A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.

http://cars9.uchicago.edu/xafs_school/Material/Articles/Horae%20JSR2005.pdf

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT.

Bacterial biosorbents and biosorption

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.

http://dzumenvis.nic.in/Physiology/pdf/Metals,%20minerals%20and%20microbes.pdf

Metals, minerals and microbes: geomicrobiology and bioremediation

A review on the adsorption of heavy metals by clay minerals, with special focus on the past decade

/pdf/processes-of-carbonate-precipitation-in-modern-microbial-176vfhaypi.pdf

Processes of carbonate precipitation in modern microbial mats

A chemical equilibrium model for metal adsorption onto bacterial surfaces

In this study, we conducted synchrotron radiation Fourier transform infrared (IR) spectroscopy, potentiometric titration, and metal sorption experiments to characterize metal-cyanobacteria sorption reactions. Infrared spectra were collected with samples in solution for intact cyanobacterial filaments and separated exopolymeric sheath material to examine the deprotonation reactions of cell surface functional groups. The infrared spectra of intact cells sequentially titrated from pH 3.2 to 6.5 display an increase in peak intensity and area at 1400 cm(-1) corresponding to vibrational COO- frequencies from the formation of deprotonated carboxyl surface sites. Similarly, bulk acid-base titration of cyanobacterial filaments and sheath material indicates that the concentration of proton-active surface sites is higher on the cell wall compared to the overlying sheath. A three-site model provides an excellent fit to the titration curves of both intact cells and sheath material with corresponding pKa values of 4.7 +/- 0.4, 6.6 +/- 0.2, 9.2 +/- 0.3 and 4.8 +/- 0.3, 6.5 +/- 0.1, 8.7 +/- 0.2, respectively. Finally, Cu2+, Cd2+, and Pb2+ sorption experiments were conducted as a function of pH, and a site-specific surface complexation model was used to describe the metal sorption data. The modeling indicates that metal ions are partitioned between the exopolymer sheath and cell wall and that the carboxyl groups on the cyanobacterial cell wall are the dominant sink for metals at near neutral pH. These results demonstrate that the cyanobacterial surfaces are complex structures which contain distinct surface layers, each with unique molecular functional groups and metal binding properties.

http://homepages.see.leeds.ac.uk/~earlgb/Publications/Yee_et_al_EST_2004.pdf

Nathan Yee

Papers

A chemical equilibrium model for metal adsorption onto bacterial surfaces

Characterization of metal-cyanobacteria sorption reactions: a combined macroscopic and infrared spectroscopic investigation

Cd adsorption onto bacterial surfaces: A universal adsorption edge?

X-ray absorption fine structure determination of pH-dependent U-bacterial cell wall interactions

Experimental study of the pH, ionic strength, and reversibility behavior of bacteria–mineral adsorption