Microbial reductive transformation of phyllosilicate Fe(III) and U(VI) in fluvial subsurface sediments.

The microbial reduction of Fe(III) and U(VI) was investigated in shallow aquifer sediments collected from subsurface flood deposits near the Hanford Reach of the Columbia River in Washington State. Increases in 0.5 N HCl-extractable Fe(II) were observed in incubated sediments and (57)Fe Mössbauer spectroscopy revealed that Fe(III) associated with phyllosilicates and pyroxene was reduced to Fe(II). Aqueous uranium(VI) concentrations decreased in subsurface sediments incubated in sulfate-containing synthetic groundwater with the rate and extent being greater in sediment amended with organic carbon. X-ray absorption spectroscopy of bioreduced sediments indicated that 67-77% of the U signal was U(VI), probably as an adsorbed species associated with a new or modified reactive mineral phase. Phylotypes within the Deltaproteobacteria were more common in Hanford sediments incubated with U(VI) than without, and in U(VI)-free incubations, members of the Clostridiales were dominant with sulfate-reducing phylotypes more common in the sulfate-amended sediments. These results demonstrate the potential for anaerobic reduction of phyllosilicate Fe(III) and sulfate in Hanford unconfined aquifer sediments and biotransformations involving reduction and adsorption leading to decreased aqueous U concentrations.

Pathways of aqueous Cr(VI) attenuation in a slightly alkaline oxic subsurface.

Column experiments combined with geochemical modeling, microscopic inspections, spectroscopic interrogations, and wet chemical extractions were used to study sediment-dependent Cr(VI) desorption, physical location, mineral association, and attenuation mechanism(s) in four freshly or naturally aged contaminated sediments exposed to concentrated Cr(VI) waste fluids. Results showed that majority of Cr(VI) mass was easily removed from the sediments (equilibrium site K(d) varied from 0 to 0.33 mL g(-1) and equilibrium site fraction was greater than 95%). Long tailings of time-dependent Cr(VI) concentrations above maximum contaminant level of 1.9 micromol L(-1) were also observed (kinetically controlled fraction K(d) and desorption reaction half-lives varied from 0 to 45 mL g(-1), and from 76.1 to 126 h, respectively). Microscopic and spectroscopic measurements confirmed that Cr was concentrated within fine-grained coatings in small areas mainly rich in phyllosilicates that contained both Cr(III) and Cr(VI). However, Cr(VI) reduction was neither significant nor complete. Under slightly alkaline and oxic conditions, contaminant Cr in the sediments occurred: (i) In the highly mobile pool (over 95% of total Cr); (ii) In the slow and time-dependent releasing pool, which served as long-term source of contamination; (iii) As reduced Cr(III) which most likely formed during Cr(VI) reaction with aqueous, sorbed, or structural Fe(II).

Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes.

Evolutionarily conserved noncoding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. However, detecting and visualizing compositionally similar cis-element clusters in the context of conserved sequences is challenging. We have explored potential solutions and developed an algorithm and visualization method that combines the results of conserved sequence analyses (BLASTZ) with those of transcription factor binding site analyses (MatInspector) (http://trafac.chmcc.org). We define hits as the density of co-occurring cis-element transcription factor (TF)-binding sites measured within a 200-bp moving average window through phylogenetically conserved regions. The results are depicted as a Regulogram, in which the hit count is plotted as a function of position within each of the two genomic regions of the aligned orthologs. Within a high-scoring region, the relative arrangement of shared cis-elements within compositionally similar TF-binding site clusters is depicted in a Trafacgram. On the basis of analyses of several training data sets, the approach also allows for the detection of similarities in composition and relative arrangement of cis-element clusters within nonorthologous genes, promoters, and enhancers that exhibit coordinate regulatory properties. Known functional regulatory regions of nonorthologous and less-conserved orthologous genes frequently showed cis-element shuffling, demonstrating that compositional similarity can be more sensitive than sequence similarity. These results show that combining sequence similarity with cis-element compositional similarity provides a powerful aid for the identification of potential control regions.