Geology topics

S.M. Webb

Publications and source records attributed to S.M. Webb.

4 recordsLinked to original sources

USGS2011

A bacterium that can grow by using arsenic instead of phosphorus

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

Science↗

USGS2009

Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick × 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-Å basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn–Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mn oxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments.

Geochimica et Cosmochimica Acta↗

USGS2008

Weathering of the Rio Blanco quartz diorite, Luquillo Mountains, Puerto Rico: Coupling oxidation, dissolution, and fracturing

In the mountainous Rio Icacos watershed in northeastern Puerto Rico, quartz diorite bedrock weathers spheroidally, producing a 0.2-2 m thick zone of partially weathered rock layers (???2.5 cm thickness each) called rindlets, which form concentric layers around corestones. Spheroidal fracturing has been modeled to occur when a weathering reaction with a positive ??V of reaction builds up elastic strain energy. The rates of spheroidal fracturing and saprolite formation are therefore controlled by the rate of the weathering reaction. Chemical, petrographic, and spectroscopic evidence demonstrates that biotite oxidation is the most likely fracture-inducing reaction. This reaction occurs with an expansion in d (0 0 1) from 10.0 to 10.5 A??, forming 'altered biotite'. Progressive biotite oxidation across the rindlet zone was inferred from thin sections and gradients in K and Fe(II). Using the gradient in Fe(II) and constraints based on cosmogenic age dates, we calculated a biotite oxidation reaction rate of 8.2 ?? 10-14 mol biotite m-2 s-1. Biotite oxidation was documented within the bedrock corestone by synchrotron X-ray microprobe fluorescence imaging and XANES. X-ray microprobe images of Fe(II) and Fe(III) at 2 ??m resolution revealed that oxidized zones within individual biotite crystals are the first evidence of alteration of the otherwise unaltered corestone. Fluids entering along fractures lead to the dissolution of plagioclase within the rindlet zone. Within 7 cm surrounding the rindlet-saprolite interface, hornblende dissolves to completion at a rate of 6.3 ?? 10-13 mol hornblende m-2 s-1: the fastest reported rate of hornblende weathering in the field. This rate is consistent with laboratory-derived hornblende dissolution rates. By revealing the coupling of these mineral weathering reactions to fracturing and porosity formation we are able to describe the process by which the quartz diorite bedrock disaggregates and forms saprolite. In the corestone, biotite oxidation induces spheroidal fracturing, facilitating the influx of fluids that react with other minerals, dissolving plagioclase and chlorite, creating additional porosity, and eventually dissolving hornblende and precipitating secondary minerals. The thickness of the resultant saprolite is maintained at steady state by a positive feedback between the denudation rate and the weathering advance rate driven by the concentration of pore water O2 at the bedrock-saprolite interface. ?? 2008 Elsevier Ltd. All rights reserved.

Geochimica et Cosmochimica Acta↗

USGS2005

Determination of uranyl incorporation into biogenic manganese oxides using X-ray absorption spectroscopy and scattering

Βiogenic manganese oxides are common and an important source of reactive mineral surfaces in the environment that may be potentially enhanced in bioremediation cases to improve natural attenuation. Experiments were performed in which the uranyl ion, UO 2 2+ (U(VI)), at various concentrations was present during manganese oxide biogenesis. At all concentrations, there was strong uptake of U onto the oxides. Synchrotron-based extended X-ray absorption fine structure (EXAFS) spectroscopy and X-ray diffraction (XRD) studies were carried out to determine the molecular-scale mechanism by which uranyl is incorporated into the oxide and how this incorporation affects the resulting manganese oxide structure and mineralogy. The EXAFS experiments show that at low concentrations (<0.3 mol % U, <1 μM U(VI) in solution), U(VI) is present as a strong bidentate surface complex. At high concentrations (>2 mol % U, >4 μM U(VI) in solution), the presence of U(VI) affects the stability and structure of the Mn oxide to form poorly ordered Mn oxide tunnel structures, similar to todorokite. EXAFS modeling shows that uranyl is present in these oxides predominantly in the tunnels of the Mn oxide structure in a tridentate complex. Observations by XRD corroborate these results. Structural incorporation may lead to more stable U(VI) sequestration that may be suitable for remediation uses. These observations, combined with the very high uptake capacity of the Mn oxides, imply that Mn-oxidizing bacteria may significantly influence dissolved U(VI) concentrations in impacted waters via sorption and incorporation into Mn oxide biominerals.

Environmental Science & Technology↗