Satish C. B. Myneni

Elucidation of Functional Groups on Gram-Positive and Gram-Negative Bacterial Surfaces Using Infrared Spectroscopy

Surface functional group chemistry of intact Gram-positive and Gram-negative bacterial cells and their isolated cell walls was examined as a function of pH, growth phase, and growth media (for intact cells only) using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Infrared spectra of aqueous model organic molecules, representatives of the common functional groups found in bacterial cell walls (i.e., hydroxyl, carboxyl, phosphoryl, and amide groups), were also examined in order to assist the interpretation of the infrared spectra of bacterial samples. The surface sensitivity of the ATR-FTIR spectroscopic technique was evaluated using diatom cells, which possess a several-nanometers-thick layer of glycoprotein on their silica shells. The ATR-FTIR spectra of bacterial surfaces exhibit carboxyl, amide, phosphate, and carbohydrate related features, and these are identical for both Gram-positive and Gram-negative cells. These results provide direct evidence to the previously held conviction that the negative charge of bacterial surfaces is derived from the deprotonation of both carboxylates and phosphates. Variation in solution pH has only a minor effect on the secondary structure of the cell wall proteins. The cell surface functional group chemistry is altered neither by the growth phase nor by the growth medium of bacteria. This study reveals the universality of the functional group chemistry of bacterial cell surfaces.

Experimental and theoretical vibrational spectroscopic evaluation of arsenate coordination in aqueous solutions, solids, and at mineral-water interfaces

Arsenate (AsO43−) is a common species in oxidizing aquatic systems and hydrothermal fluids, and its solubility and partitioning into different mineral phases are determined by the nature of AsO43− coordination, solution pH, type of soluble cations, and H2O structure at the mineral-fluid interfaces. While the vibrational spectroscopy has been widely used in examining the AsO43− coordination chemistry, insufficient knowledge on the correlation of AsO43− molecular structure and its vibrational spectra impeded the complete spectral interpretation. In this paper, we evaluated the vibrational spectroscopy of AsO43− in solutions, crystals, and sorbed on mineral surfaces using theoretical (semiempirical, for aqueous species) and experimental studies, with emphasis on the protonation, hydration, and metal complexation influence on the As-O symmetric stretching vibrations. Theoretical predictions are in excellent agreement with the experimental studies and helped in the evaluation of vibrational modes of several arsenate-complexes and in the interpretation of experimental spectra. These vibrational spectroscopic studies (IR, Raman) suggest that the symmetry of AsO43− polyhedron is strongly distorted, and its As-O vibrations are affected by protonation and the relative influence on AsO43− structure decreases in the order: H+ ≫ cation ≥ H2O. For all AsO43− complexes, the As-OX symmetric stretching (X = metal, H+, H2O; ≤820 cm−1) shifted to lower wavenumbers when compared to that of uncomplexed AsO43−. In addition, the As-OH symmetric stretching of protonated arsenates in aqueous solutions shift to higher energies with increasing protonation (<720, <770, <790 cm−1 for HAsO42−, H2AsO4−, and H3AsO40, respectively). The protonated arsenates in crystalline solids show the same trend with little variation in As-OH symmetric stretching vibrations. Since metal complexation of protonated AsO43− does not influence the As-OH vibrations significantly, deducing symmetry information from their vibrational spectra is difficult. However, for metal unprotonated-AsO43− complexes, the shifts in As-OM (M = metal) vibrations are influenced only by the nature of complexing cation and the type of coordination, and hence the AsO43− coordination environment can be interpreted directly from the splitting of As-O degenerate vibrations and relative shifts in the As-OM modes. This information is critical in evaluating the structure of AsO43− sorption complexes at the solid-water interfaces. The vibrational spectra of other tetrahedral oxoanions are expected to be along similar lines.

Spectroscopic probing of local hydrogen-bonding structures in liquid water

We have studied the electronic structure of liquid water using x-ray absorption spectroscopy at the oxygen K edge. Since the x-ray absorption process takes less than a femtosecond, it allows probing of the molecular orbital structure of frozen, local geometries of water molecules at a timescale that has not previously been accessible. Our results indicate that the electronic structure of liquid water is significantly different from that of the solid and gaseous forms, resulting in a pronounced pre-edge feature below the main absorption edge in the spectrum. Theoretical calculations of these spectra suggest that this feature originates from specific configurations of water, for which the H-bond is broken on the H-donating site of the water molecule. This study provides a fingerprint for identifying broken donating H-bonds in the liquid and shows that an unsaturated H-bonding environment exists for a dominating fraction of the water molecules.

VIBRATIONAL SPECTROSCOPY OF FUNCTIONAL GROUP CHEMISTRY AND ARSENATE COORDINATION IN ETTRINGITE

The functional group chemistry and coordination of AsO43−-sorption complexes in ettringite [Ca6Al2(SO4)3(OH)12·26H2O] were evaluated as a function of sorption type (adsorption, coprecipitation) and pH using Raman and Fourier Transform infrared (FTIR) spectroscopies. The reactive functional groups of ettringite, ≡Al-OH, ≡Ca-OH2, and ≡Ca2-OH exhibit broad overlapping OH bands in the range 3600–3200 cm−1, prohibiting separation of component vibrational bands. The SO42− polyhedra of the channels are present in three crystallographically different sites and exhibit weakly split S-O asymmetric stretch at 1136 cm−1 (with several components) and symmetric stretch at 1016, 1008, and 989 cm−1. During AsO43− adsorption, the vibrational spectra of SO42− were least affected, and the OH stretching intensities around 3600 cm−1 decreased with an increase in AsO43− sorption. In contrast, the S-O symmetric stretch at 1016 and 1008 cm−1 were almost completely removed, and the OH vibrations were relatively unaffected during AsO43−-coprecipitation. The As-O asymmetric stretch of sorbed AsO43− are split and occur as overlapping peaks around 870 cm−1. The As-Ocomplexed stretching vibrations are at ∼800 cm−1. The low pH samples (pH = 10.3–11.0) exhibit distinct As-OH stretching vibrations at 748 cm−1, indicating that some of the sorbed AsO43− ions are protonated. These spectral features demonstrate that AsO43− directly interacts with ettringite surface sites during adsorption and substitute inside the channels during coprecipitation (preferentially for two of the three sites). The energy position of the As-O symmetric stretch vibrations suggest that the AsO43− polyhedra interacts predominantly with ≡Ca-OH2 and ≡Ca2-OH sites rather than with ≡Al-OH sites. Sorption of more than one type of As species was evident in low pH (<11.0) samples.

A SCANNING TRANSMISSION X-RAY MICROSCOPE FOR MATERIALS SCIENCE SPECTROMICROSCOPY AT THE ADVANCED LIGHT SOURCE

Design and performance of a scanning transmission x-ray microscope (STXM) at the Advanced Light Source is described. This instrument makes use of a high brightness undulator beamline and extends the STXM technique to new areas of research. After 2.5 years of development it is now an operational tool for research in polymer science, environmental chemistry, and magnetic materials.

Natural niche for organohalide-respiring Chloroflexi.

ABSTRACT The phylum Chloroflexi contains several isolated bacteria that have been found to respire a diverse array of halogenated anthropogenic chemicals. The distribution and role of these Chloroflexi in uncontaminated terrestrial environments, where abundant natural organohalogens could function as potential electron acceptors, have not been studied. Soil samples (116 total, including 6 sectioned cores) from a range of uncontaminated sites were analyzed for the number of Dehalococcoides-like Chloroflexi 16S rRNA genes present. Dehalococcoides-like Chloroflexi populations were detected in all but 13 samples. The concentrations of organochlorine ([organochlorine]), inorganic chloride, and total organic carbon (TOC) were obtained for 67 soil core sections. The number of Dehalococcoides-like Chloroflexi 16S rRNA genes positively correlated with [organochlorine]/TOC while the number of Bacteria 16S rRNA genes did not. Dehalococcoides-like Chloroflexi were also observed to increase in number with a concomitant accumulation of chloride when cultured with an enzymatically produced mixture of organochlorines. This research provides evidence that organohalide-respiring Chloroflexi are widely distributed as part of uncontaminated terrestrial ecosystems, they are correlated with the fraction of TOC present as organochlorines, and they increase in abundance while dechlorinating organochlorines. These findings suggest that organohalide-respiring Chloroflexi may play an integral role in the biogeochemical chlorine cycle.

Role of S/Se ratio in chemical bonding of As-S-Se glasses investigated by raman, x-ray photoelectron, and extended x-ray absorption fine structure spectroscopies

Chalcogenide glasses have attracted considerable attention and found various applications due to their infrared transparency and other optical properties. The As–S–Se chalcogenide glass, with its large glass-formation domain and favorable nonlinear property, is a promising candidate system for tailoring important optical properties through modification of glass composition. In this context, a systematic study on ternary As–S–Se glass, chalcogen-rich versus well-studied stochiometric compositions, has been carried out using three different techniques: Raman spectroscopy, x-ray photoelectron spectroscopy, and extended x-ray absorption fine structure spectroscopy. These complementary techniques lead to a consistent understanding of the role of S∕Se ratio in chalcogen-rich As–S–Se glasses, as compared to stochiometric composition, and to provide insight into the structural units (such as the mixed pyramidal units) and evidence for the existence of homopolar bonds (such as Se–Se, S–S, and Se–S), which are the ...

Overexpression and characterization of an iron storage and DNA-binding Dps protein from Trichodesmium erythraeum

ABSTRACT Although the role of iron in marine productivity has received a great deal of attention, no iron storage protein has been isolated from a marine microorganism previously. We describe an Fe-binding protein belonging to the Dps family (DNA binding protein from starved cells) in the N2-fixing marine cyanobacterium Trichodesmium erythraeum. A dps gene encoding a protein with significant levels of identity to members of the Dps family was identified in the genome of T. erythraeum. This gene codes for a putative DpsT. erythraeurm protein (Dpstery) with 69% primary amino acid sequence similarity to Synechococcus DpsA. We expressed and purified Dpstery, and we found that Dpstery, like other Dps proteins, is able to bind Fe and DNA and protect DNA from degradation by DNase. We also found that Dpstery binds phosphate, like other ferritin family proteins. Fe K near-edge X-ray absorption of Dpstery indicated that it has an iron core that resembles that of horse spleen ferritin.

Chemically and Geographically distinct solid-phase iron pools in the Southern Ocean

Swimming in Iron Pools Because iron is essential for marine phytoplankton growth, its availability limits the primary productivity of the oceans. Iron is typically bioavailable only when present in a dissolved state; however, a large fraction of the total iron in the oceans exists as tiny solid-phase particles ranging in size from a few nanometers to a few micrometers. von der Heyden et al. (p. 1199) used high-resolution x-ray microscopy and spectroscopy to characterize the distribution of iron particles along two transects of the Southern Ocean. Analysis of a number of individual particles reveals strong variation in iron oxidation state, particle mineralogy, and substitution of aluminum for iron—all of which control the solubility, and hence bioavailability, of iron. The distribution and composition of fine-grained marine iron particles vary strongly with location. Iron is a limiting nutrient in many parts of the oceans, including the unproductive regions of the Southern Ocean. Although the dominant fraction of the marine iron pool occurs in the form of solid-phase particles, its chemical speciation and mineralogy are challenging to characterize on a regional scale. We describe a diverse array of iron particles, ranging from 20 to 700 nanometers in diameter, in the waters of the Southern Ocean euphotic zone. Distinct variations in the oxidation state and composition of these iron particles exist between the coasts of South Africa and Antarctica, with different iron pools occurring in different frontal zones. These speciation variations can result in solubility differences that may affect the production of bioavailable dissolved iron.

Nanoscale Transforming Mineral Phases in Fresh Nacre

Nacre, or mother-of-pearl, the iridescent inner layer of many mollusk shells, is a biomineral lamellar composite of aragonite (CaCO3) and organic sheets. Biomineralization frequently occurs via transient amorphous precursor phases, crystallizing into the final stable biomineral. In nacre, despite extensive attempts, amorphous calcium carbonate (ACC) precursors have remained elusive. They were inferred from non-nacre-forming larval shells, or from a residue of amorphous material surrounding mature gastropod nacre tablets, and have only once been observed in bivalve nacre. Here we present the first direct observation of ACC precursors to nacre formation, obtained from the growth front of nacre in gastropod shells from red abalone (Haliotis rufescens), using synchrotron spectromicroscopy. Surprisingly, the abalone nacre data show the same ACC phases that are precursors to calcite (CaCO3) formation in sea urchin spicules, and not proto-aragonite or poorly crystalline aragonite (pAra), as expected for aragonitic nacre. In contrast, we find pAra in coral.