improved understanding of the selectivity and sorption kenetics of a range of ion-exchange resins that remove uranium from both low- and high-nitrate-containing groundwaters with varying pHs.

Distribution of uranium contamination in weathered fractured saprolite/shale and ground water.

The objective of this study was to determine how structure, stratigraphy, and weathering influence fate and transport of contaminants (particularly U) in the ground water and geologic material at the Department of Energy (DOE) Environmental Remediation Sciences Department (ERSD) Field Research Center (FRC). Several cores were collected near four former unlined adjoining waste disposal ponds. The cores were collected, described, analyzed for U, and compared with ground water geochemistry from surrounding multilevel wells. At some locations, acidic U-contaminated ground water was found to preferentially flow in small remnant fractures weathering the surrounding shale (nitric acid extractable U [U(NA)] usually < 50 mg kg(-1)) into thin (<25 cm) Fe oxide-rich clayey seams that retain U (U(NA) 239 to 375 mg kg(-1)). However, greatest contaminant transport occurs in a 2 to 3 m thick more permeable stratigraphic transition zone located between two less permeable, and generally less contaminated zones consisting of (i) overlying unconsolidated saprolite (U(NA) < 0.01 to 200 mg kg(-1)) and (ii) underlying less-weathered bedrock (U(NA) generally < 0.01 to 7 mg kg(-1)). In this transition zone, acidic (pH < 4) U-enriched ground water (U of 38 mg L(-1)) has weathered away calcite veins resulting in greater porosity, higher hydraulic conductivity, and higher U contamination (U(NA) 106 to 745 mg kg(-1)) of the weathered interbedded shale and sandstone. These characteristics of the transition zone produce an interval with a high flux of contaminants that could be targeted for remediation.

Inhibition by an extract of Ocimum sanctum of DNA-binding activity of 7,12-dimethylbenz[a]anthracene in rat hepatocytes in vitro.

Ocimum sanctum is a traditional medicinal plant. Previous studies have shown that extracts of O. sanctum inhibit the induction of skin papillomas in mice by 7,12-dimethylbenz[a]anthracene (DMBA). In the present study, primary cultures of rat hepatocytes were treated with 0-500 microg of O. sanctum extract for 24 h and then with DMBA (10 or 50 microg) for 18 h. Cells were then harvested and their DNA was isolated and analyzed by 32P-postlabelling. A significant reduction in the levels of DMBA-DNA adducts was observed in all cultures pretreated with O. sanctum extract. This effect was more pronounced at the lower dose of DMBA (10 microg). Hepatocytes which were treated with the highest dose of extract (500 microg) showed a maximum reduction of 93% in the mean values of DMBA-DNA adducts. The viability of the cells was not adversely affected by pretreatment with extract. Our findings suggest that O. sanctum leaf extract blocks or suppresses the events associated with chemical carcinogenesis by inhibiting metabolic activation of the carcinogen.

DNA adduct formation in mice following treatment with used engine oil and identification of some of the major adducts by 32P-postlabelling.

Used engine oil from a petrol-powered vehicle was fractionated by column chromatography into seven parts for which the major polycyclic aromatic hydrocarbon (PAH) components were determined by GC. Topical treatment of mice with the fractions and 32P-postlabelling of the skin DNA resulted in the detection of multiple adduct spots on TLC for some, but not all, of the fractions. The majority of the DNA binding capacity of the used engine oil was possessed by the first three fractions, (equivalent to 25, 15 and 14.5%, respectively) of the adduct forming ability of the unfractionated oil. The chromatographic mobilities of the adduct spots induced by these fractions were compared to those produced by unfractionated used engine oil. In addition, mice were also treated topically with reference PAHs, either singly or as mixtures, dissolved in unused oil at the concentrations at which they were present in the used oil. Comparisons were made between the chromatographic mobilities of the adducts formed in mouse skin DNA by synthetic mixtures with those formed by the used oil. From these data, some of the major adducts produced by treatment with used engine oil are suggested to be formed by reactive metabolites of benzo[b]naphtho[1,2-d]thiophene, benzo[c]phenanthrene, benzo[g,h,i]fluoranthene, chrysene, benzo[a]pyrene and benzo[g,h,i]perylene.

Evaluation of DNA-binding activity of hydroxyanthraquinones occurring in Rubia tinctorum L.

The naturally-occurring anthraquinones (AQs), alizarin (1,2-dihydroxyanthraquinone) and lucidin (1,3-dihydroxy-2-hydroxymethylanthraquinone), were incubated with DNA in the presence of S9 mix. The isolated DNA was analysed by 32P-postlabelling for the presence of aromatic adducts. Only lucidin formed up to five different DNA adducts in the range from 0.995 to 3.05 adducts/10(8) nucleotides. Lucidin was also incubated with polynucleotides poly[d(A-T)] and polydG*polydC in the presence of S9 mix. Analysis of polydG*polydC revealed a similar adduct pattern to that obtained with lucidin-modified DNA. Alizarin, lucidin, a glycoside mixture containing alizarinprimeveroside and lucidinprimeveroside, and Rubia Teep (a herbal drug made from Rubia tinctorum containing lucidin) were incubated with primary rat hepatocytes for 24 h and the isolated DNA was analysed by 32P-postlabelling. Lucidin, the glycoside mixture and Rubia Teep gave rise to DNA adducts, but alizarin did not. Male Parkes mice were treated orally for 4 days with alizarin (10 mg/d), lucidin (2 mg/d), the glycoside mixture (20 mg/d) or Rubia Teep (1/2 tablet/d) and DNA was isolated from liver, kidney, duodenum and colon. Analysis by 32P-postlabelling revealed that lucidin, the glycoside mixture and Rubia Teep, but not alizarin, formed DNA adducts in all the tissues examined but that the adduct patterns were organ-specific.

DNA adducts in human and mouse skin maintained in short-term culture and treated with petrol and diesel engine lubricating oils.

Human and mouse skin samples maintained in short-term organ culture were treated topically with used engine oils from petrol- and diesel-powered vehicles. Mice were also treated topically in vivo for comparison. DNA was isolated and analysed by 32P-postlabelling and the labeled DNA digests were resolved on polyethyleneimine-cellulose tlc sheets. A large number of radioactive adduct spots were observed in DNA from skin treated with the used petrol-engine oil, indicating the formation of adducts by many components of the complex oil mixture. Total adduct levels were similar in mouse skin (both in vivo and in vitro) and in human skin, although qualitative differences in the adduct maps were apparent between the human and mouse skin DNA. Treatment with the used diesel engine oil produced adduct levels no greater than that of control samples in mouse skin (in vivo and in vitro), although significant levels were found in human skin DNA from one donor. The results correlate well with the carcinogenic activity of these oils in experimental animals, helping to substantiate the conclusion that petrol engine oils (but not diesel engine oils) may present a carcinogenic risk to man if appropriate measures to minimise skin contact are not observed.

Analysis of the polycyclic aromatic hydrocarbon content of petrol and diesel engine lubricating oils and determination of DNA adducts in topically treated mice by 32P-postlabelling.

Engine lubricating oils are known to accumulate carcinogenic polycyclic aromatic hydrocarbons (PAHs) during engine running. Oils from nine petrol-powered and 11 diesel-powered vehicles, in addition to samples of unused oil, were analysed for PAH content and ability to form DNA adducts when applied topically to mouse skin. The levels of 19 PAHs, determined by GC, were in total, approximately 22 times higher in used oils from petrol engines than in oils from diesel engines. Male Parkes mice were treated with 50 microliters of oil daily for 4 days before they were killed and DNA isolated from skin and lung tissue. DNA samples were analysed by nuclease P1-enhanced 32P-postlabelling. Used oils from both diesel and petrol engines showed several adduct spots on PEI-cellulose plates at total adduct levels of up to 0.57 fmol/microgram DNA [approximately 60 times greater than in experiments with samples of unused oil in which adduct levels (0.01-0.02 fmol adducts/microgram DNA) were close to the limit of detection]. Higher adduct levels were generally formed by petrol engine oils than by diesel engine oils. Lung DNA contained similar total adduct levels to those in skin although the adduct maps were less complex. Total adduct levels correlated with extent of oil use in the engine, the total PAH concentration in oils and with the concentrations of certain individual PAHs present in the oils. An adduct spot that co-eluted with that of the major benzo[a]pyrene-DNA adduct accounted for 9-26% of the total adducts in skin DNA, and approximately 8% of the adducts in lung DNA, of mice treated with petrol engine oils. A major, and as yet unidentified, adduct spot comprised up to 30% of the total adducts in skin DNA, and up to 89% of the total adducts in lung DNA, of these animals.

Formation of DNA adducts in the skin of psoriasis patients, in human skin in organ culture, and in mouse skin and lung following topical application of coal-tar and juniper tar.

Preparations of coal-tar and juniper tar (cade oil) that are used in the treatment of psoriasis are known to contain numerous potentially carcinogenic polycyclic aromatic hydrocarbons (PAH). Evidence of covalent binding to DNA by components of these mixtures was sought in a) human skin biopsy samples from 12 psoriasis patients receiving therapy with these agents, b) human skin explants maintained in organ culture and treated topically with the tars, and c) the skin and lungs of mice treated with repeated doses of the formulations following the regimen used in the clinic. DNA was isolated from the human and mouse tissues and digested enzymically to mononucleotides. 32P-Post-labeling analysis revealed the presence of aromatic DNA adducts in the biopsy samples at levels of up to 0.4 fmol total adducts/microgram DNA. Treatment of human skin in organ culture produced similar levels of adducts, while treatment with dithranol, a non-mutagenic therapeutic agent, resulted in chromatograms indistinguishable from those from untreated controls. In mouse skin, coal-tar ointment and juniper tar gave similar DNA adduct levels, with a similar time-course of removal: maximum levels (0.5 fmol/microgram DNA) at 24 h after the final treatment declined rapidly to 0.05 fmol/microgram at 7 d, thereafter declining slowly over the succeeding 25 d. However, while coal-tar ointment produced only very low levels of adducts in mouse lung (less than 0.03 fmol/microgram DNA), juniper tar produced adducts at a high level (0.7 fmol/microgram DNA) that were persistent in this tissue. These results provide direct evidence for the formation of potentially carcinogenic DNA damage in human and mouse tissue by components of these therapeutic tar preparations.

32P-postlabelling analysis of DNA adducts in the skin of mice treated with petrol and diesel engine lubricating oils and exhaust condensates.

Samples of unused or used petrol and diesel engine lubricating oils were applied to the shaved dorsal skin of 4- to 6-week-old male Parkes mice, either as a single treatment (50 microliters/mouse) or as four consecutive daily treatments (50 microliters/application). DNA isolated from the skin 24 h after the final treatment was digested to 3'-mononucleotides and analysed by 32P-postlabelling for the presence of aromatic adducts. Enhancement of sensitivity using butanol extraction or nuclease P1 digestion of the DNA hydrolysates led to the detection of up to eight adduct spots on polyethyleneimine-cellulose thin-layer chromatograms with samples of DNA from skin treated with used engine oils, at levels of 40-150 amol total adducts/micrograms DNA. Multiple treatments with the used oils gave rise to similar patterns of adducts in lung DNA. A single treatment of mouse skin with petrol engine exhaust condensate (50 microliters), or diesel engine exhaust condensate (50 microliters), containing 20 and 46 micrograms benzo[a]pyrene (BaP)/g respectively, gave rise to approximately 75 amol total adducts/micrograms DNA in skin. A significant proportion, 31 and 48% respectively, of the adducts formed by the petrol and diesel engine exhaust condensates co-chromatographed with the major BaP-DNA adduct, but with the used engine oils, only petrol engine oil, and not diesel engine oil, produced significant amounts of an adduct (22% of total) that corresponded to the BaP-DNA adduct.