Biomedical subjects

James P McKinley

Publications and source records attributed to James P McKinley.

7 recordsLinked to original sources

PubMed2006

Uranium and technetium bio-immobilization in intermediate-scale physical models of an in situ bio-barrier.

We investigated the long-term effects of ethanol addition on U and Tc mobility in groundwater flowing through intermediate-scale columns packed with uncontaminated sediments. The columns were operated above-ground at a contaminated field site to serve as physical models of an in situ bio-barrierfor U and Tc removal from groundwater. Groundwater containing 4 microM U and 520 pM Tc was pumped through the columns for 20 months. One column received additions of ethanol to stimulate activity of indigenous microorganisms; a second column received no ethanol and served as a control. U(VI) and Tc(VII) removal was sustained for 20 months (approximately 189 pore volumes) in the stimulated column under sulfate- and Fe(III)-reducing conditions. Less apparent microbial activity and only minor removal of U(VI) and Tc(VII) were observed in the control. Sequential sediment extractions and XANES spectra confirmed that U(IV) was present in the stimulated column, although U(IV) was also detected in the control; extremely low concentrations precluded detection of Tc(IV) in any sample. These results provide additional evidence that bio-immobilization may be effective for removing U and Tc from groundwater. However, long-term effectiveness of bio-immobilization may be limited by hydraulic conductivity reductions or depletion of bioavailable Fe(III).

Bacteria↗

PubMed2006

Changes in uranium speciation through a depth sequence of contaminated Hanford sediments.

The disposal of basic sodium aluminate and acidic U(VI)-Cu(ll) wastes in the now-dry North and South 300 A Process Ponds atthe Hanford site resulted in a groundwater plume of U(VI). To gain insight into the geochemical processes that occurred during waste disposal and those affecting the current and future fate and transport of this uranium plume, the solid-phase speciation of uranium in a depth sequence of sediments from the base of the North Process Pond through the vadose zone to groundwater was investigated using standard chemical and mineralogical analyses, electron and X-ray microprobe measurements, and X-ray absorption fine structure spectroscopy. Near-surface sediments contained uranium coprecipitated with calcite, which formed due to overneutralization of the waste ponds with base (NaOH). At intermediate depths in the vadose zone, metatorbernite [Cu(UO2PO4)2 x 8H2O] precipitated, likely during pond operations. Uranium occurred predominantly sorbed onto phyllosilicates in the deeper vadose zone and groundwater; sorbed uranium was also an important component at intermediate depths. Since the calcite-bearing pond sediments have been removed in remediation efforts, uranium fate and transport will be controlled primarily by desorption of the sorbed uranium and dissolution of metatorbernite.

Adsorption↗

PubMed2006

Application of nonlinear analysis methods for identifying relationships between microbial community structure and groundwater geochemistry.

The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.

Bacteria↗

PubMed2006

Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environment.

A multilevel sampler (MLS) was emplaced in a borehole straddling anaerobic, sulfate-rich Cretaceous-era shale and sandstone rock formations approximately 200 m below ground surface at Cerro Negro, New Mexico. Sterile quartzite sand contained in chambers in the sampler allowed in situ colonization and recovery of nucleic acids for molecular analyses. Denaturing gradient gel electrophoresis and 16S rRNA gene cloning results indicated a homogeneously distributed bacterial community across the shale-sandstone interface. delta-Proteobacteria sequences were common at all depths, and were dominated by members of the Geobacteraceae family (Pelobacter, Desulphuromonas and Geobacter). Other members of this group are capable of dissimilatory Fe(III) and/or S degrees reduction, but not sulfate reduction. RNA hybridization data also suggested that Fe(III)-/S degrees -reducing bacteria were predominant. These findings are striking considering the lack of significant concentrations of these electron acceptors in this environment. The next most abundant bacterial group indicated was the sulfate reducers, including Desulfobacterium, Desulfocapsa and Desulfobulbus. Sequences related to fermenters, denitrifiers and acetogens were also recovered. The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale.

Base Sequence↗

PubMed2004

Microscale distribution of cesium sorbed to biotite and muscovite.

Individual 1-3 mm biotite and muscovite clasts from Hanford sediment were contacted with 0.08 M CsNO3. They were examined using electron or X-ray microprobe methods, as intact specimens or sectioned perpendicular to their basal planes. Cs+ was observed to preferentially sorb to mica edges, steps on mica surfaces, or fractured regions. The localization of Cs conformed to hypothesized strong binding to frayed edge sites in preference to sites on basal planes. In section, Cs+ was found to penetrate the mica interior, forming discrete zones of concentration, particularly in muscovite. In biotite, Cs was more abundant, permeating the clasts, but also forming discrete zones of higher concentration. Concentrated Cs on both clast edges and within clast interiors corresponded to microscopic but relatively extensive zones where K was depleted. The localization of sorbed Cs in areas where K was depleted suggested that weathering reactions had caused the formation of frayed edge sites within the micas. Cs+ accessed crystal interiors by diffusion along channels following crystal defects, cracks, or partings where pore fluids had previously migrated to form the interior alteration zones. On the nanometer scale, areas with localized Cs were disrupted, confirming that frayed edge sites were developed in clast interiors.

Adsorption↗

PubMed2003

Biogeochemical processes and microbial characteristics across groundwater-surface water boundaries of the Hanford Reach of the Columbia River.

Biogeochemical processes within riverbed hyporheic zones (HZ) can potentially impact the fate and transport of contaminants. We evaluated a modified freeze core technique for the collection of intact cobble-bed samples from the Columbia River HZ along a stretch of the Hanford Reach in Washington State and investigated microbiological and geochemical parameters of corresponding frozen and unfrozen samples. During three sampling periods (March, May, and November 2000), relatively high numbers of viable aerobic heterotrophic bacteria were recovered from both unfrozen (10(6)-10(7) cfu/g) and frozen samples (10(5)-10(6) cfu/g). Relatively large populations of sulfate-, nitrate-, and iron-reducing bacteria were present, and significant concentrations of acid-volatile sulfide were measured in some samples, indicating that anoxic regions exist within this zone. Cr(VI), a priority groundwater pollutant on adjacent U.S. Department of Energy lands, was probably removed from solution in HZ samples by a combination of microbial activity and chemical reduction, presumably via products of anaerobic microbial metabolism. These results suggest that biogeochemical processes in the Columbia River HZ may contribute to the natural attenuation of Cr(VI). Although freezing modestly diminished recovery of viable bacteria, freeze core techniques proved reliable for the collection of intact hyporheic sediments.

Biodegradation, Environmental↗

PubMed2003

Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock.

Subsurface microbial community structure in relation to geochemical gradients and lithology was investigated using a combination of molecular phylogenetic and geochemical analyses. Discreet groundwater and substratum samples were obtained from depths ranging from 182 to 190 m beneath the surface at approximately 10-cm intervals using a multilevel sampler (MLS) that straddled Cretaceous shale and sandstone formations at a site in the southern San Juan Basin in New Mexico. DNA and RNA were extracted directly from quartzite sand substratum loaded into individual cells of the MLS and colonized in situ. Polymerase chain reaction (PCR)-mediated T-RFLP analysis of archaeal rRNA genes (rDNA) in conjunction with partial sequencing analysis of archaeal rDNA libraries and quantitative RNA hybridization with oligonucleotide probes were used to probe community structure and function. Although total microbial populations remained relatively constant over the entire depth interval sampled, significant shifts in archaeal populations, predominantly methanogens, were observed. These shifts coincided with the geochemical transition from relatively high methane (26 mM), low sulphate (< 3 mg l(-1)) conditions in the region adjacent to the organic matter-rich shale to relatively low-methane (< 0.5 mM), high-sulphate (48 mg l(-1)) conditions in the organic-poor sandstone beneath the shale. These results indicated that active, phylogenetically diverse archaeal communities were present in the subsurface Cretaceous rock environment at this site and that major archaeal clades shifted dramatically over scales of tens of centimetres, corresponding to changes in the lithology and geochemical gradients.

Archaea↗